tool blast algorithm: Topics by Science.gov

Sample records for tool blast algorithm

A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm

PubMed Central

Guo, Xinyu; Wang, Hong; Devabhaktuni, Vijay

2012-01-01

A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. These implementations completed the first and second step of BLAST architecture and achieved significant speedup comparing with previously published architectures. PMID:25969747
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

PubMed Central

2012-01-01

Background 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. Results We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers. This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers. Conclusions We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the specificity threshold and other primer properties. This tool is publicly available at http://www.ncbi.nlm.nih.gov/tools/primer-blast. PMID:22708584
H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs.

PubMed

Ye, Weicai; Chen, Ying; Zhang, Yongdong; Xu, Yuesheng

2017-04-15

The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled seed-extension algorithm for better performance on GPUs, and offers a performance tuning mechanism for better efficiency among various CPUs and GPUs combinations. H-BLAST produces identical alignment results as NCBI-BLAST and its computational speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10 (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST. https://github.com/Yeyke/H-BLAST.git. yux06@syr.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
muBLASTP: database-indexed protein sequence search on multicore CPUs.

PubMed

Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

2016-11-04

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.
Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

PubMed

Goonesekere, Nalin Cw

2009-01-01

The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.
miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

PubMed Central

Kim, You Jung; Boyd, Andrew; Athey, Brian D.; Patel, Jignesh M.

2005-01-01

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users. PMID:16061938
Computer assisted blast design and assessment tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cameron, A.R.; Kleine, T.H.; Forsyth, W.W.

1995-12-31

In general the software required by a blast designer includes tools that graphically present blast designs (surface and underground), can analyze a design or predict its result, and can assess blasting results. As computers develop and computer literacy continues to rise the development of and use of such tools will spread. An example of the tools that are becoming available includes: Automatic blast pattern generation and underground ring design; blast design evaluation in terms of explosive distribution and detonation simulation; fragmentation prediction; blast vibration prediction and minimization; blast monitoring for assessment of dynamic performance; vibration measurement, display and signal processing;more » evaluation of blast results in terms of fragmentation; and risk and reliability based blast assessment. The authors have identified a set of criteria that are essential in choosing appropriate software blasting tools.« less
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

PubMed

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L; Sherman, Westley A; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-06-15

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296
A Homogenization Approach for Design and Simulation of Blast Resistant Composites

NASA Astrophysics Data System (ADS)

Sheyka, Michael

Structural composites have been used in aerospace and structural engineering due to their high strength to weight ratio. Composite laminates have been successfully and extensively used in blast mitigation. This dissertation examines the use of the homogenization approach to design and simulate blast resistant composites. Three case studies are performed to examine the usefulness of different methods that may be used in designing and optimizing composite plates for blast resistance. The first case study utilizes a single degree of freedom system to simulate the blast and a reliability based approach. The first case study examines homogeneous plates and the optimal stacking sequence and plate thicknesses are determined. The second and third case studies use the homogenization method to calculate the properties of composite unit cell made of two different materials. The methods are integrated with dynamic simulation environments and advanced optimization algorithms. The second case study is 2-D and uses an implicit blast simulation, while the third case study is 3-D and simulates blast using the explicit blast method. Both case studies 2 and 3 rely on multi-objective genetic algorithms for the optimization process. Pareto optimal solutions are determined in case studies 2 and 3. Case study 3 is an integrative method for determining optimal stacking sequence, microstructure and plate thicknesses. The validity of the different methods such as homogenization, reliability, explicit blast modeling and multi-objective genetic algorithms are discussed. Possible extension of the methods to include strain rate effects and parallel computation is also examined.
Biosequence Similarity Search on the Mercury System

PubMed Central

Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

2007-01-01

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. PMID:18846267
HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

PubMed

O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

2015-04-01

The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. Copyright © 2015 Elsevier Inc. All rights reserved.
Improved mine blast algorithm for optimal cost design of water distribution systems

NASA Astrophysics Data System (ADS)

Sadollah, Ali; Guen Yoo, Do; Kim, Joong Hoon

2015-12-01

The design of water distribution systems is a large class of combinatorial, nonlinear optimization problems with complex constraints such as conservation of mass and energy equations. Since feasible solutions are often extremely complex, traditional optimization techniques are insufficient. Recently, metaheuristic algorithms have been applied to this class of problems because they are highly efficient. In this article, a recently developed optimizer called the mine blast algorithm (MBA) is considered. The MBA is improved and coupled with the hydraulic simulator EPANET to find the optimal cost design for water distribution systems. The performance of the improved mine blast algorithm (IMBA) is demonstrated using the well-known Hanoi, New York tunnels and Balerma benchmark networks. Optimization results obtained using IMBA are compared to those using MBA and other optimizers in terms of their minimum construction costs and convergence rates. For the complex Balerma network, IMBA offers the cheapest network design compared to other optimization algorithms.
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

PubMed Central

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L.; Sherman, Westley A.; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-01-01

Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. PMID:22531216
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE PAGES

Yim, Won Cheol; Cushman, John C.

2017-07-22

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 andmore » 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. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yim, Won Cheol; Cushman, John C.

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 andmore » 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. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less
A Novel Approach for Blast-Induced Flyrock Prediction Based on Imperialist Competitive Algorithm and Artificial Neural Network

PubMed Central

Marto, Aminaton; Jahed Armaghani, Danial; Tonnizam Mohamad, Edy; Makhtar, Ahmad Mahir

2014-01-01

Flyrock is one of the major disturbances induced by blasting which may cause severe damage to nearby structures. This phenomenon has to be precisely predicted and subsequently controlled through the changing in the blast design to minimize potential risk of blasting. The scope of this study is to predict flyrock induced by blasting through a novel approach based on the combination of imperialist competitive algorithm (ICA) and artificial neural network (ANN). For this purpose, the parameters of 113 blasting operations were accurately recorded and flyrock distances were measured for each operation. By applying the sensitivity analysis, maximum charge per delay and powder factor were determined as the most influential parameters on flyrock. In the light of this analysis, two new empirical predictors were developed to predict flyrock distance. For a comparison purpose, a predeveloped backpropagation (BP) ANN was developed and the results were compared with those of the proposed ICA-ANN model and empirical predictors. The results clearly showed the superiority of the proposed ICA-ANN model in comparison with the proposed BP-ANN model and empirical approaches. PMID:25147856
A novel approach for blast-induced flyrock prediction based on imperialist competitive algorithm and artificial neural network.

PubMed

Marto, Aminaton; Hajihassani, Mohsen; Armaghani, Danial Jahed; Mohamad, Edy Tonnizam; Makhtar, Ahmad Mahir

2014-01-01

Flyrock is one of the major disturbances induced by blasting which may cause severe damage to nearby structures. This phenomenon has to be precisely predicted and subsequently controlled through the changing in the blast design to minimize potential risk of blasting. The scope of this study is to predict flyrock induced by blasting through a novel approach based on the combination of imperialist competitive algorithm (ICA) and artificial neural network (ANN). For this purpose, the parameters of 113 blasting operations were accurately recorded and flyrock distances were measured for each operation. By applying the sensitivity analysis, maximum charge per delay and powder factor were determined as the most influential parameters on flyrock. In the light of this analysis, two new empirical predictors were developed to predict flyrock distance. For a comparison purpose, a predeveloped backpropagation (BP) ANN was developed and the results were compared with those of the proposed ICA-ANN model and empirical predictors. The results clearly showed the superiority of the proposed ICA-ANN model in comparison with the proposed BP-ANN model and empirical approaches.
Effective channel estimation and efficient symbol detection for multi-input multi-output underwater acoustic communications

NASA Astrophysics Data System (ADS)

Ling, Jun

Achieving reliable underwater acoustic communications (UAC) has long been recognized as a challenging problem owing to the scarce bandwidth available and the reverberant spread in both time and frequency domains. To pursue high data rates, we consider a multi-input multi-output (MIMO) UAC system, and our focus is placed on two main issues regarding a MIMO UAC system: (1) channel estimation, which involves the design of the training sequences and the development of a reliable channel estimation algorithm, and (2) symbol detection, which requires interference cancelation schemes due to simultaneous transmission from multiple transducers. To enhance channel estimation performance, we present a cyclic approach for designing training sequences with good auto- and cross-correlation properties, and a channel estimation algorithm called the iterative adaptive approach (IAA). Sparse channel estimates can be obtained by combining IAA with the Bayesian information criterion (BIC). Moreover, we present sparse learning via iterative minimization (SLIM) and demonstrate that SLIM gives similar performance to IAA but at a much lower computational cost. Furthermore, an extension of the SLIM algorithm is introduced to estimate the sparse and frequency modulated acoustic channels. The extended algorithm is referred to as generalization of SLIM (GoSLIM). Regarding symbol detection, a linear minimum mean-squared error based detection scheme, called RELAX-BLAST, which is a combination of vertical Bell Labs layered space-time (V-BLAST) algorithm and the cyclic principle of the RELAX algorithm, is presented and it is shown that RELAX-BLAST outperforms V-BLAST. We show that RELAX-BLAST can be implemented efficiently by making use of the conjugate gradient method and diagonalization properties of circulant matrices. This fast implementation approach requires only simple fast Fourier transform operations and facilitates parallel implementations. The effectiveness of the proposed MIMO schemes is verified by both computer simulations and experimental results obtained by analyzing the measurements acquired in multiple in-water experiments.

NCBI BLAST+ integrated into Galaxy.

PubMed

Cock, Peter J A; Chilton, John M; Grüning, Björn; Johnson, James E; Soranzo, Nicola

2015-01-01

The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible. This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.
Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

PubMed Central

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

PubMed Central

Dowd, Scot E; Zaragoza, Joaquin; Rodriguez, Javier R; Oliver, Melvin J; Payton, Paxton R

2005-01-01

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. PMID:15819992
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

PubMed

von Grotthuss, Marcin; Plewczynski, Dariusz; Ginalski, Krzysztof; Rychlewski, Leszek; Shakhnovich, Eugene I

2006-02-06

The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF.
Investigation of blast-induced traumatic brain injury.

PubMed

Taylor, Paul A; Ludwigsen, John S; Ford, Corey C

2014-01-01

Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear.
Investigation of blast-induced traumatic brain injury

PubMed Central

Ludwigsen, John S.; Ford, Corey C.

2014-01-01

Objective Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. Methods This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. Results The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. Conclusions The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear. PMID:24766453
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU.

PubMed

Zhang, Jing; Wang, Hao; Feng, Wu-Chun

2017-01-01

BLAST, short for Basic Local Alignment Search Tool, is a ubiquitous tool used in the life sciences for pairwise sequence search. However, with the advent of next-generation sequencing (NGS), whether at the outset or downstream from NGS, the exponential growth of sequence databases is outstripping our ability to analyze the data. While recent studies have utilized the graphics processing unit (GPU) to speedup the BLAST algorithm for searching protein sequences (i.e., BLASTP), these studies use coarse-grained parallelism, where one sequence alignment is mapped to only one thread. Such an approach does not efficiently utilize the capabilities of a GPU, particularly due to the irregularity of BLASTP in both execution paths and memory-access patterns. To address the above shortcomings, we present a fine-grained approach to parallelize BLASTP, where each individual phase of sequence search is mapped to many threads on a GPU. This approach, which we refer to as cuBLASTP, reorders data-access patterns and reduces divergent branches of the most time-consuming phases (i.e., hit detection and ungapped extension). In addition, cuBLASTP optimizes the remaining phases (i.e., gapped extension and alignment with trace back) on a multicore CPU and overlaps their execution with the phases running on the GPU.
Phylogenetic profiles reveal structural/functional determinants of TRPC3 signal-sensing antennae

PubMed Central

Ko, Kyung Dae; Bhardwaj, Gaurav; Hong, Yoojin; Chang, Gue Su; Kiselyov, Kirill

2009-01-01

Biochemical assessment of channel structure/function is incredibly challenging. Developing computational tools that provide these data would enable translational research, accelerating mechanistic experimentation for the bench scientist studying ion channels. Starting with the premise that protein sequence encodes information about structure, function and evolution (SF&E), we developed a unified framework for inferring SF&E from sequence information using a knowledge-based approach. The Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST) provides phylogenetic profiles that can model, ab initio, SF&E relationships of biological sequences at the whole protein, single domain and single-amino acid level.1,2 In our recent paper,4 we have applied GDDA-BLAST analysis to study canonical TRP (TRPC) channels1 and empirically validated predicted lipid-binding and trafficking activities contained within the TRPC3 TRP_2 domain of unknown function. Overall, our in silico, in vitro, and in vivo experiments support a model in which TRPC3 has signal-sensing antennae which are adorned with lipid-binding, trafficking and calmodulin regulatory domains. In this Addendum, we correlate our functional domain analysis with the cryo-EM structure of TRPC3.3 In addition, we synthesize recent studies with our new findings to provide a refined model on the mechanism(s) of TRPC3 activation/deactivation. PMID:19704910
First-Principle Simulation of Blast Barrier Effectiveness for the Development of Simplified Design Tools

DTIC Science & Technology

2010-12-01

Simulation of Free -Field Blast ........................................................................45 27. (a) Peak Incident Pressure and (b...several types of problems involving blast propagation. Mastin et al. (1995) compared CTH simulations to free -field incident pressure as predicted by...a measure of accuracy and efficiency. To provide this direct comparison, a series of 2D-axisymmetric free -field air blast simulations were
Time difference of arrival to blast localization of potential chemical/biological event on the move

NASA Astrophysics Data System (ADS)

Morcos, Amir; Desai, Sachi; Peltzer, Brian; Hohil, Myron E.

2007-10-01

Integrating a sensor suite with ability to discriminate potential Chemical/Biological (CB) events from high-explosive (HE) events employing a standalone acoustic sensor with a Time Difference of Arrival (TDOA) algorithm we developed a cueing mechanism for more power intensive and range limited sensing techniques. Enabling the event detection algorithm to locate to a blast event using TDOA we then provide further information of the event as either Launch/Impact and if CB/HE. The added information is provided to a range limited chemical sensing system that exploits spectroscopy to determine the contents of the chemical event. The main innovation within this sensor suite is the system will provide this information on the move while the chemical sensor will have adequate time to determine the contents of the event from a safe stand-off distance. The CB/HE discrimination algorithm exploits acoustic sensors to provide early detection and identification of CB attacks. Distinct characteristics arise within the different airburst signatures because HE warheads emphasize concussive and shrapnel effects, while CB warheads are designed to disperse their contents over large areas, therefore employing a slower burning, less intense explosive to mix and spread their contents. Differences characterized by variations in the corresponding peak pressure and rise time of the blast, differences in the ratio of positive pressure amplitude to the negative amplitude, and variations in the overall duration of the resulting waveform. The discrete wavelet transform (DWT) is used to extract the predominant components of these characteristics from air burst signatures at ranges exceeding 3km. Highly reliable discrimination is achieved with a feed-forward neural network classifier trained on a feature space derived from the distribution of wavelet coefficients and higher frequency details found within different levels of the multiresolution decomposition. The development of an adaptive noise floor to provide early event detection assists in minimizing the false alarm rate and increasing the confidence whether the event is blast event or back ground noise. The integration of these algorithms with the TDOA algorithm provides a complex suite of algorithms that can give early warning detection and highly reliable look direction from a great stand-off distance for a moving vehicle to determine if a candidate blast event is CB and if CB what is the composition of the resulting cloud.
StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/
High-fidelity simulations of blast loadings in urban environments using an overset meshing strategy

NASA Astrophysics Data System (ADS)

Wang, X.; Remotigue, M.; Arnoldus, Q.; Janus, M.; Luke, E.; Thompson, D.; Weed, R.; Bessette, G.

2017-05-01

Detailed blast propagation and evolution through multiple structures representing an urban environment were simulated using the code Loci/BLAST, which employs an overset meshing strategy. The use of overset meshes simplifies mesh generation by allowing meshes for individual component geometries to be generated independently. Detailed blast propagation and evolution through multiple structures, wave reflection and interaction between structures, and blast loadings on structures were simulated and analyzed. Predicted results showed good agreement with experimental data generated by the US Army Engineer Research and Development Center. Loci/BLAST results were also found to compare favorably to simulations obtained using the Second-Order Hydrodynamic Automatic Mesh Refinement Code (SHAMRC). The results obtained demonstrated that blast reflections in an urban setting significantly increased the blast loads on adjacent buildings. Correlations of computational results with experimental data yielded valuable insights into the physics of blast propagation, reflection, and interaction under an urban setting and verified the use of Loci/BLAST as a viable tool for urban blast analysis.
Improvements in the Protein Identifier Cross-Reference service.

PubMed

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.
Prediction of blast-induced air overpressure: a hybrid AI-based predictive model.

PubMed

Jahed Armaghani, Danial; Hajihassani, Mohsen; Marto, Aminaton; Shirani Faradonbeh, Roohollah; Mohamad, Edy Tonnizam

2015-11-01

Blast operations in the vicinity of residential areas usually produce significant environmental problems which may cause severe damage to the nearby areas. Blast-induced air overpressure (AOp) is one of the most important environmental impacts of blast operations which needs to be predicted to minimize the potential risk of damage. This paper presents an artificial neural network (ANN) optimized by the imperialist competitive algorithm (ICA) for the prediction of AOp induced by quarry blasting. For this purpose, 95 blasting operations were precisely monitored in a granite quarry site in Malaysia and AOp values were recorded in each operation. Furthermore, the most influential parameters on AOp, including the maximum charge per delay and the distance between the blast-face and monitoring point, were measured and used to train the ICA-ANN model. Based on the generalized predictor equation and considering the measured data from the granite quarry site, a new empirical equation was developed to predict AOp. For comparison purposes, conventional ANN models were developed and compared with the ICA-ANN results. The results demonstrated that the proposed ICA-ANN model is able to predict blast-induced AOp more accurately than other presented techniques.
Compositional Verification with Abstraction, Learning, and SAT Solving

DTIC Science & Technology

2015-05-01

arithmetic, and bit-vectors (currently, via bit-blasting). The front-end is based on an existing tool called UFO [8] which converts C programs to the Horn...supports propositional logic, linear arithmetic, and bit-vectors (via bit-blasting). The front-end is based on the tool UFO [8]. It encodes safety of...tool UFO [8]. The encoding in Horn-SMT only uses the theory of Linear Rational Arithmetic. All experiments were carried out on an Intel R© CoreTM2 Quad
Spreadsheet Assessment Tool v. 2.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, David J.; Martinez, Ruben

2016-03-03

The Spreadsheet Assessment Tool (SAT) is an easy to use, blast assessment tool that is intended to estimate the potential risk due to an explosive attack on a blood irradiator. The estimation of risk is based on the methodology, assumptions, and results of a detailed blast effects assessment study that is summarized in Sandia National Laboratories Technical Report SAND2015-6166. Risk as defined in the report and as used in the SAT is: "The potential risk of creating an air blast-induced vent opening at a buildings envelope surface". Vent openings can be created at a buildings envelope through the failure ofmore » an exterior building component—like a wall, window, or door—due to an explosive sabotage of an irradiator within the building. To estimate risk, the tool requires that users obtain and input information pertaining to the building's characteristics and the irradiator location. The tool also suggests several prescriptive mitigation strategies that can be considered to reduce risk. Given the variability in civilian building construction practices, the input parameters used by this tool may not apply to all buildings being assessed. The tool should not be used as a substitute for engineering judgment. The tool is intended for assessment purposes only.« less
Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

PubMed Central

Nichio, Bruno T. L.; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology. PMID:29163633
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives.

PubMed

Nichio, Bruno T L; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology.

Single Pass Streaming BLAST on FPGAs*†

PubMed Central

Herbordt, Martin C.; Model, Josh; Sukhwani, Bharat; Gu, Yongfeng; VanCourt, Tom

2008-01-01

Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST. PMID:19081828
The Effects of Explosive Blast as Compared to Post-traumatic Stress Disorder on Brain Function and Structure

DTIC Science & Technology

2013-04-01

Neuropsychology (AACN). Chicago , Illinois. One of the challenges in assessing the essential neural features of mild TBI in veterans is that... Chicago , Illinois. The tool, preliminarily called the Minnesota Blast Exposure Screening Tool (MN-BEST; see Figure 12), complements current screening...the AACN. Chicago , Illinois. Examination of the number of post-concussive symptoms endorsed by the entire National Guard sample indicates that
blastjs: a BLAST+ wrapper for Node.js.

PubMed

Page, Martin; MacLean, Dan; Schudoma, Christian

2016-02-27

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possible and therefore requires only a minimal amount of code in the client application. The library is freely available under the MIT license at https://github.com/teammaclean/blastjs.
Quantifying the Effect of Fast Charger Deployments on Electric Vehicle Utility and Travel Patterns via Advanced Simulation: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, E.; Neubauer, J.; Burton, E.

The disparate characteristics between conventional (CVs) and battery electric vehicles (BEVs) in terms of driving range, refill/recharge time, and availability of refuel/recharge infrastructure inherently limit the relative utility of BEVs when benchmarked against traditional driver travel patterns. However, given a high penetration of high-power public charging combined with driver tolerance for rerouting travel to facilitate charging on long-distance trips, the difference in utility between CVs and BEVs could be marginalized. We quantify the relationships between BEV utility, the deployment of fast chargers, and driver tolerance for rerouting travel and extending travel durations by simulating BEVs operated over real-world travel patternsmore » using the National Renewable Energy Laboratory's Battery Lifetime Analysis and Simulation Tool for Vehicles (BLAST-V). With support from the U.S. Department of Energy's Vehicle Technologies Office, BLAST-V has been developed to include algorithms for estimating the available range of BEVs prior to the start of trips, for rerouting baseline travel to utilize public charging infrastructure when necessary, and for making driver travel decisions for those trips in the presence of available public charging infrastructure, all while conducting advanced vehicle simulations that account for battery electrical, thermal, and degradation response. Results from BLAST-V simulations on vehicle utility, frequency of inserted stops, duration of charging events, and additional time and distance necessary for rerouting travel are presented to illustrate how BEV utility and travel patterns can be affected by various fast charge deployments.« less
The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

PubMed

Orsini, Massimiliano; Carcangiu, Simone; Cuccuru, Gianmauro; Uva, Paolo; Tramontano, Anna

2013-01-01

BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104
Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264
Manganese-Enhanced Magnetic Resonance Imaging as a Diagnostic and Dispositional Tool after Mild-Moderate Blast Traumatic Brain Injury

PubMed Central

Schaefer, Michele L.; Wester, Brock; Lee, Yi-Chien; Boggs, Nathan; Conner, Howard A.; Merkle, Andrew C.; Fricke, Stanley T.; Albanese, Chris; Koliatsos, Vassilis E.

2016-01-01

Abstract Traumatic brain injury (TBI) caused by explosive munitions, known as blast TBI, is the signature injury in recent military conflicts in Iraq and Afghanistan. Diagnostic evaluation of TBI, including blast TBI, is based on clinical history, symptoms, and neuropsychological testing, all of which can result in misdiagnosis or underdiagnosis of this condition, particularly in the case of TBI of mild-to-moderate severity. Prognosis is currently determined by TBI severity, recurrence, and type of pathology, and also may be influenced by promptness of clinical intervention when more effective treatments become available. An important task is prevention of repetitive TBI, particularly when the patient is still symptomatic. For these reasons, the establishment of quantitative biological markers can serve to improve diagnosis and preventative or therapeutic management. In this study, we used a shock-tube model of blast TBI to determine whether manganese-enhanced magnetic resonance imaging (MEMRI) can serve as a tool to accurately and quantitatively diagnose mild-to-moderate blast TBI. Mice were subjected to a 30 psig blast and administered a single dose of MnCl2 intraperitoneally. Longitudinal T1-magnetic resonance imaging (MRI) performed at 6, 24, 48, and 72 h and at 14 and 28 days revealed a marked signal enhancement in the brain of mice exposed to blast, compared with sham controls, at nearly all time-points. Interestingly, when mice were protected with a polycarbonate body shield during blast exposure, the marked increase in contrast was prevented. We conclude that manganese uptake can serve as a quantitative biomarker for TBI and that MEMRI is a minimally-invasive quantitative approach that can aid in the accurate diagnosis and management of blast TBI. In addition, the prevention of the increased uptake of manganese by body protection strongly suggests that the exposure of an individual to blast risk could benefit from the design of improved body armor. PMID:26414591
Manganese-Enhanced Magnetic Resonance Imaging as a Diagnostic and Dispositional Tool after Mild-Moderate Blast Traumatic Brain Injury.

PubMed

Rodriguez, Olga; Schaefer, Michele L; Wester, Brock; Lee, Yi-Chien; Boggs, Nathan; Conner, Howard A; Merkle, Andrew C; Fricke, Stanley T; Albanese, Chris; Koliatsos, Vassilis E

2016-04-01

Traumatic brain injury (TBI) caused by explosive munitions, known as blast TBI, is the signature injury in recent military conflicts in Iraq and Afghanistan. Diagnostic evaluation of TBI, including blast TBI, is based on clinical history, symptoms, and neuropsychological testing, all of which can result in misdiagnosis or underdiagnosis of this condition, particularly in the case of TBI of mild-to-moderate severity. Prognosis is currently determined by TBI severity, recurrence, and type of pathology, and also may be influenced by promptness of clinical intervention when more effective treatments become available. An important task is prevention of repetitive TBI, particularly when the patient is still symptomatic. For these reasons, the establishment of quantitative biological markers can serve to improve diagnosis and preventative or therapeutic management. In this study, we used a shock-tube model of blast TBI to determine whether manganese-enhanced magnetic resonance imaging (MEMRI) can serve as a tool to accurately and quantitatively diagnose mild-to-moderate blast TBI. Mice were subjected to a 30 psig blast and administered a single dose of MnCl2 intraperitoneally. Longitudinal T1-magnetic resonance imaging (MRI) performed at 6, 24, 48, and 72 h and at 14 and 28 days revealed a marked signal enhancement in the brain of mice exposed to blast, compared with sham controls, at nearly all time-points. Interestingly, when mice were protected with a polycarbonate body shield during blast exposure, the marked increase in contrast was prevented. We conclude that manganese uptake can serve as a quantitative biomarker for TBI and that MEMRI is a minimally-invasive quantitative approach that can aid in the accurate diagnosis and management of blast TBI. In addition, the prevention of the increased uptake of manganese by body protection strongly suggests that the exposure of an individual to blast risk could benefit from the design of improved body armor.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Preece, D.S.; Knudsen, S.D.

The spherical element computer code DMC (Distinct Motion Code) used to model rock motion resulting from blasting has been enhanced to allow routine computer simulations of bench blasting. The enhancements required for bench blast simulation include: (1) modifying the gas flow portion of DMC, (2) adding a new explosive gas equation of state capability, (3) modifying the porosity calculation, and (4) accounting for blastwell spacing parallel to the face. A parametric study performed with DMC shows logical variation of the face velocity as burden, spacing, blastwell diameter and explosive type are varied. These additions represent a significant advance in themore » capability of DMC which will not only aid in understanding the physics involved in blasting but will also become a blast design tool. 8 refs., 7 figs., 1 tab.« less
Reconstruction of improvised explosive device blast loading to personnel in the open

NASA Astrophysics Data System (ADS)

Wiri, Suthee; Needham, Charles

2016-05-01

Significant advances in reconstructing attacks by improvised explosive devices (IEDs) and other blast events are reported. A high-fidelity three-dimensional computational fluid dynamics tool, called Second-order Hydrodynamic Automatic Mesh Refinement Code, was used for the analysis. Computer-aided design models for subjects or vehicles in the scene accurately represent geometries of objects in the blast field. A wide range of scenario types and blast exposure levels were reconstructed including free field blast, enclosed space of vehicle cabin, IED attack on a vehicle, buried charges, recoilless rifle operation, rocket-propelled grenade attack and missile attack with single subject or multiple subject exposure to pressure levels from ˜ 27.6 kPa (˜ 4 psi) to greater than 690 kPa (>100 psi). To create a full 3D pressure time-resolved reconstruction of a blast event for injury and blast exposure analysis, a combination of intelligence data and Blast Gauge data can be used to reconstruct an actual in-theatre blast event. The methodology to reconstruct an event and the "lessons learned" from multiple reconstructions in open space are presented. The analysis uses records of blast pressure at discrete points, and the output is a spatial and temporal blast load distribution for all personnel involved.
Sirius PSB: a generic system for analysis of biological sequences.

PubMed

Koh, Chuan Hock; Lin, Sharene; Jedd, Gregory; Wong, Limsoon

2009-12-01

Computational tools are essential components of modern biological research. For example, BLAST searches can be used to identify related proteins based on sequence homology, or when a new genome is sequenced, prediction models can be used to annotate functional sites such as transcription start sites, translation initiation sites and polyadenylation sites and to predict protein localization. Here we present Sirius Prediction Systems Builder (PSB), a new computational tool for sequence analysis, classification and searching. Sirius PSB has four main operations: (1) Building a classifier, (2) Deploying a classifier, (3) Search for proteins similar to query proteins, (4) Preliminary and post-prediction analysis. Sirius PSB supports all these operations via a simple and interactive graphical user interface. Besides being a convenient tool, Sirius PSB has also introduced two novelties in sequence analysis. Firstly, genetic algorithm is used to identify interesting features in the feature space. Secondly, instead of the conventional method of searching for similar proteins via sequence similarity, we introduced searching via features' similarity. To demonstrate the capabilities of Sirius PSB, we have built two prediction models - one for the recognition of Arabidopsis polyadenylation sites and another for the subcellular localization of proteins. Both systems are competitive against current state-of-the-art models based on evaluation of public datasets. More notably, the time and effort required to build each model is greatly reduced with the assistance of Sirius PSB. Furthermore, we show that under certain conditions when BLAST is unable to find related proteins, Sirius PSB can identify functionally related proteins based on their biophysical similarities. Sirius PSB and its related supplements are available at: http://compbio.ddns.comp.nus.edu.sg/~sirius.
Investigation of earth borne vibrations due to highway traffic and/or construction blasting : final report.

DOT National Transportation Integrated Search

1986-06-01

This study was undertaken to determine the magnitude of ground vibrations produced by traffic and/or construction blasting. Such information could provide a tool in defense of legal claims concerning physical damage to nearby properties. An engineeri...
A service-based BLAST command tool supported by cloud infrastructures.

PubMed

Carrión, Abel; Blanquer, Ignacio; Hernández, Vicente

2012-01-01

Notwithstanding the benefits of distributed-computing infrastructures for empowering bioinformatics analysis tools with the needed computing and storage capability, the actual use of these infrastructures is still low. Learning curves and deployment difficulties have reduced the impact on the wide research community. This article presents a porting strategy of BLAST based on a multiplatform client and a service that provides the same interface as sequential BLAST, thus reducing learning curve and with minimal impact on their integration on existing workflows. The porting has been done using the execution and data access components from the EC project Venus-C and the Windows Azure infrastructure provided in this project. The results obtained demonstrate a low overhead on the global execution framework and reasonable speed-up and cost-efficiency with respect to a sequential version.
Grit blasting nozzle fabricated from mild tool steel proves satisfactory

NASA Technical Reports Server (NTRS)

Mc Farland, J. E.; Turbitt, B.

1966-01-01

Dry blasting with glass beads through a nozzle assembly descales both the outside and inside surfaces of tubes of Inconel 718 used for the distribution of gaseous oxygen. The inside of the nozzle is coated with polyurethane and the deflector with a commercially available liquid urethane rubber.
40 CFR Appendix B to Part 438 - Oily Operations Definitions

Code of Federal Regulations, 2011 CFR

2011-07-01

... part. Abrasive blasting includes bead, grit, shot, and sand blasting, and may be performed either dry... between different polarity electrodes, one the part and the other the tool, separated by a small gap. The... mechanical processes such as hammer forging, shot peening, peening, coining, high-energy-rate forming...
40 CFR Appendix B to Part 438 - Oily Operations Definitions

Code of Federal Regulations, 2013 CFR

2013-07-01

... against the part. Abrasive blasting includes bead, grit, shot, and sand blasting, and may be performed... between different polarity electrodes, one the part and the other the tool, separated by a small gap. The... mechanical processes such as hammer forging, shot peening, peening, coining, high-energy-rate forming...
40 CFR Appendix B to Part 438 - Oily Operations Definitions

Code of Federal Regulations, 2014 CFR

2014-07-01

... against the part. Abrasive blasting includes bead, grit, shot, and sand blasting, and may be performed... between different polarity electrodes, one the part and the other the tool, separated by a small gap. The... mechanical processes such as hammer forging, shot peening, peening, coining, high-energy-rate forming...
40 CFR Appendix B to Part 438 - Oily Operations Definitions

Code of Federal Regulations, 2012 CFR

2012-07-01

... against the part. Abrasive blasting includes bead, grit, shot, and sand blasting, and may be performed... between different polarity electrodes, one the part and the other the tool, separated by a small gap. The... mechanical processes such as hammer forging, shot peening, peening, coining, high-energy-rate forming...
40 CFR Appendix B to Part 438 - Oily Operations Definitions

Code of Federal Regulations, 2010 CFR

2010-07-01

... part. Abrasive blasting includes bead, grit, shot, and sand blasting, and may be performed either dry... between different polarity electrodes, one the part and the other the tool, separated by a small gap. The... mechanical processes such as hammer forging, shot peening, peening, coining, high-energy-rate forming...

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.
Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
Correlative analysis of head kinematics and brain's tissue response: a computational approach toward understanding the mechanisms of blast TBI

NASA Astrophysics Data System (ADS)

Sarvghad-Moghaddam, H.; Rezaei, A.; Ziejewski, M.; Karami, G.

2017-11-01

Upon impingement of blast waves on the head, stress waves generated at the interface of the skull are transferred into the cranium and the brain tissue and may cause mild to severe blast traumatic brain injury. The intensity of the shock front, defined by the blast overpressure (BoP), that is, the blast-induced peak static overpressure, significantly affects head kinematics as well as the tissue responses of the brain. While evaluation of global linear and rotational accelerations may be feasible, an experimental determination of dynamic responses of the brain in terms of intracranial pressure (ICP), maximum shear stress (MSS), and maximum principal strain (MPS) is almost impossible. The main objective of this study is to investigate possible correlations between head accelerations and the brain's ICP, MSS, and MPS. To this end, three different blasts were simulated by modeling the detonation of 70, 200, and 500 g of TNT at a fixed distance from the head, corresponding to peak BoPs of 0.52, 1.2, and 2 MPa, respectively. A nonlinear multi-material finite element algorithm was implemented in the LS-DYNA explicit solver. Fluid-solid interaction between the blast waves and head was modeled using a penalty-based method. Strong correlations were found between the brain's dynamic responses and both global linear and rotational accelerations at different blast intensities (R^{2 }≥98%), implying that global kinematic parameters of the head might be strong predictors of brain tissue biomechanical parameters.
Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

PubMed Central

Diener, Stephen E; Houfek, Thomas D; Kalat, Sam E; Windham, DE; Burke, Mark; Opperman, Charles; Dean, Ralph A

2005-01-01

Background - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. Results - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. Conclusion - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists. PMID:15958161
BLAST for Behind-the-Meter Applications Lite Tool | Transportation Research

Science.gov Websites

provided by NREL's PV Watts calculator. A generic utility rate structure framework makes it possible to the BLAST documentation for proper CSV formatting. Rate structure values Define demand charges and energy costs to best represent your utility rate structure of interest. Demand charges and energy costs
Blast furnace supervision and control system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remorino, M.; Lingiardi, O.; Zecchi, M.

1997-12-31

On December 1992, a group of companies headed by Techint, took over Somisa, the state-owned integrated steel plant located at San Nicolas, Province of Buenos Aires, Argentina, culminating an ambitious government privatization scheme. The blast furnace 2 went into a full reconstruction and relining in January 1995. After a 140 MU$ investment the new blast furnace 2 was started in September 1995. After more than one year of operation of the blast furnace the system has proven itself useful and reliable. The main reasons for the success of the system are: same use interface for all blast furnace areas --more » operation, process, maintenance and management, (full horizontal and vertical integration); and full accessibility to all information and process tools though some restrictions apply to field commands (people empowerment). The paper describes the central system.« less
Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429
The Prediction of the Gas Utilization Ratio Based on TS Fuzzy Neural Network and Particle Swarm Optimization

PubMed Central

Jiang, Haihe; Yin, Yixin; Xiao, Wendong; Zhao, Baoyong

2018-01-01

Gas utilization ratio (GUR) is an important indicator that is used to evaluate the energy consumption of blast furnaces (BFs). Currently, the existing methods cannot predict the GUR accurately. In this paper, we present a novel data-driven model for predicting the GUR. The proposed approach utilized both the TS fuzzy neural network (TS-FNN) and the particle swarm algorithm (PSO) to predict the GUR. The particle swarm algorithm (PSO) is applied to optimize the parameters of the TS-FNN in order to decrease the error caused by the inaccurate initial parameter. This paper also applied the box graph (Box-plot) method to eliminate the abnormal value of the raw data during the data preprocessing. This method can deal with the data which does not obey the normal distribution which is caused by the complex industrial environments. The prediction results demonstrate that the optimization model based on PSO and the TS-FNN approach achieves higher prediction accuracy compared with the TS-FNN model and SVM model and the proposed approach can accurately predict the GUR of the blast furnace, providing an effective way for the on-line blast furnace distribution control. PMID:29461469
The Prediction of the Gas Utilization Ratio based on TS Fuzzy Neural Network and Particle Swarm Optimization.

PubMed

Zhang, Sen; Jiang, Haihe; Yin, Yixin; Xiao, Wendong; Zhao, Baoyong

2018-02-20

Gas utilization ratio (GUR) is an important indicator that is used to evaluate the energy consumption of blast furnaces (BFs). Currently, the existing methods cannot predict the GUR accurately. In this paper, we present a novel data-driven model for predicting the GUR. The proposed approach utilized both the TS fuzzy neural network (TS-FNN) and the particle swarm algorithm (PSO) to predict the GUR. The particle swarm algorithm (PSO) is applied to optimize the parameters of the TS-FNN in order to decrease the error caused by the inaccurate initial parameter. This paper also applied the box graph (Box-plot) method to eliminate the abnormal value of the raw data during the data preprocessing. This method can deal with the data which does not obey the normal distribution which is caused by the complex industrial environments. The prediction results demonstrate that the optimization model based on PSO and the TS-FNN approach achieves higher prediction accuracy compared with the TS-FNN model and SVM model and the proposed approach can accurately predict the GUR of the blast furnace, providing an effective way for the on-line blast furnace distribution control.
Monte Carlo simulation as a tool to predict blasting fragmentation based on the Kuz Ram model

NASA Astrophysics Data System (ADS)

Morin, Mario A.; Ficarazzo, Francesco

2006-04-01

Rock fragmentation is considered the most important aspect of production blasting because of its direct effects on the costs of drilling and blasting and on the economics of the subsequent operations of loading, hauling and crushing. Over the past three decades, significant progress has been made in the development of new technologies for blasting applications. These technologies include increasingly sophisticated computer models for blast design and blast performance prediction. Rock fragmentation depends on many variables such as rock mass properties, site geology, in situ fracturing and blasting parameters and as such has no complete theoretical solution for its prediction. However, empirical models for the estimation of size distribution of rock fragments have been developed. In this study, a blast fragmentation Monte Carlo-based simulator, based on the Kuz-Ram fragmentation model, has been developed to predict the entire fragmentation size distribution, taking into account intact and joints rock properties, the type and properties of explosives and the drilling pattern. Results produced by this simulator were quite favorable when compared with real fragmentation data obtained from a blast quarry. It is anticipated that the use of Monte Carlo simulation will increase our understanding of the effects of rock mass and explosive properties on the rock fragmentation by blasting, as well as increase our confidence in these empirical models. This understanding will translate into improvements in blasting operations, its corresponding costs and the overall economics of open pit mines and rock quarries.
Preliminary Research on Possibilities of Drilling Process Robotization

NASA Astrophysics Data System (ADS)

Pawel, Stefaniak; Jacek, Wodecki; Jakubiak, Janusz; Zimroz, Radoslaw

2017-12-01

Nowadays, drilling & blasting is crucial technique for deposit excavation using in hard rock mining. Unfortunately, such approach requires qualified staff to perform, and consequently there is a serious risk related to rock mechanics when using explosives. Negative influence of explosives usage on safety issues of underground mine is a main cause of mining demands related to elimination of people from production area. Other aspects worth taking into consideration are drilling precision according to drilling pattern, blasting effectiveness, improvement of drilling tool reliability etc. In the literature different drilling support solutions are well-known in terms of positioning support systems, anti-jamming systems or cavity detection systems. For many years, teleoperation of drilling process is also developed. Unfortunately, available technologies have so far not fully met the industries expectation in hard rock. Mine of the future is expected to incorporate robotic system instead of current approaches. In this paper we present preliminary research related to robotization of drilling process and possibilities of its application in underground mine condition. A test rig has been proposed. To simulate drilling process several key assumptions have been accepted. As a result, algorithms for automation of drilling process have been proposed and tested on the test rig. Experiences gathered so far underline that there is a need for further developing robotic system for drilling process.
Numerical simulation of blast wave propagation in vicinity of standalone prism on flat plate

NASA Astrophysics Data System (ADS)

Valger, Svetlana; Fedorova, Natalya; Fedorov, Alexander

2018-03-01

In the paper, numerical simulation of shock wave propagation in the vicinity of a standalone prism and a prism with a cavity in front of it was carried out. The modeling was based on the solution of 3D Euler equations and Fluent software was used as a main computational tool. The algorithm for local dynamic mesh adaptation to high gradients of pressure was applied. The initial stage of the explosion of condensed explosive was described with the help of "Compressed balloon method". The research allowed describing the characteristic stages of the blast in a semi-closed space, the structure of secondary shock waves and their interaction with obstacles. The numerical approach in Fluent based on combining inviscid gas dynamics methods and "Compressed balloon method" was compared with the method which had been used by the authors earlier with the help of AUTODYN and which is based on the use of the hydrodynamic model of a material to describe state of detonation products. For the problem of shock wave propagation in the vicinity of standalone prism the comparison of the simulation results obtained using both the methods with the experimental data was performed on the dependence of static pressure and effective momentum on time for the characteristic points located on prism walls.
Name that Gene: A Meaningful Computer-Based Genetics Classroom Activity that Incorporates Tolls Used by Real Research Scientists

ERIC Educational Resources Information Center

Wefer, Stephen H.

2003-01-01

"Name That Gene" is a simple classroom activity that incorporates bioinformatics (available biological information) into the classroom using "Basic Logical Alignment Search Tool (BLAST)." An excellent classroom activity involving bioinformatics and "BLAST" has been previously explored using sequences from bacteria, but it is tailored for college…
Laser cleaning of steel for paint removal

NASA Astrophysics Data System (ADS)

Chen, G. X.; Kwee, T. J.; Tan, K. P.; Choo, Y. S.; Hong, M. H.

2010-11-01

Paint removal is an important part of steel processing for marine and offshore engineering. For centuries, a blasting techniques have been widely used for this surface preparation purpose. But conventional blasting always has intrinsic problems, such as noise, explosion risk, contaminant particles, vibration, and dust. In addition, processing wastes often cause environmental problems. In recent years, laser cleaning has attracted much research effort for its significant advantages, such as precise treatment, and high selectivity and flexibility in comparison with conventional cleaning techniques. In the present study, we use this environmentally friendly technique to overcome the problems of conventional blasting. Processed samples are examined with optical microscopes and other surface characterization tools. Experimental results show that laser cleaning can be a good alternative candidate to conventional blasting.
Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840
Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941
StrBioLib: a Java library for development of custom computationalstructural biology applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less
Explosively driven air blast in a conical shock tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, Joel B., E-mail: joel.b.stewart2.civ@mail.mil; Pecora, Collin, E-mail: collin.r.pecora.civ@mail.mil

2015-03-15

Explosively driven shock tubes present challenges in terms of safety concerns and expensive upkeep of test facilities but provide more realistic approximations to the air blast resulting from free-field detonations than those provided by gas-driven shock tubes. Likewise, the geometry of conical shock tubes can naturally approximate a sector cut from a spherically symmetric blast, leading to a better agreement with the blast profiles of free-field detonations when compared to those provided by shock tubes employing constant cross sections. The work presented in this article documents the design, fabrication, and testing of an explosively driven conical shock tube whose goalmore » was to closely replicate the blast profile seen from a larger, free-field detonation. By constraining the blast through a finite area, large blasts (which can add significant damage and safety constraints) can be simulated using smaller explosive charges. The experimental data presented herein show that a close approximation to the free-field air blast profile due to a 1.5 lb charge of C4 at 76 in. can be achieved by using a 0.032 lb charge in a 76-in.-long conical shock tube (which translates to an amplification factor of nearly 50). Modeling and simulation tools were used extensively in designing this shock tube to minimize expensive fabrication costs.« less
Remote operated vehicle with CO{sub 2} blasting (ROVCO{sub 2}): Volume 1. Final report, September 1993--July 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-06-01

This report documents the second phase of the Remote Operated Vehicle with CO{sub 2} Blasting (ROVCO{sub 2}) Program. The ROVCO{sub 2} Program`s goal is to develop and demonstrate a tool to improve the productivity of concrete floor decontamination. The second phase integrated non-developmental subsystems on to the ROVCO{sub 2} system and performed quantitative decontamination effectiveness, productivity, and reliability testings. The report documents these development activities and the analysis of cost and performance. The results show that the ROVCO{sub 2} system is an efficient decontamination tool.
Diffusion Tensor Imaging Reveals White Matter Injury in a Rat Model of Repetitive Blast-Induced Traumatic Brain Injury

PubMed Central

Calabrese, Evan; Du, Fu; Garman, Robert H.; Johnson, G. Allan; Riccio, Cory; Tong, Lawrence C.

2014-01-01

Abstract Blast-induced traumatic brain injury (bTBI) is one of the most common combat-related injuries seen in U.S. military personnel, yet relatively little is known about the underlying mechanisms of injury. In particular, the effects of the primary blast pressure wave are poorly understood. Animal models have proven invaluable for the study of primary bTBI, because it rarely occurs in isolation in human subjects. Even less is known about the effects of repeated primary blast wave exposure, but existing data suggest cumulative increases in brain damage with a second blast. MRI and, in particular, diffusion tensor imaging (DTI), have become important tools for assessing bTBI in both clinical and preclinical settings. Computational statistical methods such as voxelwise analysis have shown promise in localizing and quantifying bTBI throughout the brain. In this study, we use voxelwise analysis of DTI to quantify white matter injury in a rat model of repetitive primary blast exposure. Our results show a significant increase in microstructural damage with a second blast exposure, suggesting that primary bTBI may sensitize the brain to subsequent injury. PMID:24392843

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

PubMed Central

Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

2014-01-01

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

PubMed Central

2009-01-01

Background ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. Results The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence alignment algorithm which reassembles and evaluates high scoring pairs provided from the BLAST algorithm. Rapid assembly on and replacement of the template genome by sequence reads or mapped ESTs is achieved. This is illustrated (i) by data from Staphylococci as well as from a Blattabacteria sequencing effort, (ii) mapping single cell sequencing reads is shown for poribacteria to sister phylum representative Rhodopirellula Baltica SH1. The algorithm has been implemented in a web-server accessible at http://jane.bioapps.biozentrum.uni-wuerzburg.de. Conclusion Rapid prokaryotic EST mapping or mapping of sequence reads is achieved applying JANE even without knowing the cognate genome sequence. PMID:19943962
STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882
Physics-Based Simulation and Experiment on Blast Protection of Infill Walls and Sandwich Composites Using New Generation of Nano Particle Reinforced Materials

NASA Astrophysics Data System (ADS)

Irshidat, Mohammad

A critical issue for the development of nanotechnology is our ability to understand, model, and simulate the behavior of small structures and to make the connection between nano structure properties and their macroscopic functions. Material modeling and simulation helps to understand the process, to set the objectives that could guide laboratory efforts, and to control material structures, properties, and processes at physical implementation. These capabilities are vital to engineering design at the component and systems level. In this research, experimental-computational-analytical program was employed to investigate the performance of the new generation of polymeric nano-composite materials, like nano-particle reinforced elastomeric materials (NPREM), for the protection of masonry structures against blast loads. New design tools for using these kinds of materials to protect Infill Walls (e.g. masonry walls) against blast loading were established. These tools were also extended to cover other type of panels like sandwich composites. This investigation revealed that polymeric nano composite materials are strain rate sensitive and have large amount of voids distributed randomly inside the materials. Results from blast experiments showed increase in ultimate flexural resistance achieved by both unreinforced and nano reinforced polyurea retrofit systems applied to infill masonry walls. It was also observed that a thin elastomeric coating on the interior face of the walls could be effective at minimizing the fragmentation resulting from blast. More conclusions are provided with recommended future research.
Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

2009-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.
Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

PubMed Central

Andreakis, Nikos; Høj, Lone; Kearns, Philip; Hall, Michael R.; Ericson, Gavin; Cobb, Rose E.; Gordon, Benjamin R.; Evans-Illidge, Elizabeth

2015-01-01

Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters. PMID:26308620
35. INTERIOR VIEW, WHEELBRATORFRYE SHOT PEENER FOR REMOVAL OF RUST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

35. INTERIOR VIEW, WHEELBRATOR-FRYE SHOT PEENER FOR REMOVAL OF RUST AND SCALE; NOTE TOOLS ARE TUMBLED WITH BLASTED WITH LEAD SHOT TO CLEAN SURFACES - Warwood Tool Company, Foot of Nineteenth Street, Wheeling, Ohio County, WV
Injury representation against ballistic threats using three novel numerical models.

PubMed

Breeze, Johno; Fryer, R; Pope, D; Clasper, J

2017-06-01

Injury modelling of ballistic threats is a valuable tool for informing policy on personal protective equipment and other injury mitigation methods. Currently, the Ministry of Defence (MoD) and Centre for Protection of National Infrastructure (CPNI) are focusing on the development of three interlinking numerical models, each of a different fidelity, to answer specific questions on current threats. High-fidelity models simulate the physical events most realistically, and will be used in the future to test the medical effectiveness of personal armour systems. They are however generally computationally intensive, slow running and much of the experimental data to base their algorithms on do not yet exist. Medium fidelity models, such as the personnel vulnerability simulation (PVS), generally use algorithms based on physical or engineering estimations of interaction. This enables a reasonable representation of reality and greatly speeds up runtime allowing full assessments of the entire body area to be undertaken. Low-fidelity models such as the human injury predictor (HIP) tool generally use simplistic algorithms to make injury predictions. Individual scenarios can be run very quickly and hence enable statistical casualty assessments of large groups, where significant uncertainty concerning the threat and affected population exist. HIP is used to simulate the blast and penetrative fragmentation effects of a terrorist detonation of an improvised explosive device within crowds of people in metropolitan environments. This paper describes the collaboration between MoD and CPNI using an example of all three fidelities of injury model and to highlight future areas of research that are required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.

