Fuzzy support vector machines for adaptive Morse code recognition.

PubMed

Yang, Cheng-Hong; Jin, Li-Cheng; Chuang, Li-Yeh

2006-11-01

Morse code is now being harnessed for use in rehabilitation applications of augmentative-alternative communication and assistive technology, facilitating mobility, environmental control and adapted worksite access. In this paper, Morse code is selected as a communication adaptive device for persons who suffer from muscle atrophy, cerebral palsy or other severe handicaps. A stable typing rate is strictly required for Morse code to be effective as a communication tool. Therefore, an adaptive automatic recognition method with a high recognition rate is needed. The proposed system uses both fuzzy support vector machines and the variable-degree variable-step-size least-mean-square algorithm to achieve these objectives. We apply fuzzy memberships to each point, and provide different contributions to the decision learning function for support vector machines. Statistical analyses demonstrated that the proposed method elicited a higher recognition rate than other algorithms in the literature.

Multipath search coding of stationary signals with applications to speech

NASA Astrophysics Data System (ADS)

Fehn, H. G.; Noll, P.

1982-04-01

This paper deals with the application of multipath search coding (MSC) concepts to the coding of stationary memoryless and correlated sources, and of speech signals, at a rate of one bit per sample. Use is made of three MSC classes: (1) codebook coding, or vector quantization, (2) tree coding, and (3) trellis coding. This paper explains the performances of these coders and compares them both with those of conventional coders and with rate-distortion bounds. The potentials of MSC coding strategies are demonstrated by illustrations. The paper reports also on results of MSC coding of speech, where both the strategy of adaptive quantization and of adaptive prediction were included in coder design.

TA-GC cloning: A new simple and versatile technique for the directional cloning of PCR products for recombinant protein expression.

PubMed

Niarchos, Athanasios; Siora, Anastasia; Konstantinou, Evangelia; Kalampoki, Vasiliki; Lagoumintzis, George; Poulas, Konstantinos

2017-01-01

During the last few decades, the recombinant protein expression finds more and more applications. The cloning of protein-coding genes into expression vectors is required to be directional for proper expression, and versatile in order to facilitate gene insertion in multiple different vectors for expression tests. In this study, the TA-GC cloning method is proposed, as a new, simple and efficient method for the directional cloning of protein-coding genes in expression vectors. The presented method features several advantages over existing methods, which tend to be relatively more labour intensive, inflexible or expensive. The proposed method relies on the complementarity between single A- and G-overhangs of the protein-coding gene, obtained after a short incubation with T4 DNA polymerase, and T and C overhangs of the novel vector pET-BccI, created after digestion with the restriction endonuclease BccI. The novel protein-expression vector pET-BccI also facilitates the screening of transformed colonies for recombinant transformants. Evaluation experiments of the proposed TA-GC cloning method showed that 81% of the transformed colonies contained recombinant pET-BccI plasmids, and 98% of the recombinant colonies expressed the desired protein. This demonstrates that TA-GC cloning could be a valuable method for cloning protein-coding genes in expression vectors.

TA-GC cloning: A new simple and versatile technique for the directional cloning of PCR products for recombinant protein expression

PubMed Central

Niarchos, Athanasios; Siora, Anastasia; Konstantinou, Evangelia; Kalampoki, Vasiliki; Poulas, Konstantinos

2017-01-01

During the last few decades, the recombinant protein expression finds more and more applications. The cloning of protein-coding genes into expression vectors is required to be directional for proper expression, and versatile in order to facilitate gene insertion in multiple different vectors for expression tests. In this study, the TA-GC cloning method is proposed, as a new, simple and efficient method for the directional cloning of protein-coding genes in expression vectors. The presented method features several advantages over existing methods, which tend to be relatively more labour intensive, inflexible or expensive. The proposed method relies on the complementarity between single A- and G-overhangs of the protein-coding gene, obtained after a short incubation with T4 DNA polymerase, and T and C overhangs of the novel vector pET-BccI, created after digestion with the restriction endonuclease BccI. The novel protein-expression vector pET-BccI also facilitates the screening of transformed colonies for recombinant transformants. Evaluation experiments of the proposed TA-GC cloning method showed that 81% of the transformed colonies contained recombinant pET-BccI plasmids, and 98% of the recombinant colonies expressed the desired protein. This demonstrates that TA-GC cloning could be a valuable method for cloning protein-coding genes in expression vectors. PMID:29091919

Optimizing fusion PIC code performance at scale on Cori Phase 2

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

Koskela, T. S.; Deslippe, J.

In this paper we present the results of optimizing the performance of the gyrokinetic full-f fusion PIC code XGC1 on the Cori Phase Two Knights Landing system. The code has undergone substantial development to enable the use of vector instructions in its most expensive kernels within the NERSC Exascale Science Applications Program. We study the single-node performance of the code on an absolute scale using the roofline methodology to guide optimization efforts. We have obtained 2x speedups in single node performance due to enabling vectorization and performing memory layout optimizations. On multiple nodes, the code is shown to scale wellmore » up to 4000 nodes, near half the size of the machine. We discuss some communication bottlenecks that were identified and resolved during the work.« less

Performance of a Bounce-Averaged Global Model of Super-Thermal Electron Transport in the Earth's Magnetic Field

NASA Technical Reports Server (NTRS)

McGuire, Tim

1998-01-01

In this paper, we report the results of our recent research on the application of a multiprocessor Cray T916 supercomputer in modeling super-thermal electron transport in the earth's magnetic field. In general, this mathematical model requires numerical solution of a system of partial differential equations. The code we use for this model is moderately vectorized. By using Amdahl's Law for vector processors, it can be verified that the code is about 60% vectorized on a Cray computer. Speedup factors on the order of 2.5 were obtained compared to the unvectorized code. In the following sections, we discuss the methodology of improving the code. In addition to our goal of optimizing the code for solution on the Cray computer, we had the goal of scalability in mind. Scalability combines the concepts of portabilty with near-linear speedup. Specifically, a scalable program is one whose performance is portable across many different architectures with differing numbers of processors for many different problem sizes. Though we have access to a Cray at this time, the goal was to also have code which would run well on a variety of architectures.

MHD thrust vectoring of a rocket engine

NASA Astrophysics Data System (ADS)

Labaune, Julien; Packan, Denis; Tholin, Fabien; Chemartin, Laurent; Stillace, Thierry; Masson, Frederic

2016-09-01

In this work, the possibility to use MagnetoHydroDynamics (MHD) to vectorize the thrust of a solid propellant rocket engine exhaust is investigated. Using a magnetic field for vectoring offers a mass gain and a reusability advantage compared to standard gimbaled, elastomer-joint systems. Analytical and numerical models were used to evaluate the flow deviation with a 1 Tesla magnetic field inside the nozzle. The fluid flow in the resistive MHD approximation is calculated using the KRONOS code from ONERA, coupling the hypersonic CFD platform CEDRE and the electrical code SATURNE from EDF. A critical parameter of these simulations is the electrical conductivity, which was evaluated using a set of equilibrium calculations with 25 species. Two models were used: local thermodynamic equilibrium and frozen flow. In both cases, chlorine captures a large fraction of free electrons, limiting the electrical conductivity to a value inadequate for thrust vectoring applications. However, when using chlorine-free propergols with 1% in mass of alkali, an MHD thrust vectoring of several degrees was obtained.

Transferring ecosystem simulation codes to supercomputers

NASA Technical Reports Server (NTRS)

Skiles, J. W.; Schulbach, C. H.

1995-01-01

Many ecosystem simulation computer codes have been developed in the last twenty-five years. This development took place initially on main-frame computers, then mini-computers, and more recently, on micro-computers and workstations. Supercomputing platforms (both parallel and distributed systems) have been largely unused, however, because of the perceived difficulty in accessing and using the machines. Also, significant differences in the system architectures of sequential, scalar computers and parallel and/or vector supercomputers must be considered. We have transferred a grassland simulation model (developed on a VAX) to a Cray Y-MP/C90. We describe porting the model to the Cray and the changes we made to exploit the parallelism in the application and improve code execution. The Cray executed the model 30 times faster than the VAX and 10 times faster than a Unix workstation. We achieved an additional speedup of 30 percent by using the compiler's vectoring and 'in-line' capabilities. The code runs at only about 5 percent of the Cray's peak speed because it ineffectively uses the vector and parallel processing capabilities of the Cray. We expect that by restructuring the code, it could execute an additional six to ten times faster.

Conditional Entropy-Constrained Residual VQ with Application to Image Coding

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Chung, Wilson C.; Smith, Mark J. T.

1996-01-01

This paper introduces an extension of entropy-constrained residual vector quantization (VQ) where intervector dependencies are exploited. The method, which we call conditional entropy-constrained residual VQ, employs a high-order entropy conditioning strategy that captures local information in the neighboring vectors. When applied to coding images, the proposed method is shown to achieve better rate-distortion performance than that of entropy-constrained residual vector quantization with less computational complexity and lower memory requirements. Moreover, it can be designed to support progressive transmission in a natural way. It is also shown to outperform some of the best predictive and finite-state VQ techniques reported in the literature. This is due partly to the joint optimization between the residual vector quantizer and a high-order conditional entropy coder as well as the efficiency of the multistage residual VQ structure and the dynamic nature of the prediction.

Determination of coronal magnetic fields from vector magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1992-01-01

The determination of coronal magnetic fields from vector magnetograms, including the development and application of algorithms to determine force-free coronal fields above selected observations of active regions is studied. Two additional active regions were selected and analyzed. The restriction of periodicity in the 3-D code which is used to determine the coronal field was removed giving the new code variable mesh spacing and is thus able to provide a more realistic description of coronal fields. The NOAA active region AR5747 of 20 Oct. 1989 was studied. A brief account of progress during the research performed is reported.

Automatically Preparing Safe SQL Queries

NASA Astrophysics Data System (ADS)

Bisht, Prithvi; Sistla, A. Prasad; Venkatakrishnan, V. N.

We present the first sound program source transformation approach for automatically transforming the code of a legacy web application to employ PREPARE statements in place of unsafe SQL queries. Our approach therefore opens the way for eradicating the SQL injection threat vector from legacy web applications.

Optimal source coding, removable noise elimination, and natural coordinate system construction for general vector sources using replicator neural networks

NASA Astrophysics Data System (ADS)

Hecht-Nielsen, Robert

1997-04-01

A new universal one-chart smooth manifold model for vector information sources is introduced. Natural coordinates (a particular type of chart) for such data manifolds are then defined. Uniformly quantized natural coordinates form an optimal vector quantization code for a general vector source. Replicator neural networks (a specialized type of multilayer perceptron with three hidden layers) are the introduced. As properly configured examples of replicator networks approach minimum mean squared error (e.g., via training and architecture adjustment using randomly chosen vectors from the source), these networks automatically develop a mapping which, in the limit, produces natural coordinates for arbitrary source vectors. The new concept of removable noise (a noise model applicable to a wide variety of real-world noise processes) is then discussed. Replicator neural networks, when configured to approach minimum mean squared reconstruction error (e.g., via training and architecture adjustment on randomly chosen examples from a vector source, each with randomly chosen additive removable noise contamination), in the limit eliminate removable noise and produce natural coordinates for the data vector portions of the noise-corrupted source vectors. Consideration regarding selection of the dimension of a data manifold source model and the training/configuration of replicator neural networks are discussed.

Electromagnetic Fields of a Uniform Sphere in a Uniform Conducting Medium with Application to Dipole Sources

DTIC Science & Technology

1991-09-01

12b. DISTRIBUTION CODE Approved for public release; distribution is unlimited. 13. ABSTRACT (Maximum 200 words) Vector spherical harmonic expansions are...electric and magnetic field vectors from E rand B - r alone. Genural expressions are given relating the scattered field expansion coefficients to the source...Prescnbed by ANSI Std. Z39-18 29W-102 NCSC TR 426-90 CONTENTS Pag o INTRODUCTION 1 BACKGROUND 1 ANGULAR MOMENTUM OPERATOR AND VECTOR SPHERICAL

Vector processing efficiency of plasma MHD codes by use of the FACOM 230-75 APU

NASA Astrophysics Data System (ADS)

Matsuura, T.; Tanaka, Y.; Naraoka, K.; Takizuka, T.; Tsunematsu, T.; Tokuda, S.; Azumi, M.; Kurita, G.; Takeda, T.

1982-06-01

In the framework of pipelined vector architecture, the efficiency of vector processing is assessed with respect to plasma MHD codes in nuclear fusion research. By using a vector processor, the FACOM 230-75 APU, the limit of the enhancement factor due to parallelism of current vector machines is examined for three numerical codes based on a fluid model. Reasonable speed-up factors of approximately 6,6 and 4 times faster than the highly optimized scalar version are obtained for ERATO (linear stability code), AEOLUS-R1 (nonlinear stability code) and APOLLO (1-1/2D transport code), respectively. Problems of the pipelined vector processors are discussed from the viewpoint of restructuring, optimization and choice of algorithms. In conclusion, the important concept of "concurrency within pipelined parallelism" is emphasized.

Fusion PIC code performance analysis on the Cori KNL system

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

Koskela, Tuomas S.; Deslippe, Jack; Friesen, Brian

We study the attainable performance of Particle-In-Cell codes on the Cori KNL system by analyzing a miniature particle push application based on the fusion PIC code XGC1. We start from the most basic building blocks of a PIC code and build up the complexity to identify the kernels that cost the most in performance and focus optimization efforts there. Particle push kernels operate at high AI and are not likely to be memory bandwidth or even cache bandwidth bound on KNL. Therefore, we see only minor benefits from the high bandwidth memory available on KNL, and achieving good vectorization ismore » shown to be the most beneficial optimization path with theoretical yield of up to 8x speedup on KNL. In practice we are able to obtain up to a 4x gain from vectorization due to limitations set by the data layout and memory latency.« less

CFD code evaluation for internal flow modeling

NASA Technical Reports Server (NTRS)

Chung, T. J.

1990-01-01

Research on the computational fluid dynamics (CFD) code evaluation with emphasis on supercomputing in reacting flows is discussed. Advantages of unstructured grids, multigrids, adaptive methods, improved flow solvers, vector processing, parallel processing, and reduction of memory requirements are discussed. As examples, researchers include applications of supercomputing to reacting flow Navier-Stokes equations including shock waves and turbulence and combustion instability problems associated with solid and liquid propellants. Evaluation of codes developed by other organizations are not included. Instead, the basic criteria for accuracy and efficiency have been established, and some applications on rocket combustion have been made. Research toward an ultimate goal, the most accurate and efficient CFD code, is in progress and will continue for years to come.

Learning Compact Binary Face Descriptor for Face Recognition.

PubMed

Lu, Jiwen; Liong, Venice Erin; Zhou, Xiuzhuang; Zhou, Jie

2015-10-01

Binary feature descriptors such as local binary patterns (LBP) and its variations have been widely used in many face recognition systems due to their excellent robustness and strong discriminative power. However, most existing binary face descriptors are hand-crafted, which require strong prior knowledge to engineer them by hand. In this paper, we propose a compact binary face descriptor (CBFD) feature learning method for face representation and recognition. Given each face image, we first extract pixel difference vectors (PDVs) in local patches by computing the difference between each pixel and its neighboring pixels. Then, we learn a feature mapping to project these pixel difference vectors into low-dimensional binary vectors in an unsupervised manner, where 1) the variance of all binary codes in the training set is maximized, 2) the loss between the original real-valued codes and the learned binary codes is minimized, and 3) binary codes evenly distribute at each learned bin, so that the redundancy information in PDVs is removed and compact binary codes are obtained. Lastly, we cluster and pool these binary codes into a histogram feature as the final representation for each face image. Moreover, we propose a coupled CBFD (C-CBFD) method by reducing the modality gap of heterogeneous faces at the feature level to make our method applicable to heterogeneous face recognition. Extensive experimental results on five widely used face datasets show that our methods outperform state-of-the-art face descriptors.

Security authentication using phase-encoded nanoparticle structures and polarized light.

PubMed

Carnicer, Artur; Hassanfiroozi, Amir; Latorre-Carmona, Pedro; Huang, Yi-Pai; Javidi, Bahram

2015-01-15

Phase-encoded nanostructures such as quick response (QR) codes made of metallic nanoparticles are suggested to be used in security and authentication applications. We present a polarimetric optical method able to authenticate random phase-encoded QR codes. The system is illuminated using polarized light, and the QR code is encoded using a phase-only random mask. Using classification algorithms, it is possible to validate the QR code from the examination of the polarimetric signature of the speckle pattern. We used Kolmogorov-Smirnov statistical test and Support Vector Machine algorithms to authenticate the phase-encoded QR codes using polarimetric signatures.

Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.

PubMed

Wilson, Mandy L; Okumoto, Sakiko; Adam, Laura; Peccoud, Jean

2014-01-15

Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains. Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language. The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.

Multiprocessing MCNP on an IBM RS/6000 cluster

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

McKinney, G.W.; West, J.T.

1993-01-01

The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors (P) and the fraction of task time that multiprocesses (f), can be formulated using Amdahl's Law S ((f,P) = 1 f + f/P). However, for most applications this theoretical limit cannot be achieved, due to additional terms not included in Amdahl's Law. Monte Carlo transport is a natural candidate for multiprocessing, since the particle tracks are generally independent and the precision of the result increases as the square root of the number of particles tracked.« less

Discrete Data Transfer Technique for Fluid-Structure Interaction

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2007-01-01

This paper presents a general three-dimensional algorithm for data transfer between dissimilar meshes. The algorithm is suitable for applications of fluid-structure interaction and other high-fidelity multidisciplinary analysis and optimization. Because the algorithm is independent of the mesh topology, we can treat structured and unstructured meshes in the same manner. The algorithm is fast and accurate for transfer of scalar or vector fields between dissimilar surface meshes. The algorithm is also applicable for the integration of a scalar field (e.g., coefficients of pressure) on one mesh and injection of the resulting vectors (e.g., force vectors) onto another mesh. The author has implemented the algorithm in a C++ computer code. This paper contains a complete formulation of the algorithm with a few selected results.

A Performance Evaluation of the Cray X1 for Scientific Applications

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Borrill, Julian; Canning, Andrew; Carter, Jonathan; Djomehri, M. Jahed; Shan, Hongzhang; Skinner, David

2004-01-01

The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end capability and cost effectiveness. However, the recent development of massively parallel vector systems is having a significant effect on the supercomputing landscape. In this paper, we compare the performance of the recently released Cray X1 vector system with that of the cacheless NEC SX-6 vector machine, and the superscalar cache-based IBM Power3 and Power4 architectures for scientific applications. Overall results demonstrate that the X1 is quite promising, but performance improvements are expected as the hardware, systems software, and numerical libraries mature. Code reengineering to effectively utilize the complex architecture may also lead to significant efficiency enhancements.

Helper-dependent adenoviral vectors for liver-directed gene therapy

PubMed Central

Brunetti-Pierri, Nicola; Ng, Philip

2011-01-01

Helper-dependent adenoviral (HDAd) vectors devoid of all viral-coding sequences are promising non-integrating vectors for liver-directed gene therapy because they have a large cloning capacity, can efficiently transduce a wide variety of cell types from various species independent of the cell cycle and can result in long-term transgene expression without chronic toxicity. The main obstacle preventing clinical applications of HDAd for liver-directed gene therapy is the host innate inflammatory response against the vector capsid proteins that occurs shortly after intravascular vector administration resulting in acute toxicity, the severity of which is dependent on vector dose. Intense efforts have been focused on elucidating the factors involved in this acute response and various strategies have been investigated to improve the therapeutic index of HDAd vectors. These strategies have yielded encouraging results with the potential for clinical translation. PMID:21470977

Vectorization, threading, and cache-blocking considerations for hydrocodes on emerging architectures

DOE PAGES

Fung, J.; Aulwes, R. T.; Bement, M. T.; ...

2015-07-14

This work reports on considerations for improving computational performance in preparation for current and expected changes to computer architecture. The algorithms studied will include increasingly complex prototypes for radiation hydrodynamics codes, such as gradient routines and diffusion matrix assembly (e.g., in [1-6]). The meshes considered for the algorithms are structured or unstructured meshes. The considerations applied for performance improvements are meant to be general in terms of architecture (not specifically graphical processing unit (GPUs) or multi-core machines, for example) and include techniques for vectorization, threading, tiling, and cache blocking. Out of a survey of optimization techniques on applications such asmore » diffusion and hydrodynamics, we make general recommendations with a view toward making these techniques conceptually accessible to the applications code developer. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.« less

[Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

PubMed

Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

2012-01-01

Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

A Performance Evaluation of the Cray X1 for Scientific Applications

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Borrill, Julian; Canning, Andrew; Carter, Jonathan; Djomehri, M. Jahed; Shan, Hongzhang; Skinner, David

2003-01-01

The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end capability and capacity computers because of their generality, scalability, and cost effectiveness. However, the recent development of massively parallel vector systems is having a significant effect on the supercomputing landscape. In this paper, we compare the performance of the recently-released Cray X1 vector system with that of the cacheless NEC SX-6 vector machine, and the superscalar cache-based IBM Power3 and Power4 architectures for scientific applications. Overall results demonstrate that the X1 is quite promising, but performance improvements are expected as the hardware, systems software, and numerical libraries mature. Code reengineering to effectively utilize the complex architecture may also lead to significant efficiency enhancements.

Interframe vector wavelet coding technique

NASA Astrophysics Data System (ADS)

Wus, John P.; Li, Weiping

1997-01-01

Wavelet coding is often used to divide an image into multi- resolution wavelet coefficients which are quantized and coded. By 'vectorizing' scalar wavelet coding and combining this with vector quantization (VQ), vector wavelet coding (VWC) can be implemented. Using a finite number of states, finite-state vector quantization (FSVQ) takes advantage of the similarity between frames by incorporating memory into the video coding system. Lattice VQ eliminates the potential mismatch that could occur using pre-trained VQ codebooks. It also eliminates the need for codebook storage in the VQ process, thereby creating a more robust coding system. Therefore, by using the VWC coding method in conjunction with the FSVQ system and lattice VQ, the formulation of a high quality very low bit rate coding systems is proposed. A coding system using a simple FSVQ system where the current state is determined by the previous channel symbol only is developed. To achieve a higher degree of compression, a tree-like FSVQ system is implemented. The groupings are done in this tree-like structure from the lower subbands to the higher subbands in order to exploit the nature of subband analysis in terms of the parent-child relationship. Class A and Class B video sequences from the MPEG-IV testing evaluations are used in the evaluation of this coding method.

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

Sharma, Vishal C.; Gopalakrishnan, Ganesh; Krishnamoorthy, Sriram

The systems resilience research community has developed methods to manually insert additional source-program level assertions to trap errors, and also devised tools to conduct fault injection studies for scalar program codes. In this work, we contribute the first vector oriented LLVM-level fault injector VULFI to help study the effects of faults in vector architectures that are of growing importance, especially for vectorizing loops. Using VULFI, we conduct a resiliency study of nine real-world vector benchmarks using Intel’s AVX and SSE extensions as the target vector instruction sets, and offer the first reported understanding of how faults affect vector instruction sets.more » We take this work further toward automating the insertion of resilience assertions during compilation. This is based on our observation that during intermediate (e.g., LLVM-level) code generation to handle full and partial vectorization, modern compilers exploit (and explicate in their code-documentation) critical invariants. These invariants are turned into error-checking code. We confirm the efficacy of these automatically inserted low-overhead error detectors for vectorized for-loops.« less

Multiprocessing MCNP on an IBN RS/6000 cluster

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

McKinney, G.W.; West, J.T.

1993-01-01

The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors P and the fraction f of task time that multiprocesses, can be formulated using Amdahl's law: S(f, P) =1/(1-f+f/P). However, for most applications, this theoretical limit cannot be achieved because of additional terms (e.g., multitasking overhead, memory overlap, etc.) that are not included in Amdahl's law. Monte Carlo transport is a natural candidate for multiprocessing because the particle tracks are generally independent, and the precision of the result increases as the square Foot of the number of particles tracked.« less

Multiprocessing MCNP on an IBM RS/6000 cluster

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

McKinney, G.W.; West, J.T.

1993-03-01

The advent of high-performance computer systems has brought to maturity programming concepts like vectorization, multiprocessing, and multitasking. While there are many schools of thought as to the most significant factor in obtaining order-of-magnitude increases in performance, such speedup can only be achieved by integrating the computer system and application code. Vectorization leads to faster manipulation of arrays by overlapping instruction CPU cycles. Discrete ordinates codes, which require the solving of large matrices, have proved to be major benefactors of vectorization. Monte Carlo transport, on the other hand, typically contains numerous logic statements and requires extensive redevelopment to benefit from vectorization.more » Multiprocessing and multitasking provide additional CPU cycles via multiple processors. Such systems are generally designed with either common memory access (multitasking) or distributed memory access. In both cases, theoretical speedup, as a function of the number of processors (P) and the fraction of task time that multiprocesses (f), can be formulated using Amdahl`s Law S ((f,P) = 1 f + f/P). However, for most applications this theoretical limit cannot be achieved, due to additional terms not included in Amdahl`s Law. Monte Carlo transport is a natural candidate for multiprocessing, since the particle tracks are generally independent and the precision of the result increases as the square root of the number of particles tracked.« less

Vector Adaptive/Predictive Encoding Of Speech

NASA Technical Reports Server (NTRS)

Chen, Juin-Hwey; Gersho, Allen

1989-01-01

Vector adaptive/predictive technique for digital encoding of speech signals yields decoded speech of very good quality after transmission at coding rate of 9.6 kb/s and of reasonably good quality at 4.8 kb/s. Requires 3 to 4 million multiplications and additions per second. Combines advantages of adaptive/predictive coding, and code-excited linear prediction, yielding speech of high quality but requires 600 million multiplications and additions per second at encoding rate of 4.8 kb/s. Vector adaptive/predictive coding technique bridges gaps in performance and complexity between adaptive/predictive coding and code-excited linear prediction.

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes.

PubMed

Burke, James M; Kincaid, Rodney P; Aloisio, Francesca; Welch, Nicole; Sullivan, Christopher S

2017-09-29

Short hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, typical U6/H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression. This can limit the efficacy and/or number of delivery vector options, particularly when delivery of multiple gene/shRNA combinations is required. Here, we develop a compact shRNA (cshRNA) expression system based on retroviral microRNA (miRNA) gene architecture that uses RNAP III type II promoters. We demonstrate that cshRNAs coded from as little as 100 bps of total coding space can precisely generate small interfering RNAs (siRNAs) that are active in the RNA-induced silencing complex (RISC). We provide an algorithm with a user-friendly interface to design cshRNAs for desired target genes. This cshRNA expression system reduces the coding space required for shRNA expression by >2-fold as compared to the typical U6/H1 promoters, which may facilitate therapeutic RNAi applications where delivery vector space is limiting. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Vector and Raster Data Storage Based on Morton Code

NASA Astrophysics Data System (ADS)

Zhou, G.; Pan, Q.; Yue, T.; Wang, Q.; Sha, H.; Huang, S.; Liu, X.

2018-05-01

Even though geomatique is so developed nowadays, the integration of spatial data in vector and raster formats is still a very tricky problem in geographic information system environment. And there is still not a proper way to solve the problem. This article proposes a method to interpret vector data and raster data. In this paper, we saved the image data and building vector data of Guilin University of Technology to Oracle database. Then we use ADO interface to connect database to Visual C++ and convert row and column numbers of raster data and X Y of vector data to Morton code in Visual C++ environment. This method stores vector and raster data to Oracle Database and uses Morton code instead of row and column and X Y to mark the position information of vector and raster data. Using Morton code to mark geographic information enables storage of data make full use of storage space, simultaneous analysis of vector and raster data more efficient and visualization of vector and raster more intuitive. This method is very helpful for some situations that need to analyse or display vector data and raster data at the same time.

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

PubMed

Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

2017-10-03

Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes.

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes

PubMed Central

Peng, Hui; Lan, Chaowang; Liu, Yuansheng; Liu, Tao; Blumenstein, Michael; Li, Jinyan

2017-01-01

Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures. This idea is supported by our observation that some substructures (e.g., the chromosome 6 p-arm) are highly preferred by disease-related protein coding genes, while some (e.g., the 21 p-arm) are not favored at all. The second sub-vector is 30-dimensional, characterizing the distribution of disease gene enriched KEGG pathways in comparison with our manually created pathway groups. The second sub-vector complements with the first one to differentiate between various diseases. Our prediction method outperforms the state-of-the-art methods on benchmark datasets for prioritizing disease related lncRNA genes. The method also works well when only the sequence information of an lncRNA gene is known, or even when a given disease has no currently recognized long non-coding genes. PMID:29108274

Carbon Nanotube Growth Rate Regression using Support Vector Machines and Artificial Neural Networks

DTIC Science & Technology

2014-03-27

intensity D peak. Reprinted with permission from [38]. The SVM classifier is trained using custom written Java code leveraging the Sequential Minimal...Society Encog is a machine learning framework for Java , C++ and .Net applications that supports Bayesian Networks, Hidden Markov Models, SVMs and ANNs [13...SVM classifiers are trained using Weka libraries and leveraging custom written Java code. The data set is created as an Attribute Relationship File

The Design of a Templated C++ Small Vector Class for Numerical Computing

NASA Technical Reports Server (NTRS)

Moran, Patrick J.

2000-01-01

We describe the design and implementation of a templated C++ class for vectors. The vector class is templated both for vector length and vector component type; the vector length is fixed at template instantiation time. The vector implementation is such that for a vector of N components of type T, the total number of bytes required by the vector is equal to N * size of (T), where size of is the built-in C operator. The property of having a size no bigger than that required by the components themselves is key in many numerical computing applications, where one may allocate very large arrays of small, fixed-length vectors. In addition to the design trade-offs motivating our fixed-length vector design choice, we review some of the C++ template features essential to an efficient, succinct implementation. In particular, we highlight some of the standard C++ features, such as partial template specialization, that are not supported by all compilers currently. This report provides an inventory listing the relevant support currently provided by some key compilers, as well as test code one can use to verify compiler capabilities.

Design and implementation of a cartographic client application for mobile devices using SVG Tiny and J2ME

NASA Astrophysics Data System (ADS)

Hui, L.; Behr, F.-J.; Schröder, D.

2006-10-01

The dissemination of digital geospatial data is available now on mobile devices such as PDAs (personal digital assistants) and smart-phones etc. The mobile devices which support J2ME (Java 2 Micro Edition) offer users and developers one open interface, which they can use to develop or download the software according their own demands. Currently WMS (Web Map Service) can afford not only traditional raster image, but also the vector image. SVGT (Scalable Vector Graphics Tiny) is one subset of SVG (Scalable Vector Graphics) and because of its precise vector information, original styling and small file size, SVGT format is fitting well for the geographic mapping purpose, especially for the mobile devices which has bandwidth net connection limitation. This paper describes the development of a cartographic client for the mobile devices, using SVGT and J2ME technology. Mobile device will be simulated on the desktop computer for a series of testing with WMS, for example, send request and get the responding data from WMS and then display both vector and raster format image. Analyzing and designing of System structure such as user interface and code structure are discussed, the limitation of mobile device should be taken into consideration for this applications. The parsing of XML document which is received from WMS after the GetCapabilities request and the visual realization of SVGT and PNG (Portable Network Graphics) image are important issues in codes' writing. At last the client was tested on Nokia S40/60 mobile phone successfully.

Holographic implementation of a binary associative memory for improved recognition

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Somnath; Ghosh, Ajay; Datta, Asit K.

1998-03-01

Neural network associate memory has found wide application sin pattern recognition techniques. We propose an associative memory model for binary character recognition. The interconnection strengths of the memory are binary valued. The concept of sparse coding is sued to enhance the storage efficiency of the model. The question of imposed preconditioning of pattern vectors, which is inherent in a sparsely coded conventional memory, is eliminated by using a multistep correlation technique an the ability of correct association is enhanced in a real-time application. A potential optoelectronic implementation of the proposed associative memory is also described. The learning and recall is possible by using digital optical matrix-vector multiplication, where full use of parallelism and connectivity of optics is made. A hologram is used in the experiment as a longer memory (LTM) for storing all input information. The short-term memory or the interconnection weight matrix required during the recall process is configured by retrieving the necessary information from the holographic LTM.

The use of computer-generated color graphic images for transient thermal analysis. [for hypersonic aircraft

NASA Technical Reports Server (NTRS)

Edwards, C. L. W.; Meissner, F. T.; Hall, J. B.

1979-01-01

Color computer graphics techniques were investigated as a means of rapidly scanning and interpreting large sets of transient heating data. The data presented were generated to support the conceptual design of a heat-sink thermal protection system (TPS) for a hypersonic research airplane. Color-coded vector and raster displays of the numerical geometry used in the heating calculations were employed to analyze skin thicknesses and surface temperatures of the heat-sink TPS under a variety of trajectory flight profiles. Both vector and raster displays proved to be effective means for rapidly identifying heat-sink mass concentrations, regions of high heating, and potentially adverse thermal gradients. The color-coded (raster) surface displays are a very efficient means for displaying surface-temperature and heating histories, and thereby the more stringent design requirements can quickly be identified. The related hardware and software developments required to implement both the vector and the raster displays for this application are also discussed.

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

DOE PAGES

O'keefe, Matthew; Parr, Terence; Edgar, B. Kevin; ...

1995-01-01

Massively parallel processors (MPPs) hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. Wemore » have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.« less

Production of SV40-derived vectors.

PubMed

Strayer, David S; Mitchell, Christine; Maier, Dawn A; Nichols, Carmen N

2010-06-01

Recombinant simian virus 40 (rSV40)-derived vectors are particularly useful for gene delivery to bone marrow progenitor cells and their differentiated derivatives, certain types of epithelial cells (e.g., hepatocytes), and central nervous system neurons and microglia. They integrate rapidly into cellular DNA to provide long-term gene expression in vitro and in vivo in both resting and dividing cells. Here we describe a protocol for production and purification of these vectors. These procedures require only packaging cells (e.g., COS-7) and circular vector genome DNA. Amplification involves repeated infection of packaging cells with vector produced by transfection. Cotransfection is not required in any step. Viruses are purified by centrifugation using discontinuous sucrose or cesium chloride (CsCl) gradients and resulting vectors are replication-incompetent and contain no detectable wild-type SV40 revertants. These approaches are simple, give reproducible results, and may be used to generate vectors that are deleted only for large T antigen (Tag), or for all SV40-coding sequences capable of carrying up to 5 kb of foreign DNA. These vectors are best applied to long-term expression of proteins normally encoded by mammalian cells or by viruses that infect mammalian cells, or of untranslated RNAs (e.g., RNA interference). The preparative approaches described facilitate application of these vectors and allow almost any laboratory to exploit their strengths for diverse gene delivery applications.

Vector quantization for efficient coding of upper subbands

NASA Technical Reports Server (NTRS)

Zeng, W. J.; Huang, Y. F.

1994-01-01

This paper examines the application of vector quantization (VQ) to exploit both intra-band and inter-band redundancy in subband coding. The focus here is on the exploitation of inter-band dependency. It is shown that VQ is particularly suitable and effective for coding the upper subbands. Three subband decomposition-based VQ coding schemes are proposed here to exploit the inter-band dependency by making full use of the extra flexibility of VQ approach over scalar quantization. A quadtree-based variable rate VQ (VRVQ) scheme which takes full advantage of the intra-band and inter-band redundancy is first proposed. Then, a more easily implementable alternative based on an efficient block-based edge estimation technique is employed to overcome the implementational barriers of the first scheme. Finally, a predictive VQ scheme formulated in the context of finite state VQ is proposed to further exploit the dependency among different subbands. A VRVQ scheme proposed elsewhere is extended to provide an efficient bit allocation procedure. Simulation results show that these three hybrid techniques have advantages, in terms of peak signal-to-noise ratio (PSNR) and complexity, over other existing subband-VQ approaches.

Global MHD simulation of magnetosphere using HPF

NASA Astrophysics Data System (ADS)

Ogino, T.

We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5% using 56 PEs of Fujitsu VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

Neighboring block based disparity vector derivation for multiview compatible 3D-AVC

NASA Astrophysics Data System (ADS)

Kang, Jewon; Chen, Ying; Zhang, Li; Zhao, Xin; Karczewicz, Marta

2013-09-01

3D-AVC being developed under Joint Collaborative Team on 3D Video Coding (JCT-3V) significantly outperforms the Multiview Video Coding plus Depth (MVC+D) which simultaneously encodes texture views and depth views with the multiview extension of H.264/AVC (MVC). However, when the 3D-AVC is configured to support multiview compatibility in which texture views are decoded without depth information, the coding performance becomes significantly degraded. The reason is that advanced coding tools incorporated into the 3D-AVC do not perform well due to the lack of a disparity vector converted from the depth information. In this paper, we propose a disparity vector derivation method utilizing only the information of texture views. Motion information of neighboring blocks is used to determine a disparity vector for a macroblock, so that the derived disparity vector is efficiently used for the coding tools in 3D-AVC. The proposed method significantly improves a coding gain of the 3D-AVC in the multiview compatible mode about 20% BD-rate saving in the coded views and 26% BD-rate saving in the synthesized views on average.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexander E; Gschwind, Michael K; Gunnels, John A

2013-10-29

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexandre E [Chappaqua, NY; Gschwind, Michael K [Chappaqua, NY; Gunnels, John A [Yorktown Heights, NY

2012-08-28

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Low-rate image coding using vector quantization

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

Makur, A.

1990-01-01

This thesis deals with the development and analysis of a computationally simple vector quantization image compression system for coding monochrome images at low bit rate. Vector quantization has been known to be an effective compression scheme when a low bit rate is desirable, but the intensive computation required in a vector quantization encoder has been a handicap in using it for low rate image coding. The present work shows that, without substantially increasing the coder complexity, it is indeed possible to achieve acceptable picture quality while attaining a high compression ratio. Several modifications to the conventional vector quantization coder aremore » proposed in the thesis. These modifications are shown to offer better subjective quality when compared to the basic coder. Distributed blocks are used instead of spatial blocks to construct the input vectors. A class of input-dependent weighted distortion functions is used to incorporate psychovisual characteristics in the distortion measure. Computationally simple filtering techniques are applied to further improve the decoded image quality. Finally, unique designs of the vector quantization coder using electronic neural networks are described, so that the coding delay is reduced considerably.« less

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

Singer product apertures-A coded aperture system with a fast decoding algorithm

NASA Astrophysics Data System (ADS)

Byard, Kevin; Shutler, Paul M. E.

2017-06-01

A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

Applications of Signal Processing in Digital Communications. Appendix.

DTIC Science & Technology

1991-04-01

we get a separable alphabet with 128 vectors (see Fig. 3). Among It is seen that the effect of R on a two-dimencional vector hem, 32 have energy 3c 2...and 96 have energy b2 + 2c 2. is to rotate it by an angle 21r/M, and the effect of T is to The average energy is 1. exchange its components. This...Sh, S, are two elements of It, the intradistance set associ- generating the code are d.ose associated to nlane ritalins ated with the coset Si! Include

Global Magnetohydrodynamic Simulation Using High Performance FORTRAN on Parallel Computers

NASA Astrophysics Data System (ADS)

Ogino, T.

High Performance Fortran (HPF) is one of modern and common techniques to achieve high performance parallel computation. We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5 VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

A progressive data compression scheme based upon adaptive transform coding: Mixture block coding of natural images

NASA Technical Reports Server (NTRS)

Rost, Martin C.; Sayood, Khalid

1991-01-01

A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.

Progressive low-bitrate digital color/monochrome image coding by neuro-fuzzy clustering

NASA Astrophysics Data System (ADS)

Mitra, Sunanda; Meadows, Steven

1997-10-01

Color image coding at low bit rates is an area of research that is just being addressed in recent literature since the problems of storage and transmission of color images are becoming more prominent in many applications. Current trends in image coding exploit the advantage of subband/wavelet decompositions in reducing the complexity in optimal scalar/vector quantizer (SQ/VQ) design. Compression ratios (CRs) of the order of 10:1 to 20:1 with high visual quality have been achieved by using vector quantization of subband decomposed color images in perceptually weighted color spaces. We report the performance of a recently developed adaptive vector quantizer, namely, AFLC-VQ for effective reduction in bit rates while maintaining high visual quality of reconstructed color as well as monochrome images. For 24 bit color images, excellent visual quality is maintained upto a bit rate reduction to approximately 0.48 bpp (for each color plane or monochrome 0.16 bpp, CR 50:1) by using the RGB color space. Further tuning of the AFLC-VQ, and addition of an entropy coder module after the VQ stage results in extremely low bit rates (CR 80:1) for good quality, reconstructed images. Our recent study also reveals that for similar visual quality, RGB color space requires less bits/pixel than either the YIQ, or HIS color space for storing the same information when entropy coding is applied. AFLC-VQ outperforms other standard VQ and adaptive SQ techniques in retaining visual fidelity at similar bit rate reduction.

The ASC Sequoia Programming Model

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

Seager, M

2008-08-06

In the late 1980's and early 1990's, Lawrence Livermore National Laboratory was deeply engrossed in determining the next generation programming model for the Integrated Design Codes (IDC) beyond vectorization for the Cray 1s series of computers. The vector model, developed in mid 1970's first for the CDC 7600 and later extended from stack based vector operation to memory to memory operations for the Cray 1s, lasted approximately 20 years (See Slide 5). The Cray vector era was deemed an extremely long lived era as it allowed vector codes to be developed over time (the Cray 1s were faster in scalarmore » mode than the CDC 7600) with vector unit utilization increasing incrementally over time. The other attributes of the Cray vector era at LLNL were that we developed, supported and maintained the Operating System (LTSS and later NLTSS), communications protocols (LINCS), Compilers (Civic Fortran77 and Model), operating system tools (e.g., batch system, job control scripting, loaders, debuggers, editors, graphics utilities, you name it) and math and highly machine optimized libraries (e.g., SLATEC, and STACKLIB). Although LTSS was adopted by Cray for early system generations, they later developed COS and UNICOS operating systems and environment on their own. In the late 1970s and early 1980s two trends appeared that made the Cray vector programming model (described above including both the hardware and system software aspects) seem potentially dated and slated for major revision. These trends were the appearance of low cost CMOS microprocessors and their attendant, departmental and mini-computers and later workstations and personal computers. With the wide spread adoption of Unix in the early 1980s, it appeared that LLNL (and the other DOE Labs) would be left out of the mainstream of computing without a rapid transition to these 'Killer Micros' and modern OS and tools environments. The other interesting advance in the period is that systems were being developed with multiple 'cores' in them and called Symmetric Multi-Processor or Shared Memory Processor (SMP) systems. The parallel revolution had begun. The Laboratory started a small 'parallel processing project' in 1983 to study the new technology and its application to scientific computing with four people: Tim Axelrod, Pete Eltgroth, Paul Dubois and Mark Seager. Two years later, Eugene Brooks joined the team. This team focused on Unix and 'killer micro' SMPs. Indeed, Eugene Brooks was credited with coming up with the 'Killer Micro' term. After several generations of SMP platforms (e.g., Sequent Balance 8000 with 8 33MHz MC32032s, Allian FX8 with 8 MC68020 and FPGA based Vector Units and finally the BB&N Butterfly with 128 cores), it became apparent to us that the killer micro revolution would indeed take over Crays and that we definitely needed a new programming and systems model. The model developed by Mark Seager and Dale Nielsen focused on both the system aspects (Slide 3) and the code development aspects (Slide 4). Although now succinctly captured in two attached slides, at the time there was tremendous ferment in the research community as to what parallel programming model would emerge, dominate and survive. In addition, we wanted a model that would provide portability between platforms of a single generation but also longevity over multiple--and hopefully--many generations. Only after we developed the 'Livermore Model' and worked it out in considerable detail did it become obvious that what we came up with was the right approach. In a nutshell, the applications programming model of the Livermore Model posited that SMP parallelism would ultimately not scale indefinitely and one would have to bite the bullet and implement MPI parallelism within the Integrated Design Code (IDC). We also had a major emphasis on doing everything in a completely standards based, portable methodology with POSIX/Unix as the target environment. We decided against specialized libraries like STACKLIB for performance, but kept as many general purpose, portable math libraries as were needed by the codes. Third, we assumed that the SMPs in clusters would evolve in time to become more powerful, feature rich and, in particular, offer more cores. Thus, we focused on OpenMP, and POSIX PThreads for programming SMP parallelism. These code porting efforts were lead by Dale Nielsen, A-Division code group leader, and Randy Christensen, B-Division code group leader. Most of the porting effort revolved removing 'Crayisms' in the codes: artifacts of LTSS/NLTSS, Civic compiler extensions beyond Fortran77, IO libraries and dealing with new code control languages (we switched to Perl and later to Python). Adding MPI to the codes was initially problematic and error prone because the programmers used MPI directly and sprinkled the calls throughout the code.« less

Low-complexity video encoding method for wireless image transmission in capsule endoscope.

PubMed

Takizawa, Kenichi; Hamaguchi, Kiyoshi

2010-01-01

This paper presents a low-complexity video encoding method applicable for wireless image transmission in capsule endoscopes. This encoding method is based on Wyner-Ziv theory, in which side information available at a transmitter is treated as side information at its receiver. Therefore complex processes in video encoding, such as estimation of the motion vector, are moved to the receiver side, which has a larger-capacity battery. As a result, the encoding process is only to decimate coded original data through channel coding. We provide a performance evaluation for a low-density parity check (LDPC) coding method in the AWGN channel.

Vector Potential Generation for Numerical Relativity Simulations

NASA Astrophysics Data System (ADS)

Silberman, Zachary; Faber, Joshua; Adams, Thomas; Etienne, Zachariah; Ruchlin, Ian

2017-01-01

Many different numerical codes are employed in studies of highly relativistic magnetized accretion flows around black holes. Based on the formalisms each uses, some codes evolve the magnetic field vector B, while others evolve the magnetic vector potential A, the two being related by the curl: B=curl(A). Here, we discuss how to generate vector potentials corresponding to specified magnetic fields on staggered grids, a surprisingly difficult task on finite cubic domains. The code we have developed solves this problem in two ways: a brute-force method, whose scaling is nearly linear in the number of grid cells, and a direct linear algebra approach. We discuss the success both algorithms have in generating smooth vector potential configurations and how both may be extended to more complicated cases involving multiple mesh-refinement levels. NSF ACI-1550436

Insertion of operation-and-indicate instructions for optimized SIMD code

DOEpatents

Eichenberger, Alexander E; Gara, Alan; Gschwind, Michael K

2013-06-04

Mechanisms are provided for inserting indicated instructions for tracking and indicating exceptions in the execution of vectorized code. A portion of first code is received for compilation. The portion of first code is analyzed to identify non-speculative instructions performing designated non-speculative operations in the first code that are candidates for replacement by replacement operation-and-indicate instructions that perform the designated non-speculative operations and further perform an indication operation for indicating any exception conditions corresponding to special exception values present in vector register inputs to the replacement operation-and-indicate instructions. The replacement is performed and second code is generated based on the replacement of the at least one non-speculative instruction. The data processing system executing the compiled code is configured to store special exception values in vector output registers, in response to a speculative instruction generating an exception condition, without initiating exception handling.

Parallel-vector computation for structural analysis and nonlinear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.

1990-01-01

Practical engineering application can often be formulated in the form of a constrained optimization problem. There are several solution algorithms for solving a constrained optimization problem. One approach is to convert a constrained problem into a series of unconstrained problems. Furthermore, unconstrained solution algorithms can be used as part of the constrained solution algorithms. Structural optimization is an iterative process where one starts with an initial design, a finite element structure analysis is then performed to calculate the response of the system (such as displacements, stresses, eigenvalues, etc.). Based upon the sensitivity information on the objective and constraint functions, an optimizer such as ADS or IDESIGN, can be used to find the new, improved design. For the structural analysis phase, the equation solver for the system of simultaneous, linear equations plays a key role since it is needed for either static, or eigenvalue, or dynamic analysis. For practical, large-scale structural analysis-synthesis applications, computational time can be excessively large. Thus, it is necessary to have a new structural analysis-synthesis code which employs new solution algorithms to exploit both parallel and vector capabilities offered by modern, high performance computers such as the Convex, Cray-2 and Cray-YMP computers. The objective of this research project is, therefore, to incorporate the latest development in the parallel-vector equation solver, PVSOLVE into the widely popular finite-element production code, such as the SAP-4. Furthermore, several nonlinear unconstrained optimization subroutines have also been developed and tested under a parallel computer environment. The unconstrained optimization subroutines are not only useful in their own right, but they can also be incorporated into a more popular constrained optimization code, such as ADS.

A hybrid LBG/lattice vector quantizer for high quality image coding

NASA Technical Reports Server (NTRS)

Ramamoorthy, V.; Sayood, K.; Arikan, E. (Editor)

1991-01-01

It is well known that a vector quantizer is an efficient coder offering a good trade-off between quantization distortion and bit rate. The performance of a vector quantizer asymptotically approaches the optimum bound with increasing dimensionality. A vector quantized image suffers from the following types of degradations: (1) edge regions in the coded image contain staircase effects, (2) quasi-constant or slowly varying regions suffer from contouring effects, and (3) textured regions lose details and suffer from granular noise. All three of these degradations are due to the finite size of the code book, the distortion measures used in the design, and due to the finite training procedure involved in the construction of the code book. In this paper, we present an adaptive technique which attempts to ameliorate the edge distortion and contouring effects.

Fast image interpolation for motion estimation using graphics hardware

NASA Astrophysics Data System (ADS)

Kelly, Francis; Kokaram, Anil

2004-05-01

Motion estimation and compensation is the key to high quality video coding. Block matching motion estimation is used in most video codecs, including MPEG-2, MPEG-4, H.263 and H.26L. Motion estimation is also a key component in the digital restoration of archived video and for post-production and special effects in the movie industry. Sub-pixel accurate motion vectors can improve the quality of the vector field and lead to more efficient video coding. However sub-pixel accuracy requires interpolation of the image data. Image interpolation is a key requirement of many image processing algorithms. Often interpolation can be a bottleneck in these applications, especially in motion estimation due to the large number pixels involved. In this paper we propose using commodity computer graphics hardware for fast image interpolation. We use the full search block matching algorithm to illustrate the problems and limitations of using graphics hardware in this way.