PubMed

Liu, Yongchao; Wirawan, Adrianto; Schmidt, Bertil

2013-04-04

The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases. We present CUDASW++ 3.0, a fast Smith-Waterman protein database search algorithm, which couples CPU and GPU SIMD instructions and carries out concurrent CPU and GPU computations. For the CPU computation, this algorithm employs SSE-based vector execution units as accelerators. For the GPU computation, we have investigated for the first time a GPU SIMD parallelization, which employs CUDA PTX SIMD video instructions to gain more data parallelism beyond the SIMT execution model. Moreover, sequence alignment workloads are automatically distributed over CPUs and GPUs based on their respective compute capabilities. Evaluation on the Swiss-Prot database shows that CUDASW++ 3.0 gains a performance improvement over CUDASW++ 2.0 up to 2.9 and 3.2, with a maximum performance of 119.0 and 185.6 GCUPS, on a single-GPU GeForce GTX 680 and a dual-GPU GeForce GTX 690 graphics card, respectively. In addition, our algorithm has demonstrated significant speedups over other top-performing tools: SWIPE and BLAST+. CUDASW++ 3.0 is written in CUDA C++ and PTX assembly languages, targeting GPUs based on the Kepler architecture. This algorithm obtains significant speedups over its predecessor: CUDASW++ 2.0, by benefiting from the use of CPU and GPU SIMD instructions as well as the concurrent execution on CPUs and GPUs. The source code and the simulated data are available at http://cudasw.sourceforge.net.
Modelling and Testing of Blast Effect On the Structures

NASA Astrophysics Data System (ADS)

Figuli, Lucia; Jangl, Štefan; Papán, Daniel

2016-10-01

As a blasting agent in the blasting and mining engineering, has been using one of so called new generation of explosives which offer greater flexibility in their range and application, and such explosive is ANFO. It is type of explosive consists of an oxidiser and a fuel (ammonium nitrate and fuel oil). One of such ANFO explosives which are industrially made in Slovakia is POLONIT. The explosive is a mixture of ammonium nitrate, methyl esters of higher fatty acids, vegetable oil and red dye. The paper deals with the analysis of structure subjected to the blast load created by the explosion of POLONIT charge. First part of paper is describing behaviour and characteristic of blast wave generated from the blast (detonation characteristics, physical characteristics, time-history diagram etc.) and the second part presents the behaviour of such loaded structures, because of the analysis of such dynamical loaded structure is required knowing the parameters of blast wave, its effect on structure and the tools for the solution of dynamic analysis. The real field tests of three different weight of charges and two different structures were done. The explosive POLONIT was used together with 25 g of ignition explosive PLNp10. Analytical and numerical model of blast loaded structure is compared with the results obtained from the field tests (is compared with the corresponding experimental accelerations). For the modelling structures were approximated as a one-degree system of freedom (SDOF), where the blast wave was estimated with linear decay and exponential decay using positive and negative phase of blast wave. Numerical solution of the steel beam dynamic response was performed via FEM (Finite Element Method) using standard software Visual FEA.
Microstructural consequences of blast lung injury characterised with digital volume correlation

NASA Astrophysics Data System (ADS)

Arora, Hari; Nila, Alex; Vitharana, Kalpani; Sherwood, Joseph M.; Nguyen, Thuy-Tien N.; Karunaratne, Angelo; Mohammed, Idris K.; Bodey, Andrew J.; Hellyer, Peter J.; Overby, Darryl R.; Schroter, Robert C.; Hollis, Dave

2017-12-01

This study focuses on microstructural changes that occur within the mammalian lung when subject to blast and how these changes influence strain distributions within the tissue. Shock tube experiments were performed to generate the blast injured specimens (cadaveric Sprague-Dawley rats). Blast overpressures of 100 kPa and 180 kPa were studied. Synchrotron tomography imaging was used to capture volumetric image data of lungs. Specimens were ventilated using a custom-built system to study multiple inflation pressures during each tomography scan. This data enabled the first digital volume correlation (DVC) measurements in lung tissue to be performed. Quantitative analysis was performed to describe the damaged architecture of the lung. No clear changes in the microstructure of the tissue morphology were observed due to controlled low to moderate level blast exposure. However, significant focal sites of injury were observed using DVC, which allowed detection of bias and concentration in the patterns of strain level. Morphological analysis corroborated the findings, illustrating that the focal damage caused by a blast can give rise to diffuse influence across the tissue. It is important to characterise the non-instantly fatal doses of blast, given the transient nature of blast lung in the clinical setting. This research has highlighted the need for better understanding of focal injury and its zone of influence (alveolar inter-dependency and neighbouring tissue burden as a result of focal injury). Digital volume correlation techniques show great promise as a tool to advance this endeavour, providing a new perspective on lung mechanics post-blast.
Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

PubMed Central

Pride, David T; Schoenfeld, Thomas

2008-01-01

Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes. Conclusion That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis. PMID:18798991
Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

PubMed

Pride, David T; Schoenfeld, Thomas

2008-09-17

Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes. That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.
Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis.

PubMed

Aparicio, G; Götz, S; Conesa, A; Segrelles, D; Blanquer, I; García, J M; Hernandez, V; Robles, M; Talon, M

2006-01-01

The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.
Automated information system for analysis and prediction of production situations in blast furnace plant

NASA Astrophysics Data System (ADS)

Lavrov, V. V.; Spirin, N. A.

2016-09-01

Advances in modern science and technology are inherently connected with the development, implementation, and widespread use of computer systems based on mathematical modeling. Algorithms and computer systems are gaining practical significance solving a range of process tasks in metallurgy of MES-level (Manufacturing Execution Systems - systems controlling industrial process) of modern automated information systems at the largest iron and steel enterprises in Russia. This fact determines the necessity to develop information-modeling systems based on mathematical models that will take into account the physics of the process, the basics of heat and mass exchange, the laws of energy conservation, and also the peculiarities of the impact of technological and standard characteristics of raw materials on the manufacturing process data. Special attention in this set of operations for metallurgic production is devoted to blast-furnace production, as it consumes the greatest amount of energy, up to 50% of the fuel used in ferrous metallurgy. The paper deals with the requirements, structure and architecture of BF Process Engineer's Automated Workstation (AWS), a computer decision support system of MES Level implemented in the ICS of the Blast Furnace Plant at Magnitogorsk Iron and Steel Works. It presents a brief description of main model subsystems as well as assumptions made in the process of mathematical modelling. Application of the developed system allows the engineering and process staff to analyze online production situations in the blast furnace plant, to solve a number of process tasks related to control of heat, gas dynamics and slag conditions of blast-furnace smelting as well as to calculate the optimal composition of blast-furnace slag, which eventually results in increasing technical and economic performance of blast-furnace production.
Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia.

PubMed

Elder, A; Bomken, S; Wilson, I; Blair, H J; Cockell, S; Ponthan, F; Dormon, K; Pal, D; Heidenreich, O; Vormoor, J

2017-12-01

High frequencies of blasts in primary acute lymphoblastic leukaemia (ALL) samples have the potential to induce leukaemia and to engraft mice. However, it is unclear how individual ALL cells each contribute to drive leukaemic development in a bulk transplant and the extent to which these blasts vary functionally. We used cellular barcoding as a fate mapping tool to track primograft ALL blasts in vivo. Our results show that high numbers of ALL founder cells contribute at similar frequencies to leukaemic propagation over serial transplants, without any clear evidence of clonal succession. These founder cells also exhibit equal capacity to home and engraft to different organs, although stochastic processes may alter the composition in restrictive niches. Our findings enhance the stochastic stem cell model of ALL by demonstrating equal functional abilities of singular ALL blasts and show that successful treatment strategies must eradicate the entire leukaemic cell population.
[siRNAs with high specificity to the target: a systematic design by CRM algorithm].

PubMed

Alsheddi, T; Vasin, L; Meduri, R; Randhawa, M; Glazko, G; Baranova, A

2008-01-01

'Off-target' silencing effect hinders the development of siRNA-based therapeutic and research applications. Common solution to this problem is an employment of the BLAST that may miss significant alignments or an exhaustive Smith-Waterman algorithm that is very time-consuming. We have developed a Comprehensive Redundancy Minimizer (CRM) approach for mapping all unique sequences ("targets") 9-to-15 nt in size within large sets of sequences (e.g. transcriptomes). CRM outputs a list of potential siRNA candidates for every transcript of the particular species. These candidates could be further analyzed by traditional "set-of-rules" types of siRNA designing tools. For human, 91% of transcripts are covered by candidate siRNAs with kernel targets of N = 15. We tested our approach on the collection of previously described experimentally assessed siRNAs and found that the correlation between efficacy and presence in CRM-approved set is significant (r = 0.215, p-value = 0.0001). An interactive database that contains a precompiled set of all human siRNA candidates with minimized redundancy is available at http://129.174.194.243. Application of the CRM-based filtering minimizes potential "off-target" silencing effects and could improve routine siRNA applications.
Development of GP and GEP models to estimate an environmental issue induced by blasting operation.

PubMed

Faradonbeh, Roohollah Shirani; Hasanipanah, Mahdi; Amnieh, Hassan Bakhshandeh; Armaghani, Danial Jahed; Monjezi, Masoud

2018-05-21

Air overpressure (AOp) is one of the most adverse effects induced by blasting in the surface mines and civil projects. So, proper evaluation and estimation of the AOp is important for minimizing the environmental problems resulting from blasting. The main aim of this study is to estimate AOp produced by blasting operation in Miduk copper mine, Iran, developing two artificial intelligence models, i.e., genetic programming (GP) and gene expression programming (GEP). Then, the accuracy of the GP and GEP models has been compared to multiple linear regression (MLR) and three empirical models. For this purpose, 92 blasting events were investigated, and subsequently, the AOp values were carefully measured. Moreover, in each operation, the values of maximum charge per delay and distance from blast points, as two effective parameters on the AOp, were measured. After predicting by the predictive models, their performance prediction was checked in terms of variance account for (VAF), coefficient of determination (CoD), and root mean square error (RMSE). Finally, it was found that the GEP with VAF of 94.12%, CoD of 0.941, and RMSE of 0.06 is a more precise model than other predictive models for the AOp prediction in the Miduk copper mine, and it can be introduced as a new powerful tool for estimating the AOp resulting from blasting.

De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

PubMed Central

Gulvik, Christopher A.; Effler, T. Chad; Wilhelm, Steven W.; Buchan, Alison

2012-01-01

Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications. PMID:23189198
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

PubMed Central

Ebhardt, H Alexander; Wiese, Kay C; Unrau, Peter J

2006-01-01

Background DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. Results Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on Conclusion Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]. PMID:16584563
BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

PubMed

Worley, K C; Wiese, B A; Smith, R F

1995-09-01

BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).
Study of consumer fireworks post-blast residues by ATR-FTIR.

PubMed

Martín-Alberca, Carlos; Zapata, Félix; Carrascosa, Héctor; Ortega-Ojeda, Fernando E; García-Ruiz, Carmen

2016-03-01

Specific analytical procedures are requested for the forensic analysis of pre- and post-blast consumer firework samples, which present significant challenges. Up to date, vibrational spectroscopic techniques such as Fourier transform infrared spectroscopy (FTIR) have not been tested for the analysis of post-blast residues in spite of their interesting strengths for the forensic field. Therefore, this work proposes a simple and fast procedure for the sampling and analysis of consumer firework post-blast residues by a portable FTIR instrument with an Attenuated Total Reflection (ATR) accessory. In addition, the post-blast residues spectra of several consumer fireworks were studied in order to achieve the identification of their original chemical compositions. Hence, this work analysed 22 standard reagents usually employed to make consumer fireworks, or because they are related to their combustion products. Then, 5 different consumer fireworks were exploded, and their residues were sampled with dry cotton swabs and directly analysed by ATR-FTIR. In addition, their pre-blast fuses and charges were also analysed in order to stablish a proper comparison. As a result, the identification of the original chemical compositions of the post-blast samples was obtained. Some of the compounds found were potassium chlorate, barium nitrate, potassium nitrate, potassium perchlorate or charcoal. An additional study involving chemometric tools found that the results might greatly depend on the swab head type used for the sampling, and its sampling efficiency. The proposed procedure could be used as a complementary technique for the analysis of consumer fireworks post-blast residues. Copyright © 2015 Elsevier B.V. All rights reserved.
Effects of Blast Overpressure on Neurons and Glial Cells in Rat Organotypic Hippocampal Slice Cultures

PubMed Central

Miller, Anna P.; Shah, Alok S.; Aperi, Brandy V.; Budde, Matthew D.; Pintar, Frank A.; Tarima, Sergey; Kurpad, Shekar N.; Stemper, Brian D.; Glavaski-Joksimovic, Aleksandra

2015-01-01

Due to recent involvement in military conflicts, and an increase in the use of explosives, there has been an escalation in the incidence of blast-induced traumatic brain injury (bTBI) among US military personnel. Having a better understanding of the cellular and molecular cascade of events in bTBI is prerequisite for the development of an effective therapy that currently is unavailable. The present study utilized organotypic hippocampal slice cultures (OHCs) exposed to blast overpressures of 150 kPa (low) and 280 kPa (high) as an in vitro bTBI model. Using this model, we further characterized the cellular effects of the blast injury. Blast-evoked cell death was visualized by a propidium iodide (PI) uptake assay as early as 2 h post-injury. Quantification of PI staining in the cornu Ammonis 1 and 3 (CA1 and CA3) and the dentate gyrus regions of the hippocampus at 2, 24, 48, and 72 h following blast exposure revealed significant time dependent effects. OHCs exposed to 150 kPa demonstrated a slow increase in cell death plateauing between 24 and 48 h, while OHCs from the high-blast group exhibited a rapid increase in cell death already at 2 h, peaking at ~24 h post-injury. Measurements of lactate dehydrogenase release into the culture medium also revealed a significant increase in cell lysis in both low- and high-blast groups compared to sham controls. OHCs were fixed at 72 h post-injury and immunostained for markers against neurons, astrocytes, and microglia. Labeling OHCs with PI, neuronal, and glial markers revealed that the blast-evoked extensive neuronal death and to a lesser extent loss of glial cells. Furthermore, our data demonstrated activation of astrocytes and microglial cells in low- and high-blasted OHCs, which reached a statistically significant difference in the high-blast group. These data confirmed that our in vitro bTBI model is a useful tool for studying cellular and molecular changes after blast exposure. PMID:25729377
Epidemiological Study of Mild Traumatic Brain Injury Sequelae Caused by Blast Exposure During Operations Iraqi Freedom and Enduring Freedom

DTIC Science & Technology

2014-11-01

Emily Lynn, BA Research Assistant April, 2010. (Departed program: July, 2012) Jasmine Smith, BA Research Assistant June, 2010 (Departed Program...final diagnostic algorithm represents the study clinicians’ collective interpretation of 10 the interview data. In essence , it provides a clinician
Modeling Blast Loading on Buried Reinforced Concrete Structures with Zapotec

DOE PAGES

Bessette, Greg C.

2008-01-01

A coupled Euler-Lagrange solution approach is used to model the response of a buried reinforced concrete structure subjected to a close-in detonation of a high explosive charge. The coupling algorithm is discussed along with a set of benchmark calculations involving detonations in clay and sand.
Controlled Low-Pressure Blast-Wave Exposure Causes Distinct Behavioral and Morphological Responses Modelling Mild Traumatic Brain Injury, Post-Traumatic Stress Disorder, and Comorbid Mild Traumatic Brain Injury-Post-Traumatic Stress Disorder.

PubMed

Zuckerman, Amitai; Ram, Omri; Ifergane, Gal; Matar, Michael A; Sagi, Ram; Ostfeld, Ishay; Hoffman, Jay R; Kaplan, Zeev; Sadot, Oren; Cohen, Hagit

2017-01-01

The intense focus in the clinical literature on the mental and neurocognitive sequelae of explosive blast-wave exposure, especially when comorbid with post-traumatic stress-related disorders (PTSD) is justified, and warrants the design of translationally valid animal studies to provide valid complementary basic data. We employed a controlled experimental blast-wave paradigm in which unanesthetized animals were exposed to visual, auditory, olfactory, and tactile effects of an explosive blast-wave produced by exploding a thin copper wire. By combining cognitive-behavioral paradigms and ex vivo brain MRI to assess mild traumatic brain injury (mTBI) phenotype with a validated behavioral model for PTSD, complemented by morphological assessments, this study sought to examine our ability to evaluate the biobehavioral effects of low-intensity blast overpressure on rats, in a translationally valid manner. There were no significant differences between blast- and sham-exposed rats on motor coordination and strength, or sensory function. Whereas most male rats exposed to the blast-wave displayed normal behavioral and cognitive responses, 23.6% of the rats displayed a significant retardation of spatial learning acquisition, fulfilling criteria for mTBI-like responses. In addition, 5.4% of the blast-exposed animals displayed an extreme response in the behavioral tasks used to define PTSD-like criteria, whereas 10.9% of the rats developed both long-lasting and progressively worsening behavioral and cognitive "symptoms," suggesting comorbid PTSD-mTBI-like behavioral and cognitive response patterns. Neither group displayed changes on MRI. Exposure to experimental blast-wave elicited distinct behavioral and morphological responses modelling mTBI-like, PTSD-like, and comorbid mTBI-PTSD-like responses. This experimental animal model can be a useful tool for elucidating neurobiological mechanisms underlying the effects of blast-wave-induced mTBI and PTSD and comorbid mTBI-PTSD.
The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
A multi-band spectral subtraction-based algorithm for real-time noise cancellation applied to gunshot acoustics

NASA Astrophysics Data System (ADS)

Ramos, António L. L.; Holm, Sverre; Gudvangen, Sigmund; Otterlei, Ragnvald

2013-06-01

Acoustical sniper positioning is based on the detection and direction-of-arrival estimation of the shockwave and the muzzle blast acoustical signals. In real-life situations, the detection and direction-of-arrival estimation processes is usually performed under the influence of background noise sources, e.g., vehicles noise, and might result in non-negligible inaccuracies than can affect the system performance and reliability negatively, specially when detecting the muzzle sound under long range distance and absorbing terrains. This paper introduces a multi-band spectral subtraction based algorithm for real-time noise reduction, applied to gunshot acoustical signals. The ballistic shockwave and the muzzle blast signals exhibit distinct frequency contents that are affected differently by additive noise. In most real situations, the noise component is colored and a multi-band spectral subtraction approach for noise reduction contributes to reducing the presence of artifacts in denoised signals. The proposed algorithm is tested using a dataset generated by combining signals from real gunshots and real vehicle noise. The noise component was generated using a steel tracked military tank running on asphalt and includes, therefore, the sound from the vehicle engine, which varies slightly in frequency over time according to the engine's rpm, and the sound from the steel tracks as the vehicle moves.
Bombings specific triage (Bost Tool) tool and its application by healthcare professionals.

PubMed

Sanjay, Jaiswal; Ankur, Verma; Tamorish, Kole

2015-01-01

Bombing is a unique incident which produces unique patterns, multiple and occult injuries. Death often is a result of combined blast, ballistic and thermal effect injuries. Various natures of injury, self referrals and arrival by private transportation may lead to "wrong triage" in the emergency department. In India there has been an increase in incidence of bombing in the last 15 years. There is no documented triage tool from the National Disaster Management Authority of India for Bombings. We have tried to develop an ideal bombing specific triage tool which will guide the right patients to the right place at the right time and save more lives. There are three methods of studying the triage tool: 1) real disaster; 2) mock drill; 3) table top exercise. In this study, a table top exercise method was selected. There are two groups, each consisting of an emergency physician, a nurse and a paramedic. By using the proportion test, we found that correct triaging was significantly different (P=0.005) in proportion between the two groups: group B (80%) with triage tool performed better in triaging the bomb blast victims than group A (50%) without the bombing specific triage tool performed. Development of bombing specific triage tool can reduce under triaging.
Bombings specific triage (Bost Tool) tool and its application by healthcare professionals

PubMed Central

Sanjay, Jaiswal; Ankur, Verma; Tamorish, Kole

2015-01-01

BACKGROUND: Bombing is a unique incident which produces unique patterns, multiple and occult injuries. Death often is a result of combined blast, ballistic and thermal effect injuries. Various natures of injury, self referrals and arrival by private transportation may lead to “wrong triage” in the emergency department. In India there has been an increase in incidence of bombing in the last 15 years. There is no documented triage tool from the National Disaster Management Authority of India for Bombings. We have tried to develop an ideal bombing specific triage tool which will guide the right patients to the right place at the right time and save more lives. METHODS: There are three methods of studying the triage tool: 1) real disaster; 2) mock drill; 3) table top exercise. In this study, a table top exercise method was selected. There are two groups, each consisting of an emergency physician, a nurse and a paramedic. RESULTS: By using the proportion test, we found that correct triaging was significantly different (P=0.005) in proportion between the two groups: group B (80%) with triage tool performed better in triaging the bomb blast victims than group A (50%) without the bombing specific triage tool performed. CONCLUSION: Development of bombing specific triage tool can reduce under triaging. PMID:26693264
Performance Evaluation Test of the Rapid Area Preparation Tool (RAPTOR)

DTIC Science & Technology

2008-12-01

the standard SETCO tires. A blast test of the new SETCO tire is scheduled for the spring of...Washington, DC 20301-2500 Performance Evaluation Test of the Rapid Area Preparation Tool (RAPTOR) December 2008 Prepared ...2008 to 00-00-2008 4. TITLE AND SUBTITLE Performance Evaluation Test of the Rapid Area Preparation Tool (RAPTOR) 5a. CONTRACT NUMBER 5b.
Finding similar nucleotide sequences using network BLAST searches.

PubMed

Ladunga, Istvan

2009-06-01

The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge.
Interphase FISH for BCR-ABL1 rearrangement on neutrophils: A decisive tool to discriminate a lymphoid blast crisis of chronic myeloid leukemia from a de novo BCR-ABL1 positive acute lymphoblastic leukemia.

PubMed

Balducci, Estelle; Loosveld, Marie; Rahal, Ilhem; Boudjarane, John; Alazard, Emilie; Missirian, Chantal; Lafage-Pochitaloff, Marina; Michel, Gérard; Zattara, Hélène

2018-02-01

Discrimination between lymphoid blast crisis of chronic myeloid leukemia (CML) and de novo BCR-ABL1 positive acute lymphoblastic leukemia (ALL) represents a diagnostic challenge because this distinction has a major incidence on the management of patients. Here, we report an uncommon pediatric case of ALL with cryptic ins(22;9)(q11;q34q34) and p190-type BCR-ABL1 transcript. We performed interphase fluorescence in situ hybridization (FISH) for BCR-ABL1 rearrangement on blood neutrophils, which was positive consistent with the diagnosis of lymphoid blast crisis of CML. This case illustrates the major interest of interphase FISH for BCR-ABL1 rearrangement on blood neutrophils as a decisive method to discriminate a lymphoid blast crisis of CML from a de novo BCR-ABL1 positive ALL. Copyright © 2017 John Wiley & Sons, Ltd.
Analysis of MINIE2013 Explosion Air-Blast Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnurr, Julie M.; Rodgers, Arthur J.; Kim, Keehoon

We report analysis of air-blast overpressure measurements from the MINIE2013 explosive experiments. The MINIE2013 experiment involved a series of nearly 70 near-surface (height-ofburst, HOB, ranging from -1 to +4 m) low-yield (W=2-20 kg TNT equivalent) chemical highexplosives tests that were recorded at local distances (230 m – 28.5 km). Many of the W and HOB combinations were repeated, allowing for quantification of the variability in air-blast features and corresponding yield estimates. We measured canonical signal features (peak overpressure, impulse per unit area, and positive pulse duration) from the air-blast data and compared these to existing air-blast models. Peak overpressure measurementsmore » showed good agreement with the models at close ranges but tended to attenuate more rapidly at longer range (~ 1 km), which is likely caused by upward refraction of acoustic waves due to a negative vertical gradient of sound speed. We estimated yields of the MINIE2013 explosions using the Integrated Yield Determination Tool (IYDT). Errors of the estimated yields were on average within 30% of the reported yields, and there were no significant differences in the accuracy of the IYDT predictions grouped by yield. IYDT estimates tend to be lower than ground truth yields, possibly because of reduced overpressure amplitudes by upward refraction. Finally, we report preliminary results on a development of a new parameterized air-blast waveform.« less
SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.
Ubiquitin Carboxy-Terminal Hydrolase-L1 as a Serum Neurotrauma Biomarker for Exposure to Occupational Low-Level Blast

PubMed Central

Carr, Walter; Yarnell, Angela M.; Ong, Ricardo; Walilko, Timothy; Kamimori, Gary H.; da Silva, Uade; McCarron, Richard M.; LoPresti, Matthew L.

2015-01-01

Repeated exposure to low-level blast is a characteristic of a few select occupations and there is concern that such occupational exposures present risk for traumatic brain injury. These occupations include specialized military and law enforcement units that employ controlled detonation of explosive charges for the purpose of tactical entry into secured structures. The concern for negative effects from blast exposure is based on rates of operator self-reported headache, sleep disturbance, working memory impairment, and other concussion-like symptoms. A challenge in research on this topic has been the need for improved assessment tools to empirically evaluate the risk associated with repeated exposure to blast overpressure levels commonly considered to be too low in magnitude to cause acute injury. Evaluation of serum-based neurotrauma biomarkers provides an objective measure that is logistically feasible for use in field training environments. Among candidate biomarkers, ubiquitin carboxy-terminal hydrolase-L1 (UCH-L1) has some empirical support and was evaluated in this study. We used daily blood draws to examine acute change in UCH-L1 among 108 healthy military personnel who were exposed to repeated low-level blast across a 2-week period. These research volunteers also wore pressure sensors to record blast exposures, wrist actigraphs to monitor sleep patterns, and completed daily behavioral assessments of symptomology, postural stability, and neurocognitive function. UCH-L1 levels were elevated as a function of participating in the 2-week training with explosives, but the correlation of UCH-L1 elevation and blast magnitude was weak and inconsistent. Also, UCH-L1 elevations did not correlate with deficits in behavioral measures. These results provide some support for including UCH-L1 as a measure of central nervous system effects from exposure to low-level blast. However, the weak relation observed suggests that additional indicators of blast effect are needed. PMID:25852633
Continuum modeling of neuronal cell under blast loading

PubMed Central

Jérusalem, Antoine; Dao, Ming

2012-01-01

Traumatic brain injuries have recently been put under the spotlight as one of the most important causes of accidental brain dysfunctions. Significant experimental and modeling efforts are thus ongoing to study the associated biological, mechanical and physical mechanisms. In the field of cell mechanics, progresses are also being made at the experimental and modeling levels to better characterize many of the cell functions such as differentiation, growth, migration and death, among others. The work presented here aims at bridging both efforts by proposing a continuum model of neuronal cell submitted to blast loading. In this approach, cytoplasm, nucleus and membrane (plus cortex) are differentiated in a representative cell geometry, and different material constitutive models are adequately chosen for each one. The material parameters are calibrated against published experimental work of cell nanoindentation at multiple rates. The final cell model is ultimately subjected to blast loading within a complete fluid-structure interaction computational framework. The results are compared to the nanoindentation simulation and the specific effects of the blast wave on the pressure and shear levels at the interfaces are identified. As a conclusion, the presented model successfully captures some of the intrinsic intracellular phenomena occurring during its deformation under blast loading and potentially leading to cell damage. It suggests more particularly the localization of damage at the nucleus membrane similarly to what has already been observed at the overall cell membrane. This degree of damage is additionally predicted to be worsened by a longer blast positive phase duration. As a conclusion, the proposed model ultimately provides a new three dimensional computational tool to evaluate intracellular damage during blast loading. PMID:22562014
Why Choose This One? Factors in Scientists' Selection of Bioinformatics Tools

ERIC Educational Resources Information Center

Bartlett, Joan C.; Ishimura, Yusuke; Kloda, Lorie A.

2011-01-01

Purpose: The objective was to identify and understand the factors involved in scientists' selection of preferred bioinformatics tools, such as databases of gene or protein sequence information (e.g., GenBank) or programs that manipulate and analyse biological data (e.g., BLAST). Methods: Eight scientists maintained research diaries for a two-week…

DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins.

PubMed

Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Banchariya, Anjali; Rao, Atmakuri Ramakrishna

2017-03-24

Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the proteins encoded from certain class of genes of the insects. To distinguish the insecticide resistant proteins from non-resistant proteins, no computational tool is available till date. Thus, development of such a computational tool will be helpful in predicting the insecticide resistant proteins, which can be targeted for developing appropriate insecticides. Five different sets of feature viz., amino acid composition (AAC), di-peptide composition (DPC), pseudo amino acid composition (PAAC), composition-transition-distribution (CTD) and auto-correlation function (ACF) were used to map the protein sequences into numeric feature vectors. The encoded numeric vectors were then used as input in support vector machine (SVM) for classification of insecticide resistant and non-resistant proteins. Higher accuracies were obtained under RBF kernel than that of other kernels. Further, accuracies were observed to be higher for DPC feature set as compared to others. The proposed approach achieved an overall accuracy of >90% in discriminating resistant from non-resistant proteins. Further, the two classes of resistant proteins i.e., detoxification-based and target-based were discriminated from non-resistant proteins with >95% accuracy. Besides, >95% accuracy was also observed for discrimination of proteins involved in detoxification- and target-based resistance mechanisms. The proposed approach not only outperformed Blastp, PSI-Blast and Delta-Blast algorithms, but also achieved >92% accuracy while assessed using an independent dataset of 75 insecticide resistant proteins. This paper presents the first computational approach for discriminating the insecticide resistant proteins from non-resistant proteins. Based on the proposed approach, an online prediction server DIRProt has also been developed for computational prediction of insecticide resistant proteins, which is accessible at http://cabgrid.res.in:8080/dirprot/ . The proposed approach is believed to supplement the efforts needed to develop dynamic insecticides in wet-lab by targeting the insecticide resistant proteins.
How effective are DNA barcodes in the identification of African rainforest trees?

PubMed

Parmentier, Ingrid; Duminil, Jérôme; Kuzmina, Maria; Philippe, Morgane; Thomas, Duncan W; Kenfack, David; Chuyong, George B; Cruaud, Corinne; Hardy, Olivier J

2013-01-01

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.
How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

PubMed Central

Parmentier, Ingrid; Duminil, Jérôme; Kuzmina, Maria; Philippe, Morgane; Thomas, Duncan W.; Kenfack, David; Chuyong, George B.; Cruaud, Corinne; Hardy, Olivier J.

2013-01-01

Background DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. Methodology/Principal Findings We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. Conclusions/Significance Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications. PMID:23565134
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

PubMed Central

Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko

2015-01-01

Abstract Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. PMID:25948579
Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790
Prediction of subcellular localization of eukaryotic proteins using position-specific profiles and neural network with weighted inputs.

PubMed

Zou, Lingyun; Wang, Zhengzhi; Huang, Jiaomin

2007-12-01

Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles (PSP) have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific Iterative-Basic Local Alignment Search Tool (PSI-BLAST) has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and 1st-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network (PSP-WNN). The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.
Blasting vibrations control: The shortcomings of traditional methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vuillaume, P.M.; Kiszlo, M.; Bernard, T.

1996-12-31

In the context of its studies for the French ministry of the environment and for the French national coal board, INERIS (the French institute for the industrial environment and hazards, formerly CERCHAR) has made a complete critical survey of the methods generally used to reduce the levels of blasting vibrations. It is generally acknowledged that the main parameter to control vibrations is the so-called instantaneous charge, or charge per delay. This should be reduced as much as possible in order to diminish vibration levels. On account of this, the use of a new generation of blasting devices, such as non-electricmore » detonators or electronic sequential timers has been developed since the seventies. INERIS has collected data from about 900 blasts in 2 quarries and 3 open pit mines. These data include input parameters such as borehole diameter, burden, spacing, charge per hole, charge per delay, total fired charge, etc ... They also include output measurements, such as vibration peak particle velocities, and main frequencies. These data have been analyzed with the help of multi variable statistical tools. Blasting tests were undertaken to evaluate new methods of vibrations control, such as the superposition of vibration signals. These methods appear to be accurate in many critical cases, but certainly would be highly improved with a better accuracy of firing delays. The development of electronic detonators seems to be the way of the future for a better blasting control.« less
BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu
The Future of Sustainable Transportation | Transportation Research | NREL

Science.gov Websites

lithium-ion batteries need to be dramatically cut for electric vehicles (EVs) to reach a wider audience pledge to provide workplace charging. New Tool Helps Optimize Battery Lifespan While upfront costs of . NREL's new Battery Lifetime Analysis and Simulation Tool (BLAST) suite makes it possible to predict long
An automated genotyping tool for enteroviruses and noroviruses.

PubMed

Kroneman, A; Vennema, H; Deforche, K; v d Avoort, H; Peñaranda, S; Oberste, M S; Vinjé, J; Koopmans, M

2011-06-01

Molecular techniques are established as routine in virological laboratories and virus typing through (partial) sequence analysis is increasingly common. Quality assurance for the use of typing data requires harmonization of genotype nomenclature, and agreement on target genes, depending on the level of resolution required, and robustness of methods. To develop and validate web-based open-access typing-tools for enteroviruses and noroviruses. An automated web-based typing algorithm was developed, starting with BLAST analysis of the query sequence against a reference set of sequences from viruses in the family Picornaviridae or Caliciviridae. The second step is phylogenetic analysis of the query sequence and a sub-set of the reference sequences, to assign the enterovirus type or norovirus genotype and/or variant, with profile alignment, construction of phylogenetic trees and bootstrap validation. Typing is performed on VP1 sequences of Human enterovirus A to D, and ORF1 and ORF2 sequences of genogroup I and II noroviruses. For validation, we used the tools to automatically type sequences in the RIVM and CDC enterovirus databases and the FBVE norovirus database. Using the typing-tools, 785(99%) of 795 Enterovirus VP1 sequences, and 8154(98.5%) of 8342 norovirus sequences were typed in accordance with previously used methods. Subtyping into variants was achieved for 4439(78.4%) of 5838 NoV GII.4 sequences. The online typing-tools reliably assign genotypes for enteroviruses and noroviruses. The use of phylogenetic methods makes these tools robust to ongoing evolution. This should facilitate standardized genotyping and nomenclature in clinical and public health laboratories, thus supporting inter-laboratory comparisons. Copyright © 2011 Elsevier B.V. All rights reserved.
On the formation of Friedlander waves in a compressed-gas-driven shock tube

PubMed Central

Tasissa, Abiy F.; Hautefeuille, Martin; Fitek, John H.; Radovitzky, Raúl A.

2016-01-01

Compressed-gas-driven shock tubes have become popular as a laboratory-scale replacement for field blast tests. The well-known initial structure of the Riemann problem eventually evolves into a shock structure thought to resemble a Friedlander wave, although this remains to be demonstrated theoretically. In this paper, we develop a semi-analytical model to predict the key characteristics of pseudo blast waves forming in a shock tube: location where the wave first forms, peak over-pressure, decay time and impulse. The approach is based on combining the solutions of the two different types of wave interactions that arise in the shock tube after the family of rarefaction waves in the Riemann solution interacts with the closed end of the tube. The results of the analytical model are verified against numerical simulations obtained with a finite volume method. The model furnishes a rational approach to relate shock tube parameters to desired blast wave characteristics, and thus constitutes a useful tool for the design of shock tubes for blast testing. PMID:27118888
Development of a Portable Tool for Screening Neuromotor Sequelae From Repetitive Low-Level Blast Exposure.

PubMed

Rhea, Christopher K; Kuznetsov, Nikita A; Ross, Scott E; Long, Benjamin; Jakiela, Jason T; Bailie, Jason M; Yanagi, Matthew A; Haran, F Jay; Wright, W Geoffrey; Robins, Rebecca K; Sargent, Paul D; Duckworth, Joshua L

2017-03-01

Blast exposure is a prevalent cause of mild traumatic brain injury (mTBI) in military personnel in combat. However, it is more common for a service member to be exposed to a low-level blast (LLB) that does not result in a clinically diagnosable mTBI. Recent research suggests that repetitive LLB exposure can result in symptomology similar to symptoms observed after mTBI. This manuscript reports on the use of an Android-based smartphone application (AccWalker app) to capture changes in neuromotor functioning after blast exposure. Active duty U.S. Navy personnel (N = 59) performed a stepping-in-place task before repetitive LLB exposure (heavy weapons training), and again immediately after, 24 hours after, and 72 to 96 hours after the completion of the training. The AccWalker app revealed that there are changes in neuromotor functioning after LLB exposure (slower self-selected movement pace and increased stride time variability) in participants who experienced neurocognitive decline. These data suggest that neurocognitive and neuromotor decline can occur after repeated LLB exposure. Reprint & Copyright © 2017 Association of Military Surgeons of the U.S.
CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens.

PubMed

Qiu, Tianyi; Yang, Yiyan; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan; Tang, Kailin; Xu, Jianqing; Cao, Zhiwei

2018-05-02

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination. Application to dengue-related data demonstrates high harmonization between the computed clusters and the experimental serological data, undetectable by classical grouping. CE-BLAST identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus, precisely corroborated by experimental data. The high performance of the pathogens without the experimental binding data suggests the potential utility of CE-BLAST to rapidly design cross-protective vaccines or promptly determine the efficacy of the currently marketed vaccine against emerging pathogens, which are the critical factors for containing emerging disease outbreaks.
Simulation of adaptive semi-active magnetorheological seat damper for vehicle occupant blast protection

NASA Astrophysics Data System (ADS)

Yoo, Jin-Hyeong; Murugan, Muthuvel; Wereley, Norman M.

2013-04-01

This study investigates a lumped-parameter human body model which includes lower leg in seated posture within a quarter-car model for blast injury assessment simulation. To simulate the shock acceleration of the vehicle, mine blast analysis was conducted on a generic land vehicle crew compartment (sand box) structure. For the purpose of simulating human body dynamics with non-linear parameters, a physical model of a lumped-parameter human body within a quarter car model was implemented using multi-body dynamic simulation software. For implementing the control scheme, a skyhook algorithm was made to work with the multi-body dynamic model by running a co-simulation with the control scheme software plug-in. The injury criteria and tolerance levels for the biomechanical effects are discussed for each of the identified vulnerable body regions, such as the relative head displacement and the neck bending moment. The desired objective of this analytical model development is to study the performance of adaptive semi-active magnetorheological damper that can be used for vehicle-occupant protection technology enhancements to the seat design in a mine-resistant military vehicle.
Dynamic programming algorithms for biological sequence comparison.

PubMed

Pearson, W R; Miller, W

1992-01-01

Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.
Usage of density analysis based on micro-CT for studying lung injury associated with burn-blast combined injury.

PubMed

Chang, Yang; Zhang, Dong-Hai; Hu, Quan; Liu, Ling-Ying; Yu, Yong-Hui; Chai, Jia-Ke

2018-02-12

Burn-blast combined injury is a kind of injury caused by heat and blast at the same time. The lung injury after burn-blast combined injuries is of primary importance, and investigation of lung injury is needed in the clinical care of patients. Computed tomography (CT) is one of the standard tools used to observe the anatomical basis and pathophysiology of acute lung injury. We applied a method of fast 3D (three-dimensional) reconstruction to calculate the density value of the lung injury by CT analysis. Blast-injury group (BL group), burn-injury group (B group), burn-blast combined injury group (BBL group), and sham control group (C group) were established. Each group had 16 rats. The three-dimensional images of the lung tissue were obtained at 6h, 24h, and 48h according to the CT value. The average density of the whole lung, left lung, and right lung were measured. The lung tissues were paraffin-embedded and HE stained. Smith scoring was performed according to the pathological findings. In the BBL group, the density of the lung tissue was higher than those of the BL group and B group (P<0.01). The lung tissue density values at 24h after injury were higher than those at 6h and 48h after injury (P<0.01). Pathological results confirmed the changes of density analysis of the lung tissue. The results have indicated that density analysis through a CT scan can be used as a way to evaluate lung injury in a burn-blast injury. Copyright © 2018 Elsevier Ltd and ISBI. All rights reserved.
Oxy-acetylene driven laboratory scale shock tubes for studying blast wave effects

NASA Astrophysics Data System (ADS)

Courtney, Amy C.; Andrusiv, Lubov P.; Courtney, Michael W.

2012-04-01

This paper describes the development and characterization of modular, oxy-acetylene driven laboratory scale shock tubes. Such tools are needed to produce realistic blast waves in a laboratory setting. The pressure-time profiles measured at 1 MHz using high-speed piezoelectric pressure sensors have relevant durations and show a true shock front and exponential decay characteristic of free-field blast waves. Descriptions are included for shock tube diameters of 27-79 mm. A range of peak pressures from 204 kPa to 1187 kPa (with 0.5-5.6% standard error of the mean) were produced by selection of the driver section diameter and distance from the shock tube opening. The peak pressures varied predictably with distance from the shock tube opening while maintaining both a true blast wave profile and relevant pulse duration for distances up to about one diameter from the shock tube opening. This shock tube design provides a more realistic blast profile than current compression-driven shock tubes, and it does not have a large jet effect. In addition, operation does not require specialized personnel or facilities like most blast-driven shock tubes, which reduces operating costs and effort and permits greater throughput and accessibility. It is expected to be useful in assessing the response of various sensors to shock wave loading; assessing the reflection, transmission, and absorption properties of candidate armor materials; assessing material properties at high rates of loading; assessing the response of biological materials to shock wave exposure; and providing a means to validate numerical models of the interaction of shock waves with structures. All of these activities have been difficult to pursue in a laboratory setting due in part to lack of appropriate means to produce a realistic blast loading profile.
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

PubMed Central

2011-01-01

Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance. PMID:21631914
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

PubMed

Rognes, Torbjørn

2011-06-01

The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.
Accelerated time-resolved three-dimensional MR velocity mapping of blood flow patterns in the aorta using SENSE and k-t BLAST.

PubMed

Stadlbauer, Andreas; van der Riet, Wilma; Crelier, Gerard; Salomonowitz, Erich

2010-07-01

To assess the feasibility and potential limitations of the acceleration techniques SENSE and k-t BLAST for time-resolved three-dimensional (3D) velocity mapping of aortic blood flow. Furthermore, to quantify differences in peak velocity versus heart phase curves. Time-resolved 3D blood flow patterns were investigated in eleven volunteers and two patients suffering from aortic diseases with accelerated PC-MR sequences either in combination with SENSE (R=2) or k-t BLAST (6-fold). Both sequences showed similar data acquisition times and hence acceleration efficiency. Flow-field streamlines were calculated and visualized using the GTFlow software tool in order to reconstruct 3D aortic blood flow patterns. Differences between the peak velocities from single-slice PC-MRI experiments using SENSE 2 and k-t BLAST 6 were calculated for the whole cardiac cycle and averaged for all volunteers. Reconstruction of 3D flow patterns in volunteers revealed attenuations in blood flow dynamics for k-t BLAST 6 compared to SENSE 2 in terms of 3D streamlines showing fewer and less distinct vortices and reduction in peak velocity, which is caused by temporal blurring. Solely by time-resolved 3D MR velocity mapping in combination with SENSE detected pathologic blood flow patterns in patients with aortic diseases. For volunteers, we found a broadening and flattering of the peak velocity versus heart phase diagram between the two acceleration techniques, which is an evidence for the temporal blurring of the k-t BLAST approach. We demonstrated the feasibility of SENSE and detected potential limitations of k-t BLAST when used for time-resolved 3D velocity mapping. The effects of higher k-t BLAST acceleration factors have to be considered for application in 3D velocity mapping. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

Code Verification Results of an LLNL ASC Code on Some Tri-Lab Verification Test Suite Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, S R; Bihari, B L; Salari, K

As scientific codes become more complex and involve larger numbers of developers and algorithms, chances for algorithmic implementation mistakes increase. In this environment, code verification becomes essential to building confidence in the code implementation. This paper will present first results of a new code verification effort within LLNL's B Division. In particular, we will show results of code verification of the LLNL ASC ARES code on the test problems: Su Olson non-equilibrium radiation diffusion, Sod shock tube, Sedov point blast modeled with shock hydrodynamics, and Noh implosion.
PMD compensation in multilevel coded-modulation schemes with coherent detection using BLAST algorithm and iterative polarization cancellation.

PubMed

Djordjevic, Ivan B; Xu, Lei; Wang, Ting

2008-09-15

We present two PMD compensation schemes suitable for use in multilevel (M>or=2) block-coded modulation schemes with coherent detection. The first scheme is based on a BLAST-type polarization-interference cancellation scheme, and the second scheme is based on iterative polarization cancellation. Both schemes use the LDPC codes as channel codes. The proposed PMD compensations schemes are evaluated by employing coded-OFDM and coherent detection. When used in combination with girth-10 LDPC codes those schemes outperform polarization-time coding based OFDM by 1 dB at BER of 10(-9), and provide two times higher spectral efficiency. The proposed schemes perform comparable and are able to compensate even 1200 ps of differential group delay with negligible penalty.
Iterative MMSE Detection for MIMO/BLAST DS-CDMA Systems in Frequency Selective Fading Channels - Achieving High Performance in Fully Loaded Systems

NASA Astrophysics Data System (ADS)

Silva, João Carlos; Souto, Nuno; Cercas, Francisco; Dinis, Rui

A MMSE (Minimum Mean Square Error) DS-CDMA (Direct Sequence-Code Division Multiple Access) receiver coupled with a low-complexity iterative interference suppression algorithm was devised for a MIMO/BLAST (Multiple Input, Multiple Output / Bell Laboratories Layered Space Time) system in order to improve system performance, considering frequency selective fading channels. The scheme is compared against the simple MMSE receiver, for both QPSK and 16QAM modulations, under SISO (Single Input, Single Output) and MIMO systems, the latter with 2Tx by 2Rx and 4Tx by 4Rx (MIMO order 2 and 4 respectively) antennas. To assess its performance in an existing system, the uncoded UMTS HSDPA (High Speed Downlink Packet Access) standard was considered.
Application of neural networks for the prediction of rock fragmentation in Chadormalu iron mine / Zastosowanie sieci neuronowych do prognozowania stopnia rozdrobnienia skał w kopalni rud żelaza w Chadormalu

NASA Astrophysics Data System (ADS)

Monjezi, Masoud; Ahmadi, Zabiholla; Khandelwal, Manoj

2012-12-01

Most open-pit mining operations employ blasting for primary breakage of the in-situ rock mass. Inappropriate blasting techniques can result in excessive damage to the wall rock, decreasing stability and increasing water influx. In addition, it will result in either over and/or under breakage of rocks. The presence of over broken rocks can result in decreased wall stability and require additional excavation. In contrast, the presence of under broken rocks may require secondary blasting and additional crushing. Since blasting is a major cost factor, both cases (under and over breakage) create additional costs reflected in the increase of the operation and maintenance of the machinery. Quick and accurate measurements of fragment size distribution are essential for managing fragmented rock and other materials. Various fragmentation measurement techniques are available and are being used by industry/researchers but most of the methods are time consuming and not precise. An ideally performed blasting operation enormously influences the overall mining cost. This aim can be achieved by proper prediction and attenuation of fragmentation. Prediction of fragmentation is essential for optimizing blasting operation. Poor performance of the empirical models for predicting fragmentation has urged the application of new approaches. In this paper, artificial neural network (ANN) method is implemented to develop a model to predict rock fragmentation size distribution due to blasting in Chadormalu iron mine, Iran. In the development of the proposed ANN model, ten parameters such as UCS, drilling rate, water content, burden, spacing, stemming, hole diameter, bench height, powder factor and charge per delay were incorporated. Training and testing of the model was performed by the back-propagation algorithm using 97 datasets. A four-layer ANN was found to be optimum with architecture of 10-7-5-1. A comparison has made between measured results of fragmentation with predicted results of fragmentation by ANN and multiple regression model. Sensitivity analysis was also performed to understand the effect of each influencing parameters on rock fragmentation.
Considerations for animal models of blast-related traumatic brain injury and chronic traumatic encephalopathy.

PubMed

Goldstein, Lee E; McKee, Ann C; Stanton, Patric K

2014-01-01

The association of military blast exposure and brain injury was first appreciated in World War I as commotio cerebri, and later as shell shock. Similar injuries sustained in modern military conflicts are now classified as mild traumatic brain injury (TBI). Recent research has yielded new insights into the mechanisms by which blast exposure leads to acute brain injury and chronic sequelae, including postconcussive syndrome, post-traumatic stress disorder, post-traumatic headache, and chronic traumatic encephalopathy, a tau protein neurodegenerative disease. Impediments to delivery of effective medical care for individuals affected by blast-related TBI include: poor insight into the heterogeneity of neurological insults induced by blast exposure; limited understanding of the mechanisms by which blast exposure injures the brain and triggers sequelae; failure to appreciate interactive injuries that affect frontal lobe function, pituitary regulation, and neurovegetative homeostasis; unknown influence of genetic risk factors, prior trauma, and comorbidities; absence of validated diagnostic criteria and clinical nosology that differentiate clinical endophenotypes; and lack of empirical evidence to guide medical management and therapeutic intervention. While clinicopathological analysis can provide evidence of correlative association, experimental use of animal models remains the primary tool for establishing causal mechanisms of disease. However, the TBI field is confronted by a welter of animal models with varying clinical relevance, thereby impeding scientific coherence and hindering translational progress. Animal models of blast TBI will be far more translationally useful if experimental emphasis focuses on accurate reproduction of clinically relevant endpoints (output) rather than scaled replication of idealized blast shockwaves (input). The utility of an animal model is dependent on the degree to which the model recapitulates pathophysiological mechanisms, neuropathological features, and neurological sequelae observed in the corresponding human disorder. Understanding the purpose of an animal model and the criteria by which experimental results derived from the model are validated are critical components for useful animal modeling. Animal models that reliably demonstrate clinically relevant endpoints will expedite development of new treatments, diagnostics, preventive measures, and rehabilitative strategies for individuals affected by blast TBI and its aftermath.
Considerations for animal models of blast-related traumatic brain injury and chronic traumatic encephalopathy

PubMed Central

2014-01-01

The association of military blast exposure and brain injury was first appreciated in World War I as commotio cerebri, and later as shell shock. Similar injuries sustained in modern military conflicts are now classified as mild traumatic brain injury (TBI). Recent research has yielded new insights into the mechanisms by which blast exposure leads to acute brain injury and chronic sequelae, including postconcussive syndrome, post-traumatic stress disorder, post-traumatic headache, and chronic traumatic encephalopathy, a tau protein neurodegenerative disease. Impediments to delivery of effective medical care for individuals affected by blast-related TBI include: poor insight into the heterogeneity of neurological insults induced by blast exposure; limited understanding of the mechanisms by which blast exposure injures the brain and triggers sequelae; failure to appreciate interactive injuries that affect frontal lobe function, pituitary regulation, and neurovegetative homeostasis; unknown influence of genetic risk factors, prior trauma, and comorbidities; absence of validated diagnostic criteria and clinical nosology that differentiate clinical endophenotypes; and lack of empirical evidence to guide medical management and therapeutic intervention. While clinicopathological analysis can provide evidence of correlative association, experimental use of animal models remains the primary tool for establishing causal mechanisms of disease. However, the TBI field is confronted by a welter of animal models with varying clinical relevance, thereby impeding scientific coherence and hindering translational progress. Animal models of blast TBI will be far more translationally useful if experimental emphasis focuses on accurate reproduction of clinically relevant endpoints (output) rather than scaled replication of idealized blast shockwaves (input). The utility of an animal model is dependent on the degree to which the model recapitulates pathophysiological mechanisms, neuropathological features, and neurological sequelae observed in the corresponding human disorder. Understanding the purpose of an animal model and the criteria by which experimental results derived from the model are validated are critical components for useful animal modeling. Animal models that reliably demonstrate clinically relevant endpoints will expedite development of new treatments, diagnostics, preventive measures, and rehabilitative strategies for individuals affected by blast TBI and its aftermath. PMID:25478023
AutoFACT: An Automatic Functional Annotation and Classification Tool

PubMed Central

Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

2005-01-01

Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

PubMed

Brandt, Bernd W; Heringa, Jaap; Leunissen, Jack A M

2008-07-01

With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files contain sequence and coordinate information. Residues present in the sequence can be absent from the coordinate section, which means their position in space is unknown. Similarity searches are routinely carried out against sequences taken from PDB SEQRES. However, there no distinction is made between residues that have a known or unknown position in the 3D protein structure. We present a FASTA sequence database that is produced by combining the sequence and coordinate information. All residues absent from the PDB coordinate section are masked with lower-case letters, thereby providing a view of these residues in the context of the entire protein sequence, which facilitates inspecting 'missing' regions. We also provide a masked version of the CATH domain database. A user-friendly BLAST interface is available for similarity searching. In contrast to standard (stand-alone) BLAST output, which only contains upper-case letters, our output retains the lower-case letters of the masked regions. Thus, our server can be used to perform BLAST searching case-sensitively. Here, we have applied it to the study of missing regions in their sequence context. SEQATOMS is available at http://www.bioinformatics.nl/tools/seqatoms/.
Optimization of Sinter Plant Operating Conditions Using Advanced Multivariate Statistics: Intelligent Data Processing

NASA Astrophysics Data System (ADS)

Fernández-González, Daniel; Martín-Duarte, Ramón; Ruiz-Bustinza, Íñigo; Mochón, Javier; González-Gasca, Carmen; Verdeja, Luis Felipe

2016-08-01

Blast furnace operators expect to get sinter with homogenous and regular properties (chemical and mechanical), necessary to ensure regular blast furnace operation. Blends for sintering also include several iron by-products and other wastes that are obtained in different processes inside the steelworks. Due to their source, the availability of such materials is not always consistent, but their total production should be consumed in the sintering process, to both save money and recycle wastes. The main scope of this paper is to obtain the least expensive iron ore blend for the sintering process, which will provide suitable chemical and mechanical features for the homogeneous and regular operation of the blast furnace. The systematic use of statistical tools was employed to analyze historical data, including linear and partial correlations applied to the data and fuzzy clustering based on the Sugeno Fuzzy Inference System to establish relationships among the available variables.
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

PubMed

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.
Detecting false positive sequence homology: a machine learning approach.

PubMed

Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Bybee, Seth M

2016-02-24

Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

PubMed

Bonizzoni, Paola; Rizzi, Raffaella; Pesole, Graziano

2005-10-05

Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.
Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563
Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

PubMed Central

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

PubMed

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/
A Monte Carlo Approach to Modeling the Breakup of the Space Launch System EM-1 Core Stage with an Integrated Blast and Fragment Catalogue

NASA Technical Reports Server (NTRS)

Richardson, Erin; Hays, M. J.; Blackwood, J. M.; Skinner, T.