Effective Vectorization with OpenMP 4.5

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

Huber, Joseph N.; Hernandez, Oscar R.; Lopez, Matthew Graham

This paper describes how the Single Instruction Multiple Data (SIMD) model and its extensions in OpenMP work, and how these are implemented in different compilers. Modern processors are highly parallel computational machines which often include multiple processors capable of executing several instructions in parallel. Understanding SIMD and executing instructions in parallel allows the processor to achieve higher performance without increasing the power required to run it. SIMD instructions can significantly reduce the runtime of code by executing a single operation on large groups of data. The SIMD model is so integral to the processor s potential performance that, if SIMDmore » is not utilized, less than half of the processor is ever actually used. Unfortunately, using SIMD instructions is a challenge in higher level languages because most programming languages do not have a way to describe them. Most compilers are capable of vectorizing code by using the SIMD instructions, but there are many code features important for SIMD vectorization that the compiler cannot determine at compile time. OpenMP attempts to solve this by extending the C++/C and Fortran programming languages with compiler directives that express SIMD parallelism. OpenMP is used to pass hints to the compiler about the code to be executed in SIMD. This is a key resource for making optimized code, but it does not change whether or not the code can use SIMD operations. However, in many cases critical functions are limited by a poor understanding of how SIMD instructions are actually implemented, as SIMD can be implemented through vector instructions or simultaneous multi-threading (SMT). We have found that it is often the case that code cannot be vectorized, or is vectorized poorly, because the programmer does not have sufficient knowledge of how SIMD instructions work.« less

Vector quantization

NASA Technical Reports Server (NTRS)

Gray, Robert M.

1989-01-01

During the past ten years Vector Quantization (VQ) has developed from a theoretical possibility promised by Shannon's source coding theorems into a powerful and competitive technique for speech and image coding and compression at medium to low bit rates. In this survey, the basic ideas behind the design of vector quantizers are sketched and some comments made on the state-of-the-art and current research efforts.

Memorization of Sequences of Movements of the Right or the Left Hand by Right- and Left-Handers: Vector Coding.

PubMed

Bobrova, E V; Bogacheva, I N; Lyakhovetskii, V A; Fabinskaja, A A; Fomina, E V

2017-01-01

In order to test the hypothesis of hemisphere specialization for different types of information coding (the right hemisphere, for positional coding; the left one, for vector coding), we analyzed the errors of right and left-handers during a task involving the memorization of sequences of movements by the left or the right hand, which activates vector coding by changing the order of movements in memorized sequences. The task was first performed by the right or the left hand, then by the opposite hand. It was found that both'right- and left-handers use the information about the previous movements of the dominant hand, but not of the non-dom" inant one. After changing the hand, right-handers use the information about previous movements of the second hand, while left-handers do not. We compared our results with the data of previous experiments, in which positional coding was activated, and concluded that both right- and left-handers use vector coding for memorizing the sequences of their dominant hands and positional coding for memorizing the sequences of non-dominant hand. No similar patterns of errors were found between right- and left-handers after changing the hand, which suggests that in right- and left-handersthe skills are transferred in different ways depending on the type of coding.

Vector quantizer based on brightness maps for image compression with the polynomial transform

NASA Astrophysics Data System (ADS)

Escalante-Ramirez, Boris; Moreno-Gutierrez, Mauricio; Silvan-Cardenas, Jose L.

2002-11-01

We present a vector quantization scheme acting on brightness fields based on distance/distortion criteria correspondent with psycho-visual aspects. These criteria quantify sensorial distortion between vectors that represent either portions of a digital image or alternatively, coefficients of a transform-based coding system. In the latter case, we use an image representation model, namely the Hermite transform, that is based on some of the main perceptual characteristics of the human vision system (HVS) and in their response to light stimulus. Energy coding in the brightness domain, determination of local structure, code-book training and local orientation analysis are all obtained by means of the Hermite transform. This paper, for thematic reasons, is divided in four sections. The first one will shortly highlight the importance of having newer and better compression algorithms. This section will also serve to explain briefly the most relevant characteristics of the HVS, advantages and disadvantages related with the behavior of our vision in front of ocular stimulus. The second section shall go through a quick review of vector quantization techniques, focusing their performance on image treatment, as a preview for the image vector quantizer compressor actually constructed in section 5. Third chapter was chosen to concentrate the most important data gathered on brightness models. The building of this so-called brightness maps (quantification of the human perception on the visible objects reflectance), in a bi-dimensional model, will be addressed here. The Hermite transform, a special case of polynomial transforms, and its usefulness, will be treated, in an applicable discrete form, in the fourth chapter. As we have learned from previous works 1, Hermite transform has showed to be a useful and practical solution to efficiently code the energy within an image block, deciding which kind of quantization is to be used upon them (whether scalar or vector). It will also be a unique tool to structurally classify the image block within a given lattice. This particular operation intends to be one of the main contributions of this work. The fifth section will fuse the proposals derived from the study of the three main topics- addressed in the last sections- in order to propose an image compression model that takes advantage of vector quantizers inside the brightness transformed domain to determine the most important structures, finding the energy distribution inside the Hermite domain. Sixth and last section will show some results obtained while testing the coding-decoding model. The guidelines to evaluate the image compressing performance were the compression ratio, SNR and psycho-visual quality. Some conclusions derived from the research and possible unexplored paths will be shown on this section as well.

TOUGH+ v1.5 Core Code

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

Moridis, George J.

TOUGH+ v1.5 is a numerical code for the simulation of multi-phase, multi-component flow and transport of mass and heat through porous and fractured media, and represents the third update of the code since its first release [Moridis et al., 2008]. TOUGH+ is a successor to the TOUGH2 [Pruess et al., 1991; 2012] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstations, PC, Macintosh). TOUGH+ v1.5 employs dynamic memory allocation, thus minimizing storage requirements. It has amore » completely modular structure, follows the tenets of Object-Oriented Programming (OOP), and involves the advanced features of FORTRAN 95/2003, i.e., modules, derived data types, the use of pointers, lists and trees, data encapsulation, defined operators and assignments, operator extension and overloading, use of generic procedures, and maximum use of the powerful intrinsic vector and matrix processing operations. TOUGH+ v1.5 is the core code for its family of applications, i.e., the part of the code that is common to all its applications. It provides a description of the underlying physics and thermodynamics of non-isothermal flow, of the mathematical and numerical approaches, as well as a detailed explanation of the general (common to all applications) input requirements, options, capabilities and output specifications. The core code cannot run by itself: it needs to be coupled with the code for the specific TOUGH+ application option that describes a particular type of problem. The additional input requirements specific to a particular TOUGH+ application options and related illustrative examples can be found in the corresponding User's Manual.« less

Improved dense trajectories for action recognition based on random projection and Fisher vectors

NASA Astrophysics Data System (ADS)

Ai, Shihui; Lu, Tongwei; Xiong, Yudian

2018-03-01

As an important application of intelligent monitoring system, the action recognition in video has become a very important research area of computer vision. In order to improve the accuracy rate of the action recognition in video with improved dense trajectories, one advanced vector method is introduced. Improved dense trajectories combine Fisher Vector with Random Projection. The method realizes the reduction of the characteristic trajectory though projecting the high-dimensional trajectory descriptor into the low-dimensional subspace based on defining and analyzing Gaussian mixture model by Random Projection. And a GMM-FV hybrid model is introduced to encode the trajectory feature vector and reduce dimension. The computational complexity is reduced by Random Projection which can drop Fisher coding vector. Finally, a Linear SVM is used to classifier to predict labels. We tested the algorithm in UCF101 dataset and KTH dataset. Compared with existed some others algorithm, the result showed that the method not only reduce the computational complexity but also improved the accuracy of action recognition.

Vectorization of a classical trajectory code on a floating point systems, Inc. Model 164 attached processor.

PubMed

Kraus, Wayne A; Wagner, Albert F

1986-04-01

A triatomic classical trajectory code has been modified by extensive vectorization of the algorithms to achieve much improved performance on an FPS 164 attached processor. Extensive timings on both the FPS 164 and a VAX 11/780 with floating point accelerator are presented as a function of the number of trajectories simultaneously run. The timing tests involve a potential energy surface of the LEPS variety and trajectories with 1000 time steps. The results indicate that vectorization results in timing improvements on both the VAX and the FPS. For larger numbers of trajectories run simultaneously, up to a factor of 25 improvement in speed occurs between VAX and FPS vectorized code. Copyright © 1986 John Wiley & Sons, Inc.

Multispectral code excited linear prediction coding and its application in magnetic resonance images.

PubMed

Hu, J H; Wang, Y; Cahill, P T

1997-01-01

This paper reports a multispectral code excited linear prediction (MCELP) method for the compression of multispectral images. Different linear prediction models and adaptation schemes have been compared. The method that uses a forward adaptive autoregressive (AR) model has been proven to achieve a good compromise between performance, complexity, and robustness. This approach is referred to as the MFCELP method. Given a set of multispectral images, the linear predictive coefficients are updated over nonoverlapping three-dimensional (3-D) macroblocks. Each macroblock is further divided into several 3-D micro-blocks, and the best excitation signal for each microblock is determined through an analysis-by-synthesis procedure. The MFCELP method has been applied to multispectral magnetic resonance (MR) images. To satisfy the high quality requirement for medical images, the error between the original image set and the synthesized one is further specified using a vector quantizer. This method has been applied to images from 26 clinical MR neuro studies (20 slices/study, three spectral bands/slice, 256x256 pixels/band, 12 b/pixel). The MFCELP method provides a significant visual improvement over the discrete cosine transform (DCT) based Joint Photographers Expert Group (JPEG) method, the wavelet transform based embedded zero-tree wavelet (EZW) coding method, and the vector tree (VT) coding method, as well as the multispectral segmented autoregressive moving average (MSARMA) method we developed previously.

Polarized skylight navigation in insects: model and electrophysiology of e-vector coding by neurons in the central complex.

PubMed

Sakura, Midori; Lambrinos, Dimitrios; Labhart, Thomas

2008-02-01

Many insects exploit skylight polarization for visual compass orientation or course control. As found in crickets, the peripheral visual system (optic lobe) contains three types of polarization-sensitive neurons (POL neurons), which are tuned to different ( approximately 60 degrees diverging) e-vector orientations. Thus each e-vector orientation elicits a specific combination of activities among the POL neurons coding any e-vector orientation by just three neural signals. In this study, we hypothesize that in the presumed orientation center of the brain (central complex) e-vector orientation is population-coded by a set of "compass neurons." Using computer modeling, we present a neural network model transforming the signal triplet provided by the POL neurons to compass neuron activities coding e-vector orientation by a population code. Using intracellular electrophysiology and cell marking, we present evidence that neurons with the response profile of the presumed compass neurons do indeed exist in the insect brain: each of these compass neuron-like (CNL) cells is activated by a specific e-vector orientation only and otherwise remains silent. Morphologically, CNL cells are tangential neurons extending from the lateral accessory lobe to the lower division of the central body. Surpassing the modeled compass neurons in performance, CNL cells are insensitive to the degree of polarization of the stimulus between 99% and at least down to 18% polarization and thus largely disregard variations of skylight polarization due to changing solar elevations or atmospheric conditions. This suggests that the polarization vision system includes a gain control circuit keeping the output activity at a constant level.

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1994-01-01

The unequal error protection capabilities of convolutional and trellis codes are studied. In certain environments, a discrepancy in the amount of error protection placed on different information bits is desirable. Examples of environments which have data of varying importance are a number of speech coding algorithms, packet switched networks, multi-user systems, embedded coding systems, and high definition television. Encoders which provide more than one level of error protection to information bits are called unequal error protection (UEP) codes. In this work, the effective free distance vector, d, is defined as an alternative to the free distance as a primary performance parameter for UEP convolutional and trellis encoders. For a given (n, k), convolutional encoder, G, the effective free distance vector is defined as the k-dimensional vector d = (d(sub 0), d(sub 1), ..., d(sub k-1)), where d(sub j), the j(exp th) effective free distance, is the lowest Hamming weight among all code sequences that are generated by input sequences with at least one '1' in the j(exp th) position. It is shown that, although the free distance for a code is unique to the code and independent of the encoder realization, the effective distance vector is dependent on the encoder realization.

Decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H. Lee; Ganti, Anand; Resnick, David R

2013-10-22

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

Design, decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H Lee; Ganti, Anand; Resnick, David R

2014-06-17

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

Decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H Lee; Ganti, Anand; Resnick, David R

2014-11-18

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

User's guide for vectorized code EQUIL for calculating equilibrium chemistry on Control Data STAR-100 computer

NASA Technical Reports Server (NTRS)

Kumar, A.; Graves, R. A., Jr.; Weilmuenster, K. J.

1980-01-01

A vectorized code, EQUIL, was developed for calculating the equilibrium chemistry of a reacting gas mixture on the Control Data STAR-100 computer. The code provides species mole fractions, mass fractions, and thermodynamic and transport properties of the mixture for given temperature, pressure, and elemental mass fractions. The code is set up for the electrons H, He, C, O, N system of elements. In all, 24 chemical species are included.

Application of Polarization to the MODIS Aerosol Retrieval Over Land

NASA Technical Reports Server (NTRS)

Levy, Robert C.; Remer, Lorraine R.; Kaufman, Yoram J.

2004-01-01

Reflectance measurements in the visible and infrared wavelengths, from the Moderate Resolution Imaging Spectroradiometer (MODIS), are used to derive aerosol optical thicknesses (AOT) and aerosol properties over land surfaces. The measured spectral reflectance is compared with lookup tables, containing theoretical reflectance calculated by radiative transfer (RT) code. Specifically, this RT code calculates top of the atmosphere (TOA) intensities based on a scalar treatment of radiation, neglecting the effects of polarization. In the red and near infrared (NIR) wavelengths the use of the scalar RT code is of sufficient accuracy to model TOA reflectance. However, in the blue, molecular and aerosol scattering dominate the TOA signal. Here, polarization effects can be large, and should be included in the lookup table derivation. Using a RT code that allows for both vector and scalar calculations, we examine the reflectance differences at the TOA, with and without polarization. We find that the differences in blue channel TOA reflectance (vector - scalar) may reach values of 0.01 or greater, depending on the sun/surface/sensor scattering geometry. Reflectance errors of this magnitude translate to AOT differences of 0.1, which is a very large error, especially when the actual AOT is low. As a result of this study, the next version of aerosol retrieval from MODIS over land will include polarization.

Roofline Analysis in the Intel® Advisor to Deliver Optimized Performance for applications on Intel® Xeon Phi™ Processor

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

Koskela, Tuomas S.; Lobet, Mathieu; Deslippe, Jack

In this session we show, in two case studies, how the roofline feature of Intel Advisor has been utilized to optimize the performance of kernels of the XGC1 and PICSAR codes in preparation for Intel Knights Landing architecture. The impact of the implemented optimizations and the benefits of using the automatic roofline feature of Intel Advisor to study performance of large applications will be presented. This demonstrates an effective optimization strategy that has enabled these science applications to achieve up to 4.6 times speed-up and prepare for future exascale architectures. # Goal/Relevance of Session The roofline model [1,2] is amore » powerful tool for analyzing the performance of applications with respect to the theoretical peak achievable on a given computer architecture. It allows one to graphically represent the performance of an application in terms of operational intensity, i.e. the ratio of flops performed and bytes moved from memory in order to guide optimization efforts. Given the scale and complexity of modern science applications, it can often be a tedious task for the user to perform the analysis on the level of functions or loops to identify where performance gains can be made. With new Intel tools, it is now possible to automate this task, as well as base the estimates of peak performance on measurements rather than vendor specifications. The goal of this session is to demonstrate how the roofline feature of Intel Advisor can be used to balance memory vs. computation related optimization efforts and effectively identify performance bottlenecks. A series of typical optimization techniques: cache blocking, structure refactoring, data alignment, and vectorization illustrated by the kernel cases will be addressed. # Description of the codes ## XGC1 The XGC1 code [3] is a magnetic fusion Particle-In-Cell code that uses an unstructured mesh for its Poisson solver that allows it to accurately resolve the edge plasma of a magnetic fusion device. After recent optimizations to its collision kernel [4], most of the computing time is spent in the electron push (pushe) kernel, where these optimization efforts have been focused. The kernel code scaled well with MPI+OpenMP but had almost no automatic compiler vectorization, in part due to indirect memory addresses and in part due to low trip counts of low-level loops that would be candidates for vectorization. Particle blocking and sorting have been implemented to increase trip counts of low-level loops and improve memory locality, and OpenMP directives have been added to vectorize compute-intensive loops that were identified by Advisor. The optimizations have improved the performance of the pushe kernel 2x on Haswell processors and 1.7x on KNL. The KNL node-for-node performance has been brought to within 30% of a NERSC Cori phase I Haswell node and we expect to bridge this gap by reducing the memory footprint of compute intensive routines to improve cache reuse. ## PICSAR is a Fortran/Python high-performance Particle-In-Cell library targeting at MIC architectures first designed to be coupled with the PIC code WARP for the simulation of laser-matter interaction and particle accelerators. PICSAR also contains a FORTRAN stand-alone kernel for performance studies and benchmarks. A MPI domain decomposition is used between NUMA domains and a tile decomposition (cache-blocking) handled by OpenMP has been added for shared-memory parallelism and better cache management. The so-called current deposition and field gathering steps that compose the PIC time loop constitute major hotspots that have been rewritten to enable more efficient vectorization. Particle communications between tiles and MPI domain has been merged and parallelized. All considered, these improvements provide speedups of 3.1 for order 1 and 4.6 for order 3 interpolation shape factors on KNL configured in SNC4 quadrant flat mode. Performance is similar between a node of cori phase 1 and KNL at order 1 and better on KNL by a factor 1.6 at order 3 with the considered test case (homogeneous thermal plasma).« less

A border-ownership model based on computational electromagnetism.

PubMed

Zainal, Zaem Arif; Satoh, Shunji

2018-03-01

The mathematical relation between a vector electric field and its corresponding scalar potential field is useful to formulate computational problems of lower/middle-order visual processing, specifically related to the assignment of borders to the side of the object: so-called border ownership (BO). BO coding is a key process for extracting the objects from the background, allowing one to organize a cluttered scene. We propose that the problem is solvable simultaneously by application of a theorem of electromagnetism, i.e., "conservative vector fields have zero rotation, or "curl." We hypothesize that (i) the BO signal is definable as a vector electric field with arrowheads pointing to the inner side of perceived objects, and (ii) its corresponding scalar field carries information related to perceived order in depth of occluding/occluded objects. A simple model was developed based on this computational theory. Model results qualitatively agree with object-side selectivity of BO-coding neurons, and with perceptions of object order. The model update rule can be reproduced as a plausible neural network that presents new interpretations of existing physiological results. Results of this study also suggest that T-junction detectors are unnecessary to calculate depth order. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Vaccine application of recombinant herpesviruses].

PubMed

Yokoyama, N; Xuan, X; Mikami, T

2000-04-01

Recently, genetic engineering using recombinant DNA techniques has been applied to design new viral vaccines in order to reduce some problems which the present viral vaccines have. Up to now, many viruses have been investigated for development of recombinant attenuated vaccines or live viral vectors for delivery of foreign genes coding immunogenic antigens. In this article, we introduced the new vaccine strategy using genetically engineered herpesviruses.

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016.

PubMed

Kyalo, David; Amratia, Punam; Mundia, Clara W; Mbogo, Charles M; Coetzee, Maureen; Snow, Robert W

2017-01-01

Background : Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods : We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results : The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion : We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for African national malaria control programmes planning their future control and elimination strategies.

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016

PubMed Central

Kyalo, David; Amratia, Punam; Mundia, Clara W.; Mbogo, Charles M.; Coetzee, Maureen; Snow, Robert W.

2017-01-01

Background: Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods: We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results: The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion: We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for African national malaria control programmes planning their future control and elimination strategies. PMID:28884158

Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants

PubMed Central

Perilla-Henao, Laura M.; Casteel, Clare L.

2016-01-01

Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant–virus–vector interactions has flourished in recent years, plant–bacteria–vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant–bacteria–vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and ‘Candidatus Phytoplasma spp.’. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector–plant–bacteria interactions. PMID:27555855

More About Vector Adaptive/Predictive Coding Of Speech

NASA Technical Reports Server (NTRS)

Jedrey, Thomas C.; Gersho, Allen

1992-01-01

Report presents additional information about digital speech-encoding and -decoding system described in "Vector Adaptive/Predictive Encoding of Speech" (NPO-17230). Summarizes development of vector adaptive/predictive coding (VAPC) system and describes basic functions of algorithm. Describes refinements introduced enabling receiver to cope with errors. VAPC algorithm implemented in integrated-circuit coding/decoding processors (codecs). VAPC and other codecs tested under variety of operating conditions. Tests designed to reveal effects of various background quiet and noisy environments and of poor telephone equipment. VAPC found competitive with and, in some respects, superior to other 4.8-kb/s codecs and other codecs of similar complexity.

A performance comparison of the Cray-2 and the Cray X-MP

NASA Technical Reports Server (NTRS)

Schmickley, Ronald; Bailey, David H.

1986-01-01

A suite of thirteen large Fortran benchmark codes were run on Cray-2 and Cray X-MP supercomputers. These codes were a mix of compute-intensive scientific application programs (mostly Computational Fluid Dynamics) and some special vectorized computation exercise programs. For the general class of programs tested on the Cray-2, most of which were not specially tuned for speed, the floating point operation rates varied under a variety of system load configurations from 40 percent up to 125 percent of X-MP performance rates. It is concluded that the Cray-2, in the original system configuration studied (without memory pseudo-banking) will run untuned Fortran code, on average, about 70 percent of X-MP speeds.

Monte Carlo simulation of Ising models by multispin coding on a vector computer

NASA Astrophysics Data System (ADS)

Wansleben, Stephan; Zabolitzky, John G.; Kalle, Claus

1984-11-01

Rebbi's efficient multispin coding algorithm for Ising models is combined with the use of the vector computer CDC Cyber 205. A speed of 21.2 million updates per second is reached. This is comparable to that obtained by special- purpose computers.

Advanced Design of Dumbbell-shaped Genetic Minimal Vectors Improves Non-coding and Coding RNA Expression.

PubMed

Jiang, Xiaoou; Yu, Han; Teo, Cui Rong; Tan, Genim Siu Xian; Goh, Sok Chin; Patel, Parasvi; Chua, Yiqiang Kevin; Hameed, Nasirah Banu Sahul; Bertoletti, Antonio; Patzel, Volker

2016-09-01

Dumbbell-shaped DNA minimal vectors lacking nontherapeutic genes and bacterial sequences are considered a stable, safe alternative to viral, nonviral, and naked plasmid-based gene-transfer systems. We investigated novel molecular features of dumbbell vectors aiming to reduce vector size and to improve the expression of noncoding or coding RNA. We minimized small hairpin RNA (shRNA) or microRNA (miRNA) expressing dumbbell vectors in size down to 130 bp generating the smallest genetic expression vectors reported. This was achieved by using a minimal H1 promoter with integrated transcriptional terminator transcribing the RNA hairpin structure around the dumbbell loop. Such vectors were generated with high conversion yields using a novel protocol. Minimized shRNA-expressing dumbbells showed accelerated kinetics of delivery and transcription leading to enhanced gene silencing in human tissue culture cells. In primary human T cells, minimized miRNA-expressing dumbbells revealed higher stability and triggered stronger target gene suppression as compared with plasmids and miRNA mimics. Dumbbell-driven gene expression was enhanced up to 56- or 160-fold by implementation of an intron and the SV40 enhancer compared with control dumbbells or plasmids. Advanced dumbbell vectors may represent one option to close the gap between durable expression that is achievable with integrating viral vectors and short-term effects triggered by naked RNA.

Validation of a recombinant human bactericidal/permeability-increasing protein (hBPI) expression vector using murine mammary gland tumor cells and the early development of hBPI transgenic goat embryos.

PubMed

Gui, Tao; Liu, Xing; Tao, Jia; Chen, Jianwen; Li, Yunsheng; Zhang, Meiling; Wu, Ronghua; Zhang, Yuanliang; Peng, Kaisong; Liu, Ya; Zhang, Xiaorong; Zhang, Yunhai

2013-12-01

Human bactericidal/permeability-increasing protein (hBPI) is the only antibacterial peptide which acts against both gram-negative bacteria and neutralizes endotoxins in human polymorphonuclear neutrophils; therefore, hBPI is of great value in clinical applications. In the study, we constructed a hBPI expression vector (pBC1-Loxp-Neo-Loxp-hBPI) containing the full-length hBPI coding sequence which could be specifically expressed in the mammary gland. To validate the function of the vector, in vitro cultured C127 (mouse mammary Carcinoma Cells) were transfected with the vector, and the transgenic cell clones were selected to express hBPI by hormone induction. The mRNA and protein expression of hBPI showed that the constructed vector was effective and suitable for future application in producing mammary gland bioreactor. Then, female and male goat fibroblasts were transfected with the vector, and two male and two female transgenic clonal cell lines were obtained. Using the transgenic cell lines as nuclear donors for somatic cell nuclear transfer, the reconstructed goat embryos produced from all four clones could develop to blastocysts in vitro. In conclusion, we constructed and validated an efficient mammary gland-specific hBPI expression vector, pBC1-Loxp-Neo-Loxp-hBPI, and transgenic hBPI goat embryos were successfully produced, laying foundations for future production of recombinant hBPI in goat mammary gland. Copyright © 2013 Elsevier B.V. All rights reserved.

Development of Peritoneal Tumor-Targeting Vector by In Vivo Screening with a Random Peptide-Displaying Adenovirus Library

PubMed Central

Yoshida, Kimiko; Goto, Naoko; Ohnami, Shumpei; Aoki, Kazunori

2012-01-01

The targeting of gene transfer at the cell-entry level is one of the most attractive challenges in vector development. However, attempts to redirect adenovirus vectors to alternative receptors by engineering the capsid-coding region have shown limited success, because the proper targeting ligands on the cells of interest are generally unknown. To overcome this limitation, we have constructed a random peptide library displayed on the adenoviral fiber knob, and have successfully selected targeted vectors by screening the library on cancer cell lines in vitro. The infection of targeted vectors was considered to be mediated by specific receptors on target cells. However, the expression levels and kinds of cell surface receptors may be substantially different between in vitro culture and in vivo tumor tissue. Here, we screened the peptide display-adenovirus library in the peritoneal dissemination model of AsPC-1 pancreatic cancer cells. The vector displaying a selected peptide (PFWSGAV) showed higher infectivity in the AsPC-1 peritoneal tumors but not in organs and other peritoneal tumors as compared with a non-targeted vector. Furthermore, the infectivity of the PFWSGAV-displaying vector for AsPC-1 peritoneal tumors was significantly higher than that of a vector displaying a peptide selected by in vitro screening, indicating the usefulness of in vivo screening in exploring the targeting vectors. This vector-screening system can facilitate the development of targeted adenovirus vectors for a variety of applications in medicine. PMID:23029088

Gain-adaptive vector quantization for medium-rate speech coding

NASA Technical Reports Server (NTRS)

Chen, J.-H.; Gersho, A.

1985-01-01

A class of adaptive vector quantizers (VQs) that can dynamically adjust the 'gain' of codevectors according to the input signal level is introduced. The encoder uses a gain estimator to determine a suitable normalization of each input vector prior to VQ coding. The normalized vectors have reduced dynamic range and can then be more efficiently coded. At the receiver, the VQ decoder output is multiplied by the estimated gain. Both forward and backward adaptation are considered and several different gain estimators are compared and evaluated. An approach to optimizing the design of gain estimators is introduced. Some of the more obvious techniques for achieving gain adaptation are substantially less effective than the use of optimized gain estimators. A novel design technique that is needed to generate the appropriate gain-normalized codebook for the vector quantizer is introduced. Experimental results show that a significant gain in segmental SNR can be obtained over nonadaptive VQ with a negligible increase in complexity.

The solution of linear systems of equations with a structural analysis code on the NAS CRAY-2

NASA Technical Reports Server (NTRS)

Poole, Eugene L.; Overman, Andrea L.

1988-01-01

Two methods for solving linear systems of equations on the NAS Cray-2 are described. One is a direct method; the other is an iterative method. Both methods exploit the architecture of the Cray-2, particularly the vectorization, and are aimed at structural analysis applications. To demonstrate and evaluate the methods, they were installed in a finite element structural analysis code denoted the Computational Structural Mechanics (CSM) Testbed. A description of the techniques used to integrate the two solvers into the Testbed is given. Storage schemes, memory requirements, operation counts, and reformatting procedures are discussed. Finally, results from the new methods are compared with results from the initial Testbed sparse Choleski equation solver for three structural analysis problems. The new direct solvers described achieve the highest computational rates of the methods compared. The new iterative methods are not able to achieve as high computation rates as the vectorized direct solvers but are best for well conditioned problems which require fewer iterations to converge to the solution.

Portable implementation model for CFD simulations. Application to hybrid CPU/GPU supercomputers

NASA Astrophysics Data System (ADS)

Oyarzun, Guillermo; Borrell, Ricard; Gorobets, Andrey; Oliva, Assensi

2017-10-01

Nowadays, high performance computing (HPC) systems experience a disruptive moment with a variety of novel architectures and frameworks, without any clarity of which one is going to prevail. In this context, the portability of codes across different architectures is of major importance. This paper presents a portable implementation model based on an algebraic operational approach for direct numerical simulation (DNS) and large eddy simulation (LES) of incompressible turbulent flows using unstructured hybrid meshes. The strategy proposed consists in representing the whole time-integration algorithm using only three basic algebraic operations: sparse matrix-vector product, a linear combination of vectors and dot product. The main idea is based on decomposing the nonlinear operators into a concatenation of two SpMV operations. This provides high modularity and portability. An exhaustive analysis of the proposed implementation for hybrid CPU/GPU supercomputers has been conducted with tests using up to 128 GPUs. The main objective consists in understanding the challenges of implementing CFD codes on new architectures.

Pulse Vector-Excitation Speech Encoder

NASA Technical Reports Server (NTRS)

Davidson, Grant; Gersho, Allen

1989-01-01

Proposed pulse vector-excitation speech encoder (PVXC) encodes analog speech signals into digital representation for transmission or storage at rates below 5 kilobits per second. Produces high quality of reconstructed speech, but with less computation than required by comparable speech-encoding systems. Has some characteristics of multipulse linear predictive coding (MPLPC) and of code-excited linear prediction (CELP). System uses mathematical model of vocal tract in conjunction with set of excitation vectors and perceptually-based error criterion to synthesize natural-sounding speech.

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

The nondeterministic divide

NASA Technical Reports Server (NTRS)

Charlesworth, Arthur

1990-01-01

The nondeterministic divide partitions a vector into two non-empty slices by allowing the point of division to be chosen nondeterministically. Support for high-level divide-and-conquer programming provided by the nondeterministic divide is investigated. A diva algorithm is a recursive divide-and-conquer sequential algorithm on one or more vectors of the same range, whose division point for a new pair of recursive calls is chosen nondeterministically before any computation is performed and whose recursive calls are made immediately after the choice of division point; also, access to vector components is only permitted during activations in which the vector parameters have unit length. The notion of diva algorithm is formulated precisely as a diva call, a restricted call on a sequential procedure. Diva calls are proven to be intimately related to associativity. Numerous applications of diva calls are given and strategies are described for translating a diva call into code for a variety of parallel computers. Thus diva algorithms separate logical correctness concerns from implementation concerns.

Chemical application of diffusion quantum Monte Carlo

NASA Technical Reports Server (NTRS)

Reynolds, P. J.; Lester, W. A., Jr.

1984-01-01

The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. This approach is receiving increasing attention in chemical applications as a result of its high accuracy. However, reducing statistical uncertainty remains a priority because chemical effects are often obtained as small differences of large numbers. As an example, the single-triplet splitting of the energy of the methylene molecule CH sub 2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on the VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX, are discussed. The computational time dependence obtained versus the number of basis functions is discussed and this is compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures.

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1, Introducing a Python Edition

NASA Astrophysics Data System (ADS)

Barron, Eric G.; Kaplan, G. H.; Bangert, J.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2011-01-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source-code library that provides common astrometric quantities and transformations. NOVAS calculations are accurate at the sub-milliarcsecond level. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and, currently, mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to harness the object-oriented nature of the Python language, and will implement the ability to handle large quantities of objects or observers using the array functionality in NumPy (a third-party scientific package for Python). NOVAS 3.1 also adds a module to transform GCRS vectors to the ITRS; the ITRS to GCRS transformation was already provided in NOVAS 3.0. The module that corrects an ITRS vector for polar motion has been modified to undo that correction upon demand. In the C edition, the ephemeris-access functions have been revised for use on 64-bit systems and for improved performance in general. NOVAS, including documentation, is available from the USNO website (http://www.usno.navy.mil/USNO/astronomical-applications/software-products/novas).

Massively parallel data processing for quantitative total flow imaging with optical coherence microscopy and tomography

NASA Astrophysics Data System (ADS)

Sylwestrzak, Marcin; Szlag, Daniel; Marchand, Paul J.; Kumar, Ashwin S.; Lasser, Theo

2017-08-01

We present an application of massively parallel processing of quantitative flow measurements data acquired using spectral optical coherence microscopy (SOCM). The need for massive signal processing of these particular datasets has been a major hurdle for many applications based on SOCM. In view of this difficulty, we implemented and adapted quantitative total flow estimation algorithms on graphics processing units (GPU) and achieved a 150 fold reduction in processing time when compared to a former CPU implementation. As SOCM constitutes the microscopy counterpart to spectral optical coherence tomography (SOCT), the developed processing procedure can be applied to both imaging modalities. We present the developed DLL library integrated in MATLAB (with an example) and have included the source code for adaptations and future improvements. Catalogue identifier: AFBT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 913552 No. of bytes in distributed program, including test data, etc.: 270876249 Distribution format: tar.gz Programming language: CUDA/C, MATLAB. Computer: Intel x64 CPU, GPU supporting CUDA technology. Operating system: 64-bit Windows 7 Professional. Has the code been vectorized or parallelized?: Yes, CPU code has been vectorized in MATLAB, CUDA code has been parallelized. RAM: Dependent on users parameters, typically between several gigabytes and several tens of gigabytes Classification: 6.5, 18. Nature of problem: Speed up of data processing in optical coherence microscopy Solution method: Utilization of GPU for massively parallel data processing Additional comments: Compiled DLL library with source code and documentation, example of utilization (MATLAB script with raw data) Running time: 1,8 s for one B-scan (150 × faster in comparison to the CPU data processing time)

Supercomputers for engineering analysis

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

Goudreau, G.L.; Benson, D.J.; Hallquist, J.O.

1986-07-01

The Cray-1 and Cray X-MP/48 experience in engineering computations at the Lawrence Livermore National Laboratory is surveyed. The fully vectorized explicit DYNA and implicit NIKE finite element codes are discussed with respect to solid and structural mechanics. The main efficiencies for production analyses are currently obtained by simple CFT compiler exploitation of pipeline architecture for inner do-loop optimization. Current developmet of outer-loop multitasking is also discussed. Applications emphasis will be on 3D examples spanning earth penetrator loads analysis, target lethality assessment, and crashworthiness. The use of a vectorized large deformation shell element in both DYNA and NIKE has substantially expandedmore » 3D nonlinear capability. 25 refs., 7 figs.« less

Digital TV processing system

NASA Technical Reports Server (NTRS)

1975-01-01

Two digital video data compression systems directly applicable to the Space Shuttle TV Communication System were described: (1) For the uplink, a low rate monochrome data compressor is used. The compression is achieved by using a motion detection technique in the Hadamard domain. To transform the variable source rate into a fixed rate, an adaptive rate buffer is provided. (2) For the downlink, a color data compressor is considered. The compression is achieved first by intra-color transformation of the original signal vector, into a vector which has lower information entropy. Then two-dimensional data compression techniques are applied to the Hadamard transformed components of this last vector. Mathematical models and data reliability analyses were also provided for the above video data compression techniques transmitted over a channel encoded Gaussian channel. It was shown that substantial gains can be achieved by the combination of video source and channel coding.

Documentation of the GLAS fourth order general calculation model. Volume 3: Vectorized code for the Cyber 205

NASA Technical Reports Server (NTRS)

Kalnay, E.; Balgovind, R.; Chao, W.; Edelmann, D.; Pfaendtner, J.; Takacs, L.; Takano, K.

1983-01-01

Volume 3 of a 3-volume technical memoranda which contains documentation of the GLAS fourth order genera circulation model is presented. The volume contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A dictionary of FORTRAN variables used in the Scalar Version, and listings of the FORTRAN Code compiled with the C-option, are included. Cross reference maps of local variables are included for each subroutine.

Speech coding, reconstruction and recognition using acoustics and electromagnetic waves

DOEpatents

Holzrichter, J.F.; Ng, L.C.

1998-03-17

The use of EM radiation in conjunction with simultaneously recorded acoustic speech information enables a complete mathematical coding of acoustic speech. The methods include the forming of a feature vector for each pitch period of voiced speech and the forming of feature vectors for each time frame of unvoiced, as well as for combined voiced and unvoiced speech. The methods include how to deconvolve the speech excitation function from the acoustic speech output to describe the transfer function each time frame. The formation of feature vectors defining all acoustic speech units over well defined time frames can be used for purposes of speech coding, speech compression, speaker identification, language-of-speech identification, speech recognition, speech synthesis, speech translation, speech telephony, and speech teaching. 35 figs.

Speech coding, reconstruction and recognition using acoustics and electromagnetic waves

DOEpatents

Holzrichter, John F.; Ng, Lawrence C.

1998-01-01

The use of EM radiation in conjunction with simultaneously recorded acoustic speech information enables a complete mathematical coding of acoustic speech. The methods include the forming of a feature vector for each pitch period of voiced speech and the forming of feature vectors for each time frame of unvoiced, as well as for combined voiced and unvoiced speech. The methods include how to deconvolve the speech excitation function from the acoustic speech output to describe the transfer function each time frame. The formation of feature vectors defining all acoustic speech units over well defined time frames can be used for purposes of speech coding, speech compression, speaker identification, language-of-speech identification, speech recognition, speech synthesis, speech translation, speech telephony, and speech teaching.

Horizontal vectorization of electron repulsion integrals.

PubMed

Pritchard, Benjamin P; Chow, Edmond

2016-10-30

We present an efficient implementation of the Obara-Saika algorithm for the computation of electron repulsion integrals that utilizes vector intrinsics to calculate several primitive integrals concurrently in a SIMD vector. Initial benchmarks display a 2-4 times speedup with AVX instructions over comparable scalar code, depending on the basis set. Speedup over scalar code is found to be sensitive to the level of contraction of the basis set, and is best for (lAlB|lClD) quartets when lD  = 0 or lB=lD=0, which makes such a vectorization scheme particularly suitable for density fitting. The basic Obara-Saika algorithm, how it is vectorized, and the performance bottlenecks are analyzed and discussed. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Vectors a Fortran 90 module for 3-dimensional vector and dyadic arithmetic

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

Brock, B.C.

1998-02-01

A major advance contained in the new Fortran 90 language standard is the ability to define new data types and the operators associated with them. Writing computer code to implement computations with real and complex three-dimensional vectors and dyadics is greatly simplified if the equations can be implemented directly, without the need to code the vector arithmetic explicitly. The Fortran 90 module described here defines new data types for real and complex 3-dimensional vectors and dyadics, along with the common operations needed to work with these objects. Routines to allow convenient initialization and output of the new types are alsomore » included. In keeping with the philosophy of data abstraction, the details of the implementation of the data types are maintained private, and the functions and operators are made generic to simplify the combining of real, complex, single- and double-precision vectors and dyadics.« less

PERI - Auto-tuning Memory Intensive Kernels for Multicore

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

Bailey, David H; Williams, Samuel; Datta, Kaushik

2008-06-24

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to Sparse Matrix Vector Multiplication (SpMV), the explicit heat equation PDE on a regular grid (Stencil), and a lattice Boltzmann application (LBMHD). We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Xeon Clovertown, AMD Opteron Barcelona, Sun Victoria Falls, and the Sony-Toshiba-IBM (STI) Cell. Rather than hand-tuning each kernel for each system, we developmore » a code generator for each kernel that allows us to identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned kernel applications often achieve a better than 4X improvement compared with the original code. Additionally, we analyze a Roofline performance model for each platform to reveal hardware bottlenecks and software challenges for future multicore systems and applications.« less

Automated Detection and Analysis of Interplanetary Shocks Running Real-Time on the Web

NASA Astrophysics Data System (ADS)

Vorotnikov, V.; Smith, C. W.; Hu, Q.; Szabo, A.; Skoug, R. M.; Cohen, C. M.; Davis, A. J.

2008-05-01

The ACE real-time data stream provides web-based now-casting capabilities for solar wind conditions upstream of Earth. We have built a fully automated code that finds and analyzes interplanetary shocks as they occur and posts their solutions on the Web for possible real-time application to space weather nowcasting. Shock analysis algorithms based on the Rankine-Hugoniot jump conditions exist and are in wide-spread use today for the interactive analysis of interplanetary shocks yielding parameters such as shock speed and propagation direction and shock strength in the form of compression ratios. At a previous meeting we reported on efforts to develop a fully automated code that used ACE Level-2 (science quality) data to prove the applicability and correctness of the code and the associated shock-finder. We have since adapted the code to run ACE RTSW data provided by NOAA. This data lacks the full 3-dimensional velocity vector for the solar wind and contains only a single component wind speed. We show that by assuming the wind velocity to be radial strong shock solutions remain essentially unchanged and the analysis performs as well as it would if 3-D velocity components were available. This is due, at least in part, to the fact that strong shocks tend to have nearly radial shock normals and it is the strong shocks that are most effective in space weather applications. Strong shocks are the only shocks that concern us in this application. The code is now running on the Web and the results are available to all.

Simulations of linear and Hamming codes using SageMath

NASA Astrophysics Data System (ADS)

Timur, Tahta D.; Adzkiya, Dieky; Soleha

2018-03-01

Digital data transmission over a noisy channel could distort the message being transmitted. The goal of coding theory is to ensure data integrity, that is, to find out if and where this noise has distorted the message and what the original message was. Data transmission consists of three stages: encoding, transmission, and decoding. Linear and Hamming codes are codes that we discussed in this work, where encoding algorithms are parity check and generator matrix, and decoding algorithms are nearest neighbor and syndrome. We aim to show that we can simulate these processes using SageMath software, which has built-in class of coding theory in general and linear codes in particular. First we consider the message as a binary vector of size k. This message then will be encoded to a vector with size n using given algorithms. And then a noisy channel with particular value of error probability will be created where the transmission will took place. The last task would be decoding, which will correct and revert the received message back to the original message whenever possible, that is, if the number of error occurred is smaller or equal to the correcting radius of the code. In this paper we will use two types of data for simulations, namely vector and text data.

Speech coding, reconstruction and recognition using acoustics and electromagnetic waves

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

Holzrichter, J.F.; Ng, L.C.

The use of EM radiation in conjunction with simultaneously recorded acoustic speech information enables a complete mathematical coding of acoustic speech. The methods include the forming of a feature vector for each pitch period of voiced speech and the forming of feature vectors for each time frame of unvoiced, as well as for combined voiced and unvoiced speech. The methods include how to deconvolve the speech excitation function from the acoustic speech output to describe the transfer function each time frame. The formation of feature vectors defining all acoustic speech units over well defined time frames can be used formore » purposes of speech coding, speech compression, speaker identification, language-of-speech identification, speech recognition, speech synthesis, speech translation, speech telephony, and speech teaching. 35 figs.« less

Experimental Study of an Axisymmetric Dual Throat Fluidic Thrust Vectoring Nozzle for Supersonic Aircraft Application

NASA Technical Reports Server (NTRS)

Flamm, Jeffrey D.; Deere, Karen A.; Mason, Mary L.; Berrier, Bobby L.; Johnson, Stuart K.

2007-01-01

An axisymmetric version of the Dual Throat Nozzle concept with a variable expansion ratio has been studied to determine the impacts on thrust vectoring and nozzle performance. The nozzle design, applicable to a supersonic aircraft, was guided using the unsteady Reynolds-averaged Navier-Stokes computational fluid dynamics code, PAB3D. The axisymmetric Dual Throat Nozzle concept was tested statically in the Jet Exit Test Facility at the NASA Langley Research Center. The nozzle geometric design variables included circumferential span of injection, cavity length, cavity convergence angle, and nozzle expansion ratio for conditions corresponding to take-off and landing, mid climb and cruise. Internal nozzle performance and thrust vectoring performance was determined for nozzle pressure ratios up to 10 with secondary injection rates up to 10 percent of the primary flow rate. The 60 degree span of injection generally performed better than the 90 degree span of injection using an equivalent injection area and number of holes, in agreement with computational results. For injection rates less than 7 percent, thrust vector angle for the 60 degree span of injection was 1.5 to 2 degrees higher than the 90 degree span of injection. Decreasing cavity length improved thrust ratio and discharge coefficient, but decreased thrust vector angle and thrust vectoring efficiency. Increasing cavity convergence angle from 20 to 30 degrees increased thrust vector angle by 1 degree over the range of injection rates tested, but adversely affected system thrust ratio and discharge coefficient. The dual throat nozzle concept generated the best thrust vectoring performance with an expansion ratio of 1.0 (a cavity in between two equal minimum areas). The variable expansion ratio geometry did not provide the expected improvements in discharge coefficient and system thrust ratio throughout the flight envelope of typical a supersonic aircraft. At mid-climb and cruise conditions, the variable geometry design compromised thrust vector angle achieved, but some thrust vector control would be available, potentially for aircraft trim. The fixed area, expansion ratio of 1.0, Dual Throat Nozzle provided the best overall compromise for thrust vectoring and nozzle internal performance over the range of NPR tested compared to the variable geometry Dual Throat Nozzle.

Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

Software packages for spatial data often implement a hybrid approach of interpreted and compiled programming languages. The compiled parts are usually written in C, C++, or Fortran, and are efficient in terms of computational speed and memory usage. Conversely, the interpreted part serves as a convenient user-interface and calls the compiled code for computationally demanding operations. The price paid for the user friendliness of the interpreted component is-besides performance-the limited access to low level and optimized code. An example of such a restriction is the 64-bit vector support of the widely used statistical language R. On the R side, users do not need to change existing code and may not even notice the extension. On the other hand, interfacing 64-bit compiled code efficiently is challenging. Since many R packages for spatial data could benefit from 64-bit vectors, we investigate strategies to efficiently pass 64-bit vectors to compiled languages. More precisely, we show how to simply extend existing R packages using the foreign function interface to seamlessly support 64-bit vectors. This extension is shown with the sparse matrix algebra R package spam. The new capabilities are illustrated with an example of GIMMS NDVI3g data featuring a parametric modeling approach for a non-stationary covariance matrix.

Single-Step Conversion of Cells to Retrovirus Vector Producers with Herpes Simplex Virus–Epstein-Barr Virus Hybrid Amplicons

PubMed Central

Sena-Esteves, Miguel; Saeki, Yoshinaga; Camp, Sara M.; Chiocca, E. Antonio; Breakefield, Xandra O.

1999-01-01

We report here on the development and characterization of a novel herpes simplex virus type 1 (HSV-1) amplicon-based vector system which takes advantage of the host range and retention properties of HSV–Epstein-Barr virus (EBV) hybrid amplicons to efficiently convert cells to retrovirus vector producer cells after single-step transduction. The retrovirus genes gag-pol and env (GPE) and retroviral vector sequences were modified to minimize sequence overlap and cloned into an HSV-EBV hybrid amplicon. Retrovirus expression cassettes were used to generate the HSV-EBV-retrovirus hybrid vectors, HERE and HERA, which code for the ecotropic and the amphotropic envelopes, respectively. Retrovirus vector sequences encoding lacZ were cloned downstream from the GPE expression unit. Transfection of 293T/17 cells with amplicon plasmids yielded retrovirus titers between 106 and 107 transducing units/ml, while infection of the same cells with amplicon vectors generated maximum titers 1 order of magnitude lower. Retrovirus titers were dependent on the extent of transduction by amplicon vectors for the same cell line, but different cell lines displayed varying capacities to produce retrovirus vectors even at the same transduction efficiencies. Infection of human and dog primary gliomas with this system resulted in the production of retrovirus vectors for more than 1 week and the long-term retention and increase in transgene activity over time in these cell populations. Although the efficiency of this system still has to be determined in vivo, many applications are foreseeable for this approach to gene delivery. PMID:10559361

GAMERA - The New Magnetospheric Code

NASA Astrophysics Data System (ADS)

Lyon, J.; Sorathia, K.; Zhang, B.; Merkin, V. G.; Wiltberger, M. J.; Daldorff, L. K. S.

2017-12-01

The Lyon-Fedder-Mobarry (LFM) code has been a main-line magnetospheric simulation code for 30 years. The code base, designed in the age of memory to memory vector ma- chines,is still in wide use for science production but needs upgrading to ensure the long term sustainability. In this presentation, we will discuss our recent efforts to update and improve that code base and also highlight some recent results. The new project GAM- ERA, Grid Agnostic MHD for Extended Research Applications, has kept the original design characteristics of the LFM and made significant improvements. The original de- sign included high order numerical differencing with very aggressive limiting, the ability to use arbitrary, but logically rectangular, grids, and maintenance of div B = 0 through the use of the Yee grid. Significant improvements include high-order upwinding and a non-clipping limiter. One other improvement with wider applicability is an im- proved averaging technique for the singularities in polar and spherical grids. The new code adopts a hybrid structure - multi-threaded OpenMP with an overarching MPI layer for large scale and coupled applications. The MPI layer uses a combination of standard MPI and the Global Array Toolkit from PNL to provide a lightweight mechanism for coupling codes together concurrently. The single processor code is highly efficient and can run magnetospheric simulations at the default CCMC resolution faster than real time on a MacBook pro. We have run the new code through the Athena suite of tests, and the results compare favorably with the codes available to the astrophysics community. LFM/GAMERA has been applied to many different situations ranging from the inner and outer heliosphere and magnetospheres of Venus, the Earth, Jupiter and Saturn. We present example results the Earth's magnetosphere including a coupled ring current (RCM), the magnetospheres of Jupiter and Saturn, and the inner heliosphere.

Development and Evaluation of Vectorised and Multi-Core Event Reconstruction Algorithms within the CMS Software Framework

NASA Astrophysics Data System (ADS)

Hauth, T.; Innocente and, V.; Piparo, D.

2012-12-01

The processing of data acquired by the CMS detector at LHC is carried out with an object-oriented C++ software framework: CMSSW. With the increasing luminosity delivered by the LHC, the treatment of recorded data requires extraordinary large computing resources, also in terms of CPU usage. A possible solution to cope with this task is the exploitation of the features offered by the latest microprocessor architectures. Modern CPUs present several vector units, the capacity of which is growing steadily with the introduction of new processor generations. Moreover, an increasing number of cores per die is offered by the main vendors, even on consumer hardware. Most recent C++ compilers provide facilities to take advantage of such innovations, either by explicit statements in the programs sources or automatically adapting the generated machine instructions to the available hardware, without the need of modifying the existing code base. Programming techniques to implement reconstruction algorithms and optimised data structures are presented, that aim to scalable vectorization and parallelization of the calculations. One of their features is the usage of new language features of the C++11 standard. Portions of the CMSSW framework are illustrated which have been found to be especially profitable for the application of vectorization and multi-threading techniques. Specific utility components have been developed to help vectorization and parallelization. They can easily become part of a larger common library. To conclude, careful measurements are described, which show the execution speedups achieved via vectorised and multi-threaded code in the context of CMSSW.

Benchmark tests on the digital equipment corporation Alpha AXP 21164-based AlphaServer 8400, including a comparison of optimized vector and superscalar processing

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

Wasserman, H.J.

1996-02-01

The second generation of the Digital Equipment Corp. (DEC) DECchip Alpha AXP microprocessor is referred to as the 21164. From the viewpoint of numerically-intensive computing, the primary difference between it and its predecessor, the 21064, is that the 21164 has twice the multiply/add throughput per clock period (CP), a maximum of two floating point operations (FLOPS) per CP vs. one for 21064. The AlphaServer 8400 is a shared-memory multiprocessor server system that can accommodate up to 12 CPUs and up to 14 GB of memory. In this report we will compare single processor performance of the 8400 system with thatmore » of the International Business Machines Corp. (IBM) RISC System/6000 POWER-2 microprocessor running at 66 MHz, the Silicon Graphics, Inc. (SGI) MIPS R8000 microprocessor running at 75 MHz, and the Cray Research, Inc. CRAY J90. The performance comparison is based on a set of Fortran benchmark codes that represent a portion of the Los Alamos National Laboratory supercomputer workload. The advantage of using these codes, is that the codes also span a wide range of computational characteristics, such as vectorizability, problem size, and memory access pattern. The primary disadvantage of using them is that detailed, quantitative analysis of performance behavior of all codes on all machines is difficult. One important addition to the benchmark set appears for the first time in this report. Whereas the older version was written for a vector processor, the newer version is more optimized for microprocessor architectures. Therefore, we have for the first time, an opportunity to measure performance on a single application using implementations that expose the respective strengths of vector and superscalar architecture. All results in this report are from single processors. A subsequent article will explore shared-memory multiprocessing performance of the 8400 system.« less

Image coding using entropy-constrained residual vector quantization

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Smith, Mark J. T.; Barnes, Christopher F.

1993-01-01

The residual vector quantization (RVQ) structure is exploited to produce a variable length codeword RVQ. Necessary conditions for the optimality of this RVQ are presented, and a new entropy-constrained RVQ (ECRVQ) design algorithm is shown to be very effective in designing RVQ codebooks over a wide range of bit rates and vector sizes. The new EC-RVQ has several important advantages. It can outperform entropy-constrained VQ (ECVQ) in terms of peak signal-to-noise ratio (PSNR), memory, and computation requirements. It can also be used to design high rate codebooks and codebooks with relatively large vector sizes. Experimental results indicate that when the new EC-RVQ is applied to image coding, very high quality is achieved at relatively low bit rates.

Vector platforms for gene therapy of inherited retinopathies

PubMed Central

Trapani, Ivana; Puppo, Agostina; Auricchio, Alberto

2014-01-01

Inherited retinopathies (IR) are common untreatable blinding conditions. Most of them are inherited as monogenic disorders, due to mutations in genes expressed in retinal photoreceptors (PR) and in retinal pigment epithelium (RPE). The retina’s compatibility with gene transfer has made transduction of different retinal cell layers in small and large animal models via viral and non-viral vectors possible. The ongoing identification of novel viruses as well as modifications of existing ones based either on rational design or directed evolution have generated vector variants with improved transduction properties. Dozens of promising proofs of concept have been obtained in IR animal models with both viral and non-viral vectors, and some of them have been relayed to clinical trials. To date, recombinant vectors based on the adeno-associated virus (AAV) represent the most promising tool for retinal gene therapy, given their ability to efficiently deliver therapeutic genes to both PR and RPE and their excellent safety and efficacy profiles in humans. However, AAVs’ limited cargo capacity has prevented application of the viral vector to treatments requiring transfer of genes with a coding sequence larger than 5 kb. Vectors with larger capacity, i.e. nanoparticles, adenoviral and lentiviral vectors are being exploited for gene transfer to the retina in animal models and, more recently, in humans. This review focuses on the available platforms for retinal gene therapy to fight inherited blindness, highlights their main strengths and examines the efforts to overcome some of their limitations. PMID:25124745

Context-Aware Local Binary Feature Learning for Face Recognition.

PubMed

Duan, Yueqi; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

2018-05-01

In this paper, we propose a context-aware local binary feature learning (CA-LBFL) method for face recognition. Unlike existing learning-based local face descriptors such as discriminant face descriptor (DFD) and compact binary face descriptor (CBFD) which learn each feature code individually, our CA-LBFL exploits the contextual information of adjacent bits by constraining the number of shifts from different binary bits, so that more robust information can be exploited for face representation. Given a face image, we first extract pixel difference vectors (PDV) in local patches, and learn a discriminative mapping in an unsupervised manner to project each pixel difference vector into a context-aware binary vector. Then, we perform clustering on the learned binary codes to construct a codebook, and extract a histogram feature for each face image with the learned codebook as the final representation. In order to exploit local information from different scales, we propose a context-aware local binary multi-scale feature learning (CA-LBMFL) method to jointly learn multiple projection matrices for face representation. To make the proposed methods applicable for heterogeneous face recognition, we present a coupled CA-LBFL (C-CA-LBFL) method and a coupled CA-LBMFL (C-CA-LBMFL) method to reduce the modality gap of corresponding heterogeneous faces in the feature level, respectively. Extensive experimental results on four widely used face datasets clearly show that our methods outperform most state-of-the-art face descriptors.

Efficient biprediction decision scheme for fast high efficiency video coding encoding

NASA Astrophysics Data System (ADS)

Park, Sang-hyo; Lee, Seung-ho; Jang, Euee S.; Jun, Dongsan; Kang, Jung-Won

2016-11-01

An efficient biprediction decision scheme of high efficiency video coding (HEVC) is proposed for fast-encoding applications. For low-delay video applications, bidirectional prediction can be used to increase compression performance efficiently with previous reference frames. However, at the same time, the computational complexity of the HEVC encoder is significantly increased due to the additional biprediction search. Although a some research has attempted to reduce this complexity, whether the prediction is strongly related to both motion complexity and prediction modes in a coding unit has not yet been investigated. A method that avoids most compression-inefficient search points is proposed so that the computational complexity of the motion estimation process can be dramatically decreased. To determine if biprediction is critical, the proposed method exploits the stochastic correlation of the context of prediction units (PUs): the direction of a PU and the accuracy of a motion vector. Through experimental results, the proposed method showed that the time complexity of biprediction can be reduced to 30% on average, outperforming existing methods in view of encoding time, number of function calls, and memory access.

Advanced Doubling Adding Method for Radiative Transfer in Planetary Atmospheres

NASA Astrophysics Data System (ADS)

Liu, Quanhua; Weng, Fuzhong

2006-12-01

The doubling adding method (DA) is one of the most accurate tools for detailed multiple-scattering calculations. The principle of the method goes back to the nineteenth century in a problem dealing with reflection and transmission by glass plates. Since then the doubling adding method has been widely used as a reference tool for other radiative transfer models. The method has never been used in operational applications owing to tremendous demand on computational resources from the model. This study derives an analytical expression replacing the most complicated thermal source terms in the doubling adding method. The new development is called the advanced doubling adding (ADA) method. Thanks also to the efficiency of matrix and vector manipulations in FORTRAN 90/95, the advanced doubling adding method is about 60 times faster than the doubling adding method. The radiance (i.e., forward) computation code of ADA is easily translated into tangent linear and adjoint codes for radiance gradient calculations. The simplicity in forward and Jacobian computation codes is very useful for operational applications and for the consistency between the forward and adjoint calculations in satellite data assimilation.

Pre-coding assisted generation of a frequency quadrupled optical vector D-band millimeter wave with one Mach-Zehnder modulator.

PubMed

Zhou, Wen; Li, Xinying; Yu, Jianjun

2017-10-30

We propose QPSK millimeter-wave (mm-wave) vector signal generation for D-band based on balanced precoding-assisted photonic frequency quadrupling technology employing a single intensity modulator without an optical filter. The intensity MZM is driven by a balanced pre-coding 37-GHz QPSK RF signal. The modulated optical subcarriers are directly sent into the single ended photodiode to generate 148-GHz QPSK vector signal. We experimentally demonstrate 1-Gbaud 148-GHz QPSK mm-wave vector signal generation, and investigate the bit-error-rate (BER) performance of the vector signals at 148-GHz. The experimental results show that the BER value can be achieved as low as 1.448 × 10 -3 when the optical power into photodiode is 8.8dBm. To the best of our knowledge, it is the first time to realize the frequency-quadrupling vector mm-wave signal generation at D-band based on only one MZM without an optical filter.

Low bit rate coding of Earth science images

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Chung, Wilson C.; Smith, Mark J. T.

1993-01-01

In this paper, the authors discuss compression based on some new ideas in vector quantization and their incorporation in a sub-band coding framework. Several variations are considered, which collectively address many of the individual compression needs within the earth science community. The approach taken in this work is based on some recent advances in the area of variable rate residual vector quantization (RVQ). This new RVQ method is considered separately and in conjunction with sub-band image decomposition. Very good results are achieved in coding a variety of earth science images. The last section of the paper provides some comparisons that illustrate the improvement in performance attributable to this approach relative the the JPEG coding standard.

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

DOE PAGES

Vincenti, H.; Lobet, M.; Lehe, R.; ...

2016-09-19

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD registermore » length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries:  OpenMP > 4.0 Nature of problem: Exascale architectures will have many-core processors per node with long vector data registers capable of performing one single instruction on multiple data during one clock cycle. Data register lengths are expected to double every four years and this pushes for new portable solutions for efficiently vectorizing Particle-In-Cell codes on these future many-core architectures. One of the main hotspot routines of the PIC algorithm is the current/charge deposition for which there is no efficient and portable vector algorithm. Solution method: Here we provide an efficient and portable vector algorithm of current/charge deposition routines that uses a new data structure, which significantly reduces gather/scatter operations. Vectorization is controlled using OpenMP 4.0 compiler directives for vectorization which ensures portability across different architectures. Restrictions: Here we do not provide the full PIC algorithm with an executable but only vector routines for current/charge deposition. These scalar/vector routines can be used as library routines in your 3D Particle-In-Cell code. However, to get the best performances out of vector routines you have to satisfy the two following requirements: (1) Your code should implement particle tiling (as explained in the manuscript) to allow for maximized cache reuse and reduce memory accesses that can hinder vector performances. The routines can be used directly on each particle tile. (2) You should compile your code with a Fortran 90 compiler (e.g Intel, gnu or cray) and provide proper alignment flags and compiler alignment directives (more details in README file).« less

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

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

Vincenti, H.; Lobet, M.; Lehe, R.

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD registermore » length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries:  OpenMP > 4.0 Nature of problem: Exascale architectures will have many-core processors per node with long vector data registers capable of performing one single instruction on multiple data during one clock cycle. Data register lengths are expected to double every four years and this pushes for new portable solutions for efficiently vectorizing Particle-In-Cell codes on these future many-core architectures. One of the main hotspot routines of the PIC algorithm is the current/charge deposition for which there is no efficient and portable vector algorithm. Solution method: Here we provide an efficient and portable vector algorithm of current/charge deposition routines that uses a new data structure, which significantly reduces gather/scatter operations. Vectorization is controlled using OpenMP 4.0 compiler directives for vectorization which ensures portability across different architectures. Restrictions: Here we do not provide the full PIC algorithm with an executable but only vector routines for current/charge deposition. These scalar/vector routines can be used as library routines in your 3D Particle-In-Cell code. However, to get the best performances out of vector routines you have to satisfy the two following requirements: (1) Your code should implement particle tiling (as explained in the manuscript) to allow for maximized cache reuse and reduce memory accesses that can hinder vector performances. The routines can be used directly on each particle tile. (2) You should compile your code with a Fortran 90 compiler (e.g Intel, gnu or cray) and provide proper alignment flags and compiler alignment directives (more details in README file).« less

iTOUGH2 Universal Optimization Using the PEST Protocol

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

Finsterle, S.A.

2010-07-01

iTOUGH2 (http://www-esd.lbl.gov/iTOUGH2) is a computer program for parameter estimation, sensitivity analysis, and uncertainty propagation analysis [Finsterle, 2007a, b, c]. iTOUGH2 contains a number of local and global minimization algorithms for automatic calibration of a model against measured data, or for the solution of other, more general optimization problems (see, for example, Finsterle [2005]). A detailed residual and estimation uncertainty analysis is conducted to assess the inversion results. Moreover, iTOUGH2 can be used to perform a formal sensitivity analysis, or to conduct Monte Carlo simulations for the examination for prediction uncertainties. iTOUGH2's capabilities are continually enhanced. As the name implies, iTOUGH2more » is developed for use in conjunction with the TOUGH2 forward simulator for nonisothermal multiphase flow in porous and fractured media [Pruess, 1991]. However, iTOUGH2 provides FORTRAN interfaces for the estimation of user-specified parameters (see subroutine USERPAR) based on user-specified observations (see subroutine USEROBS). These user interfaces can be invoked to add new parameter or observation types to the standard set provided in iTOUGH2. They can also be linked to non-TOUGH2 models, i.e., iTOUGH2 can be used as a universal optimization code, similar to other model-independent, nonlinear parameter estimation packages such as PEST [Doherty, 2008] or UCODE [Poeter and Hill, 1998]. However, to make iTOUGH2's optimization capabilities available for use with an external code, the user is required to write some FORTRAN code that provides the link between the iTOUGH2 parameter vector and the input parameters of the external code, and between the output variables of the external code and the iTOUGH2 observation vector. While allowing for maximum flexibility, the coding requirement of this approach limits its applicability to those users with FORTRAN coding knowledge. To make iTOUGH2 capabilities accessible to many application models, the PEST protocol [Doherty, 2007] has been implemented into iTOUGH2. This protocol enables communication between the application (which can be a single 'black-box' executable or a script or batch file that calls multiple codes) and iTOUGH2. The concept requires that for the application model: (1) Input is provided on one or more ASCII text input files; (2) Output is returned to one or more ASCII text output files; (3) The model is run using a system command (executable or script/batch file); and (4) The model runs to completion without any user intervention. For each forward run invoked by iTOUGH2, select parameters cited within the application model input files are then overwritten with values provided by iTOUGH2, and select variables cited within the output files are extracted and returned to iTOUGH2. It should be noted that the core of iTOUGH2, i.e., its optimization routines and related analysis tools, remains unchanged; it is only the communication format between input parameters, the application model, and output variables that are borrowed from PEST. The interface routines have been provided by Doherty [2007]. The iTOUGH2-PEST architecture is shown in Figure 1. This manual contains installation instructions for the iTOUGH2-PEST module, and describes the PEST protocol as well as the input formats needed in iTOUGH2. Examples are provided that demonstrate the use of model-independent optimization and analysis using iTOUGH2.« less

Coordination analysis of players' distribution in football using cross-correlation and vector coding techniques.

PubMed

Moura, Felipe Arruda; van Emmerik, Richard E A; Santana, Juliana Exel; Martins, Luiz Eduardo Barreto; Barros, Ricardo Machado Leite de; Cunha, Sergio Augusto

2016-12-01

The purpose of this study was to investigate the coordination between teams spread during football matches using cross-correlation and vector coding techniques. Using a video-based tracking system, we obtained the trajectories of 257 players during 10 matches. Team spread was calculated as functions of time. For a general coordination description, we calculated the cross-correlation between the signals. Vector coding was used to identify the coordination patterns between teams during offensive sequences that ended in shots on goal or defensive tackles. Cross-correlation showed that opponent teams have a tendency to present in-phase coordination, with a short time lag. During offensive sequences, vector coding results showed that, although in-phase coordination dominated, other patterns were observed. We verified that during the early stages, offensive sequences ending in shots on goal present greater anti-phase and attacking team phase periods, compared to sequences ending in tackles. Results suggest that the attacking team may seek to present a contrary behaviour of its opponent (or may lead the adversary behaviour) in the beginning of the attacking play, regarding to the distribution strategy, to increase the chances of a shot on goal. The techniques allowed detecting the coordination patterns between teams, providing additional information about football dynamics and players' interaction.

Overview of the relevant CFD work at Thiokol Corporation

NASA Technical Reports Server (NTRS)

Chwalowski, Pawel; Loh, Hai-Tien

1992-01-01

An in-house developed proprietary advanced computational fluid dynamics code called SHARP (Trademark) is a primary tool for many flow simulations and design analyses. The SHARP code is a time dependent, two dimensional (2-D) axisymmetric numerical solution technique for the compressible Navier-Stokes equations. The solution technique in SHARP uses a vectorizable implicit, second order accurate in time and space, finite volume scheme based on an upwind flux-difference splitting of a Roe-type approximated Riemann solver, Van Leer's flux vector splitting, and a fourth order artificial dissipation scheme with a preconditioning to accelerate the flow solution. Turbulence is simulated by an algebraic model, and ultimately the kappa-epsilon model. Some other capabilities of the code are 2-D two-phase Lagrangian particle tracking and cell blockages. Extensive development and testing has been conducted on the 3-D version of the code with flow, combustion, and turbulence interactions. The emphasis here is on the specific applications of SHARP in Solid Rocket Motor design. Information is given in viewgraph form.

A Low-Storage-Consumption XML Labeling Method for Efficient Structural Information Extraction

NASA Astrophysics Data System (ADS)

Liang, Wenxin; Takahashi, Akihiro; Yokota, Haruo

Recently, labeling methods to extract and reconstruct the structural information of XML data, which are important for many applications such as XPath query and keyword search, are becoming more attractive. To achieve efficient structural information extraction, in this paper we propose C-DO-VLEI code, a novel update-friendly bit-vector encoding scheme, based on register-length bit operations combining with the properties of Dewey Order numbers, which cannot be implemented in other relevant existing schemes such as ORDPATH. Meanwhile, the proposed method also achieves lower storage consumption because it does not require either prefix schema or any reserved codes for node insertion. We performed experiments to evaluate and compare the performance and storage consumption of the proposed method with those of the ORDPATH method. Experimental results show that the execution times for extracting depth information and parent node labels using the C-DO-VLEI code are about 25% and 15% less, respectively, and the average label size using the C-DO-VLEI code is about 24% smaller, comparing with ORDPATH.

A Code Generation Approach for Auto-Vectorization in the Spade Compiler

NASA Astrophysics Data System (ADS)

Wang, Huayong; Andrade, Henrique; Gedik, Buğra; Wu, Kun-Lung

We describe an auto-vectorization approach for the Spade stream processing programming language, comprising two ideas. First, we provide support for vectors as a primitive data type. Second, we provide a C++ library with architecture-specific implementations of a large number of pre-vectorized operations as the means to support language extensions. We evaluate our approach with several stream processing operators, contrasting Spade's auto-vectorization with the native auto-vectorization provided by the GNU gcc and Intel icc compilers.

Vector systems for prenatal gene therapy: principles of retrovirus vector design and production.

PubMed

Howe, Steven J; Chandrashekran, Anil

2012-01-01

Vectors derived from the Retroviridae family have several attributes required for successful gene delivery. Retroviral vectors have an adequate payload size for the coding regions of most genes; they are safe to handle and simple to produce. These vectors can be manipulated to target different cell types with low immunogenicity and can permanently insert genetic information into the host cells' genome. Retroviral vectors have been used in gene therapy clinical trials and successfully applied experimentally in vitro, in vivo, and in utero.

Initial Kernel Timing Using a Simple PIM Performance Model

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Block, Gary L.; Springer, Paul L.; Sterling, Thomas; Brockman, Jay B.; Callahan, David

2005-01-01

This presentation will describe some initial results of paper-and-pencil studies of 4 or 5 application kernels applied to a processor-in-memory (PIM) system roughly similar to the Cascade Lightweight Processor (LWP). The application kernels are: * Linked list traversal * Sun of leaf nodes on a tree * Bitonic sort * Vector sum * Gaussian elimination The intent of this work is to guide and validate work on the Cascade project in the areas of compilers, simulators, and languages. We will first discuss the generic PIM structure. Then, we will explain the concepts needed to program a parallel PIM system (locality, threads, parcels). Next, we will present a simple PIM performance model that will be used in the remainder of the presentation. For each kernel, we will then present a set of codes, including codes for a single PIM node, and codes for multiple PIM nodes that move data to threads and move threads to data. These codes are written at a fairly low level, between assembly and C, but much closer to C than to assembly. For each code, we will present some hand-drafted timing forecasts, based on the simple PIM performance model. Finally, we will conclude by discussing what we have learned from this work, including what programming styles seem to work best, from the point-of-view of both expressiveness and performance.

Increasing the computational efficient of digital cross correlation by a vectorization method

NASA Astrophysics Data System (ADS)

Chang, Ching-Yuan; Ma, Chien-Ching

2017-08-01

This study presents a vectorization method for use in MATLAB programming aimed at increasing the computational efficiency of digital cross correlation in sound and images, resulting in a speedup of 6.387 and 36.044 times compared with performance values obtained from looped expression. This work bridges the gap between matrix operations and loop iteration, preserving flexibility and efficiency in program testing. This paper uses numerical simulation to verify the speedup of the proposed vectorization method as well as experiments to measure the quantitative transient displacement response subjected to dynamic impact loading. The experiment involved the use of a high speed camera as well as a fiber optic system to measure the transient displacement in a cantilever beam under impact from a steel ball. Experimental measurement data obtained from the two methods are in excellent agreement in both the time and frequency domain, with discrepancies of only 0.68%. Numerical and experiment results demonstrate the efficacy of the proposed vectorization method with regard to computational speed in signal processing and high precision in the correlation algorithm. We also present the source code with which to build MATLAB-executable functions on Windows as well as Linux platforms, and provide a series of examples to demonstrate the application of the proposed vectorization method.

User's guide for NASCRIN: A vectorized code for calculating two-dimensional supersonic internal flow fields

NASA Technical Reports Server (NTRS)

Kumar, A.

1984-01-01

A computer program NASCRIN has been developed for analyzing two-dimensional flow fields in high-speed inlets. It solves the two-dimensional Euler or Navier-Stokes equations in conservation form by an explicit, two-step finite-difference method. An explicit-implicit method can also be used at the user's discretion for viscous flow calculations. For turbulent flow, an algebraic, two-layer eddy-viscosity model is used. The code is operational on the CDC CYBER 203 computer system and is highly vectorized to take full advantage of the vector-processing capability of the system. It is highly user oriented and is structured in such a way that for most supersonic flow problems, the user has to make only a few changes. Although the code is primarily written for supersonic internal flow, it can be used with suitable changes in the boundary conditions for a variety of other problems.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2003-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2004-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

The development of an explicit thermochemical nonequilibrium algorithm and its application to compute three dimensional AFE flowfields

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

This study presents a three-dimensional explicit, finite-difference, shock-capturing numerical algorithm applied to viscous hypersonic flows in thermochemical nonequilibrium. The algorithm employs a two-temperature physical model. Equations governing the finite-rate chemical reactions are fully-coupled to the gas dynamic equations using a novel coupling technique. The new coupling method maintains stability in the explicit, finite-rate formulation while allowing relatively large global time steps. The code uses flux-vector accuracy. Comparisons with experimental data and other numerical computations verify the accuracy of the present method. The code is used to compute the three-dimensional flowfield over the Aeroassist Flight Experiment (AFE) vehicle at one of its trajectory points.

Energy scaling advantages of resistive memory crossbar based computation and its application to sparse coding

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

Agarwal, Sapan; Quach, Tu -Thach; Parekh, Ojas

In this study, the exponential increase in data over the last decade presents a significant challenge to analytics efforts that seek to process and interpret such data for various applications. Neural-inspired computing approaches are being developed in order to leverage the computational properties of the analog, low-power data processing observed in biological systems. Analog resistive memory crossbars can perform a parallel read or a vector-matrix multiplication as well as a parallel write or a rank-1 update with high computational efficiency. For an N × N crossbar, these two kernels can be O(N) more energy efficient than a conventional digital memory-basedmore » architecture. If the read operation is noise limited, the energy to read a column can be independent of the crossbar size (O(1)). These two kernels form the basis of many neuromorphic algorithms such as image, text, and speech recognition. For instance, these kernels can be applied to a neural sparse coding algorithm to give an O(N) reduction in energy for the entire algorithm when run with finite precision. Sparse coding is a rich problem with a host of applications including computer vision, object tracking, and more generally unsupervised learning.« less

Energy scaling advantages of resistive memory crossbar based computation and its application to sparse coding

DOE PAGES

Agarwal, Sapan; Quach, Tu -Thach; Parekh, Ojas; ...

2016-01-06

In this study, the exponential increase in data over the last decade presents a significant challenge to analytics efforts that seek to process and interpret such data for various applications. Neural-inspired computing approaches are being developed in order to leverage the computational properties of the analog, low-power data processing observed in biological systems. Analog resistive memory crossbars can perform a parallel read or a vector-matrix multiplication as well as a parallel write or a rank-1 update with high computational efficiency. For an N × N crossbar, these two kernels can be O(N) more energy efficient than a conventional digital memory-basedmore » architecture. If the read operation is noise limited, the energy to read a column can be independent of the crossbar size (O(1)). These two kernels form the basis of many neuromorphic algorithms such as image, text, and speech recognition. For instance, these kernels can be applied to a neural sparse coding algorithm to give an O(N) reduction in energy for the entire algorithm when run with finite precision. Sparse coding is a rich problem with a host of applications including computer vision, object tracking, and more generally unsupervised learning.« less

CAVE: A computer code for two-dimensional transient heating analysis of conceptual thermal protection systems for hypersonic vehicles

NASA Technical Reports Server (NTRS)

Rathjen, K. A.

1977-01-01

A digital computer code CAVE (Conduction Analysis Via Eigenvalues), which finds application in the analysis of two dimensional transient heating of hypersonic vehicles is described. The CAVE is written in FORTRAN 4 and is operational on both IBM 360-67 and CDC 6600 computers. The method of solution is a hybrid analytical numerical technique that is inherently stable permitting large time steps even with the best of conductors having the finest of mesh size. The aerodynamic heating boundary conditions are calculated by the code based on the input flight trajectory or can optionally be calculated external to the code and then entered as input data. The code computes the network conduction and convection links, as well as capacitance values, given basic geometrical and mesh sizes, for four generations (leading edges, cooled panels, X-24C structure and slabs). Input and output formats are presented and explained. Sample problems are included. A brief summary of the hybrid analytical-numerical technique, which utilizes eigenvalues (thermal frequencies) and eigenvectors (thermal mode vectors) is given along with aerodynamic heating equations that have been incorporated in the code and flow charts.

Language Recognition via Sparse Coding

DTIC Science & Technology

2016-09-08

a posteriori (MAP) adaptation scheme that further optimizes the discriminative quality of sparse-coded speech fea - tures. We empirically validate the...significantly improve the discriminative quality of sparse-coded speech fea - tures. In Section 4, we evaluate the proposed approaches against an i-vector

Rapid production of functionalized recombinant proteins: marrying ligation independent cloning and in vitro protein ligation.

PubMed

Kushnir, Susanna; Marsac, Yoann; Breitling, Reinhard; Granovsky, Igor; Brok-Volchanskaya, Vera; Goody, Roger S; Becker, Christian F W; Alexandrov, Kirill

2006-01-01

Functional genomics and proteomics have been very active fields since the sequencing of several genomes was completed. To assign a physiological role to the newly discovered coding genes with unknown function, new generic methods for protein production, purification, and targeted functionalization are needed. This work presents a new vector, pCYSLIC, that allows rapid generation of Escherichia coli expression constructs via ligation-independent cloning (LIC). The vector is designed to facilitate protein purification by either Ni-NTA or GSH affinity chromatography. Subsequent proteolytic removal of affinity tags liberates an N-terminal cysteine residue that is then used for covalent modification of the target protein with different biophysical probes via protein ligation. The described system has been tested on 36 mammalian Rab GTPases, and it was demonstrated that recombinant GTPases produced with pCYSLIC could be efficiently modified with fluorescein or biotin in vitro. Finally, LIC was compared with the recently developed In-Fusion cloning method, and it was demonstrated that In-Fusion provides superior flexibility in choice of expression vector. By the application of In-Fusion cloning Cys-Rab6A GTPase with an N-terminal cysteine residue was generated employing unmodified pET30a vector and TVMV protease.

Supporting the Virtual Soldier With a Physics-Based Software Architecture

DTIC Science & Technology

2005-06-01

simple approach taken here). Rather, this paper demonstrates how existing solution schemes can rapidly expand; it embraces all theoretical solution... bodyj . In (5) the superscript ’T’ accompanying a vector denotes the transposition of the vector. The constraint force and moment are defined as F C=Z1 a a...FE codes as there are meshes, and the requested MD code. This is described next. Exactly how the PM instantiated each physics process became an issue

New syndrome decoder for (n, 1) convolutional codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

The letter presents a new syndrome decoding algorithm for the (n, 1) convolutional codes (CC) that is different and simpler than the previous syndrome decoding algorithm of Schalkwijk and Vinck. The new technique uses the general solution of the polynomial linear Diophantine equation for the error polynomial vector E(D). A recursive, Viterbi-like, algorithm is developed to find the minimum weight error vector E(D). An example is given for the binary nonsystematic (2, 1) CC.

Armored long non-coding RNA MEG3 targeting EGFR based on recombinant MS2 bacteriophage virus-like particles against hepatocellular carcinoma.

PubMed

Chang, Le; Wang, Guojing; Jia, Tingting; Zhang, Lei; Li, Yulong; Han, Yanxi; Zhang, Kuo; Lin, Guigao; Zhang, Rui; Li, Jinming; Wang, Lunan

2016-04-26

Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers worldwide. However, the treatment of patients with HCC is particularly challenging. Long non-coding RNA maternally expressed gene 3 (MEG3) has been identified as a potential suppressor of several types of tumors, but the delivery of long RNA remains problematic, limiting its applications. In the present study, we designed a novel delivery system based on MS2 virus-like particles (VLPs) crosslinked with GE11 polypeptide. This vector was found to be fast, effective and safe for the targeted delivery of lncRNA MEG3 RNA to the epidermal growth factor receptor (EGFR)-positive HCC cell lines without the activation of EGFR downstream pathways, and significantly attenuated both in vitro and in vivo tumor cell growth. Our study also revealed that the targeted delivery was mainly dependent on clathrin-mediated endocytosis and MEG3 RNA suppresses tumor growth mainly via increasing the expression of p53 and its downstream gene GDF15, but decreasing the expression of MDM2. Thus, this vector is promising as a novel delivery system and may facilitate a new approach to lncRNA based cancer therapy.

Vector-matrix-quaternion, array and arithmetic packages: All HAL/S functions implemented in Ada

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Kwong, David D.

1986-01-01

The HAL/S avionics programmers have enjoyed a variety of tools built into a language tailored to their special requirements. Ada is designed for a broader group of applications. Rather than providing built-in tools, Ada provides the elements with which users can build their own. Standard avionic packages remain to be developed. These must enable programmers to code in Ada as they have coded in HAL/S. The packages under development at JPL will provide all of the vector-matrix, array, and arithmetic functions described in the HAL/S manuals. In addition, the linear algebra package will provide all of the quaternion functions used in Shuttle steering and Galileo attitude control. Furthermore, using Ada's extensibility, many quaternion functions are being implemented as infix operations; equivalent capabilities were never implemented in HAL/S because doing so would entail modifying the compiler and expanding the language. With these packages, many HAL/S expressions will compile and execute in Ada, unchanged. Others can be converted simply by replacing the implicit HAL/S multiply operator with the Ada *. Errors will be trapped and identified. Input/output will be convenient and readable.

Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.

PubMed

Jenkins, Adam M; Waterhouse, Robert M; Muskavitch, Marc A T

2015-04-23

Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus. Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles. This study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.

Optimization of large matrix calculations for execution on the Cray X-MP vector supercomputer

NASA Technical Reports Server (NTRS)

Hornfeck, William A.

1988-01-01

A considerable volume of large computational computer codes were developed for NASA over the past twenty-five years. This code represents algorithms developed for machines of earlier generation. With the emergence of the vector supercomputer as a viable, commercially available machine, an opportunity exists to evaluate optimization strategies to improve the efficiency of existing software. This result is primarily due to architectural differences in the latest generation of large-scale machines and the earlier, mostly uniprocessor, machines. A sofware package being used by NASA to perform computations on large matrices is described, and a strategy for conversion to the Cray X-MP vector supercomputer is also described.

Thyra Abstract Interface Package

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

Bartlett, Roscoe A.

2005-09-01

Thrya primarily defines a set of abstract C++ class interfaces needed for the development of abstract numerical atgorithms (ANAs) such as iterative linear solvers, transient solvers all the way up to optimization. At the foundation of these interfaces are abstract C++ classes for vectors, vector spaces, linear operators and multi-vectors. Also included in the Thyra package is C++ code for creating concrete vector, vector space, linear operator, and multi-vector subclasses as well as other utilities to aid in the development of ANAs. Currently, very general and efficient concrete subclass implementations exist for serial and SPMD in-core vectors and multi-vectors. Codemore » also currently exists for testing objects and providing composite objects such as product vectors.« less

The fourfold way of the genetic code.

PubMed

Jiménez-Montaño, Miguel Angel

2009-11-01

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.

Method and System for Temporal Filtering in Video Compression Systems

NASA Technical Reports Server (NTRS)

Lu, Ligang; He, Drake; Jagmohan, Ashish; Sheinin, Vadim

2011-01-01

Three related innovations combine improved non-linear motion estimation, video coding, and video compression. The first system comprises a method in which side information is generated using an adaptive, non-linear motion model. This method enables extrapolating and interpolating a visual signal, including determining the first motion vector between the first pixel position in a first image to a second pixel position in a second image; determining a second motion vector between the second pixel position in the second image and a third pixel position in a third image; determining a third motion vector between the first pixel position in the first image and the second pixel position in the second image, the second pixel position in the second image, and the third pixel position in the third image using a non-linear model; and determining a position of the fourth pixel in a fourth image based upon the third motion vector. For the video compression element, the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a decoder. The encoder converts the source frame into a space-frequency representation, estimates the conditional statistics of at least one vector of space-frequency coefficients with similar frequencies, and is conditioned on previously encoded data. It estimates an encoding rate based on the conditional statistics and applies a Slepian-Wolf code with the computed encoding rate. The method for decoding includes generating a side-information vector of frequency coefficients based on previously decoded source data and encoder statistics and previous reconstructions of the source frequency vector. It also performs Slepian-Wolf decoding of a source frequency vector based on the generated side-information and the Slepian-Wolf code bits. The video coding element includes receiving a first reference frame having a first pixel value at a first pixel position, a second reference frame having a second pixel value at a second pixel position, and a third reference frame having a third pixel value at a third pixel position. It determines a first motion vector between the first pixel position and the second pixel position, a second motion vector between the second pixel position and the third pixel position, and a fourth pixel value for a fourth frame based upon a linear or nonlinear combination of the first pixel value, the second pixel value, and the third pixel value. A stationary filtering process determines the estimated pixel values. The parameters of the filter may be predetermined constants.

Adaptive Hybrid Picture Coding. Volume 2.

DTIC Science & Technology

1985-02-01

ooo5 V.a Measurement Vector ..eho..............57 V.b Size Variable o .entroi* Vector .......... .- 59 V * c Shape Vector .Ř 0-60o oe 6 I V~d...the Program for the Adaptive Line of Sight Method .i.. 18.. o ... .... .... 1 B Details of the Feature Vector FormationProgram .. o ...oo..-....- .122 C ...shape recognition is analogous to recognition of curves in space. Therefore, well known concepts and theorems from differential geometry can be 34 . o

Pulse Code Modulation (PCM) encoder handbook for Aydin Vector MMP-900 series system

NASA Technical Reports Server (NTRS)

Raphael, David

1995-01-01

This handbook explicates the hardware and software properties of a time division multiplex system. This system is used to sample analog and digital data. The data is then merged with frame synchronization information to produce a serial pulse coded modulation (PCM) bit stream. Information in this handbook is required by users to design congruous interface and attest effective utilization of this encoder system. Aydin Vector provides all of the components for these systems to Goddard Space Flight Center/Wallops Flight Facility.

The magnetic universe through vector potential SPMHD simulations

NASA Astrophysics Data System (ADS)

Stasyszyn, F. A.

2017-10-01

The use of Smoothed Particle Magneto Hydrodynamics (SPMHD) is getting nowadays more and more common in Astrophysics. From galaxy clusters to neutron starts, there are multiple applications already existing in the literature. I will review some of the common methods used and highlight the successful approach of using vector potentials to describe the evolution of the magnetic fields. The latter have some interesting advantages, and their results challenge previous findings, being the magnetic divergence problem naturally vanished. We select a few examples to discuss some areas of interest. First, we show some Galaxy Clusters from the MUSIC project. These cosmological simulations are done with the usual sub-grid recipes, as radiative cooling and star formation, being the first ones obtained with an SPH code in a self consistent way. This demonstrates the robustness of the new method in a variety of astrophysical scenarios.

Documentation of the GLAS fourth order general circulation model. Volume 2: Scalar code

NASA Technical Reports Server (NTRS)

Kalnay, E.; Balgovind, R.; Chao, W.; Edelmann, D.; Pfaendtner, J.; Takacs, L.; Takano, K.

1983-01-01

Volume 2, of a 3 volume technical memoranda contains a detailed documentation of the GLAS fourth order general circulation model. Volume 2 contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A variable name dictionary for the scalar code, and code listings are outlined.

A VLSI chip set for real time vector quantization of image sequences

NASA Technical Reports Server (NTRS)

Baker, Richard L.

1989-01-01

The architecture and implementation of a VLSI chip set that vector quantizes (VQ) image sequences in real time is described. The chip set forms a programmable Single-Instruction, Multiple-Data (SIMD) machine which can implement various vector quantization encoding structures. Its VQ codebook may contain unlimited number of codevectors, N, having dimension up to K = 64. Under a weighted least squared error criterion, the engine locates at video rates the best code vector in full-searched or large tree searched VQ codebooks. The ability to manipulate tree structured codebooks, coupled with parallelism and pipelining, permits searches in as short as O (log N) cycles. A full codebook search results in O(N) performance, compared to O(KN) for a Single-Instruction, Single-Data (SISD) machine. With this VLSI chip set, an entire video code can be built on a single board that permits realtime experimentation with very large codebooks.

Method and system for efficient video compression with low-complexity encoder

NASA Technical Reports Server (NTRS)

Chen, Jun (Inventor); He, Dake (Inventor); Sheinin, Vadim (Inventor); Jagmohan, Ashish (Inventor); Lu, Ligang (Inventor)

2012-01-01

Disclosed are a method and system for video compression, wherein the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a video decoder, wherein the method for encoding includes the steps of converting a source frame into a space-frequency representation; estimating conditional statistics of at least one vector of space-frequency coefficients; estimating encoding rates based on the said conditional statistics; and applying Slepian-Wolf codes with the said computed encoding rates. The preferred method for decoding includes the steps of; generating a side-information vector of frequency coefficients based on previously decoded source data, encoder statistics, and previous reconstructions of the source frequency vector; and performing Slepian-Wolf decoding of at least one source frequency vector based on the generated side-information, the Slepian-Wolf code bits and the encoder statistics.

A comparative study of history-based versus vectorized Monte Carlo methods in the GPU/CUDA environment for a simple neutron eigenvalue problem

NASA Astrophysics Data System (ADS)

Liu, Tianyu; Du, Xining; Ji, Wei; Xu, X. George; Brown, Forrest B.

2014-06-01

For nuclear reactor analysis such as the neutron eigenvalue calculations, the time consuming Monte Carlo (MC) simulations can be accelerated by using graphics processing units (GPUs). However, traditional MC methods are often history-based, and their performance on GPUs is affected significantly by the thread divergence problem. In this paper we describe the development of a newly designed event-based vectorized MC algorithm for solving the neutron eigenvalue problem. The code was implemented using NVIDIA's Compute Unified Device Architecture (CUDA), and tested on a NVIDIA Tesla M2090 GPU card. We found that although the vectorized MC algorithm greatly reduces the occurrence of thread divergence thus enhancing the warp execution efficiency, the overall simulation speed is roughly ten times slower than the history-based MC code on GPUs. Profiling results suggest that the slow speed is probably due to the memory access latency caused by the large amount of global memory transactions. Possible solutions to improve the code efficiency are discussed.

Livermore Compiler Analysis Loop Suite

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

Hornung, R. D.

2013-03-01

LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermoremore » Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

An adaptive vector quantization scheme

NASA Technical Reports Server (NTRS)

Cheung, K.-M.

1990-01-01

Vector quantization is known to be an effective compression scheme to achieve a low bit rate so as to minimize communication channel bandwidth and also to reduce digital memory storage while maintaining the necessary fidelity of the data. However, the large number of computations required in vector quantizers has been a handicap in using vector quantization for low-rate source coding. An adaptive vector quantization algorithm is introduced that is inherently suitable for simple hardware implementation because it has a simple architecture. It allows fast encoding and decoding because it requires only addition and subtraction operations.

Coding for parallel execution of hardware-in-the-loop millimeter-wave scene generation models on multicore SIMD processor architectures

NASA Astrophysics Data System (ADS)

Olson, Richard F.

2013-05-01

Rendering of point scatterer based radar scenes for millimeter wave (mmW) seeker tests in real-time hardware-in-the-loop (HWIL) scene generation requires efficient algorithms and vector-friendly computer architectures for complex signal synthesis. New processor technology from Intel implements an extended 256-bit vector SIMD instruction set (AVX, AVX2) in a multi-core CPU design providing peak execution rates of hundreds of GigaFLOPS (GFLOPS) on one chip. Real world mmW scene generation code can approach peak SIMD execution rates only after careful algorithm and source code design. An effective software design will maintain high computing intensity emphasizing register-to-register SIMD arithmetic operations over data movement between CPU caches or off-chip memories. Engineers at the U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) applied two basic parallel coding methods to assess new 256-bit SIMD multi-core architectures for mmW scene generation in HWIL. These include use of POSIX threads built on vector library functions and more portable, highlevel parallel code based on compiler technology (e.g. OpenMP pragmas and SIMD autovectorization). Since CPU technology is rapidly advancing toward high processor core counts and TeraFLOPS peak SIMD execution rates, it is imperative that coding methods be identified which produce efficient and maintainable parallel code. This paper describes the algorithms used in point scatterer target model rendering, the parallelization of those algorithms, and the execution performance achieved on an AVX multi-core machine using the two basic parallel coding methods. The paper concludes with estimates for scale-up performance on upcoming multi-core technology.

Speech coding at low to medium bit rates

NASA Astrophysics Data System (ADS)

Leblanc, Wilfred Paul

1992-09-01

Improved search techniques coupled with improved codebook design methodologies are proposed to improve the performance of conventional code-excited linear predictive coders for speech. Improved methods for quantizing the short term filter are developed by employing a tree search algorithm and joint codebook design to multistage vector quantization. Joint codebook design procedures are developed to design locally optimal multistage codebooks. Weighting during centroid computation is introduced to improve the outlier performance of the multistage vector quantizer. Multistage vector quantization is shown to be both robust against input characteristics and in the presence of channel errors. Spectral distortions of about 1 dB are obtained at rates of 22-28 bits/frame. Structured codebook design procedures for excitation in code-excited linear predictive coders are compared to general codebook design procedures. Little is lost using significant structure in the excitation codebooks while greatly reducing the search complexity. Sparse multistage configurations are proposed for reducing computational complexity and memory size. Improved search procedures are applied to code-excited linear prediction which attempt joint optimization of the short term filter, the adaptive codebook, and the excitation. Improvements in signal to noise ratio of 1-2 dB are realized in practice.

Reflectance Prediction Modelling for Residual-Based Hyperspectral Image Coding

PubMed Central

Xiao, Rui; Gao, Junbin; Bossomaier, Terry

2016-01-01

A Hyperspectral (HS) image provides observational powers beyond human vision capability but represents more than 100 times the data compared to a traditional image. To transmit and store the huge volume of an HS image, we argue that a fundamental shift is required from the existing “original pixel intensity”-based coding approaches using traditional image coders (e.g., JPEG2000) to the “residual”-based approaches using a video coder for better compression performance. A modified video coder is required to exploit spatial-spectral redundancy using pixel-level reflectance modelling due to the different characteristics of HS images in their spectral and shape domain of panchromatic imagery compared to traditional videos. In this paper a novel coding framework using Reflectance Prediction Modelling (RPM) in the latest video coding standard High Efficiency Video Coding (HEVC) for HS images is proposed. An HS image presents a wealth of data where every pixel is considered a vector for different spectral bands. By quantitative comparison and analysis of pixel vector distribution along spectral bands, we conclude that modelling can predict the distribution and correlation of the pixel vectors for different bands. To exploit distribution of the known pixel vector, we estimate a predicted current spectral band from the previous bands using Gaussian mixture-based modelling. The predicted band is used as the additional reference band together with the immediate previous band when we apply the HEVC. Every spectral band of an HS image is treated like it is an individual frame of a video. In this paper, we compare the proposed method with mainstream encoders. The experimental results are fully justified by three types of HS dataset with different wavelength ranges. The proposed method outperforms the existing mainstream HS encoders in terms of rate-distortion performance of HS image compression. PMID:27695102

Creation of fully vectorized FORTRAN code for integrating the movement of dust grains in interplanetary environments

NASA Technical Reports Server (NTRS)

Colquitt, Walter

1989-01-01

The main objective is to improve the performance of a specific FORTRAN computer code from the Planetary Sciences Division of NASA/Johnson Space Center when used on a modern vectorizing supercomputer. The code is used to calculate orbits of dust grains that separate from comets and asteroids. This code accounts for influences of the sun and 8 planets (neglecting Pluto), solar wind, and solar light pressure including Poynting-Robertson drag. Calculations allow one to study the motion of these particles as they are influenced by the Earth or one of the other planets. Some of these particles become trapped just beyond the Earth for long periods of time. These integer period resonances vary from 3 orbits of the Earth and 2 orbits of the particles to as high as 14 to 13.

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

Skeletonization and Partitioning of Digital Images Using Discrete Morse Theory.

PubMed

Delgado-Friedrichs, Olaf; Robins, Vanessa; Sheppard, Adrian

2015-03-01

We show how discrete Morse theory provides a rigorous and unifying foundation for defining skeletons and partitions of grayscale digital images. We model a grayscale image as a cubical complex with a real-valued function defined on its vertices (the voxel values). This function is extended to a discrete gradient vector field using the algorithm presented in Robins, Wood, Sheppard TPAMI 33:1646 (2011). In the current paper we define basins (the building blocks of a partition) and segments of the skeleton using the stable and unstable sets associated with critical cells. The natural connection between Morse theory and homology allows us to prove the topological validity of these constructions; for example, that the skeleton is homotopic to the initial object. We simplify the basins and skeletons via Morse-theoretic cancellation of critical cells in the discrete gradient vector field using a strategy informed by persistent homology. Simple working Python code for our algorithms for efficient vector field traversal is included. Example data are taken from micro-CT images of porous materials, an application area where accurate topological models of pore connectivity are vital for fluid-flow modelling.

Time-variant analysis of rotorcraft systems dynamics - An exploitation of vector processors

NASA Technical Reports Server (NTRS)

Amirouche, F. M. L.; Xie, M.; Shareef, N. H.

1993-01-01

In this paper a generalized algorithmic procedure is presented for handling constraints in mechanical transmissions. The latter are treated as multibody systems of interconnected rigid/flexible bodies. The constraint Jacobian matrices are generated automatically and suitably updated in time, depending on the geometrical and kinematical constraint conditions describing the interconnection between shafts or gears. The type of constraints are classified based on the interconnection of the bodies by assuming that one or more points of contact exist between them. The effects due to elastic deformation of the flexible bodies are included by allowing each body element to undergo small deformations. The procedure is based on recursively formulated Kane's dynamical equations of motion and the finite element method, including the concept of geometrical stiffening effects. The method is implemented on an IBM-3090-600j vector processor with pipe-lining capabilities. A significant increase in the speed of execution is achieved by vectorizing the developed code in computationally intensive areas. An example consisting of two meshing disks rotating at high angular velocity is presented. Applications are intended for the study of the dynamic behavior of helicopter transmissions.