2014-01-01

The Liquid Propellant Fragment Overpressure Acceleration Model (L-FOAM) is a tool developed by Bangham Engineering Incorporated (BEi) that produces a representative debris cloud from an exploding liquid-propellant launch vehicle. Here it is applied to the Core Stage (CS) of the National Aeronautics and Space Administration (NASA) Space Launch System (SLS launch vehicle). A combination of Probability Density Functions (PDF) based on empirical data from rocket accidents and applicable tests, as well as SLS specific geometry are combined in a MATLAB script to create unique fragment catalogues each time L-FOAM is run-tailored for a Monte Carlo approach for risk analysis. By accelerating the debris catalogue with the BEi blast model for liquid hydrogen / liquid oxygen explosions, the result is a fully integrated code that models the destruction of the CS at a given point in its trajectory and generates hundreds of individual fragment catalogues with initial imparted velocities. The BEi blast model provides the blast size (radius) and strength (overpressure) as probabilities based on empirical data and anchored with analytical work. The coupling of the L-FOAM catalogue with the BEi blast model is validated with a simulation of the Project PYRO S-IV destruct test. When running a Monte Carlo simulation, L-FOAM can accelerate all catalogues with the same blast (mean blast, 2 s blast, etc.), or vary the blast size and strength based on their respective probabilities. L-FOAM then propagates these fragments until impact with the earth. Results from L-FOAM include a description of each fragment (dimensions, weight, ballistic coefficient, type and initial location on the rocket), imparted velocity from the blast, and impact data depending on user desired application. LFOAM application is for both near-field (fragment impact to escaping crew capsule) and far-field (fragment ground impact footprint) safety considerations. The user is thus able to use statistics from a Monte Carlo set of L-FOAM catalogues to quantify risk for a multitude of potential CS destruct scenarios. Examples include the effect of warning time on the survivability of an escaping crew capsule or the maximum fragment velocities generated by the ignition of leaking propellants in internal cavities.
About creation of machines for rock destruction with formation of apertures of various cross-sections

NASA Astrophysics Data System (ADS)

Zhukov, I. A.; Dvornikov, L. T.; Nikitenko, S. M.

2016-04-01

The article presents the results of the experimental research of the high strength rock destruction by a bladeless tool. Rational circuit designs of disposing of indenters in the impact part of the drill bits and a diamond tool are justified. New constructive solutions of reinforcing bladeless drill bits, which allow drilling blast-holes of the various cross-section, are shown.
Analysis of dynamical response of air blast loaded safety device

NASA Astrophysics Data System (ADS)

Tropkin, S. N.; Tlyasheva, R. R.; Bayazitov, M. I.; Kuzeev, I. R.

2018-03-01

Equipment of many oil and gas processing plants in the Russian Federation is considerably worn-out. This causes the decrease of reliability and durability of equipment and rises the accident rate. An air explosion is the one of the most dangerous cases for plants in oil and gas industry, usually caused by uncontrolled emission and inflammation of oil products. Air explosion can lead to significant danger for life and health of plant staff, so it necessitates safety device usage. A new type of a safety device is designed. Numerical simulation is necessary to analyse design parameters and performance of the safety device, subjected to air blast loading. Coupled fluid-structure interaction analysis is performed to determine strength of the protective device and its performance. The coupled Euler-Lagrange method, allowable in Abaqus by SIMULIA, is selected as the most appropriate analysis tool to study blast wave interaction with the safety device. Absorption factors of blast wave are evaluated for the safety device. This factors allow one to assess efficiency of the safety device, and its main structural component – dampener. Usage of CEL allowed one to model fast and accurately the dampener behaviour, and to develop the parametric model to determine safety device sizes.
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

PubMed

Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

2015-07-01

Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Colour image segmentation using unsupervised clustering technique for acute leukemia images

NASA Astrophysics Data System (ADS)

Halim, N. H. Abd; Mashor, M. Y.; Nasir, A. S. Abdul; Mustafa, N.; Hassan, R.

2015-05-01

Colour image segmentation has becoming more popular for computer vision due to its important process in most medical analysis tasks. This paper proposes comparison between different colour components of RGB(red, green, blue) and HSI (hue, saturation, intensity) colour models that will be used in order to segment the acute leukemia images. First, partial contrast stretching is applied on leukemia images to increase the visual aspect of the blast cells. Then, an unsupervised moving k-means clustering algorithm is applied on the various colour components of RGB and HSI colour models for the purpose of segmentation of blast cells from the red blood cells and background regions in leukemia image. Different colour components of RGB and HSI colour models have been analyzed in order to identify the colour component that can give the good segmentation performance. The segmented images are then processed using median filter and region growing technique to reduce noise and smooth the images. The results show that segmentation using saturation component of HSI colour model has proven to be the best in segmenting nucleus of the blast cells in acute leukemia image as compared to the other colour components of RGB and HSI colour models.
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.
Supra-aortic arteries: three-dimensional time-resolved k-t BLAST contrast-enhanced MRA using a nondedicated body coil at 3 tesla in acute ischemic stroke.

PubMed

Ferré, Jean-Christophe; Raoult, Hélène; Breil, Stéphane; Carsin-Nicol, Béatrice; Ronzière, Thomas; Gauvrit, Jean-Yves

2014-11-01

To assess the image quality and diagnostic performance achieved by using supra-aortic 3D-TR-CE-k-t BLAST MRA and a nondedicated body coil as compared with conventional CE-MRA in patients with acute ischemic stroke. In this prospective study, 36 consecutive patients with a suspected acute ischemic stroke underwent both k-t BLAST MRA and conventional CE-MRA. Image quality was assessed using visual and quantitative criteria and the techniques were compared. Both techniques were compared for degree of visual and quantitative measurement of carotid stenosis. Delineation of vessel lumen and overall diagnostic confidence were significantly better with CE-MRA, respectively 3.4 ± 0.5 and 3.3 ± 0.6 (mean score ± SD), than with k-t BLAST MRA, respectively 2.8 ± 0.4 and 2.9 ± 0.5 (P < 0.02). SNR and CNR were significantly higher for k-t BLAST MRA, respectively 33.5 ± 19.3 and 27.9 ± 19.3, than for CE-MRA, respectively 25.7 ± 10 and 20.4 ± 8.4 (P < 0.03). Intertechnique agreement was good for carotid stenosis characterization (κ = .763). For the 14 relevant stenosis, stenosis measurements were highly correlated between techniques (0.96; P < 0.0001). The Bland-Altman plot showed a low bias in assessment of the degree of stenosis (mean bias 2.1% ± 7.7). k-t BLAST MRA using a nondedicated coil offering and dynamic information was a effective diagnostic tool for detection and characterization of carotid stenosis. © 2013 Wiley Periodicals, Inc.
Single-subject-based whole-brain MEG slow-wave imaging approach for detecting abnormality in patients with mild traumatic brain injury

PubMed Central

Huang, Ming-Xiong; Nichols, Sharon; Baker, Dewleen G.; Robb, Ashley; Angeles, Annemarie; Yurgil, Kate A.; Drake, Angela; Levy, Michael; Song, Tao; McLay, Robert; Theilmann, Rebecca J.; Diwakar, Mithun; Risbrough, Victoria B.; Ji, Zhengwei; Huang, Charles W.; Chang, Douglas G.; Harrington, Deborah L.; Muzzatti, Laura; Canive, Jose M.; Christopher Edgar, J.; Chen, Yu-Han; Lee, Roland R.

2014-01-01

Traumatic brain injury (TBI) is a leading cause of sustained impairment in military and civilian populations. However, mild TBI (mTBI) can be difficult to detect using conventional MRI or CT. Injured brain tissues in mTBI patients generate abnormal slow-waves (1–4 Hz) that can be measured and localized by resting-state magnetoencephalography (MEG). In this study, we develop a voxel-based whole-brain MEG slow-wave imaging approach for detecting abnormality in patients with mTBI on a single-subject basis. A normative database of resting-state MEG source magnitude images (1–4 Hz) from 79 healthy control subjects was established for all brain voxels. The high-resolution MEG source magnitude images were obtained by our recent Fast-VESTAL method. In 84 mTBI patients with persistent post-concussive symptoms (36 from blasts, and 48 from non-blast causes), our method detected abnormalities at the positive detection rates of 84.5%, 86.1%, and 83.3% for the combined (blast-induced plus with non-blast causes), blast, and non-blast mTBI groups, respectively. We found that prefrontal, posterior parietal, inferior temporal, hippocampus, and cerebella areas were particularly vulnerable to head trauma. The result also showed that MEG slow-wave generation in prefrontal areas positively correlated with personality change, trouble concentrating, affective lability, and depression symptoms. Discussion is provided regarding the neuronal mechanisms of MEG slow-wave generation due to deafferentation caused by axonal injury and/or blockages/limitations of cholinergic transmission in TBI. This study provides an effective way for using MEG slow-wave source imaging to localize affected areas and supports MEG as a tool for assisting the diagnosis of mTBI. PMID:25009772
Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease.

PubMed

Selisana, S M; Yanoria, M J; Quime, B; Chaipanya, C; Lu, G; Opulencia, R; Wang, G-L; Mitchell, T; Correll, J; Talbot, N J; Leung, H; Zhou, B

2017-06-01

Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.
GeneMachine: gene prediction and sequence annotation.

PubMed

Makalowska, I; Ryan, J F; Baxevanis, A D

2001-09-01

A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of what is essentially 'anonymous DNA'. As these programs apply inherently different criteria to the question of what is and is not a coding region, multiple algorithms should be used in the course of positional cloning and positional candidate projects to assure that all potential coding regions within a previously-identified critical region are identified. We have developed a gene identification tool called GeneMachine which allows users to query multiple exon and gene prediction programs in an automated fashion. BLAST searches are also performed in order to see whether a previously-characterized coding region corresponds to a region in the query sequence. A suite of Perl programs and modules are used to run MZEF, GENSCAN, GRAIL 2, FGENES, RepeatMasker, Sputnik, and BLAST. The results of these runs are then parsed and written into ASN.1 format. Output files can be opened using NCBI Sequin, in essence using Sequin as both a workbench and as a graphical viewer. The main feature of GeneMachine is that the process is fully automated; the user is only required to launch GeneMachine and then open the resulting file with Sequin. Annotations can then be made to these results prior to submission to GenBank, thereby increasing the intrinsic value of these data. GeneMachine is freely-available for download at http://genome.nhgri.nih.gov/genemachine. A public Web interface to the GeneMachine server for academic and not-for-profit users is available at http://genemachine.nhgri.nih.gov. The Web supplement to this paper may be found at http://genome.nhgri.nih.gov/genemachine/supplement/.
Development of feedback-speed-control system of fixed-abrasive tool for mat-surface fabrication

NASA Astrophysics Data System (ADS)

Yanagihara, K.; Kita, R.

2018-01-01

This study deals with the new method to fabricate a mat-surface by using fixed-abrasive tool. Mat-surface is a surface with microscopic irregularities whose dimensions are close to the wavelengths of visible light (400-700 nanometers). In order to develop the new method to fabricate mat-surface without pre-masking and large scale back up facility, utilization of fixed-abrasive tool is discussed. The discussion clarifies that abrasives in shot blasting are given kinetic energy along to only plunge-direction while excluding traverse-direction. If the relative motion between tool and work in fixed-abrasive process can be realized as that in blasting, mat-surface will be accomplished with fixed-abrasive process. To realize the proposed idea, new surface-fabrication system to which is adopted feedback-speed-control of abrasive wheel has been designed. The system consists of micro-computer unit (MPU), work-speed sensor, fixed-abrasive wheel, and wheel driving unit. The system can control relative speed between work and wheel in optimum range to produce mat-surface. Finally experiment to verify the developed system is carried out. The results of experiments show that the developed system is effective and it can produce the surface from grinding to mat-surface seamlessly.
Blackjack

DTIC Science & Technology

2012-05-01

astar (C++) path finding algorithms.  bwaves (Fortran) simulation of blast waves in 3D transonic transient laminar viscous flow.  bzip2 (C) in...search based on Profile Hidden Markov Models.  lbm (C) implementation of Lattice Boltzman Method for simulation of incompressible fluids in 3D...to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE
Simulating Underbelly Blast Events using Abaqus/Explicit - CEL

DTIC Science & Technology

2013-01-15

describe the material. As a result, a Langragian treatment of the structure is preferred. Therefore, a finite element solver with the capability of...algorithm is a two part process in which all material is deformed with a Lagrange treatment in a given time increment. This is followed by a remapping...accurately describe the material response of geological materials subjected to high impulse loading (i.e. shock events). The hydrostatic behavior of
Crustal thickness variations across the Blue Ridge mountains, southern Appalachians: an alternative procedure for migrating wide-angle reflection data

Treesearch

Robert B. Hawman

2008-01-01

Migration of wide-angle reflections generated by quarry blasts suggests that crustal thickness increases from 38 km beneath the Carolina Terrane to 47â51 km along the southeastern flank of the Blue Ridge. The migration algorithm, developed for generating single-fold images from explosions and earthquakes recorded with isolated, short-aperture arrays, uses the localized...
Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine

PubMed Central

Mankga, Ledile T.; Yessoufou, Kowiyou; Moteetee, Annah M.; Daru, Barnabas H.; van der Bank, Michelle

2013-01-01

Abstract Medicinal plants cover a broad range of taxa, which may be phylogenetically less related but morphologically very similar. Such morphological similarity between species may lead to misidentification and inappropriate use. Also the substitution of a medicinal plant by a cheaper alternative (e.g. other non-medicinal plant species), either due to misidentification, or deliberately to cheat consumers, is an issue of growing concern. In this study, we used DNA barcoding to identify commonly used medicinal plants in South Africa. Using the core plant barcodes, matK and rbcLa, obtained from processed and poorly conserved materials sold at the muthi traditional medicine market, we tested efficacy of the barcodes in species discrimination. Based on genetic divergence, PCR amplification efficiency and BLAST algorithm, we revealed varied discriminatory potentials for the DNA barcodes. In general, the barcodes exhibited high discriminatory power, indicating their effectiveness in verifying the identity of the most common plant species traded in South African medicinal markets. BLAST algorithm successfully matched 61% of the queries against a reference database, suggesting that most of the information supplied by sellers at traditional medicinal markets in South Africa is correct. Our findings reinforce the utility of DNA barcoding technique in limiting false identification that can harm public health. PMID:24453559
Delay-and-sum beamforming for direction of arrival estimation applied to gunshot acoustics

NASA Astrophysics Data System (ADS)

Ramos, António L. L.; Holm, Sverre; Gudvangen, Sigmund; Otterlei, Ragnvald

2011-06-01

Sniper positioning systems described in the literature use a two-step algorithm to estimate the sniper's location. First, the shockwave and the muzzle blast acoustic signatures must be detected and recognized, followed by an estimation of their respective direction-of-arrival (DOA). Second, the actual sniper's position is calculated based on the estimated DOA via an iterative algorithm that varies from system to system. The overall performance of such a system, however, is highly compromised when the first step is not carried out successfully. Currently available systems rely on a simple calculation of differences of time-of-arrival to estimate angles-of-arrival. This approach, however, lacks robustness by not taking full advantage of the array of sensors. This paper shows how the delay-and-sum beamforming technique can be applied to estimate the DOA for both the shockwave and the muzzle blast. The method has the twofold advantage of 1) adding an array gain of 10 logM, i.e., an increased SNR of 6 dB for a 4-microphone array, which is equivalent to doubling the detection range assuming free-field propagation; and 2) offering improved robustness in handling single- and multi-shots events as well as reflections by taking advantage of the spatial filtering capability.
A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less
Expanding the species and chemical diversity of Penicillium section Cinnamopurpurea

USDA-ARS?s Scientific Manuscript database

A set of isolates genetically similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a Basic Local Alignment Search Tool (BLAST) search of internal transcribed spacer (ITS) similarity among described (GenBank) and undescribed Penicillium isolates...
Battery Lifetime Analysis and Simulation Tool (BLAST) Documentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neubauer, J.

2014-12-01

The deployment and use of lithium-ion (Li-ion) batteries in automotive and stationary energy storage applications must be optimized to justify their high up-front costs. Given that batteries degrade with use and storage, such optimizations must evaluate many years of operation. As the degradation mechanisms are sensitive to temperature, state-of-charge (SOC) histories, current levels, and cycle depth and frequency, it is important to model both the battery and the application to a high level of detail to ensure battery response is accurately predicted. To address these issues, the National Renewable Energy Laboratory (NREL) has developed the Battery Lifetime Analysis and Simulationmore » Tool (BLAST) suite. This suite of tools pairs NREL’s high-fidelity battery degradation model with a battery electrical and thermal performance model, application-specific electrical and thermal performance models of the larger system (e.g., an electric vehicle), application-specific system use data (e.g., vehicle travel patterns and driving data), and historic climate data from cities across the United States. This provides highly realistic long-term predictions of battery response and thereby enables quantitative comparisons of varied battery use strategies.« less
Squid - a simple bioinformatics grid.

PubMed

Carvalho, Paulo C; Glória, Rafael V; de Miranda, Antonio B; Degrave, Wim M

2005-08-03

BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example.
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments

PubMed Central

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Koo, JaeHyung; Kim, Min-Soo

2016-01-01

Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com. PMID:27154272
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

PubMed Central

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov. PMID:22064861
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.

PubMed Central

Borodovsky, M; Rudd, K E; Koonin, E V

1994-01-01

The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database, totaling 1,278 'intergenic' sequences of the combined length of 359,279 basepairs, were analyzed using computer-assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 354 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 208 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 182 ORFs as probable genes was supported by GeneMark and BLAST, comprising 51.4% of the GeneMark 'hits' and 87.5% of the BLAST 'hits'. 73 putative new genes, comprising 20.6% of the GeneMark predictions, belong to ancient conserved protein families that include both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins, and different types of regulatory proteins. Images PMID:7984428
CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

PubMed Central

Tan, Mui Fern; Jakubovics, Nick S.; Wee, Wei Yee; Mutha, Naresh V. R.; Wong, Guat Jah; Ang, Mia Yang; Yazdi, Amir Hessam; Choo, Siew Woh

2014-01-01

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/. PMID:24466021

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

PubMed Central

Liu, Yongchao; Maskell, Douglas L; Schmidt, Bertil

2009-01-01

Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card) provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. PMID:19416548
Dice and DNA

ERIC Educational Resources Information Center

Wernersson, Rasmus

2007-01-01

An important part of teaching students how to use the BLAST tool for searching large sequence databases, is to train the students to think critically about the quality of the sequence hits found--both in terms of the statistical significance and how informative the individual hits are. This paper describes how generating truly random sequences by…
CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.
Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis*

PubMed Central

Wojtuszkiewicz, Anna; Schuurhuis, Gerrit J.; Kessler, Floortje L.; Piersma, Sander R.; Knol, Jaco C.; Pham, Thang V.; Jansen, Gerrit; Musters, René J. P.; van Meerloo, Johan; Assaraf, Yehuda G.; Kaspers, Gertjan J. L.; Zweegman, Sonja; Cloos, Jacqueline; Jimenez, Connie R.

2016-01-01

Expression of apoptosis-regulating proteins (B-cell CLL/lymphoma 2 - BCL-2, Myeloid Cell Leukemia 1 - MCL-1, BCL-2 like 1 - BCL-X and BCL-2-associated X protein - BAX) in acute myeloid leukemia (AML) blasts at diagnosis is associated with disease-free survival. We previously found that the initially high apoptosis-resistance of AML cells decreased after therapy, while regaining high levels at relapse. Herein, we further explored this aspect of dynamic apoptosis regulation in AML. First, we showed that the intraindividual ex vivo apoptosis-related profiles of normal lymphocytes and AML blasts within the bone marrow of AML patients were highly correlated. The expression values of apoptosis-regulating proteins were far beyond healthy control lymphocytes, which implicates the influence of microenvironmental factors. Second, we demonstrated that apoptosis-resistant primary AML blasts, as opposed to apoptosis-sensitive cells, were able to up-regulate BCL-2 expression in sensitive AML blasts in contact cultures (p = 0.0067 and p = 1.0, respectively). Using secretome proteomics, we identified novel proteins possibly engaged in apoptosis regulation. Intriguingly, this analysis revealed that major functional protein clusters engaged in global gene regulation, including mRNA splicing, protein translation, and chromatin remodeling, were more abundant (p = 4.01E-06) in secretomes of apoptosis-resistant AML. These findings were confirmed by subsequent extracellular vesicle proteomics. Finally, confocal-microscopy-based colocalization studies show that splicing factors-containing vesicles secreted by high AAI cells are taken up by low AAI cells. The current results constitute the first comprehensive analysis of proteins released by apoptosis-resistant and sensitive primary AML cells. Together, the data point to vesicle-mediated release of global gene regulatory protein clusters as a plausible novel mechanism of induction of apoptosis resistance. Deciphering the modes of communication between apoptosis-resistant blasts may in perspective lead to the discovery of prognostic tools and development of novel therapeutic interventions, aimed at limiting or overcoming therapy resistance. PMID:26801919
Simulation Engine for Fluid Solid Interaction Problems and its Application to the Modelling of Air Blast Hazards in Block Cave Mining.

NASA Astrophysics Data System (ADS)

Galindo Torres, S. A.; Scheuermann, A.; Ruest, M.

2016-12-01

Air blasts that may occur in a block caving mining operation represent a significant hazard for personnel as well as to mining infrastructure. Uncontrolled caving of a large volume of broken rock into a mine void causes compression of the air within, forcing it to flow at high velocities into connecting tunnels such as extraction points beneath the cave or observation points intersecting the cave. This high velocity flow of air can cause injury to personnel and significant damage to equipment. In this presentation, we introduce a simulation engine for the air blast problem. The solid material is modelled using the Discrete Element Method (DEM) and the fluid (air) is modelled using the Lattice Boltzmann Method (LBM). The combined DEM-LBM approach has been introduced by our group at the University of Queensland[1]. LBM allows us to introduce an appropriate equation of state for the air that simulates compressibility as a function of the speed of sound. Validation examples are presented to justify the use of this tool for an air blasting situation. A section view of one simulation is provided in Fig 1. An investigation into the risk of developing air pockets as a function of fragment size distribution is also conducted and described. The fragment size distribution can be assessed during mining and the risk of air pockets forming (and consequently of air blast occurring) can be deduced and mitigation measures put in place. The effect of other key variables that can be determined from geotechnical investigations, such as fracture frequency, are also systematically explored. It is expected that the results of this study can elucidate key features of the air blasting phenomenon in order to formulate safer mining protocols. references 1. Galindo-Torres, S.A., A coupled Discrete Element Lattice Boltzmann Method for the simulation of fluid-solid interaction with particles of general shapes. Computer Methods in Applied Mechanics and Engineering, 2013. 265(0): p. 107-119.
TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.
Isotopic Fingerprints of Iron-Cyanide Complexes in the Environment.

PubMed

Mansfeldt, Tim; Höhener, Patrick

2016-07-19

Tracing the origin of iron-cyanide complexes in the environment is important because these compounds are potentially toxic. We determined the stable isotopic compositions of cyanide-carbon (CCN) and cyanide-nitrogen (NCN) in 127 contaminated solids and 11 samples of contaminated groundwater from coal carbonization sites, blast furnace operations, and commercial cyanide applications. Coal-carbonization-related cyanides had unique high mean δ(13)CCN values of -10.5 ± 3.5‰ for the solids and -16.1 ± 1.2‰ for the groundwater samples, while the values for blast furnace sludge (-26.9 ± 1.5‰), commercial cyanides (-26.0 ± 3.0‰), and their corresponding groundwaters were significantly lower. Determination of δ(13)CCN is a promising tool for identifying the source of cyanide contamination. However, for coal carbonization sites, historical research into the manufacturing process is necessary because a nonconventional gas works site exhibited exceptionally low δ(13)CCN values of -22.7 ± 1.7‰. The δ(15)NCN values for samples related to coal carbonization and blast furnaces overlapped within a range of +0.1 to +10.3‰, but very high δ(15)NCN values seemed to be indicative for a cyanide source in the blast furnace. In contrast, commercial cyanides tend to have lower δ(15)NCN values of -5.6 to +1.9‰ in solids and -0.5 to +3.0‰ in the groundwater.
Efficacy of dry-ice blasting in preventive maintenance of auto robotic assemblies

NASA Astrophysics Data System (ADS)

Baluch, Nazim; Mohtar, Shahimi; Abdullah, Che Sobry

2016-08-01

Welding robots are extensively applied in the automotive assemblies and `Spot Welding' is the most common welding application found in the auto stamping assembly manufacturing. Every manufacturing process is subject to variations - with resistance welding, these include; part fit up, part thickness variations, misaligned electrodes, variations in coating materials or thickness, sealers, weld force variations, shunting, machine tooling degradation; and slag and spatter damage. All welding gun tips undergo wear; an elemental part of the process. Though adaptive resistance welding control automatically compensates to keep production and quality up to the levels needed as gun tips undergo wear so that the welds remain reliable; the system cannot compensate for deterioration caused by the slag and spatter on the part holding fixtures, sensors, and gun tips. To cleanse welding robots of slag and spatter, dry-ice blasting has proven to be an effective remedy. This paper describes Spot welding process, analyses the slag and spatter formation during robotic welding of stamping assemblies, and concludes that the dry ice blasting process's utility in cleansing of welding robots in auto stamping plant operations is paramount and exigent.
BiDiBlast: comparative genomics pipeline for the PC.

PubMed

de Almeida, João M G C F

2010-06-01

Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license. Copyright 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.
AGORA : Organellar genome annotation from the amino acid and nucleotide references.

PubMed

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.
Performance analysis of an OAM multiplexing-based MIMO FSO system over atmospheric turbulence using space-time coding with channel estimation.

PubMed

Zhang, Yan; Wang, Ping; Guo, Lixin; Wang, Wei; Tian, Hongxin

2017-08-21

The average bit error rate (ABER) performance of an orbital angular momentum (OAM) multiplexing-based free-space optical (FSO) system with multiple-input multiple-output (MIMO) architecture has been investigated over atmospheric turbulence considering channel estimation and space-time coding. The impact of different types of space-time coding, modulation orders, turbulence strengths, receive antenna numbers on the transmission performance of this OAM-FSO system is also taken into account. On the basis of the proposed system model, the analytical expressions of the received signals carried by the k-th OAM mode of the n-th receive antenna for the vertical bell labs layered space-time (V-Blast) and space-time block codes (STBC) are derived, respectively. With the help of channel estimator carrying out with least square (LS) algorithm, the zero-forcing criterion with ordered successive interference cancellation criterion (ZF-OSIC) equalizer of V-Blast scheme and Alamouti decoder of STBC scheme are adopted to mitigate the performance degradation induced by the atmospheric turbulence. The results show that the ABERs obtained by channel estimation have excellent agreement with those of turbulence phase screen simulations. The ABERs of this OAM multiplexing-based MIMO system deteriorate with the increase of turbulence strengths. And both V-Blast and STBC schemes can significantly improve the system performance by mitigating the distortions of atmospheric turbulence as well as additive white Gaussian noise (AWGN). In addition, the ABER performances of both space-time coding schemes can be further enhanced by increasing the number of receive antennas for the diversity gain and STBC outperforms V-Blast in this system for data recovery. This work is beneficial to the OAM FSO system design.
A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model

PubMed Central

Pinthong, Watthanai; Muangruen, Panya

2016-01-01

Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software. PMID:27547555
Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

ERIC Educational Resources Information Center

Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

2007-01-01

We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…
Map showing relative ease of excavation in the Salina quadrangle, Utah

USGS Publications Warehouse

Williams, Paul L.

1972-01-01

This map shows the relative ease (or difficulty) with which rocks and surficial deposits can be excavated. Because of rapidly changing technology of excavation and considerable local variability of many rock units, it is not practical to specifically categorize rock units according to type of equipment needed for their excavations. However, it may be stated in general that rock units classed as very easy and easy can in most places be excavated by hand tools and by light machinery such as backhoes and small bulldozers; units included in easy to difficult require blasting and (or) heavy machinery such as rippers and large bulldozers for resistant rocks, and hand tools or light power equipment for soft rocks; and units classes as difficult and very difficult probably require blasting and heavy machinery.The excavation units shown here are based on map units of the geologic map of the Salina quadrangle. Where bedrock is mantled with thin unmapped surficial deposits, ease of excavation shown is that of the bedrock, not that of the thin surficial mantle; where surficial deposits are mapped, ease of excavation shown is that of surficial deposits.
Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.

PubMed

Ordulu, Zehra; Wong, Kristen E; Currall, Benjamin B; Ivanov, Andrew R; Pereira, Shahrin; Althari, Sara; Gusella, James F; Talkowski, Michael E; Morton, Cynthia C

2014-05-01

With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Improving pairwise comparison of protein sequences with domain co-occurrence

PubMed Central

Gascuel, Olivier

2018-01-01

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498
Battlefield Acoustic Sensing, Multimodal Sensing, and Networked Sensing for Intelligence, Surveillance, and Reconnaissance (ISR) Applications

DTIC Science & Technology

2015-09-01

seen in Fig. 9, were placed at the rear of the vehicle to minimize the noise and vibration from the engine and its intake and exhaust from the...Specific/unique algorithm approaches attempted and results 4) Observations related to wind noise rejection and/or effects 5) Limitations of technology 6...After a certain time, the muzzle blast is detected, which results from the exit of the munition at the muzzle. Figure 6 shows an example of a single
NORSAR detection processing system

NASA Astrophysics Data System (ADS)

Loughran, L. B.

1987-05-01

This Semiannual Technical Summary describes the operation, maintenance and research activities at the Norwegian Seismic Array (NORSAR). Investigations into further potential improvements in the NORSAR array processing system have continued. A new Detection Processor (DP) program has developed and tested in an off-line mode. This program is flexible enough to conduct both NORSAR and NORESS detection processing as is done today, besides incorporating improved algorithms. A wide-band slowness estimation technique has been investigated by processing data from several events from the same location. Ten quarry blasts at a dam construction site in western Russia and sixteen Semipalatinsk nuclear explosions were selected. The major conclusion from this study is that employing a wider frequency band clearly tends to increase the stability of the slowness estimates, provided the signal-to-noise ratio is adequate over the band of interest. The stability was found, particularly for Pn, to be remarkably good for the western Norway quarry blasts when using a fixed frequency band for each phase for all ten events.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.

PubMed

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Koo, JaeHyung; Kim, Min-Soo

2016-07-08

Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Seismic Search Engine: A distributed database for mining large scale seismic data

NASA Astrophysics Data System (ADS)

Liu, Y.; Vaidya, S.; Kuzma, H. A.

2009-12-01

The International Monitoring System (IMS) of the CTBTO collects terabytes worth of seismic measurements from many receiver stations situated around the earth with the goal of detecting underground nuclear testing events and distinguishing them from other benign, but more common events such as earthquakes and mine blasts. The International Data Center (IDC) processes and analyzes these measurements, as they are collected by the IMS, to summarize event detections in daily bulletins. Thereafter, the data measurements are archived into a large format database. Our proposed Seismic Search Engine (SSE) will facilitate a framework for data exploration of the seismic database as well as the development of seismic data mining algorithms. Analogous to GenBank, the annotated genetic sequence database maintained by NIH, through SSE, we intend to provide public access to seismic data and a set of processing and analysis tools, along with community-generated annotations and statistical models to help interpret the data. SSE will implement queries as user-defined functions composed from standard tools and models. Each query is compiled and executed over the database internally before reporting results back to the user. Since queries are expressed with standard tools and models, users can easily reproduce published results within this framework for peer-review and making metric comparisons. As an illustration, an example query is “what are the best receiver stations in East Asia for detecting events in the Middle East?” Evaluating this query involves listing all receiver stations in East Asia, characterizing known seismic events in that region, and constructing a profile for each receiver station to determine how effective its measurements are at predicting each event. The results of this query can be used to help prioritize how data is collected, identify defective instruments, and guide future sensor placements.
A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.
A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

Background The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Results Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from Conclusion This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language. PMID:18251993
Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW).

PubMed

Gálvez, Sergio; Ferusic, Adis; Esteban, Francisco J; Hernández, Pilar; Caballero, Juan A; Dorado, Gabriel

2016-10-01

The Smith-Waterman algorithm has a great sensitivity when used for biological sequence-database searches, but at the expense of high computing-power requirements. To overcome this problem, there are implementations in literature that exploit the different hardware-architectures available in a standard PC, such as GPU, CPU, and coprocessors. We introduce an application that splits the original database-search problem into smaller parts, resolves each of them by executing the most efficient implementations of the Smith-Waterman algorithms in different hardware architectures, and finally unifies the generated results. Using non-overlapping hardware allows simultaneous execution, and up to 2.58-fold performance gain, when compared with any other algorithm to search sequence databases. Even the performance of the popular BLAST heuristic is exceeded in 78% of the tests. The application has been tested with standard hardware: Intel i7-4820K CPU, Intel Xeon Phi 31S1P coprocessors, and nVidia GeForce GTX 960 graphics cards. An important increase in performance has been obtained in a wide range of situations, effectively exploiting the available hardware.
Advance Planning Briefing for Industry. Technology Requirements Briefings

DTIC Science & Technology

2009-02-17

procedure drills through complex multiplayer interactions representative of a motorcade under heavy attack. The tool shall provide a first-person...Integrated Munitions Effect Assessment IMI Interactive Multimedia Instruction IP Internet Protocol IPE Intelligence Preparation of the Environment IR...CTTSO Programs and Mission Areas/Subgroups 13 Requirement Descriptions Blast Effects and Mitigation (BX) 16 Chemical, Biological, Radiological, and
Dynamic Analysis of Tunnel in Weathered Rock Subjected to Internal Blast Loading

NASA Astrophysics Data System (ADS)

Tiwari, Rohit; Chakraborty, Tanusree; Matsagar, Vasant

2016-11-01

The present study deals with three-dimensional nonlinear finite element (FE) analyses of a tunnel in rock with reinforced concrete (RC) lining subjected to internal blast loading. The analyses have been performed using the coupled Eulerian-Lagrangian analysis tool available in FE software Abaqus/Explicit. Rock and RC lining are modeled using three-dimensional Lagrangian elements. Beam elements have been used to model reinforcement in RC lining. Three different rock types with different weathering conditions have been used to understand the response of rock when subjected to blast load. The trinitrotoluene (TNT) explosive and surrounding air have been modeled using the Eulerian elements. The Drucker-Prager plasticity model with strain rate-dependent material properties has been used to simulate the stress-strain response of rock. The concrete damaged plasticity model and Johnson-Cook plasticity model have been used for the simulation of stress-strain response of concrete and steel, respectively. The explosive (TNT) has been modeled using Jones-Wilkins-Lee (JWL) equation of state. The analysis results have been studied for stresses, deformation and damage of RC lining and the surrounding rock. It is observed that damage in RC lining results in higher stress in rock. Rocks with low modulus and high weathering conditions show higher attenuation of shock wave. Higher amount of ground shock wave propagation is observed in case of less weathered rock. Ground heave is observed under blast loading for tunnel close to ground surface.
Design and Implementation of an Underwater Sound Recording Device

PubMed Central

Martinez, Jayson J.; Myers, Josh R.; Carlson, Thomas J.; Deng, Z. Daniel; Rohrer, John S.; Caviggia, Kurt A.; Woodley, Christa M.; Weiland, Mark A.

2011-01-01

To monitor the underwater sound and pressure waves generated by anthropogenic activities such as underwater blasting and pile driving, an autonomous system was designed to record underwater acoustic signals. The underwater sound recording device (USR) allows for connections of two hydrophones or other dynamic pressure sensors, filters high frequency noise out of the collected signals, has a gain that can be independently set for each sensor, and allows for 2 h of data collection. Two versions of the USR were created: a submersible model deployable to a maximum depth of 300 m, and a watertight but not fully submersible model. Tests were performed on the USR in the laboratory using a data acquisition system to send single-frequency sinusoidal voltages directly to each component. These tests verified that the device operates as designed and performs as well as larger commercially available data acquisition systems, which are not suited for field use. On average, the designed gain values differed from the actual measured gain values by about 0.35 dB. A prototype of the device was used in a case study to measure blast pressures while investigating the effect of underwater rock blasting on juvenile Chinook salmon and rainbow trout. In the case study, maximum positive pressure from the blast was found to be significantly correlated with frequency of injury for individual fish. The case study also demonstrated that the device withstood operation in harsh environments, making it a valuable tool for collecting field measurements. PMID:22164089
Application of learning to rank to protein remote homology detection.

PubMed

Liu, Bin; Chen, Junjie; Wang, Xiaolong

2015-11-01

Protein remote homology detection is one of the fundamental problems in computational biology, aiming to find protein sequences in a database of known structures that are evolutionarily related to a given query protein. Some computational methods treat this problem as a ranking problem and achieve the state-of-the-art performance, such as PSI-BLAST, HHblits and ProtEmbed. This raises the possibility to combine these methods to improve the predictive performance. In this regard, we are to propose a new computational method called ProtDec-LTR for protein remote homology detection, which is able to combine various ranking methods in a supervised manner via using the Learning to Rank (LTR) algorithm derived from natural language processing. Experimental results on a widely used benchmark dataset showed that ProtDec-LTR can achieve an ROC1 score of 0.8442 and an ROC50 score of 0.9023 outperforming all the individual predictors and some state-of-the-art methods. These results indicate that it is correct to treat protein remote homology detection as a ranking problem, and predictive performance improvement can be achieved by combining different ranking approaches in a supervised manner via using LTR. For users' convenience, the software tools of three basic ranking predictors and Learning to Rank algorithm were provided at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR/home/ bliu@insun.hit.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
29 CFR 1926.909 - Firing the blast.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Firing the blast. (a) A code of blasting signals equivalent to Table U-1, shall be posted on one or more... blasts 5 minutes prior to blast signal. Blast Signal—A series of short blasts 1 minute prior to the shot...
29 CFR 1926.909 - Firing the blast.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Firing the blast. (a) A code of blasting signals equivalent to Table U-1, shall be posted on one or more... blasts 5 minutes prior to blast signal. Blast Signal—A series of short blasts 1 minute prior to the shot...
29 CFR 1926.909 - Firing the blast.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Firing the blast. (a) A code of blasting signals equivalent to Table U-1, shall be posted on one or more... blasts 5 minutes prior to blast signal. Blast Signal—A series of short blasts 1 minute prior to the shot...
29 CFR 1926.909 - Firing the blast.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Firing the blast. (a) A code of blasting signals equivalent to Table U-1, shall be posted on one or more... blasts 5 minutes prior to blast signal. Blast Signal—A series of short blasts 1 minute prior to the shot...
29 CFR 1926.909 - Firing the blast.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Firing the blast. (a) A code of blasting signals equivalent to Table U-1, shall be posted on one or more... blasts 5 minutes prior to blast signal. Blast Signal—A series of short blasts 1 minute prior to the shot...
Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.
Improvement of Thermal Interruption Capability in Self-blast Interrupting Chamber for New 245kV-50kA GCB

NASA Astrophysics Data System (ADS)

Shinkai, Takeshi; Koshiduka, Tadashi; Mori, Tadashi; Uchii, Toshiyuki; Tanaka, Tsutomu; Ikeda, Hisatoshi

Current zero measurements are performed for 245kV-50kA-60Hz short line fault (L90) interruption tests with a self-blast interrupting chamber (double volume system) which has the interrupting capability up to 245kV-50kA-50Hz L90. Lower L90 interruption capability is observed for longer arcing time although very high pressure rise is obtained. It may be caused by higher blowing temperature and lower blowing density for longer arcing time. Interruption criteria and a optimization method of the chamber design are discussed to improve L90 interruption capability with it. The new chambers are designed at 245kV-50kA-60Hz to improve gas density in thermal volume for long arcing time. 245kV-50kA-60Hz L90 interruptions are performed with the new chamber. The suggested optimization method is an efficient tool for the self-blast interrupting chamber design although study of computing methods is required to calculate arc conductance around current zero as a direct criterion for L90 interruption capability with higher accuracy.
Development of a 3D numerical methodology for fast prediction of gun blast induced loading

NASA Astrophysics Data System (ADS)

Costa, E.; Lagasco, F.

2014-05-01

In this paper, the development of a methodology based on semi-empirical models from the literature to carry out 3D prediction of pressure loading on surfaces adjacent to a weapon system during firing is presented. This loading is consequent to the impact of the blast wave generated by the projectile exiting the muzzle bore. When exceeding a pressure threshold level, loading is potentially capable to induce unwanted damage to nearby hard structures as well as frangible panels or electronic equipment. The implemented model shows the ability to quickly predict the distribution of the blast wave parameters over three-dimensional complex geometry surfaces when the weapon design and emplacement data as well as propellant and projectile characteristics are available. Considering these capabilities, the use of the proposed methodology is envisaged as desirable in the preliminary design phase of the combat system to predict adverse effects and then enable to identify the most appropriate countermeasures. By providing a preliminary but sensitive estimate of the operative environmental loading, this numerical means represents a good alternative to more powerful, but time consuming advanced computational fluid dynamics tools, which use can, thus, be limited to the final phase of the design.
BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

PubMed Central

Manavski, Svetlin A; Valle, Giorgio

2008-01-01

Background Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic programming approach that explores all the possible alignments between two sequences; as a result it returns the optimal local alignment. Unfortunately, the computational cost is very high, requiring a number of operations proportional to the product of the length of two sequences. Furthermore, the exponential growth of protein and DNA databases makes the Smith-Waterman algorithm unrealistic for searching similarities in large sets of sequences. For these reasons heuristic approaches such as those implemented in FASTA and BLAST tend to be preferred, allowing faster execution times at the cost of reduced sensitivity. The main motivation of our work is to exploit the huge computational power of commonly available graphic cards, to develop high performance solutions for sequence alignment. Results In this paper we present what we believe is the fastest solution of the exact Smith-Waterman algorithm running on commodity hardware. It is implemented in the recently released CUDA programming environment by NVidia. CUDA allows direct access to the hardware primitives of the last-generation Graphics Processing Units (GPU) G80. Speeds of more than 3.5 GCUPS (Giga Cell Updates Per Second) are achieved on a workstation running two GeForce 8800 GTX. Exhaustive tests have been done to compare our implementation to SSEARCH and BLAST, running on a 3 GHz Intel Pentium IV processor. Our solution was also compared to a recently published GPU implementation and to a Single Instruction Multiple Data (SIMD) solution. These tests show that our implementation performs from 2 to 30 times faster than any other previous attempt available on commodity hardware. Conclusions The results show that graphic cards are now sufficiently advanced to be used as efficient hardware accelerators for sequence alignment. Their performance is better than any alternative available on commodity hardware platforms. The solution presented in this paper allows large scale alignments to be performed at low cost, using the exact Smith-Waterman algorithm instead of the largely adopted heuristic approaches. PMID:18387198
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.

PubMed

Gibbons, Theodore R; Mount, Stephen M; Cooper, Endymion D; Delwiche, Charles F

2015-07-10

Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been the centerpiece of several popular applications. Each of these approaches generates an undirected graph that represents sequences as nodes connected to each other by edges weighted with a BLAST-based metric. MCL is then used to infer clusters of homologous proteins by analyzing these graphs. The various approaches differ only by how they weight the edges, yet there has been very little direct examination of the relative performance of alternative edge-weighting metrics. This study compares the performance of four BLAST-based edge-weighting metrics: the bit score, bit score ratio (BSR), bit score over anchored length (BAL), and negative common log of the expectation value (NLE). Performance is tested using the Extended CEGMA KOGs (ECK) database, which we introduce here. All metrics performed similarly when analyzing full-length sequences, but dramatic differences emerged as progressively larger fractions of the test sequences were split into fragments. The BSR and BAL successfully rescued subsets of clusters by strengthening certain types of alignments between fragmented sequences, but also shifted the largest correct scores down near the range of scores generated from spurious alignments. This penalty outweighed the benefits in most test cases, and was greatly exacerbated by increasing the MCL inflation parameter, making these metrics less robust than the bit score or the more popular NLE. Notably, the bit score performed as well or better than the other three metrics in all scenarios. The results provide a strong case for use of the bit score, which appears to offer equivalent or superior performance to the more popular NLE. The insight that MCL-based clustering methods can be improved using a more tractable edge-weighting metric will greatly simplify future implementations. We demonstrate this with our own minimalist Python implementation: Porthos, which uses only standard libraries and can process a graph with 25 m + edges connecting the 60 k + KOG sequences in half a minute using less than half a gigabyte of memory.
Reliable classification of high explosive and chemical/biological artillery using acoustic sensors

NASA Astrophysics Data System (ADS)

Desai, Sachi V.; Hohil, Myron E.; Bass, Henry E.; Chambers, Jim

2005-05-01

Feature extraction methods based on the discrete wavelet transform and multiresolution analysis are used to develop a robust classification algorithm that reliably discriminates between conventional and simulated chemical/biological artillery rounds via acoustic signals produced during detonation utilizing a generic acoustic sensor. Based on the transient properties of the signature blast distinct characteristics arise within the different acoustic signatures because high explosive warheads emphasize concussive and shrapnel effects, while chemical/biological warheads are designed to disperse their contents over large areas, therefore employing a slower burning, less intense explosive to mix and spread their contents. The ensuing blast waves are readily characterized by variations in the corresponding peak pressure and rise time of the blast, differences in the ratio of positive pressure amplitude to the negative amplitude, and variations in the overall duration of the resulting waveform. Unique attributes can also be identified that depend upon the properties of the gun tube, projectile speed at the muzzle, and the explosive burn rates of the warhead. The algorithm enables robust classification of various airburst signatures using acoustics. It is capable of being integrated within an existing chemical/biological sensor, a stand-alone generic sensor, or a part of a disparate sensor suite. When emplaced in high-threat areas, this added capability would further provide field personal with advanced battlefield knowledge without the aide of so-called "sniffer" sensors that rely upon air particle information based on direct contact with possible contaminated air. In this work, the discrete wavelet transform is used to extract the predominant components of these characteristics from air burst signatures at ranges exceeding 2km while maintaining temporal sequence of the data to keep relevance to the transient differences of the airburst signatures. Highly reliable discrimination is achieved with a feedforward neural network classifier trained on a feature space derived from the distribution of wavelet coefficients and higher frequency details found within different levels of the multiresolution decomposition the neural network then is capable of classifying new airburst signatures as Chemical/Biological or High Explosive.

Simultaneous Scheduling of Jobs, AGVs and Tools Considering Tool Transfer Times in Multi Machine FMS By SOS Algorithm

NASA Astrophysics Data System (ADS)

Sivarami Reddy, N.; Ramamurthy, D. V., Dr.; Prahlada Rao, K., Dr.

2017-08-01

This article addresses simultaneous scheduling of machines, AGVs and tools where machines are allowed to share the tools considering transfer times of jobs and tools between machines, to generate best optimal sequences that minimize makespan in a multi-machine Flexible Manufacturing System (FMS). Performance of FMS is expected to improve by effective utilization of its resources, by proper integration and synchronization of their scheduling. Symbiotic Organisms Search (SOS) algorithm is a potent tool which is a better alternative for solving optimization problems like scheduling and proven itself. The proposed SOS algorithm is tested on 22 job sets with makespan as objective for scheduling of machines and tools where machines are allowed to share tools without considering transfer times of jobs and tools and the results are compared with the results of existing methods. The results show that the SOS has outperformed. The same SOS algorithm is used for simultaneous scheduling of machines, AGVs and tools where machines are allowed to share tools considering transfer times of jobs and tools to determine the best optimal sequences that minimize makespan.
A Preliminary Investigation of Traumatically Induced Axonal Injury in a Three-Dimensional (3-D) Finite Element Model (FEM) of the Human Head During Blast-Loading

DTIC Science & Technology

2013-07-01

are reconstructed from DTI data. An algorithm was previously developed by ARL to import diffusion-weighted imaging data (in this case, DTI data...this study contained ocular cavities in the facial bone, but lacked both openings on the sphenoid for the optic canals. This could potentially alter...Cellular Response. J of Trauma , 2009, 67, 1113–1122. 3. MacDonald, C., Johnson, A.; Cooper, D.; Malone, T.; Sorrell, J.; Shimony, J.; Parsons, M
Low-cost blast wave generator for studies of hearing loss and brain injury: blast wave effects in closed spaces.

PubMed

Newman, Andrew J; Hayes, Sarah H; Rao, Abhiram S; Allman, Brian L; Manohar, Senthilvelan; Ding, Dalian; Stolzberg, Daniel; Lobarinas, Edward; Mollendorf, Joseph C; Salvi, Richard

2015-03-15

Military personnel and civilians living in areas of armed conflict have increased risk of exposure to blast overpressures that can cause significant hearing loss and/or brain injury. The equipment used to simulate comparable blast overpressures in animal models within laboratory settings is typically very large and prohibitively expensive. To overcome the fiscal and space limitations introduced by previously reported blast wave generators, we developed a compact, low-cost blast wave generator to investigate the effects of blast exposures on the auditory system and brain. The blast wave generator was constructed largely from off the shelf components, and reliably produced blasts with peak sound pressures of up to 198dB SPL (159.3kPa) that were qualitatively similar to those produced from muzzle blasts or explosions. Exposure of adult rats to 3 blasts of 188dB peak SPL (50.4kPa) resulted in significant loss of cochlear hair cells, reduced outer hair cell function and a decrease in neurogenesis in the hippocampus. Existing blast wave generators are typically large, expensive, and are not commercially available. The blast wave generator reported here provides a low-cost method of generating blast waves in a typical laboratory setting. This compact blast wave generator provides scientists with a low cost device for investigating the biological mechanisms involved in blast wave injury to the rodent cochlea and brain that may model many of the damaging effects sustained by military personnel and civilians exposed to intense blasts. Copyright © 2015 Elsevier B.V. All rights reserved.
Low-Cost Blast Wave Generator for Studies of Hearing Loss and Brain Injury: Blast Wave Effects in Closed Spaces

PubMed Central

Newman, Andrew J.; Hayes, Sarah H.; Rao, Abhiram S.; Allman, Brian L.; Manohar, Senthilvelan; Ding, Dalian; Stolzberg, Daniel; Lobarinas, Edward; Mollendorf, Joseph C.; Salvi, Richard

2015-01-01

Background Military personnel and civilians living in areas of armed conflict have increased risk of exposure to blast overpressures that can cause significant hearing loss and/or brain injury. The equipment used to simulate comparable blast overpressures in animal models within laboratory settings is typically very large and prohibitively expensive. New Method To overcome the fiscal and space limitations introduced by previously reported blast wave generators, we developed a compact, low-cost blast wave generator to investigate the effects of blast exposures on the auditory system and brain. Results The blast wave generator was constructed largely from off the shelf components, and reliably produced blasts with peak sound pressures of up to 198 dB SPL (159.3 kPa) that were qualitatively similar to those produced from muzzle blasts or explosions. Exposure of adult rats to 3 blasts of 188 dB peak SPL (50.4 kPa) resulted in significant loss of cochlear hair cells, reduced outer hair cell function and a decrease in neurogenesis in the hippocampus. Comparison to existing methods Existing blast wave generators are typically large, expensive, and are not commercially available. The blast wave generator reported here provides a low-cost method of generating blast waves in a typical laboratory setting. Conclusions This compact blast wave generator provides scientists with a low cost device for investigating the biological mechanisms involved in blast wave injury to the rodent cochlea and brain that may model many of the damaging effects sustained by military personnel and civilians exposed to intense blasts. PMID:25597910
Fake ballistics and real explosions: field-scale experiments on the ejection and emplacement of volcanic bombs during vent-clearing explosive activity

NASA Astrophysics Data System (ADS)

Taddeucci, J.; Valentine, G.; Gaudin, D.; Graettinger, A. H.; Lube, G.; Kueppers, U.; Sonder, I.; White, J. D.; Ross, P.; Bowman, D. C.

2013-12-01

Ballistics - bomb-sized pyroclasts that travel from volcanic source to final emplacement position along ballistic trajectories - represent a prime source of volcanic hazard, but their emplacement range, size, and density is useful to inverse model key eruption parameters related to their initial ejection velocity. Models and theory, however, have so far focused on the trajectory of ballistics after leaving the vent, neglecting the complex dynamics of their initial acceleration phase in the vent/conduit. Here, we use field-scale buried explosion experiments to study the ground-to-ground ballistic emplacement of particles through their entire acceleration-deceleration cycle. Twelve blasts were performed at the University at Buffalo Large Scale Experimental Facility with a range of scaled depths (burial depth divided by the cubic root of the energy of the explosive charge) and crater configurations. In all runs, ballistic analogs were placed on the ground surface at variable distance from the vertical projection of the buried charge, resulting in variable ejection angle. The chosen analogs are tennis and ping-pong balls filled with different materials, covering a limited range of sizes and densities. The analogs are tracked in multiple high-speed and high-definition videos, while Particle Image Velocimetry is used to detail ground motion in response to the buried blasts. In addition, after each blast the emplacement position of all analog ballistics was mapped with respect to the blast location. Preliminary results show the acceleration history of ballistics to be quite variable, from very short and relatively simple acceleration coupled with ground motion, to more complex, multi-stage accelerations possibly affected not only by the initial ground motion but also by variable coupling with the gas-particle mixture generated by the blasts. Further analysis of the experimental results is expected to provide new interpretative tools for ballistic deposits and better hazard assessment, with particular emphasis for the case of vent-opening eruptions driven by explosive gas expansion beneath loose debris.
High resolution seismic tomography imaging of Ireland with quarry blast data

NASA Astrophysics Data System (ADS)

Arroucau, P.; Lebedev, S.; Bean, C. J.; Grannell, J.