Reverse genetics of measles virus and resulting multivalent recombinant vaccines: applications of recombinant measles viruses.

PubMed

Billeter, M A; Naim, H Y; Udem, S A

2009-01-01

An overview is given on the development of technologies to allow reverse genetics of RNA viruses, i.e., the rescue of viruses from cDNA, with emphasis on nonsegmented negative-strand RNA viruses (Mononegavirales), as exemplified for measles virus (MV). Primarily, these technologies allowed site-directed mutagenesis, enabling important insights into a variety of aspects of the biology of these viruses. Concomitantly, foreign coding sequences were inserted to (a) allow localization of virus replication in vivo through marker gene expression, (b) develop candidate multivalent vaccines against measles and other pathogens, and (c) create candidate oncolytic viruses. The vector use of these viruses was experimentally encouraged by the pronounced genetic stability of the recombinants unexpected for RNA viruses, and by the high load of insertable genetic material, in excess of 6 kb. The known assets, such as the small genome size of the vector in comparison to DNA viruses proposed as vectors, the extensive clinical experience of attenuated MV as vaccine with a proven record of high safety and efficacy, and the low production cost per vaccination dose are thus favorably complemented.

Novel Integration of Frame Rate Up Conversion and HEVC Coding Based on Rate-Distortion Optimization.

PubMed

Guo Lu; Xiaoyun Zhang; Li Chen; Zhiyong Gao

2018-02-01

Frame rate up conversion (FRUC) can improve the visual quality by interpolating new intermediate frames. However, high frame rate videos by FRUC are confronted with more bitrate consumption or annoying artifacts of interpolated frames. In this paper, a novel integration framework of FRUC and high efficiency video coding (HEVC) is proposed based on rate-distortion optimization, and the interpolated frames can be reconstructed at encoder side with low bitrate cost and high visual quality. First, joint motion estimation (JME) algorithm is proposed to obtain robust motion vectors, which are shared between FRUC and video coding. What's more, JME is embedded into the coding loop and employs the original motion search strategy in HEVC coding. Then, the frame interpolation is formulated as a rate-distortion optimization problem, where both the coding bitrate consumption and visual quality are taken into account. Due to the absence of original frames, the distortion model for interpolated frames is established according to the motion vector reliability and coding quantization error. Experimental results demonstrate that the proposed framework can achieve 21% ~ 42% reduction in BDBR, when compared with the traditional methods of FRUC cascaded with coding.

Kablammo: an interactive, web-based BLAST results visualizer.

PubMed

Wintersinger, Jeff A; Wasmuth, James D

2015-04-15

Kablammo is a web-based application that produces interactive, vector-based visualizations of sequence alignments generated by BLAST. These visualizations can illustrate many features, including shared protein domains, chromosome structural modifications and genome misassembly. Kablammo can be used at http://kablammo.wasmuthlab.org. For a local installation, the source code and instructions are available under the MIT license at http://github.com/jwintersinger/kablammo. jeff@wintersinger.org. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Efficiency of VIGS and gene expression in a novel bipartite potexvirus vector delivery system as a function of strength of TGB1 silencing suppression.

PubMed

Lim, Hyoun-Sub; Vaira, Anna Maria; Domier, Leslie L; Lee, Sung Chul; Kim, Hong Gi; Hammond, John

2010-06-20

We have developed plant virus-based vectors for virus-induced gene silencing (VIGS) and protein expression, based on Alternanthera mosaic virus (AltMV), for infection of a wide range of host plants including Nicotiana benthamiana and Arabidopsis thaliana by either mechanical inoculation of in vitro transcripts or via agroinfiltration. In vivo transcripts produced by co-agroinfiltration of bacteriophage T7 RNA polymerase resulted in T7-driven AltMV infection from a binary vector in the absence of the Cauliflower mosaic virus 35S promoter. An artificial bipartite viral vector delivery system was created by separating the AltMV RNA-dependent RNA polymerase and Triple Gene Block (TGB)123-Coat protein (CP) coding regions into two constructs each bearing the AltMV 5' and 3' non-coding regions, which recombined in planta to generate a full-length AltMV genome. Substitution of TGB1 L(88)P, and equivalent changes in other potexvirus TGB1 proteins, affected RNA silencing suppression efficacy and suitability of the vectors from protein expression to VIGS. Published by Elsevier Inc.

Neural networks for data compression and invariant image recognition

NASA Technical Reports Server (NTRS)

Gardner, Sheldon

1989-01-01

An approach to invariant image recognition (I2R), based upon a model of biological vision in the mammalian visual system (MVS), is described. The complete I2R model incorporates several biologically inspired features: exponential mapping of retinal images, Gabor spatial filtering, and a neural network associative memory. In the I2R model, exponentially mapped retinal images are filtered by a hierarchical set of Gabor spatial filters (GSF) which provide compression of the information contained within a pixel-based image. A neural network associative memory (AM) is used to process the GSF coded images. We describe a 1-D shape function method for coding of scale and rotationally invariant shape information. This method reduces image shape information to a periodic waveform suitable for coding as an input vector to a neural network AM. The shape function method is suitable for near term applications on conventional computing architectures equipped with VLSI FFT chips to provide a rapid image search capability.

Fast space-varying convolution using matrix source coding with applications to camera stray light reduction.

PubMed

Wei, Jianing; Bouman, Charles A; Allebach, Jan P

2014-05-01

Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.

Pulse Code Modulation (PCM) encoder handbook for Aydin Vector MMP-600 series system

NASA Technical Reports Server (NTRS)

Currier, S. F.; Powell, W. R.

1986-01-01

The hardware and software characteristics of a time division multiplex system are described. The system is used to sample analog and digital data. The data is merged with synchronization information to produce a serial pulse coded modulation (PCM) bit stream. Information presented herein is required by users to design compatible interfaces and assure effective utilization of this encoder system. GSFC/Wallops Flight Facility has flown approximately 50 of these systems through 1984 on sounding rockets with no inflight failures. Aydin Vector manufactures all of the components for these systems.

NPS-NRL-Rice-UIUC Collaboration on Navy Atmosphere-Ocean Coupled Models on Many-Core Computer Architectures Annual Report

DTIC Science & Technology

2014-09-30

portability is difficult to achieve on future supercomputers that use various type of accelerators (GPUs, Xeon - Phi , and SIMD etc). All of these...bottlenecks of NUMA. For example, in the CG code the state vector was originally stored as q(1 : Nvar ,1 : Npoin) where Nvar are the number of...a Global Grid Point (GGP) storage. On the other hand, in the DG code the state vector is typically stored as q(1 : Nvar ,1 : Npts,1 : Nelem) where

Magnetic resonance image compression using scalar-vector quantization

NASA Astrophysics Data System (ADS)

Mohsenian, Nader; Shahri, Homayoun

1995-12-01

A new coding scheme based on the scalar-vector quantizer (SVQ) is developed for compression of medical images. SVQ is a fixed-rate encoder and its rate-distortion performance is close to that of optimal entropy-constrained scalar quantizers (ECSQs) for memoryless sources. The use of a fixed-rate quantizer is expected to eliminate some of the complexity issues of using variable-length scalar quantizers. When transmission of images over noisy channels is considered, our coding scheme does not suffer from error propagation which is typical of coding schemes which use variable-length codes. For a set of magnetic resonance (MR) images, coding results obtained from SVQ and ECSQ at low bit-rates are indistinguishable. Furthermore, our encoded images are perceptually indistinguishable from the original, when displayed on a monitor. This makes our SVQ based coder an attractive compression scheme for picture archiving and communication systems (PACS), currently under consideration for an all digital radiology environment in hospitals, where reliable transmission, storage, and high fidelity reconstruction of images are desired.

Novel Approaches for the Treatment of Familial Hypercholesterolemia: Current Status and Future Challenges.

PubMed

Jiang, Long; Wang, Lu-Ya; Cheng, Xiao-Shu

2018-06-13

Familial hypercholesterolemia (FH) is an autosomal-dominant disorder that is characterized by high plasma low-density lipoprotein cholesterol (LDL-c) levels and an increased risk of cardiovascular disease. Despite the use of high-dose statins and the recent addition of proprotein convertase subtilisin/kexin type 9 inhibitors as a treatment option, many patients with homozygous FH fail to achieve optimal reductions of LDL-c levels. Gene therapy has become one of the most promising research directions for contemporary life sciences and is a potential treatment option for FH. Recent studies have confirmed the efficacy of a recombinant adeno-associated virus 8 vector expressing the human LDL-c receptor gene in a mouse model, and this vector is currently in phase 2 clinical trials. Much progress has also been achieved in the fields of antisense oligonucleotide- and small interfering RNA-based gene therapies, which are in phase 1-2 clinical trials. In addition, novel approaches, such as the use of minicircle DNA vectors, microRNAs, long non-coding RNAs, and the CRISPR/Cas9 gene-editing system, have shown great potential for FH therapy. However, the delivery system, immunogenicity, accuracy, and specificity of gene therapies limit their clinical applications. In this article, we discuss the current status of gene therapy and recent advances that will likely affect the clinical application of gene therapy for the treatment of FH.

Gravitational and Magnetic Anomaly Inversion Using a Tree-Based Geometry Representation

DTIC Science & Technology

2009-06-01

find successive mini- ized vectors. Throughout this paper, the term iteration refers to a ingle loop through a stage of the global scheme, not...BOX 12211 RESEARCH TRIANGLE PARK NC 27709-2211 5 NAVAL RESEARCH LAB E R FRANCHI CODE 7100 M H ORR CODE 7120 J A BUCARO CODE 7130

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: Path radiance

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Matarrese, Raffaella; Klemm, Frank J., Jr.

2006-09-01

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part I: path radiance.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Matarrese, Raffaella; Klemm, Frank J

2006-09-10

A vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), which enables accounting for radiation polarization, has been developed and validated against a Monte Carlo code, Coulson's tabulated values, and MOBY (Marine Optical Buoy System) water-leaving reflectance measurements. The developed code was also tested against the scalar codes SHARM, DISORT, and MODTRAN to evaluate its performance in scalar mode and the influence of polarization. The obtained results have shown a good agreement of 0.7% in comparison with the Monte Carlo code, 0.2% for Coulson's tabulated values, and 0.001-0.002 for the 400-550 nm region for the MOBY reflectances. Ignoring the effects of polarization led to large errors in calculated top-of-atmosphere reflectances: more than 10% for a molecular atmosphere and up to 5% for an aerosol atmosphere. This new version of 6S is intended to replace the previous scalar version used for calculation of lookup tables in the MODIS (Moderate Resolution Imaging Spectroradiometer) atmospheric correction algorithm.

Adaptation and optimization of a line-by-line radiative transfer program for the STAR-100 (STARSMART)

NASA Technical Reports Server (NTRS)

Rarig, P. L.

1980-01-01

A program to calculate upwelling infrared radiation was modified to operate efficiently on the STAR-100. The modified software processes specific test cases significantly faster than the initial STAR-100 code. For example, a midlatitude summer atmospheric model is executed in less than 2% of the time originally required on the STAR-100. Furthermore, the optimized program performs extra operations to save the calculated absorption coefficients. Some of the advantages and pitfalls of virtual memory and vector processing are discussed along with strategies used to avoid loss of accuracy and computing power. Results from the vectorized code, in terms of speed, cost, and relative error with respect to serial code solutions are encouraging.

Transformable Rhodobacter strains, method for producing transformable Rhodobacter strains

DOEpatents

Laible, Philip D.; Hanson, Deborah K.

2018-05-08

The invention provides an organism for expressing foreign DNA, the organism engineered to accept standard DNA carriers. The genome of the organism codes for intracytoplasmic membranes and features an interruption in at least one of the genes coding for restriction enzymes. Further provided is a system for producing biological materials comprising: selecting a vehicle to carry DNA which codes for the biological materials; determining sites on the vehicle's DNA sequence susceptible to restriction enzyme cleavage; choosing an organism to accept the vehicle based on that organism not acting upon at least one of said vehicle's sites; engineering said vehicle to contain said DNA; thereby creating a synthetic vector; and causing the synthetic vector to enter the organism so as cause expression of said DNA.

Recursive optimal pruning with applications to tree structured vector quantizers

NASA Technical Reports Server (NTRS)

Kiang, Shei-Zein; Baker, Richard L.; Sullivan, Gary J.; Chiu, Chung-Yen

1992-01-01

A pruning algorithm of Chou et al. (1989) for designing optimal tree structures identifies only those codebooks which lie on the convex hull of the original codebook's operational distortion rate function. The authors introduce a modified version of the original algorithm, which identifies a large number of codebooks having minimum average distortion, under the constraint that, in each step, only modes having no descendents are removed from the tree. All codebooks generated by the original algorithm are also generated by this algorithm. The new algorithm generates a much larger number of codebooks in the middle- and low-rate regions. The additional codebooks permit operation near the codebook's operational distortion rate function without time sharing by choosing from the increased number of available bit rates. Despite the statistical mismatch which occurs when coding data outside the training sequence, these pruned codebooks retain their performance advantage over full search vector quantizers (VQs) for a large range of rates.

Some Remarks on GMRES for Transport Theory

NASA Technical Reports Server (NTRS)

Patton, Bruce W.; Holloway, James Paul

2003-01-01

We review some work on the application of GMRES to the solution of the discrete ordinates transport equation in one-dimension. We note that GMRES can be applied directly to the angular flux vector, or it can be applied to only a vector of flux moments as needed to compute the scattering operator of the transport equation. In the former case we illustrate both the delights and defects of ILU right-preconditioners for problems with anisotropic scatter and for problems with upscatter. When working with flux moments we note that GMRES can be used as an accelerator for any existing transport code whose solver is based on a stationary fixed-point iteration, including transport sweeps and DSA transport sweeps. We also provide some numerical illustrations of this idea. We finally show how space can be traded for speed by taking multiple transport sweeps per GMRES iteration. Key Words: transport equation, GMRES, Krylov subspace

Time variant analysis of large scale constrained rotorcraft systems dynamics - An exploitation of IBM-3090 vector-processor's pipe-lining feature

NASA Technical Reports Server (NTRS)

Amirouche, F. M. L.; Shareef, N. H.; Xie, M.

1991-01-01

A generalized algorithmic procedure is presented for handling the constraints in transmissions, which are treated as a multibody system of interconnected rigid/flexible bodies. The type of constraints are classified based on the interconnection of the bodies, assuming one or more points of contact to exist between them. The method is explained through flow charts and configuration/interaction tables. A significant increase in speed of execution is achieved by vectorizing the developed code in computationally intensive areas. The study of an example consisting of two meshing disks rotating at high angular velocity is carried out. The dynamic behavior of the constraint forces associated with the generalized coordinates of the system are plotted by selecting various modes. Applications are intended for the study of dynamic and subsequent prediction of constraint forces at the gear teeth contacting points in helicopter transmissions with the aim of improving performance dependability.

Vectorized schemes for conical potential flow using the artificial density method

NASA Technical Reports Server (NTRS)

Bradley, P. F.; Dwoyer, D. L.; South, J. C., Jr.; Keen, J. M.

1984-01-01

A method is developed to determine solutions to the full-potential equation for steady supersonic conical flow using the artificial density method. Various update schemes used generally for transonic potential solutions are investigated. The schemes are compared for speed and robustness. All versions of the computer code have been vectorized and are currently running on the CYBER-203 computer. The update schemes are vectorized, where possible, either fully (explicit schemes) or partially (implicit schemes). Since each version of the code differs only by the update scheme and elements other than the update scheme are completely vectorizable, comparisons of computational effort and convergence rate among schemes are a measure of the specific scheme's performance. Results are presented for circular and elliptical cones at angle of attack for subcritical and supercritical crossflows.

An efficient system for reliably transmitting image and video data over low bit rate noisy channels

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.; Huang, Y. F.; Stevenson, Robert L.

1994-01-01

This research project is intended to develop an efficient system for reliably transmitting image and video data over low bit rate noisy channels. The basic ideas behind the proposed approach are the following: employ statistical-based image modeling to facilitate pre- and post-processing and error detection, use spare redundancy that the source compression did not remove to add robustness, and implement coded modulation to improve bandwidth efficiency and noise rejection. Over the last six months, progress has been made on various aspects of the project. Through our studies of the integrated system, a list-based iterative Trellis decoder has been developed. The decoder accepts feedback from a post-processor which can detect channel errors in the reconstructed image. The error detection is based on the Huber Markov random field image model for the compressed image. The compression scheme used here is that of JPEG (Joint Photographic Experts Group). Experiments were performed and the results are quite encouraging. The principal ideas here are extendable to other compression techniques. In addition, research was also performed on unequal error protection channel coding, subband vector quantization as a means of source coding, and post processing for reducing coding artifacts. Our studies on unequal error protection (UEP) coding for image transmission focused on examining the properties of the UEP capabilities of convolutional codes. The investigation of subband vector quantization employed a wavelet transform with special emphasis on exploiting interband redundancy. The outcome of this investigation included the development of three algorithms for subband vector quantization. The reduction of transform coding artifacts was studied with the aid of a non-Gaussian Markov random field model. This results in improved image decompression. These studies are summarized and the technical papers included in the appendices.

BSIFT: toward data-independent codebook for large scale image search.

PubMed

Zhou, Wengang; Li, Houqiang; Hong, Richang; Lu, Yijuan; Tian, Qi

2015-03-01

Bag-of-Words (BoWs) model based on Scale Invariant Feature Transform (SIFT) has been widely used in large-scale image retrieval applications. Feature quantization by vector quantization plays a crucial role in BoW model, which generates visual words from the high- dimensional SIFT features, so as to adapt to the inverted file structure for the scalable retrieval. Traditional feature quantization approaches suffer several issues, such as necessity of visual codebook training, limited reliability, and update inefficiency. To avoid the above problems, in this paper, a novel feature quantization scheme is proposed to efficiently quantize each SIFT descriptor to a descriptive and discriminative bit-vector, which is called binary SIFT (BSIFT). Our quantizer is independent of image collections. In addition, by taking the first 32 bits out from BSIFT as code word, the generated BSIFT naturally lends itself to adapt to the classic inverted file structure for image indexing. Moreover, the quantization error is reduced by feature filtering, code word expansion, and query sensitive mask shielding. Without any explicit codebook for quantization, our approach can be readily applied in image search in some resource-limited scenarios. We evaluate the proposed algorithm for large scale image search on two public image data sets. Experimental results demonstrate the index efficiency and retrieval accuracy of our approach.

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing

PubMed Central

Davidsson, Marcus; Diaz-Fernandez, Paula; Schwich, Oliver D.; Torroba, Marcos; Wang, Gang; Björklund, Tomas

2016-01-01

Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode. PMID:27874090

Deep Hashing for Scalable Image Search.

PubMed

Lu, Jiwen; Liong, Venice Erin; Zhou, Jie

2017-05-01

In this paper, we propose a new deep hashing (DH) approach to learn compact binary codes for scalable image search. Unlike most existing binary codes learning methods, which usually seek a single linear projection to map each sample into a binary feature vector, we develop a deep neural network to seek multiple hierarchical non-linear transformations to learn these binary codes, so that the non-linear relationship of samples can be well exploited. Our model is learned under three constraints at the top layer of the developed deep network: 1) the loss between the compact real-valued code and the learned binary vector is minimized, 2) the binary codes distribute evenly on each bit, and 3) different bits are as independent as possible. To further improve the discriminative power of the learned binary codes, we extend DH into supervised DH (SDH) and multi-label SDH by including a discriminative term into the objective function of DH, which simultaneously maximizes the inter-class variations and minimizes the intra-class variations of the learned binary codes with the single-label and multi-label settings, respectively. Extensive experimental results on eight widely used image search data sets show that our proposed methods achieve very competitive results with the state-of-the-arts.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part II. Homogeneous Lambertian and anisotropic surfaces.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F

2007-07-10

This is the second part of the validation effort of the recently developed vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), primarily used for the calculation of look-up tables in the Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric correction algorithm. The 6SV1 code was tested against a Monte Carlo code and Coulson's tabulated values for molecular and aerosol atmospheres bounded by different Lambertian and anisotropic surfaces. The code was also tested in scalar mode against the scalar code SHARM to resolve the previous 6S accuracy issues in the case of an anisotropic surface. All test cases were characterized by good agreement between the 6SV1 and the other codes: The overall relative error did not exceed 0.8%. The study also showed that ignoring the effects of radiation polarization in the atmosphere led to large errors in the simulated top-of-atmosphere reflectances: The maximum observed error was approximately 7.2% for both Lambertian and anisotropic surfaces.

Validation of a vector version of the 6S radiative transfer code for atmospheric correction of satellite data. Part II. Homogeneous Lambertian and anisotropic surfaces

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.

2007-07-01

This is the second part of the validation effort of the recently developed vector version of the 6S (Second Simulation of a Satellite Signal in the Solar Spectrum) radiative transfer code (6SV1), primarily used for the calculation of look-up tables in the Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric correction algorithm. The 6SV1 code was tested against a Monte Carlo code and Coulson's tabulated values for molecular and aerosol atmospheres bounded by different Lambertian and anisotropic surfaces. The code was also tested in scalar mode against the scalar code SHARM to resolve the previous 6S accuracy issues in the case of an anisotropic surface. All test cases were characterized by good agreement between the 6SV1 and the other codes: The overall relative error did not exceed 0.8%. The study also showed that ignoring the effects of radiation polarization in the atmosphere led to large errors in the simulated top-of-atmosphere reflectances: The maximum observed error was approximately 7.2% for both Lambertian and anisotropic surfaces.

Parallel processors and nonlinear structural dynamics algorithms and software

NASA Technical Reports Server (NTRS)

Belytschko, Ted

1990-01-01

Techniques are discussed for the implementation and improvement of vectorization and concurrency in nonlinear explicit structural finite element codes. In explicit integration methods, the computation of the element internal force vector consumes the bulk of the computer time. The program can be efficiently vectorized by subdividing the elements into blocks and executing all computations in vector mode. The structuring of elements into blocks also provides a convenient way to implement concurrency by creating tasks which can be assigned to available processors for evaluation. The techniques were implemented in a 3-D nonlinear program with one-point quadrature shell elements. Concurrency and vectorization were first implemented in a single time step version of the program. Techniques were developed to minimize processor idle time and to select the optimal vector length. A comparison of run times between the program executed in scalar, serial mode and the fully vectorized code executed concurrently using eight processors shows speed-ups of over 25. Conjugate gradient methods for solving nonlinear algebraic equations are also readily adapted to a parallel environment. A new technique for improving convergence properties of conjugate gradients in nonlinear problems is developed in conjunction with other techniques such as diagonal scaling. A significant reduction in the number of iterations required for convergence is shown for a statically loaded rigid bar suspended by three equally spaced springs.

Efficient diagonalization of the sparse matrices produced within the framework of the UK R-matrix molecular codes

NASA Astrophysics Data System (ADS)

Galiatsatos, P. G.; Tennyson, J.

2012-11-01

The most time consuming step within the framework of the UK R-matrix molecular codes is that of the diagonalization of the inner region Hamiltonian matrix (IRHM). Here we present the method that we follow to speed up this step. We use shared memory machines (SMM), distributed memory machines (DMM), the OpenMP directive based parallel language, the MPI function based parallel language, the sparse matrix diagonalizers ARPACK and PARPACK, a variation for real symmetric matrices of the official coordinate sparse matrix format and finally a parallel sparse matrix-vector product (PSMV). The efficient application of the previous techniques rely on two important facts: the sparsity of the matrix is large enough (more than 98%) and in order to get back converged results we need a small only part of the matrix spectrum.

Drop-out phagemid vector for switching from phage displayed affinity reagents to expression formats.

PubMed

Pershad, Kritika; Sullivan, Mark A; Kay, Brian K

2011-05-15

Affinity reagents that are generated by phage display are typically subcloned into an expression vector for further biochemical characterization. This insert transfer process is time consuming and laborious especially if many inserts are to be subcloned. To simplify the transfer process, we have constructed a "drop-out" phagemid vector that can be rapidly converted to an expression vector by a simple restriction enzyme digestion with MfeI (to "drop-out" the gene III coding sequence), which generates alkaline phosphatase (AP) fusions of the affinity reagents on religation. Subsequently, restriction digestion with AscI drops out the AP coding region and religation generates affinity reagents with a C-terminal six-histidine tag. To validate the usefulness of this vector, four different human single chain Fragments of variable regions (scFv) were tested, three of which show specific binding to three zebrafish (Danio rerio) proteins, namely suppression of tumorigenicity 13, recoverin, and Ppib and the fourth binds to human Lactoferrin protein. For each of the constructs tested, the gene III and AP drop-out efficiency was between 90% and 100%. This vector is especially useful in speeding up the downstream screening of affinity reagents and bypassing the time-consuming subcloning experiments. Copyright © 2011 Elsevier Inc. All rights reserved.

A vector based on the SV40 origin of replication and chromosomal S/MARs replicates episomally in CHO cells.

PubMed Central

Piechaczek, C; Fetzer, C; Baiker, A; Bode, J; Lipps, H J

1999-01-01

We have developed an episomal replicating expression vector in which the SV40 gene coding for the large T-antigen was replaced by chromosomal scaffold/matrix attached regions. Southern analysis as well as vector rescue experiments in CHO cells and in Escherichia coli demonstrate that the vector replicates episomally in CHO cells. It occurs in a very low copy number in the cells and is stably maintained over more than 100 generations without selection pressure. PMID:9862961

Medical Image Compression Based on Vector Quantization with Variable Block Sizes in Wavelet Domain

PubMed Central

Jiang, Huiyan; Ma, Zhiyuan; Hu, Yang; Yang, Benqiang; Zhang, Libo

2012-01-01

An optimized medical image compression algorithm based on wavelet transform and improved vector quantization is introduced. The goal of the proposed method is to maintain the diagnostic-related information of the medical image at a high compression ratio. Wavelet transformation was first applied to the image. For the lowest-frequency subband of wavelet coefficients, a lossless compression method was exploited; for each of the high-frequency subbands, an optimized vector quantization with variable block size was implemented. In the novel vector quantization method, local fractal dimension (LFD) was used to analyze the local complexity of each wavelet coefficients, subband. Then an optimal quadtree method was employed to partition each wavelet coefficients, subband into several sizes of subblocks. After that, a modified K-means approach which is based on energy function was used in the codebook training phase. At last, vector quantization coding was implemented in different types of sub-blocks. In order to verify the effectiveness of the proposed algorithm, JPEG, JPEG2000, and fractal coding approach were chosen as contrast algorithms. Experimental results show that the proposed method can improve the compression performance and can achieve a balance between the compression ratio and the image visual quality. PMID:23049544

Medical image compression based on vector quantization with variable block sizes in wavelet domain.

PubMed

Jiang, Huiyan; Ma, Zhiyuan; Hu, Yang; Yang, Benqiang; Zhang, Libo

2012-01-01

An optimized medical image compression algorithm based on wavelet transform and improved vector quantization is introduced. The goal of the proposed method is to maintain the diagnostic-related information of the medical image at a high compression ratio. Wavelet transformation was first applied to the image. For the lowest-frequency subband of wavelet coefficients, a lossless compression method was exploited; for each of the high-frequency subbands, an optimized vector quantization with variable block size was implemented. In the novel vector quantization method, local fractal dimension (LFD) was used to analyze the local complexity of each wavelet coefficients, subband. Then an optimal quadtree method was employed to partition each wavelet coefficients, subband into several sizes of subblocks. After that, a modified K-means approach which is based on energy function was used in the codebook training phase. At last, vector quantization coding was implemented in different types of sub-blocks. In order to verify the effectiveness of the proposed algorithm, JPEG, JPEG2000, and fractal coding approach were chosen as contrast algorithms. Experimental results show that the proposed method can improve the compression performance and can achieve a balance between the compression ratio and the image visual quality.

User's and test case manual for FEMATS

NASA Technical Reports Server (NTRS)

Chatterjee, Arindam; Volakis, John; Nurnberger, Mike; Natzke, John

1995-01-01

The FEMATS program incorporates first-order edge-based finite elements and vector absorbing boundary conditions into the scattered field formulation for computation of the scattering from three-dimensional geometries. The code has been validated extensively for a large class of geometries containing inhomogeneities and satisfying transition conditions. For geometries that are too large for the workstation environment, the FEMATS code has been optimized to run on various supercomputers. Currently, FEMATS has been configured to run on the HP 9000 workstation, vectorized for the Cray Y-MP, and parallelized to run on the Kendall Square Research (KSR) architecture and the Intel Paragon.

High Order Entropy-Constrained Residual VQ for Lossless Compression of Images

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Smith, Mark J. T.; Scales, Allen

1995-01-01

High order entropy coding is a powerful technique for exploiting high order statistical dependencies. However, the exponentially high complexity associated with such a method often discourages its use. In this paper, an entropy-constrained residual vector quantization method is proposed for lossless compression of images. The method consists of first quantizing the input image using a high order entropy-constrained residual vector quantizer and then coding the residual image using a first order entropy coder. The distortion measure used in the entropy-constrained optimization is essentially the first order entropy of the residual image. Experimental results show very competitive performance.

New Syndrome Decoding Techniques for the (n, K) Convolutional Codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

This paper presents a new syndrome decoding algorithm for the (n,k) convolutional codes (CC) which differs completely from an earlier syndrome decoding algorithm of Schalkwijk and Vinck. The new algorithm is based on the general solution of the syndrome equation, a linear Diophantine equation for the error polynomial vector E(D). The set of Diophantine solutions is a coset of the CC. In this error coset a recursive, Viterbi-like algorithm is developed to find the minimum weight error vector (circumflex)E(D). An example, illustrating the new decoding algorithm, is given for the binary nonsystemmatic (3,1)CC.

Simplified Syndrome Decoding of (n, 1) Convolutional Codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1983-01-01

A new syndrome decoding algorithm for the (n, 1) convolutional codes (CC) that is different and simpler than the previous syndrome decoding algorithm of Schalkwijk and Vinck is presented. The new algorithm uses the general solution of the polynomial linear Diophantine equation for the error polynomial vector E(D). This set of Diophantine solutions is a coset of the CC space. A recursive or Viterbi-like algorithm is developed to find the minimum weight error vector cirumflex E(D) in this error coset. An example illustrating the new decoding algorithm is given for the binary nonsymmetric (2,1)CC.

Bounded-Angle Iterative Decoding of LDPC Codes

NASA Technical Reports Server (NTRS)

Dolinar, Samuel; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush

2009-01-01

Bounded-angle iterative decoding is a modified version of conventional iterative decoding, conceived as a means of reducing undetected-error rates for short low-density parity-check (LDPC) codes. For a given code, bounded-angle iterative decoding can be implemented by means of a simple modification of the decoder algorithm, without redesigning the code. Bounded-angle iterative decoding is based on a representation of received words and code words as vectors in an n-dimensional Euclidean space (where n is an integer).

Vector coding of wavelet-transformed images

NASA Astrophysics Data System (ADS)

Zhou, Jun; Zhi, Cheng; Zhou, Yuanhua

1998-09-01

Wavelet, as a brand new tool in signal processing, has got broad recognition. Using wavelet transform, we can get octave divided frequency band with specific orientation which combines well with the properties of Human Visual System. In this paper, we discuss the classified vector quantization method for multiresolution represented image.

Achieving High Performance on the i860 Microprocessor

NASA Technical Reports Server (NTRS)

Lee, King; Kutler, Paul (Technical Monitor)

1998-01-01

The i860 is a high performance microprocessor used in the Intel Touchstone project. This paper proposes a paradigm for programming the i860 that is modelled on the vector instructions of the Cray computers. Fortran callable assembler subroutines were written that mimic the concurrent vector instructions of the Cray. Cache takes the place of vector registers. Using this paradigm we have achieved twice the performance of compiled code on a traditional solve.

Interactive computer modeling of combustion chemistry and coalescence-dispersion modeling of turbulent combustion

NASA Technical Reports Server (NTRS)

Pratt, D. T.

1984-01-01

An interactive computer code for simulation of a high-intensity turbulent combustor as a single point inhomogeneous stirred reactor was developed from an existing batch processing computer code CDPSR. The interactive CDPSR code was used as a guide for interpretation and direction of DOE-sponsored companion experiments utilizing Xenon tracer with optical laser diagnostic techniques to experimentally determine the appropriate mixing frequency, and for validation of CDPSR as a mixing-chemistry model for a laboratory jet-stirred reactor. The coalescence-dispersion model for finite rate mixing was incorporated into an existing interactive code AVCO-MARK I, to enable simulation of a combustor as a modular array of stirred flow and plug flow elements, each having a prescribed finite mixing frequency, or axial distribution of mixing frequency, as appropriate. Further increase the speed and reliability of the batch kinetics integrator code CREKID was increased by rewriting in vectorized form for execution on a vector or parallel processor, and by incorporating numerical techniques which enhance execution speed by permitting specification of a very low accuracy tolerance.

A Real-Time Interference Monitoring Technique for GNSS Based on a Twin Support Vector Machine Method.

PubMed

Li, Wutao; Huang, Zhigang; Lang, Rongling; Qin, Honglei; Zhou, Kai; Cao, Yongbin

2016-03-04

Interferences can severely degrade the performance of Global Navigation Satellite System (GNSS) receivers. As the first step of GNSS any anti-interference measures, interference monitoring for GNSS is extremely essential and necessary. Since interference monitoring can be considered as a classification problem, a real-time interference monitoring technique based on Twin Support Vector Machine (TWSVM) is proposed in this paper. A TWSVM model is established, and TWSVM is solved by the Least Squares Twin Support Vector Machine (LSTWSVM) algorithm. The interference monitoring indicators are analyzed to extract features from the interfered GNSS signals. The experimental results show that the chosen observations can be used as the interference monitoring indicators. The interference monitoring performance of the proposed method is verified by using GPS L1 C/A code signal and being compared with that of standard SVM. The experimental results indicate that the TWSVM-based interference monitoring is much faster than the conventional SVM. Furthermore, the training time of TWSVM is on millisecond (ms) level and the monitoring time is on microsecond (μs) level, which make the proposed approach usable in practical interference monitoring applications.

A Real-Time Interference Monitoring Technique for GNSS Based on a Twin Support Vector Machine Method

PubMed Central

Li, Wutao; Huang, Zhigang; Lang, Rongling; Qin, Honglei; Zhou, Kai; Cao, Yongbin

2016-01-01

Interferences can severely degrade the performance of Global Navigation Satellite System (GNSS) receivers. As the first step of GNSS any anti-interference measures, interference monitoring for GNSS is extremely essential and necessary. Since interference monitoring can be considered as a classification problem, a real-time interference monitoring technique based on Twin Support Vector Machine (TWSVM) is proposed in this paper. A TWSVM model is established, and TWSVM is solved by the Least Squares Twin Support Vector Machine (LSTWSVM) algorithm. The interference monitoring indicators are analyzed to extract features from the interfered GNSS signals. The experimental results show that the chosen observations can be used as the interference monitoring indicators. The interference monitoring performance of the proposed method is verified by using GPS L1 C/A code signal and being compared with that of standard SVM. The experimental results indicate that the TWSVM-based interference monitoring is much faster than the conventional SVM. Furthermore, the training time of TWSVM is on millisecond (ms) level and the monitoring time is on microsecond (μs) level, which make the proposed approach usable in practical interference monitoring applications. PMID:26959020

Studies on image compression and image reconstruction

NASA Technical Reports Server (NTRS)

Sayood, Khalid; Nori, Sekhar; Araj, A.

1994-01-01

During this six month period our works concentrated on three, somewhat different areas. We looked at and developed a number of error concealment schemes for use in a variety of video coding environments. This work is described in an accompanying (draft) Masters thesis. In the thesis we describe application of this techniques to the MPEG video coding scheme. We felt that the unique frame ordering approach used in the MPEG scheme would be a challenge to any error concealment/error recovery technique. We continued with our work in the vector quantization area. We have also developed a new type of vector quantizer, which we call a scan predictive vector quantization. The scan predictive VQ was tested on data processed at Goddard to approximate Landsat 7 HRMSI resolution and compared favorably with existing VQ techniques. A paper describing this work is included. The third area is concerned more with reconstruction than compression. While there is a variety of efficient lossless image compression schemes, they all have a common property that they use past data to encode future data. This is done either via taking differences, context modeling, or by building dictionaries. When encoding large images, this common property becomes a common flaw. When the user wishes to decode just a portion of the image, the requirement that the past history be available forces the decoding of a significantly larger portion of the image than desired by the user. Even with intelligent partitioning of the image dataset, the number of pixels decoded may be four times the number of pixels requested. We have developed an adaptive scanning strategy which can be used with any lossless compression scheme and which lowers the additional number of pixels to be decoded to about 7 percent of the number of pixels requested! A paper describing these results is included.

Advances in image compression and automatic target recognition; Proceedings of the Meeting, Orlando, FL, Mar. 30, 31, 1989

NASA Technical Reports Server (NTRS)

Tescher, Andrew G. (Editor)

1989-01-01

Various papers on image compression and automatic target recognition are presented. Individual topics addressed include: target cluster detection in cluttered SAR imagery, model-based target recognition using laser radar imagery, Smart Sensor front-end processor for feature extraction of images, object attitude estimation and tracking from a single video sensor, symmetry detection in human vision, analysis of high resolution aerial images for object detection, obscured object recognition for an ATR application, neural networks for adaptive shape tracking, statistical mechanics and pattern recognition, detection of cylinders in aerial range images, moving object tracking using local windows, new transform method for image data compression, quad-tree product vector quantization of images, predictive trellis encoding of imagery, reduced generalized chain code for contour description, compact architecture for a real-time vision system, use of human visibility functions in segmentation coding, color texture analysis and synthesis using Gibbs random fields.

Facile manipulation of protein localization in fission yeast through binding of GFP-binding protein to GFP.

PubMed

Chen, Ying-Hui; Wang, Gao-Yuan; Hao, Hao-Chao; Chao, Chun-Jiang; Wang, Yamei; Jin, Quan-Wen

2017-03-01

GFP-binding protein (or GBP) has been recently developed in various systems and organisms as an efficient tool to purify GFP-fusion proteins. Due to the high affinity between GBP and GFP or GFP variants, this GBP-based approach is also ideally suited to alter the localization of functional proteins in live cells. In order to facilitate the wide use of the GBP-targeting approach in the fission yeast Schizosaccharomyces pombe , we developed a set of pFA6a-, pJK148- and pUC119-based vectors containing GBP- or GBP-mCherry-coding sequences and variants of inducible nmt1 or constitutive adh1 promoters that result in different levels of expression. The GBP or GBP-mCherry fragments can serve as cassettes for N- or C-terminal genomic tagging of genes of interest. We illustrated the application of these vectors in the construction of yeast strains with Dma1 or Cdc7 tagged with GBP-mCherry and efficient targeting of Dma1- or Cdc7-GBP-mCherry to the spindle pole body by Sid4-GFP. This series of vectors should help to facilitate the application of the GBP-targeting approach in manipulating protein localization and the analysis of gene function in fission yeast, at the level of single genes, as well as at a systematic scale. © 2017. Published by The Company of Biologists Ltd.

COMPUTATION OF GLOBAL PHOTOCHEMISTRY WITH SMVGEAR II (R823186)

EPA Science Inventory

A computer model was developed to simulate global gas-phase photochemistry. The model solves chemical equations with SMVGEAR II, a sparse-matrix, vectorized Gear-type code. To obtain SMVGEAR II, the original SMVGEAR code was modified to allow computation of different sets of chem...

Developement of an Optimum Interpolation Analysis Method for the CYBER 205

NASA Technical Reports Server (NTRS)

Nestler, M. S.; Woollen, J.; Brin, Y.

1985-01-01

A state-of-the-art technique to assimilate the diverse observational database obtained during FGGE, and thus create initial conditions for numerical forecasts is described. The GLA optimum interpolation (OI) analysis method analyzes pressure, winds, and temperature at sea level, mixing ratio at six mandatory pressure levels up to 300 mb, and heights and winds at twelve levels up to 50 mb. Conversion to the CYBER 205 required a major re-write of the Amdahl OI code to take advantage of the CYBER vector processing capabilities. Structured programming methods were used to write the programs and this has resulted in a modular, understandable code. Among the contributors to the increased speed of the CYBER code are a vectorized covariance-calculation routine, an extremely fast matrix equation solver, and an innovative data search and sort technique.

Cloning and Sequencing of Defective Particles Derived from the Autonomous Parvovirus Minute Virus of Mice for the Construction of Vectors with Minimal cis-Acting Sequences

PubMed Central

Clément, Nathalie; Avalosse, Bernard; El Bakkouri, Karim; Velu, Thierry; Brandenburger, Annick

2001-01-01

The production of wild-type-free stocks of recombinant parvovirus minute virus of mice [MVM(p)] is difficult due to the presence of homologous sequences in vector and helper genomes that cannot easily be eliminated from the overlapping coding sequences. We have therefore cloned and sequenced spontaneously occurring defective particles of MVM(p) with very small genomes to identify the minimal cis-acting sequences required for DNA amplification and virus production. One of them has lost all capsid-coding sequences but is still able to replicate in permissive cells when nonstructural proteins are provided in trans by a helper plasmid. Vectors derived from this particle produce stocks with no detectable wild-type MVM after cotransfection with new, matched, helper plasmids that present no homology downstream from the transgene. PMID:11152501

Necessary conditions for the optimality of variable rate residual vector quantizers

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Smith, Mark J. T.; Barnes, Christopher F.

1993-01-01

Residual vector quantization (RVQ), or multistage VQ, as it is also called, has recently been shown to be a competitive technique for data compression. The competitive performance of RVQ reported in results from the joint optimization of variable rate encoding and RVQ direct-sum code books. In this paper, necessary conditions for the optimality of variable rate RVQ's are derived, and an iterative descent algorithm based on a Lagrangian formulation is introduced for designing RVQ's having minimum average distortion subject to an entropy constraint. Simulation results for these entropy-constrained RVQ's (EC-RVQ's) are presented for memory less Gaussian, Laplacian, and uniform sources. A Gauss-Markov source is also considered. The performance is superior to that of entropy-constrained scalar quantizers (EC-SQ's) and practical entropy-constrained vector quantizers (EC-VQ's), and is competitive with that of some of the best source coding techniques that have appeared in the literature.

Visual information processing II; Proceedings of the Meeting, Orlando, FL, Apr. 14-16, 1993

NASA Technical Reports Server (NTRS)

Huck, Friedrich O. (Editor); Juday, Richard D. (Editor)

1993-01-01

Various papers on visual information processing are presented. Individual topics addressed include: aliasing as noise, satellite image processing using a hammering neural network, edge-detetion method using visual perception, adaptive vector median filters, design of a reading test for low-vision image warping, spatial transformation architectures, automatic image-enhancement method, redundancy reduction in image coding, lossless gray-scale image compression by predictive GDF, information efficiency in visual communication, optimizing JPEG quantization matrices for different applications, use of forward error correction to maintain image fidelity, effect of peanoscanning on image compression. Also discussed are: computer vision for autonomous robotics in space, optical processor for zero-crossing edge detection, fractal-based image edge detection, simulation of the neon spreading effect by bandpass filtering, wavelet transform (WT) on parallel SIMD architectures, nonseparable 2D wavelet image representation, adaptive image halftoning based on WT, wavelet analysis of global warming, use of the WT for signal detection, perfect reconstruction two-channel rational filter banks, N-wavelet coding for pattern classification, simulation of image of natural objects, number-theoretic coding for iconic systems.

A CPU benchmark for protein crystallographic refinement.

PubMed

Bourne, P E; Hendrickson, W A

1990-01-01

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

New syndrome decoding techniques for the (n, k) convolutional codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1984-01-01

This paper presents a new syndrome decoding algorithm for the (n, k) convolutional codes (CC) which differs completely from an earlier syndrome decoding algorithm of Schalkwijk and Vinck. The new algorithm is based on the general solution of the syndrome equation, a linear Diophantine equation for the error polynomial vector E(D). The set of Diophantine solutions is a coset of the CC. In this error coset a recursive, Viterbi-like algorithm is developed to find the minimum weight error vector (circumflex)E(D). An example, illustrating the new decoding algorithm, is given for the binary nonsystemmatic (3, 1)CC. Previously announced in STAR as N83-34964

(Re)engineering Earth System Models to Expose Greater Concurrency for Ultrascale Computing: Practice, Experience, and Musings

NASA Astrophysics Data System (ADS)

Mills, R. T.

2014-12-01

As the high performance computing (HPC) community pushes towards the exascale horizon, the importance and prevalence of fine-grained parallelism in new computer architectures is increasing. This is perhaps most apparent in the proliferation of so-called "accelerators" such as the Intel Xeon Phi or NVIDIA GPGPUs, but the trend also holds for CPUs, where serial performance has grown slowly and effective use of hardware threads and vector units are becoming increasingly important to realizing high performance. This has significant implications for weather, climate, and Earth system modeling codes, many of which display impressive scalability across MPI ranks but take relatively little advantage of threading and vector processing. In addition to increasing parallelism, next generation codes will also need to address increasingly deep hierarchies for data movement: NUMA/cache levels, on node vs. off node, local vs. wide neighborhoods on the interconnect, and even in the I/O system. We will discuss some approaches (grounded in experiences with the Intel Xeon Phi architecture) for restructuring Earth science codes to maximize concurrency across multiple levels (vectors, threads, MPI ranks), and also discuss some novel approaches for minimizing expensive data movement/communication.

Transcoding method from H.264/AVC to high efficiency video coding based on similarity of intraprediction, interprediction, and motion vector

NASA Astrophysics Data System (ADS)

Liu, Mei-Feng; Zhong, Guo-Yun; He, Xiao-Hai; Qing, Lin-Bo

2016-09-01

Currently, most video resources on line are encoded in the H.264/AVC format. More fluent video transmission can be obtained if these resources are encoded in the newest international video coding standard: high efficiency video coding (HEVC). In order to improve the video transmission and storage on line, a transcoding method from H.264/AVC to HEVC is proposed. In this transcoding algorithm, the coding information of intraprediction, interprediction, and motion vector (MV) in H.264/AVC video stream are used to accelerate the coding in HEVC. It is found through experiments that the region of interprediction in HEVC overlaps that in H.264/AVC. Therefore, the intraprediction for the region in HEVC, which is interpredicted in H.264/AVC, can be skipped to reduce coding complexity. Several macroblocks in H.264/AVC are combined into one PU in HEVC when the MV difference between two of the macroblocks in H.264/AVC is lower than a threshold. This method selects only one coding unit depth and one prediction unit (PU) mode to reduce the coding complexity. An MV interpolation method of combined PU in HEVC is proposed according to the areas and distances between the center of one macroblock in H.264/AVC and that of the PU in HEVC. The predicted MV accelerates the motion estimation for HEVC coding. The simulation results show that our proposed algorithm achieves significant coding time reduction with a little loss in bitrates distortion rate, compared to the existing transcoding algorithms and normal HEVC coding.

Multitasking the INS3D-LU code on the Cray Y-MP

NASA Technical Reports Server (NTRS)

Fatoohi, Rod; Yoon, Seokkwan

1991-01-01

This paper presents the results of multitasking the INS3D-LU code on eight processors. The code is a full Navier-Stokes solver for incompressible fluid in three dimensional generalized coordinates using a lower-upper symmetric-Gauss-Seidel implicit scheme. This code has been fully vectorized on oblique planes of sweep and parallelized using autotasking with some directives and minor modifications. The timing results for five grid sizes are presented and analyzed. The code has achieved a processing rate of over one Gflops.

Multi-GPU and multi-CPU accelerated FDTD scheme for vibroacoustic applications

NASA Astrophysics Data System (ADS)

Francés, J.; Otero, B.; Bleda, S.; Gallego, S.; Neipp, C.; Márquez, A.; Beléndez, A.

2015-06-01

The Finite-Difference Time-Domain (FDTD) method is applied to the analysis of vibroacoustic problems and to study the propagation of longitudinal and transversal waves in a stratified media. The potential of the scheme and the relevance of each acceleration strategy for massively computations in FDTD are demonstrated in this work. In this paper, we propose two new specific implementations of the bi-dimensional scheme of the FDTD method using multi-CPU and multi-GPU, respectively. In the first implementation, an open source message passing interface (OMPI) has been included in order to massively exploit the resources of a biprocessor station with two Intel Xeon processors. Moreover, regarding CPU code version, the streaming SIMD extensions (SSE) and also the advanced vectorial extensions (AVX) have been included with shared memory approaches that take advantage of the multi-core platforms. On the other hand, the second implementation called the multi-GPU code version is based on Peer-to-Peer communications available in CUDA on two GPUs (NVIDIA GTX 670). Subsequently, this paper presents an accurate analysis of the influence of the different code versions including shared memory approaches, vector instructions and multi-processors (both CPU and GPU) and compares them in order to delimit the degree of improvement of using distributed solutions based on multi-CPU and multi-GPU. The performance of both approaches was analysed and it has been demonstrated that the addition of shared memory schemes to CPU computing improves substantially the performance of vector instructions enlarging the simulation sizes that use efficiently the cache memory of CPUs. In this case GPU computing is slightly twice times faster than the fine tuned CPU version in both cases one and two nodes. However, for massively computations explicit vector instructions do not worth it since the memory bandwidth is the limiting factor and the performance tends to be the same than the sequential version with auto-vectorisation and also shared memory approach. In this scenario GPU computing is the best option since it provides a homogeneous behaviour. More specifically, the speedup of GPU computing achieves an upper limit of 12 for both one and two GPUs, whereas the performance reaches peak values of 80 GFlops and 146 GFlops for the performance for one GPU and two GPUs respectively. Finally, the method is applied to an earth crust profile in order to demonstrate the potential of our approach and the necessity of applying acceleration strategies in these type of applications.