2017-12-01

Local earthquake tomography is a well established tool to image geological structure at depth. That technique, however, is difficult to apply in slowly deforming regions, where local earthquakes are typically rare and of small magnitude, resulting in sparse data sampling. The natural earthquake seismicity of Ireland is very low. That due to quarry and mining blasts, on the other hand, is high and homogeneously distributed. As a consequence, and thanks to the dense and nearly uniform coverage achieved in the past ten years by temporary and permanent broadband seismological stations, the quarry blasts offer an alternative approach for high resolution seismic imaging of the crust and uppermost mantle beneath Ireland. We detected about 1,500 quarry blasts in Ireland and Northern Ireland between 2011 and 2014, for which we manually picked more than 15,000 P- and 20,000 S-wave first arrival times. The anthropogenic, explosive origin of those events was unambiguously assessed based on location, occurrence time and waveform characteristics. Here, we present a preliminary 3D tomographic model obtained from the inversion of 3,800 P-wave arrival times associated with a subset of 500 events observed in 2011, using FMTOMO tomographic code. Forward modeling is performed with the Fast Marching Method (FMM) and the inverse problem is solved iteratively using a gradient-based subspace inversion scheme after careful selection of damping and smoothing regularization parameters. The results illuminate the geological structure of Ireland from deposit to crustal scale in unprecedented detail, as demonstrated by sensitivity analysis, source relocation with the 3D velocity model and comparisons with surface geology.
SCAR marker specific to detect Magnaporthe grisea infecting finger millets (Eleusine coracana).

PubMed

Gnanasing Jesumaharaja, L; Manikandan, R; Raguchander, T

2016-09-01

To determine the molecular variability and develop specific Sequence Characterized Amplified Region (SCAR) marker for the detection of Magnaporthe grisea causing blast disease in finger millet. Random amplified polymorphic DNA (RAPD) was performed with 14 isolates of M. grisea using 20 random primers. SCAR marker was developed for accurate and specific detection of M. grisea infecting only finger millets. The genetic similarity coefficient within each group and variation between the groups was observed. Among the primers, OPF-08 generated a RAPD polymorphic profile that showed common fragment of 478 bp in all the isolates. This fragment was cloned and sequenced. SCAR primers, Mg-SCAR-FP and Mg-SCAR-RP, were designed using sequence of the cloned product. The specificity of the SCAR primers was evaluated using purified DNA from M. grisea isolates from finger millets and other pathogens viz., Pyricularia oryzae, Colletotrichum gloeosporioides, Colletotrichum falcatum and Colletotrichum capcisi infecting different crops. The SCAR primers amplified only specific 460 bp fragment from DNA of M. grisea isolates and this fragment was not amplified in other pathogens tested. SCAR primers distinguish blast disease of finger millet from rice as there is no amplification in the rice blast pathogen. PCR-based SCAR marker is a convenient tool for specific and rapid detection of M. grisea in finger millets. Genetic diversity in fungal population helps in developing a suitable SCAR marker to identify the blast pathogen at the early stage of infection. © 2016 The Society for Applied Microbiology.
A dynamic scheduling algorithm for singe-arm two-cluster tools with flexible processing times

NASA Astrophysics Data System (ADS)

Li, Xin; Fung, Richard Y. K.

2018-02-01

This article presents a dynamic algorithm for job scheduling in two-cluster tools producing multi-type wafers with flexible processing times. Flexible processing times mean that the actual times for processing wafers should be within given time intervals. The objective of the work is to minimize the completion time of the newly inserted wafer. To deal with this issue, a two-cluster tool is decomposed into three reduced single-cluster tools (RCTs) in a series based on a decomposition approach proposed in this article. For each single-cluster tool, a dynamic scheduling algorithm based on temporal constraints is developed to schedule the newly inserted wafer. Three experiments have been carried out to test the dynamic scheduling algorithm proposed, comparing with the results the 'earliest starting time' heuristic (EST) adopted in previous literature. The results show that the dynamic algorithm proposed in this article is effective and practical.
LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

PubMed

Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

2018-05-07

Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.
Numerical simulation of long-duration blast wave evolution in confined facilities

NASA Astrophysics Data System (ADS)

Togashi, F.; Baum, J. D.; Mestreau, E.; Löhner, R.; Sunshine, D.

2010-10-01

The objective of this research effort was to investigate the quasi-steady flow field produced by explosives in confined facilities. In this effort we modeled tests in which a high explosive (HE) cylindrical charge was hung in the center of a room and detonated. The HEs used for the tests were C-4 and AFX 757. While C-4 is just slightly under-oxidized and is typically modeled as an ideal explosive, AFX 757 includes a significant percentage of aluminum particles, so long-time afterburning and energy release must be considered. The Lawrence Livermore National Laboratory (LLNL)-produced thermo-chemical equilibrium algorithm, “Cheetah”, was used to estimate the remaining burnable detonation products. From these remaining species, the afterburning energy was computed and added to the flow field. Computations of the detonation and afterburn of two HEs in the confined multi-room facility were performed. The results demonstrate excellent agreement with available experimental data in terms of blast wave time of arrival, peak shock amplitude, reverberation, and total impulse (and hence, total energy release, via either the detonation or afterburn processes.
HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.
Optimizing Blasting’s Air Overpressure Prediction Model using Swarm Intelligence

NASA Astrophysics Data System (ADS)

Nur Asmawisham Alel, Mohd; Ruben Anak Upom, Mark; Asnida Abdullah, Rini; Hazreek Zainal Abidin, Mohd

2018-04-01

Air overpressure (AOp) resulting from blasting can cause damage and nuisance to nearby civilians. Thus, it is important to be able to predict AOp accurately. In this study, 8 different Artificial Neural Network (ANN) were developed for the purpose of prediction of AOp. The ANN models were trained using different variants of Particle Swarm Optimization (PSO) algorithm. AOp predictions were also made using an empirical equation, as suggested by United States Bureau of Mines (USBM), to serve as a benchmark. In order to develop the models, 76 blasting operations in Hulu Langat were investigated. All the ANN models were found to outperform the USBM equation in three performance metrics; root mean square error (RMSE), mean absolute percentage error (MAPE) and coefficient of determination (R2). Using a performance ranking method, MSO-Rand-Mut was determined to be the best prediction model for AOp with a performance metric of RMSE=2.18, MAPE=1.73% and R2=0.97. The result shows that ANN models trained using PSO are capable of predicting AOp with great accuracy.
Effects of visualization on algorithm comprehension

NASA Astrophysics Data System (ADS)

Mulvey, Matthew

Computer science students are expected to learn and apply a variety of core algorithms which are an essential part of the field. Any one of these algorithms by itself is not necessarily extremely complex, but remembering the large variety of algorithms and the differences between them is challenging. To address this challenge, we present a novel algorithm visualization tool designed to enhance students understanding of Dijkstra's algorithm by allowing them to discover the rules of the algorithm for themselves. It is hoped that a deeper understanding of the algorithm will help students correctly select, adapt and apply the appropriate algorithm when presented with a problem to solve, and that what is learned here will be applicable to the design of other visualization tools designed to teach different algorithms. Our visualization tool is currently in the prototype stage, and this thesis will discuss the pedagogical approach that informs its design, as well as the results of some initial usability testing. Finally, to clarify the direction for further development of the tool, four different variations of the prototype were implemented, and the instructional effectiveness of each was assessed by having a small sample participants use the different versions of the prototype and then take a quiz to assess their comprehension of the algorithm.
27 CFR 555.220 - Table of separation distances of ammonium nitrate and blasting agents from explosives or blasting...

Code of Federal Regulations, 2010 CFR

2010-04-01

... distances of ammonium nitrate and blasting agents from explosives or blasting agents. 555.220 Section 555... ammonium nitrate and blasting agents from explosives or blasting agents. Table: Department of Defense... Not over Minimum separation distance of acceptor from donor when barricaded (ft.) Ammonium nitrate...
27 CFR 555.220 - Table of separation distances of ammonium nitrate and blasting agents from explosives or blasting...

Code of Federal Regulations, 2011 CFR

2011-04-01

... distances of ammonium nitrate and blasting agents from explosives or blasting agents. 555.220 Section 555... ammonium nitrate and blasting agents from explosives or blasting agents. Table: Department of Defense... Not over Minimum separation distance of acceptor from donor when barricaded (ft.) Ammonium nitrate...
27 CFR 555.220 - Table of separation distances of ammonium nitrate and blasting agents from explosives or blasting...

Code of Federal Regulations, 2012 CFR

2012-04-01

... distances of ammonium nitrate and blasting agents from explosives or blasting agents. 555.220 Section 555... ammonium nitrate and blasting agents from explosives or blasting agents. Table: Department of Defense... Not over Minimum separation distance of acceptor from donor when barricaded (ft.) Ammonium nitrate...
27 CFR 555.220 - Table of separation distances of ammonium nitrate and blasting agents from explosives or blasting...

Code of Federal Regulations, 2013 CFR

2013-04-01

... distances of ammonium nitrate and blasting agents from explosives or blasting agents. 555.220 Section 555... ammonium nitrate and blasting agents from explosives or blasting agents. Table: Department of Defense... Not over Minimum separation distance of acceptor from donor when barricaded (ft.) Ammonium nitrate...
27 CFR 555.220 - Table of separation distances of ammonium nitrate and blasting agents from explosives or blasting...

Code of Federal Regulations, 2014 CFR

2014-04-01

... distances of ammonium nitrate and blasting agents from explosives or blasting agents. 555.220 Section 555... ammonium nitrate and blasting agents from explosives or blasting agents. Table: Department of Defense... Not over Minimum separation distance of acceptor from donor when barricaded (ft.) Ammonium nitrate...
An Empirical Derivation of the Run Time of the Bubble Sort Algorithm.

ERIC Educational Resources Information Center

Gonzales, Michael G.

1984-01-01

Suggests a moving pictorial tool to help teach principles in the bubble sort algorithm. Develops such a tool applied to an unsorted list of numbers and describes a method to derive the run time of the algorithm. The method can be modified to run the times of various other algorithms. (JN)
Department of Defense Interface Standard Electromagnetic Environmental Effects Requirements for Systems

DTIC Science & Technology

2002-12-19

effective tool in evaluating IMI. A5.2.2 Shipboard internal electromagnetic environment (EME). For ship applications, electric fields (peak V/m-rms...effects waveform parameters ........................................ 9 MIL-STD-464A v CONTENTS Page TABLES 2B Electromagnetic fields from near...blasting of hardware. 3.8 Lightning indirect effects. Electrical transients induced by lightning due to coupling of electromagnetic fields . 3.9

Linking blast physics to biological outcomes in mild traumatic brain injury: Narrative review and preliminary report of an open-field blast model.

PubMed

Song, Hailong; Cui, Jiankun; Simonyi, Agnes; Johnson, Catherine E; Hubler, Graham K; DePalma, Ralph G; Gu, Zezong

2018-03-15

Blast exposures are associated with traumatic brain injury (TBI) and blast-induced TBIs are common injuries affecting military personnel. Department of Defense and Veterans Administration (DoD/VA) reports for TBI indicated that the vast majority (82.3%) has been mild TBI (mTBI)/concussion. mTBI and associated posttraumatic stress disorders (PTSD) have been called "the invisible injury" of the current conflicts in Iraq and Afghanistan. These injuries induce varying degrees of neuropathological alterations and, in some cases, chronic cognitive, behavioral and neurological disorders. Appropriate animal models of blast-induced TBI will not only assist the understanding of physical characteristics of the blast, but also help to address the potential mechanisms. This report provides a brief overview of physical principles of blast, injury mechanisms related to blast exposure, current blast animal models, and the neurological behavioral and neuropathological findings related to blast injury in experimental settings. We describe relationships between blast peak pressures and the observed injuries. We also report preliminary use of a highly reproducible and intensity-graded blast murine model carried out in open-field with explosives, and describe physical and pathological findings in this experimental model. Our results indicate close relationships between blast intensities and neuropathology and behavioral deficits, particularly at low level blast intensities relevant to mTBI. Copyright © 2016 Elsevier B.V. All rights reserved.
Blasting for abandoned-mine land reclamation (closure of individual subsidence features and erratic, undocumented underground coal-mine workings). Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Workman, J.L.; Thompson, J.

1991-01-01

The study has examined the feasibility of blasting for mitigating various abandoned mine land features on AML sites. The investigation included extensive field trial blasts at sites in North Dakota and Montana. A blasting technique was used that was based on spherical cratering concepts. At the Beulah, North Dakota site thirteen individual vertical openings (sinkholes) were blasted with the intent to fill the voids. The blasts were designed to displace material laterally into the void. Good success was had in filling the sinkholes. At the White site in Montana erratic underground rooms with no available documentation were collapsed. An aditmore » leading into the mine was also blasted. Both individual room blasting and area pattern blasting were studied. A total of eight blasts were fired on the one acre area. Exploration requirements and costs were found to be extensive.« less
Hydrodynamic Modeling of Air Blast Propagation from the Humble Redwood Chemical High Explosive Detonations Using GEODYN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chipman, V D

Two-dimensional axisymmetric hydrodynamic models were developed using GEODYN to simulate the propagation of air blasts resulting from a series of high explosive detonations conducted at Kirtland Air Force Base in August and September of 2007. Dubbed Humble Redwood I (HR-1), these near-surface chemical high explosive detonations consisted of seven shots of varying height or depth of burst. Each shot was simulated numerically using GEODYN. An adaptive mesh refinement scheme based on air pressure gradients was employed such that the mesh refinement tracked the advancing shock front where sharp discontinuities existed in the state variables, but allowed the mesh to sufficientlymore » relax behind the shock front for runtime efficiency. Comparisons of overpressure, sound speed, and positive phase impulse from the GEODYN simulations were made to the recorded data taken from each HR-1 shot. Where the detonations occurred above ground or were shallowly buried (no deeper than 1 m), the GEODYN model was able to simulate the sound speeds, peak overpressures, and positive phase impulses to within approximately 1%, 23%, and 6%, respectively, of the actual recorded data, supporting the use of numerical simulation of the air blast as a forensic tool in determining the yield of an otherwise unknown explosion.« less
Machining of Aircraft Titanium with Abrasive-Waterjets for Fatigue Critical Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, H. T.; Hovanski, Yuri; Dahl, Michael E.

2010-10-04

Laboratory tests were conducted to determine the fatigue performance of AWJ-machined aircraft titanium. Dog-bone specimens machined with AWJs were prepared and tested with and without sanding and dry-grit blasting with Al2O3 as secondary processes. The secondary processes were applied to remove the visual appearance of AWJ-generated striations and to clean up the garnet embedment. The fatigue performance of AWJ-machined specimens was compared with baseline specimens machined with CNC milling. Fatigue test results not only confirmed the findings of the aluminum dog-bone specimens but also further enhance the fatigue performance. In addition, titanium is known to be notoriously difficult to cutmore » with contact tools while AWJs cut it 34% faster than stainless steel. AWJ cutting and dry-grit blasting are shown to be a preferred combination for processing aircraft titanium that is fatigue critical.« less
Radiological-Pathological Correlations Following Blast-Related Traumatic Brain Injury in the Whole Human Brain Using ex Vivo Diffusion Tensor Imaging

DTIC Science & Technology

2014-01-01

were as follows: Blast TBI: Suicide drug overdose – blast years prior Ruptured aneurysm – blast years prior intraventricular hemorrhage...drug overdose Suicide blunt trauma - fall Cancer Cardiac Arrest Tissue fixation was highly variable because cases were obtained from 4 different...blast years prior Civilian Blast DOA Non-blast TBI: MVA – DOA MVA – DOS Suicide – NFL – GSW to chest Cardiac Arrest – NFL Controls: Suicide
PEPlife: A Repository of the Half-life of Peptides

NASA Astrophysics Data System (ADS)

Mathur, Deepika; Prakash, Satya; Anand, Priya; Kaur, Harpreet; Agrawal, Piyush; Mehta, Ayesha; Kumar, Rajesh; Singh, Sandeep; Raghava, Gajendra P. S.

2016-11-01

Short half-life is one of the key challenges in the field of therapeutic peptides. Various studies have reported enhancement in the stability of peptides using methods like chemical modifications, D-amino acid substitution, cyclization, replacement of labile aminos acids, etc. In order to study this scattered data, there is a pressing need for a repository dedicated to the half-life of peptides. To fill this lacuna, we have developed PEPlife (http://crdd.osdd.net/raghava/peplife), a manually curated resource of experimentally determined half-life of peptides. PEPlife contains 2229 entries covering 1193 unique peptides. Each entry provides detailed information of the peptide, like its name, sequence, half-life, modifications, the experimental assay for determining half-life, biological nature and activity of the peptide. We also maintain SMILES and structures of peptides. We have incorporated web-based modules to offer user-friendly data searching and browsing in the database. PEPlife integrates numerous tools to perform various types of analysis such as BLAST, Smith-Waterman algorithm, GGSEARCH, Jalview and MUSTANG. PEPlife would augment the understanding of different factors that affect the half-life of peptides like modifications, sequence, length, route of delivery of the peptide, etc. We anticipate that PEPlife will be useful for the researchers working in the area of peptide-based therapeutics.
Fragment Size Distribution of Blasted Rock Mass

NASA Astrophysics Data System (ADS)

Jug, Jasmin; Strelec, Stjepan; Gazdek, Mario; Kavur, Boris

2017-12-01

Rock mass is a heterogeneous material, and the heterogeneity of rock causes sizes distribution of fragmented rocks in blasting. Prediction of blasted rock mass fragmentation has a significant role in the overall economics of opencast mines. Blasting as primary fragmentation can significantly decrease the cost of loading, transport, crushing and milling operations. Blast fragmentation chiefly depends on the specific blast design (geometry of blast holes drilling, the quantity and class of explosive, the blasting form, the timing and partition, etc.) and on the properties of the rock mass (including the uniaxial compressive strength, the rock mass elastic Young modulus, the rock discontinuity characteristics and the rock density). Prediction and processing of blasting results researchers can accomplish by a variety of existing software’s and models, one of them is the Kuz-Ram model, which is possibly the most widely used approach to estimating fragmentation from blasting. This paper shows the estimation of fragmentation using the "SB" program, which was created by the authors. Mentioned program includes the Kuz-Ram model. Models of fragmentation are confirmed and calibrated by comparing the estimated fragmentation with actual post-blast fragmentation from image processing techniques. In this study, the Kuz-Ram fragmentation model has been used for an open-pit limestone quarry in Dalmatia, southern Croatia. The resulting calibrated value of the rock factor enables the quality prognosis of fragmentation in further blasting works, with changed drilling geometry and blast design parameters. It also facilitates simulation in the program to optimize blasting works and get the desired fragmentations of the blasted rock mass.
Chronic Traumatic Encephalopathy in Blast-Exposed Military Veterans and a Blast Neurotrauma Mouse Model

PubMed Central

Goldstein, Lee E.; Fisher, Andrew M.; Tagge, Chad A.; Zhang, Xiao-Lei; Velisek, Libor; Sullivan, John A.; Upreti, Chirag; Kracht, Jonathan M.; Ericsson, Maria; Wojnarowicz, Mark W.; Goletiani, Cezar J.; Maglakelidze, Giorgi M.; Casey, Noel; Moncaster, Juliet A.; Minaeva, Olga; Moir, Robert D.; Nowinski, Christopher J.; Stern, Robert A.; Cantu, Robert C.; Geiling, James; Blusztajn, Jan K.; Wolozin, Benjamin L.; Ikezu, Tsuneya; Stein, Thor D.; Budson, Andrew E.; Kowall, Neil W.; Chargin, David; Sharon, Andre; Saman, Sudad; Hall, Garth F.; Moss, William C.; Cleveland, Robin O.; Tanzi, Rudolph E.; Stanton, Patric K.; McKee, Ann C.

2013-01-01

Blast exposure is associated with traumatic brain injury (TBI), neuropsychiatric symptoms, and long-term cognitive disability. We examined a case series of postmortem brains from U.S. military veterans exposed to blast and/or concussive injury. We found evidence of chronic traumatic encephalopathy (CTE), a tau protein–linked neurodegenerative disease, that was similar to the CTE neuropathology observed in young amateur American football players and a professional wrestler with histories of concussive injuries. We developed a blast neurotrauma mouse model that recapitulated CTE-linked neuropathology in wild-type C57BL/6 mice 2 weeks after exposure to a single blast. Blast-exposed mice demonstrated phosphorylated tauopathy, myelinated axonopathy, microvasculopathy, chronic neuroinflammation, and neurodegeneration in the absence of macroscopic tissue damage or hemorrhage. Blast exposure induced persistent hippocampal-dependent learning and memory deficits that persisted for at least 1 month and correlated with impaired axonal conduction and defective activity-dependent long-term potentiation of synaptic transmission. Intracerebral pressure recordings demonstrated that shock waves traversed the mouse brain with minimal change and without thoracic contributions. Kinematic analysis revealed blast-induced head oscillation at accelerations sufficient to cause brain injury. Head immobilization during blast exposure prevented blast-induced learning and memory deficits. The contribution of blast wind to injurious head acceleration may be a primary injury mechanism leading to blast-related TBI and CTE. These results identify common pathogenic determinants leading to CTE in blast-exposed military veterans and head-injured athletes and additionally provide mechanistic evidence linking blast exposure to persistent impairments in neurophysiological function, learning, and memory. PMID:22593173
Chronic traumatic encephalopathy in blast-exposed military veterans and a blast neurotrauma mouse model.

PubMed

Goldstein, Lee E; Fisher, Andrew M; Tagge, Chad A; Zhang, Xiao-Lei; Velisek, Libor; Sullivan, John A; Upreti, Chirag; Kracht, Jonathan M; Ericsson, Maria; Wojnarowicz, Mark W; Goletiani, Cezar J; Maglakelidze, Giorgi M; Casey, Noel; Moncaster, Juliet A; Minaeva, Olga; Moir, Robert D; Nowinski, Christopher J; Stern, Robert A; Cantu, Robert C; Geiling, James; Blusztajn, Jan K; Wolozin, Benjamin L; Ikezu, Tsuneya; Stein, Thor D; Budson, Andrew E; Kowall, Neil W; Chargin, David; Sharon, Andre; Saman, Sudad; Hall, Garth F; Moss, William C; Cleveland, Robin O; Tanzi, Rudolph E; Stanton, Patric K; McKee, Ann C

2012-05-16

Blast exposure is associated with traumatic brain injury (TBI), neuropsychiatric symptoms, and long-term cognitive disability. We examined a case series of postmortem brains from U.S. military veterans exposed to blast and/or concussive injury. We found evidence of chronic traumatic encephalopathy (CTE), a tau protein-linked neurodegenerative disease, that was similar to the CTE neuropathology observed in young amateur American football players and a professional wrestler with histories of concussive injuries. We developed a blast neurotrauma mouse model that recapitulated CTE-linked neuropathology in wild-type C57BL/6 mice 2 weeks after exposure to a single blast. Blast-exposed mice demonstrated phosphorylated tauopathy, myelinated axonopathy, microvasculopathy, chronic neuroinflammation, and neurodegeneration in the absence of macroscopic tissue damage or hemorrhage. Blast exposure induced persistent hippocampal-dependent learning and memory deficits that persisted for at least 1 month and correlated with impaired axonal conduction and defective activity-dependent long-term potentiation of synaptic transmission. Intracerebral pressure recordings demonstrated that shock waves traversed the mouse brain with minimal change and without thoracic contributions. Kinematic analysis revealed blast-induced head oscillation at accelerations sufficient to cause brain injury. Head immobilization during blast exposure prevented blast-induced learning and memory deficits. The contribution of blast wind to injurious head acceleration may be a primary injury mechanism leading to blast-related TBI and CTE. These results identify common pathogenic determinants leading to CTE in blast-exposed military veterans and head-injured athletes and additionally provide mechanistic evidence linking blast exposure to persistent impairments in neurophysiological function, learning, and memory.
MCMC-ODPR: primer design optimization using Markov Chain Monte Carlo sampling.

PubMed

Kitchen, James L; Moore, Jonathan D; Palmer, Sarah A; Allaby, Robin G

2012-11-05

Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base.
MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling

PubMed Central

2012-01-01

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base. PMID:23126469
On the Propagation and Interaction of Spherical Blast Waves

NASA Technical Reports Server (NTRS)

Kandula, Max; Freeman, Robert

2007-01-01

The characteristics and the scaling laws of isolated spherical blast waves have been briefly reviewed. Both self-similar solutions and numerical solutions of isolated blast waves are discussed. Blast profiles in the near-field (strong shock region) and the far-field (weak shock region) are examined. Particular attention is directed at the blast overpressure and shock propagating speed. Consideration is also given to the interaction of spherical blast waves. Test data for the propagation and interaction of spherical blast waves emanating from explosives placed in the vicinity of a solid propellant stack are presented. These data are discussed with regard to the scaling laws concerning the decay of blast overpressure.
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

PubMed

Simonyan, Vahan; Mazumder, Raja

2014-09-30

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

PubMed Central

Simonyan, Vahan; Mazumder, Raja

2014-01-01

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. PMID:25271953
Blast waves and how they interact with structures.

PubMed

Cullis, I G

2001-02-01

The paper defines and describes blast waves, their interaction with a structure and its subsequent response. Explosions generate blast waves, which need not be due to explosives. A blast wave consists of two parts: a shock wave and a blast wind. The paper explains how shock waves are formed and their basic properties. The physics of blast waves is non-linear and therefore non-intuitive. To understand how an explosion generates a blast wave a numerical modelling computer code, called a hydrocode has to be employed. This is briefly explained and the cAst Eulerian hydrocode is used to illustrate the formation and propagation of the blast wave generated by a 1 kg sphere of TNT explosive detonated 1 m above the ground. The paper concludes with a discussion of the response of a structure to a blast wave and shows that this response is governed by the structures natural frequency of vibration compared to the duration of the blast wave. The basic concepts introduced are illustrated in a second simulation that introduces two structures into the blast field of the TNT charge.
Brain Vulnerability to Repeated Blast Overpressure and Polytrauma

DTIC Science & Technology

2015-10-01

characterization of the mouse model of repeated blast also found no cumula- tive effect of repeated blast on cortical levels of reactive oxygen species [39]. C...overpressure in rats to investigate the cumulative effects of multiple blast exposures on neurologic status, neurobehavioral function, and brain...preclinical model of blast overpressure in rats to investigate the cumulative effects of multiple blast exposures using neurological, neurochemical
Dynamic Modelling of Fault Slip Induced by Stress Waves due to Stope Production Blasts

NASA Astrophysics Data System (ADS)

Sainoki, Atsushi; Mitri, Hani S.

2016-01-01

Seismic events can take place due to the interaction of stress waves induced by stope production blasts with faults located in close proximity to stopes. The occurrence of such seismic events needs to be controlled to ensure the safety of the mine operators and the underground mine workings. This paper presents the results of a dynamic numerical modelling study of fault slip induced by stress waves resulting from stope production blasts. First, the calibration of a numerical model having a single blast hole is performed using a charge weight scaling law to determine blast pressure and damping coefficient of the rockmass. Subsequently, a numerical model of a typical Canadian metal mine encompassing a fault parallel to a tabular ore deposit is constructed, and the simulation of stope extraction sequence is carried out with static analyses until the fault exhibits slip burst conditions. At that point, the dynamic analysis begins by applying the calibrated blast pressure to the stope wall in the form of velocities generated by the blast holes. It is shown from the results obtained from the dynamic analysis that the stress waves reflected on the fault create a drop of normal stresses acting on the fault, which produces a reduction in shear stresses while resulting in fault slip. The influence of blast sequences on the behaviour of the fault is also examined assuming several types of blast sequences. Comparison of the blast sequence simulation results indicates that performing simultaneous blasts symmetrically induces the same level of seismic events as separate blasts, although seismic energy is more rapidly released when blasts are performed symmetrically. On the other hand when nine blast holes are blasted simultaneously, a large seismic event is induced, compared to the other two blasts. It is concluded that the separate blasts might be employed under the adopted geological conditions. The developed methodology and procedure to arrive at an ideal blast sequence can be applied to other mines where faults are found in the vicinity of stopes.
Relationship between orientation to a blast and pressure wave propagation inside the rat brain.

PubMed

Chavko, Mikulas; Watanabe, Tomas; Adeeb, Saleena; Lankasky, Jason; Ahlers, Stephen T; McCarron, Richard M

2011-01-30

Exposure to a blast wave generated during an explosion may result in brain damage and related neurological impairments. Several mechanisms by which the primary blast wave can damage the brain have been proposed, including: (1) a direct effect of the shock wave on the brain causing tissue damage by skull flexure and propagation of stress and shear forces; and (2) an indirect transfer of kinetic energy from the blast, through large blood vessels and cerebrospinal fluid (CSF), to the central nervous system. To address a basic question related to the mechanisms of blast brain injury, pressure was measured inside the brains of rats exposed to a low level of blast (~35kPa), while positioned in three different orientations with respect to the primary blast wave; head facing blast, right side exposed to blast and head facing away from blast. Data show different patterns and durations of the pressure traces inside the brain, depending on the rat orientation to blast. Frontal exposures (head facing blast) resulted in pressure traces of higher amplitude and longer duration, suggesting direct transmission and reflection of the pressure inside the brain (dynamic pressure transfer). The pattern of the pressure wave inside the brain in the head facing away from blast exposures assumes contribution of the static pressure, similar to hydrodynamic pressure to the pressure wave inside the brain. Published by Elsevier B.V.
Numerical Study of the Reduction Process in an Oxygen Blast Furnace

NASA Astrophysics Data System (ADS)

Zhang, Zongliang; Meng, Jiale; Guo, Lei; Guo, Zhancheng

2016-02-01

Based on computational fluid dynamics, chemical reaction kinetics, principles of transfer in metallurgy, and other principles, a multi-fluid model for a traditional blast furnace was established. The furnace conditions were simulated with this multi-fluid mathematical model, and the model was verified with the comparison of calculation and measurement. Then a multi-fluid model for an oxygen blast furnace in the gasifier-full oxygen blast furnace process was established based on this traditional blast furnace model. With the established multi-fluid model for an oxygen blast furnace, the basic characteristics of iron ore reduction process in the oxygen blast furnace were summarized, including the changing process of the iron ore reduction degree and the compositions of the burden, etc. The study found that compared to the traditional blast furnace, the magnetite reserve zone in the furnace shaft under oxygen blast furnace condition was significantly reduced, which is conducive to the efficient operation of blast furnace. In order to optimize the oxygen blast furnace design and operating parameters, the iron ore reduction process in the oxygen blast furnace was researched under different shaft tuyere positions, different recycling gas temperatures, and different allocation ratios of recycling gas between the hearth tuyere and the shaft tuyere. The results indicate that these three factors all have a substantial impact on the ore reduction process in the oxygen blast furnace. Moderate shaft tuyere position, high recycling gas temperature, and high recycling gas allocation ratio between hearth and shaft could significantly promote the reduction of iron ore, reduce the scope of the magnetite reserve zone, and improve the performance of oxygen blast furnace. Based on the above findings, the recommendations for improvement of the oxygen blast furnace design and operation were proposed.
Low-Level Blast Exposure Increases Transient Receptor Potential Vanilloid 1 (TRPV1) Expression in the Rat Cornea

PubMed Central

Por, Elaine D.; Choi, Jae-Hyek; Lund, Brian J.

2016-01-01

ABSTRACT Background: Blast-related ocular injuries sustained by military personnel have led to rigorous efforts to elucidate the effects of blast exposure on neurosensory function. Recent studies have provided some insight into cognitive and visual deficits sustained following blast exposure; however, limited data are available on the effects of blast on pain and inflammatory processes. Investigation of these secondary effects of blast exposure is necessary to fully comprehend the complex pathophysiology of blast-related injuries. The overall purpose of this study is to determine the effects of single and repeated blast exposure on pain and inflammatory mediators in ocular tissues. Methods: A compressed air shock tube was used to deliver a single or repeated blast (68.0 ± 2.7 kPa) to anesthetized rats daily for 5 days. Immunohistochemistry was performed on ocular tissues to determine the expression of the transient receptor potential vanilloid 1 (TRPV1) channel, calcitonin gene-related peptide (CGRP), substance P (SP), and endothelin-1 (ET-1) following single and repeated blast exposure. Neutrophil infiltration and myeloperoxidase (MPO) expression were also assessed in blast tissues via immunohistochemistry and enzyme-linked immunosorbent assay (ELISA) analysis, respectively. Results: TRPV1 expression was increased in rat corneas exposed to both single and repeated blast. Increased secretion of CGRP, SP, and ET-1 was also detected in rat corneas as compared to control. Moreover, repeated blast exposure resulted in neutrophil infiltration in the cornea and stromal layer as compared to control animals. Conclusion: Single and repeated blast exposure resulted in increased expression of TRPV1, CGRP, SP, and ET-1 as well as neutrophil infiltration. Collectively, these findings provide novel insight into the activation of pain and inflammation signaling mediators following blast exposure. PMID:27049881

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

PubMed

Lagnel, Jacques; Tsigenopoulos, Costas S; Iliopoulos, Ioannis

2009-03-15

NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. Supplementary data are available at Bioinformatics online.
Hull Form Design and Optimization Tool Development

DTIC Science & Technology

2012-07-01

global minimum. The algorithm accomplishes this by using a method known as metaheuristics which allows the algorithm to examine a large area by...further development of these tools including the implementation and testing of a new optimization algorithm , the improvement of a rapid hull form...under the 2012 Naval Research Enterprise Intern Program. 15. SUBJECT TERMS hydrodynamic, hull form, generation, optimization, algorithm
New algorithms for motion error detection of numerical control machine tool by laser tracking measurement on the basis of GPS principle.

PubMed

Wang, Jindong; Chen, Peng; Deng, Yufen; Guo, Junjie

2018-01-01

As a three-dimensional measuring instrument, the laser tracker is widely used in industrial measurement. To avoid the influence of angle measurement error on the overall measurement accuracy, the multi-station and time-sharing measurement with a laser tracker is introduced on the basis of the global positioning system (GPS) principle in this paper. For the proposed method, how to accurately determine the coordinates of each measuring point by using a large amount of measured data is a critical issue. Taking detecting motion error of a numerical control machine tool, for example, the corresponding measurement algorithms are investigated thoroughly. By establishing the mathematical model of detecting motion error of a machine tool with this method, the analytical algorithm concerning on base station calibration and measuring point determination is deduced without selecting the initial iterative value in calculation. However, when the motion area of the machine tool is in a 2D plane, the coefficient matrix of base station calibration is singular, which generates a distortion result. In order to overcome the limitation of the original algorithm, an improved analytical algorithm is also derived. Meanwhile, the calibration accuracy of the base station with the improved algorithm is compared with that with the original analytical algorithm and some iterative algorithms, such as the Gauss-Newton algorithm and Levenberg-Marquardt algorithm. The experiment further verifies the feasibility and effectiveness of the improved algorithm. In addition, the different motion areas of the machine tool have certain influence on the calibration accuracy of the base station, and the corresponding influence of measurement error on the calibration result of the base station depending on the condition number of coefficient matrix are analyzed.
New algorithms for motion error detection of numerical control machine tool by laser tracking measurement on the basis of GPS principle

NASA Astrophysics Data System (ADS)

Wang, Jindong; Chen, Peng; Deng, Yufen; Guo, Junjie

2018-01-01

As a three-dimensional measuring instrument, the laser tracker is widely used in industrial measurement. To avoid the influence of angle measurement error on the overall measurement accuracy, the multi-station and time-sharing measurement with a laser tracker is introduced on the basis of the global positioning system (GPS) principle in this paper. For the proposed method, how to accurately determine the coordinates of each measuring point by using a large amount of measured data is a critical issue. Taking detecting motion error of a numerical control machine tool, for example, the corresponding measurement algorithms are investigated thoroughly. By establishing the mathematical model of detecting motion error of a machine tool with this method, the analytical algorithm concerning on base station calibration and measuring point determination is deduced without selecting the initial iterative value in calculation. However, when the motion area of the machine tool is in a 2D plane, the coefficient matrix of base station calibration is singular, which generates a distortion result. In order to overcome the limitation of the original algorithm, an improved analytical algorithm is also derived. Meanwhile, the calibration accuracy of the base station with the improved algorithm is compared with that with the original analytical algorithm and some iterative algorithms, such as the Gauss-Newton algorithm and Levenberg-Marquardt algorithm. The experiment further verifies the feasibility and effectiveness of the improved algorithm. In addition, the different motion areas of the machine tool have certain influence on the calibration accuracy of the base station, and the corresponding influence of measurement error on the calibration result of the base station depending on the condition number of coefficient matrix are analyzed.
Shock tubes and blast injury modeling.

PubMed

Ning, Ya-Lei; Zhou, Yuan-Guo

2015-01-01

Explosive blast injury has become the most prevalent injury in recent military conflicts and terrorist attacks. The magnitude of this kind of polytrauma is complex due to the basic physics of blast and the surrounding environments. Therefore, development of stable, reproducible and controllable animal model using an ideal blast simulation device is the key of blast injury research. The present review addresses the modeling of blast injury and applications of shock tubes.
Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection

PubMed Central

Tanweer, Fatah A.; Rafii, Mohd Y.; Sijam, Kamaruzaman; Rahim, Harun A.; Ahmed, Fahim; Ashkani, Sadegh; Latif, Mohammad A.

2015-01-01

Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013
A Multi-Mode Shock Tube for Investigation of Blast-Induced Traumatic Brain Injury

PubMed Central

Reneer, Dexter V.; Hisel, Richard D.; Hoffman, Joshua M.; Kryscio, Richard J.; Lusk, Braden T.

2011-01-01

Abstract Blast-induced mild traumatic brain injury (bTBI) has become increasingly common in recent military conflicts. The mechanisms by which non-impact blast exposure results in bTBI are incompletely understood. Current small animal bTBI models predominantly utilize compressed air-driven membrane rupture as their blast wave source, while large animal models use chemical explosives. The pressure-time signature of each blast mode is unique, making it difficult to evaluate the contributions of the different components of the blast wave to bTBI when using a single blast source. We utilized a multi-mode shock tube, the McMillan blast device, capable of utilizing compressed air- and compressed helium-driven membrane rupture, and the explosives oxyhydrogen and cyclotrimethylenetrinitramine (RDX, the primary component of C-4 plastic explosives) as the driving source. At similar maximal blast overpressures, the positive pressure phase of compressed air-driven blasts was longer, and the positive impulse was greater, than those observed for shockwaves produced by other driving sources. Helium-driven shockwaves more closely resembled RDX blasts, but by displacing air created a hypoxic environment within the shock tube. Pressure-time traces from oxyhydrogen-driven shockwaves were very similar those produced by RDX, although they resulted in elevated carbon monoxide levels due to combustion of the polyethylene bag used to contain the gases within the shock tube prior to detonation. Rats exposed to compressed air-driven blasts had more pronounced vascular damage than those exposed to oxyhydrogen-driven blasts of the same peak overpressure, indicating that differences in blast wave characteristics other than peak overpressure may influence the extent of bTBI. Use of this multi-mode shock tube in small animal models will enable comparison of the extent of brain injury with the pressure-time signature produced using each blast mode, facilitating evaluation of the blast wave components contributing to bTBI. PMID:21083431
Effects of Low-Level Blast Exposure on the Nervous System: Is There Really a Controversy?

PubMed Central

Elder, Gregory A.; Stone, James R.; Ahlers, Stephen T.

2014-01-01

High-pressure blast waves can cause extensive CNS injury in human beings. However, in combat settings, such as Iraq and Afghanistan, lower level exposures associated with mild traumatic brain injury (mTBI) or subclinical exposure have been much more common. Yet controversy exists concerning what traits can be attributed to low-level blast, in large part due to the difficulty of distinguishing blast-related mTBI from post-traumatic stress disorder (PTSD). We describe how TBI is defined in human beings and the problems posed in using current definitions to recognize blast-related mTBI. We next consider the problem of applying definitions of human mTBI to animal models, in particular that TBI severity in human beings is defined in relation to alteration of consciousness at the time of injury, which typically cannot be assessed in animals. However, based on outcome assessments, a condition of “low-level” blast exposure can be defined in animals that likely approximates human mTBI or subclinical exposure. We review blast injury modeling in animals noting that inconsistencies in experimental approach have contributed to uncertainty over the effects of low-level blast. Yet, animal studies show that low-level blast pressure waves are transmitted to the brain. In brain, low-level blast exposures cause behavioral, biochemical, pathological, and physiological effects on the nervous system including the induction of PTSD-related behavioral traits in the absence of a psychological stressor. We review the relationship of blast exposure to chronic neurodegenerative diseases noting the paradoxical lowering of Abeta by blast, which along with other observations suggest that blast-related TBI is pathophysiologically distinct from non-blast TBI. Human neuroimaging studies show that blast-related mTBI is associated with a variety of chronic effects that are unlikely to be explained by co-morbid PTSD. We conclude that abundant evidence supports low-level blast as having long-term effects on the nervous system. PMID:25566175
A multi-mode shock tube for investigation of blast-induced traumatic brain injury.

PubMed

Reneer, Dexter V; Hisel, Richard D; Hoffman, Joshua M; Kryscio, Richard J; Lusk, Braden T; Geddes, James W

2011-01-01

Blast-induced mild traumatic brain injury (bTBI) has become increasingly common in recent military conflicts. The mechanisms by which non-impact blast exposure results in bTBI are incompletely understood. Current small animal bTBI models predominantly utilize compressed air-driven membrane rupture as their blast wave source, while large animal models use chemical explosives. The pressure-time signature of each blast mode is unique, making it difficult to evaluate the contributions of the different components of the blast wave to bTBI when using a single blast source. We utilized a multi-mode shock tube, the McMillan blast device, capable of utilizing compressed air- and compressed helium-driven membrane rupture, and the explosives oxyhydrogen and cyclotrimethylenetrinitramine (RDX, the primary component of C-4 plastic explosives) as the driving source. At similar maximal blast overpressures, the positive pressure phase of compressed air-driven blasts was longer, and the positive impulse was greater, than those observed for shockwaves produced by other driving sources. Helium-driven shockwaves more closely resembled RDX blasts, but by displacing air created a hypoxic environment within the shock tube. Pressure-time traces from oxyhydrogen-driven shockwaves were very similar those produced by RDX, although they resulted in elevated carbon monoxide levels due to combustion of the polyethylene bag used to contain the gases within the shock tube prior to detonation. Rats exposed to compressed air-driven blasts had more pronounced vascular damage than those exposed to oxyhydrogen-driven blasts of the same peak overpressure, indicating that differences in blast wave characteristics other than peak overpressure may influence the extent of bTBI. Use of this multi-mode shock tube in small animal models will enable comparison of the extent of brain injury with the pressure-time signature produced using each blast mode, facilitating evaluation of the blast wave components contributing to bTBI.
Transcriptional profiling in rat hair follicles following simulated Blast insult: a new diagnostic tool for traumatic brain injury.

PubMed

Zhang, Jing; Carnduff, Lisa; Norman, Grant; Josey, Tyson; Wang, Yushan; Sawyer, Thomas W; Martyniuk, Christopher J; Langlois, Valerie S

2014-01-01

With wide adoption of explosive-dependent weaponry during military activities, Blast-induced neurotrauma (BINT)-induced traumatic brain injury (TBI) has become a significant medical issue. Therefore, a robust and accessible biomarker system is in demand for effective and efficient TBI diagnosis. Such systems will also be beneficial to studies of TBI pathology. Here we propose the mammalian hair follicles as a potential candidate. An Advanced Blast Simulator (ABS) was developed to generate shock waves simulating traumatic conditions on brains of rat model. Microarray analysis was performed in hair follicles to identify the gene expression profiles that are associated with shock waves. Gene set enrichment analysis (GSEA) and sub-network enrichment analysis (SNEA) were used to identify cell processes and molecular signaling cascades affected by simulated bomb blasts. Enrichment analyses indicated that genes with altered expression levels were involved in central nervous system (CNS)/peripheral nervous system (PNS) responses as well as signal transduction including Ca2+, K+-transportation-dependent signaling, Toll-Like Receptor (TLR) signaling and Mitogen Activated Protein Kinase (MAPK) signaling cascades. Many of the pathways identified as affected by shock waves in the hair follicles have been previously reported to be TBI responsive in other organs such as brain and blood. The results suggest that the hair follicle has some common TBI responsive molecular signatures to other tissues. Moreover, various TBI-associated diseases were identified as preferentially affected using a gene network approach, indicating that the hair follicle may be capable of reflecting comprehensive responses to TBI conditions. Accordingly, the present study demonstrates that the hair follicle is a potentially viable system for rapid and non-invasive TBI diagnosis.
Development of unidentified dna-specific hif 1α gene of lizard (hemidactylus platyurus) which plays a role in tissue regeneration process

NASA Astrophysics Data System (ADS)

Novianti, T.; Sadikin, M.; Widia, S.; Juniantito, V.; Arida, E. A.

2018-03-01

Development of unidentified specific gene is essential to analyze the availability these genes in biological process. Identification unidentified specific DNA of HIF 1α genes is important to analyze their contribution in tissue regeneration process in lizard tail (Hemidactylus platyurus). Bioinformatics and PCR techniques are relatively an easier method to identify an unidentified gene. The most widely used method is BLAST (Basic Local Alignment Sequence Tools) method for alignment the sequences from the other organism. BLAST technique is online software from website https://blast.ncbi.nlm.nih.gov/Blast.cgi that capable to generate the similar sequences from closest kinship to distant kindship. Gecko japonicus is a species that it has closest kinship with H. platyurus. Comparing HIF 1 α gene sequence of G. japonicus with the other species used multiple alignment methods from Mega7 software. Conserved base areas were identified using Clustal IX method. Primary DNA of HIF 1 α gene was design by Primer3 software. HIF 1α gene of lizard (H. platyurus) was successfully amplified using a real-time PCR machine by primary DNA that we had designed from Gecko japonicus. Identification unidentified gene of HIF 1a lizard has been done successfully with multiple alignment method. The study was conducted by analyzing during the growth of tail on day 1, 3, 5, 7, 10, 13 and 17 of lizard tail after autotomy. Process amplification of HIF 1α gene was described by CT value in real time PCR machine. HIF 1α expression of gene is quantified by Livak formula. Chi-square statistic test is 0.000 which means that there is a different expression of HIF 1 α gene in every growth day treatment.
Transcriptional Profiling in Rat Hair Follicles following Simulated Blast Insult: A New Diagnostic Tool for Traumatic Brain Injury

PubMed Central

Zhang, Jing; Carnduff, Lisa; Norman, Grant; Josey, Tyson; Wang, Yushan; Sawyer, Thomas W.; Martyniuk, Christopher J.; Langlois, Valerie S.

2014-01-01

With wide adoption of explosive-dependent weaponry during military activities, Blast-induced neurotrauma (BINT)-induced traumatic brain injury (TBI) has become a significant medical issue. Therefore, a robust and accessible biomarker system is in demand for effective and efficient TBI diagnosis. Such systems will also be beneficial to studies of TBI pathology. Here we propose the mammalian hair follicles as a potential candidate. An Advanced Blast Simulator (ABS) was developed to generate shock waves simulating traumatic conditions on brains of rat model. Microarray analysis was performed in hair follicles to identify the gene expression profiles that are associated with shock waves. Gene set enrichment analysis (GSEA) and sub-network enrichment analysis (SNEA) were used to identify cell processes and molecular signaling cascades affected by simulated bomb blasts. Enrichment analyses indicated that genes with altered expression levels were involved in central nervous system (CNS)/peripheral nervous system (PNS) responses as well as signal transduction including Ca2+, K+-transportation-dependent signaling, Toll-Like Receptor (TLR) signaling and Mitogen Activated Protein Kinase (MAPK) signaling cascades. Many of the pathways identified as affected by shock waves in the hair follicles have been previously reported to be TBI responsive in other organs such as brain and blood. The results suggest that the hair follicle has some common TBI responsive molecular signatures to other tissues. Moreover, various TBI-associated diseases were identified as preferentially affected using a gene network approach, indicating that the hair follicle may be capable of reflecting comprehensive responses to TBI conditions. Accordingly, the present study demonstrates that the hair follicle is a potentially viable system for rapid and non-invasive TBI diagnosis. PMID:25136963
Prospective Molecular Characterization of Burn Wound Colonization: Novel Tools and Analysis

DTIC Science & Technology

2014-02-01

from patients with endocarditis and wound/soft tissue infections, have been sequenced and an initial analysis performed. Finally, enrollment in the...Price LB. Analysis of S. aureus isolates from endocarditis and skin/soft tissue infections A strict blast search was performed on the S. aureus...targets differentiating the cellulitis and endocarditis isolates. This was followed with a basic Pearson’s Chi-squared test with Yates’ continuity
GUM Analysis for TIMS Isotopic Ratios in BEP0 Graphite Qualification Samples, Round 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerlach, David C.; Heasler, Patrick G.; Reid, Bruce D.

In May 2007, one set of three samples from NBL were addressed to Steve Petersen for TIMS analysis, and included BEP0 samples numbered 27008, 30986, and 50846. All cores were trimmed by tooling, and lightly cleaned by CO2 pellet blasting. Small discs were cut from the second set of samples for SIMS analysis, with the remainder of each used for TIMS preparation.
PANDA: Protein function prediction using domain architecture and affinity propagation.

PubMed

Wang, Zheng; Zhao, Chenguang; Wang, Yiheng; Sun, Zheng; Wang, Nan

2018-02-22

We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .
Temporal compressive imaging for video

NASA Astrophysics Data System (ADS)

Zhou, Qun; Zhang, Linxia; Ke, Jun

2018-01-01

In many situations, imagers are required to have higher imaging speed, such as gunpowder blasting analysis and observing high-speed biology phenomena. However, measuring high-speed video is a challenge to camera design, especially, in infrared spectrum. In this paper, we reconstruct a high-frame-rate video from compressive video measurements using temporal compressive imaging (TCI) with a temporal compression ratio T=8. This means that, 8 unique high-speed temporal frames will be obtained from a single compressive frame using a reconstruction algorithm. Equivalently, the video frame rates is increased by 8 times. Two methods, two-step iterative shrinkage/threshold (TwIST) algorithm and the Gaussian mixture model (GMM) method, are used for reconstruction. To reduce reconstruction time and memory usage, each frame of size 256×256 is divided into patches of size 8×8. The influence of different coded mask to reconstruction is discussed. The reconstruction qualities using TwIST and GMM are also compared.
Herpetomonas spp. isolated from tomato fruits (Lycopersicon esculentum) in southern Spain.

PubMed

Marín, Clotilde; Fabre, Sandrine; Sánchez-Moreno, Manuel; Dollet, Michel

2007-05-01

A flagellate of the family Trypanosomatidae was isolated from fruits of Lycopersicon esculentum (tomato) in southeastern Spain. The isolate was successfully adapted to in vitro culture in monophasic media. The morphology showed the kinetoplast to be positioned towards the middle of the body, and the typical opistomastigote form characteristic of members of the genus Herpetomonas. Amplification of the mini-exon gene was negative, whilst for the 5S ribosomal rRNA gene the result was positive. The DNA sequence was obtained and its alignment with other trypasomatids, obtained using the BLAST algorithm, suggested it was closely related to Herpetomonas samuelpessoai.
30 CFR 780.13 - Operation plan: Blasting.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Operation plan: Blasting. 780.13 Section 780.13... SURFACE MINING PERMIT APPLICATIONS-MINIMUM REQUIREMENTS FOR RECLAMATION AND OPERATION PLAN § 780.13 Operation plan: Blasting. (a) Blasting plan. Each application shall contain a blasting plan for the proposed...
30 CFR 77.1910 - Explosives and blasting; general.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Explosives and blasting; general. 77.1910... COAL MINES Slope and Shaft Sinking § 77.1910 Explosives and blasting; general. (a) Light and power circuits shall be disconnected or removed from the blasting area before charging and blasting. (b) All...
29 CFR 1926.914 - Definitions applicable to this subpart.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., including but not limited to trucks, trailers, rail cars, barges, and vessels. (i) Detonating cord—A... caps, electric blasting caps, delay electric blasting caps, and nonelectric delay blasting caps. (k) Electric blasting cap—A blasting cap designed for and capable of detonation by means of an electric current...

Utilization of Seismic and Infrasound Signals for Characterizing Mining Explosions

DTIC Science & Technology

2001-10-01

different types of mining operations exist, ranging from surface coal cast blasting to hard rock fragmentation blasting in porphyry copper mines. The study...both seismic and infrasound signals. The seismic coupling of large-scale cast blasts in Wyoming, copper fragmentation blasts in Arizona and New Mexico...mining explosions from the copper fragmentation blasts in SE Arizona were observed at Los Alamos. Detected events were among the largest of the blasts
Quantitative electroencephalography in a swine model of blast-induced brain injury.

PubMed

Chen, Chaoyang; Zhou, Chengpeng; Cavanaugh, John M; Kallakuri, Srinivasu; Desai, Alok; Zhang, Liying; King, Albert I

2017-01-01

Electroencephalography (EEG) was used to examine brain activity abnormalities earlier after blast exposure using a swine model to develop a qEEG data analysis protocol. Anaesthetized swine were exposed to 420-450 Kpa blast overpressure and survived for 3 days after blast. EEG recordings were performed at 15 minutes before the blast and 15 minutes, 30 minutes, 2 hours and 1, 2 and 3 days post-blast using surface recording electrodes and a Biopac 4-channel data acquisition system. Off-line quantitative EEG (qEEG) data analysis was performed to determine qEEG changes. Blast induced qEEG changes earlier after blast exposure, including a decrease of mean amplitude (MAMP), an increase of delta band power, a decrease of alpha band root mean square (RMS) and a decrease of 90% spectral edge frequency (SEF90). This study demonstrated that qEEG is sensitive for cerebral injury. The changes of qEEG earlier after the blast indicate the potential of utilization of multiple parameters of qEEG for diagnosis of blast-induced brain injury. Early detection of blast induced brain injury will allow early screening and assessment of brain abnormalities in soldiers to enable timely therapeutic intervention.
Water flow algorithm decision support tool for travelling salesman problem

NASA Astrophysics Data System (ADS)

Kamarudin, Anis Aklima; Othman, Zulaiha Ali; Sarim, Hafiz Mohd

2016-08-01

This paper discuss about the role of Decision Support Tool in Travelling Salesman Problem (TSP) for helping the researchers who doing research in same area will get the better result from the proposed algorithm. A study has been conducted and Rapid Application Development (RAD) model has been use as a methodology which includes requirement planning, user design, construction and cutover. Water Flow Algorithm (WFA) with initialization technique improvement is used as the proposed algorithm in this study for evaluating effectiveness against TSP cases. For DST evaluation will go through usability testing conducted on system use, quality of information, quality of interface and overall satisfaction. Evaluation is needed for determine whether this tool can assists user in making a decision to solve TSP problems with the proposed algorithm or not. Some statistical result shown the ability of this tool in term of helping researchers to conduct the experiments on the WFA with improvements TSP initialization.
Repeat low-level blast exposure increases transient receptor potential vanilloid 1 (TRPV1) and endothelin-1 (ET-1) expression in the trigeminal ganglion

PubMed Central

Burke, Teresa A.; Doyle Brackley, Allison; Jeske, Nathaniel A.; Cleland, Jeffery M.; Lund, Brian J.

2017-01-01

Blast-associated sensory and cognitive trauma sustained by military service members is an area of extensively studied research. Recent studies in our laboratory have revealed that low-level blast exposure increased expression of transient receptor potential vanilloid 1 (TRPV1) and endothelin-1 (ET-1), proteins well characterized for their role in mediating pain transmission, in the cornea. Determining the functional consequences of these alterations in protein expression is critical to understanding blast-related sensory trauma. Thus, the purpose of this study was to examine TRPV1 and ET-1 expression in ocular associated sensory tissues following primary and tertiary blast. A rodent model of blast injury was used in which anesthetized animals, unrestrained or restrained, received a single or repeat blast (73.8 ± 5.5 kPa) from a compressed air shock tube once or daily for five consecutive days, respectively. Behavioral and functional analyses were conducted to assess blast effects on nocifensive behavior and TRPV1 activity. Immunohistochemistry and Western Blot were also performed with trigeminal ganglia (TG) to determine TRPV1, ET-1 and glial fibrillary associated protein (GFAP) expression following blast. Increased TRPV1, ET-1 and GFAP were detected in the TG of animals exposed to repeat blast. Increased nocifensive responses were also observed in animals exposed to repeat, tertiary blast as compared to single blast and control. Moreover, decreased TRPV1 desensitization was observed in TG neurons exposed to repeat blast. Repeat, tertiary blast resulted in increased TRPV1, ET-1 and GFAP expression in the TG, enhanced nociception and decreased TRPV1 desensitization. PMID:28797041
22 CFR 121.11 - Military demolition blocks and blasting caps.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Military demolition blocks and blasting caps... blasting caps. Military demolition blocks and blasting caps referred to in Category IV(a) do not include the following articles: (a) Electric squibs. (b) No. 6 and No. 8 blasting caps, including electric...
30 CFR 817.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 817.11. The operator shall...
30 CFR 816.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-SURFACE MINING ACTIVITIES § 816.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 816.11. The operator shall— (1...
30 CFR 817.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 817.11. The operator shall...
30 CFR 816.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-SURFACE MINING ACTIVITIES § 816.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 816.11. The operator shall— (1...
30 CFR 816.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-SURFACE MINING ACTIVITIES § 816.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 816.11. The operator shall— (1...
30 CFR 817.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 817.11. The operator shall...
30 CFR 817.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 817.11. The operator shall...
30 CFR 817.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 817.11. The operator shall...
30 CFR 816.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-SURFACE MINING ACTIVITIES § 816.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 816.11. The operator shall— (1...
30 CFR 816.66 - Use of explosives: Blasting signs, warnings, and access control.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Use of explosives: Blasting signs, warnings... STANDARDS-SURFACE MINING ACTIVITIES § 816.66 Use of explosives: Blasting signs, warnings, and access control. (a) Blasting signs. Blasting signs shall meet the specifications of § 816.11. The operator shall— (1...
29 CFR 1926.905 - Loading of explosives or blasting agents.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 8 2010-07-01 2010-07-01 false Loading of explosives or blasting agents. 1926.905 Section... Explosives § 1926.905 Loading of explosives or blasting agents. (a) Procedures that permit safe and efficient... have contained explosives or blasting agents. (g) No explosives or blasting agents shall be left...
Comment on "chronic traumatic encephalopathy in blast-exposed military veterans and a blast neurotrauma mouse model".

PubMed

Tsao, Jack W

2012-10-24

In their recent paper, Goldstein et al. show murine brain tau neuropathology after explosive blast with head rotation but do not present additional evidence that would delineate whether this neuropathology was principally caused by blast exposure alone or by blast exposure plus head rotational injury.
Blast injury research models

PubMed Central

Kirkman, E.; Watts, S.; Cooper, G.

2011-01-01

Blast injuries are an increasing problem in both military and civilian practice. Primary blast injury to the lungs (blast lung) is found in a clinically significant proportion of casualties from explosions even in an open environment, and in a high proportion of severely injured casualties following explosions in confined spaces. Blast casualties also commonly suffer secondary and tertiary blast injuries resulting in significant blood loss. The presence of hypoxaemia owing to blast lung complicates the process of fluid resuscitation. Consequently, prolonged hypotensive resuscitation was found to be incompatible with survival after combined blast lung and haemorrhage. This article describes studies addressing new forward resuscitation strategies involving a hybrid blood pressure profile (initially hypotensive followed later by normotensive resuscitation) and the use of supplemental oxygen to increase survival and reduce physiological deterioration during prolonged resuscitation. Surprisingly, hypertonic saline dextran was found to be inferior to normal saline after combined blast injury and haemorrhage. New strategies have therefore been developed to address the needs of blast-injured casualties and are likely to be particularly useful under circumstances of enforced delayed evacuation to surgical care. PMID:21149352
Human Injury Criteria for Underwater Blasts

PubMed Central

Lance, Rachel M.; Capehart, Bruce; Kadro, Omar; Bass, Cameron R.

2015-01-01

Underwater blasts propagate further and injure more readily than equivalent air blasts. Development of effective personal protection and countermeasures, however, requires knowledge of the currently unknown human tolerance to underwater blast. Current guidelines for prevention of underwater blast injury are not based on any organized injury risk assessment, human data or experimental data. The goal of this study was to derive injury risk assessments for underwater blast using well-characterized human underwater blast exposures in the open literature. The human injury dataset was compiled using 34 case reports on underwater blast exposure to 475 personnel, dating as early as 1916. Using severity ratings, computational reconstructions of the blasts, and survival information from a final set of 262 human exposures, injury risk models were developed for both injury severity and risk of fatality as functions of blast impulse and blast peak overpressure. Based on these human data, we found that the 50% risk of fatality from underwater blast occurred at 302±16 kPa-ms impulse. Conservatively, there is a 20% risk of pulmonary injury at a kilometer from a 20 kg charge. From a clinical point of view, this new injury risk model emphasizes the large distances possible for potential pulmonary and gut injuries in water compared with air. This risk value is the first impulse-based fatality risk calculated from human data. The large-scale inconsistency between the blast exposures in the case reports and the guidelines available in the literature prior to this study further underscored the need for this new guideline derived from the unique dataset of actual injuries in this study. PMID:26606655
Effect of Human and Sheep Lung Orientation on Primary Blast Injury Induced by Single Blast

DTIC Science & Technology

2010-09-01

may be injured by m ore than one of these mechanisms in any given event. Primary blast in juries ( PBI ) are exclusively caused by the blast...overpressure. A PBI usually affects air-containing organs such as t he lung, ears and gastrointestinal tract. Secon dary blast injuries are caused by...orientation on blast injuries predicted in human and sheep models. From th is study, it is predicted that the greatest reduction in lung PBI may be

Evaluation of the Effectiveness of Wet Blast Cleaning Methods of Surface Preparation

DTIC Science & Technology

1985-06-01

for Air Abrasive Wet Blast: Complete System Water Abrasive Mixing Chamber in Slurry Blast Unit Schematic of unit Control Unit Slurry Blast — Air/Water...this discussion we present some general. user guidelines regarding what to look for in con- sidering the use or purchase of wet blasting equipment...These units use compressed air as the medium to propel the eroding material. They differ from air abrasive wet blast units in that the abrasive is mixed
Simulation of blast-induced, early-time intracranial wave physics leading to traumatic brain injury.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Paul Allen; Ford, Corey C.

U.S. soldiers are surviving blast and impacts due to effective body armor, trauma evacuation and care. Blast injuries are the leading cause of traumatic brain injury (TBI) in military personnel returning from combat. Understanding of Primary Blast Injury may be needed to develop better means of blast mitigation strategies. The objective of this paper is to investigate the effects of blast direction and strength on the resulting mechanical stress and wave energy distributions generated in the brain.
Current advance methods for the identification of blast resistance genes in rice.

PubMed

Tanweer, Fatah A; Rafii, Mohd Y; Sijam, Kamaruzaman; Rahim, Harun A; Ahmed, Fahim; Latif, Mohammad A

2015-05-01

Rice blast caused by Magnaporthe oryzae is one of the most devastating diseases of rice around the world and crop losses due to blast are considerably high. Many blast resistant rice varieties have been developed by classical plant breeding and adopted by farmers in various rice-growing countries. However, the variability in the pathogenicity of the blast fungus according to environment made blast disease a major concern for farmers, which remains a threat to the rice industry. With the utilization of molecular techniques, plant breeders have improved rice production systems and minimized yield losses. In this article, we have summarized the current advanced molecular techniques used for controlling blast disease. With the advent of new technologies like marker-assisted selection, molecular mapping, map-based cloning, marker-assisted backcrossing and allele mining, breeders have identified more than 100 Pi loci and 350 QTL in rice genome responsible for blast disease. These Pi genes and QTLs can be introgressed into a blast-susceptible cultivar through marker-assisted backcross breeding. These molecular techniques provide timesaving, environment friendly and labour-cost-saving ways to control blast disease. The knowledge of host-plant interactions in the frame of blast disease will lead to develop resistant varieties in the future. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.
Comparison of Some Blast Vibration Predictors for Blasting in Underground Drifts and Some Observations

NASA Astrophysics Data System (ADS)

Bhagwat, Vaibhab Pramod; Dey, Kaushik

2016-04-01

Drilling and blasting are the most economical excavation techniques in underground drifts driven through hard rock formation. Burn cut is the most popular drill pattern, used in this case, to achieve longer advance per blast round. The ground vibration generated due to the propagation of blast waves on the detonation of explosive during blasting is the principal cause for structural and rock damage. Thus, ground vibration is a point of concern for the blasting engineers. The ground vibration from a blast is measured using a seismograph placed at the blast monitoring station. The measured vibrations, in terms of peak particle velocity, are related to the maximum charge detonated at one instant and the distance of seismograph from the blast point. The ground vibrations from a number of blast rounds of varying charge/delay and distances are monitored. A number of scaling factors of these dependencies (viz. Distance and maximum charge/delay) have been proposed by different researchers, namely, square root, cube root, CMRI, Langefors and Kihlstrom, Ghosh-Daemon, Indian standard etc. Scaling factors of desired type are computed for all the measured blast rounds. Regression analysis is carried out between the scaling factors and peak particle velocities to establish the coefficients of the vibration predictor equation. Then, the developed predictor equation is used for designing the blast henceforth. Director General of Mine Safety, India, specified that ground vibrations from eight to ten blast rounds of varying charge/delay and distances should be monitored to develop a predictor equation; however, there is no guideline about the type of scaling factor to be used. Further to this, from the statistical point of view, a regression analysis on a small sample population cannot be accepted without the testing of hypothesis. To show the importance of the above, in this paper, seven scaling factors are considered for blast data set of a hard-rock underground drift using burn-cut blast design. The possible step by step approach to establish a vibration predictor equation is also proposed.
Functional Interactions of Major Rice Blast Resistance Genes Pi-ta with Pi-b and Minor Blast Resistance QTLs

USDA-ARS?s Scientific Manuscript database

Major blast resistance (R) genes confer resistance in a gene-for-gene manner. However, little information is available on interactions between R genes. In this study, interactions between two rice blast R genes, Pi-ta and Pi-b, and other minor blast resistance quantitative trait locus (QTLs) were in...
30 CFR 56.6605 - Isolation of blasting circuits.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Extraneous Electricity § 56.6605 Isolation of blasting circuits. Lead wires and blasting lines shall be... sources of stray or static electricity. Blasting circuits shall be protected from any contact between...
30 CFR 56.6605 - Isolation of blasting circuits.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Extraneous Electricity § 56.6605 Isolation of blasting circuits. Lead wires and blasting lines shall be... sources of stray or static electricity. Blasting circuits shall be protected from any contact between...
30 CFR 56.6605 - Isolation of blasting circuits.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Extraneous Electricity § 56.6605 Isolation of blasting circuits. Lead wires and blasting lines shall be... sources of stray or static electricity. Blasting circuits shall be protected from any contact between...
30 CFR 56.6605 - Isolation of blasting circuits.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Extraneous Electricity § 56.6605 Isolation of blasting circuits. Lead wires and blasting lines shall be... sources of stray or static electricity. Blasting circuits shall be protected from any contact between...
30 CFR 56.6605 - Isolation of blasting circuits.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Extraneous Electricity § 56.6605 Isolation of blasting circuits. Lead wires and blasting lines shall be... sources of stray or static electricity. Blasting circuits shall be protected from any contact between...
Color changing photonic crystals detect blast exposure

PubMed Central

Cullen, D. Kacy; Xu, Yongan; Reneer, Dexter V.; Browne, Kevin D.; Geddes, James W.; Yang, Shu; Smith, Douglas H.

2010-01-01

Blast-induced traumatic brain injury (bTBI) is the “signature wound” of the current wars in Iraq and Afghanistan. However, with no objective information of relative blast exposure, warfighters with bTBI may not receive appropriate medical care and are at risk of being returned to the battlefield. Accordingly, we have created a colorimetric blast injury dosimeter (BID) that exploits material failure of photonic crystals to detect blast exposure. Appearing like a colored sticker, the BID is fabricated in photosensitive polymers via multi-beam interference lithography. Although very stable in the presence of heat, cold or physical impact, sculpted micro- and nano-structures of the BID are physically altered in a precise manner by blast exposure, resulting in color changes that correspond with blast intensity. This approach offers a lightweight, power-free sensor that can be readily interpreted by the naked eye. Importantly, with future refinement this technology may be deployed to identify soldiers exposed to blast at levels suggested to be supra-threshold for non-impact blast-induced mild TBI. PMID:21040795
Blast optimization for improved dragline productivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humphreys, M.; Baldwin, G.

1994-12-31

A project aimed at blast optimization for large open pit coal mines is utilizing blast monitoring and analysis techniques, advanced dragline monitoring equipment, and blast simulation software, to assess the major controlling factors affecting both blast performance and subsequent dragline productivity. This has involved collaborative work between the explosives supplier, mine operator, monitoring equipment manufacturer, and a mining research organization. The results from trial blasts and subsequently monitored dragline production have yielded promising results and continuing studies are being conducted as part of a blast optimization program. It should be stressed that the optimization of blasting practices for improved draglinemore » productivity is a site specific task, achieved through controlled and closely monitored procedures. The benefits achieved at one location can not be simply transferred to another minesite unless similar improvement strategies are first implemented.« less
Modelling the Source of Blasting for the Numerical Simulation of Blast-Induced Ground Vibrations: A Review

NASA Astrophysics Data System (ADS)

Ainalis, Daniel; Kaufmann, Olivier; Tshibangu, Jean-Pierre; Verlinden, Olivier; Kouroussis, Georges

2017-01-01

The mining and construction industries have long been faced with considerable attention and criticism in regard to the effects of blasting. The generation of ground vibrations is one of the most significant factors associated with blasting and is becoming increasingly important as mining sites are now regularly located near urban areas. This is of concern to not only the operators of the mine but also residents. Mining sites are subjected to an inevitable compromise: a production blast is designed to fragment the utmost amount of rock possible; however, any increase in the blast can generate ground vibrations which can propagate great distances and cause structural damage or discomfort to residents in surrounding urban areas. To accurately predict the propagation of ground vibrations near these sensitive areas, the blasting process and surrounding environment must be characterised and understood. As an initial step, an accurate model of the source of blast-induced vibrations is required. This paper presents a comprehensive review of the approaches to model the blasting source in order to critically evaluate developments in the field. An overview of the blasting process and description of the various factors which influence the blast performance and subsequent ground vibrations are also presented. Several approaches to analytically model explosives are discussed. Ground vibration prediction methods focused on seed waveform and charge weight scaling techniques are presented. Finally, numerical simulations of the blasting source are discussed, including methods to estimate blasthole wall pressure time-history, and hydrodynamic codes.
Assessment of Blasting Performance Using Electronic Vis-à-Vis Shock Tube Detonators in Strong Garnet Biotite Sillimanite Gneiss Formations

NASA Astrophysics Data System (ADS)

Sharma, Suresh Kumar; Rai, Piyush

2016-04-01

This paper presents a comparative investigation of the shock tube and electronic detonating systems practised in bench blasting. The blast trials were conducted on overburden rocks of Garnet Biotite Sillimanite Gneiss formations in one of the largest metalliferous mine of India. The study revealed that the choice of detonating system was crucial in deciding the fragment size and its distribution within the blasted muck-piles. The fragment size and its distribution affected the digging rate of excavators. Also, the shape of the blasted muck-pile was found to be related to the degree of fragmentation. From the present work, it may be inferred that in electronic detonation system, timely release of explosive energy resulted in better overall blasting performance. Hence, the precision in delay time must be considered in designing blast rounds in such overburden rock formations. State-of-art image analysis, GPS based muck-pile profile plotting techniques were rigorously used in the investigation. The study revealed that a mean fragment size (K50) value for shock tube detonated blasts (0.55-0.59 m) was higher than that of electronically detonated blasts (0.43-0.45 m). The digging rate of designated shovels (34 m3) with electronically detonated blasts was consistently more than 5000 t/h, which was almost 13 % higher in comparison to shock tube detonated blasts. Furthermore, favourable muck-pile shapes were witnessed in electronically detonated blasts from the observations made on the dozer performance.
AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts.

PubMed

Lavorgna, Giovanni; Triunfo, Riccardo; Santoni, Federico; Orfanelli, Ugo; Noci, Sara; Bulfone, Alessandro; Zanetti, Gianluigi; Casari, Giorgio

2005-07-01

An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at http://bioinfo.crs4.it/AH2.0.
Validation of the AVM Blast Computational Modeling and Simulation Tool Set

DTIC Science & Technology

2015-08-04

by-construction" methodology is powerful and would not be possible without high -level design languages to support validation and verification. [1,4...to enable the making of informed design decisions.  Enable rapid exploration of the design trade-space for high -fidelity requirements tradeoffs...live-fire tests, the jump height of the target structure is recorded by using either high speed cameras or a string pot. A simple projectile motion
Use of the rectus abdominis muscle flap to fill a retroperitoneal defect following blast injury.

PubMed

Talarczyk, Matthew R; Ricci, Michael A

2009-02-01

Wartime injuries from explosive devices have created the need for atypical responses to devastating and unusual injuries. We report a case of an explosive abdominal injury that produced a huge defect in the posterior abdominal wall which was ultimately repaired with a rectus abdominus flap, an usual use of this versatile muscle flap. The rectus abdominus muscle may be another tool available for the repair of wartime injuries.
LibKiSAO: a Java library for Querying KiSAO.

PubMed

Zhukova, Anna; Adams, Richard; Laibe, Camille; Le Novère, Nicolas

2012-09-24

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characteristics, parameters and inter-relationships. KiSAO enables the unambiguous identification of algorithms from simulation descriptions. Information about analogous methods having similar characteristics and about algorithm parameters incorporated into KiSAO is desirable for simulation tools. To retrieve this information programmatically an application programming interface (API) for KiSAO is needed. We developed libKiSAO, a Java library to enable querying of the KiSA Ontology. It implements methods to retrieve information about simulation algorithms stored in KiSAO, their characteristics and parameters, and methods to query the algorithm hierarchy and search for similar algorithms providing comparable results for the same simulation set-up. Using libKiSAO, simulation tools can make logical inferences based on this knowledge and choose the most appropriate algorithm to perform a simulation. LibKiSAO also enables simulation tools to handle a wider range of simulation descriptions by determining which of the available methods are similar and can be used instead of the one indicated in the simulation description if that one is not implemented. LibKiSAO enables Java applications to easily access information about simulation algorithms, their characteristics and parameters stored in the OWL-encoded Kinetic Simulation Algorithm Ontology. LibKiSAO can be used by simulation description editors and simulation tools to improve reproducibility of computational simulation tasks and facilitate model re-use.
Innovative Composite Structure Design for Blast Protection

DTIC Science & Technology

2007-01-01

2007-01-0483 Innovative Composite Structure Design for Blast Protection Dongying Jiang, Yuanyuan Liu MKP Structural Design Associates, Inc...protect vehicle and occupants against various explosives. The multi-level and multi-scenario blast simulation and design system integrates three major...numerical simulation of a BTR composite under a blast event. The developed blast simulation and design system will enable the prediction, design, and
Accelerated Profile HMM Searches

PubMed Central

Eddy, Sean R.

2011-01-01

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

Vascular and Inflammatory Factors in the Pathophysiology of Blast-Induced Brain Injury

PubMed Central

Elder, Gregory A.; Gama Sosa, Miguel A.; De Gasperi, Rita; Stone, James Radford; Dickstein, Dara L.; Haghighi, Fatemeh; Hof, Patrick R.; Ahlers, Stephen T.

2015-01-01

Blast-related traumatic brain injury (TBI) has received much recent attention because of its frequency in the conflicts in Iraq and Afghanistan. This renewed interest has led to a rapid expansion of clinical and animal studies related to blast. In humans, high-level blast exposure is associated with a prominent hemorrhagic component. In animal models, blast exerts a variety of effects on the nervous system including vascular and inflammatory effects that can be seen with even low-level blast exposures which produce minimal or no neuronal pathology. Acutely, blast exposure in animals causes prominent vasospasm and decreased cerebral blood flow along with blood-brain barrier breakdown and increased vascular permeability. Besides direct effects on the central nervous system, evidence supports a role for a thoracically mediated effect of blast; whereby, pressure waves transmitted through the systemic circulation damage the brain. Chronically, a vascular pathology has been observed that is associated with alterations of the vascular extracellular matrix. Sustained microglial and astroglial reactions occur after blast exposure. Markers of a central and peripheral inflammatory response are found for sustained periods after blast injury and include elevation of inflammatory cytokines and other inflammatory mediators. At low levels of blast exposure, a microvascular pathology has been observed in the presence of an otherwise normal brain parenchyma, suggesting that the vasculature may be selectively vulnerable to blast injury. Chronic immune activation in brain following vascular injury may lead to neurobehavioral changes in the absence of direct neuronal pathology. Strategies aimed at preventing or reversing vascular damage or modulating the immune response may improve the chronic neuropsychiatric symptoms associated with blast-related TBI. PMID:25852632
Experimental Investigation on the Basic Law of the Fracture Spatial Morphology for Water Pressure Blasting in a Drillhole Under True Triaxial Stress

NASA Astrophysics Data System (ADS)

Huang, Bingxiang; Li, Pengfeng

2015-07-01

The present literature on the morphology of water pressure blasting fractures in drillholes is not sufficient and does not take triaxial confining stress into account. Because the spatial morphology of water pressure blasting fractures in drillholes is not clear, the operations lack an exact basis. Using a large true triaxial water pressure blasting experimental system and an acoustic emission 3-D positioning system, water pressure blasting experiments on cement mortar test blocks (300 mm × 300 mm × 300 mm) were conducted to study the associated basic law of the fracture spatial morphology. The experimental results show that water pressure blasting does not always generate bubble pulsation. After water pressure blasting under true triaxial stress, a crushed compressive zone and a blasting fracture zone are formed from the inside, with the blasting section of the naked drillhole as the center, to the outside. The shape of the outer edges of the two zones is ellipsoidal. The range of the blasting fracture is large in the radial direction of the drillhole, where the surrounding pressure is large, i.e., the range of the blasting fracture in the drillhole radial cross-section is approximately ellipsoidal. The rock near the drillhole wall is affected by a tensile stress wave caused by the test block boundary reflection, resulting in more flake fractures appearing in the fracturing crack surface in the drillhole axial direction and parallel to the boundary surface. The flake fracture is thin, presenting a small-range flake fracture. The spatial morphology of the water pressure blasting fracture in the drillhole along the axial direction is similar to a wide-mouth Chinese bottle: the crack extent is large near the drillhole orifice, gradually narrows inward along the drillhole axial direction, and then increases into an approximate ellipsoid in the internal naked blasting section. Based on the causes of the crack generation, the blasting cracks are divided into three zones: the blasting shock zone, the axial extension zone, and the orifice influence zone. The explosion shock zone is the range that is directly impacted by the explosive shock waves. The axial extension zone is the axial crack area with uniform width, which is formed when the blasting fracture in the edge of the explosion shock zone extends along the drillhole wall. The extension of the orifice influence zone is very large because the explosion stress waves reflect at the free face and generate tensile stress waves. In the water pressure blasting of the drillhole, the sealing section should be lengthened to allow the drillhole blasting cracks to extend sufficiently under the long-time effect of the blasting stress field of quasi-hydrostatic pressure.
Parametric analysis of the biomechanical response of head subjected to the primary blast loading--a data mining approach.

PubMed

Zhu, Feng; Kalra, Anil; Saif, Tal; Yang, Zaihan; Yang, King H; King, Albert I

2016-01-01

Traumatic brain injury due to primary blast loading has become a signature injury in recent military conflicts and terrorist activities. Extensive experimental and computational investigations have been conducted to study the interrelationships between intracranial pressure response and intrinsic or 'input' parameters such as the head geometry and loading conditions. However, these relationships are very complicated and are usually implicit and 'hidden' in a large amount of simulation/test data. In this study, a data mining method is proposed to explore such underlying information from the numerical simulation results. The heads of different species are described as a highly simplified two-part (skull and brain) finite element model with varying geometric parameters. The parameters considered include peak incident pressure, skull thickness, brain radius and snout length. Their interrelationship and coupling effect are discovered by developing a decision tree based on the large simulation data-set. The results show that the proposed data-driven method is superior to the conventional linear regression method and is comparable to the nonlinear regression method. Considering its capability of exploring implicit information and the relatively simple relationships between response and input variables, the data mining method is considered to be a good tool for an in-depth understanding of the mechanisms of blast-induced brain injury. As a general method, this approach can also be applied to other nonlinear complex biomechanical systems.
Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes.

PubMed

Xie, Lei; Wang, Ying Wei; Guan, Shan Yue; Xie, Li Jing; Long, Xin; Sun, Cheng Ye

2014-10-01

Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (matK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. The primer universality of all the three markers was high. Except in the case of ITS for Hemerocallis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method. DNA barcoding technique provides us a fast tool for clinical identification of poisonous plants in China. We suggest matK, rbcL, ITS used in combination as DNA barcodes for authentication of poisonous plants. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.
Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

NASA Astrophysics Data System (ADS)

Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

2014-12-01

The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.
Educational Tool for Optimal Controller Tuning Using Evolutionary Strategies

ERIC Educational Resources Information Center

Carmona Morales, D.; Jimenez-Hornero, J. E.; Vazquez, F.; Morilla, F.

2012-01-01

In this paper, an optimal tuning tool is presented for control structures based on multivariable proportional-integral-derivative (PID) control, using genetic algorithms as an alternative to traditional optimization algorithms. From an educational point of view, this tool provides students with the necessary means to consolidate their knowledge on…
Catastrophic eruptions of the directed-blast type at Mount St. Helens, bezymianny and Shiveluch volcanoes

USGS Publications Warehouse

Bogoyavlenskaya, G.E.; Braitseva, O.A.; Melekestsev, I.V.; Kiriyanov, V. Yu; Dan, Miller C.

1985-01-01

This paper describes catastrophic eruptions of Mount St. Helens (1980), Bezymianny (1955-1956), and Shiveluch (1964) volcanoes. A detailed description of eruption stages and their products, as well as the quantitative characteristics of the eruptive process are given. The eruptions under study belong to the directed-blast type. This type is characterized by the catastrophic character of the climatic stage during which a directed blast, accompanied by edifice destruction, the profound ejection of juvenile pyroclastics and the formation of pyroclastic flows, occur. The climatic stage of all three eruptions has similar characteristics, such as duration, kinetic energy of blast (1017-1018 J), the initial velocity of debris ejection, morphology and size of newly-formed craters. But there are also certain differences. At Mount St. Helens the directed blast was preceeded by failure of the edifice and these events produced separable deposits, namely debris avalanche and directed blast deposits which are composed of different materials and have different volumes, thickness and distribution. At Bezymianny, failure did not precede the blast and the whole mass of debris of the old edifice was outburst only by blast. The resulting deposits, represented by the directed blast agglomerate and sand facies, have characteristics of both the debris avalanche and the blast deposit at Mount St. Helens. At Shiveluch directed-blast deposits are represented only by the directed-blast agglomerate; the directed-blast sand facies, or blast proper, seen at Mount St. Helens is absent. During the period of Plinian activity, the total volumes of juvenile material erupted at Mount St. Helens and at Besymianny were roughly comparable and exceeded the volume of juvenile material erupted at Shiveluch, However, the volume of pyroclastic-flow deposits erupted at Mount St. Helens was much less. The heat energy of all three eruptions is comparable: 1.3 ?? 1018, 3.8-4.8 ?? 1018 and 1 ?? 1017 J for Shiveluch, Bezymianny, and Mount St. Helens, respectively. ?? 1985.
De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.
Support Vector Machine Model for Automatic Detection and Classification of Seismic Events

NASA Astrophysics Data System (ADS)

Barros, Vesna; Barros, Lucas

2016-04-01

The automated processing of multiple seismic signals to detect, localize and classify seismic events is a central tool in both natural hazards monitoring and nuclear treaty verification. However, false detections and missed detections caused by station noise and incorrect classification of arrivals are still an issue and the events are often unclassified or poorly classified. Thus, machine learning techniques can be used in automatic processing for classifying the huge database of seismic recordings and provide more confidence in the final output. Applied in the context of the International Monitoring System (IMS) - a global sensor network developed for the Comprehensive Nuclear-Test-Ban Treaty (CTBT) - we propose a fully automatic method for seismic event detection and classification based on a supervised pattern recognition technique called the Support Vector Machine (SVM). According to Kortström et al., 2015, the advantages of using SVM are handleability of large number of features and effectiveness in high dimensional spaces. Our objective is to detect seismic events from one IMS seismic station located in an area of high seismicity and mining activity and classify them as earthquakes or quarry blasts. It is expected to create a flexible and easily adjustable SVM method that can be applied in different regions and datasets. Taken a step further, accurate results for seismic stations could lead to a modification of the model and its parameters to make it applicable to other waveform technologies used to monitor nuclear explosions such as infrasound and hydroacoustic waveforms. As an authorized user, we have direct access to all IMS data and bulletins through a secure signatory account. A set of significant seismic waveforms containing different types of events (e.g. earthquake, quarry blasts) and noise is being analysed to train the model and learn the typical pattern of the signal from these events. Moreover, comparing the performance of the support-vector network to various classical learning algorithms used before in seismic detection and classification is an essential final step to analyze the advantages and disadvantages of the model.
Fragmentation, Cost and Environmental Effects of Plaster Stemming Method for Blasting at A Basalt Quarry

NASA Astrophysics Data System (ADS)

Cevizci, Halim

2014-10-01

In this study, the plaster stemming application for blasting at a basalt quarry is studied. Drill cuttings are generally used in open pits and quarries as the most common stemming material since these are most readily available at blast sites. However, dry drill cuttings eject very easily from blastholes without offering much resistance to blast energy. The plaster stemming method has been found to be better than the drill cuttings stemming method due to increased confinement inside the hole and better utilization of blast explosive energy in the rock. The main advantage of the new stemming method is the reduction in the cost of blasting. At a basalt quarry, blasting costs per unit volume of rock were reduced to 15% by increasing burden and spacing distances. In addition, better fragmentation was obtained by using the plaster stemming method. Blast trials showed that plaster stemming produced finer material. In the same blast tests, +30 cm size fragments were reduced to 47.3% of the total, compared to 32.6% in the conventional method of drill cuttings stemming. With this method of stemming, vibration and air shock values increased slightly due to more blast energy being available for rock breakage but generally these increased values were small and stayed under the permitted limit for blast damage criteria unless measuring distance is too close.
Otologic blast injuries due to the Kenya embassy bombing.

PubMed

Helling, Eric Robert

2004-11-01

Otologic injuries are frequently associated with large blasts. On August 7, 1998, a large truck bomb exploded next to the U.S. Embassy in Nairobi, Kenya. Initial patient findings and care are reviewed. Five months later, an otologic screening and care mission was then sent to comprehensively screen all remaining blast victims on site in Nairobi and to determine degree of persistent injury. Surgical care appropriate for an outpatient environment was provided. Five of 14 tympanic membranes without intervention failed to heal, while 3 of 3 with previous intervention had. Blast injury severity did not correlate to distance from blast epicenter. This may be due to channeling of the blast through the embassy building and an unpredictable pattern of blast overpressure within the building. It is recommended that comprehensive otologic screening be performed after blast events to identify occult injuries and improve outcomes. Early intervention for tympanic membrane perforation (suctioning, eversion of perforations, and paper patch) is recommended.
Effect of Stemming to Burden Ratio and Powder Factor on Blast Induced Rock Fragmentation- A Case Study

NASA Astrophysics Data System (ADS)

Prasad, Sandeep; Choudhary, B. S.; Mishra, A. K.

2017-08-01

Rock fragmentation size is very important parameters for economical point of view in any surface mining. Rock fragment size direct effects on the costs of drilling, blasting, loading, secondary blasting and crushing. The main purpose of this study is to investigate effect of blast design parameters such as burden, blast hole length, stemming length, and powder factor on rock fragmentation. The fragment sizes (MFS, K50, m), and maximum fragment size (K95, m) of rock were determined by using the computer software. For every blast, after blasting operation, the images of whole muck pile are captured and there images were used for fragmentation analysis by using the Fragalyst software. It was observed that the optimal fragment size (MFS, K50, m and maximum fragment size, K95, m) of rock depends strongly on the blast design parameters and explosive parameters.
CRISPR/Cas9-Mediated Gene Editing in Rice (Oryza sativa L. japonica cv. Katy) for Stable Resistance against Blast Fungus (Magnaporthe oryzae)

USDA-ARS?s Scientific Manuscript database

Rice blast is a recurring and devastating disease in the USA and worldwide. In the USA, the blast-resistance (R) genes found in a tropical japonica cultivar, Katy, reduce blast damages from 1990 to present. The cultivar is still used as a principal donor of blast R genes in developing numerous elit...
VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.
Myeloblastic and lymphoblastic markers in acute undifferentiated leukemia and chronic myelogenous leukemia in blast crisis.

PubMed

Shumak, K H; Baker, M A; Taub, R N; Coleman, M S

1980-11-01

Blast cells were obtained from 17 patients with acute undifferentiated leukemia and 13 patients with chronic myelogenous leukemia in blast crisis. The blasts were tested with anti-i serum in cytotoxicity tests and with antisera to myeloblastic leukemia-associated antigens in immunofluorescence tests. The terminal deoxynucleotidyl transferase (TDT) content of the blasts was also measured. Lymphoblasts react strongly with anti-i, do not react with anti-myeloblast serum, and have high levels of TDT; myeloblasts react weakly with anti-i, do not react with anti-myeloblast serum, and have very low levels of TDT. Of the 17 patients with acute undifferentiated leukemia, there were six with blasts which reacted like lymphoblasts, six with blasts which reacted like myeloblasts, and five with blasts bearing different combinations of these lymphoblastic and myeloblastic markers. Eight of the 11 patients with lymphoblastic or mixed lymphoblastic-myeloblastic markers, but only one of the six with myeloblastic markers, achieved complete or partial remission in response to therapy. Thus, in acute undifferentiated leukemia, classification of blasts with these markers may be of prognostic value. Of the 13 patients with chronic myelogenous leukemia in blast crises, the markers were concordant (for myeloblasts) in only two cases. Three of the 13 patients had TDT-positive blasts, but the reactions of these cells with anti-i and with anti-myeloblast serum differed from those seen with lymphoblasts from patients with acute lymphoblastic leukemia. Although the cell involved in "lymphoid" blast crisis of chronic myelogenous leukemia is similar in many respects to that involved in acute lymphoblastic leukemia, these cells are not identical.
An RES-Based Model for Risk Assessment and Prediction of Backbreak in Bench Blasting

NASA Astrophysics Data System (ADS)

Faramarzi, F.; Ebrahimi Farsangi, M. A.; Mansouri, H.

2013-07-01

Most blasting operations are associated with various forms of energy loss, emerging as environmental side effects of rock blasting, such as flyrock, vibration, airblast, and backbreak. Backbreak is an adverse phenomenon in rock blasting operations, which imposes risk and increases operation expenses because of safety reduction due to the instability of walls, poor fragmentation, and uneven burden in subsequent blasts. In this paper, based on the basic concepts of a rock engineering systems (RES) approach, a new model for the prediction of backbreak and the risk associated with a blast is presented. The newly suggested model involves 16 effective parameters on backbreak due to blasting, while retaining simplicity as well. The data for 30 blasts, carried out at Sungun copper mine, western Iran, were used to predict backbreak and the level of risk corresponding to each blast by the RES-based model. The results obtained were compared with the backbreak measured for each blast, which showed that the level of risk achieved is in consistence with the backbreak measured. The maximum level of risk [vulnerability index (VI) = 60] was associated with blast No. 2, for which the corresponding average backbreak was the highest achieved (9.25 m). Also, for blasts with levels of risk under 40, the minimum average backbreaks (<4 m) were observed. Furthermore, to evaluate the model performance for backbreak prediction, the coefficient of correlation ( R 2) and root mean square error (RMSE) of the model were calculated ( R 2 = 0.8; RMSE = 1.07), indicating the good performance of the model.
Rodent model of direct cranial blast injury.

PubMed

Kuehn, Reed; Simard, Philippe F; Driscoll, Ian; Keledjian, Kaspar; Ivanova, Svetlana; Tosun, Cigdem; Williams, Alicia; Bochicchio, Grant; Gerzanich, Volodymyr; Simard, J Marc

2011-10-01

Traumatic brain injury resulting from an explosive blast is one of the most serious wounds suffered by warfighters, yet the effects of explosive blast overpressure directly impacting the head are poorly understood. We developed a rodent model of direct cranial blast injury (dcBI), in which a blast overpressure could be delivered exclusively to the head, precluding indirect brain injury via thoracic transmission of the blast wave. We constructed and validated a Cranium Only Blast Injury Apparatus (COBIA) to deliver blast overpressures generated by detonating .22 caliber cartridges of smokeless powder. Blast waveforms generated by COBIA replicated those recorded within armored vehicles penetrated by munitions. Lethal dcBI (LD(50) ∼ 515 kPa) was associated with: (1) apparent brainstem failure, characterized by immediate opisthotonus and apnea leading to cardiac arrest that could not be overcome by cardiopulmonary resuscitation; (2) widespread subarachnoid hemorrhages without cortical contusions or intracerebral or intraventricular hemorrhages; and (3) no pulmonary abnormalities. Sub-lethal dcBI was associated with: (1) apnea lasting up to 15 sec, with transient abnormalities in oxygen saturation; (2) very few delayed deaths; (3) subarachnoid hemorrhages, especially in the path of the blast wave; (4) abnormal immunolabeling for IgG, cleaved caspase-3, and β-amyloid precursor protein (β-APP), and staining for Fluoro-Jade C, all in deep brain regions away from the subarachnoid hemorrhages, but in the path of the blast wave; and (5) abnormalities on the accelerating Rotarod that persisted for the 1 week period of observation. We conclude that exposure of the head alone to severe explosive blast predisposes to significant neurological dysfunction.
Concussive brain injury from explosive blast

PubMed Central

de Lanerolle, Nihal C; Hamid, Hamada; Kulas, Joseph; Pan, Jullie W; Czlapinski, Rebecca; Rinaldi, Anthony; Ling, Geoffrey; Bandak, Faris A; Hetherington, Hoby P

2014-01-01

Objective Explosive blast mild traumatic brain injury (mTBI) is associated with a variety of symptoms including memory impairment and posttraumatic stress disorder (PTSD). Explosive shock waves can cause hippocampal injury in a large animal model. We recently reported a method for detecting brain injury in soldiers with explosive blast mTBI using magnetic resonance spectroscopic imaging (MRSI). This method is applied in the study of veterans exposed to blast. Methods The hippocampus of 25 veterans with explosive blast mTBI, 20 controls, and 12 subjects with PTSD but without exposure to explosive blast were studied using MRSI at 7 Tesla. Psychiatric and cognitive assessments were administered to characterize the neuropsychiatric deficits and compare with findings from MRSI. Results Significant reductions in the ratio of N-acetyl aspartate to choline (NAA/Ch) and N-acetyl aspartate to creatine (NAA/Cr) (P < 0.05) were found in the anterior portions of the hippocampus with explosive blast mTBI in comparison to control subjects and were more pronounced in the right hippocampus, which was 15% smaller in volume (P < 0.05). Decreased NAA/Ch and NAA/Cr were not influenced by comorbidities – PTSD, depression, or anxiety. Subjects with PTSD without blast had lesser injury, which tended to be in the posterior hippocampus. Explosive blast mTBI subjects had a reduction in visual memory compared to PTSD without blast. Interpretation The region of the hippocampus injured differentiates explosive blast mTBI from PTSD. MRSI is quite sensitive in detecting and localizing regions of neuronal injury from explosive blast associated with memory impairment. PMID:25493283
Assessment of the Effect of Blast Hole Diameter on the Number of Oversize Boulders Using ANN Model

NASA Astrophysics Data System (ADS)

Dhekne, Prakash; Pradhan, Manoj; Jade, Ravi Krishnarao

2016-04-01

Now-a-days, blasts are planned using large diameter blast holes. The loading density (kg/m) and subsequently the energy available for the breakage of the rockmass increase with the diameter. The in-hole velocity of detonation (VoD) of non-ideal explosive also boosts up with the increase in diameter till the optimum diameter is reached. The increase in the energy content and in-hole VoD cause a sizable effect on the rock fragmentation. The effect can be assessed by counting the number of oversize boulders. This paper explains as to how the technique of artificial neural network modeling was used to predict the number of oversize boulders resulting from ANFO and SME blasts with blast holes of different diameters. The results from ANFO blasts indicated that there was no significant variation in the number of oversize boulders with the diameter whereas a perceptible variation was noticed in case of SME blasts with the change in the diameter. The change in the number of oversize boulders in ANFO blasts was negligible because mean energy factor remained almost same even when the diameter of the blast holes was altered. The decrease in the number of oversize boulders in SME blasts was on account of increase in mean energy factor when the blast hole diameter was increased. The increase in the in-hole VoD due to increase in the diameter of the hole was not found to have an effect on the generation of oversize boulders as this increase was not substantial both in SME and ANFO blasts.
Dry ice blasting

NASA Astrophysics Data System (ADS)

Lonergan, Jeffrey M.

1992-04-01

As legal and societal pressures against the use of hazardous waste generating materials has increased, so has the motivation to find safe, effective, and permanent replacements. Dry ice blasting is a technology which uses CO2 pellets as a blasting medium. The use of CO2 for cleaning and stripping operations offers potential for significant environmental, safety, and productivity improvements over grit blasting, plastic media blasting, and chemical solvent cleaning. Because CO2 pellets break up and sublime upon impact, there is no expended media to dispose of. Unlike grit or plastic media blasting which produce large quantities of expended media, the only waste produced by CO2 blasting is the material removed. The quantity of hazardous waste produced, and thus the cost of hazardous waste disposal is significantly reduced.

Computational modeling of blast exposure associated with recoilless weapons combat training

NASA Astrophysics Data System (ADS)

Wiri, S.; Ritter, A. C.; Bailie, J. M.; Needham, C.; Duckworth, J. L.

2017-11-01

Military personnel are exposed to blast as part of routine combat training with shoulder-fired recoilless rifles. These weapons fire large-caliber ammunitions capable of disabling structures and uparmored vehicles (e.g., tanks). Scientific, medical, and military leaders are beginning to recognize the blast overpressure from these shoulder-fired weapons may result in acute and even long-term physiological effects to military personnel. However, the back blast generated from the Carl Gustav and Shoulder-launched Multipurpose Assault Weapon (SMAW) shoulder-fired weapons on the weapon operator has not been quantified. By quantifying and modeling the full-body blast exposure from these weapons, better injury correlations can be constructed. Blast exposure data from the Carl Gustav and SMAW were used to calibrate a propellant burn source term for computational simulations of blast exposure on operators of these shoulder-mounted weapon systems. A propellant burn model provided the source term for each weapon to capture blast effects. Blast data from personnel-mounted gauges during weapon firing were used to create initial, high-fidelity 3D computational fluid dynamic simulations using SHAMRC (Second-order Hydrodynamic Automatic Mesh Refinement Code). These models were then improved upon using data collected from static blast sensors positioned around the military personnel while weapons were utilized in actual combat training. The final simulation models for both the Carl Gustav and SMAW were in good agreement with the data collected from the personnel-mounted and static pressure gauges. Using the final simulation results, contour maps were created for peak overpressure and peak overpressure impulse experienced by military personnel firing the weapon as well as those assisting with firing of those weapons. Reconstruction of the full-body blast loading enables a more accurate assessment of the cause of potential mechanisms of injury due to air blast even for subjects not wearing blast gauges themselves. By accurately understanding the blast exposure and its variations across an individual, more meaningful correlations with physiologic response including potential TBI spectrum physiology associated with sub-concussive blast exposure can be established. As blast injury thresholds become better defined, results from these reconstructions can provide important insights into approaches for reducing possible risk of injury to personnel operating shoulder-launched weapons.
Dynamic response analysis of surrounding rock under the continuous blasting seismic wave

NASA Astrophysics Data System (ADS)

Gao, P. F.; Zong, Q.; Xu, Y.; Fu, J.

2017-10-01

The blasting vibration that is caused by blasting excavation will generate a certain degree of negative effect on the stability of surrounding rock in underground engineering. A dynamic response analysis of surrounding rock under the continuous blasting seismic wave is carried out to optimize blasting parameters and guide underground engineering construction. Based on the theory of wavelet analysis, the reconstructed signals of each layer of different frequency bands are obtained by db8 wavelet decomposition. The difference of dynamic response of the continuous blasting seismic wave at a certain point caused by different blasting sources is discussed. The signal in the frequency band of natural frequency of the surrounding rock shows a certain degree of amplification effect deduced from the dynamic response characteristics of the surrounding rock under the influence of continuous blasting seismic wave. Continuous blasting operations in a fixed space will lead to the change of internal structure of the surrounding rock. It may result in the decline of natural frequency of the whole surrounding rock and it is also harmful for the stability of the surrounding rock.
Bomb blast mass casualty incidents: initial triage and management of injuries.

PubMed

Goh, S H

2009-01-01

Bomb blast injuries are no longer confined to battlefields. With the ever present threat of terrorism, we should always be prepared for bomb blasts. Bomb blast injuries tend to affect air-containing organs more, as the blast wave tends to exert a shearing force on air-tissue interfaces. Commonly-injured organs include the tympanic membranes, the sinuses, the lungs and the bowel. Of these, blast lung injury is the most challenging to treat. The clinical picture is a mix of acute respiratory distress syndrome and air embolism, and the institution of positive pressure ventilation in the presence of low venous pressures could cause systemic arterial air embolism. The presence of a tympanic membrane perforation is not a reliable indicator of the presence of a blast injury in the other air-containing organs elsewhere. Radiological imaging of the head, chest and abdomen help with the early identification of blast lung injury, head injury, abdominal injury, eye and sinus injuries, as well as any penetration by foreign bodies. In addition, it must be borne in mind that bomb blasts could also be used to disperse radiological and chemical agents.
Unified Lambert Tool for Massively Parallel Applications in Space Situational Awareness

NASA Astrophysics Data System (ADS)

Woollands, Robyn M.; Read, Julie; Hernandez, Kevin; Probe, Austin; Junkins, John L.

2018-03-01

This paper introduces a parallel-compiled tool that combines several of our recently developed methods for solving the perturbed Lambert problem using modified Chebyshev-Picard iteration. This tool (unified Lambert tool) consists of four individual algorithms, each of which is unique and better suited for solving a particular type of orbit transfer. The first is a Keplerian Lambert solver, which is used to provide a good initial guess (warm start) for solving the perturbed problem. It is also used to determine the appropriate algorithm to call for solving the perturbed problem. The arc length or true anomaly angle spanned by the transfer trajectory is the parameter that governs the automated selection of the appropriate perturbed algorithm, and is based on the respective algorithm convergence characteristics. The second algorithm solves the perturbed Lambert problem using the modified Chebyshev-Picard iteration two-point boundary value solver. This algorithm does not require a Newton-like shooting method and is the most efficient of the perturbed solvers presented herein, however the domain of convergence is limited to about a third of an orbit and is dependent on eccentricity. The third algorithm extends the domain of convergence of the modified Chebyshev-Picard iteration two-point boundary value solver to about 90% of an orbit, through regularization with the Kustaanheimo-Stiefel transformation. This is the second most efficient of the perturbed set of algorithms. The fourth algorithm uses the method of particular solutions and the modified Chebyshev-Picard iteration initial value solver for solving multiple revolution perturbed transfers. This method does require "shooting" but differs from Newton-like shooting methods in that it does not require propagation of a state transition matrix. The unified Lambert tool makes use of the General Mission Analysis Tool and we use it to compute thousands of perturbed Lambert trajectories in parallel on the Space Situational Awareness computer cluster at the LASR Lab, Texas A&M University. We demonstrate the power of our tool by solving a highly parallel example problem, that is the generation of extremal field maps for optimal spacecraft rendezvous (and eventual orbit debris removal). In addition we demonstrate the need for including perturbative effects in simulations for satellite tracking or data association. The unified Lambert tool is ideal for but not limited to space situational awareness applications.
Algorithms for optimizing the treatment of depression: making the right decision at the right time.

PubMed

Adli, M; Rush, A J; Möller, H-J; Bauer, M

2003-11-01

Medication algorithms for the treatment of depression are designed to optimize both treatment implementation and the appropriateness of treatment strategies. Thus, they are essential tools for treating and avoiding refractory depression. Treatment algorithms are explicit treatment protocols that provide specific therapeutic pathways and decision-making tools at critical decision points throughout the treatment process. The present article provides an overview of major projects of algorithm research in the field of antidepressant therapy. The Berlin Algorithm Project and the Texas Medication Algorithm Project (TMAP) compare algorithm-guided treatments with treatment as usual. The Sequenced Treatment Alternatives to Relieve Depression Project (STAR*D) compares different treatment strategies in treatment-resistant patients.
Mathematical model of blasting schemes management in mining operations in presence of random disturbances

NASA Astrophysics Data System (ADS)

Kazakova, E. I.; Medvedev, A. N.; Kolomytseva, A. O.; Demina, M. I.