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers

DOE PAGES

Wang, Bei; Ethier, Stephane; Tang, William; ...

2017-06-29

The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability ofmore » the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon Phi (MIC) co-processors and performance comparisons with state-of-the-art homogeneous HPC systems such as Blue Gene/Q. New discovery science capabilities in the magnetic fusion energy application domain are enabled, including investigations of Ion-Temperature-Gradient (ITG) driven turbulence simulations with unprecedented spatial resolution and long temporal duration. Performance studies with realistic fusion experimental parameters are carried out on multiple supercomputing systems spanning a wide range of cache capacities, cache-sharing configurations, memory bandwidth, interconnects and network topologies. These performance comparisons using a realistic discovery-science-capable domain application code provide valuable insights on optimization techniques across one of the broadest sets of current high-end computing platforms worldwide.« less

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers

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

Wang, Bei; Ethier, Stephane; Tang, William

The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability ofmore » the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon Phi (MIC) co-processors and performance comparisons with state-of-the-art homogeneous HPC systems such as Blue Gene/Q. New discovery science capabilities in the magnetic fusion energy application domain are enabled, including investigations of Ion-Temperature-Gradient (ITG) driven turbulence simulations with unprecedented spatial resolution and long temporal duration. Performance studies with realistic fusion experimental parameters are carried out on multiple supercomputing systems spanning a wide range of cache capacities, cache-sharing configurations, memory bandwidth, interconnects and network topologies. These performance comparisons using a realistic discovery-science-capable domain application code provide valuable insights on optimization techniques across one of the broadest sets of current high-end computing platforms worldwide.« less

Gene inactivation in the plant pathogen Glomerella cingulata: three strategies for the disruption of the pectin lyase gene pnlA.

PubMed

Bowen, J K; Templeton, M D; Sharrock, K R; Crowhurst, R N; Rikkerink, E H

1995-01-20

The feasibility of performing routine transformation-mediated mutagenesis in Glomerella cingulata was analysed by adopting three one-step gene disruption strategies targeted at the pectin lyase gene pnlA. The efficiencies of disruption following transformation with gene replacement- or gene truncation-disruption vectors were compared. To effect replacement-disruption, G. cingulata was transformed with a vector carrying DNA from the pnlA locus in which the majority of the coding sequence had been replaced by the gene for hygromycin B resistance. Two of the five transformants investigated contained an inactivated pnlA gene (pnlA-); both also contained ectopically integrated vector sequences. The efficacy of gene disruption by transformation with two gene truncation-disruption vectors was also assessed. Both vectors carried at 5' and 3' truncated copy of the pnlA coding sequence, adjacent to the gene for hygromycin B resistance. The promoter sequences controlling the selectable marker differed in the two vectors. In one vector the homologous G. cingulata gpdA promoter controlled hygromycin B phosphotransferase expression (homologous truncation vector), whereas in the second vector promoter elements were from the Aspergillus nidulans gpdA gene (heterologous truncation vector). Following transformation with the homologous truncation vector, nine transformants were analysed by Southern hybridisation; no transformants contained a disrupted pnlA gene. Of nineteen heterologous truncation vector transformants, three contained a disrupted pnlA gene; Southern analysis revealed single integrations of vector sequence at pnlA in two of these transformants. pnlA mRNA was not detected by Northern hybridisation in pnlA- transformants. pnlA- transformants failed to produce a PNLA protein with a pI identical to one normally detected in wild-type isolates by silver and activity staining of isoelectric focussing gels. Pathogenesis on Capsicum and apple was unaffected by disruption of the pnlA gene, indicating that the corresponding gene product, PNLA, is not essential for pathogenicity. Gene disruption is a feasible method for selectively mutating defined loci in G. cingulata for functional analysis of the corresponding gene products.

Multi-Modulator for Bandwidth-Efficient Communication

NASA Technical Reports Server (NTRS)

Gray, Andrew; Lee, Dennis; Lay, Norman; Cheetham, Craig; Fong, Wai; Yeh, Pen-Shu; King, Robin; Ghuman, Parminder; Hoy, Scott; Fisher, Dave

2009-01-01

A modulator circuit board has recently been developed to be used in conjunction with a vector modulator to generate any of a large number of modulations for bandwidth-efficient radio transmission of digital data signals at rates than can exceed 100 Mb/s. The modulations include quadrature phaseshift keying (QPSK), offset quadrature phase-shift keying (OQPSK), Gaussian minimum-shift keying (GMSK), and octonary phase-shift keying (8PSK) with square-root raised-cosine pulse shaping. The figure is a greatly simplified block diagram showing the relationship between the modulator board and the rest of the transmitter. The role of the modulator board is to encode the incoming data stream and to shape the resulting pulses, which are fed as inputs to the vector modulator. The combination of encoding and pulse shaping in a given application is chosen to maximize the bandwidth efficiency. The modulator board includes gallium arsenide serial-to-parallel converters at its input end. A complementary metal oxide/semiconductor (CMOS) field-programmable gate array (FPGA) performs the coding and modulation computations and utilizes parallel processing in doing so. The results of the parallel computation are combined and converted to pulse waveforms by use of gallium arsenide parallel-to-serial converters integrated with digital-to-analog converters. Without changing the hardware, one can configure the modulator to produce any of the designed combinations of coding and modulation by loading the appropriate bit configuration file into the FPGA.

Recent update of the RPLUS2D/3D codes

NASA Technical Reports Server (NTRS)

Tsai, Y.-L. Peter

1991-01-01

The development of the RPLUS2D/3D codes is summarized. These codes utilize LU algorithms to solve chemical non-equilibrium flows in a body-fitted coordinate system. The motivation behind the development of these codes is the need to numerically predict chemical non-equilibrium flows for the National AeroSpace Plane Program. Recent improvements include vectorization method, blocking algorithms for geometric flexibility, out-of-core storage for large-size problems, and an LU-SW/UP combination for CPU-time efficiency and solution quality.

Quantization of high dimensional Gaussian vector using permutation modulation with application to information reconciliation in continuous variable QKD

NASA Astrophysics Data System (ADS)

Daneshgaran, Fred; Mondin, Marina; Olia, Khashayar

This paper is focused on the problem of Information Reconciliation (IR) for continuous variable Quantum Key Distribution (QKD). The main problem is quantization and assignment of labels to the samples of the Gaussian variables observed at Alice and Bob. Trouble is that most of the samples, assuming that the Gaussian variable is zero mean which is de-facto the case, tend to have small magnitudes and are easily disturbed by noise. Transmission over longer and longer distances increases the losses corresponding to a lower effective Signal-to-Noise Ratio (SNR) exasperating the problem. Quantization over higher dimensions is advantageous since it allows for fractional bit per sample accuracy which may be needed at very low SNR conditions whereby the achievable secret key rate is significantly less than one bit per sample. In this paper, we propose to use Permutation Modulation (PM) for quantization of Gaussian vectors potentially containing thousands of samples. PM is applied to the magnitudes of the Gaussian samples and we explore the dependence of the sign error probability on the magnitude of the samples. At very low SNR, we may transmit the entire label of the PM code from Bob to Alice in Reverse Reconciliation (RR) over public channel. The side information extracted from this label can then be used by Alice to characterize the sign error probability of her individual samples. Forward Error Correction (FEC) coding can be used by Bob on each subset of samples with similar sign error probability to aid Alice in error correction. This can be done for different subsets of samples with similar sign error probabilities leading to an Unequal Error Protection (UEP) coding paradigm.

Fluid-solid interaction: benchmarking of an external coupling of ANSYS with CFX for cardiovascular applications.

PubMed

Hose, D R; Lawford, P V; Narracott, A J; Penrose, J M T; Jones, I P

2003-01-01

Fluid-solid interaction is a primary feature of cardiovascular flows. There is increasing interest in the numerical solution of these systems as the extensive computational resource required for such studies becomes available. One form of coupling is an external weak coupling of separate solid and fluid mechanics codes. Information about the stress tensor and displacement vector at the wetted boundary is passed between the codes, and an iterative scheme is employed to move towards convergence of these parameters at each time step. This approach has the attraction that separate codes with the most extensive functionality for each of the separate phases can be selected, which might be important in the context of the complex rheology and contact mechanics that often feature in cardiovascular systems. Penrose and Staples describe a weak coupling of CFX for computational fluid mechanics to ANSYS for solid mechanics, based on a simple Jacobi iteration scheme. It is important to validate the coupled numerical solutions. An extensive analytical study of flow in elastic-walled tubes was carried out by Womersley in the late 1950s. This paper describes the performance of the coupling software for the straight elastic-walled tube, and compares the results with Womersley's analytical solutions. It also presents preliminary results demonstrating the application of the coupled software in the context of a stented vessel.

Plasmid Vectors and Molecular Building Blocks for the Development of Genetic Manipulation Tools for Trypanosoma cruzi

PubMed Central

Bouvier, León A.; Cámara, María de los Milagros; Canepa, Gaspar E.; Miranda, Mariana R.; Pereira, Claudio A.

2013-01-01

The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted. PMID:24205392

Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

USGS Publications Warehouse

Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

2013-01-01

The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

Coxsackievirus B3 vaccines: use as an expression vector for prevention of myocarditis.

PubMed

Henke, Andreas; Jarasch, Nadine; Wutzler, Peter

2008-12-01

Coxsackievirus B3 (CVB3), a member of the Picornaviridae family, is considered to be one of the most important infectious agents to cause virus-induced myocarditis. Despite improvements in studying virus pathology, structure and molecular biology, as well as the diagnosis of this disease, there is still no virus-specific drug or vaccine in clinical use. During the last 20 years many investigations have been performed to develop classic and modern immunization techniques against CVB3-induced heart disease. One promising approach among others includes the insertion of coding sequences of cytokines into the viral genome. The application of an IFN-gamma-expressing recombinant coxsackievirus vector is especially efficient against CVB3-induced myocarditis. Beside direct IFN-gamma-mediated antiviral effects, the local and simultaneous expression of IFN-gamma by the virus itself activates the immune system in a strong and long-lasting manner, which protects animals completely against subsequent lethal infections independently of the age of the immunized individual and the route of vaccine administration.

An emergence of coordinated communication in populations of agents.

PubMed

Kvasnicka, V; Pospichal, J

1999-01-01

The purpose of this article is to demonstrate that coordinated communication spontaneously emerges in a population composed of agents that are capable of specific cognitive activities. Internal states of agents are characterized by meaning vectors. Simple neural networks composed of one layer of hidden neurons perform cognitive activities of agents. An elementary communication act consists of the following: (a) two agents are selected, where one of them is declared the speaker and the other the listener; (b) the speaker codes a selected meaning vector onto a sequence of symbols and sends it to the listener as a message; and finally, (c) the listener decodes this message into a meaning vector and adapts his or her neural network such that the differences between speaker and listener meaning vectors are decreased. A Darwinian evolution enlarged by ideas from the Baldwin effect and Dawkins' memes is simulated by a simple version of an evolutionary algorithm without crossover. The agent fitness is determined by success of the mutual pairwise communications. It is demonstrated that agents in the course of evolution gradually do a better job of decoding received messages (they are closer to meaning vectors of speakers) and all agents gradually start to use the same vocabulary for the common communication. Moreover, if agent meaning vectors contain regularities, then these regularities are manifested also in messages created by agent speakers, that is, similar parts of meaning vectors are coded by similar symbol substrings. This observation is considered a manifestation of the emergence of a grammar system in the common coordinated communication.

Hill Ciphers over Near-Fields

ERIC Educational Resources Information Center

Farag, Mark

2007-01-01

Hill ciphers are linear codes that use as input a "plaintext" vector [p-right arrow above] of size n, which is encrypted with an invertible n x n matrix E to produce a "ciphertext" vector [c-right arrow above] = E [middle dot] [p-right arrow above]. Informally, a near-field is a triple [left angle bracket]N; +, *[right angle bracket] that…

Reliable Wireless Broadcast with Linear Network Coding for Multipoint-to-Multipoint Real-Time Communications

NASA Astrophysics Data System (ADS)

Kondo, Yoshihisa; Yomo, Hiroyuki; Yamaguchi, Shinji; Davis, Peter; Miura, Ryu; Obana, Sadao; Sampei, Seiichi

This paper proposes multipoint-to-multipoint (MPtoMP) real-time broadcast transmission using network coding for ad-hoc networks like video game networks. We aim to achieve highly reliable MPtoMP broadcasting using IEEE 802.11 media access control (MAC) that does not include a retransmission mechanism. When each node detects packets from the other nodes in a sequence, the correctly detected packets are network-encoded, and the encoded packet is broadcasted in the next sequence as a piggy-back for its native packet. To prevent increase of overhead in each packet due to piggy-back packet transmission, network coding vector for each node is exchanged between all nodes in the negotiation phase. Each user keeps using the same coding vector generated in the negotiation phase, and only coding information that represents which user signal is included in the network coding process is transmitted along with the piggy-back packet. Our simulation results show that the proposed method can provide higher reliability than other schemes using multi point relay (MPR) or redundant transmissions such as forward error correction (FEC). We also implement the proposed method in a wireless testbed, and show that the proposed method achieves high reliability in a real-world environment with a practical degree of complexity when installed on current wireless devices.

Exact first order scattering correction for vector radiative transfer in coupled atmosphere and ocean systems

NASA Astrophysics Data System (ADS)

Zhai, Peng-Wang; Hu, Yongxiang; Josset, Damien B.; Trepte, Charles R.; Lucker, Patricia L.; Lin, Bing

2012-06-01

We have developed a Vector Radiative Transfer (VRT) code for coupled atmosphere and ocean systems based on the successive order of scattering (SOS) method. In order to achieve efficiency and maintain accuracy, the scattering matrix is expanded in terms of the Wigner d functions and the delta fit or delta-M technique is used to truncate the commonly-present large forward scattering peak. To further improve the accuracy of the SOS code, we have implemented the analytical first order scattering treatment using the exact scattering matrix of the medium in the SOS code. The expansion and truncation techniques are kept for higher order scattering. The exact first order scattering correction was originally published by Nakajima and Takana.1 A new contribution of this work is to account for the exact secondary light scattering caused by the light reflected by and transmitted through the rough air-sea interface.

Learning dictionaries of sparse codes of 3D movements of body joints for real-time human activity understanding.

PubMed

Qi, Jin; Yang, Zhiyong

2014-01-01

Real-time human activity recognition is essential for human-robot interactions for assisted healthy independent living. Most previous work in this area is performed on traditional two-dimensional (2D) videos and both global and local methods have been used. Since 2D videos are sensitive to changes of lighting condition, view angle, and scale, researchers begun to explore applications of 3D information in human activity understanding in recently years. Unfortunately, features that work well on 2D videos usually don't perform well on 3D videos and there is no consensus on what 3D features should be used. Here we propose a model of human activity recognition based on 3D movements of body joints. Our method has three steps, learning dictionaries of sparse codes of 3D movements of joints, sparse coding, and classification. In the first step, space-time volumes of 3D movements of body joints are obtained via dense sampling and independent component analysis is then performed to construct a dictionary of sparse codes for each activity. In the second step, the space-time volumes are projected to the dictionaries and a set of sparse histograms of the projection coefficients are constructed as feature representations of the activities. Finally, the sparse histograms are used as inputs to a support vector machine to recognize human activities. We tested this model on three databases of human activities and found that it outperforms the state-of-the-art algorithms. Thus, this model can be used for real-time human activity recognition in many applications.

First experience of vectorizing electromagnetic physics models for detector simulation

NASA Astrophysics Data System (ADS)

Amadio, G.; Apostolakis, J.; Bandieramonte, M.; Bianchini, C.; Bitzes, G.; Brun, R.; Canal, P.; Carminati, F.; de Fine Licht, J.; Duhem, L.; Elvira, D.; Gheata, A.; Jun, S. Y.; Lima, G.; Novak, M.; Presbyterian, M.; Shadura, O.; Seghal, R.; Wenzel, S.

2015-12-01

The recent emergence of hardware architectures characterized by many-core or accelerated processors has opened new opportunities for concurrent programming models taking advantage of both SIMD and SIMT architectures. The GeantV vector prototype for detector simulations has been designed to exploit both the vector capability of mainstream CPUs and multi-threading capabilities of coprocessors including NVidia GPUs and Intel Xeon Phi. The characteristics of these architectures are very different in terms of the vectorization depth, parallelization needed to achieve optimal performance or memory access latency and speed. An additional challenge is to avoid the code duplication often inherent to supporting heterogeneous platforms. In this paper we present the first experience of vectorizing electromagnetic physics models developed for the GeantV project.

Integrated Design Analysis and Optimisation of Aircraft Structures (L’Analyse pour la Conception Integree et l’Optimisation des Structures d’Aeronefs)

DTIC Science & Technology

1992-02-01

Division (Code RM) ONERA Office of Aeronautics & Space Technology 29 ave de la Division Leclerc NASA Hq 92320 Chfitillon Washington DC 20546 France United...Vector of thickness variables. V’ = [ t2 ........ tN Vector of thickness changes. AV ’= [rt, 5t2 ......... tNJ TI 7-9 Vector of strain derivatives. F...ds, ds, I d, 1i’,= dt, dr2 ........ dt--N Vector of buckling derivatives. dX d). , dt1 dt2 dtN Then 5F= Vs’i . AV and SX V,’. AV The linearised

Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

PubMed

Rong, Y; Padron, A V; Hagerty, K J; Nelson, N; Chi, S; Keyhani, N O; Katz, J; Datta, S P A; Gomes, C; McLamore, E S

2018-04-30

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae.

PubMed

Gritz, L; Davies, J

1983-11-01

The plasmid-borne gene hph coding for hygromycin B phosphotransferase (HPH) in Escherichia coli has been identified and its nucleotide sequence determined. The hph gene is 1026 nucleotides long, coding for a protein with a predicted Mr of 39 000. The hph gene was placed in a shuttle plasmid vector, downstream from the promoter region of the cyc 1 gene of Saccharomyces cerevisiae, and an hph construction containing a single AUG in the 5' noncoding region allowed direct selection following transformation in yeast and in E. coli. Thus the hph gene can be used in cloning vectors for both pro- and eukaryotes.

A series of vectors to construct lacZ fusions for the study of gene expression in Schizosaccharomyces pombe.

PubMed

Lafuente, M J; Petit, T; Gancedo, C

1997-12-22

We have constructed a series of plasmids to facilitate the fusion of promoters with or without coding regions of genes of Schizosaccharomyces pombe to the lacZ gene of Escherichia coli. These vectors carry a multiple cloning region in which fission yeast DNA may be inserted in three different reading frames with respect to the coding region of lacZ. The plasmids were constructed with the ura4+ or the his3+ marker of S. pombe. Functionality of the plasmids was tested measuring in parallel the expression of fructose 1,6-bisphosphatase and beta-galactosidase under the control of the fbp1+ promoter in different conditions.

Universal Decoder for PPM of any Order

NASA Technical Reports Server (NTRS)

Moision, Bruce E.

2010-01-01

A recently developed algorithm for demodulation and decoding of a pulse-position- modulation (PPM) signal is suitable as a basis for designing a single hardware decoding apparatus to be capable of handling any PPM order. Hence, this algorithm offers advantages of greater flexibility and lower cost, in comparison with prior such algorithms, which necessitate the use of a distinct hardware implementation for each PPM order. In addition, in comparison with the prior algorithms, the present algorithm entails less complexity in decoding at large orders. An unavoidably lengthy presentation of background information, including definitions of terms, is prerequisite to a meaningful summary of this development. As an aid to understanding, the figure illustrates the relevant processes of coding, modulation, propagation, demodulation, and decoding. An M-ary PPM signal has M time slots per symbol period. A pulse (signifying 1) is transmitted during one of the time slots; no pulse (signifying 0) is transmitted during the other time slots. The information intended to be conveyed from the transmitting end to the receiving end of a radio or optical communication channel is a K-bit vector u. This vector is encoded by an (N,K) binary error-correcting code, producing an N-bit vector a. In turn, the vector a is subdivided into blocks of m = log2(M) bits and each such block is mapped to an M-ary PPM symbol. The resultant coding/modulation scheme can be regarded as equivalent to a nonlinear binary code. The binary vector of PPM symbols, x is transmitted over a Poisson channel, such that there is obtained, at the receiver, a Poisson-distributed photon count characterized by a mean background count nb during no-pulse time slots and a mean signal-plus-background count of ns+nb during a pulse time slot. In the receiver, demodulation of the signal is effected in an iterative soft decoding process that involves consideration of relationships among photon counts and conditional likelihoods of m-bit vectors of coded bits. Inasmuch as the likelihoods of all the m-bit vectors of coded bits mapping to the same PPM symbol are correlated, the best performance is obtained when the joint mbit conditional likelihoods are utilized. Unfortunately, the complexity of decoding, measured in the number of operations per bit, grows exponentially with m, and can thus become prohibitively expensive for large PPM orders. For a system required to handle multiple PPM orders, the cost is even higher because it is necessary to have separate decoding hardware for each order. This concludes the prerequisite background information. In the present algorithm, the decoding process as described above is modified by, among other things, introduction of an lbit marginalizer sub-algorithm. The term "l-bit marginalizer" signifies that instead of m-bit conditional likelihoods, the decoder computes l-bit conditional likelihoods, where l is fixed. Fixing l, regardless of the value of m, makes it possible to use a single hardware implementation for any PPM order. One could minimize the decoding complexity and obtain an especially simple design by fixing l at 1, but this would entail some loss of performance. An intermediate solution is to fix l at some value, greater than 1, that may be less than or greater than m. This solution makes it possible to obtain the desired flexibility to handle any PPM order while compromising between complexity and loss of performance.

PETSc Users Manual Revision 3.3

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

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.4

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

Balay, S.; Brown, J.; Buschelman, K.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

PETSc Users Manual Revision 3.5

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

Balay, S.; Abhyankar, S.; Adams, M.

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms neededmore » within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. ;For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.« less

Wireless Intrusion Detection

DTIC Science & Technology

2007-03-01

32 4.4 Algorithm Pseudo - Code ...................................................................................34 4.5 WIND Interface With a...difference estimates of xc temporal derivatives, or by using a polynomial fit to the previous values of xc. 34 4.4 ALGORITHM PSEUDO - CODE Pseudo ...Phase Shift Keying DQPSK Differential Quadrature Phase Shift Keying EVM Error Vector Magnitude FFT Fast Fourier Transform FPGA Field Programmable

Poly ICLC increases the potency of a replication-defective human adenovirus vectored foot-and-mouth disease vaccine

USDA-ARS?s Scientific Manuscript database

Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hoofed animals. We have previously demonstrated that a replication-defective human adenovirus 5 vector carrying the FMDV capsid coding region of serotype A24 Cruzeiro (Ad5-CI-A24-2B) protects swine and cattle against FM...

Effects of insertion sites in a Newcastle disease virus vector on foreign gene expression through an internal ribosomal entry site

USDA-ARS?s Scientific Manuscript database

Newcastle disease virus (NDV), avian paramyxovirus type 1, has been developed as a vector to express foreign genes for vaccine and gene therapy purposes. The foreign genes are usually inserted into a non-coding region of the NDV genome as an independent transcription unit (ITU), which potentially a...

[Sendai virus vector: vector development and its application to health care and biotechnology].

PubMed

Iida, Akihiro

2007-06-01

Sendai virus (SeV) is an enveloped virus with a nonsegmented negative-strand RNA genome and a member of the paramyxovirus family. We have developed SeV vector which has shown a high efficiently of gene transfer and expression of foreign genes to a wide range of dividing and non-dividing mammalian cells and tissues. One of the characteristics of the vector is that the genome is located exclusively in the cytoplasm of infected cells and does not go through a DNA phase; thus there is no concern about unwanted integration of foreign sequences into chromosomal DNA. Therefore, this new class of "cytoplasmic RNA vector", an RNA vector with cytoplasmic expression, is expected to be a safer and more efficient viral vector than existing vectors for application to human therapy in various fields including gene therapy and vaccination. In this review, I describe development of Sendai virus vector, its application in the field of biotechnology and clinical application aiming to treat for a large number of diseases including cancer, cardiovascular disease, infectious diseases and neurologic disorders.

A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research

PubMed Central

Miano, Joseph M.; Zhu, Qiuyu Martin; Lowenstein, Charles J.

2016-01-01

Previous efforts to target the mouse genome for the addition, subtraction, or substitution of biologically informative sequences required complex vector design and a series of arduous steps only a handful of labs could master. The facile and inexpensive clustered regularly interspaced short palindromic repeats (CRISPR) method has now superseded traditional means of genome modification such that virtually any lab can quickly assemble reagents for developing new mouse models for cardiovascular research. Here we briefly review the history of CRISPR in prokaryotes, highlighting major discoveries leading to its formulation for genome modification in the animal kingdom. Core components of CRISPR technology are reviewed and updated. Practical pointers for two-component and three-component CRISPR editing are summarized with a number of applications in mice including frameshift mutations, deletion of enhancers and non-coding genes, nucleotide substitution of protein-coding and gene regulatory sequences, incorporation of loxP sites for conditional gene inactivation, and epitope tag integration. Genotyping strategies are presented and topics of genetic mosaicism and inadvertent targeting discussed. Finally, clinical applications and ethical considerations are addressed as the biomedical community eagerly embraces this astonishing innovation in genome editing to tackle previously intractable questions. PMID:27102963

MultiElec: A MATLAB Based Application for MEA Data Analysis.

PubMed

Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

2015-01-01

We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

Spin Resonances for Stored Deuteron Beams in COSY. Vector Polarization. Tracking with Spink

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

Luccio,A.; Lehrach, A.

2008-04-01

Results of measurements of vector and tensor polarization of a deuteron beam in the storage ring COSY have been published by the SPIN{at}COSY collaboration. In this experiment a RF Dipole was used that produced spin flip. The strength of the RFD-induced depolarizing resonance was calculated from the amount of spin flipping and the results shown in the figures of the cited paper. In this note we present the simulation of the experimental data (vector polarization) with the spin tracking code Spink.

Constrained motion estimation-based error resilient coding for HEVC

NASA Astrophysics Data System (ADS)

Guo, Weihan; Zhang, Yongfei; Li, Bo

2018-04-01

Unreliable communication channels might lead to packet losses and bit errors in the videos transmitted through it, which will cause severe video quality degradation. This is even worse for HEVC since more advanced and powerful motion estimation methods are introduced to further remove the inter-frame dependency and thus improve the coding efficiency. Once a Motion Vector (MV) is lost or corrupted, it will cause distortion in the decoded frame. More importantly, due to motion compensation, the error will propagate along the motion prediction path, accumulate over time, and significantly degrade the overall video presentation quality. To address this problem, we study the problem of encoder-sider error resilient coding for HEVC and propose a constrained motion estimation scheme to mitigate the problem of error propagation to subsequent frames. The approach is achieved by cutting off MV dependencies and limiting the block regions which are predicted by temporal motion vector. The experimental results show that the proposed method can effectively suppress the error propagation caused by bit errors of motion vector and can improve the robustness of the stream in the bit error channels. When the bit error probability is 10-5, an increase of the decoded video quality (PSNR) by up to1.310dB and on average 0.762 dB can be achieved, compared to the reference HEVC.

Development of Sendai Virus Vectors and their Potential Applications in Gene Therapy and Regenerative Medicine

PubMed Central

Nakanishi, Mahito; Otsu, Makoto

2012-01-01

Gene delivery/expression vectors have been used as fundamental technologies in gene therapy since the 1980s. These technologies are also being applied in regenerative medicine as tools to reprogram cell genomes to a pluripotent state and to other cell lineages. Rapid progress in these new research areas and expectations for their translation into clinical applications have facilitated the development of more sophisticated gene delivery/expression technologies. Since its isolation in 1953 in Japan, Sendai virus (SeV) has been widely used as a research tool in cell biology and in industry, but the application of SeV as a recombinant viral vector has been investigated only recently. Recombinant SeV vectors have various unique characteristics, such as low pathogenicity, powerful capacity for gene expression and a wide host range. In addition, the cytoplasmic gene expression mediated by this vector is advantageous for applications, in that chromosomal integration of exogenous genes can be undesirable. In this review, we introduce a brief historical background on the development of recombinant SeV vectors and describe their current applications in gene therapy. We also describe the application of SeV vectors in advanced nuclear reprogramming and introduce a defective and persistent SeV vector (SeVdp) optimized for such reprogramming. PMID:22920683

Space shuttle main engine numerical modeling code modifications and analysis

NASA Technical Reports Server (NTRS)

Ziebarth, John P.

1988-01-01

The user of computational fluid dynamics (CFD) codes must be concerned with the accuracy and efficiency of the codes if they are to be used for timely design and analysis of complicated three-dimensional fluid flow configurations. A brief discussion of how accuracy and efficiency effect the CFD solution process is given. A more detailed discussion of how efficiency can be enhanced by using a few Cray Research Inc. utilities to address vectorization is presented and these utilities are applied to a three-dimensional Navier-Stokes CFD code (INS3D).

Evaluation Method for Service Branding Using Word-of-Mouth Data

NASA Astrophysics Data System (ADS)

Shirahada, Kunio; Kosaka, Michitaka

Development and spread of internet technology contributes service firms to obtaining the high capability of brand information transmission as well as relative customer feedback data collection. In this paper, we propose a new evaluation method for service branding using firms and consumers data on the internet. Based on service marketing 7Ps (Product, Price, Place, Promotion, People, Physical evidence, Process) which are the key viewpoints for branding, we develop a brand evaluation system including coding methods for Word-of-Mouth (WoM) and corporate introductory information on the internet to identify both customer's service value recognition vector and firm's service value proposition vector. Our system quantitatively clarify both customer's service value recognition of the firm and firm's strength in service value proposition, thereby analyzing service brand communication gaps between firm and consumers. We applied this system to Japanese Ryokan hotel industry. Using six ryokan-hotels' data on Jyaran-net and Rakuten travel, we made totally 983 codes from WoM information and analyzed their service brand value according to three price based categories. As a result, we found that the characteristics of customers' service value recognition vector differ according to the price categories. In addition, the system clarified that there is a firm that has a different service value proposition vector from customers' recognition vector. This helps to analyze corporate service brand strategy and has a significance as a system technology supporting service management.

A portable approach for PIC on emerging architectures

NASA Astrophysics Data System (ADS)

Decyk, Viktor

2016-03-01

A portable approach for designing Particle-in-Cell (PIC) algorithms on emerging exascale computers, is based on the recognition that 3 distinct programming paradigms are needed. They are: low level vector (SIMD) processing, middle level shared memory parallel programing, and high level distributed memory programming. In addition, there is a memory hierarchy associated with each level. Such algorithms can be initially developed using vectorizing compilers, OpenMP, and MPI. This is the approach recommended by Intel for the Phi processor. These algorithms can then be translated and possibly specialized to other programming models and languages, as needed. For example, the vector processing and shared memory programming might be done with CUDA instead of vectorizing compilers and OpenMP, but generally the algorithm itself is not greatly changed. The UCLA PICKSC web site at http://www.idre.ucla.edu/ contains example open source skeleton codes (mini-apps) illustrating each of these three programming models, individually and in combination. Fortran2003 now supports abstract data types, and design patterns can be used to support a variety of implementations within the same code base. Fortran2003 also supports interoperability with C so that implementations in C languages are also easy to use. Finally, main codes can be translated into dynamic environments such as Python, while still taking advantage of high performing compiled languages. Parallel languages are still evolving with interesting developments in co-Array Fortran, UPC, and OpenACC, among others, and these can also be supported within the same software architecture. Work supported by NSF and DOE Grants.

A compositional reservoir simulator on distributed memory parallel computers

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

Rame, M.; Delshad, M.

1995-12-31

This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. Amore » portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented.« less

World-wide precision airports for SVS

NASA Astrophysics Data System (ADS)

Schiefele, Jens; Lugsch, Bill; Launer, Marc; Baca, Diana

2004-08-01

Future cockpit and aviation applications require high quality airport databases. Accuracy, resolution, integrity, completeness, traceability, and timeliness [1] are key requirements. For most aviation applications, attributed vector databases are needed. The geometry is based on points, lines, and closed polygons. To document the needs for aviation industry RTCA and EUROCAE developed in a joint committee, the DO-272/ED-99 document. It states industry needs for data features, attributes, coding, and capture rules for Airport Mapping Databases (AMDB). This paper describes the technical approach Jeppesen has taken to generate a world-wide set of three-hundred AMDB airports. All AMDB airports are DO-200A/ED-76 [1] and DO-272/ED-99 [2] compliant. Jeppesen airports have a 5m (CE90) accuracy and an 10-3 integrity. World-wide all AMDB data is delivered in WGS84 coordinates. Jeppesen continually updates the databases.

78 FR 14367 - Market Vectors ETF Trust, et al.; Notice of Application

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-05

...] Market Vectors ETF Trust, et al.; Notice of Application February 27, 2013. AGENCY: Securities and... companies and unit investment trusts outside of the same group of investment companies as the series to...-feeder structure. Applicants: Market Vectors ETF Trust (the ``Trust''), Van Eck Associates Corporation...

Computational Investigation of Fluidic Counterflow Thrust Vectoring

NASA Technical Reports Server (NTRS)

Hunter, Craig A.; Deere, Karen A.

1999-01-01

A computational study of fluidic counterflow thrust vectoring has been conducted. Two-dimensional numerical simulations were run using the computational fluid dynamics code PAB3D with two-equation turbulence closure and linear Reynolds stress modeling. For validation, computational results were compared to experimental data obtained at the NASA Langley Jet Exit Test Facility. In general, computational results were in good agreement with experimental performance data, indicating that efficient thrust vectoring can be obtained with low secondary flow requirements (less than 1% of the primary flow). An examination of the computational flowfield has revealed new details about the generation of a countercurrent shear layer, its relation to secondary suction, and its role in thrust vectoring. In addition to providing new information about the physics of counterflow thrust vectoring, this work appears to be the first documented attempt to simulate the counterflow thrust vectoring problem using computational fluid dynamics.

RNAi screening of subtracted transcriptomes reveals tumor suppression by taurine-activated GABAA receptors involved in volume regulation

PubMed Central

van Nierop, Pim; Vormer, Tinke L.; Foijer, Floris; Verheij, Joanne; Lodder, Johannes C.; Andersen, Jesper B.; Mansvelder, Huibert D.; te Riele, Hein

2018-01-01

To identify coding and non-coding suppressor genes of anchorage-independent proliferation by efficient loss-of-function screening, we have developed a method for enzymatic production of low complexity shRNA libraries from subtracted transcriptomes. We produced and screened two LEGO (Low-complexity by Enrichment for Genes shut Off) shRNA libraries that were enriched for shRNA vectors targeting coding and non-coding polyadenylated transcripts that were reduced in transformed Mouse Embryonic Fibroblasts (MEFs). The LEGO shRNA libraries included ~25 shRNA vectors per transcript which limited off-target artifacts. Our method identified 79 coding and non-coding suppressor transcripts. We found that taurine-responsive GABAA receptor subunits, including GABRA5 and GABRB3, were induced during the arrest of non-transformed anchor-deprived MEFs and prevented anchorless proliferation. We show that taurine activates chloride currents through GABAA receptors on MEFs, causing seclusion of cell volume in large membrane protrusions. Volume seclusion from cells by taurine correlated with reduced proliferation and, conversely, suppression of this pathway allowed anchorage-independent proliferation. In human cholangiocarcinomas, we found that several proteins involved in taurine signaling via GABAA receptors were repressed. Low GABRA5 expression typified hyperproliferative tumors, and loss of taurine signaling correlated with reduced patient survival, suggesting this tumor suppressive mechanism operates in vivo. PMID:29787571

Optimizing ATLAS code with different profilers

NASA Astrophysics Data System (ADS)

Kama, S.; Seuster, R.; Stewart, G. A.; Vitillo, R. A.

2014-06-01

After the current maintenance period, the LHC will provide higher energy collisions with increased luminosity. In order to keep up with these higher rates, ATLAS software needs to speed up substantially. However, ATLAS code is composed of approximately 6M lines, written by many different programmers with different backgrounds, which makes code optimisation a challenge. To help with this effort different profiling tools and techniques are being used. These include well known tools, such as the Valgrind suite and Intel Amplifier; less common tools like Pin, PAPI, and GOoDA; as well as techniques such as library interposing. In this paper we will mainly focus on Pin tools and GOoDA. Pin is a dynamic binary instrumentation tool which can obtain statistics such as call counts, instruction counts and interrogate functions' arguments. It has been used to obtain CLHEP Matrix profiles, operations and vector sizes for linear algebra calculations which has provided the insight necessary to achieve significant performance improvements. Complimenting this, GOoDA, an in-house performance tool built in collaboration with Google, which is based on hardware performance monitoring unit events, is used to identify hot-spots in the code for different types of hardware limitations, such as CPU resources, caches, or memory bandwidth. GOoDA has been used in improvement of the performance of new magnetic field code and identification of potential vectorization targets in several places, such as Runge-Kutta propagation code.

High-capacity 'gutless' adenoviral vectors.

PubMed

Kochanek, S; Schiedner, G; Volpers, C

2001-10-01

Adenoviral vectors are promising gene transfer vehicles for different gene therapy applications. High-capacity adenoviral (HC-Ad) vectors address some of the problems that have been observed with replication-defective, E1-deleted first-generation adenoviral vectors: toxicity and immunogenicity due to viral gene expression and 7 to 8 kb capacity limit for the transport of therapeutic DNA. This review summarizes HC-Ad vector-related publications from the past 18 months that are mainly concerned with vector design/production and in vivo applications in different murine models.

Geographic Information Systems: A Primer

DTIC Science & Technology

1990-10-01

AVAILABILITY OF REPORT Approved for public release; distribution 2b DECLASSjFICATION/ DOWNGRADING SCHEDULE unlimited. 4 PERFORMING ORGANIZATION REPORT...utilizing sophisticated integrated databases (usually vector-based), avoid the indirect value coding scheme by recognizing names or direct magnitudes...intricate involvement required by the operator in order to establish a functional coding scheme . A simple raster system, in which cell values indicate

Development of a Newcastle disease virus vector expressing a foreign gene through an internal ribosomal entry site provides direct proof for a sequential transcription mechanism

USDA-ARS?s Scientific Manuscript database

Objectives: Newcastle disease virus (NDV), a member of the Paramxoviridae family, has been developed as a vector to express foreign genes for vaccine and gene therapy purposes. The foreign genes are usually inserted into a non-coding region of the NDV genome as an independent transcription unit (ITU...

Modeling Interferometric Structures with Birefringent Elements: A Linear Vector-Space Formalism

DTIC Science & Technology

2013-11-12

Annapolis, Maryland ViNceNt J. Urick FraNk BUcholtz Photonics Technology Branch Optical Sciences Division i REPORT DOCUMENTATION PAGE Form...a Linear Vector-Space Formalism Nicholas J. Frigo,1 Vincent J. Urick , and Frank Bucholtz Naval Research Laboratory, Code 5650 4555 Overlook Avenue, SW...Annapolis, MD Unclassified Unlimited Unclassified Unlimited Unclassified Unlimited Unclassified Unlimited 29 Vincent J. Urick (202) 767-9352 Coupled mode

Computation of transonic potential flow about 3 dimensional inlets, ducts, and bodies

NASA Technical Reports Server (NTRS)

Reyhner, T. A.

1982-01-01

An analysis was developed and a computer code, P465 Version A, written for the prediction of transonic potential flow about three dimensional objects including inlet, duct, and body geometries. Finite differences and line relaxation are used to solve the complete potential flow equation. The coordinate system used for the calculations is independent of body geometry. Cylindrical coordinates are used for the computer code. The analysis is programmed in extended FORTRAN 4 for the CYBER 203 vector computer. The programming of the analysis is oriented toward taking advantage of the vector processing capabilities of this computer. Comparisons of computed results with experimental measurements are presented to verify the analysis. Descriptions of program input and output formats are also presented.

SIMD Optimization of Linear Expressions for Programmable Graphics Hardware

PubMed Central

Bajaj, Chandrajit; Ihm, Insung; Min, Jungki; Oh, Jinsang

2009-01-01

The increased programmability of graphics hardware allows efficient graphical processing unit (GPU) implementations of a wide range of general computations on commodity PCs. An important factor in such implementations is how to fully exploit the SIMD computing capacities offered by modern graphics processors. Linear expressions in the form of ȳ = Ax̄ + b̄, where A is a matrix, and x̄, ȳ and b̄ are vectors, constitute one of the most basic operations in many scientific computations. In this paper, we propose a SIMD code optimization technique that enables efficient shader codes to be generated for evaluating linear expressions. It is shown that performance can be improved considerably by efficiently packing arithmetic operations into four-wide SIMD instructions through reordering of the operations in linear expressions. We demonstrate that the presented technique can be used effectively for programming both vertex and pixel shaders for a variety of mathematical applications, including integrating differential equations and solving a sparse linear system of equations using iterative methods. PMID:19946569

Documentation of a graphical display program for the saturated- unsaturated transport (SUTRA) finite-element simulation model

USGS Publications Warehouse

Souza, W.R.

1987-01-01

This report documents a graphical display program for the U. S. Geological Survey finite-element groundwater flow and solute transport model. Graphic features of the program, SUTRA-PLOT (SUTRA-PLOT = saturated/unsaturated transport), include: (1) plots of the finite-element mesh, (2) velocity vector plots, (3) contour plots of pressure, solute concentration, temperature, or saturation, and (4) a finite-element interpolator for gridding data prior to contouring. SUTRA-PLOT is written in FORTRAN 77 on a PRIME 750 computer system, and requires Version 9.0 or higher of the DISSPLA graphics library. The program requires two input files: the SUTRA input data list and the SUTRA simulation output listing. The program is menu driven and specifications for individual types of plots are entered and may be edited interactively. Installation instruction, a source code listing, and a description of the computer code are given. Six examples of plotting applications are used to demonstrate various features of the plotting program. (Author 's abstract)

Applications Performance on NAS Intel Paragon XP/S - 15#

NASA Technical Reports Server (NTRS)

Saini, Subhash; Simon, Horst D.; Copper, D. M. (Technical Monitor)

1994-01-01

The Numerical Aerodynamic Simulation (NAS) Systems Division received an Intel Touchstone Sigma prototype model Paragon XP/S- 15 in February, 1993. The i860 XP microprocessor with an integrated floating point unit and operating in dual -instruction mode gives peak performance of 75 million floating point operations (NIFLOPS) per second for 64 bit floating point arithmetic. It is used in the Paragon XP/S-15 which has been installed at NAS, NASA Ames Research Center. The NAS Paragon has 208 nodes and its peak performance is 15.6 GFLOPS. Here, we will report on early experience using the Paragon XP/S- 15. We have tested its performance using both kernels and applications of interest to NAS. We have measured the performance of BLAS 1, 2 and 3 both assembly-coded and Fortran coded on NAS Paragon XP/S- 15. Furthermore, we have investigated the performance of a single node one-dimensional FFT, a distributed two-dimensional FFT and a distributed three-dimensional FFT Finally, we measured the performance of NAS Parallel Benchmarks (NPB) on the Paragon and compare it with the performance obtained on other highly parallel machines, such as CM-5, CRAY T3D, IBM SP I, etc. In particular, we investigated the following issues, which can strongly affect the performance of the Paragon: a. Impact of the operating system: Intel currently uses as a default an operating system OSF/1 AD from the Open Software Foundation. The paging of Open Software Foundation (OSF) server at 22 MB to make more memory available for the application degrades the performance. We found that when the limit of 26 NIB per node out of 32 MB available is reached, the application is paged out of main memory using virtual memory. When the application starts paging, the performance is considerably reduced. We found that dynamic memory allocation can help applications performance under certain circumstances. b. Impact of data cache on the i860/XP: We measured the performance of the BLAS both assembly coded and Fortran coded. We found that the measured performance of assembly-coded BLAS is much less than what memory bandwidth limitation would predict. The influence of data cache on different sizes of vectors is also investigated using one-dimensional FFTs. c. Impact of processor layout: There are several different ways processors can be laid out within the two-dimensional grid of processors on the Paragon. We have used the FFT example to investigate performance differences based on processors layout.

A Comprehensive C++ Controller for a Magnetically Supported Vertical Rotor. 1.0

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.

2001-01-01

This manual describes the new FATMaCC (Five-Axis, Three-Magnetic-Bearing Control Code). The FATMaCC (pronounced "fat mak") is a versatile control code that possesses many desirable features that were not available in previous in-house controllers. The ultimate goal in designing this code was to achieve full rotor levitation and control at a loop time of 50 microsec. Using a 1-GHz processor, the code will control a five-axis system in either a decentralized or a more elegant centralized (modal control) mode at a loop time of 56 microsec. In addition, it will levitate and control (with only minor modification to the input/output wiring) a two-axis and/or a four-axis system. Stable rotor levitation and control of any of the systems mentioned above are accomplished through appropriate key presses to modify parameters, such as stiffness, damping, and bias. A signal generation block provides 11 excitation signals. An excitation signal is then superimposed on the radial bearing x- and y-control signals, thus producing a resultant force vector. By modulating the signals on the bearing x- and y-axes with a cosine and a sine function, respectively, a radial excitation force vector is made to rotate 360 deg. about the bearing geometric center. The rotation of the force vector is achieved manually by using key press or automatically by engaging the "one-per-revolution" feature. Rotor rigid body modes can be excited by using the excitation module. Depending on the polarities of the excitation signal in each radial bearing, the bounce or tilt mode will be excited.

Bearing performance degradation assessment based on time-frequency code features and SOM network

NASA Astrophysics Data System (ADS)

Zhang, Yan; Tang, Baoping; Han, Yan; Deng, Lei

2017-04-01

Bearing performance degradation assessment and prognostics are extremely important in supporting maintenance decision and guaranteeing the system’s reliability. To achieve this goal, this paper proposes a novel feature extraction method for the degradation assessment and prognostics of bearings. Features of time-frequency codes (TFCs) are extracted from the time-frequency distribution using a hybrid procedure based on short-time Fourier transform (STFT) and non-negative matrix factorization (NMF) theory. An alternative way to design the health indicator is investigated by quantifying the similarity between feature vectors using a self-organizing map (SOM) network. On the basis of this idea, a new health indicator called time-frequency code quantification error (TFCQE) is proposed to assess the performance degradation of the bearing. This indicator is constructed based on the bearing real-time behavior and the SOM model that is previously trained with only the TFC vectors under the normal condition. Vibration signals collected from the bearing run-to-failure tests are used to validate the developed method. The comparison results demonstrate the superiority of the proposed TFCQE indicator over many other traditional features in terms of feature quality metrics, incipient degradation identification and achieving accurate prediction. Highlights • Time-frequency codes are extracted to reflect the signals’ characteristics. • SOM network served as a tool to quantify the similarity between feature vectors. • A new health indicator is proposed to demonstrate the whole stage of degradation development. • The method is useful for extracting the degradation features and detecting the incipient degradation. • The superiority of the proposed method is verified using experimental data.

The Adenovirus Genome Contributes to the Structural Stability of the Virion

PubMed Central

Saha, Bratati; Wong, Carmen M.; Parks, Robin J.

2014-01-01

Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design. PMID:25254384

The Helioseismic and Magnetic Imager (HMI) Vector Magnetic Field Pipeline: Overview and Performance

NASA Astrophysics Data System (ADS)

Hoeksema, J. Todd; Liu, Yang; Hayashi, Keiji; Sun, Xudong; Schou, Jesper; Couvidat, Sebastien; Norton, Aimee; Bobra, Monica; Centeno, Rebecca; Leka, K. D.; Barnes, Graham; Turmon, Michael

2014-09-01

The Helioseismic and Magnetic Imager (HMI) began near-continuous full-disk solar measurements on 1 May 2010 from the Solar Dynamics Observatory (SDO). An automated processing pipeline keeps pace with observations to produce observable quantities, including the photospheric vector magnetic field, from sequences of filtergrams. The basic vector-field frame list cadence is 135 seconds, but to reduce noise the filtergrams are combined to derive data products every 720 seconds. The primary 720 s observables were released in mid-2010, including Stokes polarization parameters measured at six wavelengths, as well as intensity, Doppler velocity, and the line-of-sight magnetic field. More advanced products, including the full vector magnetic field, are now available. Automatically identified HMI Active Region Patches (HARPs) track the location and shape of magnetic regions throughout their lifetime. The vector field is computed using the Very Fast Inversion of the Stokes Vector (VFISV) code optimized for the HMI pipeline; the remaining 180∘ azimuth ambiguity is resolved with the Minimum Energy (ME0) code. The Milne-Eddington inversion is performed on all full-disk HMI observations. The disambiguation, until recently run only on HARP regions, is now implemented for the full disk. Vector and scalar quantities in the patches are used to derive active region indices potentially useful for forecasting; the data maps and indices are collected in the SHARP data series, hmi.sharp_720s. Definitive SHARP processing is completed only after the region rotates off the visible disk; quick-look products are produced in near real time. Patches are provided in both CCD and heliographic coordinates. HMI provides continuous coverage of the vector field, but has modest spatial, spectral, and temporal resolution. Coupled with limitations of the analysis and interpretation techniques, effects of the orbital velocity, and instrument performance, the resulting measurements have a certain dynamic range and sensitivity and are subject to systematic errors and uncertainties that are characterized in this report.

National malaria vector control policy: an analysis of the decision to scale-up larviciding in Nigeria.