2017-11-01

The paper presents a mathematical model of blasting schemes management in presence of random disturbances. Based on the lemmas and theorems proved, a control functional is formulated, which is stable. A universal classification of blasting schemes is developed. The main classification attributes are suggested: the orientation in plan the charging wells rows relatively the block of rocks; the presence of cuts in the blasting schemes; the separation of the wells series onto elements; the sequence of the blasting. The periodic regularity of transition from one Short-delayed scheme of blasting to another is proved.
Blast pulmonaire primaire chez le brûlé. a propos d’un cas et revue de la littérature

PubMed Central

Siah, S.; Emane, A.; Bertin-Maghit, M.

2016-01-01

Summary Le blast est à l’origine de lésions spécifiques pour lesquelles une prise en charge spécialisée est nécessaire. Après une explosion on peut observer des lésions de blast primaire, liées à l’onde de choc, secondaire par polycriblage et tertiaire par projection du patient. Les blasts secondaire et tertiaire sont plus fréquents que le blast primaire et peuvent entraîner un polytraumatisme. Dans 5% des cas, on retrouve des brûlures pouvant faire partie du blast quaternaire, qui regroupe toutes les lésions d’autres mécanismes que ceux précités. La prise en charge des lésions secondaires et tertiaires de blast est comparable à celle des traumatisés graves. Le blast pulmonaire primaire aggrave le pronostic des blessés les plus graves mais impose rarement une prise en charge spécifique. La connaissance des particularités physiopathologiques et lésionnelles permet de mieux traiter les blastés et brûlés graves survivants. Nous rapportons une observation de blast pulmonaire primaire chez un brûlé. PMID:28149247
Reduction of optically observed artillery blast wave trajectories using low dimensionality models

NASA Astrophysics Data System (ADS)

Steward, Bryan J.; Gross, Kevin C.; Perram, Glen P.

2011-05-01

Muzzle blast trajectories from firings of a 152 mm caliber gun howitzer were obtained with high-speed optical imagers and used to assess the fidelity with which low dimensionality models can be used for data reduction. Characteristic flow regions were defined for the blast waves. The near-field region was estimated to extend to 0.98 - 1.25 meters from the muzzle and the far-field region was estimated to begin at 2.61 - 3.31 meters. Blast wave geometries and radial trajectories were collected in the near through far-fields with visible imagers operating at 1,600 Hz. Beyond the near-field the blast waves exhibited a near-spherical geometry in which the major axis of the blast lay along the axis of the gun barrel and measured within 95% of the minor axis. Several blast wave propagation models were applied to the mid and far-field data to determine their ability to reduce the blast wave trajectories to fewer parameters while retaining the ability to distinguish amongst three munitions configurations. A total of 147 firings were observed and used to assess within-configuration variability relative to separation between configurations. Results show that all models perform well, and drag and point blast model parameters additionally provide insight into phenomenology of the blast.
Treatment outcomes of chronic post-traumatic headaches after mild head trauma in US soldiers: an observational study.

PubMed

Erickson, Jay C

2011-06-01

he effectiveness of medical therapies for chronic post-traumatic headaches (PTHs) attributable to mild head trauma in military troops has not been established. To determine the treatment outcomes of acute and prophylactic medical therapies prescribed for chronic PTHs after mild head trauma in US Army soldiers. A retrospective cohort study was conducted with 100 soldiers undergoing treatment for chronic PTH at a single US Army neurology clinic. Headache frequency and Migraine Disability Assessment (MIDAS) scores were determined at the initial clinic visit and then again by phone 3 months after starting headache prophylactic medication. Response rates of headache abortive medications were also determined. Treatment outcomes were compared between subjects with blast-related PTH and non-blast PTH. Ninety-nine of 100 subjects were male. Seventy-seven of 100 subjects had blast PTH and 23/100 subjects had non-blast PTH. Headache characteristics were similar for blast PTH and non-blast PTH with 96% and 95%, respectively, resembling migraine. Headache frequency among all PTH subjects decreased from 17.1 days/month at baseline to 14.5 days/month at follow-up (P = .009). Headache frequency decreased by 41% among non-blast PTH compared to 9% among blast PTH. Fifty-seven percent of non-blast PTH subjects had a 50% or greater decline in headache frequency compared to 29% of blast PTH subjects (P =.023). A significant decline in headache frequency occurred in subjects treated with topiramate (n = 29, -23%, P = .02) but not among those treated with a low-dose tricyclic antidepressant (n = 48, -12%, P = .23). Seventy percent of PTH subjects who used a triptan class medication experienced reliable headache relief within 2 hours compared to 42% of subjects using other headache abortive medications (P = .01). Triptan medications were effective for both blast PTH and non-blast PTH (66% response rate vs 86% response rate, respectively; P = .20). Headache-related disability, as measured by mean MIDAS scores, declined by 57% among all PTH subjects with no significant difference between blast PTH (-56%) and non-blast PTH (-61%). Triptan class medications are usually effective for aborting headaches in military troops with chronic PTH attributed to a concussion from a blast injury or non-blast injury. Topiramate appears to be an effective headache prophylactic therapy in military troops with chronic PTH, whereas low doses of tricyclic antidepressants appear to have little efficacy. Chronic PTH triggered by a blast injury may be less responsive to commonly prescribed headache prophylactic medications compared to non-blast PTH. These conclusions require validation by prospective, controlled clinical trials. © 2011 American Headache Society.
MannDB: A microbial annotation database for protein characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, C; Lam, M; Smith, J

2006-05-19

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-sourcemore » tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports.« less
Range Systems Simulation for the NASA Shuttle: Emphasis on Disaster and Prevention Management During Lift-Off

NASA Technical Reports Server (NTRS)

Rabelo, Lisa; Sepulveda, Jose; Moraga, Reinaldo; Compton, Jeppie; Turner, Robert

2005-01-01

This article describes a decision-making system composed of a number of safety and environmental models for the launch phase of a NASA Space Shuttle mission. The components of this distributed simulation environment represent the different systems that must collaborate to establish the Expectation of Casualties (E(sub c)) caused by a failed Space Shuttle launch and subsequent explosion (accidental or instructed) of the spacecraft shortly after liftoff. This decision-making tool employs Space Shuttle reliability models, trajectory models, a blast model, weather dissemination systems, population models, amount and type of toxicants, gas dispersion models, human response functions to toxicants, and a geographical information system. Since one of the important features of this proposed simulation environment is to measure blast, toxic, and debris effects, the clear benefits is that it can help safety managers not only estimate the population at risk, but also to help plan evacuations, make sheltering decisions, establish the resources required to provide aid and comfort, and mitigate damages in case of a disaster.
Database resources of the National Center for Biotechnology Information: 2002 update

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2002-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242
Evaluation of Algorithms for a Miles-in-Trail Decision Support Tool

NASA Technical Reports Server (NTRS)

Bloem, Michael; Hattaway, David; Bambos, Nicholas

2012-01-01

Four machine learning algorithms were prototyped and evaluated for use in a proposed decision support tool that would assist air traffic managers as they set Miles-in-Trail restrictions. The tool would display probabilities that each possible Miles-in-Trail value should be used in a given situation. The algorithms were evaluated with an expected Miles-in-Trail cost that assumes traffic managers set restrictions based on the tool-suggested probabilities. Basic Support Vector Machine, random forest, and decision tree algorithms were evaluated, as was a softmax regression algorithm that was modified to explicitly reduce the expected Miles-in-Trail cost. The algorithms were evaluated with data from the summer of 2011 for air traffic flows bound to the Newark Liberty International Airport (EWR) over the ARD, PENNS, and SHAFF fixes. The algorithms were provided with 18 input features that describe the weather at EWR, the runway configuration at EWR, the scheduled traffic demand at EWR and the fixes, and other traffic management initiatives in place at EWR. Features describing other traffic management initiatives at EWR and the weather at EWR achieved relatively high information gain scores, indicating that they are the most useful for estimating Miles-in-Trail. In spite of a high variance or over-fitting problem, the decision tree algorithm achieved the lowest expected Miles-in-Trail costs when the algorithms were evaluated using 10-fold cross validation with the summer 2011 data for these air traffic flows.
Co-blasting of titanium surfaces with an abrasive and hydroxyapatite to produce bioactive coatings: substrate and coating characterisation.

PubMed

Dunne, Conor F; Twomey, Barry; O'Neill, Liam; Stanton, Kenneth T

2014-01-01

The aim of this work is to assess the influence of two blast media on the deposition of hydroxyapatite onto a titanium substrate using a novel ambient temperature coating technique named CoBlast. CoBlast was developed to address the problems with high temperature coating techniques. The blasting media used in this study were Al2O3 and a sintered apatite powder. The prepared and coated surfaces were compared to plasma sprayed hydroxyapatite on the same substrates using the same hydroxyapatite feedstock powder. X-ray diffraction analysis revealed the coating crystallinity was the same as the original hydroxyapatite feedstock powder for the CoBlast samples while evidence of amorphous hydroxyapatite phases and β-TCP was observed in the plasma sprayed samples. The blast media type significantly influences the adhesive strength of the coating, surface roughness of both the substrate and coating and the microstructure of the substrate. The coating adhesion increased for the CoBlasted samples from 50 MPa to 60 MPa for sintered apatite powder and alumina, respectively, while plasma spray samples were significantly lower (5 MPa) when tested using a modified pull-test. In conclusion, the choice of blast medium is shown to be a key parameter in the CoBlast process. This study indicates that sintered apatite powder is the most suitable candidate for use as a blast medium in the coating of medical devices.
Blast Injuries: From Improvised Explosive Device Blasts to the Boston Marathon Bombing.

PubMed

Singh, Ajay K; Ditkofsky, Noah G; York, John D; Abujudeh, Hani H; Avery, Laura A; Brunner, John F; Sodickson, Aaron D; Lev, Michael H

2016-01-01

Although most trauma centers have experience with the imaging and management of gunshot wounds, in most regions blast wounds such as the ones encountered in terrorist attacks with the use of improvised explosive devices (IEDs) are infrequently encountered outside the battlefield. As global terrorism becomes a greater concern, it is important that radiologists, particularly those working in urban trauma centers, be aware of the mechanisms of injury and the spectrum of primary, secondary, tertiary, and quaternary blast injury patterns. Primary blast injuries are caused by barotrauma from the initial increased pressure of the explosive detonation and the rarefaction of the atmosphere immediately afterward. Secondary blast injuries are caused by debris carried by the blast wind and most often result in penetrating trauma from small shrapnel. Tertiary blast injuries are caused by the physical displacement of the victim and the wide variety of blunt or penetrating trauma sustained as a result of the patient impacting immovable objects such as surrounding cars, walls, or fences. Quaternary blast injuries include all other injuries, such as burns, crush injuries, and inhalational injuries. Radiography is considered the initial imaging modality for assessment of shrapnel and fractures. Computed tomography is the optimal test to assess penetrating chest, abdominal, and head trauma. The mechanism of blast injuries and the imaging experience of the victims of the Boston Marathon bombing are detailed, as well as musculoskeletal, neurologic, gastrointestinal, and pulmonary injury patterns from blast injuries. ©RSNA, 2016.
Acceleration-based methodology to assess the blast mitigation performance of explosive ordnance disposal helmets

NASA Astrophysics Data System (ADS)

Dionne, J. P.; Levine, J.; Makris, A.

2018-01-01

To design the next generation of blast mitigation helmets that offer increasing levels of protection against explosive devices, manufacturers must be able to rely on appropriate test methodologies and human surrogates that will differentiate the performance level of various helmet solutions and ensure user safety. Ideally, such test methodologies and associated injury thresholds should be based on widely accepted injury criteria relevant within the context of blast. Unfortunately, even though significant research has taken place over the last decade in the area of blast neurotrauma, there currently exists no agreement in terms of injury mechanisms for blast-induced traumatic brain injury. In absence of such widely accepted test methods and injury criteria, the current study presents a specific blast test methodology focusing on explosive ordnance disposal protective equipment, involving the readily available Hybrid III mannequin, initially developed for the automotive industry. The unlikely applicability of the associated brain injury criteria (based on both linear and rotational head acceleration) is discussed in the context of blast. Test results encompassing a large number of blast configurations and personal protective equipment are presented, emphasizing the possibility to develop useful correlations between blast parameters, such as the scaled distance, and mannequin engineering measurements (head acceleration). Suggestions are put forward for a practical standardized blast testing methodology taking into account limitations in the applicability of acceleration-based injury criteria as well as the inherent variability in blast testing results.
Computer applications making rapid advances in high throughput microbial proteomics (HTMP).

PubMed

Anandkumar, Balakrishna; Haga, Steve W; Wu, Hui-Fen

2014-02-01

The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery. Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification, functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway engineering and drug discovery.
Problem solving with genetic algorithms and Splicer

NASA Technical Reports Server (NTRS)

Bayer, Steven E.; Wang, Lui

1991-01-01

Genetic algorithms are highly parallel, adaptive search procedures (i.e., problem-solving methods) loosely based on the processes of population genetics and Darwinian survival of the fittest. Genetic algorithms have proven useful in domains where other optimization techniques perform poorly. The main purpose of the paper is to discuss a NASA-sponsored software development project to develop a general-purpose tool for using genetic algorithms. The tool, called Splicer, can be used to solve a wide variety of optimization problems and is currently available from NASA and COSMIC. This discussion is preceded by an introduction to basic genetic algorithm concepts and a discussion of genetic algorithm applications.
Development of a Continuous Drill and Blast Tunneling Concept, Phase II

DOT National Transportation Integrated Search

1974-05-01

A spiral drilling pattern is described which offers high efficiency drill and blast tunnelling via frequent small blasts rather than occasional large blasts. Design work is presented for a machine which would stay at the face to provide essentially c...
Assessing Neuro-Systemic & Behavioral Components in the Pathophysiology of Blast-Related Brain Injury

PubMed Central

Kobeissy, Firas; Mondello, Stefania; Tümer, Nihal; Toklu, Hale Z.; Whidden, Melissa A.; Kirichenko, Nataliya; Zhang, Zhiqun; Prima, Victor; Yassin, Walid; Anagli, John; Chandra, Namas; Svetlov, Stan; Wang, Kevin K. W.

2013-01-01

Among the U.S. military personnel, blast injury is among the leading causes of brain injury. During the past decade, it has become apparent that even blast injury as a form of mild traumatic brain injury (mTBI) may lead to multiple different adverse outcomes, such as neuropsychiatric symptoms and long-term cognitive disability. Blast injury is characterized by blast overpressure, blast duration, and blast impulse. While the blast injuries of a victim close to the explosion will be severe, majority of victims are usually at a distance leading to milder form described as mild blast TBI (mbTBI). A major feature of mbTBI is its complex manifestation occurring in concert at different organ levels involving systemic, cerebral, neuronal, and neuropsychiatric responses; some of which are shared with other forms of brain trauma such as acute brain injury and other neuropsychiatric disorders such as post-traumatic stress disorder. The pathophysiology of blast injury exposure involves complex cascades of chronic psychological stress, autonomic dysfunction, and neuro/systemic inflammation. These factors render blast injury as an arduous challenge in terms of diagnosis and treatment as well as identification of sensitive and specific biomarkers distinguishing mTBI from other non-TBI pathologies and from neuropsychiatric disorders with similar symptoms. This is due to the “distinct” but shared and partially identified biochemical pathways and neuro-histopathological changes that might be linked to behavioral deficits observed. Taken together, this article aims to provide an overview of the current status of the cellular and pathological mechanisms involved in blast overpressure injury and argues for the urgent need to identify potential biomarkers that can hint at the different mechanisms involved. PMID:24312074

Assessing neuro-systemic & behavioral components in the pathophysiology of blast-related brain injury.

PubMed

Kobeissy, Firas; Mondello, Stefania; Tümer, Nihal; Toklu, Hale Z; Whidden, Melissa A; Kirichenko, Nataliya; Zhang, Zhiqun; Prima, Victor; Yassin, Walid; Anagli, John; Chandra, Namas; Svetlov, Stan; Wang, Kevin K W

2013-11-21

Among the U.S. military personnel, blast injury is among the leading causes of brain injury. During the past decade, it has become apparent that even blast injury as a form of mild traumatic brain injury (mTBI) may lead to multiple different adverse outcomes, such as neuropsychiatric symptoms and long-term cognitive disability. Blast injury is characterized by blast overpressure, blast duration, and blast impulse. While the blast injuries of a victim close to the explosion will be severe, majority of victims are usually at a distance leading to milder form described as mild blast TBI (mbTBI). A major feature of mbTBI is its complex manifestation occurring in concert at different organ levels involving systemic, cerebral, neuronal, and neuropsychiatric responses; some of which are shared with other forms of brain trauma such as acute brain injury and other neuropsychiatric disorders such as post-traumatic stress disorder. The pathophysiology of blast injury exposure involves complex cascades of chronic psychological stress, autonomic dysfunction, and neuro/systemic inflammation. These factors render blast injury as an arduous challenge in terms of diagnosis and treatment as well as identification of sensitive and specific biomarkers distinguishing mTBI from other non-TBI pathologies and from neuropsychiatric disorders with similar symptoms. This is due to the "distinct" but shared and partially identified biochemical pathways and neuro-histopathological changes that might be linked to behavioral deficits observed. Taken together, this article aims to provide an overview of the current status of the cellular and pathological mechanisms involved in blast overpressure injury and argues for the urgent need to identify potential biomarkers that can hint at the different mechanisms involved.
Leech segmental repeats develop normally in the absence of signals from either anterior or posterior segments

NASA Technical Reports Server (NTRS)

Seaver, E. C.; Shankland, M.

2000-01-01

We have investigated whether the development of segmental repeats is autonomous in the embryo of the leech Helobdella robusta. The segmental tissues of the germinal band arise from progeny of five stem cells called teloblasts. Asymmetric divisions of the teloblasts form chains of segment founder cells (called primary blast cells) that divide in a stereotypical manner to produce differentiated descendants. Using two distinct techniques, we have looked for potential interactions between neighboring blast cell clones along the anterior-posterior axis. In one technique, we prevented the birth of primary blast cells by injection of DNase I into the teloblast, thereby depriving the last blast cell produced before the ablation of its normal posterior neighbors. We also ablated single blast cells with a laser microbeam, which allowed us to assess potential signals acting on either more anterior or more posterior primary blast cell clones. Our results suggest that interactions along the anterior-posterior axis between neighboring primary blast cell clones are not required for development of normal segmental organization within the blast cell clone. We also examined the possibility that blast cells receive redundant signals from both anterior and posterior neighboring clones and that either is sufficient for normal development. Using double blast cell laser ablations to isolate a primary blast cell clone by removal of both its anterior and its posterior neighbor, we found that the isolated clone still develops normally. These results reveal that the fundamental segmental repeat in the leech embryo, the primary blast cell clone, can develop normally in the apparent absence of signals from adjacent repeats along the anterior-posterior axis.
Is Blast Injury a Modern Phenomenon?: Early Historical Descriptions of Mining and Volcanic Traumatic Brain Injury With Relevance to Modern Terrorist Attacks and Military Warfare.

PubMed

Bowen, Lauren N; Moore, David F; Okun, Michael S

2016-03-01

Given the recent interest in blast injury spurred by returning soldiers from overseas conflicts, we sought to research the early historical descriptions of blast injuries and their treatments. Consideration was given to specific descriptions of survivors of closed head injury and their treatment. A review of the medical and nonmedical literature was undertaken, with particular emphasis on pre-1800 descriptions of volcanic eruptions and mining accidents. Compilations of accounts of the Etna eruptions dating from 126 BC were translated into English, and early mining texts from the 1600s and 1700s were reviewed. Accumulations of flammable gases were recorded in many medieval sources and this knowledge of toxic gas which could lead to blast injury was known in the mining community by 1316. No direct attribution of injuries to blast forces was present in the historical record examined before the 1300s, although mining accounts in the 1600s detail deaths due to blast. No specific descriptions of survivors of a closed head injury were found in the mining and volcanic eruption literature. Descriptions and warnings of blast forces were commonly written about in the medieval and Renaissance mining communities. Personal narratives as early as 1316 recognize the traumatic effects of blast injury. No mining or volcanic blast descriptions before 1800 detailed severe closed head injury survivors, suggesting greater mortality than morbidity from blast injury in the premodern era. This review also uncovered that there was no historical treatment or remedy recommended to survivors of blast injury. Blast explosions resulting in injury or death were frequently described, although in simplistic terminology.
Modeling the Blast Load Simulator Airblast Environment using First Principles Codes. Report 1, Blast Load Simulator Environment

DTIC Science & Technology

2016-11-01

ER D C/ G SL T R- 16 -3 1 Modeling the Blast Load Simulator Airblast Environment Using First Principles Codes Report 1, Blast Load...Simulator Airblast Environment using First Principles Codes Report 1, Blast Load Simulator Environment Gregory C. Bessette, James L. O’Daniel...evaluate several first principles codes (FPCs) for modeling airblast environments typical of those encountered in the BLS. The FPCs considered were
A Multisite Study of the Relationships between Blast Exposures and Symptom Reporting in a Post-Deployment Active Duty Military Population with Mild Traumatic Brain Injury

PubMed Central

Miller, Kelly J.; Lange, Rael T.; Cooper, Douglas B.; Tate, David F.; Bailie, Jason; Brickell, Tracey A.; French, Louis M.; Asmussen, Sarah; Kennedy, Jan E.

2014-01-01

Abstract Explosive devices have been the most frequent cause of traumatic brain injury (TBI) among deployed contemporary U.S. service members. The purpose of this study was to examine the influence of previous cumulative blast exposures (that did or did not result in TBI) on later post-concussion and post-traumatic symptom reporting after sustaining a mild TBI (MTBI). Participants were 573 service members who sustained MTBI divided into four groups by number of blast exposures (1, 2, 3, and 4–10) and a nonblast control group. Post-concussion symptoms were measured using the Neurobehavioral Symptom Inventory (NSI) and post-traumatic stress disorder (PTSD) symptoms using the Post-traumatic Checklist-Civilian version (PCL-C). Results show groups significantly differed on total NSI scores (p<0.001), where symptom endorsement increased as number of reported blast exposures increased. Total NSI scores were significantly higher for the 3– and 4–10 blast groups compared with the 1- and 2-blast groups with effect sizes ranging from small to moderate (d=0.31 to 0.63). After controlling for PTSD symptoms using the PCL-C total score, NSI total score differences remained between the 4–10-blast group and the 1- and 2-blast groups, but were less pronounced (d=0.35 and d=0.24, respectively). Analyses of NSI subscale scores using PCL-C scores as a covariate revealed significant between-blast group differences on cognitive, sensory, and somatic, but not affective symptoms. Regression analyses revealed that cumulative blast exposures accounted for a small but significant amount of the variance in total NSI scores (4.8%; p=0.009) and total PCL-C scores (2.3%; p<0.001). Among service members exposed to blast, post-concussion symptom reporting increased as a function of cumulative blast exposures. Future research will need to determine the relationship between cumulative blast exposures, symptom reporting, and neuropathological changes. PMID:25036531
Erythroleukemia shares biological features and outcome with myelodysplastic syndromes with excess blasts: a rationale for its inclusion into future classifications of myelodysplastic syndromes.

PubMed

Calvo, Xavier; Arenillas, Leonor; Luño, Elisa; Senent, Leonor; Arnan, Montserrat; Ramos, Fernando; Ardanaz, María Teresa; Pedro, Carme; Tormo, Mar; Montoro, Julia; Díez-Campelo, María; Arrizabalaga, Beatriz; Xicoy, Blanca; Bonanad, Santiago; Jerez, Andrés; Nomdedeu, Benet; Ferrer, Ana; Sanz, Guillermo F; Florensa, Lourdes

2016-12-01

Erythroleukemia was considered an acute myeloid leukemia in the 2008 World Health Organization (WHO) classification and is defined by the presence of ≥50% bone marrow erythroblasts, having <20% bone marrow blasts from total nucleated cells but ≥20% bone marrow myeloblasts from nonerythroid cells. Erythroleukemia shares clinicopathologic features with myelodysplastic syndromes, especially with erythroid-predominant myelodysplastic syndromes (≥50% bone marrow erythroblasts). The upcoming WHO revision proposes to eliminate the nonerythroid blast cell count rule and to move erythroleukemia patients into the appropriate myelodysplastic syndrome category on the basis of the absolute blast cell count. We conducted a retrospective study of patients with de novo erythroleukemia and compared their clinico-biological features and outcome with those of de novo myelodysplastic syndromes, focusing on erythroid-predominant myelodysplastic syndromes. Median overall survival of 405 erythroid-predominant myelodysplastic syndromes without excess blasts was significantly longer than that observed in 57 erythroid-predominant refractory anemias with excess blasts-1 and in 59 erythroleukemias, but no significant difference was observed between erythroid-predominant refractory anemias with excess blasts-1 and erythroleukemias. In this subset of patients with ≥50% bone marrow erythroblasts and excess blasts, the presence of a high-risk karyotype defined by the International Prognostic Scoring System or by the Revised International Prognostic Scoring System was the main prognostic factor. In the same way, the survival of 459 refractory anemias with excess blasts-2, independently of having ≥20% bone marrow blasts from nonerythroid cells or not, was almost identical to the observed in 59 erythroleukemias. Interestingly, 11 low-blast count erythroleukemias with 5 to <10% bone marrow blasts from total nucleated cells showed similar survival than the rest of erythroleukemias. Our data suggest that de novo erythroleukemia is in the spectrum of myelodysplastic syndromes with excess blasts and support its inclusion into future classifications of myelodysplastic syndromes.
Blast injury from explosive munitions.

PubMed

Cernak, I; Savic, J; Ignjatovic, D; Jevtic, M

1999-07-01

To evaluate the effect of blast in common war injuries. One thousand three hundred and three patients injured by explosive munitions and demonstrating extremity wounds without other penetrating injuries were admitted to the Military Medical Academy in Belgrade between 1991 and 1994. Of these, 665 patients (51%) had symptoms and physical signs that were compatible with the clinical diagnosis of primary blast injury, whereas the remaining 658 patients did not. Random sampling of 65 patients in the blast group during the early posttraumatic period showed statistically significant elevations in blood thromboxane A2 (TxA2), prostacyclin (PGI2), and sulfidopeptide leukotrienes compared with the random sample of 62 patients in the nonblast group. This difference could not be accounted for by differing injury severity between the groups, because the severity of wounds as measured by both the Injury Severity Score and the Red Cross Wound Classification was similar in both groups. Amongst blast patients, 200 patients (30%) had long-term (1 year) symptoms and signs reflecting central nervous system disorders. These symptoms and signs were only sporadically found in 4% of the nonblast patients. These findings indicate that primary blast injury is more common in war injuries than previously thought and that of those affected by blast, a surprisingly high proportion retain long-term neurologic disability. The elevation in eicosanoids could be used to confirm and monitor blast injury. In relation to the immediate management of patients injured by explosive weapons, it follows that particular attention should be paid to the presence and/or development of blast injury. Our findings indicate that blast is more common in war injuries than previously thought. Eicosanoid changes after blast injury suggest that blast injury causes a major physiologic stress. A variety of effects on the central nervous system suggest that blast injury could be responsible for some aspects of what is now considered to be the posttraumatic stress disorder.
Considering Bone Marrow Blasts From Nonerythroid Cellularity Improves the Prognostic Evaluation of Myelodysplastic Syndromes.

PubMed

Arenillas, Leonor; Calvo, Xavier; Luño, Elisa; Senent, Leonor; Alonso, Esther; Ramos, Fernando; Ardanaz, María Teresa; Pedro, Carme; Tormo, Mar; Marco, Víctor; Montoro, Julia; Díez-Campelo, María; Brunet, Salut; Arrizabalaga, Beatriz; Xicoy, Blanca; Andreu, Rafael; Bonanad, Santiago; Jerez, Andrés; Nomdedeu, Benet; Ferrer, Ana; Sanz, Guillermo F; Florensa, Lourdes

2016-09-20

WHO classification of myeloid malignancies is based mainly on the percentage of bone marrow (BM) blasts. This is considered from total nucleated cells (TNCs), unless there is erythroid-hyperplasia (erythroblasts ≥ 50%), calculated from nonerythroid cells (NECs). In these instances, when BM blasts are ≥ 20%, the disorder is classified as erythroleukemia, and when BM blasts are < 20%, as myelodysplastic syndrome (MDS). In the latter, the percentage of blasts is considered from TNCs. We assessed the percentage of BM blasts from TNCs and NECs in 3,692 patients with MDS from the Grupo Español de Síndromes Mielodisplásicos, 465 patients with erythroid hyperplasia (MDS-E) and 3,227 patients without erythroid hyperplasia. We evaluated the relevance of both quantifications on classification and prognostication. By enumerating blasts systematically from NECs, 22% of patients with MDS-E and 12% with MDS from the whole series diagnosed within WHO categories with < 5% BM blasts, were reclassified into higher-risk categories and showed a poorer overall survival than did those who remained in initial categories (P = .006 and P = .001, respectively). Following WHO recommendations, refractory anemia with excess blasts (RAEB)-2 diagnosis is not possible in MDS-E, as patients with 10% to < 20% BM blasts from TNCs fulfill erythroleukemia criteria; however, by considering blasts from NECs, 72 patients were recoded as RAEB-2 and showed an inferior overall survival than did patients with RAEB-1 without erythroid hyperplasia. Recalculating the International Prognostic Scoring System by enumerating blasts from NECs in MDS-E and in the overall MDS population reclassified approximately 9% of lower-risk patients into higher-risk categories, which indicated the survival expected for higher-risk patients. Regardless of the presence of erythroid hyperplasia, calculating the percentage of BM blasts from NECs improves prognostic assessment of MDS. This fact should be considered in future WHO classification reviews. © 2016 by American Society of Clinical Oncology.
Interactions and relevance of blast percentage and treatment strategy among younger and older patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS)

PubMed Central

DiNardo, Courtney D.; Garcia-Manero, Guillermo; Pierce, Sherry; Nazha, Aziz; Bueso-Ramos, Carlos; Jabbour, Elias; Ravandi, Farhad; Cortes, Jorge; Kantarjian, Hagop

2017-01-01

Acute myeloid leukemia (AML) is defined as ≥20% myeloblasts, representing a change from original guidelines where ≤30% blasts were considered as myelodysplastic syndromes (MDS), and 20–29% blasts classified as refractory anemia with excess blasts in transformation (RAEB-T). Whether the diagnostic bone marrow blast percentage has current value with regards to patient prognostication or identification of optimal treatment strategies is unclear. We retrospectively studied 1652 treatment-naïve adults with MDS or AML and ≥10% blasts from January 2000 to April 2014. Patients with 20–29% blasts were more similar to MDS patients in terms of advanced age, increased frequency of poor-risk cytogenetics, lower WBC count, and less frequent NPM1 and FLT3-ITD mutations. Median overall survival of MDS and RAEB-T were similar, 16.0 and 16.0 months, compared to 13.5 months for AML with ≥30% blasts (P =0.045). Multivariate analysis showed inferior survival with increased age (HR 1.81 age 60–69, HR 2.68 age ≥70, P < 0.0005); poor-risk cytogenetics (HR 2.25, P < 0.0005); therapy-related disease (HR 1.44, P < 0.0005); and markers of proliferative disease including WBC ≥25 × 109/L (HR 1.35, P = 0.0003), elevated LDH count (HR 1.24, P =0.0015), and peripheral blasts (HR 1.25, P =0.004). Among younger patients (≤60 years), intensive AML-type therapy resulted in similar outcomes regardless of blast percentage, suggesting this to be optimal therapy in this context. Among older patients (≥70 years), patients with 20–29% blasts had similar outcomes to patients with <20% blasts, and better than those with ≥30% blasts. In addition, among older patients, epigenetic therapy provided at least equivalent outcome to intensive chemotherapy. PMID:26799610
Interactions and relevance of blast percentage and treatment strategy among younger and older patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS).

PubMed

DiNardo, Courtney D; Garcia-Manero, Guillermo; Pierce, Sherry; Nazha, Aziz; Bueso-Ramos, Carlos; Jabbour, Elias; Ravandi, Farhad; Cortes, Jorge; Kantarjian, Hagop

2016-02-01

Acute myeloid leukemia (AML) is defined as ≥20% myeloblasts, representing a change from original guidelines where ≤30% blasts were considered as myelodysplastic syndromes (MDS), and 20-29% blasts classified as refractory anemia with excess blasts in transformation (RAEB-T). Whether the diagnostic bone marrow blast percentage has current value with regards to patient prognostication or identification of optimal treatment strategies is unclear. We retrospectively studied 1652 treatment-naïve adults with MDS or AML and ≥10% blasts from January 2000 to April 2014. Patients with 20-29% blasts were more similar to MDS patients in terms of advanced age, increased frequency of poor-risk cytogenetics, lower WBC count, and less frequent NPM1 and FLT3-ITD mutations. Median overall survival of MDS and RAEB-T were similar, 16.0 and 16.0 months, compared to 13.5 months for AML with ≥30% blasts (P = 0.045). Multivariate analysis showed inferior survival with increased age (HR 1.81 age 60-69, HR 2.68 age ≥70, P < 0.0005); poor-risk cytogenetics (HR 2.25, P < 0.0005); therapy-related disease (HR 1.44, P < 0.0005); and markers of proliferative disease including WBC ≥25 × 10(9) /L (HR 1.35, P = 0.0003), elevated LDH count (HR 1.24, P = 0.0015), and peripheral blasts (HR 1.25, P = 0.004). Among younger patients (≤60 years), intensive AML-type therapy resulted in similar outcomes regardless of blast percentage, suggesting this to be optimal therapy in this context. Among older patients (≥70 years), patients with 20-29% blasts had similar outcomes to patients with <20% blasts, and better than those with ≥30% blasts. In addition, among older patients, epigenetic therapy provided at least equivalent outcome to intensive chemotherapy. © 2015 Wiley Periodicals, Inc.
Results of tests of MTA-2 TPS on the SRB hold-down bolt blast container

NASA Technical Reports Server (NTRS)

Dean, W. G.

1982-01-01

The four solid rocket booster (SRB) hold-down posts are fastened to the mobile launch platform (MLP) with four large nuts. At liftoff the nuts are split with explosive changes to release the SRB/Shuttle. A blast container is placed over the nuts to protect the vehicle from flying debris. The blast container is a reusable part and has to be protected from aerodynamic heating during flight. The thermal protection system (TPS) used to protect these blast containers is cork. Fitting the flat cork sheet to this hemispherical shaped blast container is both time consuming and expensive. Another problem is removing the charred cork and epoxy glue from the blast containers. Replacements of this cork with another TPS material such as MTA-2 was examined. Heating rates along the centerline of the forward facing areas of the blast container were determined. The feasibility of using 1/2 in. MTA-2 on the SRB blast containers for protection from ascent, plume impingement and reentry heating is demonstrated.
Passive blast pressure sensor

DOEpatents

King, Michael J.; Sanchez, Roberto J.; Moss, William C.

2013-03-19

A passive blast pressure sensor for detecting blast overpressures of at least a predetermined minimum threshold pressure. The blast pressure sensor includes a piston-cylinder arrangement with one end of the piston having a detection surface exposed to a blast event monitored medium through one end of the cylinder and the other end of the piston having a striker surface positioned to impact a contact stress sensitive film that is positioned against a strike surface of a rigid body, such as a backing plate. The contact stress sensitive film is of a type which changes color in response to at least a predetermined minimum contact stress which is defined as a product of the predetermined minimum threshold pressure and an amplification factor of the piston. In this manner, a color change in the film arising from impact of the piston accelerated by a blast event provides visual indication that a blast overpressure encountered from the blast event was not less than the predetermined minimum threshold pressure.
Manufacture and Preparation of Test Specimens for Johnson-Cook Material Characterization

DTIC Science & Technology

2013-01-01

modeling and simulation, and will be included in the Elastic Plastic Impact Code (EPIC) library. This report describes the welding and machining...used by the government for ballistic, blast and other types of modeling and simulation, and will be included in the Elastic Plastic Impact Code (EPIC...made of H13 tool steel with a scrolled pin and shoulder (See Figure 2-3) was used however the different heat requirements of the materials required
GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

PubMed

de Sá, Pablo H C G; Miranda, Fábio; Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T J

2016-01-01

The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.
Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878
Leveraging Python Interoperability Tools to Improve Sapphire's Usability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gezahegne, A; Love, N S

2007-12-10

The Sapphire project at the Center for Applied Scientific Computing (CASC) develops and applies an extensive set of data mining algorithms for the analysis of large data sets. Sapphire's algorithms are currently available as a set of C++ libraries. However many users prefer higher level scripting languages such as Python for their ease of use and flexibility. In this report, we evaluate four interoperability tools for the purpose of wrapping Sapphire's core functionality with Python. Exposing Sapphire's functionality through a Python interface would increase its usability and connect its algorithms to existing Python tools.
Effects of geometry on blast-induced loadings

NASA Astrophysics Data System (ADS)

Moore, Christopher Dyer

Simulations of blasts in an urban environment were performed using Loci/BLAST, a full-featured fluid dynamics simulation code, and analyzed. A two-structure urban environment blast case was used to perform a mesh refinement study. Results show that mesh spacing on and around the structure must be 12.5 cm or less to resolve fluid dynamic features sufficiently to yield accurate results. The effects of confinement were illustrated by analyzing a blast initiated from the same location with and without the presence of a neighboring structure. Analysis of extreme pressures and impulses on structures showed that confinement can increase blast loading by more than 200 percent.
Predictive control of thermal state of blast furnace

NASA Astrophysics Data System (ADS)

Barbasova, T. A.; Filimonova, A. A.

2018-05-01

The work describes the structure of the model for predictive control of the thermal state of a blast furnace. The proposed model contains the following input parameters: coke rate; theoretical combustion temperature, comprising: natural gas consumption, blasting temperature, humidity, oxygen, blast furnace cooling water; blast furnace gas utilization rate. The output parameter is the cast iron temperature. The results for determining the cast iron temperature were obtained following the identification using the Hammerstein-Wiener model. The result of solving the cast iron temperature stabilization problem was provided for the calculated values of process parameters of the target area of the respective blast furnace operation mode.
An FMS Dynamic Production Scheduling Algorithm Considering Cutting Tool Failure and Cutting Tool Life

NASA Astrophysics Data System (ADS)

Setiawan, A.; Wangsaputra, R.; Martawirya, Y. Y.; Halim, A. H.

2016-02-01

This paper deals with Flexible Manufacturing System (FMS) production rescheduling due to unavailability of cutting tools caused either of cutting tool failure or life time limit. The FMS consists of parallel identical machines integrated with an automatic material handling system and it runs fully automatically. Each machine has a same cutting tool configuration that consists of different geometrical cutting tool types on each tool magazine. The job usually takes two stages. Each stage has sequential operations allocated to machines considering the cutting tool life. In the real situation, the cutting tool can fail before the cutting tool life is reached. The objective in this paper is to develop a dynamic scheduling algorithm when a cutting tool is broken during unmanned and a rescheduling needed. The algorithm consists of four steps. The first step is generating initial schedule, the second step is determination the cutting tool failure time, the third step is determination of system status at cutting tool failure time and the fourth step is the rescheduling for unfinished jobs. The approaches to solve the problem are complete-reactive scheduling and robust-proactive scheduling. The new schedules result differences starting time and completion time of each operations from the initial schedule.
Creation of a federated database of blood proteins: a powerful new tool for finding and characterizing biomarkers in serum

PubMed Central

2014-01-01

Protein biomarkers offer major benefits for diagnosis and monitoring of disease processes. Recent advances in protein mass spectrometry make it feasible to use this very sensitive technology to detect and quantify proteins in blood. To explore the potential of blood biomarkers, we conducted a thorough review to evaluate the reliability of data in the literature and to determine the spectrum of proteins reported to exist in blood with a goal of creating a Federated Database of Blood Proteins (FDBP). A unique feature of our approach is the use of a SQL database for all of the peptide data; the power of the SQL database combined with standard informatic algorithms such as BLAST and the statistical analysis system (SAS) allowed the rapid annotation and analysis of the database without the need to create special programs to manage the data. Our mathematical analysis and review shows that in addition to the usual secreted proteins found in blood, there are many reports of intracellular proteins and good agreement on transcription factors, DNA remodelling factors in addition to cellular receptors and their signal transduction enzymes. Overall, we have catalogued about 12,130 proteins identified by at least one unique peptide, and of these 3858 have 3 or more peptide correlations. The FDBP with annotations should facilitate testing blood for specific disease biomarkers. PMID:24476026

7 CFR 3201.78 - Blast media.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 15 2013-01-01 2013-01-01 false Blast media. 3201.78 Section 3201.78 Agriculture... Items § 3201.78 Blast media. (a) Definition. Abrasive particles sprayed forcefully to clean, remove... qualifying biobased blast media. By that date, Federal agencies that have the responsibility for drafting or...
7 CFR 3201.78 - Blast media.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 15 2014-01-01 2014-01-01 false Blast media. 3201.78 Section 3201.78 Agriculture... Items § 3201.78 Blast media. (a) Definition. Abrasive particles sprayed forcefully to clean, remove... qualifying biobased blast media. By that date, Federal agencies that have the responsibility for drafting or...
Temporal Progression of Visual Injury from Blast Exposure

DTIC Science & Technology

2013-09-01

carprofen one day before the blast for pain management. A baseline of vision functionality is established before the blast using the metrics...returned to the animal facility. While animals do not show signs of pain following the blast exposure, carprofen is administered the next day as a
Characterisation of interface astroglial scarring in the human brain after blast exposure: a post-mortem case series.

PubMed

Shively, Sharon Baughman; Horkayne-Szakaly, Iren; Jones, Robert V; Kelly, James P; Armstrong, Regina C; Perl, Daniel P

2016-08-01

No evidence-based guidelines are available for the definitive diagnosis or directed treatment of most blast-associated traumatic brain injuries, partly because the underlying pathology is unknown. Moreover, few neuropathological studies have addressed whether blast exposure produces unique lesions in the human brain, and if those lesions are comparable with impact-induced traumatic brain injury. We aimed to test the hypothesis that blast exposure produces unique patterns of damage, differing from that associated with impact-induced, non-blast traumatic brain injuries. In this post-mortem case series, we investigated several features of traumatic brain injuries, using clinical histopathology techniques and markers, in brain specimens from male military service members with chronic blast exposures and from those who had died shortly after severe blast exposures. We then compared these results with those from brain specimens from male civilian (ie, non-military) cases with no history of blast exposure, including cases with and without chronic impact traumatic brain injuries and cases with chronic exposure to opiates, and analysed the limited associated clinical histories of all cases. Brain specimens had been archived in tissue banks in the USA. We analysed brain specimens from five cases with chronic blast exposure, three cases with acute blast exposure, five cases with chronic impact traumatic brain injury, five cases with exposure to opiates, and three control cases with no known neurological disorders. All five cases with chronic blast exposure showed prominent astroglial scarring that involved the subpial glial plate, penetrating cortical blood vessels, grey-white matter junctions, and structures lining the ventricles; all cases of acute blast exposure showed early astroglial scarring in the same brain regions. All cases of chronic blast exposure had an antemortem diagnosis of post traumatic stress disorder. The civilian cases, with or without history of impact traumatic brain injury or a history of opiate use, did not have any astroglial scarring in the brain regions analysed. The blast exposure cases showed a distinct and previously undescribed pattern of interface astroglial scarring at boundaries between brain parenchyma and fluids, and at junctions between grey and white matter. This distinctive pattern of scarring may indicate specific areas of damage from blast exposure consistent with the general principles of blast biophysics, and further, could account for aspects of the neuropsychiatric clinical sequelae reported. The generalisability of these findings needs to be explored in future studies, as the number of cases, clinical data, and tissue availability were limited. Defense Health Program of the United States Department of Defense. Copyright © 2016 Elsevier Ltd. All rights reserved.
Rapid condition assessment of structural condition after a blast using state-space identification

NASA Astrophysics Data System (ADS)

Eskew, Edward; Jang, Shinae

2015-04-01

After a blast event, it is important to quickly quantify the structural damage for emergency operations. In order improve the speed, accuracy, and efficiency of condition assessments after a blast, the authors have previously performed work to develop a methodology for rapid assessment of the structural condition of a building after a blast. The method involved determining a post-event equivalent stiffness matrix using vibration measurements and a finite element (FE) model. A structural model was built for the damaged structure based on the equivalent stiffness, and inter-story drifts from the blast are determined using numerical simulations, with forces determined from the blast parameters. The inter-story drifts are then compared to blast design conditions to assess the structures damage. This method still involved engineering judgment in terms of determining significant frequencies, which can lead to error, especially with noisy measurements. In an effort to improve accuracy and automate the process, this paper will look into a similar method of rapid condition assessment using subspace state-space identification. The accuracy of the method will be tested using a benchmark structural model, as well as experimental testing. The blast damage assessments will be validated using pressure-impulse (P-I) diagrams, which present the condition limits across blast parameters. Comparisons between P-I diagrams generated using the true system parameters and equivalent parameters will show the accuracy of the rapid condition based blast assessments.
Lasting Retinal Injury in a Mouse Model of Blast-Induced Trauma.

PubMed

Mammadova, Najiba; Ghaisas, Shivani; Zenitsky, Gary; Sakaguchi, Donald S; Kanthasamy, Anumantha G; Greenlee, Justin J; West Greenlee, M Heather

2017-07-01

Traumatic brain injury due to blast exposure is currently the most prevalent of war injuries. Although secondary ocular blast injuries due to flying debris are more common, primary ocular blast exposure resulting from blast wave pressure has been reported among survivors of explosions, but with limited understanding of the resulting retinal pathologies. Using a compressed air-driven shock tube system, adult male and female C57BL/6 mice were exposed to blast wave pressure of 300 kPa (43.5 psi) per day for 3 successive days, and euthanized 30 days after injury. We assessed retinal tissues using immunofluorescence for glial fibrillary acidic protein, microglia-specific proteins Iba1 and CD68, and phosphorylated tau (AT-270 pThr181 and AT-180 pThr231). Primary blast wave pressure resulted in activation of Müller glia, loss of photoreceptor cells, and an increase in phosphorylated tau in retinal neurons and glia. We found that 300-kPa blasts yielded no detectable cognitive or motor deficits, and no neurochemical or biochemical evidence of injury in the striatum or prefrontal cortex, respectively. These changes were detected 30 days after blast exposure, suggesting the possibility of long-lasting retinal injury and neuronal inflammation after primary blast exposure. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
Minimization of Blast furnace Fuel Rate by Optimizing Burden and Gas Distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Chenn Zhou

2012-08-15

The goal of the research is to improve the competitive edge of steel mills by using the advanced CFD technology to optimize the gas and burden distributions inside a blast furnace for achieving the best gas utilization. A state-of-the-art 3-D CFD model has been developed for simulating the gas distribution inside a blast furnace at given burden conditions, burden distribution and blast parameters. The comprehensive 3-D CFD model has been validated by plant measurement data from an actual blast furnace. Validation of the sub-models is also achieved. The user friendly software package named Blast Furnace Shaft Simulator (BFSS) has beenmore » developed to simulate the blast furnace shaft process. The research has significant benefits to the steel industry with high productivity, low energy consumption, and improved environment.« less
Scaling bioinformatics applications on HPC.

PubMed

Mikailov, Mike; Luo, Fu-Jyh; Barkley, Stuart; Valleru, Lohit; Whitney, Stephen; Liu, Zhichao; Thakkar, Shraddha; Tong, Weida; Petrick, Nicholas

2017-12-28

Recent breakthroughs in molecular biology and next generation sequencing technologies have led to the expenential growh of the sequence databases. Researchrs use BLAST for processing these sequences. However traditional software parallelization techniques (threads, message passing interface) applied in newer versios of BLAST are not adequate for processing these sequences in timely manner. A new method for array job parallelization has been developed which offers O(T) theoretical speed-up in comparison to multi-threading and MPI techniques. Here T is the number of array job tasks. (The number of CPUs that will be used to complete the job equals the product of T multiplied by the number of CPUs used by a single task.) The approach is based on segmentation of both input datasets to the BLAST process, combining partial solutions published earlier (Dhanker and Gupta, Int J Comput Sci Inf Technol_5:4818-4820, 2014), (Grant et al., Bioinformatics_18:765-766, 2002), (Mathog, Bioinformatics_19:1865-1866, 2003). It is accordingly referred to as a "dual segmentation" method. In order to implement the new method, the BLAST source code was modified to allow the researcher to pass to the program the number of records (effective number of sequences) in the original database. The team also developed methods to manage and consolidate the large number of partial results that get produced. Dual segmentation allows for massive parallelization, which lifts the scaling ceiling in exciting ways. BLAST jobs that hitherto failed or slogged inefficiently to completion now finish with speeds that characteristically reduce wallclock time from 27 days on 40 CPUs to a single day using 4104 tasks, each task utilizing eight CPUs and taking less than 7 minutes to complete. The massive increase in the number of tasks when running an analysis job with dual segmentation reduces the size, scope and execution time of each task. Besides significant speed of completion, additional benefits include fine-grained checkpointing and increased flexibility of job submission. "Trickling in" a swarm of individual small tasks tempers competition for CPU time in the shared HPC environment, and jobs submitted during quiet periods can complete in extraordinarily short time frames. The smaller task size also allows the use of older and less powerful hardware. The CDRH workhorse cluster was commissioned in 2010, yet its eight-core CPUs with only 24GB RAM work well in 2017 for these dual segmentation jobs. Finally, these techniques are excitingly friendly to budget conscious scientific research organizations where probabilistic algorithms such as BLAST might discourage attempts at greater certainty because single runs represent a major resource drain. If a job that used to take 24 days can now be completed in less than an hour or on a space available basis (which is the case at CDRH), repeated runs for more exhaustive analyses can be usefully contemplated.
Attenuation of blast pressure behind ballistic protective vests.

PubMed

Wood, Garrett W; Panzer, Matthew B; Shridharani, Jay K; Matthews, Kyle A; Capehart, Bruce P; Myers, Barry S; Bass, Cameron R

2013-02-01

Clinical studies increasingly report brain injury and not pulmonary injury following blast exposures, despite the increased frequency of exposure to explosive devices. The goal of this study was to determine the effect of personal body armour use on the potential for primary blast injury and to determine the risk of brain and pulmonary injury following a blast and its impact on the clinical care of patients with a history of blast exposure. A shock tube was used to generate blast overpressures on soft ballistic protective vests (NIJ Level-2) and hard protective vests (NIJ Level-4) while overpressure was recorded behind the vest. Both types of vest were found to significantly decrease pulmonary injury risk following a blast for a wide range of conditions. At the highest tested blast overpressure, the soft vest decreased the behind armour overpressure by a factor of 14.2, and the hard vest decreased behind armour overpressure by a factor of 56.8. Addition of body armour increased the 50th percentile pulmonary death tolerance of both vests to higher levels than the 50th percentile for brain injury. These results suggest that ballistic protective body armour vests, especially hard body armour plates, provide substantial chest protection in primary blasts and explain the increased frequency of head injuries, without the presence of pulmonary injuries, in protected subjects reporting a history of blast exposure. These results suggest increased clinical suspicion for mild to severe brain injury is warranted in persons wearing body armour exposed to a blast with or without pulmonary injury.
An animal-to-human scaling law for blast-induced traumatic brain injury risk assessment.

PubMed

Jean, Aurélie; Nyein, Michelle K; Zheng, James Q; Moore, David F; Joannopoulos, John D; Radovitzky, Raúl

2014-10-28

Despite recent efforts to understand blast effects on the human brain, there are still no widely accepted injury criteria for humans. Recent animal studies have resulted in important advances in the understanding of brain injury due to intense dynamic loads. However, the applicability of animal brain injury results to humans remains uncertain. Here, we use advanced computational models to derive a scaling law relating blast wave intensity to the mechanical response of brain tissue across species. Detailed simulations of blast effects on the brain are conducted for different mammals using image-based biofidelic models. The intensity of the stress waves computed for different external blast conditions is compared across species. It is found that mass scaling, which successfully estimates blast tolerance of the thorax, fails to capture the brain mechanical response to blast across mammals. Instead, we show that an appropriate scaling variable must account for the mass of protective tissues relative to the brain, as well as their acoustic impedance. Peak stresses transmitted to the brain tissue by the blast are then shown to be a power function of the scaling parameter for a range of blast conditions relevant to TBI. In particular, it is found that human brain vulnerability to blast is higher than for any other mammalian species, which is in distinct contrast to previously proposed scaling laws based on body or brain mass. An application of the scaling law to recent experiments on rabbits furnishes the first physics-based injury estimate for blast-induced TBI in humans.
Forensic Seismology: constraints on terrorist bombings

NASA Astrophysics Data System (ADS)

Wallace, T. C.; Koper, K. D.

2002-05-01

Seismology has long been used as a tool to monitor and investigate explosions, both accidental and intentional. Seismic records can be used to provide a precise chronology of events, estimate the energy release in explosions and produce constraints to test various scenarios for the explosions. Truck bombs are a popular tool of terrorists, and at least two such attacks have been recorded seismically. On August 7, 1998 a truck bomb was detonated near the US embassy in Nairobi, Kenya. The bomb seriously damaging a dozen buildings, injuring more than 4000 people and causing 220 fatalities. The explosion was recorded on a short-period seismometer located north of the blast site; the blast seismogram contained body waves, Rayleigh waves and vibrations associated with the air blast. Modeling of the body and surfaces wave allowed an estimate of the origin time of the bombing, which it turn could be used as a constraint the timing of the air blasts. The speed of the air waves from an explosion depend on the air temperature and the size, or yield, of the explosion. In an effort to fully utilize the seismic recordings from such attacks, we analyzed the seismic records from a series of controlled truck bomb explosions carried out at White Sand Missile Range in New Mexico. We developed a new set of scaling laws that relate seismic and acoustic observations directly to the explosive mass (yield). These relationships give a yield of approximately 3000 kg of TNT equivalent for the Nairobi bomb. The terrorist bombing of the Murrah Federal Building in Oklahoma City in 1995 was also recorded on seismometers. One of these records showed 2 discrete surface wavetrains separated by approximately 10 seconds. Some groups seized on the seismic recordings as evidence that there were 2 explosions, and that the US government was actually behind the bombing. However, the USGS monitored the demolition of the remainder of the Murrah Building and showed that the collapse also produced 2 surface waves. The interpretation is that one group was the fundamental mode Rayleigh wave while the other was either a higher-mode surface wave or a scattered S-wave (Lg like) packet (Holzer et al, 1996). This example illustrates the utility of forensic seismology for testing various hypothesis for the explosions. As the number of permanent and temporarily installed seismometers increase in the next decade, the number of "exotic" sources recorded and investigated is grow dramatically. These studies can be very useful for investigating terrorist attacks, and developing scenarios for the crimes.
Lasting retinal injury in a mouse model of blast-induced trauma

USDA-ARS?s Scientific Manuscript database

Traumatic brain injury (TBI) due to blast exposure is currently the most prevalent of war injuries. While secondary ocular blast injuries due to flying debris are more common, primary ocular blast exposure has been reported among survivors of explosions, but with limited understanding of the resulti...
BLAST FURNACE CAST HOUSE EMISSION CONTROL TECHNOLOGY ASSESSMENT

EPA Science Inventory

The study describes the state-of-the-art of controlling fumes escaping from blast furnace cast houses. Background information is based on: a study of existing literature; visits to blast furnaces in the U.S., Japan, and Europe; meetings with an ad hoc group of experienced blast f...
29 CFR 1926.906 - Initiation of explosive charges-electric blasting.

Code of Federal Regulations, 2010 CFR

2010-07-01

... dangerous. Blasting cap leg wires shall be kept short-circuited (shunted) until they are connected into the..., in accordance with the manufacturer's recommendations. (f) Connecting wires and lead wires shall be... manufacturer of the electric blasting caps used. (o) The number of electric blasting caps connected to a...
Benchmarking protein classification algorithms via supervised cross-validation.

PubMed

Kertész-Farkas, Attila; Dhir, Somdutta; Sonego, Paolo; Pacurar, Mircea; Netoteia, Sergiu; Nijveen, Harm; Kuzniar, Arnold; Leunissen, Jack A M; Kocsor, András; Pongor, Sándor

2008-04-24

Development and testing of protein classification algorithms are hampered by the fact that the protein universe is characterized by groups vastly different in the number of members, in average protein size, similarity within group, etc. Datasets based on traditional cross-validation (k-fold, leave-one-out, etc.) may not give reliable estimates on how an algorithm will generalize to novel, distantly related subtypes of the known protein classes. Supervised cross-validation, i.e., selection of test and train sets according to the known subtypes within a database has been successfully used earlier in conjunction with the SCOP database. Our goal was to extend this principle to other databases and to design standardized benchmark datasets for protein classification. Hierarchical classification trees of protein categories provide a simple and general framework for designing supervised cross-validation strategies for protein classification. Benchmark datasets can be designed at various levels of the concept hierarchy using a simple graph-theoretic distance. A combination of supervised and random sampling was selected to construct reduced size model datasets, suitable for algorithm comparison. Over 3000 new classification tasks were added to our recently established protein classification benchmark collection that currently includes protein sequence (including protein domains and entire proteins), protein structure and reading frame DNA sequence data. We carried out an extensive evaluation based on various machine-learning algorithms such as nearest neighbor, support vector machines, artificial neural networks, random forests and logistic regression, used in conjunction with comparison algorithms, BLAST, Smith-Waterman, Needleman-Wunsch, as well as 3D comparison methods DALI and PRIDE. The resulting datasets provide lower, and in our opinion more realistic estimates of the classifier performance than do random cross-validation schemes. A combination of supervised and random sampling was used to construct model datasets, suitable for algorithm comparison.
Efficient RNA structure comparison algorithms.

PubMed

Arslan, Abdullah N; Anandan, Jithendar; Fry, Eric; Monschke, Keith; Ganneboina, Nitin; Bowerman, Jason

2017-12-01

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.
ASTROS: A multidisciplinary automated structural design tool

NASA Technical Reports Server (NTRS)

Neill, D. J.

1989-01-01

ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.
Control technology for crystalline silica exposures in construction: wet abrasive blasting.

PubMed

Golla, Vijay; Heitbrink, William

2004-03-01

This study was designed to document the effect that wet abrasive blasting has on reducing worker exposure to crystalline silica, which has been associated with silicosis and premature death. In this study, worker exposure to respirable crystalline silica was monitored during wet abrasive blasting on the exterior walls of a parking garage to remove surface concrete and expose the underlying aggregate. In this process a wet sand mix comprised of 80% dry sand and 20% water was used. Sampling and analysis revealed that the geometric mean respirable quartz concentration was 0.2 mg/m(3) for workers conducting abrasive blasting and 0.06 mg/m(3) for helpers. When abrasive blasting was conducted in areas that apparently had reduced natural ventilation, dust exposures appeared to increase. When compared with other published data, this case study suggests that wet abrasive blasting causes less exposure to crystalline silica than dry abrasive blasting.
Application of Carbon Composite Bricks for Blast Furnace Hearth

NASA Astrophysics Data System (ADS)

Zuo, Haibin; Wang, Cong; Zhang, Jianliang; Zhao, Yongan; Jiao, Kexin

Traditional refractory materials for blast furnace hearth lining are mainly composed of carbon bricks and the ceramic cup. However, these materials can't meet the demands for long service life design of blast furnaces. In this paper, a new refractory called carbon composite brick (CCB) was introduced, which combined the advantages of carbon bricks and the ceramic cup. In this case, the resistance of the CCB against corrosion was equal to the ceramic cup and the thermal conductivity of the CCB was equal to carbon bricks. From the results of more than 20 blast furnaces, the CCB could be well used in small blast furnaces and large blast furnaces. In the bad condition of low grade burden and high smelting intensity, the CCB gave full play to the role of cooling system, and effectively resisted the erosion of hot metal to improve the service life of blast furnaces.
Numerical modeling and characterization of blast waves for application in blast-induced mild traumatic brain injury research

NASA Astrophysics Data System (ADS)

Phillips, Michael G.

Human exposure to blast waves, including blast-induced traumatic brain injury, is a developing field in medical research. Experiments with explosives have many disadvantages including safety, cost, and required area for trials. Shock tubes provide an alternative method to produce free field blast wave profiles. A compressed nitrogen shock tube experiment instrumented with static and reflective pressure taps is modeled using a numerical simulation. The geometry of the numerical model is simplified and blast wave characteristics are derived based upon static and pressure profiles. The pressure profiles are analyzed along the shock tube centerline and radially away from the tube axis. The blast wave parameters found from the pressure profiles provide guidelines for spatial location of a specimen. The location could be based on multiple parameters and provides a distribution of anticipated pressure profiles experience by the specimen.

Cold blast furnace syndrome: a new source of toxic inhalation by nitrogen oxides.

PubMed

Tague, I; Llewellin, P; Burton, K; Buchan, R; Yates, D H

2004-05-01

To describe a new toxic inhalation syndrome in blast furnace workers. Fourteen workers developed acute respiratory symptoms shortly after exposure to "air blast" from blast furnace tuyeres. These included chest tightness, dyspnoea, rigors, and diaphoresis. Chest radiographs showed pulmonary infiltrates, and lung function a restrictive abnormality. This report includes a description of clinical features of the affected workers and elucidation of the probable cause of the outbreak. Clinical features and occupational hygiene measurements suggested the most likely cause was inhalation of nitrogen oxides at high pressure and temperature. While the task could not be eliminated, engineering controls were implemented to control the hazard. No further cases have occurred. "Cold blast furnace syndrome" represents a previously undescribed hazard of blast furnace work, probably due to inhalation of nitrogen oxides. It should be considered in the differential diagnosis of acute toxic inhalational injuries in blast furnace workers.
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.

PubMed

Lai, Fu-Jou; Chang, Hong-Tsun; Wu, Wei-Sheng

2015-01-01

Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to predict cooperative TF pairs in yeast. However, it is still difficult to conduct a comprehensive and objective performance comparison of different algorithms because of lacking sufficient performance indices and adequate overall performance scores. To solve this problem, in our previous study (published in BMC Systems Biology 2014), we adopted/proposed eight performance indices and designed two overall performance scores to compare the performance of 14 existing algorithms for predicting cooperative TF pairs in yeast. Most importantly, our performance comparison framework can be applied to comprehensively and objectively evaluate the performance of a newly developed algorithm. However, to use our framework, researchers have to put a lot of effort to construct it first. To save researchers time and effort, here we develop a web tool to implement our performance comparison framework, featuring fast data processing, a comprehensive performance comparison and an easy-to-use web interface. The developed tool is called PCTFPeval (Predicted Cooperative TF Pair evaluator), written in PHP and Python programming languages. The friendly web interface allows users to input a list of predicted cooperative TF pairs from their algorithm and select (i) the compared algorithms among the 15 existing algorithms, (ii) the performance indices among the eight existing indices, and (iii) the overall performance scores from two possible choices. The comprehensive performance comparison results are then generated in tens of seconds and shown as both bar charts and tables. The original comparison results of each compared algorithm and each selected performance index can be downloaded as text files for further analyses. Allowing users to select eight existing performance indices and 15 existing algorithms for comparison, our web tool benefits researchers who are eager to comprehensively and objectively evaluate the performance of their newly developed algorithm. Thus, our tool greatly expedites the progress in the research of computational identification of cooperative TF pairs.
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast

PubMed Central

2015-01-01

Background Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to predict cooperative TF pairs in yeast. However, it is still difficult to conduct a comprehensive and objective performance comparison of different algorithms because of lacking sufficient performance indices and adequate overall performance scores. To solve this problem, in our previous study (published in BMC Systems Biology 2014), we adopted/proposed eight performance indices and designed two overall performance scores to compare the performance of 14 existing algorithms for predicting cooperative TF pairs in yeast. Most importantly, our performance comparison framework can be applied to comprehensively and objectively evaluate the performance of a newly developed algorithm. However, to use our framework, researchers have to put a lot of effort to construct it first. To save researchers time and effort, here we develop a web tool to implement our performance comparison framework, featuring fast data processing, a comprehensive performance comparison and an easy-to-use web interface. Results The developed tool is called PCTFPeval (Predicted Cooperative TF Pair evaluator), written in PHP and Python programming languages. The friendly web interface allows users to input a list of predicted cooperative TF pairs from their algorithm and select (i) the compared algorithms among the 15 existing algorithms, (ii) the performance indices among the eight existing indices, and (iii) the overall performance scores from two possible choices. The comprehensive performance comparison results are then generated in tens of seconds and shown as both bar charts and tables. The original comparison results of each compared algorithm and each selected performance index can be downloaded as text files for further analyses. Conclusions Allowing users to select eight existing performance indices and 15 existing algorithms for comparison, our web tool benefits researchers who are eager to comprehensively and objectively evaluate the performance of their newly developed algorithm. Thus, our tool greatly expedites the progress in the research of computational identification of cooperative TF pairs. PMID:26677932
29 CFR 1926.906 - Initiation of explosive charges-electric blasting.

Code of Federal Regulations, 2013 CFR

2013-07-01

...” position at all times, except when firing. It shall be so designed that the firing lines to the cap circuit... blasting machine shall not be in excess of its rated capacity. Furthermore, in primary blasting, a series..., shall use only blasting galvanometers or other instruments that are specifically designed for this...
29 CFR 1926.906 - Initiation of explosive charges-electric blasting.

Code of Federal Regulations, 2014 CFR

2014-07-01

...” position at all times, except when firing. It shall be so designed that the firing lines to the cap circuit... blasting machine shall not be in excess of its rated capacity. Furthermore, in primary blasting, a series..., shall use only blasting galvanometers or other instruments that are specifically designed for this...
29 CFR 1926.906 - Initiation of explosive charges-electric blasting.

Code of Federal Regulations, 2012 CFR

2012-07-01

...” position at all times, except when firing. It shall be so designed that the firing lines to the cap circuit... blasting machine shall not be in excess of its rated capacity. Furthermore, in primary blasting, a series..., shall use only blasting galvanometers or other instruments that are specifically designed for this...
29 CFR 1926.906 - Initiation of explosive charges-electric blasting.

Code of Federal Regulations, 2011 CFR

2011-07-01

...” position at all times, except when firing. It shall be so designed that the firing lines to the cap circuit... blasting machine shall not be in excess of its rated capacity. Furthermore, in primary blasting, a series..., shall use only blasting galvanometers or other instruments that are specifically designed for this...
75 FR 4793 - Availability for Non-Exclusive, Exclusive, or Partially Exclusive Licensing of U.S. Provisional...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

... Partially Exclusive Licensing of U.S. Provisional Patent Application Concerning Blast Wave Sensor AGENCY... ``Blast Wave Sensor,'' filed January 4, 2010. The United States Government, as represented by the... wave sensors and their use to detect blast induced pressure changes, and, in particular, a blast wave...
33 CFR 83.35 - Sound signals in restricted visibility (Rule 35).

Code of Federal Regulations, 2013 CFR

2013-07-01

... more than 2 minutes two prolonged blasts in succession with an interval of about 2 seconds between them... than 2 minutes, three blasts in succession; namely, one prolonged followed by two short blasts. (d..., shall at intervals of not more than 2 minutes sound four blasts in succession; namely, one prolonged...
33 CFR 83.35 - Sound signals in restricted visibility (Rule 35).

Code of Federal Regulations, 2014 CFR

2014-07-01

... more than 2 minutes two prolonged blasts in succession with an interval of about 2 seconds between them... than 2 minutes, three blasts in succession; namely, one prolonged followed by two short blasts. (d..., shall at intervals of not more than 2 minutes sound four blasts in succession; namely, one prolonged...
33 CFR 83.35 - Sound signals in restricted visibility (Rule 35).

Code of Federal Regulations, 2012 CFR

2012-07-01

... more than 2 minutes two prolonged blasts in succession with an interval of about 2 seconds between them... than 2 minutes, three blasts in succession; namely, one prolonged followed by two short blasts. (d..., shall at intervals of not more than 2 minutes sound four blasts in succession; namely, one prolonged...
33 CFR 83.35 - Sound signals in restricted visibility (Rule 35).

Code of Federal Regulations, 2011 CFR

2011-07-01

... more than 2 minutes two prolonged blasts in succession with an interval of about 2 seconds between them... than 2 minutes, three blasts in succession; namely, one prolonged followed by two short blasts. (d..., shall at intervals of not more than 2 minutes sound four blasts in succession; namely, one prolonged...
Characterization of molecular identity and pathogenicity of rice blast fungus in Hunan province of China

USDA-ARS?s Scientific Manuscript database

Characterization of molecular identity and pathogenicity of the rice blast fungus benefits the deployment of effective blast resistance (R) genes. In order to identify blast resistance genes in rice producing areas where most of the hybrid rice is grown in Hunan province, 182 M. oryzae strains were ...
Identification of blast resistance genes for managing rice blast disease

USDA-ARS?s Scientific Manuscript database

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases worldwide. In the present study, an international set of monogenic differentials carrying 24 major blast resistance (R) genes (Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Pik-s, Pish, Pit, Pita, Pita2,...
Blast-induced tinnitus and hyperactivity in the auditory cortex of rats.

PubMed

Luo, Hao; Pace, Edward; Zhang, Jinsheng

2017-01-06

Blast exposure can cause tinnitus and hearing impairment by damaging the auditory periphery and direct impact to the brain, which trigger neural plasticity in both auditory and non-auditory centers. However, the underlying neurophysiological mechanisms of blast-induced tinnitus are still unknown. In this study, we induced tinnitus in rats using blast exposure and investigated changes in spontaneous firing and bursting activity in the auditory cortex (AC) at one day, one month, and three months after blast exposure. Our results showed that spontaneous activity in the tinnitus-positive group began changing at one month after blast exposure, and manifested as robust hyperactivity at all frequency regions at three months after exposure. We also observed an increased bursting rate in the low-frequency region at one month after blast exposure and in all frequency regions at three months after exposure. Taken together, spontaneous firing and bursting activity in the AC played an important role in blast-induced chronic tinnitus as opposed to acute tinnitus, thus favoring a bottom-up mechanism. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.
Blast investigation by fast multispectral radiometric analysis

NASA Astrophysics Data System (ADS)

Devir, A. D.; Bushlin, Y.; Mendelewicz, I.; Lessin, A. B.; Engel, M.

2011-06-01

Knowledge regarding the processes involved in blasts and detonations is required in various applications, e.g. missile interception, blasts of high-explosive materials, final ballistics and IED identification. Blasts release large amount of energy in short time duration. Some part of this energy is released as intense radiation in the optical spectral bands. This paper proposes to measure the blast radiation by a fast multispectral radiometer. The measurement is made, simultaneously, in appropriately chosen spectral bands. These spectral bands provide extensive information on the physical and chemical processes that govern the blast through the time-dependence of the molecular and aerosol contributions to the detonation products. Multi-spectral blast measurements are performed in the visible, SWIR and MWIR spectral bands. Analysis of the cross-correlation between the measured multi-spectral signals gives the time dependence of the temperature, aerosol and gas composition of the blast. Farther analysis of the development of these quantities in time may indicate on the order of the detonation and amount and type of explosive materials. Examples of analysis of measured explosions are presented to demonstrate the power of the suggested fast multispectral radiometric analysis approach.
Clinical characteristics of 15 children with juvenile myelomonocytic leukaemia who developed blast crisis: MDS Committee of Japanese Society of Paediatric Haematology/Oncology.

PubMed

Honda, Yuko; Tsuchida, Masahiro; Zaike, Yuji; Masunaga, Atsuko; Yoshimi, Ayami; Kojima, Seiji; Ito, Masafumi; Kikuchi, Akira; Nakahata, Tatsutoshi; Manabe, Atsushi

2014-06-01

Juvenile myelomonocytic leukaemia (JMML) is a rare haematopoietic stem cell disease of early childhood, which can progress to blast crisis in some children. A total of 153 children diagnosed with JMML were reported to the Myelodysplastic Syndrome Committee in Japan between 1989 and 2007; 15 of them (9·8%) had 20% or more blasts in the bone marrow (blast crisis) during the disease course. Blast crisis occurred during observation without therapy (n = 3) or with oral 6-mercaptopurine treatment (n = 9) and in relapse after haematopoietic stem cell transplantation (HSCT; n = 3). Six patients had a complex karyotype (5 including monosomy 7) and an additional three patients had isolated monosomy 7 at blast crisis. Seven patients received HSCT after blast crisis and four of them achieved remission. Eleven out of the 15 patients died; the cause of death was disease progression in 10 patients and transplant-related complication in one patient. In summary, patients with blast crisis have poor prognosis and can be cured only by HSCT. The emergence of monosomy 7 and complex karyotype may be characteristic of blast crisis in a substantial subset of children. © 2014 John Wiley & Sons Ltd.
Blast-Induced Tinnitus and Elevated Central Auditory and Limbic Activity in Rats: A Manganese-Enhanced MRI and Behavioral Study.

PubMed

Ouyang, Jessica; Pace, Edward; Lepczyk, Laura; Kaufman, Michael; Zhang, Jessica; Perrine, Shane A; Zhang, Jinsheng

2017-07-07

Blast-induced tinitus is the number one service-connected disability that currently affects military personnel and veterans. To elucidate its underlying mechanisms, we subjected 13 Sprague Dawley adult rats to unilateral 14 psi blast exposure to induce tinnitus and measured auditory and limbic brain activity using manganese-enhanced MRI (MEMRI). Tinnitus was evaluated with a gap detection acoustic startle reflex paradigm, while hearing status was assessed with prepulse inhibition (PPI) and auditory brainstem responses (ABRs). Both anxiety and cognitive functioning were assessed using elevated plus maze and Morris water maze, respectively. Five weeks after blast exposure, 8 of the 13 blasted rats exhibited chronic tinnitus. While acoustic PPI remained intact and ABR thresholds recovered, the ABR wave P1-N1 amplitude reduction persisted in all blast-exposed rats. No differences in spatial cognition were observed, but blasted rats as a whole exhibited increased anxiety. MEMRI data revealed a bilateral increase in activity along the auditory pathway and in certain limbic regions of rats with tinnitus compared to age-matched controls. Taken together, our data suggest that while blast-induced tinnitus may play a role in auditory and limbic hyperactivity, the non-auditory effects of blast and potential traumatic brain injury may also exert an effect.
Computational modeling of human head under blast in confined and open spaces: primary blast injury.

PubMed

Rezaei, A; Salimi Jazi, M; Karami, G

2014-01-01

In this paper, a computational modeling for biomechanical analysis of primary blast injuries is presented. The responses of the brain in terms of mechanical parameters under different blast spaces including open, semi-confined, and confined environments are studied. In the study, the effect of direct and indirect blast waves from the neighboring walls in the confined environments will be taken into consideration. A 50th percentile finite element head model is exposed to blast waves of different intensities. In the open space, the head experiences a sudden intracranial pressure (ICP) change, which vanishes in a matter of a few milliseconds. The situation is similar in semi-confined space, but in the confined space, the reflections from the walls will create a number of subsequent peaks in ICP with a longer duration. The analysis procedure is based on a simultaneous interaction simulation of the deformable head and its components with the blast wave propagations. It is concluded that compared with the open and semi-confined space settings, the walls in the confined space scenario enhance the risk of primary blast injuries considerably because of indirect blast waves transferring a larger amount of damaging energy to the head. Copyright © 2013 John Wiley & Sons, Ltd.
Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

NASA Technical Reports Server (NTRS)

Weber, Ryan; New, Michael H.; Fonda, Mark (Technical Monitor)

2002-01-01

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Online aptitude automatic surface quality inspection system for hot rolled strips steel

NASA Astrophysics Data System (ADS)

Lin, Jin; Xie, Zhi-jiang; Wang, Xue; Sun, Nan-Nan

2005-12-01

Defects on the surface of hot rolled steel strips are main factors to evaluate quality of steel strips, an improved image recognition algorithm are used to extract the feature of Defects on the surface of steel strips. Base on the Machine vision and Artificial Neural Networks, establish a defect recognition method to select defect on the surface of steel strips. Base on these research. A surface inspection system and advanced algorithms for image processing to hot rolled strips is developed. Preparing two different fashion to lighting, adopting line blast vidicon of CCD on the surface steel strips on-line. Opening up capacity-diagnose-system with level the surface of steel strips on line, toward the above and undersurface of steel strips with ferric oxide, injure, stamp etc of defects on the surface to analyze and estimate. Miscarriage of justice and alternate of justice rate not preponderate over 5%.Geting hold of applications on some big enterprises of steel at home. Experiment proved that this measure is feasible and effective.
Retinal ganglion cell damage in an experimental rodent model of blast-mediated traumatic brain injury.

PubMed

Mohan, Kabhilan; Kecova, Helga; Hernandez-Merino, Elena; Kardon, Randy H; Harper, Matthew M

2013-05-15

To evaluate retina and optic nerve damage following experimental blast injury. Healthy adult mice were exposed to an overpressure blast wave using a custom-built blast chamber. The effects of blast exposure on retina and optic nerve function and structure were evaluated using the pattern electroretinogram (pERG), spectral domain optical coherence tomography (OCT), and the chromatic pupil light reflex. Assessment of the pupil response to light demonstrated decreased maximum pupil constriction diameter in blast-injured mice using red light or blue light stimuli 24 hours after injury compared with baseline in the eye exposed to direct blast injury. A decrease in the pupil light reflex was not observed chronically following blast exposure. We observed a biphasic pERG decrease with the acute injury recovering by 24 hours postblast and the chronic injury appearing at 4 months postblast injury. Furthermore, at 3 months following injury, a significant decrease in the retinal nerve fiber layer was observed using OCT compared with controls. Histologic analysis of the retina and optic nerve revealed punctate regions of reduced cellularity in the ganglion cell layer and damage to optic nerves. Additionally, a significant upregulation of proteins associated with oxidative stress was observed acutely following blast exposure compared with control mice. Our study demonstrates that decrements in retinal ganglion cell responses can be detected after blast injury using noninvasive functional and structural tests. These objective responses may serve as surrogate tests for higher CNS functions following traumatic brain injury that are difficult to quantify.
Xenon Protects against Blast-Induced Traumatic Brain Injury in an In Vitro Model.

PubMed

Campos-Pires, Rita; Koziakova, Mariia; Yonis, Amina; Pau, Ashni; Macdonald, Warren; Harris, Katie; Edge, Christopher J; Franks, Nicholas P; Mahoney, Peter F; Dickinson, Robert

2018-04-15

The aim of this study was to evaluate the neuroprotective efficacy of the inert gas xenon as a treatment for patients with blast-induced traumatic brain injury in an in vitro laboratory model. We developed a novel blast traumatic brain injury model using C57BL/6N mouse organotypic hippocampal brain-slice cultures exposed to a single shockwave, with the resulting injury quantified using propidium iodide fluorescence. A shock tube blast generator was used to simulate open field explosive blast shockwaves, modeled by the Friedlander waveform. Exposure to blast shockwave resulted in significant (p < 0.01) injury that increased with peak-overpressure and impulse of the shockwave, and which exhibited a secondary injury development up to 72 h after trauma. Blast-induced propidium iodide fluorescence overlapped with cleaved caspase-3 immunofluorescence, indicating that shock-wave-induced cell death involves apoptosis. Xenon (50% atm) applied 1 h after blast exposure reduced injury 24 h (p < 0.01), 48 h (p < 0.05), and 72 h (p < 0.001) later, compared with untreated control injury. Xenon-treated injured slices were not significantly different from uninjured sham slices at 24 h and 72 h. We demonstrate for the first time that xenon treatment after blast traumatic brain injury reduces initial injury and prevents subsequent injury development in vitro. Our findings support the idea that xenon may be a potential first-line treatment for those with blast-induced traumatic brain injury.
BLAST BIOLOGY. Technical Progress Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, C.S.; Richmond, D.R.

1959-09-18

Experimental data regarding the biologic consequences of exposure to several environmental variations associated with actual and simulated explosive detonations were reviewed. Blast biology is discussed relative to primary, secondary, tentiary, and miscellaneous blast effects as those attributable, respectively, to variations in environmental pressure, trauma from blast-produced missiles (both penetrating and nonpenetrating), the consequences of physical displacement of biological targets by blast-produced winds, and hazards due to ground shock, dust, and thermal phenomena not caused by thermal radiation per se. Primary blast effects were considered, noting physical-biophysical factors contributing to the observed pathophysiology. A simple hydrostatic model was utilized diagrammatically inmore » pointing out possible etiologic mechanisms. The gross biologic response to single. "fast"-rising overpressures were described as was the tolerance of mice, rats, guinea pigs. and rabbits to "long"-duration pressure pulses rising "rapidly" in single and double steps. Data regarding biological response to "slowly" rising over-pressures of "long" duration are discussed. Attention was called to the similarities under certain circumstances between thoracic trauma from nonpenetrating missiles and that noted from air blast. The association between air emboli, increase in lung weight (hemorrhage and edema), and mortality was discussed. Data relevant to the clinical symptoms and therapy of blast injury are presented. The relation of blast hazards to nuclear explosions was assessed and one approach to predicting the maximal potential casualties from blast phenomena is presented making use of arbitrary and tentative criteria. (auth)« less
Mechanisms of Hearing Loss after Blast Injury to the Ear

PubMed Central

Cho, Sung-Il; Gao, Simon S.; Xia, Anping; Wang, Rosalie; Salles, Felipe T.; Raphael, Patrick D.; Abaya, Homer; Wachtel, Jacqueline; Baek, Jongmin; Jacobs, David; Rasband, Matthew N.; Oghalai, John S.

2013-01-01

Given the frequent use of improvised explosive devices (IEDs) around the world, the study of traumatic blast injuries is of increasing interest. The ear is the most common organ affected by blast injury because it is the body’s most sensitive pressure transducer. We fabricated a blast chamber to re-create blast profiles similar to that of IEDs and used it to develop a reproducible mouse model to study blast-induced hearing loss. The tympanic membrane was perforated in all mice after blast exposure and found to heal spontaneously. Micro-computed tomography demonstrated no evidence for middle ear or otic capsule injuries; however, the healed tympanic membrane was thickened. Auditory brainstem response and distortion product otoacoustic emission threshold shifts were found to be correlated with blast intensity. As well, these threshold shifts were larger than those found in control mice that underwent surgical perforation of their tympanic membranes, indicating cochlear trauma. Histological studies one week and three months after the blast demonstrated no disruption or damage to the intra-cochlear membranes. However, there was loss of outer hair cells (OHCs) within the basal turn of the cochlea and decreased spiral ganglion neurons (SGNs) and afferent nerve synapses. Using our mouse model that recapitulates human IED exposure, our results identify that the mechanisms underlying blast-induced hearing loss does not include gross membranous rupture as is commonly believed. Instead, there is both OHC and SGN loss that produce auditory dysfunction. PMID:23840874
High-speed imaging and small-scale explosive characterization techniques to understand effects of primary blast-induced injury on nerve cell structure and function

NASA Astrophysics Data System (ADS)

Piehler, T.; Banton, R.; Zander, N.; Duckworth, J.; Benjamin, R.; Sparks, R.

2018-01-01

Traumatic brain injury (TBI) is often associated with blast exposure. Even in the absence of penetrating injury or evidence of tissue injury on imaging, blast TBI may trigger a series of neural/glial cellular and functional changes. Unfortunately, the diagnosis and proper treatment of mild traumatic brain injury (mTBI) caused by explosive blast is challenging, as it is not easy to clinically distinguish blast from non-blast TBI on the basis of patient symptoms. Damage to brain tissue, cell, and subcellular structures continues to occur slowly and in a manner undetectable by conventional imaging techniques. The threshold shock impulse levels required to induce damage and the cumulative effects upon multiple exposures are not well characterized. Understanding how functional and structural damage from realistic blast impact at cellular and tissue levels at variable timescales after mTBI events may be vital for understanding this injury phenomenon and for linking mechanically induced structural changes with measurable effects on the nervous system. Our working hypothesis is that there is some transient physiological dysfunction occurring at cellular and subcellular levels within the central nervous system due to primary blast exposure. We have developed a novel in vitro indoor experimental system that uses real military explosive charges to more accurately represent military blast exposure and to probe the effects of primary explosive blast on dissociated neurons. We believe this system offers a controlled experimental method to analyze and characterize primary explosive blast-induced cellular injury and to understand threshold injury phenomenon. This paper will also focus on the modeling aspect of our work and how it relates to the experimental work.
Economic and Environmental Impact of Rice Blast Pathogen (Magnaporthe oryzae) Alleviation in the United States.

PubMed

Nalley, Lawton; Tsiboe, Francis; Durand-Morat, Alvaro; Shew, Aaron; Thoma, Greg

2016-01-01

Rice blast (Magnaporthe oryzae) is a key concern in combating global food insecurity given the disease is responsible for approximately 30% of rice production losses globally-the equivalent of feeding 60 million people. These losses increase the global rice price and reduce consumer welfare and food security. Rice is the staple crop for more than half the world's population so any reduction in rice blast would have substantial beneficial effects on consumer livelihoods. In 2012, researchers in the US began analyzing the feasibility of creating blast-resistant rice through cisgenic breeding. Correspondingly, our study evaluates the changes in producer, consumer, and environmental welfare, if all the rice produced in the Mid-South of the US were blast resistant through a process like cisgenics, using both international trade and environmental assessment modeling. Our results show that US rice producers would gain 69.34 million dollars annually and increase the rice supply to feed an additional one million consumers globally by eliminating blast from production in the Mid-South. These results suggest that blast alleviation could be even more significant in increasing global food security given that the US is a small rice producer by global standards and likely experiences lower losses from blast than other rice-producing countries because of its ongoing investment in production technology and management. Furthermore, results from our detailed life cycle assessment (LCA) show that producing blast-resistant rice has lower environmental (fossil fuel depletion, ecotoxicity, carcinogenics, eutrophication, acidification, global warming potential, and ozone depletion) impacts per unit of rice than non-blast resistant rice production. Our findings suggest that any reduction in blast via breeding will have significantly positive impacts on reducing global food insecurity through increased supply, as well as decreased price and environmental impacts in production.
Ultrastructural brain abnormalities and associated behavioral changes in mice after low-intensity blast exposure.

PubMed

Song, Hailong; Konan, Landry M; Cui, Jiankun; Johnson, Catherine E; Langenderfer, Martin; Grant, DeAna; Ndam, Tina; Simonyi, Agnes; White, Tommi; Demirci, Utkan; Mott, David R; Schwer, Doug; Hubler, Graham K; Cernak, Ibolja; DePalma, Ralph G; Gu, Zezong

2018-07-16

Explosive blast-induced mild traumatic brain injury (mTBI), a "signature wound" of recent military conflicts, commonly affects service members. While past blast injury studies have provided insights into TBI with moderate- to high-intensity explosions, the impact of primary low-intensity blast (LIB)-mediated pathobiology on neurological deficits requires further investigation. Our prior considerations of blast physics predicted ultrastructural injuries at nanoscale levels. Here, we provide quantitative data using a primary LIB injury murine model exposed to open field detonation of 350 g of high-energy explosive C4. We quantified ultrastructural and behavioral changes up to 30 days post blast injury (DPI). The use of an open-field experimental blast generated a primary blast wave with a peak overpressure of 6.76 PSI (46.6 kPa) at a 3-m distance from the center of the explosion, a positive phase duration of approximate 3.0 milliseconds (ms), a maximal impulse of 8.7 PSI × ms and a sharp rising time of 9 × 10 -3  ms, with no apparent impact/acceleration in exposed animals. Neuropathologically, myelinated axonal damage was observed in blast-exposed groups at 7 DPI. Using transmission electron microscopy, we observed and quantified myelin sheath defects and mitochondrial abnormalities at 7 and 30 DPI. Inverse correlations between blast intensities and neurobehavioral outcomes including motor activities, anxiety levels, nesting behavior, spatial learning and memory occurred. These observations uncover unique ultrastructural brain abnormalities and associated behavioral changes due to primary blast injury and provide key insights into its pathogenesis and potential treatment. Copyright © 2018 Elsevier B.V. All rights reserved.
Neuronal Injury and Glial Changes Are Hallmarks of Open Field Blast Exposure in Swine Frontal Lobe

PubMed Central

Kallakuri, Srinivasu; Desai, Alok; Feng, Ke; Tummala, Sharvani; Saif, Tal; Chen, Chaoyang; Zhang, Liying; Cavanaugh, John M.; King, Albert I.

2017-01-01

With the rapid increase in the number of blast induced traumatic brain injuries and associated neuropsychological consequences in veterans returning from the operations in Iraq and Afghanistan, the need to better understand the neuropathological sequelae following exposure to an open field blast exposure is still critical. Although a large body of experimental studies have attempted to address these pathological changes using shock tube models of blast injury, studies directed at understanding changes in a gyrencephalic brain exposed to a true open field blast are limited and thus forms the focus of this study. Anesthetized, male Yucatan swine were subjected to forward facing medium blast overpressure (peak side on overpressure 224–332 kPa; n = 7) or high blast overpressure (peak side on overpressure 350–403 kPa; n = 5) by detonating 3.6 kg of composition-4 charge. Sham animals (n = 5) were subjected to all the conditions without blast exposure. After a 3-day survival period, the brain was harvested and sections from the frontal lobes were processed for histological assessment of neuronal injury and glial reactivity changes. Significant neuronal injury in the form of beta amyloid precursor protein immunoreactive zones in the gray and white matter was observed in the frontal lobe sections from both the blast exposure groups. A significant increase in the number of astrocytes and microglia was also observed in the blast exposed sections compared to sham sections. We postulate that the observed acute injury changes may progress to chronic periods after blast and may contribute to short and long-term neuronal degeneration and glial mediated inflammation. PMID:28107370
Economic and Environmental Impact of Rice Blast Pathogen (Magnaporthe oryzae) Alleviation in the United States

PubMed Central

2016-01-01

Rice blast (Magnaporthe oryzae) is a key concern in combating global food insecurity given the disease is responsible for approximately 30% of rice production losses globally—the equivalent of feeding 60 million people. These losses increase the global rice price and reduce consumer welfare and food security. Rice is the staple crop for more than half the world’s population so any reduction in rice blast would have substantial beneficial effects on consumer livelihoods. In 2012, researchers in the US began analyzing the feasibility of creating blast-resistant rice through cisgenic breeding. Correspondingly, our study evaluates the changes in producer, consumer, and environmental welfare, if all the rice produced in the Mid-South of the US were blast resistant through a process like cisgenics, using both international trade and environmental assessment modeling. Our results show that US rice producers would gain 69.34 million dollars annually and increase the rice supply to feed an additional one million consumers globally by eliminating blast from production in the Mid-South. These results suggest that blast alleviation could be even more significant in increasing global food security given that the US is a small rice producer by global standards and likely experiences lower losses from blast than other rice-producing countries because of its ongoing investment in production technology and management. Furthermore, results from our detailed life cycle assessment (LCA) show that producing blast-resistant rice has lower environmental (fossil fuel depletion, ecotoxicity, carcinogenics, eutrophication, acidification, global warming potential, and ozone depletion) impacts per unit of rice than non-blast resistant rice production. Our findings suggest that any reduction in blast via breeding will have significantly positive impacts on reducing global food insecurity through increased supply, as well as decreased price and environmental impacts in production. PMID:27907101
Experimental investigation of blast mitigation and particle-blast interaction during the explosive dispersal of particles and liquids

NASA Astrophysics Data System (ADS)

Pontalier, Q.; Loiseau, J.; Goroshin, S.; Frost, D. L.

2018-04-01

The attenuation of a blast wave from a high-explosive charge surrounded by a layer of inert material is investigated experimentally in a spherical geometry for a wide range of materials. The blast wave pressure is inferred from extracting the blast wave velocity with high-speed video as well as direct measurements with pressure transducers. The mitigant consists of either a packed bed of particles, a particle bed saturated with water, or a homogeneous liquid. The reduction in peak blast wave overpressure is primarily dependent on the mitigant to explosive mass ratio, M/C, with the mitigant material properties playing a secondary role. Relative peak pressure mitigation reduces with distance and for low values of M/C (< 10) can return to unmitigated pressure levels in the mid-to-far field. Solid particles are more effective at mitigating the blast overpressure than liquids, particularly in the near field and at low values of M/C, suggesting that the energy dissipation during compaction, deformation, and fracture of the powders plays an important role. The difference in scaled arrival time of the blast and material fronts increases with M/C and scaled distance, with solid particles giving the largest separation between the blast wave and cloud of particles. Surrounding a high-explosive charge with a layer of particles reduces the positive-phase blast impulse, whereas a liquid layer has no influence on the impulse in the far field. Taking the total impulse due to the blast wave and material impact into account implies that the damage to a nearby structure may actually be augmented for a range of distances. These results should be taken into consideration in the design of explosive mitigant systems.
Relationship between changes in the cochlear blood flow and disorder of hearing function induced by blast injury in guinea pigs.

PubMed

Chen, Wei; Wang, Jianmin; Chen, Jing; Chen, Jichuan; Chen, Zhiqiang

2013-01-01

The auditory system is the most susceptible to damages from blast waves. Blast injuries always lead to varying degrees of hearing impairment. Although a disorder of the cochlear blood flow (CoBF) has been considered to be related to many pathological processes of the auditory system and to contribute to various types of hearing loss, changes in the CoBF induced by blast waves and the relationship between such changes and hearing impairment are undefined. To observe the changes in the cochlear microcirculation after exposure to an explosion blast, investigate the relationship between changes in the CoBF and hearing impairment and subsequently explore the mechanism responsible for the changes in the CoBF, we detected the perfusion of the cochlear microcirculation and hearing threshold shift after exposure to an explosion blast. Then, an N-nitro-L-arginine-methyl ester (L-NAME, NO synthase inhibitor) solution and artificial perilymph were applied to the round window (RW) of the cochlea before the blast exposure, followed by an evaluation of the CoBF and hearing function. The results indicated that the changes in the CoBF were correlated to the strength of the blast wave. The cochlear blood flow significantly increased when the peak value of the blast overpressure was greater than approximately 45 kPa, and there was no significant change in the cochlear blood flow when the peak value of the blast overpressure was less than approximately 35 kPa. Following local administration of the NO synthase inhibitor L-NAME, the increase in the CoBF induced by the blast was inhibited, and this reduction was significantly associated with the hearing threshold.
Experimental investigation of blast mitigation and particle-blast interaction during the explosive dispersal of particles and liquids

NASA Astrophysics Data System (ADS)

Pontalier, Q.; Loiseau, J.; Goroshin, S.; Frost, D. L.

2018-05-01

The attenuation of a blast wave from a high-explosive charge surrounded by a layer of inert material is investigated experimentally in a spherical geometry for a wide range of materials. The blast wave pressure is inferred from extracting the blast wave velocity with high-speed video as well as direct measurements with pressure transducers. The mitigant consists of either a packed bed of particles, a particle bed saturated with water, or a homogeneous liquid. The reduction in peak blast wave overpressure is primarily dependent on the mitigant to explosive mass ratio, M/ C, with the mitigant material properties playing a secondary role. Relative peak pressure mitigation reduces with distance and for low values of M/ C (< 10) can return to unmitigated pressure levels in the mid-to-far field. Solid particles are more effective at mitigating the blast overpressure than liquids, particularly in the near field and at low values of M/ C, suggesting that the energy dissipation during compaction, deformation, and fracture of the powders plays an important role. The difference in scaled arrival time of the blast and material fronts increases with M/ C and scaled distance, with solid particles giving the largest separation between the blast wave and cloud of particles. Surrounding a high-explosive charge with a layer of particles reduces the positive-phase blast impulse, whereas a liquid layer has no influence on the impulse in the far field. Taking the total impulse due to the blast wave and material impact into account implies that the damage to a nearby structure may actually be augmented for a range of distances. These results should be taken into consideration in the design of explosive mitigant systems.
Blasting Damage Predictions by Numerical Modeling in Siahbishe Pumped Storage Powerhouse

NASA Astrophysics Data System (ADS)

Eslami, Majid; Goshtasbi, Kamran

2018-04-01

One of the popular methods of underground and surface excavations is the use of blasting. Throughout this method of excavation, the loading resulted from blasting can be affected by different geo-mechanical and structural parameters of rock mass. Several factors affect turbulence in underground structures some of which are explosion, vibration, and stress impulses caused by the neighbouring blasting products. In investigating the blasting mechanism one should address the processes which expand with time and cause seismic events. To protect the adjoining structures against any probable deconstruction or damage, it is very important to model the blasting process prior to any actual operation. Efforts have been taken in the present study to demonstrate the potentiality of numerical methods in predicting the specified parameters in order to prevent any probable destruction. For this purpose the blasting process was modeled, according to its natural implementation, in one of the tunnels of Siahbishe dam by the 3DEC and AUTODYN 3D codes. 3DEC was used for modeling the blasting environment as well as the blast holes and AUTODYN 3D for modeling the explosion process in the blast hole. In this process the output of AUTODYN 3D, which is a result of modeling the blast hole and is in the form of stress waves, is entered into 3DEC. For analyzing the amount of destruction made by the blasting operation, the key parameter of Peak Particle Velocity was used. In the end, the numerical modeling results have been compared with the data recorded by the seismographs planted through the tunnel. As the results indicated 3DEC and AUTODYN 3D proved appropriate for analyzing such an issue. Therefore, by means of these two softwares one can analyze explosion processes prior to their implementation and make close estimation of the damage resulting from these processes.
WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.
WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410
Military blast exposure, ageing and white matter integrity

PubMed Central

Trotter, Benjamin B.; Robinson, Meghan E.; Milberg, William P.; McGlinchey, Regina E.

2015-01-01

Mild traumatic brain injury, or concussion, is associated with a range of neural changes including altered white matter structure. There is emerging evidence that blast exposure—one of the most pervasive causes of casualties in the recent overseas conflicts in Iraq and Afghanistan—is accompanied by a range of neurobiological events that may result in pathological changes to brain structure and function that occur independently of overt concussion symptoms. The potential effects of brain injury due to blast exposure are of great concern as a history of mild traumatic brain injury has been identified as a risk factor for age-associated neurodegenerative disease. The present study used diffusion tensor imaging to investigate whether military-associated blast exposure influences the association between age and white matter tissue structure integrity in a large sample of veterans of the recent conflicts (n = 190 blast-exposed; 59 without exposure) between the ages of 19 and 62 years. Tract-based spatial statistics revealed a significant blast exposure × age interaction on diffusion parameters with blast-exposed individuals exhibiting a more rapid cross-sectional age trajectory towards reduced tissue integrity. Both distinct and overlapping voxel clusters demonstrating the interaction were observed among the examined diffusion contrast measures (e.g. fractional anisotropy and radial diffusivity). The regions showing the effect on fractional anisotropy included voxels both within and beyond the boundaries of the regions exhibiting a significant negative association between fractional anisotropy and age in the entire cohort. The regional effect was sensitive to the degree of blast exposure, suggesting a ‘dose-response’ relationship between the number of blast exposures and white matter integrity. Additionally, there was an age-independent negative association between fractional anisotropy and years since most severe blast exposure in a subset of the blast-exposed group, suggesting a specific influence of time since exposure on tissue structure, and this effect was also independent of post-traumatic stress symptoms. Overall, these data suggest that blast exposure may negatively affect brain-ageing trajectories at the microstructural tissue level. Additional work examining longitudinal changes in brain tissue integrity in individuals exposed to military blast forces will be an important future direction to the initial findings presented here. PMID:26033970
Comparative Genomics and Association Mapping Approaches for Blast Resistant Genes in Finger Millet Using SSRs

PubMed Central

Babu, B. Kalyana; Dinesh, Pandey; Agrawal, Pawan K.; Sood, S.; Chandrashekara, C.; Bhatt, Jagadish C.; Kumar, Anil

2014-01-01

The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R2) of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R2. The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R2. Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars. PMID:24915067
Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs.

PubMed

Babu, B Kalyana; Dinesh, Pandey; Agrawal, Pawan K; Sood, S; Chandrashekara, C; Bhatt, Jagadish C; Kumar, Anil

2014-01-01

The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R²) of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R². The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R². Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars.
Low Level Primary Blast Injury in Rodent Brain

PubMed Central

Pun, Pamela B. L.; Kan, Enci Mary; Salim, Agus; Li, Zhaohui; Ng, Kian Chye; Moochhala, Shabbir M.; Ling, Eng-Ang; Tan, Mui Hong; Lu, Jia

2011-01-01

The incidence of blast attacks and resulting traumatic brain injuries has been on the rise in recent years. Primary blast is one of the mechanisms in which the blast wave can cause injury to the brain. The aim of this study was to investigate the effects of a single sub-lethal blast over pressure (BOP) exposure of either 48.9 kPa (7.1 psi) or 77.3 kPa (11.3 psi) to rodents in an open-field setting. Brain tissue from these rats was harvested for microarray and histopathological analyses. Gross histopathology of the brains showed that cortical neurons were “darkened” and shrunken with narrowed vasculature in the cerebral cortex day 1 after blast with signs of recovery at day 4 and day 7 after blast. TUNEL-positive cells were predominant in the white matter of the brain at day 1 after blast and double-labeling of brain tissue showed that these DNA-damaged cells were both oligodendrocytes and astrocytes but were mainly not apoptotic due to the low caspase-3 immunopositivity. There was also an increase in amyloid precursor protein immunoreactive cells in the white matter which suggests acute axonal damage. In contrast, Iba-1 staining for macrophages or microglia was not different from control post-blast. Blast exposure altered the expression of over 5786 genes in the brain which occurred mostly at day 1 and day 4 post-blast. These genes were narrowed down to 10 overlapping genes after time-course evaluation and functional analyses. These genes pointed toward signs of repair at day 4 and day 7 post-blast. Our findings suggest that the BOP levels in the study resulted in mild cellular injury to the brain as evidenced by acute neuronal, cerebrovascular, and white matter perturbations that showed signs of resolution. It is unclear whether these perturbations exist at a milder level or normalize completely and will need more investigation. Specific changes in gene expression may be further evaluated to understand the mechanism of blast-induced neurotrauma. PMID:21541261

Side scatter versus CD45 flow cytometric plot can distinguish acute leukaemia subtypes.

PubMed

Saksena, Annapurna; Gautam, Parul; Desai, Parth; Gupta, Naresh; Dubey, A P; Singh, Tejinder

2016-05-01

Flow cytometry is an important tool to diagnose acute leukaemia. Attempts are being made to find the minimal number of antibodies for correctly diagnosing acute leukaemia subtypes. The present study was designed to evaluate the analysis of side scatter (SSC) versus CD45 flow dot plot to distinguish acute myeloid leukaemia (AML) from acute lymphoblastic leukaemia (ALL), with minimal immunological markers. One hundred consecutive cases of acute leukaemia were evaluated for blast cluster on SSC versus CD45 plots. The parameters studied included visual shape, CD45 and side scatter expression, continuity with residual granulocytes/lymphocytes/monocytes and ratio of maximum width to maximum height (w/h). The final diagnosis of ALL and AML and their subtypes was made by morphology, cytochemistry and immunophenotyping. Two sample Wilcoxon rank-sum (Mann Whitney) test and Kruskal-Wallis equality-of-populations rank tests were applied to elucidate the significance of the above ratios of blast cluster for diagnosis of ALL, AML and their subtypes. Receiver operating characteristic (ROC) curves were generated and the optimal cut-offs of the w/h ratio to distinguish between ALL and AML determined. Of the 100 cases, 57 of ALL and 43 cases of AML were diagnosed. The median w/h ratio of blast population was 3.8 for ALL and 1 for AML (P<0.001). ROC had area under curve of 0.9772.The optimal cut-off of the w/h ratio for distinction of ALL from AML was found to be 1.6. Our findings suggest that if w/h ratio on SSC versus CD45 plot is less than 1.6, AML may be considered, and if it is more than 1.6, ALL may be diagnosed. Using morphometric analysis of the blast cluster on SSC versus CD45, it was possible to distinguish between ALL and AML, and their subtypes.
Advancing Research in Second Language Writing through Computational Tools and Machine Learning Techniques: A Research Agenda

ERIC Educational Resources Information Center

Crossley, Scott A.