PubMed

Tesfazghi, Kemi; Hill, Jenny; Jones, Caroline; Ranson, Hilary; Worrall, Eve

2016-02-01

New vector control tools are needed to combat insecticide resistance and reduce malaria transmission. The World Health Organization (WHO) endorses larviciding as a supplementary vector control intervention using larvicides recommended by the WHO Pesticides Evaluation Scheme (WHOPES). The decision to scale-up larviciding in Nigeria provided an opportunity to investigate the factors influencing policy adoption and assess the role that actors and evidence play in the policymaking process, in order to draw lessons that help accelerate the uptake of new methods for vector control. A retrospective policy analysis was carried out using in-depth interviews with national level policy stakeholders to establish normative national vector control policy or strategy decision-making processes and compare these with the process that led to the decision to scale-up larviciding. The interviews were transcribed, then coded and analyzed using NVivo10. Data were coded according to pre-defined themes from an analytical policy framework developed a priori. Stakeholders reported that the larviciding decision-making process deviated from the normative vector control decision-making process. National malaria policy is normally strongly influenced by WHO recommendations, but the potential of larviciding to contribute to national economic development objectives through larvicide production in Nigeria was cited as a key factor shaping the decision. The larviciding decision involved a restricted range of policy actors, and notably excluded actors that usually play advisory, consultative and evidence generation roles. Powerful actors limited the access of some actors to the policy processes and content. This may have limited the influence of scientific evidence in this policy decision. This study demonstrates that national vector control policy change can be facilitated by linking malaria control objectives to wider socioeconomic considerations and through engaging powerful policy champions to drive policy change and thereby accelerate access to new vector control tools. © The Author 2015. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Wireless visual sensor network resource allocation using cross-layer optimization

NASA Astrophysics Data System (ADS)

Bentley, Elizabeth S.; Matyjas, John D.; Medley, Michael J.; Kondi, Lisimachos P.

2009-01-01

In this paper, we propose an approach to manage network resources for a Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network where nodes monitor scenes with varying levels of motion. It uses cross-layer optimization across the physical layer, the link layer and the application layer. Our technique simultaneously assigns a source coding rate, a channel coding rate, and a power level to all nodes in the network based on one of two criteria that maximize the quality of video of the entire network as a whole, subject to a constraint on the total chip rate. One criterion results in the minimal average end-to-end distortion amongst all nodes, while the other criterion minimizes the maximum distortion of the network. Our approach allows one to determine the capacity of the visual sensor network based on the number of nodes and the quality of video that must be transmitted. For bandwidth-limited applications, one can also determine the minimum bandwidth needed to accommodate a number of nodes with a specific target chip rate. Video captured by a sensor node camera is encoded and decoded using the H.264 video codec by a centralized control unit at the network layer. To reduce the computational complexity of the solution, Universal Rate-Distortion Characteristics (URDCs) are obtained experimentally to relate bit error probabilities to the distortion of corrupted video. Bit error rates are found first by using Viterbi's upper bounds on the bit error probability and second, by simulating nodes transmitting data spread by Total Square Correlation (TSC) codes over a Rayleigh-faded DS-CDMA channel and receiving that data using Auxiliary Vector (AV) filtering.

Ritz method for transient response in systems having unsymmetric stiffness

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1989-01-01

The DMAP coding was automated to such an extent by using the device of bubble vectors, that it is useable for analyses in its present form. This feasibility study demonstrates that the Ritz Method is so compelling as to warrant coding its modules in FORTRAN and organizing the resulting coding into a new Rigid Format. Even though this Ritz technique was developed for unsymmetric stiffness matrices, it offers advantages to problems with symmetric stiffnesses. If used for the symmetric case the solution would be simplified to one set of modes, because the adjoint would be the same as the primary. Its advantage in either type of symmetry over a classical eigenvalue modal expansion is that information density per Ritz mode is far richer than per eigenvalue mode; thus far fewer modes would be needed for the same accuracy and every mode would actively participate in the response. Considerable economy can be realized in adapting Ritz vectors for modal solutions. This new Ritz capability now makes NASTRAN even more powerful than before.

Rigorous vector wave propagation for arbitrary flat media

NASA Astrophysics Data System (ADS)

Bos, Steven P.; Haffert, Sebastiaan Y.; Keller, Christoph U.

2017-08-01

Precise modelling of the (off-axis) point spread function (PSF) to identify geometrical and polarization aberrations is important for many optical systems. In order to characterise the PSF of the system in all Stokes parameters, an end-to-end simulation of the system has to be performed in which Maxwell's equations are rigorously solved. We present the first results of a python code that we are developing to perform multiscale end-to-end wave propagation simulations that include all relevant physics. Currently we can handle plane-parallel near- and far-field vector diffraction effects of propagating waves in homogeneous isotropic and anisotropic materials, refraction and reflection of flat parallel surfaces, interference effects in thin films and unpolarized light. We show that the code has a numerical precision on the order of 10-16 for non-absorbing isotropic and anisotropic materials. For absorbing materials the precision is on the order of 10-8. The capabilities of the code are demonstrated by simulating a converging beam reflecting from a flat aluminium mirror at normal incidence.

Multitasking the three-dimensional shock wave code CTH on the Cray X-MP/416

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

McGlaun, J.M.; Thompson, S.L.

1988-01-01

CTH is a software system under development at Sandia National Laboratories Albuquerque that models multidimensional, multi-material, large-deformation, strong shock wave physics. CTH was carefully designed to both vectorize and multitask on the Cray X-MP/416. All of the physics routines are vectorized except the thermodynamics and the interface tracer. All of the physics routines are multitasked except the boundary conditions. The Los Alamos National Laboratory multitasking library was used for the multitasking. The resulting code is easy to maintain, easy to understand, gives the same answers as the unitasked code, and achieves a measured speedup of approximately 3.5 on the fourmore » cpu Cray. This document discusses the design, prototyping, development, and debugging of CTH. It also covers the architecture features of CTH that enhances multitasking, granularity of the tasks, and synchronization of tasks. The utility of system software and utilities such as simulators and interactive debuggers are also discussed. 5 refs., 7 tabs.« less

Parallelisation study of a three-dimensional environmental flow model

NASA Astrophysics Data System (ADS)

O'Donncha, Fearghal; Ragnoli, Emanuele; Suits, Frank

2014-03-01

There are many simulation codes in the geosciences that are serial and cannot take advantage of the parallel computational resources commonly available today. One model important for our work in coastal ocean current modelling is EFDC, a Fortran 77 code configured for optimal deployment on vector computers. In order to take advantage of our cache-based, blade computing system we restructured EFDC from serial to parallel, thereby allowing us to run existing models more quickly, and to simulate larger and more detailed models that were previously impractical. Since the source code for EFDC is extensive and involves detailed computation, it is important to do such a port in a manner that limits changes to the files, while achieving the desired speedup. We describe a parallelisation strategy involving surgical changes to the source files to minimise error-prone alteration of the underlying computations, while allowing load-balanced domain decomposition for efficient execution on a commodity cluster. The use of conjugate gradient posed particular challenges due to implicit non-local communication posing a hindrance to standard domain partitioning schemes; a number of techniques are discussed to address this in a feasible, computationally efficient manner. The parallel implementation demonstrates good scalability in combination with a novel domain partitioning scheme that specifically handles mixed water/land regions commonly found in coastal simulations. The approach presented here represents a practical methodology to rejuvenate legacy code on a commodity blade cluster with reasonable effort; our solution has direct application to other similar codes in the geosciences.

Observations on Polar Coding with CRC-Aided List Decoding

DTIC Science & Technology

2016-09-01

9 v 1. INTRODUCTION Polar codes are a new type of forward error correction (FEC) codes, introduced by Arikan in [1], in which he...error correction (FEC) currently used and planned for use in Navy wireless communication systems. The project’s results from FY14 and FY15 are...good error- correction per- formance. We used the Tal/Vardy method of [5]. The polar encoder uses a row vector u of length N . Let uA be the subvector

Analysis and Simulation of Narrowband GPS Jamming Using Digital Excision Temporal Filtering.

DTIC Science & Technology

1994-12-01

the sequence of stored values from the P- code sampled at a 20 MHz rate. When correlated with a reference vector of the same length to simulate a GPS ...rate required for the GPS signals, (20 MHz sampling rate for the P- code signal), the personal computer (PC) used run the simulation could not perform...This subroutine is used to perform a fast FFT based 168 biased cross correlation . Written by Capt Gerry Falen, USAF, 16 AUG 94 % start of code

Navier-Stokes Simulation of Homogeneous Turbulence on the CYBER 205

NASA Technical Reports Server (NTRS)

Wu, C. T.; Ferziger, J. H.; Chapman, D. R.; Rogallo, R. S.

1984-01-01

A computer code which solves the Navier-Stokes equations for three dimensional, time-dependent, homogenous turbulence has been written for the CYBER 205. The code has options for both 64-bit and 32-bit arithmetic. With 32-bit computation, mesh sizes up to 64 (3) are contained within core of a 2 million 64-bit word memory. Computer speed timing runs were made for various vector lengths up to 6144. With this code, speeds a little over 100 Mflops have been achieved on a 2-pipe CYBER 205. Several problems encountered in the coding are discussed.

Implementation of a fast digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic

NASA Technical Reports Server (NTRS)

Habiby, Sarry F.; Collins, Stuart A., Jr.

1987-01-01

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. A Hughes liquid crystal light valve, the residue arithmetic representation, and a holographic optical memory are used to construct position coded optical look-up tables. All operations are performed in effectively one light valve response time with a potential for a high information density.

Implementation of a fast digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic.

PubMed

Habiby, S F; Collins, S A

1987-11-01

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. A Hughes liquid crystal light valve, the residue arithmetic representation, and a holographic optical memory are used to construct position coded optical look-up tables. All operations are performed in effectively one light valve response time with a potential for a high information density.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

An investigative study of multispectral data compression for remotely-sensed images using vector quantization and difference-mapped shift-coding

NASA Technical Reports Server (NTRS)

Jaggi, S.

1993-01-01

A study is conducted to investigate the effects and advantages of data compression techniques on multispectral imagery data acquired by NASA's airborne scanners at the Stennis Space Center. The first technique used was vector quantization. The vector is defined in the multispectral imagery context as an array of pixels from the same location from each channel. The error obtained in substituting the reconstructed images for the original set is compared for different compression ratios. Also, the eigenvalues of the covariance matrix obtained from the reconstructed data set are compared with the eigenvalues of the original set. The effects of varying the size of the vector codebook on the quality of the compression and on subsequent classification are also presented. The output data from the Vector Quantization algorithm was further compressed by a lossless technique called Difference-mapped Shift-extended Huffman coding. The overall compression for 7 channels of data acquired by the Calibrated Airborne Multispectral Scanner (CAMS), with an RMS error of 15.8 pixels was 195:1 (0.41 bpp) and with an RMS error of 3.6 pixels was 18:1 (.447 bpp). The algorithms were implemented in software and interfaced with the help of dedicated image processing boards to an 80386 PC compatible computer. Modules were developed for the task of image compression and image analysis. Also, supporting software to perform image processing for visual display and interpretation of the compressed/classified images was developed.

Thrust vectoring for lateral-directional stability

NASA Technical Reports Server (NTRS)

Peron, Lee R.; Carpenter, Thomas

1992-01-01

The advantages and disadvantages of using thrust vectoring for lateral-directional control and the effects of reducing the tail size of a single-engine aircraft were investigated. The aerodynamic characteristics of the F-16 aircraft were generated by using the Aerodynamic Preliminary Analysis System II panel code. The resulting lateral-directional linear perturbation analysis of a modified F-16 aircraft with various tail sizes and yaw vectoring was performed at several speeds and altitudes to determine the stability and control trends for the aircraft compared to these trends for a baseline aircraft. A study of the paddle-type turning vane thrust vectoring control system as used on the National Aeronautics and Space Administration F/A-18 High Alpha Research Vehicle is also presented.

Characterization of a Theta-Type Plasmid from Lactobacillus sakei: a Potential Basis for Low-Copy-Number Vectors in Lactobacilli

PubMed Central

Alpert, Carl-Alfred; Crutz-Le Coq, Anne-Marie; Malleret, Christine; Zagorec, Monique

2003-01-01

The complete nucleotide sequence of the 13-kb plasmid pRV500, isolated from Lactobacillus sakei RV332, was determined. Sequence analysis enabled the identification of genes coding for a putative type I restriction-modification system, two genes coding for putative recombinases of the integrase family, and a region likely involved in replication. The structural features of this region, comprising a putative ori segment containing 11- and 22-bp repeats and a repA gene coding for a putative initiator protein, indicated that pRV500 belongs to the pUCL287 subfamily of theta-type replicons. A 3.7-kb fragment encompassing this region was fused to an Escherichia coli replicon to produce the shuttle vector pRV566 and was observed to be functional in L. sakei for plasmid replication. The L. sakei replicon alone could not support replication in E. coli. Plasmid pRV500 and its derivative pRV566 were determined to be at very low copy numbers in L. sakei. pRV566 was maintained at a reasonable rate over 20 generations in several lactobacilli, such as Lactobacillus curvatus, Lactobacillus casei, and Lactobacillus plantarum, in addition to L. sakei, making it an interesting basis for developing vectors. Sequence relationships with other plasmids are described and discussed. PMID:12957947

Implementation of a digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic

NASA Technical Reports Server (NTRS)

Habiby, Sarry F.

1987-01-01

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. The objective is to demonstrate the operation of an optical processor designed to minimize computation time in performing a practical computing application. This is done by using the large array of processing elements in a Hughes liquid crystal light valve, and relying on the residue arithmetic representation, a holographic optical memory, and position coded optical look-up tables. In the design, all operations are performed in effectively one light valve response time regardless of matrix size. The features of the design allowing fast computation include the residue arithmetic representation, the mapping approach to computation, and the holographic memory. In addition, other features of the work include a practical light valve configuration for efficient polarization control, a model for recording multiple exposures in silver halides with equal reconstruction efficiency, and using light from an optical fiber for a reference beam source in constructing the hologram. The design can be extended to implement larger matrix arrays without increasing computation time.

Template protection and its implementation in 3D face recognition systems

NASA Astrophysics Data System (ADS)

Zhou, Xuebing

2007-04-01

As biometric recognition systems are widely applied in various application areas, security and privacy risks have recently attracted the attention of the biometric community. Template protection techniques prevent stored reference data from revealing private biometric information and enhance the security of biometrics systems against attacks such as identity theft and cross matching. This paper concentrates on a template protection algorithm that merges methods from cryptography, error correction coding and biometrics. The key component of the algorithm is to convert biometric templates into binary vectors. It is shown that the binary vectors should be robust, uniformly distributed, statistically independent and collision-free so that authentication performance can be optimized and information leakage can be avoided. Depending on statistical character of the biometric template, different approaches for transforming biometric templates into compact binary vectors are presented. The proposed methods are integrated into a 3D face recognition system and tested on the 3D facial images of the FRGC database. It is shown that the resulting binary vectors provide an authentication performance that is similar to the original 3D face templates. A high security level is achieved with reasonable false acceptance and false rejection rates of the system, based on an efficient statistical analysis. The algorithm estimates the statistical character of biometric templates from a number of biometric samples in the enrollment database. For the FRGC 3D face database, the small distinction of robustness and discriminative power between the classification results under the assumption of uniquely distributed templates and the ones under the assumption of Gaussian distributed templates is shown in our tests.

Engineering of baker's yeasts, E. coli and Bacillus hosts for the production of Bacillus subtilis Lipase A.

PubMed

Sánchez, Marta; Prim, Núria; Rández-Gil, Francisca; Pastor, F I Javier; Diaz, Pilar

2002-05-05

Lipases are versatile biocatalists showing multiple applications in a wide range of biotechnological processes. The gene lipA coding for Lipase A from Bacillus subtilis was isolated by PCR amplification, cloned and expressed in Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis strains, using pBR322, YEplac112 and pUB110-derived vectors, respectively. Lipase activity analysis of the recombinant strains showed that the gene can be properly expressed in all hosts assayed, this being the first time a lipase from bacterial origin can be expressed in baker's S. cerevisiae strains. An important increase of lipase production was obtained in heterologous hosts with respect to that of parental strains, indicating that the described systems can represent a useful tool to enhance productivity of the enzyme for biotechnological applications, including the use of the lipase in bread making, or as a technological additive. Copyright 2002 Wiley Periodicals, Inc.

Finite element modeling of electromagnetic fields and waves using NASTRAN

NASA Technical Reports Server (NTRS)

Moyer, E. Thomas, Jr.; Schroeder, Erwin

1989-01-01

The various formulations of Maxwell's equations are reviewed with emphasis on those formulations which most readily form analogies with Navier's equations. Analogies involving scalar and vector potentials and electric and magnetic field components are presented. Formulations allowing for media with dielectric and conducting properties are emphasized. It is demonstrated that many problems in electromagnetism can be solved using the NASTRAN finite element code. Several fundamental problems involving time harmonic solutions of Maxwell's equations with known analytic solutions are solved using NASTRAN to demonstrate convergence and mesh requirements. Mesh requirements are studied as a function of frequency, conductivity, and dielectric properties. Applications in both low frequency and high frequency are highlighted. The low frequency problems demonstrate the ability to solve problems involving media inhomogeneity and unbounded domains. The high frequency applications demonstrate the ability to handle problems with large boundary to wavelength ratios.

Novel strategy to implement active-space coupled-cluster methods

NASA Astrophysics Data System (ADS)

Rolik, Zoltán; Kállay, Mihály

2018-03-01

A new approach is presented for the efficient implementation of coupled-cluster (CC) methods including higher excitations based on a molecular orbital space partitioned into active and inactive orbitals. In the new framework, the string representation of amplitudes and intermediates is used as long as it is beneficial, but the contractions are evaluated as matrix products. Using a new diagrammatic technique, the CC equations are represented in a compact form due to the string notations we introduced. As an application of these ideas, a new automated implementation of the single-reference-based multi-reference CC equations is presented for arbitrary excitation levels. The new program can be considered as an improvement over the previous implementations in many respects; e.g., diagram contributions are evaluated by efficient vectorized subroutines. Timings for test calculations for various complete active-space problems are presented. As an application of the new code, the weak interactions in the Be dimer were studied.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study.

PubMed

Kotchenova, Svetlana Y; Vermote, Eric F; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Radiative transfer codes for atmospheric correction and aerosol retrieval: intercomparison study

NASA Astrophysics Data System (ADS)

Kotchenova, Svetlana Y.; Vermote, Eric F.; Levy, Robert; Lyapustin, Alexei

2008-05-01

Results are summarized for a scientific project devoted to the comparison of four atmospheric radiative transfer codes incorporated into different satellite data processing algorithms, namely, 6SV1.1 (second simulation of a satellite signal in the solar spectrum, vector, version 1.1), RT3 (radiative transfer), MODTRAN (moderate resolution atmospheric transmittance and radiance code), and SHARM (spherical harmonics). The performance of the codes is tested against well-known benchmarks, such as Coulson's tabulated values and a Monte Carlo code. The influence of revealed differences on aerosol optical thickness and surface reflectance retrieval is estimated theoretically by using a simple mathematical approach. All information about the project can be found at http://rtcodes.ltdri.org.

Complete mitochondrial genome of Lutzomyia (Nyssomyia) umbratilis (Diptera: Psychodidae), the main vector of Leishmania guyanensis.

PubMed

Kocher, Arthur; Gantier, Jean-Charles; Holota, Hélène; Jeziorski, Céline; Coissac, Eric; Bañuls, Anne-Laure; Girod, Romain; Gaborit, Pascal; Murienne, Jérôme

2016-11-01

The nearly complete mitochondrial genome of Lutzomyia umbratilis Ward & Fraiha, 1977 (Psychodidae: Phlebotominae), considered as the main vector of Leishmania guyanensis, is presented. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The full nuclear ribosomal RNA segment was also assembled. The mitogenome of L. umbratilis was determined to be at least 15,717 bp-long and presents an architecture found in many mitogenomes of insect (13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one non-coding region also referred as the control region). The control region contains a large repeated element of c. 370 bp and a poly-AT region of unknown length. This is the first mitogenome of Psychodidae to be described.

Combined group ECC protection and subgroup parity protection

DOEpatents

Gara, Alan G.; Chen, Dong; Heidelberger, Philip; Ohmacht, Martin

2013-06-18

A method and system are disclosed for providing combined error code protection and subgroup parity protection for a given group of n bits. The method comprises the steps of identifying a number, m, of redundant bits for said error protection; and constructing a matrix P, wherein multiplying said given group of n bits with P produces m redundant error correction code (ECC) protection bits, and two columns of P provide parity protection for subgroups of said given group of n bits. In the preferred embodiment of the invention, the matrix P is constructed by generating permutations of m bit wide vectors with three or more, but an odd number of, elements with value one and the other elements with value zero; and assigning said vectors to rows of the matrix P.

Flavivirus RNAi suppression: decoding non-coding RNA.

PubMed

Pijlman, Gorben P

2014-08-01

Flaviviruses are important human pathogens that are transmitted by invertebrate vectors, mostly mosquitoes and ticks. During replication in their vector, flaviviruses are subject to a potent innate immune response known as antiviral RNA interference (RNAi). This defense mechanism is associated with the production of small interfering (si)RNA that lead to degradation of viral RNA. To what extent flaviviruses would benefit from counteracting antiviral RNAi is subject of debate. Here, the experimental evidence to suggest the existence of flavivirus RNAi suppressors is discussed. I will highlight the putative role of non-coding, subgenomic flavivirus RNA in suppression of RNAi in insect and mammalian cells. Novel insights from ongoing research will reveal how arthropod-borne viruses modulate innate immunity including antiviral RNAi. Copyright © 2014 Elsevier B.V. All rights reserved.

Classification of HTTP Attacks: A Study on the ECML/PKDD 2007 Discovery Challenge

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

Gallagher, Brian; Eliassi-Rad, Tina

2009-07-08

As the world becomes more reliant on Web applications for commercial, financial, and medical transactions, cyber attacks on the World Wide Web are increasing in frequency and severity. Web applications provide an attractive alternative to traditional desktop applications due to their accessibility and ease of deployment. However, the accessibility of Web applications also makes them extremely vulnerable to attack. This inherent vulnerability is intensified by the distributed nature ofWeb applications and the complexity of configuring application servers. These factors have led to a proliferation of Web-based attacks, in which attackers surreptitiously inject code into HTTP requests, allowing them to executemore » arbitrary commands on remote systems and perform malicious activities such as reading, altering, or destroying sensitive data. One approach for dealing with HTTP-based attacks is to identify malicious code in incoming HTTP requests and eliminate bad requests before they are processed. Using machine learning techniques, we can build a classifier to automatically label requests as “Valid” or “Attack.” For this study, we develop a simple, but effective HTTP attack classifier, based on the vector space model used commonly for Information Retrieval. Our classifier not only separates attacks from valid requests, but can also identify specific attack types (e.g., “SQL Injection” or “Path Traversal”). We demonstrate the effectiveness of our approach through experiments on the ECML/PKDD 2007 Discovery Challenge data set. Specifically, we show that our approach achieves higher precision and recall than previous methods. In addition, our approach has a number of desirable characteristics, including robustness to missing contextual information, interpretability of models, and scalability.« less

Development and Validation of a Natural Language Processing Tool to Identify Patients Treated for Pneumonia across VA Emergency Departments.

PubMed

Jones, B E; South, B R; Shao, Y; Lu, C C; Leng, J; Sauer, B C; Gundlapalli, A V; Samore, M H; Zeng, Q

2018-01-01

Identifying pneumonia using diagnosis codes alone may be insufficient for research on clinical decision making. Natural language processing (NLP) may enable the inclusion of cases missed by diagnosis codes. This article (1) develops a NLP tool that identifies the clinical assertion of pneumonia from physician emergency department (ED) notes, and (2) compares classification methods using diagnosis codes versus NLP against a gold standard of manual chart review to identify patients initially treated for pneumonia. Among a national population of ED visits occurring between 2006 and 2012 across the Veterans Affairs health system, we extracted 811 physician documents containing search terms for pneumonia for training, and 100 random documents for validation. Two reviewers annotated span- and document-level classifications of the clinical assertion of pneumonia. An NLP tool using a support vector machine was trained on the enriched documents. We extracted diagnosis codes assigned in the ED and upon hospital discharge and calculated performance characteristics for diagnosis codes, NLP, and NLP plus diagnosis codes against manual review in training and validation sets. Among the training documents, 51% contained clinical assertions of pneumonia; in the validation set, 9% were classified with pneumonia, of which 100% contained pneumonia search terms. After enriching with search terms, the NLP system alone demonstrated a recall/sensitivity of 0.72 (training) and 0.55 (validation), and a precision/positive predictive value (PPV) of 0.89 (training) and 0.71 (validation). ED-assigned diagnostic codes demonstrated lower recall/sensitivity (0.48 and 0.44) but higher precision/PPV (0.95 in training, 1.0 in validation); the NLP system identified more "possible-treated" cases than diagnostic coding. An approach combining NLP and ED-assigned diagnostic coding classification achieved the best performance (sensitivity 0.89 and PPV 0.80). System-wide application of NLP to clinical text can increase capture of initial diagnostic hypotheses, an important inclusion when studying diagnosis and clinical decision-making under uncertainty. Schattauer GmbH Stuttgart.

OpenClimateGIS - A Web Service Providing Climate Model Data in Commonly Used Geospatial Formats

NASA Astrophysics Data System (ADS)

Erickson, T. A.; Koziol, B. W.; Rood, R. B.

2011-12-01

The goal of the OpenClimateGIS project is to make climate model datasets readily available in commonly used, modern geospatial formats used by GIS software, browser-based mapping tools, and virtual globes.The climate modeling community typically stores climate data in multidimensional gridded formats capable of efficiently storing large volumes of data (such as netCDF, grib) while the geospatial community typically uses flexible vector and raster formats that are capable of storing small volumes of data (relative to the multidimensional gridded formats). OpenClimateGIS seeks to address this difference in data formats by clipping climate data to user-specified vector geometries (i.e. areas of interest) and translating the gridded data on-the-fly into multiple vector formats. The OpenClimateGIS system does not store climate data archives locally, but rather works in conjunction with external climate archives that expose climate data via the OPeNDAP protocol. OpenClimateGIS provides a RESTful API web service for accessing climate data resources via HTTP, allowing a wide range of applications to access the climate data.The OpenClimateGIS system has been developed using open source development practices and the source code is publicly available. The project integrates libraries from several other open source projects (including Django, PostGIS, numpy, Shapely, and netcdf4-python).OpenClimateGIS development is supported by a grant from NOAA's Climate Program Office.

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Experimental Validation of a Coupled Fluid-Multibody Dynamics Model for Tanker Trucks

DTIC Science & Technology

2007-11-08

order to accurately predict the dynamic response of tanker trucks, the model must accurately account for the following effects : • Incompressible...computational code which uses a time- accurate explicit solution procedure is used to solve both the solid and fluid equations of motion. Many commercial...position vector, τ is the deviatoric stress tensor, D is the rate of deformation tensor, f r is the body force vector, r is the artificial

Dryden/Edwards 1994 Thrust-Vectoring Aircraft Fleet - F-18 HARV, X-31, F-16 MATV

NASA Technical Reports Server (NTRS)

1994-01-01

The three thrust-vectoring aircraft at Edwards, California, each capable of flying at extreme angles of attack, cruise over the California desert in formation during flight in March 1994. They are, from left, NASA's F-18 High Alpha Research Vehicle (HARV), flown by the NASA Dryden Flight Research Center; the X-31, flown by the X-31 International Test Organization (ITO) at Dryden; and the Air Force F-16 Multi-Axis Thrust Vectoring (MATV) aircraft. All three aircraft were flown in different programs and were developed independently. The NASA F-18 HARV was a testbed to produce aerodynamic data at high angles of attack to validate computer codes and wind tunnel research. The X-31 was used to study thrust vectoring to enhance close-in air combat maneuvering, while the F-16 MATV was a demonstration of how thrust vectoring could be applied to operational aircraft.

Computational Study of Fluidic Thrust Vectoring using Separation Control in a Nozzle

NASA Technical Reports Server (NTRS)

Deere, Karen; Berrier, Bobby L.; Flamm, Jeffrey D.; Johnson, Stuart K.

2003-01-01

A computational investigation of a two- dimensional nozzle was completed to assess the use of fluidic injection to manipulate flow separation and cause thrust vectoring of the primary jet thrust. The nozzle was designed with a recessed cavity to enhance the throat shifting method of fluidic thrust vectoring. The structured-grid, computational fluid dynamics code PAB3D was used to guide the design and analyze over 60 configurations. Nozzle design variables included cavity convergence angle, cavity length, fluidic injection angle, upstream minimum height, aft deck angle, and aft deck shape. All simulations were computed with a static freestream Mach number of 0.05. a nozzle pressure ratio of 3.858, and a fluidic injection flow rate equal to 6 percent of the primary flow rate. Results indicate that the recessed cavity enhances the throat shifting method of fluidic thrust vectoring and allows for greater thrust-vector angles without compromising thrust efficiency.

Extending the length and time scales of Gram-Schmidt Lyapunov vector computations

NASA Astrophysics Data System (ADS)

Costa, Anthony B.; Green, Jason R.

2013-08-01

Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram-Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N2 (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram-Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard-Jones fluids from N=100 to 1300 between Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram-Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra.

Construction of FuzzyFind Dictionary using Golay Coding Transformation for Searching Applications

NASA Astrophysics Data System (ADS)

Kowsari, Kamram

2015-03-01

searching through a large volume of data is very critical for companies, scientists, and searching engines applications due to time complexity and memory complexity. In this paper, a new technique of generating FuzzyFind Dictionary for text mining was introduced. We simply mapped the 23 bits of the English alphabet into a FuzzyFind Dictionary or more than 23 bits by using more FuzzyFind Dictionary, and reflecting the presence or absence of particular letters. This representation preserves closeness of word distortions in terms of closeness of the created binary vectors within Hamming distance of 2 deviations. This paper talks about the Golay Coding Transformation Hash Table and how it can be used on a FuzzyFind Dictionary as a new technology for using in searching through big data. This method is introduced by linear time complexity for generating the dictionary and constant time complexity to access the data and update by new data sets, also updating for new data sets is linear time depends on new data points. This technique is based on searching only for letters of English that each segment has 23 bits, and also we have more than 23-bit and also it could work with more segments as reference table.

Alpharetroviral Self-inactivating Vectors: Long-term Transgene Expression in Murine Hematopoietic Cells and Low Genotoxicity

PubMed Central

Suerth, Julia D; Maetzig, Tobias; Brugman, Martijn H; Heinz, Niels; Appelt, Jens-Uwe; Kaufmann, Kerstin B; Schmidt, Manfred; Grez, Manuel; Modlich, Ute; Baum, Christopher; Schambach, Axel

2012-01-01

Comparative integrome analyses have highlighted alpharetroviral vectors with a relatively neutral, and thus favorable, integration spectrum. However, previous studies used alpharetroviral vectors harboring viral coding sequences and intact long-terminal repeats (LTRs). We recently developed self-inactivating (SIN) alpharetroviral vectors with an advanced split-packaging design. In a murine bone marrow (BM) transplantation model we now compared alpharetroviral, gammaretroviral, and lentiviral SIN vectors and showed that all vectors transduced hematopoietic stem cells (HSCs), leading to comparable, sustained multilineage transgene expression in primary and secondary transplanted mice. Alpharetroviral integrations were decreased near transcription start sites, CpG islands, and potential cancer genes compared with gammaretroviral, and decreased in genes compared with lentiviral integrations. Analyzing the transcriptome and intragenic integrations in engrafting cells, we observed stronger correlations between in-gene integration targeting and transcriptional activity for gammaretroviral and lentiviral vectors than for alpharetroviral vectors. Importantly, the relatively “extragenic” alpharetroviral integration pattern still supported long-term transgene expression upon serial transplantation. Furthermore, sensitive genotoxicity studies revealed a decreased immortalization incidence compared with gammaretroviral and lentiviral SIN vectors. We conclude that alpharetroviral SIN vectors have a favorable integration pattern which lowers the risk of insertional mutagenesis while supporting long-term transgene expression in the progeny of transplanted HSCs. PMID:22334016

Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1:Fortran, C, and Python Editions

NASA Astrophysics Data System (ADS)

Kaplan, G. H.; Bangert, J. A.; Barron, E. G.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2012-08-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source - code library that provides common astrometric quantities and transformations to high precision. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS is used for a wide variety of applications, including the U.S. portions of The Astronomical Almanac and a number of telescope control systems. NOVAS uses IAU recommended models for Earth orientation, including the IAU 2006 precession theory, the IAU 2000A and 2000B nutation series, and diurnal rotation based on the celestial and terrestrial intermediate origins. Equinox - based quantities, such as sidereal time, are also supported. NOVAS Earth orientation calculations match those from SOFA at the sub - microarcsecond level for comparable transformations. NOVAS algorithms for aberration an d gravitational light deflection are equivalent, at the microarcsecond level, to those inherent in the current consensus VLBI delay algorithm. NOVAS can be easily connected to the JPL planetary/lunar ephemerides (e.g., DE405), and connections to IMCCE and IAA planetary ephemerides are planned. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and currently mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to exploit the object - oriented features of Python. In the Version 3.1 C edition, the ephemeris - access functions have been revised for use on 64 - bit systems and for improved performance in general. NOVAS source code, auxiliary files, and documentation are available from the USNO website (http://aa.usno.navy.mil/software/novas/novas_info.php).

Visualization of the energy flow for guided forward and backward waves in and around a fluid-loaded elastic cylindrical shell via the Poynting vector field

NASA Astrophysics Data System (ADS)

Dean, Cleon E.; Braselton, James P.

2004-05-01

Color-coded and vector-arrow grid representations of the Poynting vector field are used to show the energy flow in and around a fluid-loaded elastic cylindrical shell for both forward- and backward-propagating waves. The present work uses a method adapted from a simpler technique due to Kaduchak and Marston [G. Kaduchak and P. L. Marston, ``Traveling-wave decomposition of surface displacements associated with scattering by a cylindrical shell: Numerical evaluation displaying guided forward and backward wave properties,'' J. Acoust. Soc. Am. 98, 3501-3507 (1995)] to isolate unidirectional energy flows.

Benchmarking GPU and CPU codes for Heisenberg spin glass over-relaxation

NASA Astrophysics Data System (ADS)

Bernaschi, M.; Parisi, G.; Parisi, L.

2011-06-01

We present a set of possible implementations for Graphics Processing Units (GPU) of the Over-relaxation technique applied to the 3D Heisenberg spin glass model. The results show that a carefully tuned code can achieve more than 100 GFlops/s of sustained performance and update a single spin in about 0.6 nanoseconds. A multi-hit technique that exploits the GPU shared memory further reduces this time. Such results are compared with those obtained by means of a highly-tuned vector-parallel code on latest generation multi-core CPUs.

Understanding the Cray X1 System

NASA Technical Reports Server (NTRS)

Cheung, Samson

2004-01-01

This paper helps the reader understand the characteristics of the Cray X1 vector supercomputer system, and provides hints and information to enable the reader to port codes to the system. It provides a comparison between the basic performance of the X1 platform and other platforms that are available at NASA Ames Research Center. A set of codes, solving the Laplacian equation with different parallel paradigms, is used to understand some features of the X1 compiler. An example code from the NAS Parallel Benchmarks is used to demonstrate performance optimization on the X1 platform.

Optical image encryption based on real-valued coding and subtracting with the help of QR code

NASA Astrophysics Data System (ADS)

Deng, Xiaopeng

2015-08-01

A novel optical image encryption based on real-valued coding and subtracting is proposed with the help of quick response (QR) code. In the encryption process, the original image to be encoded is firstly transformed into the corresponding QR code, and then the corresponding QR code is encoded into two phase-only masks (POMs) by using basic vector operations. Finally, the absolute values of the real or imaginary parts of the two POMs are chosen as the ciphertexts. In decryption process, the QR code can be approximately restored by recording the intensity of the subtraction between the ciphertexts, and hence the original image can be retrieved without any quality loss by scanning the restored QR code with a smartphone. Simulation results and actual smartphone collected results show that the method is feasible and has strong tolerance to noise, phase difference and ratio between intensities of the two decryption light beams.

Application of Vectors to Relative Velocity

ERIC Educational Resources Information Center

Tin-Lam, Toh

2004-01-01

The topic 'relative velocity' has recently been introduced into the Cambridge Ordinary Level Additional Mathematics syllabus under the application of Vectors. In this note, the results of relative velocity and the 'reduction to rest' technique of teaching relative velocity are derived mathematically from vector algebra, in the hope of providing…

Urbanization, land tenure security and vector-borne Chagas disease.

PubMed

Levy, Michael Z; Barbu, Corentin M; Castillo-Neyra, Ricardo; Quispe-Machaca, Victor R; Ancca-Juarez, Jenny; Escalante-Mejia, Patricia; Borrini-Mayori, Katty; Niemierko, Malwina; Mabud, Tarub S; Behrman, Jere R; Naquira-Velarde, Cesar

2014-08-22

Modern cities represent one of the fastest growing ecosystems on the planet. Urbanization occurs in stages; each stage characterized by a distinct habitat that may be more or less susceptible to the establishment of disease vector populations and the transmission of vector-borne pathogens. We performed longitudinal entomological and epidemiological surveys in households along a 1900 × 125 m transect of Arequipa, Peru, a major city of nearly one million inhabitants, in which the transmission of Trypanosoma cruzi, the aetiological agent of Chagas disease, by the insect vector Triatoma infestans, is an ongoing problem. The transect spans a cline of urban development from established communities to land invasions. We find that the vector is tracking the development of the city, and the parasite, in turn, is tracking the dispersal of the vector. New urbanizations are free of vector infestation for decades. T. cruzi transmission is very recent and concentrated in more established communities. The increase in land tenure security during the course of urbanization, if not accompanied by reasonable and enforceable zoning codes, initiates an influx of construction materials, people and animals that creates fertile conditions for epidemics of some vector-borne diseases. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PubMed

Colwill, Karen; Wells, Clark D; Elder, Kelly; Goudreault, Marilyn; Hersi, Kadija; Kulkarni, Sarang; Hardy, W Rod; Pawson, Tony; Morin, Gregg B

2006-03-06

Recombinational systems have been developed to rapidly shuttle Open Reading Frames (ORFs) into multiple expression vectors in order to analyze the large number of cDNAs available in the post-genomic era. In the Creator system, an ORF introduced into a donor vector can be transferred with Cre recombinase to a library of acceptor vectors optimized for different applications. Usability of the Creator system is impacted by the ability to easily manipulate DNA, the number of acceptor vectors for downstream applications, and the level of protein expression from Creator vectors. To date, we have developed over 20 novel acceptor vectors that employ a variety of promoters and epitope tags commonly employed for proteomics applications and gene function analysis. We also made several enhancements to the donor vectors including addition of different multiple cloning sites to allow shuttling from pre-existing vectors and introduction of the lacZ alpha reporter gene to allow for selection. Importantly, in order to ameliorate any effects on protein expression of the loxP site between a 5' tag and ORF, we introduced a splicing event into our expression vectors. The message produced from the resulting 'Creator Splice' vector undergoes splicing in mammalian systems to remove the loxP site. Upon analysis of our Creator Splice constructs, we discovered that protein expression levels were also significantly increased. The development of new donor and acceptor vectors has increased versatility during the cloning process and made this system compatible with a wider variety of downstream applications. The modifications introduced in our Creator Splice system were designed to remove extraneous sequences due to recombination but also aided in downstream analysis by increasing protein expression levels. As a result, we can now employ epitope tags that are detected less efficiently and reduce our assay scale to allow for higher throughput. The Creator Splice system appears to be an extremely useful tool for proteomics.

Modification of the Creator recombination system for proteomics applications – improved expression by addition of splice sites

PubMed Central

Colwill, Karen; Wells, Clark D; Elder, Kelly; Goudreault, Marilyn; Hersi, Kadija; Kulkarni, Sarang; Hardy, W Rod; Pawson, Tony; Morin, Gregg B

2006-01-01

Background Recombinational systems have been developed to rapidly shuttle Open Reading Frames (ORFs) into multiple expression vectors in order to analyze the large number of cDNAs available in the post-genomic era. In the Creator system, an ORF introduced into a donor vector can be transferred with Cre recombinase to a library of acceptor vectors optimized for different applications. Usability of the Creator system is impacted by the ability to easily manipulate DNA, the number of acceptor vectors for downstream applications, and the level of protein expression from Creator vectors. Results To date, we have developed over 20 novel acceptor vectors that employ a variety of promoters and epitope tags commonly employed for proteomics applications and gene function analysis. We also made several enhancements to the donor vectors including addition of different multiple cloning sites to allow shuttling from pre-existing vectors and introduction of the lacZ alpha reporter gene to allow for selection. Importantly, in order to ameliorate any effects on protein expression of the loxP site between a 5' tag and ORF, we introduced a splicing event into our expression vectors. The message produced from the resulting 'Creator Splice' vector undergoes splicing in mammalian systems to remove the loxP site. Upon analysis of our Creator Splice constructs, we discovered that protein expression levels were also significantly increased. Conclusion The development of new donor and acceptor vectors has increased versatility during the cloning process and made this system compatible with a wider variety of downstream applications. The modifications introduced in our Creator Splice system were designed to remove extraneous sequences due to recombination but also aided in downstream analysis by increasing protein expression levels. As a result, we can now employ epitope tags that are detected less efficiently and reduce our assay scale to allow for higher throughput. The Creator Splice system appears to be an extremely useful tool for proteomics. PMID:16519801

Using the Eclipse Parallel Tools Platform to Assist Earth Science Model Development and Optimization on High Performance Computers

NASA Astrophysics Data System (ADS)

Alameda, J. C.

2011-12-01

Development and optimization of computational science models, particularly on high performance computers, and with the advent of ubiquitous multicore processor systems, practically on every system, has been accomplished with basic software tools, typically, command-line based compilers, debuggers, performance tools that have not changed substantially from the days of serial and early vector computers. However, model complexity, including the complexity added by modern message passing libraries such as MPI, and the need for hybrid code models (such as openMP and MPI) to be able to take full advantage of high performance computers with an increasing core count per shared memory node, has made development and optimization of such codes an increasingly arduous task. Additional architectural developments, such as many-core processors, only complicate the situation further. In this paper, we describe how our NSF-funded project, "SI2-SSI: A Productive and Accessible Development Workbench for HPC Applications Using the Eclipse Parallel Tools Platform" (WHPC) seeks to improve the Eclipse Parallel Tools Platform, an environment designed to support scientific code development targeted at a diverse set of high performance computing systems. Our WHPC project to improve Eclipse PTP takes an application-centric view to improve PTP. We are using a set of scientific applications, each with a variety of challenges, and using PTP to drive further improvements to both the scientific application, as well as to understand shortcomings in Eclipse PTP from an application developer perspective, to drive our list of improvements we seek to make. We are also partnering with performance tool providers, to drive higher quality performance tool integration. We have partnered with the Cactus group at Louisiana State University to improve Eclipse's ability to work with computational frameworks and extremely complex build systems, as well as to develop educational materials to incorporate into computational science and engineering codes. Finally, we are partnering with the lead PTP developers at IBM, to ensure we are as effective as possible within the Eclipse community development. We are also conducting training and outreach to our user community, including conference BOF sessions, monthly user calls, and an annual user meeting, so that we can best inform the improvements we make to Eclipse PTP. With these activities we endeavor to encourage use of modern software engineering practices, as enabled through the Eclipse IDE, with computational science and engineering applications. These practices include proper use of source code repositories, tracking and rectifying issues, measuring and monitoring code performance changes against both optimizations as well as ever-changing software stacks and configurations on HPC systems, as well as ultimately encouraging development and maintenance of testing suites -- things that have become commonplace in many software endeavors, but have lagged in the development of science applications. We view that the challenge with the increased complexity of both HPC systems and science applications demands the use of better software engineering methods, preferably enabled by modern tools such as Eclipse PTP, to help the computational science community thrive as we evolve the HPC landscape.

[Construction of the superantigen SEA transfected laryngocarcinoma cells].

PubMed

Ji, Xiaobin; Jingli, J V; Liu, Qicai; Xie, Jinghua

2013-04-01

To construct an eukaryotic expression vectors containing superantigen staphylococcal enterotoxin A (SEA) gene, and to identify its expression in laryngeal squamous carcinoma cells. SEA full-length gene fragment was obtained from ATCC13565 genome of the staphylococcus, referencing standard strains producing SEA. Coding sequence of SEA was artificially synthetized. Than, SEA gene fragments was subcloned into eukaryotic expression vector pIRES-EGFP. The recombinant plasmid pSEA-IRES-EGFP was constructed and was transfected to laryngocarcinoma Hep-2 cells. Resistant clones were screened by G418. The expression of SEA in laryngocarcinoma cells was identified with ELISA and RT-PCR method. The subclone of artificially synthetized SEA gene was subclone to eukaryotic expression vector pires-EGFP. Flanking sequence confirmed that SEA sequence was fully identical to the coding sequence of standard staphylococcus strains ATCC13565 in Genbank. After recombinant plasmid transfected to laryngocarcinoma cells, the resistant clones was obtained after screening for two weeks. The clones were selected. The specific gene fragment was obtained by RT-PCR amplification. ELISA assay confirmed that the content of SEA protein in supernatant fluid of cell culture had reached about Pg level. The recombinant eukaryotic expression vector containing superantigen SEA gene is successfully constructed, and is capable of effective expression and continued secretion of SEA protein in laryngochrcinoma Hep-2 cells after recombinant plasmid transfected to laryngocarcinoma cells.

DYNA3D: A computer code for crashworthiness engineering

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

Hallquist, J.O.; Benson, D.J.

1986-09-01

A finite element program with crashworthiness applications has been developed at LLNL. DYNA3D, an explicit, fully vectorized, finite deformation structural dynamics program, has four capabilities that are critical for the efficient and realistic modeling crash phenomena: (1) fully optimized nonlinear solid, shell, and beam elements for representing a structure; (2) a broad range of constitutive models for simulating material behavior; (3) sophisticated contact algorithms for impact interactions; (4) a rigid body capability to represent the bodies away from the impact region at a greatly reduced cost without sacrificing accuracy in the momentum calculations. Basic methodologies of the program are brieflymore » presented along with several crashworthiness calculations. Efficiencies of the Hughes-Liu and Belytschko-Tsay shell formulations are considered.« less

Using support vector machines to detect medical fraud and abuse.

PubMed

Francis, Charles; Pepper, Noah; Strong, Homer

2011-01-01

This paper examines the architecture and efficacy of Quash, an automated medical bill processing system capable of bill routing and abuse detection. Quash is designed to be used in conjunction with human auditors and a standard bill review software platform to provide a complete cost containment solution for medical claims. The primary contribution of Quash is to provide a real world speed up for medical fraud detection experts in their work. There will be a discussion of implementation details and preliminary experimental results. In this paper we are entirely focused on medical data and billing patterns that occur within the United States, though these results should be applicable to any financial transaction environment in which structured coding data can be mined.

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine.

PubMed

Sun, Lei; Liu, Hui; Zhang, Lin; Meng, Jia

2015-01-01

Functional long non-coding RNAs (lncRNAs) have been bringing novel insight into biological study, however it is still not trivial to accurately distinguish the lncRNA transcripts (LNCTs) from the protein coding ones (PCTs). As various information and data about lncRNAs are preserved by previous studies, it is appealing to develop novel methods to identify the lncRNAs more accurately. Our method lncRScan-SVM aims at classifying PCTs and LNCTs using support vector machine (SVM). The gold-standard datasets for lncRScan-SVM model training, lncRNA prediction and method comparison were constructed according to the GENCODE gene annotations of human and mouse respectively. By integrating features derived from gene structure, transcript sequence, potential codon sequence and conservation, lncRScan-SVM outperforms other approaches, which is evaluated by several criteria such as sensitivity, specificity, accuracy, Matthews correlation coefficient (MCC) and area under curve (AUC). In addition, several known human lncRNA datasets were assessed using lncRScan-SVM. LncRScan-SVM is an efficient tool for predicting the lncRNAs, and it is quite useful for current lncRNA study.

Practical somewhat-secure quantum somewhat-homomorphic encryption with coherent states

NASA Astrophysics Data System (ADS)

Tan, Si-Hui; Ouyang, Yingkai; Rohde, Peter P.

2018-04-01

We present a scheme for implementing homomorphic encryption on coherent states encoded using phase-shift keys. The encryption operations require only rotations in phase space, which commute with computations in the code space performed via passive linear optics, and with generalized nonlinear phase operations that are polynomials of the photon-number operator in the code space. This encoding scheme can thus be applied to any computation with coherent-state inputs, and the computation proceeds via a combination of passive linear optics and generalized nonlinear phase operations. An example of such a computation is matrix multiplication, whereby a vector representing coherent-state amplitudes is multiplied by a matrix representing a linear optics network, yielding a new vector of coherent-state amplitudes. By finding an orthogonal partitioning of the support of our encoded states, we quantify the security of our scheme via the indistinguishability of the encrypted code words. While we focus on coherent-state encodings, we expect that this phase-key encoding technique could apply to any continuous-variable computation scheme where the phase-shift operator commutes with the computation.

Five-way smoking status classification using text hot-spot identification and error-correcting output codes.

PubMed

Cohen, Aaron M

2008-01-01

We participated in the i2b2 smoking status classification challenge task. The purpose of this task was to evaluate the ability of systems to automatically identify patient smoking status from discharge summaries. Our submission included several techniques that we compared and studied, including hot-spot identification, zero-vector filtering, inverse class frequency weighting, error-correcting output codes, and post-processing rules. We evaluated our approaches using the same methods as the i2b2 task organizers, using micro- and macro-averaged F1 as the primary performance metric. Our best performing system achieved a micro-F1 of 0.9000 on the test collection, equivalent to the best performing system submitted to the i2b2 challenge. Hot-spot identification, zero-vector filtering, classifier weighting, and error correcting output coding contributed additively to increased performance, with hot-spot identification having by far the largest positive effect. High performance on automatic identification of patient smoking status from discharge summaries is achievable with the efficient and straightforward machine learning techniques studied here.

Cloning of cellulase genes from acidothermus cellulolyticus

DOEpatents

Lastick, deceased, Stanley M.; Tucker, Melvin P.; Grohmann, Karel

1996-01-01

A process is described for moving fragments that code for cellulase activity from the genome of A. cellulolyticus to several plasmid vectors and the subsequent expression of active cellulase acitivty in E. coli.