2013-01-01

This paper provides an agenda for replication studies focusing on second language (L2) writing and the use of natural language processing (NLP) tools and machine learning algorithms. Specifically, it introduces a range of the available NLP tools and machine learning algorithms and demonstrates how these could be used to replicate seminal studies…
A Parametric Approach to Shape Field-Relevant Blast Wave Profiles in Compressed-Gas-Driven Shock Tube

PubMed Central

Sundaramurthy, Aravind; Chandra, Namas

2014-01-01

Detonation of a high-explosive produces shock-blast wave, shrapnel, and gaseous products. While direct exposure to blast is a concern near the epicenter, shock-blast can affect subjects, even at farther distances. When a pure shock-blast wave encounters the subject, in the absence of shrapnels, fall, or gaseous products the loading is termed as primary blast loading and is the subject of this paper. The wave profile is characterized by blast overpressure, positive time duration, and impulse and called herein as shock-blast wave parameters (SWPs). These parameters in turn are uniquely determined by the strength of high explosive and the distance of the human subjects from the epicenter. The shape and magnitude of the profile determine the severity of injury to the subjects. As shown in some of our recent works (1–3), the profile not only determines the survival of the subjects (e.g., animals) but also the acute and chronic biomechanical injuries along with the following bio-chemical sequelae. It is extremely important to carefully design and operate the shock tube to produce field-relevant SWPs. Furthermore, it is vital to identify and eliminate the artifacts that are inadvertently introduced in the shock-blast profile that may affect the results. In this work, we examine the relationship between shock tube adjustable parameters (SAPs) and SWPs that can be used to control the blast profile; the results can be easily applied to many of the laboratory shock tubes. Further, replication of shock profile (magnitude and shape) can be related to field explosions and can be a standard in comparing results across different laboratories. Forty experiments are carried out by judiciously varying SAPs such as membrane thickness, breech length (66.68–1209.68 mm), measurement location, and type of driver gas (nitrogen, helium). The effects SAPs have on the resulting shock-blast profiles are shown. Also, the shock-blast profiles of a TNT explosion from ConWep software is compared with the profiles obtained from the shock tube. To conclude, our experimental results demonstrate that a compressed-gas shock tube when designed and operated carefully can replicate the blast time profiles of field explosions accurately. Such a faithful replication is an essential first step when studying the effects of blast induced neurotrauma using animal models. PMID:25520701
Nuclear Power System Architecture and Safety Study- Feasibility of Launch Pad Explosion Simulation using Radios

NASA Astrophysics Data System (ADS)

Destefanis, Stefano; Tracino, Emanuele; Giraudo, Martina

2014-06-01

During a mission involving a spacecraft using nuclear power sources (NPS), the consequences to the population induced by an accident has to be taken into account carefully.Part of the study (led by AREVA, with TAS-I as one of the involved parties) was devoted to "Worst Case Scenario Consolidation". In particular, one of the activities carried out by TAS-I had the aim of characterizing the accidental environment (explosion on launch pad or during launch) and consolidate the requirements given as input in the study. The resulting requirements became inputs for Nuclear Power Source container design.To do so, TAS-I did first an overview of the available technical literature (mostly developed in the frame of NASA Mercury / Apollo program), to identify the key parameters to be used for analytical assessment (blast pressure wave, fragments size, speed and distribution, TNT equivalent of liquid propellant).Then, a simplified Radioss model was setup, to verify both the cards needed for blast / fragment impact analysis and the consistency between preliminary results and available technical literature (Radioss is commonly used to design mine - resistant vehicles, by simulating the effect of blasts onto structural elements, and it is used in TAS-I for several types of analysis, including land impact, water impact and fluid - structure interaction).The obtained results (albeit produced by a very simplified model) are encouraging, showing that the analytical tool and the selected key parameters represent a step in the right direction.
A mobile phone based tool to identify symptoms of common childhood diseases in Ghana: development and evaluation of the integrated clinical algorithm in a cross-sectional study.

PubMed

Franke, Konstantin H; Krumkamp, Ralf; Mohammed, Aliyu; Sarpong, Nimako; Owusu-Dabo, Ellis; Brinkel, Johanna; Fobil, Julius N; Marinovic, Axel Bonacic; Asihene, Philip; Boots, Mark; May, Jürgen; Kreuels, Benno

2018-03-27

The aim of this study was the development and evaluation of an algorithm-based diagnosis-tool, applicable on mobile phones, to support guardians in providing appropriate care to sick children. The algorithm was developed on the basis of the Integrated Management of Childhood Illness (IMCI) guidelines and evaluated at a hospital in Ghana. Two hundred and thirty-seven guardians applied the tool to assess their child's symptoms. Data recorded by the tool and health records completed by a physician were compared in terms of symptom detection, disease assessment and treatment recommendation. To compare both assessments, Kappa statistics and predictive values were calculated. The tool detected the symptoms of cough, fever, diarrhoea and vomiting with good agreement to the physicians' findings (kappa = 0.64; 0.59; 0.57 and 0.42 respectively). The disease assessment barely coincided with the physicians' findings. The tool's treatment recommendation correlated with the physicians' assessments in 93 out of 237 cases (39.2% agreement, kappa = 0.11), but underestimated a child's condition in only seven cases (3.0%). The algorithm-based tool achieved reliable symptom detection and treatment recommendations were administered conformably to the physicians' assessment. Testing in domestic environment is envisaged.
Prospectively assessed clinical outcomes in concussive blast vs nonblast traumatic brain injury among evacuated US military personnel.

PubMed

Mac Donald, Christine L; Johnson, Ann M; Wierzechowski, Linda; Kassner, Elizabeth; Stewart, Theresa; Nelson, Elliot C; Werner, Nicole J; Zonies, David; Oh, John; Fang, Raymond; Brody, David L

2014-08-01

Blast injury has been identified as the signature injury in the conflicts in Iraq and Afghanistan. However it remains to be determined whether fundamental differences may exist between blast-related traumatic brain injury (TBI) and TBI due to other mechanisms. To determine similarities and differences between clinical outcomes in US military personnel with blast-related vs. non-blast-related concussive TBI and to identify the specific domains of impairment that best correlate with overall disability. Prospective cohort study involving active duty US Military personnel evacuated from Iraq or Afghanistan to Landstuhl Regional Medical Center, in Landstuhl, Germany. Four groups of participants were enrolled from 2010 to 2013: (1) blast plus impact complex TBI (n=53), (2) non-blast related TBI with injury due to other mechanisms (n=29), (3) blast-exposed controls evacuated for other medical reasons (n=27) (4) non-blast-exposed controls evacuated for other medical reasons (n=69). All patients with TBI met Department of Defense criteria for concussive (mild) TBI. The study participants were evaluated 6-12 months after injury at Washington University in St Louis. In total, 255 subjects were enrolled in the study, and 183 participated in follow-up evaluations, 5 of whom were disqualified. In-person clinical examinations included evaluation for overall disability, a standardized neurological exam, headache questionnaires, neuropsychological test battery, combat exposure and alcohol use surveys, and structured interview evaluations for post-traumatic stress disorder (PTSD) and depression. Global outcomes, headache severity, neuropsychological performance, and surprisingly even PTSD severity and depression were indistinguishable between the two TBI groups, independent of mechanism of injury. Both TBI groups had higher rates of moderate to severe overall disability than the respective control groups: 41/53 (77%) of blast plus impact TBI and 23/29 (79%) of nonblast TBI vs. 16/27 (59%) of blast-exposed controls and 28/69 (41%) of non-blast-exposed controls. In addition, blast-exposed controls had worse headaches and more severe PTSD than non-blast-exposed controls. Self-reported combat exposure intensity was higher in the blast plus impact TBI group than in nonblast TBI group and was higher in blast-exposed controls than in non-blast-exposed controls. However, combat exposure intensity did not correlate with PTSD severity in the TBI groups, but a modest positive correlation was observed in the controls. Overall outcomes were most strongly correlated with depression, headache severity, and number of abnormalities on neuropsychological testing. However a substantial fraction of the variance in overall outcome was not explained by any of the assessed measures. One potential interpretation of these results is that TBI itself, independent of injury mechanism and combat exposure intensity, is a primary driver of adverse outcomes. Many other important factors may be as yet unmeasured, and adverse outcomes following war-time injuries are difficult to fully explain. clinicaltrials.gov Identifier: NCT01313130.
Experiences on developing digital down conversion algorithms using Xilinx system generator

NASA Astrophysics Data System (ADS)

Xu, Chengfa; Yuan, Yuan; Zhao, Lizhi

2013-07-01

The Digital Down Conversion (DDC) algorithm is a classical signal processing method which is widely used in radar and communication systems. In this paper, the DDC function is implemented by Xilinx System Generator tool on FPGA. System Generator is an FPGA design tool provided by Xilinx Inc and MathWorks Inc. It is very convenient for programmers to manipulate the design and debug the function, especially for the complex algorithm. Through the developing process of DDC function based on System Generator, the results show that System Generator is a very fast and efficient tool for FPGA design.
Software Management Environment (SME): Components and algorithms

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1994-01-01

This document presents the components and algorithms of the Software Management Environment (SME), a management tool developed for the Software Engineering Branch (Code 552) of the Flight Dynamics Division (FDD) of the Goddard Space Flight Center (GSFC). The SME provides an integrated set of visually oriented experienced-based tools that can assist software development managers in managing and planning software development projects. This document describes and illustrates the analysis functions that underlie the SME's project monitoring, estimation, and planning tools. 'SME Components and Algorithms' is a companion reference to 'SME Concepts and Architecture' and 'Software Engineering Laboratory (SEL) Relationships, Models, and Management Rules.'
Measuring Intracranial Pressure and Correlation with Severity of Blast Traumatic Brain Injury

DTIC Science & Technology

2011-10-01

cannula was then filled with a sterile saline solution. The cannula cap was filled with petroleum jelly and a fiber optic pressure sensor (FOP-MIV, FISO...petroleum jelly and the fiber optic pressure sensor (FOP-MIV, Fiso Inc.) was inserted into the cannula and threaded onto the cannula pedestal. Figure 1b...neurological consequences of explosives. J. Neurol. Sci. 249:63–67, 2006. 9Henshall, B. Shock tube–versatile tool of aerodynamic research. J. Royal
The Effectiveness of Power Tool Cleaning as an Alternative to Abrasive Blasting

DTIC Science & Technology

1995-06-01

Lamar Avenue Houston, TX 77251 3M Building Service and Cleaning Products Division Building 223-65-03 St. Paul, MN 55144-1000 Marindus Company P. O...Mill Scale Removal with 3M Brand Heavy Duty RotoPeen Flap Wheel”;”Scotch-Brite” Surface Conditioning Products, 3M Building Service and Cleaning ... Products Division. 18. “The Dilemma of Removing Lead-Based Paint,” January 1988, p. 34-35. Specifications: ASTM TEST METHODS: B1 17, Salt Spray (Fog
Interfacing Computer-Assisted Drafting and Design with the Building Loads Analysis and System Thermodynamics (BLAST) Program

DTIC Science & Technology

1992-10-01

Manual CI APPENDIX D: Drawing Navigator Field Test D1 DISTRIBUTION Accesion For NTIS CRA&I OTIC TAB Unannouncea JustiteCdtOn By Distribution I "".i•I...methods replace manual methods, the automation will handle the data for the designer, thus reducing error and increasing throughput. However, the two...actively move data from one automation tool (CADD) to the other (the analysis program). This intervention involves a manual rekeying of data already in
Catalog of Existing Small Tools for Surface Preparation and Support Equipment for Blasters and Painters

DTIC Science & Technology

1977-05-01

128 lbs./ft3 Specific Gravity 3.6 Hardness (MOHS) 7 Melting Point 2900°F. Coefficient of Expansion 7 . 8 X 1 0– 6 FIGURE 3.17: Properties of...Beaumont, Texas Bethlehem Steel Corporation, San Francisco, California Bethlehem Steel Corporation, Sparrows Point , Maryland Jacksonville Shipyards...checklist can be used by operators and super- visors as a starting point for determining if the yard’s abrasive blasting facility is operating at full
Computational Modeling of Causal Mechanisms of Blast Wave Induced Traumatic Brain Injury - A Potential Tool for Injury Prevention

DTIC Science & Technology

2009-10-01

detonation and expansion of the TNT explosive materials was described using the JWL (Jones-Wilkins-Lee) equation of state (EOS) along with a high...explosive material definition (Dobratz 1981). The JWL equation is described as: Where V= ρ0 (initial density of an explosive)/ρ (density of detonation...gas). E is specific internal energy. A, B, R1, R2, ω are JWL fitting parameters (Table 2). ρ0 Detonation velocity CJ pressure Material
The practical evaluation of DNA barcode efficacy.

PubMed

Spouge, John L; Mariño-Ramírez, Leonardo

2012-01-01

This chapter describes a workflow for measuring the efficacy of a barcode in identifying species. First, assemble individual sequence databases corresponding to each barcode marker. A controlled collection of taxonomic data is preferable to GenBank data, because GenBank data can be problematic, particularly when comparing barcodes based on more than one marker. To ensure proper controls when evaluating species identification, specimens not having a sequence in every marker database should be discarded. Second, select a computer algorithm for assigning species to barcode sequences. No algorithm has yet improved notably on assigning a specimen to the species of its nearest neighbor within a barcode database. Because global sequence alignments (e.g., with the Needleman-Wunsch algorithm, or some related algorithm) examine entire barcode sequences, they generally produce better species assignments than local sequence alignments (e.g., with BLAST). No neighboring method (e.g., global sequence similarity, global sequence distance, or evolutionary distance based on a global alignment) has yet shown a notable superiority in identifying species. Finally, "the probability of correct identification" (PCI) provides an appropriate measurement of barcode efficacy. The overall PCI for a data set is the average of the species PCIs, taken over all species in the data set. This chapter states explicitly how to calculate PCI, how to estimate its statistical sampling error, and how to use data on PCR failure to set limits on how much improvements in PCR technology can improve species identification.
30 CFR 57.22605 - Blasting from the surface (V-A mines).

Code of Federal Regulations, 2013 CFR

2013-07-01

... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...
30 CFR 57.22605 - Blasting from the surface (V-A mines).

Code of Federal Regulations, 2014 CFR

2014-07-01

... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...
30 CFR 57.22605 - Blasting from the surface (V-A mines).

Code of Federal Regulations, 2012 CFR

2012-07-01

... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...
30 CFR 57.22605 - Blasting from the surface (V-A mines).

Code of Federal Regulations, 2010 CFR

2010-07-01

... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...
30 CFR 57.22605 - Blasting from the surface (V-A mines).

Code of Federal Regulations, 2011 CFR

2011-07-01

... Standards for Methane in Metal and Nonmetal Mines Explosives § 57.22605 Blasting from the surface (V-A mines). (a) All development and production blasting shall be initiated from the surface after all persons are... methane in the mine is less than 1.0 percent, persons may enter the mine, and all places blasted shall be...
Survey of rice blast race identity for blast resistance gene identification in the USA and Puerto Rico

USDA-ARS?s Scientific Manuscript database

Rice blast disease is a significant threat to stable rice production in the USA and worldwide. The major resistance gene (Pi-ta) located within a cluster of resistance genes on rice chromosome 12 has been demonstrated to confer resistance to the rice blast disease. Katy, a rice cultivar released in ...

Cerebrovascular Injury in Blast Loading

DTIC Science & Technology

2010-01-01

TITLE: Cerebrovascular injury in blast loading PRINCIPAL INVESTIGATOR: Kenneth L. Monson, PhD...SUBTITLE Cerebrovascular injury in blast loading 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-08-1-0295 5c. PROGRAM ELEMENT NUMBER 6...and pH control. 15. SUBJECT TERMS Blast brain injury; cerebrovascular injury and dysfunction; shock tube 16. SECURITY CLASSIFICATION OF: 17
Comment on "chronic traumatic encephalopathy in blast-exposed military veterans and a blast neurotrauma mouse model".

PubMed

Tisdall, Martin; Petzold, Axel

2012-10-24

In a case study, the authors report an increase in phosphorylated neurofilament heavy chain, a marker of neuroaxonal damage, in the plasma of a blast-exposed patient immediately after injury. They suggest that this phosphoprotein may be a useful body fluid indicator of acute blast traumatic brain injury.
[Indirect blast rupture of the pancreas with a primary unperforated blast injury of the duodenum].

PubMed

Ignjatović, Dragan; Ignjatović, Mile; Jevtić, Miodrag

2006-02-01

To present a patient with an indirect blast rupture of the head of pancreas, as well as with a blast contusion of the duodenum following abdominal gunshot injury. A patient with the abdominal gunshot injury was submitted to the management of the injury of the liver, gaster and the right kidney in the field hospital. The revealed rupture of the head of the pancreas and the contusion of the duodenum were managed applying the method of Whipple. Indirect blast injuries require extensive surgical interventions, especially under war conditions.
A Comparative Study of Interval Management Control Law Capabilities

NASA Technical Reports Server (NTRS)

Barmore, Bryan E.; Smith, Colin L.; Palmer, Susan O.; Abbott, Terence S.

2012-01-01

This paper presents a new tool designed to allow for rapid development and testing of different control algorithms for airborne spacing. This tool, Interval Management Modeling and Spacing Tool (IM MAST), is a fast-time, low-fidelity tool created to model the approach of aircraft to a runway, with a focus on their interactions with each other. Errors can be induced between pairs of aircraft by varying initial positions, winds, speed profiles, and altitude profiles. Results to-date show that only a few of the algorithms tested had poor behavior in the arrival and approach environment. The majority of the algorithms showed only minimal variation in performance under the test conditions. Trajectory-based algorithms showed high susceptibility to wind forecast errors, while performing marginally better than the other algorithms under other conditions. Trajectory-based algorithms have a sizable advantage, however, of being able to perform relative spacing operations between aircraft on different arrival routes and flight profiles without employing ghosting. methods. This comes at the higher cost of substantially increased complexity, however. Additionally, it was shown that earlier initiation of relative spacing operations provided more time for corrections to be made without any significant problems in the spacing operation itself. Initiating spacing farther out, however, would require more of the aircraft to begin spacing before they merge onto a common route.
Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Mavrommatis, Kostas

2017-12-22

DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.
Use of a quality improvement tool, the prioritization matrix, to identify and prioritize triage software algorithm enhancement.

PubMed

North, Frederick; Varkey, Prathiba; Caraballo, Pedro; Vsetecka, Darlene; Bartel, Greg

2007-10-11

Complex decision support software can require significant effort in maintenance and enhancement. A quality improvement tool, the prioritization matrix, was successfully used to guide software enhancement of algorithms in a symptom assessment call center.
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition

PubMed Central

Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Stafford, William Noble; Leslie, Christina

2007-01-01

Background Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, called string kernels, for use with support vector machine (SVM) classifiers. However, while some of these approaches exhibit state-of-the-art performance at the binary protein classification problem, i.e. discriminating between a particular protein class and all other classes, few of these studies have addressed the real problem of multi-class superfamily or fold recognition. Moreover, there are only limited software tools and systems for SVM-based protein classification available to the bioinformatics community. Results We present a new multi-class SVM-based protein fold and superfamily recognition system and web server called SVM-Fold, which can be found at . Our system uses an efficient implementation of a state-of-the-art string kernel for sequence profiles, called the profile kernel, where the underlying feature representation is a histogram of inexact matching k-mer frequencies. We also employ a novel machine learning approach to solve the difficult multi-class problem of classifying a sequence of amino acids into one of many known protein structural classes. Binary one-vs-the-rest SVM classifiers that are trained to recognize individual structural classes yield prediction scores that are not comparable, so that standard "one-vs-all" classification fails to perform well. Moreover, SVMs for classes at different levels of the protein structural hierarchy may make useful predictions, but one-vs-all does not try to combine these multiple predictions. To deal with these problems, our method learns relative weights between one-vs-the-rest classifiers and encodes information about the protein structural hierarchy for multi-class prediction. In large-scale benchmark results based on the SCOP database, our code weighting approach significantly improves on the standard one-vs-all method for both the superfamily and fold prediction in the remote homology setting and on the fold recognition problem. Moreover, our code weight learning algorithm strongly outperforms nearest-neighbor methods based on PSI-BLAST in terms of prediction accuracy on every structure classification problem we consider. Conclusion By combining state-of-the-art SVM kernel methods with a novel multi-class algorithm, the SVM-Fold system delivers efficient and accurate protein fold and superfamily recognition. PMID:17570145
Blast shock wave mitigation using the hydraulic energy redirection and release technology.

PubMed

Chen, Yun; Huang, Wei; Constantini, Shlomi

2012-01-01

A hydraulic energy redirection and release technology has been developed for mitigating the effects of blast shock waves on protected objects. The technology employs a liquid-filled plastic tubing as a blast overpressure transformer to transfer kinetic energy of blast shock waves into hydraulic energy in the plastic tubings. The hydraulic energy is redirected through the plastic tubings to the openings at the lower ends, and then is quickly released with the liquid flowing out through the openings. The samples of the specifically designed body armor in which the liquid-filled plastic tubings were installed vertically as the outer layer of the body armor were tested. The blast test results demonstrated that blast overpressure behind the body armor samples was remarkably reduced by 97% in 0.2 msec after the liquid flowed out of its appropriate volume through the openings. The results also suggested that a volumetric liquid surge might be created when kinetic energy of blast shock wave was transferred into hydraulic energy to cause a rapid physical movement or displacement of the liquid. The volumetric liquid surge has a strong destructive power, and can cause a noncontact, remote injury in humans (such as blast-induced traumatic brain injury and post-traumatic stress disorder) if it is created in cardiovascular system. The hydraulic energy redirection and release technology can successfully mitigate blast shock waves from the outer surface of the body armor. It should be further explored as an innovative approach to effectively protect against blast threats to civilian and military personnel.
Blast Shock Wave Mitigation Using the Hydraulic Energy Redirection and Release Technology

PubMed Central

Chen, Yun; Huang, Wei; Constantini, Shlomi

2012-01-01

A hydraulic energy redirection and release technology has been developed for mitigating the effects of blast shock waves on protected objects. The technology employs a liquid-filled plastic tubing as a blast overpressure transformer to transfer kinetic energy of blast shock waves into hydraulic energy in the plastic tubings. The hydraulic energy is redirected through the plastic tubings to the openings at the lower ends, and then is quickly released with the liquid flowing out through the openings. The samples of the specifically designed body armor in which the liquid-filled plastic tubings were installed vertically as the outer layer of the body armor were tested. The blast test results demonstrated that blast overpressure behind the body armor samples was remarkably reduced by 97% in 0.2 msec after the liquid flowed out of its appropriate volume through the openings. The results also suggested that a volumetric liquid surge might be created when kinetic energy of blast shock wave was transferred into hydraulic energy to cause a rapid physical movement or displacement of the liquid. The volumetric liquid surge has a strong destructive power, and can cause a noncontact, remote injury in humans (such as blast-induced traumatic brain injury and post-traumatic stress disorder) if it is created in cardiovascular system. The hydraulic energy redirection and release technology can successfully mitigate blast shock waves from the outer surface of the body armor. It should be further explored as an innovative approach to effectively protect against blast threats to civilian and military personnel. PMID:22745740
Retinal Ganglion Cell Damage in an Experimental Rodent Model of Blast-Mediated Traumatic Brain Injury

PubMed Central

Mohan, Kabhilan; Kecova, Helga; Hernandez-Merino, Elena; Kardon, Randy H.; Harper, Matthew M.

2013-01-01

Purpose. To evaluate retina and optic nerve damage following experimental blast injury. Methods. Healthy adult mice were exposed to an overpressure blast wave using a custom-built blast chamber. The effects of blast exposure on retina and optic nerve function and structure were evaluated using the pattern electroretinogram (pERG), spectral domain optical coherence tomography (OCT), and the chromatic pupil light reflex. Results. Assessment of the pupil response to light demonstrated decreased maximum pupil constriction diameter in blast-injured mice using red light or blue light stimuli 24 hours after injury compared with baseline in the eye exposed to direct blast injury. A decrease in the pupil light reflex was not observed chronically following blast exposure. We observed a biphasic pERG decrease with the acute injury recovering by 24 hours postblast and the chronic injury appearing at 4 months postblast injury. Furthermore, at 3 months following injury, a significant decrease in the retinal nerve fiber layer was observed using OCT compared with controls. Histologic analysis of the retina and optic nerve revealed punctate regions of reduced cellularity in the ganglion cell layer and damage to optic nerves. Additionally, a significant upregulation of proteins associated with oxidative stress was observed acutely following blast exposure compared with control mice. Conclusions. Our study demonstrates that decrements in retinal ganglion cell responses can be detected after blast injury using noninvasive functional and structural tests. These objective responses may serve as surrogate tests for higher CNS functions following traumatic brain injury that are difficult to quantify. PMID:23620426
Xenon Protects against Blast-Induced Traumatic Brain Injury in an In Vitro Model

PubMed Central

Campos-Pires, Rita; Koziakova, Mariia; Yonis, Amina; Pau, Ashni; Macdonald, Warren; Harris, Katie; Edge, Christopher J.; Franks, Nicholas P.; Mahoney, Peter F.

2018-01-01

Abstract The aim of this study was to evaluate the neuroprotective efficacy of the inert gas xenon as a treatment for patients with blast-induced traumatic brain injury in an in vitro laboratory model. We developed a novel blast traumatic brain injury model using C57BL/6N mouse organotypic hippocampal brain-slice cultures exposed to a single shockwave, with the resulting injury quantified using propidium iodide fluorescence. A shock tube blast generator was used to simulate open field explosive blast shockwaves, modeled by the Friedlander waveform. Exposure to blast shockwave resulted in significant (p < 0.01) injury that increased with peak-overpressure and impulse of the shockwave, and which exhibited a secondary injury development up to 72 h after trauma. Blast-induced propidium iodide fluorescence overlapped with cleaved caspase-3 immunofluorescence, indicating that shock-wave–induced cell death involves apoptosis. Xenon (50% atm) applied 1 h after blast exposure reduced injury 24 h (p < 0.01), 48 h (p < 0.05), and 72 h (p < 0.001) later, compared with untreated control injury. Xenon-treated injured slices were not significantly different from uninjured sham slices at 24 h and 72 h. We demonstrate for the first time that xenon treatment after blast traumatic brain injury reduces initial injury and prevents subsequent injury development in vitro. Our findings support the idea that xenon may be a potential first-line treatment for those with blast-induced traumatic brain injury. PMID:29285980
Isolated primary blast alters neuronal function with minimal cell death in organotypic hippocampal slice cultures.

PubMed

Effgen, Gwen B; Vogel, Edward W; Lynch, Kimberly A; Lobel, Ayelet; Hue, Christopher D; Meaney, David F; Bass, Cameron R Dale; Morrison, Barclay

2014-07-01

An increasing number of U.S. soldiers are diagnosed with traumatic brain injury (TBI) subsequent to exposure to blast. In the field, blast injury biomechanics are highly complex and multi-phasic. The pathobiology caused by exposure to some of these phases in isolation, such as penetrating or inertially driven injuries, has been investigated extensively. However, it is unclear whether the primary component of blast, a shock wave, is capable of causing pathology on its own. Previous in vivo studies in the rodent and pig have demonstrated that it is difficult to deliver a primary blast (i.e., shock wave only) without rapid head accelerations and potentially confounding effects of inertially driven TBI. We have previously developed a well-characterized shock tube and custom in vitro receiver for exposing organotypic hippocampal slice cultures to pure primary blast. In this study, isolated primary blast induced minimal hippocampal cell death (on average, below 14% in any region of interest), even for the most severe blasts tested (424 kPa peak pressure, 2.3 ms overpressure duration, and 248 kPa*ms impulse). In contrast, measures of neuronal function were significantly altered at much lower exposures (336 kPa, 0.84 ms, and 86.5 kPa*ms), indicating that functional changes occur at exposures below the threshold for cell death. This is the first study to investigate a tolerance for primary blast-induced brain cell death in response to a range of blast parameters and demonstrate functional deficits at subthreshold exposures for cell death.
[Confined blasting in microexplosion cystolithotripsy].

PubMed

Uchida, M

1989-03-01

This paper is the 12th report in a series of studies on the application of microexplosion to medicine and biology. Microexplosion lithotripsy is a newly developed technique in our clinic to crush urinary stones with small quantities of explosives. A systematic research project has been performed since the first report of microexplosion lithotripsy in 1977. As a result, microexplosion was successfully applied to the destruction of bladder stones in 130 cases from 1981 to 1988. In blasting to crush rocks in industrial works, two kinds of blasting are available: external charge blasting and confined blasting. The detonation power of the latter is 10 to 50 times larger than that of the former. A detruction test using several kinds of spherical form model calculus and lead azide explosive was performed. The formula to calculate the suitable explosive dose was determined experimentally as shown below. (formula; see text) Thus the theory in general industrial blasting with massive explosives was proved to be effective also in microexplosion with small explosives. An original electric drill system was developed to make a hole in stones for confined blasting. 60 cases, including 2 cases of giant bladder stones over 100 g in weight, were successfully treated by confined blasting using this system without any complication. We consider that any bladder stones, however big or however many, can be treated by microexplosion lithotripsy with confined blasting.
Blast-Induced Color Change in Photonic Crystals Corresponds with Brain Pathology

PubMed Central

Cullen, D. Kacy; Browne, Kevin D.; Xu, Yongan; Adeeb, Saleena; Wolf, John A.; McCarron, Richard M.; Yang, Shu; Chavko, Mikulas

2011-01-01

Abstract A high incidence of blast exposure is a 21st century reality in counter-insurgency warfare. However, thresholds for closed-head blast-induced traumatic brain injury (bTBI) remain unknown. Moreover, without objective information about relative blast exposure, warfighters with bTBI may not receive appropriate medical care and may remain in harm's way. Accordingly, we have engineered a blast injury dosimeter (BID) using a photonic crystalline material that changes color following blast exposure. The photonic crystals are fabricated using SU-8 via multi-beam interference laser lithography. The final BID is similar in appearance to an array of small colored stickers that may be affixed to uniforms or helmets in multiple locations. Although durable under normal conditions, the photonic crystalline micro- and nano-structure are precisely altered by blast to create a color change. These BIDs were evaluated using a rat model of bTBI, for which blast shockwave exposure was generated via a compressed air-driven shock tube. With prototype BID arrays affixed to the animals, we found that BID color changes corresponded with subtle brain pathologies, including neuronal degeneration and reactive astrocytosis. These subtle changes were most notable in the dentate gyrus of the hippocampus, cerebral cortex, and cerebellum. These data demonstrate the feasibility of using a materials-based, power-free colorimetric BID as the first self-contained blast sensor calibrated to correspond with brain pathology. PMID:22082449
Model for small arms fire muzzle blast wave propagation in air

NASA Astrophysics Data System (ADS)

Aguilar, Juan R.; Desai, Sachi V.

2011-11-01

Accurate modeling of small firearms muzzle blast wave propagation in the far field is critical to predict sound pressure levels, impulse durations and rise times, as functions of propagation distance. Such a task being relevant to a number of military applications including the determination of human response to blast noise, gunfire detection and localization, and gun suppressor design. Herein, a time domain model to predict small arms fire muzzle blast wave propagation is introduced. The model implements a Friedlander wave with finite rise time which diverges spherically from the gun muzzle. Additionally, the effects in blast wave form of thermoviscous and molecular relaxational processes, which are associated with atmospheric absorption of sound were also incorporated in the model. Atmospheric absorption of blast waves is implemented using a time domain recursive formula obtained from numerical integration of corresponding differential equations using a Crank-Nicholson finite difference scheme. Theoretical predictions from our model were compared to previously recorded real world data of muzzle blast wave signatures obtained by shooting a set different sniper weapons of varying calibers. Recordings containing gunfire acoustical signatures were taken at distances between 100 and 600 meters from the gun muzzle. Results shows that predicted blast wave slope and exponential decay agrees well with measured data. Analysis also reveals the persistency of an oscillatory phenomenon after blast overpressure in the recorded wave forms.
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

PubMed

Wang, Tianmin; Mori, Hiroshi; Zhang, Chong; Kurokawa, Ken; Xing, Xin-Hui; Yamada, Takuji

2015-03-21

Computational predictions of catalytic function are vital for in-depth understanding of enzymes. Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we hypothesized that there is a large gap between the number of known annotated enzymes and the actual number in the protein universe, which significantly limits our ability to extract additional biologically relevant functional information from the available sequencing data. To reliably expand the enzyme space, we developed DomSign, a highly accurate domain signature-based enzyme functional prediction tool to assign Enzyme Commission (EC) digits. DomSign is a top-down prediction engine that yields results comparable, or superior, to those from many benchmark EC number prediction tools, including BLASTP, when a homolog with an identity >30% is not available in the database. Performance tests showed that DomSign is a highly reliable enzyme EC number annotation tool. After multiple tests, the accuracy is thought to be greater than 90%. Thus, DomSign can be applied to large-scale datasets, with the goal of expanding the enzyme space with high fidelity. Using DomSign, we successfully increased the percentage of EC-tagged enzymes from 12% to 30% in UniProt-TrEMBL. In the Kyoto Encyclopedia of Genes and Genomes bacterial database, the percentage of EC-tagged enzymes for each bacterial genome could be increased from 26.0% to 33.2% on average. Metagenomic mining was also efficient, as exemplified by the application of DomSign to the Human Microbiome Project dataset, recovering nearly one million new EC-labeled enzymes. Our results offer preliminarily confirmation of the existence of the hypothesized huge number of "hidden enzymes" in the protein universe, the identification of which could substantially further our understanding of the metabolisms of diverse organisms and also facilitate bioengineering by providing a richer enzyme resource. Furthermore, our results highlight the necessity of using more advanced computational tools than BLAST in protein database annotations to extract additional biologically relevant functional information from the available biological sequences.
Shooter position estimation with muzzle blast and shockwave measurements from separate locations

NASA Astrophysics Data System (ADS)

Grasing, David

2016-05-01

There are two acoustical events associated with small arms fire: the muzzle blast (created by bullets being expelled from the barrel of the weapon), and the shockwave (created by bullets which exceed the speed of sound). Assuming the ballistics of a round are known, the times and directions of arrival of the acoustic events furnish sufficient information to determine the origin of the shot. Existing methods tacitly assume that it is a single sensor which makes measurements of the times and direction of arrival. If the sensor is located past the point where the bullet goes transonic or if the sensor is far off the axis of the shot line a single sensor localization become highly inaccurate due to the ill-conditioning of the localization problem. In this paper, a more general approach is taken which allows for localizations from measurements made at separate locations. There are considerable advantages to this approach, the most noteworthy of which is the improvement in localization accuracy due to the improvement in the conditioning of the problem. Additional benefits include: the potential to locate in cases where a single sensor has insufficient information, furnishing high quality initialization to data fusion algorithms, and the potential to identify the round from a set of possible rounds.
Wavelet feature extraction for reliable discrimination between high explosive and chemical/biological artillery

NASA Astrophysics Data System (ADS)

Hohil, Myron E.; Desai, Sachi V.; Bass, Henry E.; Chambers, Jim

2005-03-01

Feature extraction methods based on the discrete wavelet transform and multiresolution analysis are used to develop a robust classification algorithm that reliably discriminates between conventional and simulated chemical/biological artillery rounds via acoustic signals produced during detonation. Distinct characteristics arise within the different airburst signatures because high explosive warheads emphasize concussive and shrapnel effects, while chemical/biological warheads are designed to disperse their contents over large areas, therefore employing a slower burning, less intense explosive to mix and spread their contents. The ensuing blast waves are readily characterized by variations in the corresponding peak pressure and rise time of the blast, differences in the ratio of positive pressure amplitude to the negative amplitude, and variations in the overall duration of the resulting waveform. Unique attributes can also be identified that depend upon the properties of the gun tube, projectile speed at the muzzle, and the explosive burn rates of the warhead. In this work, the discrete wavelet transform is used to extract the predominant components of these characteristics from air burst signatures at ranges exceeding 2km. Highly reliable discrimination is achieved with a feedforward neural network classifier trained on a feature space derived from the distribution of wavelet coefficients and higher frequency details found within different levels of the multiresolution decomposition.
30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Secondary blasting (I-A, II-A, and V-A mines). 57.22608 Section 57.22608 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... blasting (I-A, II-A, and V-A mines). Prior to secondary blasting, tests for methane shall be made in the...
30 CFR 57.22608 - Secondary blasting (I-A, II-A, and V-A mines).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Secondary blasting (I-A, II-A, and V-A mines). 57.22608 Section 57.22608 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF... blasting (I-A, II-A, and V-A mines). Prior to secondary blasting, tests for methane shall be made in the...

Use of polyclonal anti-myeloperoxidase antibody in myeloid lineage determination.

PubMed

Karnik, M P; Nair, C N; Zingde, S M; Gothoskar, B P; Zachariah, L; Barbhaya, S; Advani, S H

1994-12-01

This study reports the production of a rabbit polyclonal antibody to myeloperoxidase (MPO) and its use in ascertaining the myeloid lineage of blasts in leukaemia. Comparison of the immunocytochemical stain using the anti-MPO antibody with the routine cytochemical methodology showed that the former was more sensitive. In all subtypes of acute myeloid leukaemia (AML; 72 patients, M1-M6) greater number of MPO positive blast cells were observed by immunocytochemistry, the highest being in the promyelocytic leukaemia. It was also extremely specific for cells of the myeloid lineage as it did not react with blasts from acute lymphoblastic (50 patients) and megakaryoblastic leukaemias (1 patient). In addition, it proved most useful for the lineage determination of blasts from patients with undifferentiated acute leukaemias (AUL) and those with chronic myeloid leukaemia in blast crisis (CML-BC). Out of 8 patients of AULs, 6 were classified as acute myeloblastic leukaemia due to their reactivity to the anti-MPO antibody. Similarly, out of 12 patients of chronic myeloid leukaemia in blast crisis, blasts from 8 showed reactivity to this antibody and thus could be identified as belonging to the myeloid lineage and/or of the mixed blast crisis type.
Determination of Destress Blasting Effectiveness Using Seismic Source Parameters

NASA Astrophysics Data System (ADS)

Wojtecki, Łukasz; Mendecki, Maciej J.; Zuberek, Wacaław M.

2017-12-01

Underground mining of coal seams in the Upper Silesian Coal Basin is currently performed under difficult geological and mining conditions. The mining depth, dislocations (faults and folds) and mining remnants are responsible for rockburst hazard in the highest degree. This hazard can be minimized by using active rockburst prevention, where destress blastings play an important role. Destress blastings in coal seams aim to destress the local stress concentrations. These blastings are usually performed from the longwall face to decrease the stress level ahead of the longwall. An accurate estimation of active rockburst prevention effectiveness is important during mining under disadvantageous geological and mining conditions, which affect the risk of rockburst. Seismic source parameters characterize the focus of tremor, which may be useful in estimating the destress blasting effects. Investigated destress blastings were performed in coal seam no. 507 during its longwall mining in one of the coal mines in the Upper Silesian Coal Basin under difficult geological and mining conditions. The seismic source parameters of the provoked tremors were calculated. The presented preliminary investigations enable a rapid estimation of the destress blasting effectiveness using seismic source parameters, but further analysis in other geological and mining conditions with other blasting parameters is required.
Full-scale testing of leakage of blast waves inside a partially vented room exposed to external air blast loading

NASA Astrophysics Data System (ADS)

Codina, R.; Ambrosini, D.

2018-03-01

For the last few decades, the effects of blast loading on structures have been studied by many researchers around the world. Explosions can be caused by events such as industrial accidents, military conflicts or terrorist attacks. Urban centers have been prone to various threats including car bombs, suicide attacks, and improvised explosive devices. Partially vented constructions subjected to external blast loading represent an important topic in protective engineering. The assessment of blast survivability inside structures and the development of design provisions with respect to internal elements require the study of the propagation and leakage of blast waves inside buildings. In this paper, full-scale tests are performed to study the effects of the leakage of blast waves inside a partially vented room that is subjected to different external blast loadings. The results obtained may be useful for proving the validity of different methods of calculation, both empirical and numerical. Moreover, the experimental results are compared with those computed using the empirical curves of the US Defense report/manual UFC 3-340. Finally, results of the dynamic response of the front masonry wall are presented in terms of accelerations and an iso-damage diagram.
Simulating maar-diatreme volcanic systems in bench-scale experiments

NASA Astrophysics Data System (ADS)

Andrews, R. G.; White, J. D. L.; Dürig, T.; Zimanowski, B.

2015-12-01

Maar-diatreme eruptions are incompletely understood, and explanations for the processes involved in them have been debated for decades. This study extends bench-scale analogue experiments previously conducted on maar-diatreme systems and attempts to scale the results up to both field-scale experimentation and natural volcanic systems in order to produce a reconstructive toolkit for maar volcanoes. These experimental runs produced via multiple mechanisms complex deposits that match many features seen in natural maar-diatreme deposits. The runs include deeper single blasts, series of descending discrete blasts, and series of ascending blasts. Debris-jet inception and diatreme formation are indicated by this study to involve multiple types of granular fountains within diatreme deposits produced under varying initial conditions. The individual energies of blasts in multiple-blast series are not possible to infer from the final deposits. The depositional record of blast sequences can be ascertained from the proportion of fallback sedimentation versus maar ejecta rim material, the final crater size and the degree of overturning or slumping of accessory strata. Quantitatively, deeper blasts involve a roughly equal partitioning of energy into crater excavation energy versus mass movement of juvenile material, whereas shallower blasts expend a much greater proportion of energy in crater excavation.
Neck blast disease influences grain yield and quality traits of aromatic rice.

PubMed

Khan, Mohammad Ashik Iqbal; Bhuiyan, Md Rejwan; Hossain, Md Shahadat; Sen, Partha Pratim; Ara, Anjuman; Siddique, Md Abubakar; Ali, Md Ansar

2014-11-01

A critical investigation was conducted to find out the effect of neck blast disease on yield-contributing characters, and seed quality traits of aromatic rice in Bangladesh. Both healthy and neck-blast-infected panicles of three aromatic rice cultivars (high-yielding and local) were collected and investigated at Plant Pathology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh. All of the tested varieties were highly susceptible to neck blast disease under natural conditions, though no leaf blast symptoms appear on leaves. Neck blast disease increased grain sterility percentages, reduced grain size, yield and quality traits of seeds. The degrees of yield and seed quality reduction depended on disease severity and variety's genetic make-up. Unfilled grains were the main source of seed-borne pathogen, especially for blast in the seed lot. Transmission of blast pathogen from neck (panicle base) to seed was very poor. These findings are important, especially concerning the seed certification programme in which seed lots are certified on the basis of field inspection. Finally, controlled experiments are needed to draw more critical conclusions. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.
Two-dimensional explosion experiments examining the interaction between a blast wave and a sand hill

NASA Astrophysics Data System (ADS)

Sugiyama, Y.; Izumo, M.; Ando, H.; Matsuo, A.

2018-05-01

Two-dimensional explosion experiments were conducted to discuss the interaction between a blast wave and sand and show the mitigation effect of the sand on the blast wave. The explosive used was a detonating cord 1.0 m in length, which was initiated in a sand hill shaped like a triangular prism and whose cross section was an isosceles triangle with base angles of 30°. Sand-hill heights of 30 and 60 mm were used as parameters to discuss the effect of sand mass upon blast-wave strength. The interaction of the blast wave with the sand/air interface causes multiple peaks in the blast wave, which are induced by successive transmissions at the interface. The increase in the sand mass further mitigates the blast parameters of peak overpressure and positive impulse. The results of this experiment can be utilized to validate the numerical method of solving the problem of interaction between a compressible fluid and a particle layer.
Two-dimensional explosion experiments examining the interaction between a blast wave and a sand hill

NASA Astrophysics Data System (ADS)

Sugiyama, Y.; Izumo, M.; Ando, H.; Matsuo, A.

2018-02-01

Two-dimensional explosion experiments were conducted to discuss the interaction between a blast wave and sand and show the mitigation effect of the sand on the blast wave. The explosive used was a detonating cord 1.0 m in length, which was initiated in a sand hill shaped like a triangular prism and whose cross section was an isosceles triangle with base angles of 30°. Sand-hill heights of 30 and 60 mm were used as parameters to discuss the effect of sand mass upon blast-wave strength. The interaction of the blast wave with the sand/air interface causes multiple peaks in the blast wave, which are induced by successive transmissions at the interface. The increase in the sand mass further mitigates the blast parameters of peak overpressure and positive impulse. The results of this experiment can be utilized to validate the numerical method of solving the problem of interaction between a compressible fluid and a particle layer.
Comprehensive Numerical Modeling of the Blast Furnace Ironmaking Process

NASA Astrophysics Data System (ADS)

Zhou, Chenn; Tang, Guangwu; Wang, Jichao; Fu, Dong; Okosun, Tyamo; Silaen, Armin; Wu, Bin

2016-05-01

Blast furnaces are counter-current chemical reactors, widely utilized in the ironmaking industry. Hot reduction gases injected from lower regions of the furnace ascend, reacting with the descending burden. Through this reaction process, iron ore is reduced into liquid iron that is tapped from the furnace hearth. Due to the extremely harsh environment inside the blast furnace, it is difficult to measure or observe internal phenomena during operation. Through the collaboration between steel companies and the Center for Innovation through Visualization and Simulation, multiple computational fluid dynamics (CFD) models have been developed to simulate the complex multiphase reacting flow in the three regions of the furnace, the shaft, the raceway, and the hearth. The models have been used effectively to troubleshoot and optimize blast furnace operations. In addition, the CFD models have been integrated with virtual reality. An interactive virtual blast furnace has been developed for training purpose. This paper summarizes the developments and applications of blast furnace CFD models and the virtual blast furnace.
Grit blasting and the marginal accuracy of two ceramic veneer systems--a pilot study.

PubMed

Lim, C; Ironside, J G

1997-04-01

Margins of ceramic restorations can be damaged during removal of investment materials with grit blasting and result in relatively large marginal discrepancies and excessive marginal discrepancies with greater exposure of cement to the oral environment. Subsequent dissolution of cement can encourage plaque retention, dental caries, and periodontal problems. This study compared marginal adaptation of ceramic veneers created by the refractory die technique (R), Dicor glass ceramic technique (D), and effects of grit blasting on their margins. Two groups of ceramic veneers were constructed for each system, one without grit blasting (R g and D g) and one with grit blasting (R+g and D+g). Statistical analyses revealed that grit blasting had a greater effect in reducing marginal accuracy for Dicor ceramic veneers compared with refractory die ceramic veneers.
VirSSPA- a virtual reality tool for surgical planning workflow.

PubMed

Suárez, C; Acha, B; Serrano, C; Parra, C; Gómez, T

2009-03-01

A virtual reality tool, called VirSSPA, was developed to optimize the planning of surgical processes. Segmentation algorithms for Computed Tomography (CT) images: a region growing procedure was used for soft tissues and a thresholding algorithm was implemented to segment bones. The algorithms operate semiautomati- cally since they only need seed selection with the mouse on each tissue segmented by the user. The novelty of the paper is the adaptation of an enhancement method based on histogram thresholding applied to CT images for surgical planning, which simplifies subsequent segmentation. A substantial improvement of the virtual reality tool VirSSPA was obtained with these algorithms. VirSSPA was used to optimize surgical planning, to decrease the time spent on surgical planning and to improve operative results. The success rate increases due to surgeons being able to see the exact extent of the patient's ailment. This tool can decrease operating room time, thus resulting in reduced costs. Virtual simulation was effective for optimizing surgical planning, which could, consequently, result in improved outcomes with reduced costs.
User Guidelines for the Brassica Database: BRAD.

PubMed

Wang, Xiaobo; Cheng, Feng; Wang, Xiaowu

2016-01-01

The genome sequence of Brassica rapa was first released in 2011. Since then, further Brassica genomes have been sequenced or are undergoing sequencing. It is therefore necessary to develop tools that help users to mine information from genomic data efficiently. This will greatly aid scientific exploration and breeding application, especially for those with low levels of bioinformatic training. Therefore, the Brassica database (BRAD) was built to collect, integrate, illustrate, and visualize Brassica genomic datasets. BRAD provides useful searching and data mining tools, and facilitates the search of gene annotation datasets, syntenic or non-syntenic orthologs, and flanking regions of functional genomic elements. It also includes genome-analysis tools such as BLAST and GBrowse. One of the important aims of BRAD is to build a bridge between Brassica crop genomes with the genome of the model species Arabidopsis thaliana, thus transferring the bulk of A. thaliana gene study information for use with newly sequenced Brassica crops.
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

PubMed

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

2005-04-01

We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.
Software For Genetic Algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steve E.

1992-01-01

SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.
13. BUILDING NO. 621, INTERIOR, TOP OF BLASTING TUB UNDERNEATH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. BUILDING NO. 621, INTERIOR, TOP OF BLASTING TUB UNDERNEATH SAWDUST HOPPER. BLASTING TUB HAS DOUBLE WALLS OF 3/4' THICK STEEL ARMOR PLATE. CHARGE TO BE TESTED IS BURIED IN SAWDUST WITH FLAME RESISTANT CHEMICALS. ELEVATOR BEHIND TUB CARRIES SAWDUST BACK TO TOP OF SAWDUST HOPPER AFTER TEST IS COMPLETED AND SAWDUST IN BLASTING TUB HAS BEEN SIFTED FOR SHELL FRAGMENTS. LOUVERS IN WALLS ARE HINGED FREELY SO THEY OPEN TO RELIEVE BLAST PRESSURE DURING A TEST. - Picatinny Arsenal, 600 Area, Test Areas District, State Route 15 near I-80, Dover, Morris County, NJ
Large blast and thermal simulator advanced concept driver design by computational fluid dynamics. Final report, 1987-1989

DOE Office of Scientific and Technical Information (OSTI.GOV)

Opalka, K.O.

1989-08-01

The construction of a large test facility has been proposed for simulating the blast and thermal environment resulting from nuclear explosions. This facility would be used to test the survivability and vulnerability of military equipment such as trucks, tanks, and helicopters in a simulated thermal and blast environment, and to perform research into nuclear blast phenomenology. The proposed advanced design concepts, heating of driver gas and fast-acting throat valves for wave shaping, are described and the results of CFD studies to advance these new technical concepts fro simulating decaying blast waves are reported.
Logistics Complete Round Charts: Grenades, Mines, Pyrotechnics, Rockets, Rocket Motors, Demolition Material

DTIC Science & Technology

1986-06-01

Flash 3. (342 g) Electrically Comp Actuated By Blasting Machine or Battery 5/ 8 STD 37524 Simulator, Projectile M1lSA2 0.30 7549246 MIL-S-10058 Hand...8799710 Blastin Comp (0.07 oz) Blasting (Whistle) Fuze Fuze 8-14 Frictio Friction (Burst) ’ l3AI M3A1 721 Igniter 8833721 Igniter last 5-10 8799714...8799715 iBlasti Blasting Sec FuzeN Fuze M3A1 •721 Igniter 8833721 Igniter Inst 6-10 8799714 879971 Blast Blasting See Fuze Puze N13A1 587 FrictLi 8848587
Mechanical and histological characterization of trachea tissue subjected to blast-type pressures

NASA Astrophysics Data System (ADS)

Butler, B. J.; Bo, C.; Tucker, A. W.; Jardine, A. P.; Proud, W. G.; Williams, A.; Brown, K. A.

2014-05-01

Injuries to the respiratory system can be a component of polytrauma in blast-loading injuries. Tissues located at air-liquid interfaces, including such tissues in the respiratory system, are particularly vulnerable to damage by blast overpressures. There is a lack of information about the mechanical and cellular responses that contribute to the damage of this class of tissues subjected to the high strain rates associated with blast loading. Here, we describe the results of dynamic blast-like pressure loading tests at high strain rates on freshly harvested ex vivo trachea tissue specimens.
On the Interaction and Coalescence if Spherical Blast Waves

NASA Technical Reports Server (NTRS)

Kandula, Max; Freeman, Robert J.

2005-01-01

The scaling and similarity laws concerning the propagation of isolated spherical blast waves are briefly reviewed. Both point source explosions and high pressure gas explosions are considered. Test data on blast overpressure from the interaction and coalescence of spherical blast waves emanating from explosives in the form of shaped charges of different strength placed in the vicinity of a solid propellant stack are presented. These data are discussed with regard to the scaling laws concerning the decay of blast overpressure. The results point out the possibility of detecting source explosions from far-field pressure measurements.
Electronic firing systems and methods for firing a device

DOEpatents

Frickey, Steven J [Boise, ID; Svoboda, John M [Idaho Falls, ID

2012-04-24

An electronic firing system comprising a control system, a charging system, an electrical energy storage device, a shock tube firing circuit, a shock tube connector, a blasting cap firing circuit, and a blasting cap connector. The control system controls the charging system, which charges the electrical energy storage device. The control system also controls the shock tube firing circuit and the blasting cap firing circuit. When desired, the control system signals the shock tube firing circuit or blasting cap firing circuit to electrically connect the electrical energy storage device to the shock tube connector or the blasting cap connector respectively.
Identifying persistent and characteristic features in firearm tool marks on cartridge cases

NASA Astrophysics Data System (ADS)

Ott, Daniel; Soons, Johannes; Thompson, Robert; Song, John

2017-12-01

Recent concerns about subjectivity in forensic firearm identification have motivated the development of algorithms to compare firearm tool marks that are imparted on ammunition and to generate quantitative measures of similarity. In this paper, we describe an algorithm that identifies impressed tool marks on a cartridge case that are both consistent between firings and contribute strongly to a surface similarity metric. The result is a representation of the tool mark topography that emphasizes both significant and persistent features across firings. This characteristic surface map is useful for understanding the variability and persistence of the tool marks created by a firearm and can provide improved discrimination between the comparison scores of samples fired from the same firearm and the scores of samples fired from different firearms. The algorithm also provides a convenient method for visualizing areas of similarity that may be useful in providing quantitative support for visual comparisons by trained examiners.

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