A parallel-vector algorithm for rapid structural analysis on high-performance computers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Agarwal, Tarun K.

1990-01-01

A fast, accurate Choleski method for the solution of symmetric systems of linear equations is presented. This direct method is based on a variable-band storage scheme and takes advantage of column heights to reduce the number of operations in the Choleski factorization. The method employs parallel computation in the outermost DO-loop and vector computation via the 'loop unrolling' technique in the innermost DO-loop. The method avoids computations with zeros outside the column heights, and as an option, zeros inside the band. The close relationship between Choleski and Gauss elimination methods is examined. The minor changes required to convert the Choleski code to a Gauss code to solve non-positive-definite symmetric systems of equations are identified. The results for two large-scale structural analyses performed on supercomputers, demonstrate the accuracy and speed of the method.

A parallel-vector algorithm for rapid structural analysis on high-performance computers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Agarwal, Tarun K.

1990-01-01

A fast, accurate Choleski method for the solution of symmetric systems of linear equations is presented. This direct method is based on a variable-band storage scheme and takes advantage of column heights to reduce the number of operations in the Choleski factorization. The method employs parallel computation in the outermost DO-loop and vector computation via the loop unrolling technique in the innermost DO-loop. The method avoids computations with zeros outside the column heights, and as an option, zeros inside the band. The close relationship between Choleski and Gauss elimination methods is examined. The minor changes required to convert the Choleski code to a Gauss code to solve non-positive-definite symmetric systems of equations are identified. The results for two large scale structural analyses performed on supercomputers, demonstrate the accuracy and speed of the method.

Combined group ECC protection and subgroup parity protection

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

Gara, Alan; Cheng, Dong; Heidelberger, Philip

A method and system are disclosed for providing combined error code protection and subgroup parity protection for a given group of n bits. The method comprises the steps of identifying a number, m, of redundant bits for said error protection; and constructing a matrix P, wherein multiplying said given group of n bits with P produces m redundant error correction code (ECC) protection bits, and two columns of P provide parity protection for subgroups of said given group of n bits. In the preferred embodiment of the invention, the matrix P is constructed by generating permutations of m bit widemore » vectors with three or more, but an odd number of, elements with value one and the other elements with value zero; and assigning said vectors to rows of the matrix P.« less

Automation of the guiding center expansion

NASA Astrophysics Data System (ADS)

Burby, J. W.; Squire, J.; Qin, H.

2013-07-01

We report on the use of the recently developed Mathematica package VEST (Vector Einstein Summation Tools) to automatically derive the guiding center transformation. Our Mathematica code employs a recursive procedure to derive the transformation order-by-order. This procedure has several novel features. (1) It is designed to allow the user to easily explore the guiding center transformation's numerous non-unique forms or representations. (2) The procedure proceeds entirely in cartesian position and velocity coordinates, thereby producing manifestly gyrogauge invariant results; the commonly used perpendicular unit vector fields e1,e2 are never even introduced. (3) It is easy to apply in the derivation of higher-order contributions to the guiding center transformation without fear of human error. Our code therefore stands as a useful tool for exploring subtle issues related to the physics of toroidal momentum conservation in tokamaks.

Automation of The Guiding Center Expansion

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

J. W. Burby, J. Squire and H. Qin

2013-03-19

We report on the use of the recently-developed Mathematica package VEST (Vector Einstein Summation Tools) to automatically derive the guiding center transformation. Our Mathematica code employs a recursive procedure to derive the transformation order-by-order. This procedure has several novel features. (1) It is designed to allow the user to easily explore the guiding center transformation's numerous nonunique forms or representations. (2) The procedure proceeds entirely in cartesian position and velocity coordinates, thereby producing manifestly gyrogauge invariant results; the commonly-used perpendicular unit vector fields e1, e2 are never even introduced. (3) It is easy to apply in the derivation of higher-ordermore » contributions to the guiding center transformation without fear of human error. Our code therefore stands as a useful tool for exploring subtle issues related to the physics of toroidal momentum conservation in tokamaks« less

Vector Sum Excited Linear Prediction (VSELP) speech coding at 4.8 kbps

NASA Technical Reports Server (NTRS)

Gerson, Ira A.; Jasiuk, Mark A.

1990-01-01

Code Excited Linear Prediction (CELP) speech coders exhibit good performance at data rates as low as 4800 bps. The major drawback to CELP type coders is their larger computational requirements. The Vector Sum Excited Linear Prediction (VSELP) speech coder utilizes a codebook with a structure which allows for a very efficient search procedure. Other advantages of the VSELP codebook structure is discussed and a detailed description of a 4.8 kbps VSELP coder is given. This coder is an improved version of the VSELP algorithm, which finished first in the NSA's evaluation of the 4.8 kbps speech coders. The coder uses a subsample resolution single tap long term predictor, a single VSELP excitation codebook, a novel gain quantizer which is robust to channel errors, and a new adaptive pre/postfilter arrangement.

Adaptation of multidimensional group particle tracking and particle wall-boundary condition model to the FDNS code

NASA Technical Reports Server (NTRS)

Chen, Y. S.; Farmer, R. C.

1992-01-01

A particulate two-phase flow CFD model was developed based on the FDNS code which is a pressure based predictor plus multi-corrector Navier-Stokes flow solver. Turbulence models with compressibility correction and the wall function models were employed as submodels. A finite-rate chemistry model was used for reacting flow simulation. For particulate two-phase flow simulations, a Eulerian-Lagrangian solution method using an efficient implicit particle trajectory integration scheme was developed in this study. Effects of particle-gas reaction and particle size change to agglomeration or fragmentation were not considered in this investigation. At the onset of the present study, a two-dimensional version of FDNS which had been modified to treat Lagrangian tracking of particles (FDNS-2DEL) had already been written and was operational. The FDNS-2DEL code was too slow for practical use, mainly because it had not been written in a form amenable to vectorization on the Cray, nor was the full three-dimensional form of FDNS utilized. The specific objective of this study was to reorder to calculations into long single arrays for automatic vectorization on the Cray and to implement the full three-dimensional version of FDNS to produce the FDNS-3DEL code. Since the FDNS-2DEL code was slow, a very limited number of test cases had been run with it. This study was also intended to increase the number of cases simulated to verify and improve, as necessary, the particle tracking methodology coded in FDNS.

MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

NASA Technical Reports Server (NTRS)

Taft, James R.

1999-01-01

Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

The high-level expression of human tissue plasminogen activator in the milk of transgenic mice with hybrid gene locus strategy.

PubMed

Zhou, Yanrong; Lin, Yanli; Wu, Xiaojie; Xiong, Fuyin; Lv, Yuemeng; Zheng, Tao; Huang, Peitang; Chen, Hongxing

2012-02-01

Transgene expression for the mammary gland bioreactor aimed at producing recombinant proteins requires optimized expression vector construction. Previously we presented a hybrid gene locus strategy, which was originally tested with human lactoferrin (hLF) as target transgene, and an extremely high-level expression of rhLF ever been achieved as to 29.8 g/l in mice milk. Here to demonstrate the broad application of this strategy, another 38.4 kb mWAP-htPA hybrid gene locus was constructed, in which the 3-kb genomic coding sequence in the 24-kb mouse whey acidic protein (mWAP) gene locus was substituted by the 17.4-kb genomic coding sequence of human tissue plasminogen activator (htPA), exactly from the start codon to the end codon. Corresponding five transgenic mice lines were generated and the highest expression level of rhtPA in the milk attained as to 3.3 g/l. Our strategy will provide a universal way for the large-scale production of pharmaceutical proteins in the mammary gland of transgenic animals.

PuffinPlot: A versatile, user-friendly program for paleomagnetic analysis

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Wilson, G. S.

2012-06-01

PuffinPlot is a user-friendly desktop application for analysis of paleomagnetic data, offering a unique combination of features. It runs on several operating systems, including Windows, Mac OS X, and Linux; supports both discrete and long core data; and facilitates analysis of very weakly magnetic samples. As well as interactive graphical operation, PuffinPlot offers batch analysis for large volumes of data, and a Python scripting interface for programmatic control of its features. Available data displays include demagnetization/intensity, Zijderveld, equal-area (for sample, site, and suite level demagnetization data, and for magnetic susceptibility anisotropy data), a demagnetization data table, and a natural remanent magnetization intensity histogram. Analysis types include principal component analysis, Fisherian statistics, and great-circle path intersections. The results of calculations can be exported as CSV (comma-separated value) files; graphs can be printed, and can also be saved as publication-quality vector files in SVG or PDF format. PuffinPlot is free, and the program, user manual, and fully documented source code may be downloaded from http://code.google.com/p/puffinplot/.

Back to basics: pBR322 and protein expression systems in E. coli.

PubMed

Balbás, Paulina; Bolívar, Francisco

2004-01-01

The extensive variety of plasmid-based expression systems in E. coli resulted from the fact that there is no single strategy for achieving maximal expression of every cloned gene. Although a number of strategies have been implemented to deal with problems associated to gene transcription and translation, protein folding, secretion, location, posttranslational modifications, particularities of different strains, and the like and more integrated processes have been developed, the basic plasmid-borne elements and their interaction with the particular host strain will influence the overall expression system and final productivity. Plasmid vector pBR322 is a well-established multipurpose cloning vector in laboratories worldwide, and a large number of derivatives have been created for specific applications and research purposes, including gene expression in its natural host, E. coli, and few other bacteria. The early characterization of the molecule, including its nucleotide sequence, replication and maintenance mechanisms, and determination of its coding regions, accounted for its success, not only as a universal cloning vector, but also as a provider of genes and an origin of replication for other intraspecies vectors. Since the publication of the aforementioned reviews, novel discoveries pertaining to these issues have appeared in the literature that deepen the understanding of the plasmid's features, behavior, and impact in gene expression systems, as well as some important strain characteristics that affect plasmid replication and stability. The objectives of this review include updating and discussing the new information about (1) the replication and maintenance of pBR322; (2) the host-related modulation mechanisms of plasmid replication; (3) the effects of growth rate on replication control, stability, and recombinant gene expression; (4) ways for plasmid amplification and elimination. Finally, (5) a summary of novel ancillary studies about pBR322 is presented.

Cloning of cellulase genes from Acidothermus cellulolyticus

DOEpatents

Lastick, S.M.; Tucker, M.P.; Grohmann, K.

1996-05-07

A process is described for moving fragments that code for cellulase activity from the genome of A. cellulolyticus to several plasmid vectors and the subsequent expression of active cellulase activity in E. coli. 5 figs.

A vector scanning processing technique for pulsed laser velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1989-01-01

Pulsed-laser-sheet velocimetry yields two-dimensional velocity vectors across an extended planar region of a flow. Current processing techniques offer high-precision (1-percent) velocity estimates, but can require hours of processing time on specialized array processors. Sometimes, however, a less accurate (about 5 percent) data-reduction technique which also gives unambiguous velocity vector information is acceptable. Here, a direct space-domain processing technique is described and shown to be far superior to previous methods in achieving these objectives. It uses a novel data coding and reduction technique and has no 180-deg directional ambiguity. A complex convection vortex flow was recorded and completely processed in under 2 min on an 80386-based PC, producing a two-dimensional velocity-vector map of the flowfield. Pulsed-laser velocimetry data can thus be reduced quickly and reasonably accurately, without specialized array processing hardware.

A SOFTWARE PACKAGE FOR UNSUPERVISED PATTERN RECOGNITION AND SYNOPTIC REPRESENTATION OF RESULTS: APPLICATION TO VOLCANIC TREMOR DATA OF MT ETNA

NASA Astrophysics Data System (ADS)

Langer, H. K.; Falsaperla, S. M.; Behncke, B.; Messina, A.; Spampinato, S.

2009-12-01

Artificial Intelligence (AI) has found broad applications in volcano observatories worldwide with the aim of reducing volcanic hazard. The need to process larger and larger quantity of data makes indeed AI techniques appealing for monitoring purposes. Tools based on Artificial Neural Networks and Support Vector Machine have proved to be particularly successful in the classification of seismic events and volcanic tremor changes heralding eruptive activity, such as paroxysmal explosions and lava fountaining at Stromboli and Mt Etna, Italy (e.g., Falsaperla et al., 1996; Langer et al., 2009). Moving on from the excellent results obtained from these applications, we present KKAnalysis, a MATLAB based software which combines several unsupervised pattern classification methods, exploiting routines of the SOM Toolbox 2 for MATLAB (http://www.cis.hut.fi/projects/somtoolbox). KKAnalysis is based on Self Organizing Maps (SOM) and clustering methods consisting of K-Means, Fuzzy C-Means, and a scheme based on a metrics accounting for correlation between components of the feature vector. We show examples of applications of this tool to volcanic tremor data recorded at Mt Etna between 2007 and 2009. This time span - during which Strombolian explosions, 7 episodes of lava fountaining and effusive activity occurred - is particularly interesting, as it encompassed different states of volcanic activity (i.e., non-eruptive, eruptive according to different styles) for the unsupervised classifier to identify, highlighting their development in time. Even subtle changes in the signal characteristics allow the unsupervised classifier to recognize features belonging to the different classes and stages of volcanic activity. A convenient color-code representation shows up the temporal development of the different classes of signal, making this method extremely helpful for monitoring purposes and surveillance. Though being developed for volcanic tremor classification, KKAnalysis is generally applicable to any type of physical or chemical pattern, provided that feature vectors are given in numerical form. References: Falsaperla, S., S. Graziani, G. Nunnari, and S. Spampinato (1996). Automatic classification of volcanic earthquakes by using multy-layered neural networks. Natural Hazard, 13, 205-228. Langer, H., S. Falsaperla, M. Masotti, R. Campanini, S. Spampinato, and A. Messina (2008). Synopsis of supervised and unsupervised pattern classification techniques applied to volcanic tremor data at Mt Etna, Italy. Geophys. J. Int., doi:10.1111/j.1365-246X.2009.04179.x.

Equilibrium Spline Interface (ESI) for magnetic confinement codes

NASA Astrophysics Data System (ADS)

Li, Xujing; Zakharov, Leonid E.

2017-12-01

A compact and comprehensive interface between magneto-hydrodynamic (MHD) equilibrium codes and gyro-kinetic, particle orbit, MHD stability, and transport codes is presented. Its irreducible set of equilibrium data consists of three (in the 2-D case with occasionally one extra in the 3-D case) functions of coordinates and four 1-D radial profiles together with their first and mixed derivatives. The C reconstruction routines, accessible also from FORTRAN, allow the calculation of basis functions and their first derivatives at any position inside the plasma and in its vicinity. After this all vector fields and geometric coefficients, required for the above mentioned types of codes, can be calculated using only algebraic operations with no further interpolation or differentiation.

Accelerated Modeling and New Ferroelectric Materials for Naval SONAR

DTIC Science & Technology

2004-06-01

AN other platforms was achieved. As expected, proper into BZ leads to a development of small polarization, vectorization and optimal memory usage were...polarization is due to a combination code was fully vectorized , a speed-up of 9.2 times over of large Ag off-centering and small displacements by the Pentium 4... Xeon and 6.6 times over the SGI 03K was other cations. The large Ag displacements are due to a achieved. We are currently using the X1 in production

Communication systems, transceivers, and methods for generating data based on channel characteristics

DOEpatents

Forman, Michael A; Young, Derek

2012-09-18

Examples of methods for generating data based on a communications channel are described. In one such example, a processing unit may generate a first vector representation based in part on at least two characteristics of a communications channel. A constellation having at least two dimensions may be addressed with the first vector representation to identify a first symbol associated with the first vector representation. The constellation represents a plurality of regions, each region associated with a respective symbol. The symbol may be used to generate data, which may stored in an electronic storage medium and used as a cryptographic key or a spreading code or hopping sequence in a modulation technique.

The organization of conspecific face space in nonhuman primates

PubMed Central

Parr, Lisa A.; Taubert, Jessica; Little, Anthony C.; Hancock, Peter J. B.

2013-01-01

Humans and chimpanzees demonstrate numerous cognitive specializations for processing faces, but comparative studies with monkeys suggest that these may be the result of recent evolutionary adaptations. The present study utilized the novel approach of face space, a powerful theoretical framework used to understand the representation of face identity in humans, to further explore species differences in face processing. According to the theory, faces are represented by vectors in a multidimensional space, the centre of which is defined by an average face. Each dimension codes features important for describing a face’s identity, and vector length codes the feature’s distinctiveness. Chimpanzees and rhesus monkeys discriminated male and female conspecifics’ faces, rated by humans for their distinctiveness, using a computerized task. Multidimensional scaling analyses showed that the organization of face space was similar between humans and chimpanzees. Distinctive faces had the longest vectors and were the easiest for chimpanzees to discriminate. In contrast, distinctiveness did not correlate with the performance of rhesus monkeys. The feature dimensions for each species’ face space were visualized and described using morphing techniques. These results confirm species differences in the perceptual representation of conspecific faces, which are discussed within an evolutionary framework. PMID:22670823

The solar vector error within the SNPP Common GEO code, the correction, and the effects on the VIIRS SDR RSB calibration

NASA Astrophysics Data System (ADS)

Fulbright, Jon; Anderson, Samuel; Lei, Ning; Efremova, Boryana; Wang, Zhipeng; McIntire, Jeffrey; Chiang, Kwofu; Xiong, Xiaoxiong

2014-11-01

Due to a software error, the solar and lunar vectors reported in the on-board calibrator intermediate product (OBC-IP) files for SNPP VIIRS are incorrect. The magnitude of the error is about 0.2 degree, and the magnitude is increasing by about 0.01 degree per year. This error, although small, has an effect on the radiometric calibration of the reflective solar bands (RSB) because accurate solar angles are required for calculating the screen transmission functions and for calculating the illumination of the Solar Diffuser panel. In this paper, we describe the error in the Common GEO code, and how it may be fixed. We present evidence for the error from within the OBC-IP data. We also describe the effects of the solar vector error on the RSB calibration and the Sensor Data Record (SDR). In order to perform this evaluation, we have reanalyzed the yaw-maneuver data to compute the vignetting functions required for the on-orbit SD RSB radiometric calibration. After the reanalysis, we find effect of up to 0.5% on the shortwave infrared (SWIR) RSB calibration.

Extending the length and time scales of Gram–Schmidt Lyapunov vector computations

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

Costa, Anthony B., E-mail: acosta@northwestern.edu; Green, Jason R., E-mail: jason.green@umb.edu; Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125

Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram–Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N{sup 2} (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram–Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard–Jones fluids from N=100 to 1300 betweenmore » Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram–Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra.« less

Spin Rotation of Formalism for Spin Tracking

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

Luccio,A.

The problem of which coefficients are adequate to correctly represent the spin rotation in vector spin tracking for polarized proton and deuteron beams in synchrotrons is here re-examined in the light of recent discussions. The main aim of this note is to show where some previous erroneous results originated and how to code spin rotation in a tracking code. Some analysis of a recent experiment is presented that confirm the correctness of the assumptions.

Vector radiative transfer code SORD: Performance analysis and quick start guide

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Alexander; Holben, Brent; Kokhanovsky, Alexander

2017-10-01

We present a new open source polarized radiative transfer code SORD written in Fortran 90/95. SORD numerically simulates propagation of monochromatic solar radiation in a plane-parallel atmosphere over a reflecting surface using the method of successive orders of scattering (hence the name). Thermal emission is ignored. We did not improve the method in any way, but report the accuracy and runtime in 52 benchmark scenarios. This paper also serves as a quick start user's guide for the code available from ftp://maiac.gsfc.nasa.gov/pub/skorkin, from the JQSRT website, or from the corresponding (first) author.

A 5′ Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo

PubMed Central

Lu, Jiamiao; Williams, James A.; Luke, Jeremy; Zhang, Feijie; Chu, Kirk; Kay, Mark A.

2017-01-01

We previously developed a mini-intronic plasmid (MIP) expression system in which the essential bacterial elements for plasmid replication and selection are placed within an engineered intron contained within a universal 5′ UTR noncoding exon. Like minicircle DNA plasmids (devoid of bacterial backbone sequences), MIP plasmids overcome transcriptional silencing of the transgene. However, in addition MIP plasmids increase transgene expression by 2 and often >10 times higher than minicircle vectors in vivo and in vitro. Based on these findings, we examined the effects of the MIP intronic sequences in a recombinant adeno-associated virus (AAV) vector system. Recombinant AAV vectors containing an intron with a bacterial replication origin and bacterial selectable marker increased transgene expression by 40 to 100 times in vivo when compared with conventional AAV vectors. Therefore, inclusion of this noncoding exon/intron sequence upstream of the coding region can substantially enhance AAV-mediated gene expression in vivo. PMID:27903072

Wavelet subband coding of computer simulation output using the A++ array class library

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

Bradley, J.N.; Brislawn, C.M.; Quinlan, D.J.

1995-07-01

The goal of the project is to produce utility software for off-line compression of existing data and library code that can be called from a simulation program for on-line compression of data dumps as the simulation proceeds. Naturally, we would like the amount of CPU time required by the compression algorithm to be small in comparison to the requirements of typical simulation codes. We also want the algorithm to accomodate a wide variety of smooth, multidimensional data types. For these reasons, the subband vector quantization (VQ) approach employed in has been replaced by a scalar quantization (SQ) strategy using amore » bank of almost-uniform scalar subband quantizers in a scheme similar to that used in the FBI fingerprint image compression standard. This eliminates the considerable computational burdens of training VQ codebooks for each new type of data and performing nearest-vector searches to encode the data. The comparison of subband VQ and SQ algorithms in indicated that, in practice, there is relatively little additional gain from using vector as opposed to scalar quantization on DWT subbands, even when the source imagery is from a very homogeneous population, and our subjective experience with synthetic computer-generated data supports this stance. It appears that a careful study is needed of the tradeoffs involved in selecting scalar vs. vector subband quantization, but such an analysis is beyond the scope of this paper. Our present work is focused on the problem of generating wavelet transform/scalar quantization (WSQ) implementations that can be ported easily between different hardware environments. This is an extremely important consideration given the great profusion of different high-performance computing architectures available, the high cost associated with learning how to map algorithms effectively onto a new architecture, and the rapid rate of evolution in the world of high-performance computing.« less

A Radiation Chemistry Code Based on the Greens Functions of the Diffusion Equation

NASA Technical Reports Server (NTRS)

Plante, Ianik; Wu, Honglu

2014-01-01

Ionizing radiation produces several radiolytic species such as.OH, e-aq, and H. when interacting with biological matter. Following their creation, radiolytic species diffuse and chemically react with biological molecules such as DNA. Despite years of research, many questions on the DNA damage by ionizing radiation remains, notably on the indirect effect, i.e. the damage resulting from the reactions of the radiolytic species with DNA. To simulate DNA damage by ionizing radiation, we are developing a step-by-step radiation chemistry code that is based on the Green's functions of the diffusion equation (GFDE), which is able to follow the trajectories of all particles and their reactions with time. In the recent years, simulations based on the GFDE have been used extensively in biochemistry, notably to simulate biochemical networks in time and space and are often used as the "gold standard" to validate diffusion-reaction theories. The exact GFDE for partially diffusion-controlled reactions is difficult to use because of its complex form. Therefore, the radial Green's function, which is much simpler, is often used. Hence, much effort has been devoted to the sampling of the radial Green's functions, for which we have developed a sampling algorithm This algorithm only yields the inter-particle distance vector length after a time step; the sampling of the deviation angle of the inter-particle vector is not taken into consideration. In this work, we show that the radial distribution is predicted by the exact radial Green's function. We also use a technique developed by Clifford et al. to generate the inter-particle vector deviation angles, knowing the inter-particle vector length before and after a time step. The results are compared with those predicted by the exact GFDE and by the analytical angular functions for free diffusion. This first step in the creation of the radiation chemistry code should help the understanding of the contribution of the indirect effect in the formation of DNA damage and double-strand breaks.

A Noninvasive In Vitro Monitoring System Reporting Skeletal Muscle Differentiation.

PubMed

Öztürk-Kaloglu, Deniz; Hercher, David; Heher, Philipp; Posa-Markaryan, Katja; Sperger, Simon; Zimmermann, Alice; Wolbank, Susanne; Redl, Heinz; Hacobian, Ara

2017-01-01

Monitoring of cell differentiation is a crucial aspect of cell-based therapeutic strategies depending on tissue maturation. In this study, we have developed a noninvasive reporter system to trace murine skeletal muscle differentiation. Either a secreted bioluminescent reporter (Metridia luciferase) or a fluorescent reporter (green fluorescent protein [GFP]) was placed under the control of the truncated muscle creatine kinase (MCK) basal promoter enhanced by variable numbers of upstream MCK E-boxes. The engineered pE3MCK vector, coding a triple tandem of E-Boxes and the truncated MCK promoter, showed twentyfold higher levels of luciferase activation compared with a Cytomegalovirus (CMV) promoter. This newly developed reporter system allowed noninvasive monitoring of myogenic differentiation in a straining bioreactor. Additionally, binding sequences of endogenous microRNAs (miRNAs; seed sequences) that are known to be downregulated in myogenesis were ligated as complementary seed sequences into the reporter vector to reduce nonspecific signal background. The insertion of seed sequences improved the signal-to-noise ratio up to 25% compared with pE3MCK. Due to the highly specific, fast, and convenient expression analysis for cells undergoing myogenic differentiation, this reporter system provides a powerful tool for application in skeletal muscle tissue engineering.

Sub-block motion derivation for merge mode in HEVC

NASA Astrophysics Data System (ADS)

Chien, Wei-Jung; Chen, Ying; Chen, Jianle; Zhang, Li; Karczewicz, Marta; Li, Xiang

2016-09-01

The new state-of-the-art video coding standard, H.265/HEVC, has been finalized in 2013 and it achieves roughly 50% bit rate saving compared to its predecessor, H.264/MPEG-4 AVC. In this paper, two additional merge candidates, advanced temporal motion vector predictor and spatial-temporal motion vector predictor, are developed to improve motion information prediction scheme under the HEVC structure. The proposed method allows each Prediction Unit (PU) to fetch multiple sets of motion information from multiple blocks smaller than the current PU. By splitting a large PU into sub-PUs and filling motion information for all the sub-PUs of the large PU, signaling cost of motion information could be reduced. This paper describes above-mentioned techniques in detail and evaluates their coding performance benefits based on the common test condition during HEVC development. Simulation results show that 2.4% performance improvement over HEVC can be achieved.

Locally adaptive vector quantization: Data compression with feature preservation

NASA Technical Reports Server (NTRS)

Cheung, K. M.; Sayano, M.

1992-01-01

A study of a locally adaptive vector quantization (LAVQ) algorithm for data compression is presented. This algorithm provides high-speed one-pass compression and is fully adaptable to any data source and does not require a priori knowledge of the source statistics. Therefore, LAVQ is a universal data compression algorithm. The basic algorithm and several modifications to improve performance are discussed. These modifications are nonlinear quantization, coarse quantization of the codebook, and lossless compression of the output. Performance of LAVQ on various images using irreversible (lossy) coding is comparable to that of the Linde-Buzo-Gray algorithm, but LAVQ has a much higher speed; thus this algorithm has potential for real-time video compression. Unlike most other image compression algorithms, LAVQ preserves fine detail in images. LAVQ's performance as a lossless data compression algorithm is comparable to that of Lempel-Ziv-based algorithms, but LAVQ uses far less memory during the coding process.

SAPNEW: Parallel finite element code for thin shell structures on the Alliant FX/80

NASA Astrophysics Data System (ADS)

Kamat, Manohar P.; Watson, Brian C.

1992-02-01

The results of a research activity aimed at providing a finite element capability for analyzing turbo-machinery bladed-disk assemblies in a vector/parallel processing environment are summarized. Analysis of aircraft turbofan engines is very computationally intensive. The performance limit of modern day computers with a single processing unit was estimated at 3 billions of floating point operations per second (3 gigaflops). In view of this limit of a sequential unit, performance rates higher than 3 gigaflops can be achieved only through vectorization and/or parallelization as on Alliant FX/80. Accordingly, the efforts of this critically needed research were geared towards developing and evaluating parallel finite element methods for static and vibration analysis. A special purpose code, named with the acronym SAPNEW, performs static and eigen analysis of multi-degree-of-freedom blade models built-up from flat thin shell elements.

SAPNEW: Parallel finite element code for thin shell structures on the Alliant FX/80

NASA Technical Reports Server (NTRS)

Kamat, Manohar P.; Watson, Brian C.

1992-01-01

The results of a research activity aimed at providing a finite element capability for analyzing turbo-machinery bladed-disk assemblies in a vector/parallel processing environment are summarized. Analysis of aircraft turbofan engines is very computationally intensive. The performance limit of modern day computers with a single processing unit was estimated at 3 billions of floating point operations per second (3 gigaflops). In view of this limit of a sequential unit, performance rates higher than 3 gigaflops can be achieved only through vectorization and/or parallelization as on Alliant FX/80. Accordingly, the efforts of this critically needed research were geared towards developing and evaluating parallel finite element methods for static and vibration analysis. A special purpose code, named with the acronym SAPNEW, performs static and eigen analysis of multi-degree-of-freedom blade models built-up from flat thin shell elements.

Automation of the guiding center expansion

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

Burby, J. W.; Squire, J.; Qin, H.

2013-07-15

We report on the use of the recently developed Mathematica package VEST (Vector Einstein Summation Tools) to automatically derive the guiding center transformation. Our Mathematica code employs a recursive procedure to derive the transformation order-by-order. This procedure has several novel features. (1) It is designed to allow the user to easily explore the guiding center transformation's numerous non-unique forms or representations. (2) The procedure proceeds entirely in cartesian position and velocity coordinates, thereby producing manifestly gyrogauge invariant results; the commonly used perpendicular unit vector fields e{sub 1},e{sub 2} are never even introduced. (3) It is easy to apply in themore » derivation of higher-order contributions to the guiding center transformation without fear of human error. Our code therefore stands as a useful tool for exploring subtle issues related to the physics of toroidal momentum conservation in tokamaks.« less

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.

PubMed

Pesaranghader, Ahmad; Matwin, Stan; Sokolova, Marina; Beiko, Robert G

2016-05-01

Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be focused on specific analytical tasks and concentrate on the GO terms themselves rather than considering their textual definitions. We introduce simDEF, an efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF approach builds optimized definition vectors for all relevant GO terms, and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Relative to existing similarity measures, when validated on a yeast reference database, simDEF improves correlation with sequence homology by up to 50%, shows a correlation improvement >4% with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy. Datasets, results and source code are available at http://kiwi.cs.dal.ca/Software/simDEF CONTACT: ahmad.pgh@dal.ca or beiko@cs.dal.ca 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.

Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

PubMed Central

Inui, Masayuki; Roh, Jung Hyeob; Zahn, Kenneth; Yukawa, Hideaki

2000-01-01

A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria. PMID:10618203

Accelerating molecular property calculations with nonorthonormal Krylov space methods

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

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

Accelerating molecular property calculations with nonorthonormal Krylov space methods

DOE PAGES

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.; ...

2016-05-03

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

The Advanced Software Development and Commercialization Project

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

Gallopoulos, E.; Canfield, T.R.; Minkoff, M.

1990-09-01

This is the first of a series of reports pertaining to progress in the Advanced Software Development and Commercialization Project, a joint collaborative effort between the Center for Supercomputing Research and Development of the University of Illinois and the Computing and Telecommunications Division of Argonne National Laboratory. The purpose of this work is to apply techniques of parallel computing that were pioneered by University of Illinois researchers to mature computational fluid dynamics (CFD) and structural dynamics (SD) computer codes developed at Argonne. The collaboration in this project will bring this unique combination of expertise to bear, for the first time,more » on industrially important problems. By so doing, it will expose the strengths and weaknesses of existing techniques for parallelizing programs and will identify those problems that need to be solved in order to enable wide spread production use of parallel computers. Secondly, the increased efficiency of the CFD and SD codes themselves will enable the simulation of larger, more accurate engineering models that involve fluid and structural dynamics. In order to realize the above two goals, we are considering two production codes that have been developed at ANL and are widely used by both industry and Universities. These are COMMIX and WHAMS-3D. The first is a computational fluid dynamics code that is used for both nuclear reactor design and safety and as a design tool for the casting industry. The second is a three-dimensional structural dynamics code used in nuclear reactor safety as well as crashworthiness studies. These codes are currently available for both sequential and vector computers only. Our main goal is to port and optimize these two codes on shared memory multiprocessors. In so doing, we shall establish a process that can be followed in optimizing other sequential or vector engineering codes for parallel processors.« less

GeneXplorer: an interactive web application for microarray data visualization and analysis.

PubMed

Rees, Christian A; Demeter, Janos; Matese, John C; Botstein, David; Sherlock, Gavin

2004-10-01

When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

Design of 2D time-varying vector fields.

PubMed

Chen, Guoning; Kwatra, Vivek; Wei, Li-Yi; Hansen, Charles D; Zhang, Eugene

2012-10-01

Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects.

The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis.

PubMed

Ferreira, Flávia Viana; Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; de Oliveira, Karla Pollyanna Vieira; Silva, Emanuele Guimarães; Sant'Anna, Maurício Roberto Viana; Gontijo, Nelder de Figueiredo; Kroon, Erna Geessien; Imler, Jean Luc; Marques, João Trindade

2018-06-01

Sandflies are well known vectors for Leishmania but also transmit a number of arthropod-borne viruses (arboviruses). Few studies have addressed the interaction between sandflies and arboviruses. RNA interference (RNAi) mechanisms utilize small non-coding RNAs to regulate different aspects of host-pathogen interactions. The small interfering RNA (siRNA) pathway is a broad antiviral mechanism in insects. In addition, at least in mosquitoes, another RNAi mechanism mediated by PIWI interacting RNAs (piRNAs) is activated by viral infection. Finally, endogenous microRNAs (miRNA) may also regulate host immune responses. Here, we analyzed the small non-coding RNA response to Vesicular stomatitis virus (VSV) infection in the sandfly Lutzoymia longipalpis. We detected abundant production of virus-derived siRNAs after VSV infection in adult sandflies. However, there was no production of virus-derived piRNAs and only mild changes in the expression of vector miRNAs in response to infection. We also observed abundant production of virus-derived siRNAs against two other viruses in Lutzomyia Lulo cells. Together, our results suggest that the siRNA but not the piRNA pathway mediates an antiviral response in sandflies. In agreement with this hypothesis, pre-treatment of cells with dsRNA against VSV was able to inhibit viral replication while knock-down of the central siRNA component, Argonaute-2, led to increased virus levels. Our work begins to elucidate the role of RNAi mechanisms in the interaction between L. longipalpis and viruses and should also open the way for studies with other sandfly-borne pathogens.

User's Manual for FEMOM3DR. Version 1.0

NASA Technical Reports Server (NTRS)

Reddy, C. J.

1998-01-01

FEMoM3DR is a computer code written in FORTRAN 77 to compute radiation characteristics of antennas on 3D body using combined Finite Element Method (FEM)/Method of Moments (MoM) technique. The code is written to handle different feeding structures like coaxial line, rectangular waveguide, and circular waveguide. This code uses the tetrahedral elements, with vector edge basis functions for FEM and triangular elements with roof-top basis functions for MoM. By virtue of FEM, this code can handle any arbitrary shaped three dimensional bodies with inhomogeneous lossy materials; and due to MoM the computational domain can be terminated in any arbitrary shape. The User's Manual is written to make the user acquainted with the operation of the code. The user is assumed to be familiar with the FORTRAN 77 language and the operating environment of the computers on which the code is intended to run.

Video streaming with SHVC to HEVC transcoding

NASA Astrophysics Data System (ADS)

Gudumasu, Srinivas; He, Yuwen; Ye, Yan; Xiu, Xiaoyu

2015-09-01

This paper proposes an efficient Scalable High efficiency Video Coding (SHVC) to High Efficiency Video Coding (HEVC) transcoder, which can reduce the transcoding complexity significantly, and provide a desired trade-off between the transcoding complexity and the transcoded video quality. To reduce the transcoding complexity, some of coding information, such as coding unit (CU) depth, prediction mode, merge mode, motion vector information, intra direction information and transform unit (TU) depth information, in the SHVC bitstream are mapped and transcoded to single layer HEVC bitstream. One major difficulty in transcoding arises when trying to reuse the motion information from SHVC bitstream since motion vectors referring to inter-layer reference (ILR) pictures cannot be reused directly in transcoding. Reusing motion information obtained from ILR pictures for those prediction units (PUs) will reduce the complexity of the SHVC transcoder greatly but a significant reduction in the quality of the picture is observed. Pictures corresponding to the intra refresh pictures in the base layer (BL) will be coded as P pictures in enhancement layer (EL) in the SHVC bitstream; and directly reusing the intra information from the BL for transcoding will not get a good coding efficiency. To solve these problems, various transcoding technologies are proposed. The proposed technologies offer different trade-offs between transcoding speed and transcoding quality. They are implemented on the basis of reference software SHM-6.0 and HM-14.0 for the two layer spatial scalability configuration. Simulations show that the proposed SHVC software transcoder reduces the transcoding complexity by up to 98-99% using low complexity transcoding mode when compared with cascaded re-encoding method. The transcoder performance at various bitrates with different transcoding modes are compared in terms of transcoding speed and transcoded video quality.

PIC codes for plasma accelerators on emerging computer architectures (GPUS, Multicore/Manycore CPUS)

NASA Astrophysics Data System (ADS)

Vincenti, Henri

2016-03-01

The advent of exascale computers will enable 3D simulations of a new laser-plasma interaction regimes that were previously out of reach of current Petasale computers. However, the paradigm used to write current PIC codes will have to change in order to fully exploit the potentialities of these new computing architectures. Indeed, achieving Exascale computing facilities in the next decade will be a great challenge in terms of energy consumption and will imply hardware developments directly impacting our way of implementing PIC codes. As data movement (from die to network) is by far the most energy consuming part of an algorithm future computers will tend to increase memory locality at the hardware level and reduce energy consumption related to data movement by using more and more cores on each compute nodes (''fat nodes'') that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, CPU machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. GPU's also have a reduced clock speed per core and can process Multiple Instructions on Multiple Datas (MIMD). At the software level Particle-In-Cell (PIC) codes will thus have to achieve both good memory locality and vectorization (for Multicore/Manycore CPU) to fully take advantage of these upcoming architectures. In this talk, we present the portable solutions we implemented in our high performance skeleton PIC code PICSAR to both achieve good memory locality and cache reuse as well as good vectorization on SIMD architectures. We also present the portable solutions used to parallelize the Pseudo-sepctral quasi-cylindrical code FBPIC on GPUs using the Numba python compiler.

Efficient computational methods for electromagnetic imaging with applications to 3D magnetotellurics

NASA Astrophysics Data System (ADS)

Kordy, Michal Adam

The motivation for this work is the forward and inverse problem for magnetotellurics, a frequency domain electromagnetic remote-sensing geophysical method used in mineral, geothermal, and groundwater exploration. The dissertation consists of four papers. In the first paper, we prove the existence and uniqueness of a representation of any vector field in H(curl) by a vector lying in H(curl) and H(div). It allows us to represent electric or magnetic fields by another vector field, for which nodal finite element approximation may be used in the case of non-constant electromagnetic properties. With this approach, the system matrix does not become ill-posed for low-frequency. In the second paper, we consider hexahedral finite element approximation of an electric field for the magnetotelluric forward problem. The near-null space of the system matrix for low frequencies makes the numerical solution unstable in the air. We show that the proper solution may obtained by applying a correction on the null space of the curl. It is done by solving a Poisson equation using discrete Helmholtz decomposition. We parallelize the forward code on multicore workstation with large RAM. In the next paper, we use the forward code in the inversion. Regularization of the inversion is done by using the second norm of the logarithm of conductivity. The data space Gauss-Newton approach allows for significant savings in memory and computational time. We show the efficiency of the method by considering a number of synthetic inversions and we apply it to real data collected in Cascade Mountains. The last paper considers a cross-frequency interpolation of the forward response as well as the Jacobian. We consider Pade approximation through model order reduction and rational Krylov subspace. The interpolating frequencies are chosen adaptively in order to minimize the maximum error of interpolation. Two error indicator functions are compared. We prove a theorem of almost always lucky failure in the case of the right hand analytically dependent on frequency. The operator's null space is treated by decomposing the solution into the part in the null space and orthogonal to it.

Immune Recognition of Gene Transfer Vectors: Focus on Adenovirus as a Paradigm

PubMed Central

Aldhamen, Yasser Ali; Seregin, Sergey S.; Amalfitano, Andrea

2011-01-01

Recombinant Adenovirus (Ad) based vectors have been utilized extensively as a gene transfer platform in multiple pre-clinical and clinical applications. These applications are numerous, and inclusive of both gene therapy and vaccine based approaches to human or animal diseases. The widespread utilization of these vectors in both animal models, as well as numerous human clinical trials (Ad-based vectors surpass all other gene transfer vectors relative to numbers of patients treated, as well as number of clinical trials overall), has shed light on how this virus vector interacts with both the innate and adaptive immune systems. The ability to generate and administer large amounts of this vector likely contributes not only to their ability to allow for highly efficient gene transfer, but also their elicitation of host immune responses to the vector and/or the transgene the vector expresses in vivo. These facts, coupled with utilization of several models that allow for full detection of these responses has predicted several observations made in human trials, an important point as lack of similar capabilities by other vector systems may prevent detection of such responses until only after human trials are initiated. Finally, induction of innate or adaptive immune responses by Ad vectors may be detrimental in one setting (i.e., gene therapy) and be entirely beneficial in another (i.e., prophylactic or therapeutic vaccine based applications). Herein, we review the current understanding of innate and adaptive immune responses to Ad vectors, as well some recent advances that attempt to capitalize on this understanding so as to further broaden the safe and efficient use of Ad-based gene transfer therapies in general. PMID:22566830

A Matlab Program for Textural Classification Using Neural Networks

NASA Astrophysics Data System (ADS)

Leite, E. P.; de Souza, C.

2008-12-01

A new MATLAB code that provides tools to perform classification of textural images for applications in the Geosciences is presented. The program, here coined TEXTNN, comprises the computation of variogram maps in the frequency domain for specific lag distances in the neighborhood of a pixel. The result is then converted back to spatial domain, where directional or ominidirectional semivariograms are extracted. Feature vectors are built with textural information composed of the semivariance values at these lag distances and, moreover, with histogram measures of mean, standard deviation and weighted fill-ratio. This procedure is applied to a selected group of pixels or to all pixels in an image using a moving window. A feed- forward back-propagation Neural Network can then be designed and trained on feature vectors of predefined classes (training set). The training phase minimizes the mean-squared error on the training set. Additionally, at each iteration, the mean-squared error for every validation is assessed and a test set is evaluated. The program also calculates contingency matrices, global accuracy and kappa coefficient for the three data sets, allowing a quantitative appraisal of the predictive power of the Neural Network models. The interpreter is able to select the best model obtained from a k-fold cross-validation or to use a unique split-sample data set for classification of all pixels in a given textural image. The code is opened to the geoscientific community and is very flexible, allowing the experienced user to modify it as necessary. The performance of the algorithms and the end-user program were tested using synthetic images, orbital SAR (RADARSAT) imagery for oil seepage detection, and airborne, multi-polarimetric SAR imagery for geologic mapping. The overall results proved very promising.

International standards: the World Organisation for Animal Health Terrestrial Animal Health Code.

PubMed

Thiermann, A B

2015-04-01

This paper provides a description of the international standards contained in the TerrestrialAnimal Health Code of the World Organisation for Animal Health (OIE) that relate to the prevention and control of vector-borne diseases. It identifies the rights and obligations of OIE Member Countries regarding the notification of animal disease occurrences, as well as the recommendations to be followed for a safe and efficient international trade of animals and their products.

A GIS tool for two-dimensional glacier-terminus change tracking

NASA Astrophysics Data System (ADS)

Urbanski, Jacek Andrzej

2018-02-01

This paper presents a Glacier Termini Tracking (GTT) toolbox for the two-dimensional analysis of glacier-terminus position changes. The input consists of a vector layer with several termini lines relating to the same glacier at different times. The output layers allow analyses to be conducted of glacier-terminus retreats, changes in retreats over time and along the ice face, and glacier-terminus fluctuations over time. The application of three tools from the toolbox is demonstrated via the analysis of eight glacier-terminus retreats and fluctuations at the Hornsund fjord in south Svalbard. It is proposed that this toolbox may also be useful in the study of other line features that change over time, like coastlines and rivers. The toolbox has been coded in Python and runs via ArcGIS.

Modal Test/Analysis Correlation of Space Station Structures Using Nonlinear Sensitivity

NASA Technical Reports Server (NTRS)

Gupta, Viney K.; Newell, James F.; Berke, Laszlo; Armand, Sasan

1992-01-01

The modal correlation problem is formulated as a constrained optimization problem for validation of finite element models (FEM's). For large-scale structural applications, a pragmatic procedure for substructuring, model verification, and system integration is described to achieve effective modal correlation. The space station substructure FEM's are reduced using Lanczos vectors and integrated into a system FEM using Craig-Bampton component modal synthesis. The optimization code is interfaced with MSC/NASTRAN to solve the problem of modal test/analysis correlation; that is, the problem of validating FEM's for launch and on-orbit coupled loads analysis against experimentally observed frequencies and mode shapes. An iterative perturbation algorithm is derived and implemented to update nonlinear sensitivity (derivatives of eigenvalues and eigenvectors) during optimizer iterations, which reduced the number of finite element analyses.

Modal test/analysis correlation of Space Station structures using nonlinear sensitivity

NASA Technical Reports Server (NTRS)

Gupta, Viney K.; Newell, James F.; Berke, Laszlo; Armand, Sasan

1992-01-01

The modal correlation problem is formulated as a constrained optimization problem for validation of finite element models (FEM's). For large-scale structural applications, a pragmatic procedure for substructuring, model verification, and system integration is described to achieve effective modal correlations. The space station substructure FEM's are reduced using Lanczos vectors and integrated into a system FEM using Craig-Bampton component modal synthesis. The optimization code is interfaced with MSC/NASTRAN to solve the problem of modal test/analysis correlation; that is, the problem of validating FEM's for launch and on-orbit coupled loads analysis against experimentally observed frequencies and mode shapes. An iterative perturbation algorithm is derived and implemented to update nonlinear sensitivity (derivatives of eigenvalues and eigenvectors) during optimizer iterations, which reduced the number of finite element analyses.

Substructure program for analysis of helicopter vibrations

NASA Technical Reports Server (NTRS)

Sopher, R.

1981-01-01

A substructure vibration analysis which was developed as a design tool for predicting helicopter vibrations is described. The substructure assembly method and the composition of the transformation matrix are analyzed. The procedure for obtaining solutions to the equations of motion is illustrated for the steady-state forced response solution mode, and rotor hub load excitation and impedance are analyzed. Calculation of the mass, damping, and stiffness matrices, as well as the forcing function vectors of physical components resident in the base program code, are discussed in detail. Refinement of the model is achieved by exercising modules which interface with the external program to represent rotor induced variable inflow and fuselage induced variable inflow at the rotor. The calculation of various flow fields is discussed, and base program applications are detailed.

Application of quasi-distributions for solving inverse problems of neutron and {gamma}-ray transport

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

Pogosbekyan, L.R.; Lysov, D.A.

The considered inverse problems deal with the calculation of the unknown values of nuclear installations by means of the known (goal) functionals of neutron/{gamma}-ray distributions. The example of these problems might be the calculation of the automatic control rods position as function of neutron sensors reading, or the calculation of experimentally-corrected values of cross-sections, isotopes concentration, fuel enrichment via the measured functional. The authors have developed the new method to solve inverse problem. It finds flux density as quasi-solution of the particles conservation linear system adjointed to equalities for functionals. The method is more effective compared to the one basedmore » on the classical perturbation theory. It is suitable for vectorization and it can be used successfully in optimization codes.« less

HSV as a vector in vaccine development and gene therapy.

PubMed

Marconi, Peggy; Argnani, Rafaela; Epstein, Alberto L; Manservigi, Roberto

2009-01-01

The very deep knowledge acquired on the genetics and molecular biology of herpes simplex virus (HSV), major human pathogen whose lifestyle is based on a long-term dual interaction with the infected host characterized by the existence of lytic and latent infections, has allowed the development of potential vectors for several applications in human healthcare. These include delivery and expression of human genes to cells of the nervous system, selective destruction of cancer cells, prophylaxis against infection with HSV or other infectious diseases and targeted infection of specific tissues or organs. Three different classes of vectors can be derived from HSV-1: replication-competent attenuated vectors, replication-incompetent recombinant vectors and defective helper-dependent vectors known as amplicons. This chapter highlights the current knowledge concerning design, construction and recent applications, as well as the potential and current limitations of the three different classes of HSV-1-based vectors.

Discovering and understanding the vector field using simulation in android app

NASA Astrophysics Data System (ADS)

Budi, A.; Muliyati, D.

2018-05-01

An understanding of vector field’s concepts are fundamental parts of the electrodynamics course. In this paper, we use a simple simulation that can be used to show qualitative imaging results as a variation of the vector field. Android application packages the simulation with consideration of the efficiency of use during the lecture. In addition, this simulation also trying to cover the divergences and curl concepts from the same conditions that students have a complete understanding and can distinguish concepts that have been described only mathematically. This simulation is designed to show the relationship between the field magnitude and its potential. This application can show vector field simulations in various conditions that help to improve students’ understanding of vector field concepts and their relation to particle existence around the field vector.

A repertoire of the dominant transcripts from the salivary glands of the blood-sucking bug, Triatoma dimidiata, a vector of Chagas disease

PubMed Central

Kato, Hirotomo; Jochim, Ryan C.; Gomez, Eduardo A.; Sakoda, Ryo; Iwata, Hiroyuki; Valenzuela, Jesus G.; Hashiguchi, Yoshihisa

2010-01-01

Triatoma (T.) dimidiata is a hematophagous Hemiptera and a main vector of Chagas disease. The saliva of this and other blood-sucking insects contains potent pharmacologically active components that assist them in counteracting the host hemostatic and inflammatory systems during blood feeding. To describe the repertoire of potential bioactive salivary molecules from this insect, a number of randomly selected transcripts from the salivary gland cDNA library of T. dimidiata were sequenced and analyzed. This analysis showed that 77.5% of the isolated transcripts coded for putative secreted proteins, and 89.9% of these coded for variants of the lipocalin family proteins. The most abundant transcript was a homologue of procalin, the major allergen of T. protracta saliva, and contributed more than 50% of the transcripts coding for putative secreted proteins, suggesting that it may play an important role in the blood-feeding process. Other salivary transcripts encoding lipocalin family proteins had homology to triabin (a thrombin inhibitor), triafestin (an inhibitor of kallikrein–kinin system), pallidipin (an inhibitor of collagen-induced platelet aggregation) and others with unknown function. PMID:19900580

Improved image decompression for reduced transform coding artifacts

NASA Technical Reports Server (NTRS)

Orourke, Thomas P.; Stevenson, Robert L.

1994-01-01

The perceived quality of images reconstructed from low bit rate compression is severely degraded by the appearance of transform coding artifacts. This paper proposes a method for producing higher quality reconstructed images based on a stochastic model for the image data. Quantization (scalar or vector) partitions the transform coefficient space and maps all points in a partition cell to a representative reconstruction point, usually taken as the centroid of the cell. The proposed image estimation technique selects the reconstruction point within the quantization partition cell which results in a reconstructed image which best fits a non-Gaussian Markov random field (MRF) image model. This approach results in a convex constrained optimization problem which can be solved iteratively. At each iteration, the gradient projection method is used to update the estimate based on the image model. In the transform domain, the resulting coefficient reconstruction points are projected to the particular quantization partition cells defined by the compressed image. Experimental results will be shown for images compressed using scalar quantization of block DCT and using vector quantization of subband wavelet transform. The proposed image decompression provides a reconstructed image with reduced visibility of transform coding artifacts and superior perceived quality.

Full Wave Analysis of RF Signal Attenuation in a Lossy Cave using a High Order Time Domain Vector Finite Element Method

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

Pingenot, J; Rieben, R; White, D

2004-12-06

We present a computational study of signal propagation and attenuation of a 200 MHz dipole antenna in a cave environment. The cave is modeled as a straight and lossy random rough wall. To simulate a broad frequency band, the full wave Maxwell equations are solved directly in the time domain via a high order vector finite element discretization using the massively parallel CEM code EMSolve. The simulation is performed for a series of random meshes in order to generate statistical data for the propagation and attenuation properties of the cave environment. Results for the power spectral density and phase ofmore » the electric field vector components are presented and discussed.« less

Design Specification for a Thrust-Vectoring, Actuated-Nose-Strake Flight Control Law for the High-Alpha Research Vehicle

NASA Technical Reports Server (NTRS)

Bacon, Barton J.; Carzoo, Susan W.; Davidson, John B.; Hoffler, Keith D.; Lallman, Frederick J.; Messina, Michael D.; Murphy, Patrick C.; Ostroff, Aaron J.; Proffitt, Melissa S.; Yeager, Jessie C.;

Administration of helper-dependent adenoviral vectors and sequential delivery of different vector serotype for long-term liver-directed gene transfer in baboons

PubMed Central

Morral, Núria; O’Neal, Wanda; Rice, Karen; Leland, Michele; Kaplan, Johanne; Piedra, Pedro A.; Zhou, Heshan; Parks, Robin J.; Velji, Rizwan; Aguilar-Córdova, Estuardo; Wadsworth, Samuel; Graham, Frank L.; Kochanek, Stefan; Carey, K. Dee; Beaudet, Arthur L.

1999-01-01

The efficiency of first-generation adenoviral vectors as gene delivery tools is often limited by the short duration of transgene expression, which can be related to immune responses and to toxic effects of viral proteins. In addition, readministration is usually ineffective unless the animals are immunocompromised or a different adenovirus serotype is used. Recently, adenoviral vectors devoid of all viral coding sequences (helper-dependent or gutless vectors) have been developed to avoid expression of viral proteins. In mice, liver-directed gene transfer with AdSTK109, a helper-dependent adenoviral (Ad) vector containing the human α1-antitrypsin (hAAT) gene, resulted in sustained expression for longer than 10 months with negligible toxicity to the liver. In the present report, we have examined the duration of expression of AdSTK109 in the liver of baboons and compared it to first-generation vectors expressing hAAT. Transgene expression was limited to approximately 3–5 months with the first-generation vectors. In contrast, administration of AdSTK109 resulted in transgene expression for longer than a year in two of three baboons. We have also investigated the feasibility of circumventing the humoral response to the virus by sequential administration of vectors of different serotypes. We found that the ineffectiveness of readministration due to the humoral response to an Ad5 first-generation vector was overcome by use of an Ad2-based vector expressing hAAT. These data suggest that long-term expression of transgenes should be possible by combining the reduced immunogenicity and toxicity of helper-dependent vectors with sequential delivery of vectors of different serotypes. PMID:10536005

Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control.

PubMed

Kaur, Navneet; Hasegawa, Daniel K; Ling, Kai-Shu; Wintermantel, William M

2016-10-01

The relationships between plant viruses and their vectors have evolved over the millennia, and yet, studies on viruses began <150 years ago and investigations into the virus and vector interactions even more recently. The advent of next generation sequencing, including rapid genome and transcriptome analysis, methods for evaluation of small RNAs, and the related disciplines of proteomics and metabolomics offer a significant shift in the ability to elucidate molecular mechanisms involved in virus infection and transmission by insect vectors. Genomic technologies offer an unprecedented opportunity to examine the response of insect vectors to the presence of ingested viruses through gene expression changes and altered biochemical pathways. This review focuses on the interactions between viruses and their whitefly or thrips vectors and on potential applications of genomics-driven control of the insect vectors. Recent studies have evaluated gene expression in vectors during feeding on plants infected with begomoviruses, criniviruses, and tospoviruses, which exhibit very different types of virus-vector interactions. These studies demonstrate the advantages of genomics and the potential complementary studies that rapidly advance our understanding of the biology of virus transmission by insect vectors and offer additional opportunities to design novel genetic strategies to manage insect vectors and the viruses they transmit.

The Development of the Differential MEMS Vector Hydrophone

PubMed Central

Zhang, Guojun; Liu, Mengran; Shen, Nixin; Wang, Xubo; Zhang, Wendong

2017-01-01

To solve the problem that MEMS vector hydrophones are greatly interfered with by the vibration of the platform and flow noise in applications, this paper describes a differential MEMS vector hydrophone that could simultaneously receive acoustic signals and reject acceleration signals. Theoretical and simulation analyses have been carried out. Lastly, a prototype of the differential MEMS vector hydrophone has been created and tested using a standing wave tube and a vibration platform. The results of the test show that this hydrophone has a high sensitivity, Mv = −185 dB (@ 500 Hz, 0 dB reference 1 V/μPa), which is almost the same as the previous MEMS vector hydrophones, and has a low acceleration sensitivity, Mv = −58 dB (0 dB reference 1 V/g), which has decreased by 17 dB compared with the previous MEMS vector hydrophone. The differential MEMS vector hydrophone basically meets the requirements of acoustic vector detection when it is rigidly fixed to a working platform, which lays the foundation for engineering applications of MEMS vector hydrophones. PMID:28594384

User's Manual for FEMOM3DS. Version 1.0

NASA Technical Reports Server (NTRS)

Reddy, C.J.; Deshpande, M. D.

1997-01-01

FEMOM3DS is a computer code written in FORTRAN 77 to compute electromagnetic(EM) scattering characteristics of a three dimensional object with complex materials using combined Finite Element Method (FEM)/Method of Moments (MoM) technique. This code uses the tetrahedral elements, with vector edge basis functions for FEM in the volume of the cavity and the triangular elements with the basis functions similar to that described for MoM at the outer boundary. By virtue of FEM, this code can handle any arbitrarily shaped three-dimensional cavities filled with inhomogeneous lossy materials. The User's Manual is written to make the user acquainted with the operation of the code. The user is assumed to be familiar with the FORTRAN 77 language and the operating environment of the computers on which the code is intended to run.

Tensoral for post-processing users and simulation authors

NASA Technical Reports Server (NTRS)

Dresselhaus, Eliot

1993-01-01

The CTR post-processing effort aims to make turbulence simulations and data more readily and usefully available to the research and industrial communities. The Tensoral language, which provides the foundation for this effort, is introduced here in the form of a user's guide. The Tensoral user's guide is presented in two main sections. Section one acts as a general introduction and guides database users who wish to post-process simulation databases. Section two gives a brief description of how database authors and other advanced users can make simulation codes and/or the databases they generate available to the user community via Tensoral database back ends. The two-part structure of this document conforms to the two-level design structure of the Tensoral language. Tensoral has been designed to be a general computer language for performing tensor calculus and statistics on numerical data. Tensoral's generality allows it to be used for stand-alone native coding of high-level post-processing tasks (as described in section one of this guide). At the same time, Tensoral's specialization to a minute task (namely, to numerical tensor calculus and statistics) allows it to be easily embedded into applications written partly in Tensoral and partly in other computer languages (here, C and Vectoral). Embedded Tensoral, aimed at advanced users for more general coding (e.g. of efficient simulations, for interfacing with pre-existing software, for visualization, etc.), is described in section two of this guide.

A highly optimized vectorized code for Monte Carlo simulations of SU(3) lattice gauge theories

NASA Technical Reports Server (NTRS)

Barkai, D.; Moriarty, K. J. M.; Rebbi, C.

1984-01-01

New methods are introduced for improving the performance of the vectorized Monte Carlo SU(3) lattice gauge theory algorithm using the CDC CYBER 205. Structure, algorithm and programming considerations are discussed. The performance achieved for a 16(4) lattice on a 2-pipe system may be phrased in terms of the link update time or overall MFLOPS rates. For 32-bit arithmetic, it is 36.3 microsecond/link for 8 hits per iteration (40.9 microsecond for 10 hits) or 101.5 MFLOPS.

Lattice QCD calculation using VPP500

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

Kim, Seyong; Ohta, Shigemi

1995-02-01

A new vector parallel supercomputer, Fujitsu VPP500, was installed at RIKEN earlier this year. It consists of 30 vector computers, each with 1.6 GFLOPS peak speed and 256 MB memory, connected by a crossbar switch with 400 MB/s peak data transfer rate each way between any pair of nodes. The authors developed a Fortran lattice QCD simulation code for it. It runs at about 1.1 GFLOPS sustained per node for Metropolis pure-gauge update, and about 0.8 GFLOPS sustained per node for conjugate gradient inversion of staggered fermion matrix.

Development of a GPU Compatible Version of the Fast Radiation Code RRTMG

NASA Astrophysics Data System (ADS)

Iacono, M. J.; Mlawer, E. J.; Berthiaume, D.; Cady-Pereira, K. E.; Suarez, M.; Oreopoulos, L.; Lee, D.

2012-12-01

The absorption of solar radiation and emission/absorption of thermal radiation are crucial components of the physics that drive Earth's climate and weather. Therefore, accurate radiative transfer calculations are necessary for realistic climate and weather simulations. Efficient radiation codes have been developed for this purpose, but their accuracy requirements still necessitate that as much as 30% of the computational time of a GCM is spent computing radiative fluxes and heating rates. The overall computational expense constitutes a limitation on a GCM's predictive ability if it becomes an impediment to adding new physics to or increasing the spatial and/or vertical resolution of the model. The emergence of Graphics Processing Unit (GPU) technology, which will allow the parallel computation of multiple independent radiative calculations in a GCM, will lead to a fundamental change in the competition between accuracy and speed. Processing time previously consumed by radiative transfer will now be available for the modeling of other processes, such as physics parameterizations, without any sacrifice in the accuracy of the radiative transfer. Furthermore, fast radiation calculations can be performed much more frequently and will allow the modeling of radiative effects of rapid changes in the atmosphere. The fast radiation code RRTMG, developed at Atmospheric and Environmental Research (AER), is utilized operationally in many dynamical models throughout the world. We will present the results from the first stage of an effort to create a version of the RRTMG radiation code designed to run efficiently in a GPU environment. This effort will focus on the RRTMG implementation in GEOS-5. RRTMG has an internal pseudo-spectral vector of length of order 100 that, when combined with the much greater length of the global horizontal grid vector from which the radiation code is called in GEOS-5, makes RRTMG/GEOS-5 particularly suited to achieving a significant speed improvement through GPU technology. This large number of independent cases will allow us to take full advantage of the computational power of the latest GPUs, ensuring that all thread cores in the GPU remain active, a key criterion for obtaining significant speedup. The CUDA (Compute Unified Device Architecture) Fortran compiler developed by PGI and Nvidia will allow us to construct this parallel implementation on the GPU while remaining in the Fortran language. This implementation will scale very well across various CUDA-supported GPUs such as the recently released Fermi Nvidia cards. We will present the computational speed improvements of the GPU-compatible code relative to the standard CPU-based RRTMG with respect to a very large and diverse suite of atmospheric profiles. This suite will also be utilized to demonstrate the minimal impact of the code restructuring on the accuracy of radiation calculations. The GPU-compatible version of RRTMG will be directly applicable to future versions of GEOS-5, but it is also likely to provide significant associated benefits for other GCMs that employ RRTMG.

Accuracy comparison among different machine learning techniques for detecting malicious codes

NASA Astrophysics Data System (ADS)

Narang, Komal

2016-03-01

In this paper, a machine learning based model for malware detection is proposed. It can detect newly released malware i.e. zero day attack by analyzing operation codes on Android operating system. The accuracy of Naïve Bayes, Support Vector Machine (SVM) and Neural Network for detecting malicious code has been compared for the proposed model. In the experiment 400 benign files, 100 system files and 500 malicious files have been used to construct the model. The model yields the best accuracy 88.9% when neural network is used as classifier and achieved 95% and 82.8% accuracy for sensitivity and specificity respectively.

GloVe C++ v. 1.0

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

Cox, Jonathan A.

2015-12-02

This code implements the GloVe algorithm for learning word vectors from a text corpus. It uses a modern C++ approach. This algorithm is described in the open literature in the referenced paper by Pennington, Jeffrey, Richard Socher, and Christopher D. Manning.

Simplified moment tensor analysis and unified decomposition of acoustic emission source: Application to in situ hydrofracturing test

NASA Astrophysics Data System (ADS)

Ohtsu, Masayasu

1991-04-01

An application of a moment tensor analysis to acoustic emission (AE) is studied to elucidate crack types and orientations of AE sources. In the analysis, simplified treatment is desirable, because hundreds of AE records are obtained from just one experiment and thus sophisticated treatment is realistically cumbersome. Consequently, a moment tensor inversion based on P wave amplitude is employed to determine six independent tensor components. Selecting only P wave portion from the full-space Green's function of homogeneous and isotropic material, a computer code named SiGMA (simplified Green's functions for the moment tensor analysis) is developed for the AE inversion analysis. To classify crack type and to determine crack orientation from moment tensor components, a unified decomposition of eigenvalues into a double-couple (DC) part, a compensated linear vector dipole (CLVD) part, and an isotropic part is proposed. The aim of the decomposition is to determine the proportion of shear contribution (DC) and tensile contribution (CLVD + isotropic) on AE sources and to classify cracks into a crack type of the dominant motion. Crack orientations determined from eigenvectors are presented as crack-opening vectors for tensile cracks and fault motion vectors for shear cracks, instead of stereonets. The SiGMA inversion and the unified decomposition are applied to synthetic data and AE waveforms detected during an in situ hydrofracturing test. To check the accuracy of the procedure, numerical experiments are performed on the synthetic waveforms, including cases with 10% random noise added. Results show reasonable agreement with assumed crack configurations. Although the maximum error is approximately 10% with respect to the ratios, the differences on crack orientations are less than 7°. AE waveforms detected by eight accelerometers deployed during the hydrofracturing test are analyzed. Crack types and orientations determined are in reasonable agreement with a predicted failure plane from borehole TV observation. The results suggest that tensile cracks are generated first at weak seams and then shear cracks follow on the opened joints.

Management of arthropod pathogen vectors in North America: Minimizing adverse effects on pollinators

USGS Publications Warehouse

Ginsberg, Howard; Bargar, Timothy A.; Hladik, Michelle L.; Lubelczyk, Charles

2017-01-01

Tick and mosquito management is important to public health protection. At the same time, growing concerns about declines of pollinator species raise the question of whether vector control practices might affect pollinator populations. We report the results of a task force of the North American Pollinator Protection Campaign (NAPPC) that examined potential effects of vector management practices on pollinators, and how these programs could be adjusted to minimize negative effects on pollinating species. The main types of vector control practices that might affect pollinators are landscape manipulation, biocontrol, and pesticide applications. Some current practices already minimize effects of vector control on pollinators (e.g., short-lived pesticides and application-targeting technologies). Nontarget effects can be further diminished by taking pollinator protection into account in the planning stages of vector management programs. Effects of vector control on pollinator species often depend on specific local conditions (e.g., proximity of locations with abundant vectors to concentrations of floral resources), so planning is most effective when it includes collaborations of local vector management professionals with local experts on pollinators. Interventions can then be designed to avoid pollinators (e.g., targeting applications to avoid blooming times and pollinator nesting habitats), while still optimizing public health protection. Research on efficient targeting of interventions, and on effects on pollinators of emerging technologies, will help mitigate potential deleterious effects on pollinators in future management programs. In particular, models that can predict effects of integrated pest management on vector-borne pathogen transmission, along with effects on pollinator populations, would be useful for collaborative decision-making.

The mean-square error optimal linear discriminant function and its application to incomplete data vectors

NASA Technical Reports Server (NTRS)

Walker, H. F.

1979-01-01

In many pattern recognition problems, data vectors are classified although one or more of the data vector elements are missing. This problem occurs in remote sensing when the ground is obscured by clouds. Optimal linear discrimination procedures for classifying imcomplete data vectors are discussed.

Vector calculus in non-integer dimensional space and its applications to fractal media

NASA Astrophysics Data System (ADS)

Tarasov, Vasily E.

2015-02-01

We suggest a generalization of vector calculus for the case of non-integer dimensional space. The first and second orders operations such as gradient, divergence, the scalar and vector Laplace operators for non-integer dimensional space are defined. For simplification we consider scalar and vector fields that are independent of angles. We formulate a generalization of vector calculus for rotationally covariant scalar and vector functions. This generalization allows us to describe fractal media and materials in the framework of continuum models with non-integer dimensional space. As examples of application of the suggested calculus, we consider elasticity of fractal materials (fractal hollow ball and fractal cylindrical pipe with pressure inside and outside), steady distribution of heat in fractal media, electric field of fractal charged cylinder. We solve the correspondent equations for non-integer dimensional space models.

Compute Server Performance Results

NASA Technical Reports Server (NTRS)

Stockdale, I. E.; Barton, John; Woodrow, Thomas (Technical Monitor)

1994-01-01

Parallel-vector supercomputers have been the workhorses of high performance computing. As expectations of future computing needs have risen faster than projected vector supercomputer performance, much work has been done investigating the feasibility of using Massively Parallel Processor systems as supercomputers. An even more recent development is the availability of high performance workstations which have the potential, when clustered together, to replace parallel-vector systems. We present a systematic comparison of floating point performance and price-performance for various compute server systems. A suite of highly vectorized programs was run on systems including traditional vector systems such as the Cray C90, and RISC workstations such as the IBM RS/6000 590 and the SGI R8000. The C90 system delivers 460 million floating point operations per second (FLOPS), the highest single processor rate of any vendor. However, if the price-performance ration (PPR) is considered to be most important, then the IBM and SGI processors are superior to the C90 processors. Even without code tuning, the IBM and SGI PPR's of 260 and 220 FLOPS per dollar exceed the C90 PPR of 160 FLOPS per dollar when running our highly vectorized suite,

An integrated vector system for cellular studies of phage display-derived peptides.

PubMed

Voss, Stephan D; DeGrand, Alec M; Romeo, Giulio R; Cantley, Lewis C; Frangioni, John V

2002-09-15

Peptide phage display is a method by which large numbers of diverse peptides can be screened for binding to a target of interest. Even when successful, the rate-limiting step is usually validation of peptide bioactivity using living cells. In this paper, we describe an integrated system of vectors that expedites both the screening and the characterization processes. Library construction and screening is performed using an optimized type 3 phage display vector, mJ(1), which is shown to accept peptide libraries of at least 23 amino acids in length. Peptide coding sequences are shuttled from mJ(1) into one of three families of mammalian expression vectors for cell physiological studies. The vector pAL(1) expresses phage display-derived peptides as Gal4 DNA binding domain fusion proteins for transcriptional activation studies. The vectors pG(1), pG(1)N, and pG(1)C express phage display-derived peptides as green fluorescent protein fusions targeted to the entire cell, nucleus, or cytoplasm, respectively. The vector pAP(1) expresses phage display-derived peptides as fusions to secreted placental alkaline phosphatase. Such enzyme fusions can be used as highly sensitive affinity reagents for high-throughput assays and for cloning of peptide-binding cell surface receptors. Taken together, this system of vectors should facilitate the development of phage display-derived peptides into useful biomolecules.

Range Sidelobe Response from the Use of Polyphase Signals in Spotlight Synthetic Aperture Radar

DTIC Science & Technology

2015-12-01

come to closure. I also want to thank my mother for raising me and instilling in me the work ethic and values that have propelled me through life. I...to describe the poly-phase signals at baseband. IQ notation is preferred for complex waveforms because it allows for an easy mathematical...variables. 15 Once the Frank-coded phase vector is created, the IQ signal generation discussed in Chapter II was used to generate a Frank-code phase

IEEE International Symposium Information Theory, held at Santa Monica California, February 9-12, 1981.

DTIC Science & Technology

1981-01-01

Channel and study permutation codes as a special case. ,uch a code is generated by an initial vector x, a group G of orthogonal n by n matrices, and a...random-access components, is introduced and studied . Under this scheme, the network stations are divided into groups , each of which is assigned a...IEEE INFORMATION THEORY GROUP CO-SPONSORED BY: UNION RADIO SCIENTIFIQUE INTERNATIONALE IEEE Catalog Number 81 CH 1609-7 IT 𔃻. 81 ~20 04Q SECURITY

Particle-gas dynamics in the protoplanetary nebula

NASA Technical Reports Server (NTRS)

Cuzzi, Jeffrey N.; Champney, Joelle M.; Dobrovolskis, Anthony R.

1991-01-01

In the past year we made significant progress in improving our fundamental understanding of the physics of particle-gas dynamics in the protoplanetary nebula. Having brought our code to a state of fairly robust functionality, we devoted significant effort to optimizing it for running long cases. We optimized the code for vectorization to the extent that it now runs eight times faster than before. The following subject areas are covered: physical improvements to the model; numerical results; Reynolds averaging of fluid equations; and modeling of turbulence and viscosity.

RRTMGP: A High-Performance Broadband Radiation Code for the Next Decade

DTIC Science & Technology

2014-09-30

Hardware counters were used to measure several performance metrics, including the number of double-precision (DP) floating- point operations ( FLOPs ...0.2 DP FLOPs per CPU cycle. Experience with production science code is that it is possible to achieve execution rates in the range of 0.5 to 1.0...DP FLOPs per cycle. Looking at the ratio of vectorized DP FLOPs to total DP FLOPs we see (Figure PROF) that for most of the execution time the

Abstract generalized vector quasi-equilibrium problems in noncompact Hadamard manifolds.

PubMed

Lu, Haishu; Wang, Zhihua

2017-01-01

This paper deals with the abstract generalized vector quasi-equilibrium problem in noncompact Hadamard manifolds. We prove the existence of solutions to the abstract generalized vector quasi-equilibrium problem under suitable conditions and provide applications to an abstract vector quasi-equilibrium problem, a generalized scalar equilibrium problem, a scalar equilibrium problem, and a perturbed saddle point problem. Finally, as an application of the existence of solutions to the generalized scalar equilibrium problem, we obtain a weakly mixed variational inequality and two mixed variational inequalities. The results presented in this paper unify and generalize many known results in the literature.

[Construction and expression of recombinant lentiviral vectors of AKT2,PDK1 and BAD].

PubMed

Zhu, Jing; Chen, Bo-Jiang; Huang, Na; Li, Wei-Min

2014-03-01

To construct human protein kinase B (ATK2), phosphoinositide-dependent kinase 1 (PDK1) and bcl-2-associated death protein (BAD) lentiviral expression vector, and to determine their expressions in 293T cells. Total RNA was extracted from lung cancer tissues. The full-length coding regions of human ATK2, BAD and PDK1 cDNA were amplified via RT-PCR using specific primers, subcloned into PGEM-Teasy and then sequenced for confirmation. The full-length coding sequence was cut out with a specific restriction enzyme digest and subclone into pCDF1-MCS2-EF1-copGFP. The plasmids were transfected into 293T cells using the calcium phosphate method. The over expression of AKT2, BAD and PDK1 were detected by Western blot. AKT2, PDK1 and BAD were subcloned into pCDF1-MCS2-EF1-copGFP, with an efficiency of transfection of 100%, 95%, and 90% respectively. The virus titers were 6.7 x 10(6) PFU/mL in the supernatant. After infection, the proteins of AKT2, PDK1 and BAD were detected by Western blot. The lentivial vector pCDF1-MCS2-EF1-copGFP containing AKT2, BAD and PDK1 were successfully constructed and expressed in 293T cells.

Re-engineering adenovirus vector systems to enable high-throughput analyses of gene function.

PubMed

Stanton, Richard J; McSharry, Brian P; Armstrong, Melanie; Tomasec, Peter; Wilkinson, Gavin W G

2008-12-01

With the enhanced capacity of bioinformatics to interrogate extensive banks of sequence data, more efficient technologies are needed to test gene function predictions. Replication-deficient recombinant adenovirus (Ad) vectors are widely used in expression analysis since they provide for extremely efficient expression of transgenes in a wide range of cell types. To facilitate rapid, high-throughput generation of recombinant viruses, we have re-engineered an adenovirus vector (designated AdZ) to allow single-step, directional gene insertion using recombineering technology. Recombineering allows for direct insertion into the Ad vector of PCR products, synthesized sequences, or oligonucleotides encoding shRNAs without requirement for a transfer vector Vectors were optimized for high-throughput applications by making them "self-excising" through incorporating the I-SceI homing endonuclease into the vector removing the need to linearize vectors prior to transfection into packaging cells. AdZ vectors allow genes to be expressed in their native form or with strep, V5, or GFP tags. Insertion of tetracycline operators downstream of the human cytomegalovirus major immediate early (HCMV MIE) promoter permits silencing of transgenes in helper cells expressing the tet repressor thus making the vector compatible with the cloning of toxic gene products. The AdZ vector system is robust, straightforward, and suited to both sporadic and high-throughput applications.

SnopViz, an interactive snow profile visualization tool

NASA Astrophysics Data System (ADS)

Fierz, Charles; Egger, Thomas; gerber, Matthias; Bavay, Mathias; Techel, Frank

2016-04-01

SnopViz is a visualization tool for both simulation outputs of the snow-cover model SNOWPACK and observed snow profiles. It has been designed to fulfil the needs of operational services (Swiss Avalanche Warning Service, Avalanche Canada) as well as offer the flexibility required to satisfy the specific needs of researchers. This JavaScript application runs on any modern browser and does not require an active Internet connection. The open source code is available for download from models.slf.ch where examples can also be run. Both the SnopViz library and the SnopViz User Interface will become a full replacement of the current research visualization tool SN_GUI for SNOWPACK. The SnopViz library is a stand-alone application that parses the provided input files, for example, a single snow profile (CAAML file format) or multiple snow profiles as output by SNOWPACK (PRO file format). A plugin architecture allows for handling JSON objects (JavaScript Object Notation) as well and plugins for other file formats may be added easily. The outputs are provided either as vector graphics (SVG) or JSON objects. The SnopViz User Interface (UI) is a browser based stand-alone interface. It runs in every modern browser, including IE, and allows user interaction with the graphs. SVG, the XML based standard for vector graphics, was chosen because of its easy interaction with JS and a good software support (Adobe Illustrator, Inkscape) to manipulate graphs outside SnopViz for publication purposes. SnopViz provides new visualization for SNOWPACK timeline output as well as time series input and output. The actual output format for SNOWPACK timelines was retained while time series are read from SMET files, a file format used in conjunction with the open source data handling code MeteoIO. Finally, SnopViz is able to render single snow profiles, either observed or modelled, that are provided as CAAML-file. This file format (caaml.org/Schemas/V5.0/Profiles/SnowProfileIACS) is an international standard to exchange snow profile data. It is supported by the International Association of Cryospheric Sciences (IACS) and was developed in collaboration with practitioners (Avalanche Canada).

The application of vector concepts on two skew lines

NASA Astrophysics Data System (ADS)

Alghadari, F.; Turmudi; Herman, T.

2018-01-01

The purpose of this study is knowing how to apply vector concepts on two skew lines in three-dimensional (3D) coordinate and its utilization. Several mathematical concepts have a related function for the other, but the related between the concept of vector and 3D have not applied in learning classroom. In fact, there are studies show that female students have difficulties in learning of 3D than male. It is because of personal spatial intelligence. The relevance of vector concepts creates both learning achievement and mathematical ability of male and female students enables to be balanced. The distance like on a cube, cuboid, or pyramid whose are drawn on the rectangular coordinates of a point in space. Two coordinate points of the lines can be created a vector. The vector of two skew lines has the shortest distance and the angle. Calculating of the shortest distance is started to create two vectors as a representation of line by vector position concept, next to determining a norm-vector of two vector which was obtained by cross-product, and then to create a vector from two combination of pair-points which was passed by two skew line, the shortest distance is scalar orthogonal projection of norm-vector on a vector which is a combination of pair-points. While calculating the angle are used two vectors as a representation of line to dot-product, and the inverse of cosine is yield. The utilization of its application on mathematics learning and orthographic projection method.

Targeted Knock-Down of miR21 Primary Transcripts Using snoMEN Vectors Induces Apoptosis in Human Cancer Cell Lines.

PubMed

Ono, Motoharu; Yamada, Kayo; Avolio, Fabio; Afzal, Vackar; Bensaddek, Dalila; Lamond, Angus I

2015-01-01

We have previously reported an antisense technology, 'snoMEN vectors', for targeted knock-down of protein coding mRNAs using human snoRNAs manipulated to contain short regions of sequence complementarity with the mRNA target. Here we characterise the use of snoMEN vectors to target the knock-down of micro RNA primary transcripts. We document the specific knock-down of miR21 in HeLa cells using plasmid vectors expressing miR21-targeted snoMEN RNAs and show this induces apoptosis. Knock-down is dependent on the presence of complementary sequences in the snoMEN vector and the induction of apoptosis can be suppressed by over-expression of miR21. Furthermore, we have also developed lentiviral vectors for delivery of snoMEN RNAs and show this increases the efficiency of vector transduction in many human cell lines that are difficult to transfect with plasmid vectors. Transduction of lentiviral vectors expressing snoMEN targeted to pri-miR21 induces apoptosis in human lung adenocarcinoma cells, which express high levels of miR21, but not in human primary cells. We show that snoMEN-mediated suppression of miRNA expression is prevented by siRNA knock-down of Ago2, but not by knock-down of Ago1 or Upf1. snoMEN RNAs colocalise with Ago2 in cell nuclei and nucleoli and can be co-immunoprecipitated from nuclear extracts by antibodies specific for Ago2.

Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

PubMed Central

Yu, Junying; Hu, Kejin; Smuga-Otto, Kim; Tian, Shulan; Stewart, Ron; Slukvin, Igor I.; Thomson, James A.

2009-01-01

Reprogramming differentiated human cells to induced pluripotent stem (iPS) cells has applications in basic biology, drug development, and transplantation. Human iPS cell derivation previously required vectors that integrate into the genome, which can create mutations and limit the utility of the cells in both research and clinical applications. Here we describe the derivation of human iPS cells using non-integrating episomal vectors. After removal of the episome, iPS cells completely free of vector and transgene sequences are derived that are similar to human embryonic stem (ES) cells in proliferative and developmental potential. These results demonstrate that reprogramming human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one obstacle to the clinical application of human iPS cells. PMID:19325077

High-dimensional vector semantics

NASA Astrophysics Data System (ADS)

Andrecut, M.

In this paper we explore the “vector semantics” problem from the perspective of “almost orthogonal” property of high-dimensional random vectors. We show that this intriguing property can be used to “memorize” random vectors by simply adding them, and we provide an efficient probabilistic solution to the set membership problem. Also, we discuss several applications to word context vector embeddings, document sentences similarity, and spam filtering.

A vector scanning processing technique for pulsed laser velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1989-01-01

Pulsed laser sheet velocimetry yields nonintrusive measurements of two-dimensional velocity vectors across an extended planar region of a flow. Current processing techniques offer high precision (1 pct) velocity estimates, but can require several hours of processing time on specialized array processors. Under some circumstances, a simple, fast, less accurate (approx. 5 pct), data reduction technique which also gives unambiguous velocity vector information is acceptable. A direct space domain processing technique was examined. The direct space domain processing technique was found to be far superior to any other techniques known, in achieving the objectives listed above. It employs a new data coding and reduction technique, where the particle time history information is used directly. Further, it has no 180 deg directional ambiguity. A complex convection vortex flow was recorded and completely processed in under 2 minutes on an 80386 based PC, producing a 2-D velocity vector map of the flow field. Hence, using this new space domain vector scanning (VS) technique, pulsed laser velocimetry data can be reduced quickly and reasonably accurately, without specialized array processing hardware.

The Levi-Civita Tensor and Identities in Vector Analysis. Vector Field Identities. Modules and Monographs in Undergraduate Mathematics and Its Applications Project. UMAP Unit 427.

ERIC Educational Resources Information Center

Yiu, Chang-li; Wilde, Carroll O.

Vector analysis is viewed to play a key role in many branches of engineering and the physical sciences. This unit is geared towards deriving identities and establishing "machinery" to make derivations a routine task. It is noted that the module is not an applications unit, but has as its primary objective the goal of providing science,…

Development of apple latent spherical virus-based vaccines against three tospoviruses.

PubMed

Taki, Ayano; Yamagishi, Noriko; Yoshikawa, Nobuyuki

2013-09-01

Apple latent spherical virus (ALSV) is characterized by its relatively broad host range, latency in most host plants, and ability to induce gene silencing in host plants. Herein, we focus on the above characteristic of ALSV and describe our development of ALSV vector vaccines against three tospoviruses, namely, Impatiens necrotic spot virus (INSV), Iris yellow spot virus (IYSV), and Tomato spotted wilt virus (TSWV). DNA fragments of 201 nt of three tospovirus S-RNAs (silencing suppressor (NSS) and nucleocapsid protein (N) coding regions for each tospovirus) were inserted into an ALSV-RNA2 vector to obtain six types of ALSV vector vaccines. Nicotiana benthamiana plants at the five-leaf stage were inoculated with each ALSV vector vaccine and challenged with the corresponding tospovirus species. Tospovirus-induced symptoms and tospovirus replication after challenge were significantly suppressed in plants preinoculated with all ALSV vector vaccines having the N region fragment, indicating that strong resistance was acquired after infection with ALSV vector vaccines. On the other hand, cross protection was not significant in plants preinoculated with ALSV vectors having the NSs region fragment. Similarly, inoculation with an ALSV-RNA1 vector having the N region fragment in the 3'-noncoding region, but not the NSs region fragment, induced cross protection, indicating that cross protection is via RNA silencing, not via the function of the protein derived from the N region fragment. Our approach, wherein ALSV vectors and selected target inserts are used, enables rapid establishment of ALSV vector vaccines against many pathogenic RNA viruses with known sequences. Copyright © 2013 Elsevier B.V. All rights reserved.

On the Impact of Widening Vector Registers on Sequence Alignment

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

Daily, Jeffrey A.; Kalyanaraman, Anantharaman; Krishnamoorthy, Sriram

2016-09-22

Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based onmore » striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.« less

Automated solid-phase subcloning based on beads brought into proximity by magnetic force.

PubMed

Hudson, Elton P; Nikoshkov, Andrej; Uhlen, Mathias; Rockberg, Johan

2012-01-01

In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications.

Automated Solid-Phase Subcloning Based on Beads Brought into Proximity by Magnetic Force

PubMed Central

Hudson, Elton P.; Nikoshkov, Andrej; Uhlen, Mathias; Rockberg, Johan

2012-01-01

In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications. PMID:22624028

Reciprocity relationships in vector acoustics and their application to vector field calculations.

PubMed

Deal, Thomas J; Smith, Kevin B

2017-08-01

The reciprocity equation commonly stated in underwater acoustics relates pressure fields and monopole sources. It is often used to predict the pressure measured by a hydrophone for multiple source locations by placing a source at the hydrophone location and calculating the field everywhere for that source. A similar equation that governs the orthogonal components of the particle velocity field is needed to enable this computational method to be used for acoustic vector sensors. This paper derives a general reciprocity equation that accounts for both monopole and dipole sources. This vector-scalar reciprocity equation can be used to calculate individual components of the received vector field by altering the source type used in the propagation calculation. This enables a propagation model to calculate the received vector field components for an arbitrary number of source locations with a single model run for each vector field component instead of requiring one model run for each source location. Application of the vector-scalar reciprocity principle is demonstrated with analytic solutions for a range-independent environment and with numerical solutions for a range-dependent environment using a parabolic equation model.

Elliptic-symmetry vector optical fields.

PubMed

Pan, Yue; Li, Yongnan; Li, Si-Min; Ren, Zhi-Cheng; Kong, Ling-Jun; Tu, Chenghou; Wang, Hui-Tian

2014-08-11

We present in principle and demonstrate experimentally a new kind of vector fields: elliptic-symmetry vector optical fields. This is a significant development in vector fields, as this breaks the cylindrical symmetry and enriches the family of vector fields. Due to the presence of an additional degrees of freedom, which is the interval between the foci in the elliptic coordinate system, the elliptic-symmetry vector fields are more flexible than the cylindrical vector fields for controlling the spatial structure of polarization and for engineering the focusing fields. The elliptic-symmetry vector fields can find many specific applications from optical trapping to optical machining and so on.

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

NASA Astrophysics Data System (ADS)

Vincenti, H.; Lobet, M.; Lehe, R.; Sasanka, R.; Vay, J.-L.

2017-01-01

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈ 20 pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of × 2 to × 2.5 speed-up in double precision for particle shape factor of orders 1- 3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles).

Feature Selection Method Based on Neighborhood Relationships: Applications in EEG Signal Identification and Chinese Character Recognition

PubMed Central

Zhao, Yu-Xiang; Chou, Chien-Hsing

2016-01-01

In this study, a new feature selection algorithm, the neighborhood-relationship feature selection (NRFS) algorithm, is proposed for identifying rat electroencephalogram signals and recognizing Chinese characters. In these two applications, dependent relationships exist among the feature vectors and their neighboring feature vectors. Therefore, the proposed NRFS algorithm was designed for solving this problem. By applying the NRFS algorithm, unselected feature vectors have a high priority of being added into the feature subset if the neighboring feature vectors have been selected. In addition, selected feature vectors have a high priority of being eliminated if the neighboring feature vectors are not selected. In the experiments conducted in this study, the NRFS algorithm was compared with two feature algorithms. The experimental results indicated that the NRFS algorithm can extract the crucial frequency bands for identifying rat vigilance states and identifying crucial character regions for recognizing Chinese characters. PMID:27314346

Random vectors and spatial analysis by geostatistics for geotechnical applications

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

Young, D.S.

1987-08-01

Geostatistics is extended to the spatial analysis of vector variables by defining the estimation variance and vector variogram in terms of the magnitude of difference vectors. Many random variables in geotechnology are in vectorial terms rather than scalars, and its structural analysis requires those sample variable interpolations to construct and characterize structural models. A better local estimator will result in greater quality of input models; geostatistics can provide such estimators; kriging estimators. The efficiency of geostatistics for vector variables is demonstrated in a case study of rock joint orientations in geological formations. The positive cross-validation encourages application of geostatistics tomore » spatial analysis of random vectors in geoscience as well as various geotechnical fields including optimum site characterization, rock mechanics for mining and civil structures, cavability analysis of block cavings, petroleum engineering, and hydrologic and hydraulic modelings.« less

User's manual for CBS3DS, version 1.0

NASA Astrophysics Data System (ADS)

Reddy, C. J.; Deshpande, M. D.

1995-10-01

CBS3DS is a computer code written in FORTRAN 77 to compute the backscattering radar cross section of cavity backed apertures in infinite ground plane and slots in thick infinite ground plane. CBS3DS implements the hybrid Finite Element Method (FEM) and Method of Moments (MoM) techniques. This code uses the tetrahedral elements, with vector edge basis functions for FEM in the volume of the cavity/slot and the triangular elements with the basis functions for MoM at the apertures. By virtue of FEM, this code can handle any arbitrarily shaped three-dimensional cavities filled with inhomogeneous lossy materials; due to MoM, the apertures can be of any arbitrary shape. The User's Manual is written to make the user acquainted with the operation of the code. The user is assumed to be familiar with the FORTRAN 77 language and the operating environment of the computer the code is intended to run.

A Deep Insight Into the Sialotranscriptome of the Chagas Disease Vector, Panstrongylus megistus (Hemiptera: Heteroptera)

PubMed Central

Ribeiro, José M. C.; Schwarz, Alexandra; Francischetti, Ivo M. B.

2015-01-01

Saliva of blood-sucking arthropods contains a complex cocktail of pharmacologically active compounds that assists feeding by counteracting their hosts’ hemostatic and inflammatory reactions. Panstrongylus megistus (Burmeister) is an important vector of Chagas disease in South America, but despite its importance there is only one salivary protein sequence publicly deposited in GenBank. In the present work, we used Illumina technology to disclose and publicly deposit 3,703 coding sequences obtained from the assembly of >70 million reads. These sequences should assist proteomic experiments aimed at identifying pharmacologically active proteins and immunological markers of vector exposure. A supplemental file of the transcriptome and deducted protein sequences can be obtained from http://exon.niaid.nih.gov/transcriptome/P_megistus/Pmeg-web.xlsx. PMID:26334808

Production of scandium-44 m and scandium-44 g with deuterons on calcium-44: cross section measurements and production yield calculations.

PubMed

Duchemin, C; Guertin, A; Haddad, F; Michel, N; Métivier, V

2015-09-07

HIGHLIGHTS • Production of Sc-44 m, Sc-44 g and contaminants. • Experimental values determined using the stacked-foil technique. • Thick-Target production Yield (TTY) calculations. • Comparison with the TALYS code version 1.6.Among the large number of radionuclides of medical interest, Sc-44 is promising for PET imaging. Either the ground-state Sc-44 g or the metastable-state Sc-44 m can be used for such applications, depending on the molecule used as vector. This study compares the production rates of both Sc-44 states, when protons or deuterons are used as projectiles on an enriched Calcium-44 target. This work presents the first set of data for the deuteron route. The results are compared with the TALYS code. The Thick-Target production Yields of Sc-44 m and Sc-44 g are calculated and compared with those for the proton route for three different scenarios: the production of Sc-44 g for conventional PET imaging, its production for the new 3 γ imaging technique developed at the SUBATECH laboratory and the production of a Sc-44 m/Sc-44 g in vivo generator for antibody labelling.

Fast data preprocessing with Graphics Processing Units for inverse problem solving in light-scattering measurements

NASA Astrophysics Data System (ADS)

Derkachov, G.; Jakubczyk, T.; Jakubczyk, D.; Archer, J.; Woźniak, M.

2017-07-01

Utilising Compute Unified Device Architecture (CUDA) platform for Graphics Processing Units (GPUs) enables significant reduction of computation time at a moderate cost, by means of parallel computing. In the paper [Jakubczyk et al., Opto-Electron. Rev., 2016] we reported using GPU for Mie scattering inverse problem solving (up to 800-fold speed-up). Here we report the development of two subroutines utilising GPU at data preprocessing stages for the inversion procedure: (i) A subroutine, based on ray tracing, for finding spherical aberration correction function. (ii) A subroutine performing the conversion of an image to a 1D distribution of light intensity versus azimuth angle (i.e. scattering diagram), fed from a movie-reading CPU subroutine running in parallel. All subroutines are incorporated in PikeReader application, which we make available on GitHub repository. PikeReader returns a sequence of intensity distributions versus a common azimuth angle vector, corresponding to the recorded movie. We obtained an overall ∼ 400 -fold speed-up of calculations at data preprocessing stages using CUDA codes running on GPU in comparison to single thread MATLAB-only code running on CPU.

Recent advances and future prospects for Monte Carlo

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

Brown, Forrest B

2010-01-01

The history of Monte Carlo methods is closely linked to that of computers: The first known Monte Carlo program was written in 1947 for the ENIAC; a pre-release of the first Fortran compiler was used for Monte Carlo In 1957; Monte Carlo codes were adapted to vector computers in the 1980s, clusters and parallel computers in the 1990s, and teraflop systems in the 2000s. Recent advances include hierarchical parallelism, combining threaded calculations on multicore processors with message-passing among different nodes. With the advances In computmg, Monte Carlo codes have evolved with new capabilities and new ways of use. Production codesmore » such as MCNP, MVP, MONK, TRIPOLI and SCALE are now 20-30 years old (or more) and are very rich in advanced featUres. The former 'method of last resort' has now become the first choice for many applications. Calculations are now routinely performed on office computers, not just on supercomputers. Current research and development efforts are investigating the use of Monte Carlo methods on FPGAs. GPUs, and many-core processors. Other far-reaching research is exploring ways to adapt Monte Carlo methods to future exaflop systems that may have 1M or more concurrent computational processes.« less

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes

PubMed Central

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation. PMID:28582389

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes.

PubMed

Einkemmer, Lukas

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation.

A variable rate speech compressor for mobile applications

NASA Technical Reports Server (NTRS)

Yeldener, S.; Kondoz, A. M.; Evans, B. G.

1990-01-01

One of the most promising speech coder at the bit rate of 9.6 to 4.8 kbits/s is CELP. Code Excited Linear Prediction (CELP) has been dominating 9.6 to 4.8 kbits/s region during the past 3 to 4 years. Its set back however, is its expensive implementation. As an alternative to CELP, the Base-Band CELP (CELP-BB) was developed which produced good quality speech comparable to CELP and a single chip implementable complexity as reported previously. Its robustness was also improved to tolerate errors up to 1.0 pct. and maintain intelligibility up to 5.0 pct. and more. Although, CELP-BB produces good quality speech at around 4.8 kbits/s, it has a fundamental problem when updating the pitch filter memory. A sub-optimal solution is proposed for this problem. Below 4.8 kbits/s, however, CELP-BB suffers from noticeable quantization noise as a result of the large vector dimensions used. Efficient representation of speech below 4.8 kbits/s is reported by introducing Sinusoidal Transform Coding (STC) to represent the LPC excitation which is called Sine Wave Excited LPC (SWELP). In this case, natural sounding good quality synthetic speech is obtained at around 2.4 kbits/s.

Disruptive technology for vector control: the Innovative Vector Control Consortium and the US Military join forces to explore transformative insecticide application technology for mosquito control programmes.

PubMed

Knapp, Jennifer; Macdonald, Michael; Malone, David; Hamon, Nicholas; Richardson, Jason H

2015-09-26

Malaria vector control technology has remained largely static for decades and there is a pressing need for innovative control tools and methodology to radically improve the quality and efficiency of current vector control practices. This report summarizes a workshop jointly organized by the Innovative Vector Control Consortium (IVCC) and the Armed Forces Pest Management Board (AFPMB) focused on public health pesticide application technology. Three main topics were discussed: the limitations with current tools and techniques used for indoor residual spraying (IRS), technology innovation to improve efficacy of IRS programmes, and truly disruptive application technology beyond IRS. The group identified several opportunities to improve application technology to include: insuring all IRS programmes are using constant flow valves and erosion resistant tips; introducing compression sprayer improvements that help minimize pesticide waste and human error; and moving beyond IRS by embracing the potential for new larval source management techniques and next generation technology such as unmanned "smart" spray systems. The meeting served to lay the foundation for broader collaboration between the IVCC and AFPMB and partners in industry, the World Health Organization, the Bill and Melinda Gates Foundation and others.

Adenovirus-Mediated Gene Delivery: Potential Applications for Gene and Cell-Based Therapies in the New Era of Personalized Medicine

PubMed Central

Lee, Cody S.; Bishop, Elliot S.; Zhang, Ruyi; Yu, Xinyi; Farina, Evan M.; Yan, Shujuan; Zhao, Chen; Zheng, Zongyue; Shu, Yi; Wu, Xingye; Lei, Jiayan; Li, Yasha; Zhang, Wenwen; Yang, Chao; Wu, Ke; Wu, Ying; Ho, Sherwin; Athiviraham, Aravind; Lee, Michael J.; Wolf, Jennifer Moriatis; Reid, Russell R.; He, Tong-Chuan

2017-01-01

With rapid advances in understanding molecular pathogenesis of human diseases in the era of genome sciences and systems biology, it is anticipated that increasing numbers of therapeutic genes or targets will become available for targeted therapies. Despite numerous setbacks, efficacious gene and/or cell-based therapies still hold the great promise to revolutionize the clinical management of human diseases. It is wildly recognized that poor gene delivery is the limiting factor for most in vivo gene therapies. There has been a long-lasting interest in using viral vectors, especially adenoviral vectors, to deliver therapeutic genes for the past two decades. Among all currently available viral vectors, adenovirus is the most efficient gene delivery system in a broad range of cell and tissue types. The applications of adenoviral vectors in gene delivery have greatly increased in number and efficiency since their initial development. In fact, among over 2,000 gene therapy clinical trials approved worldwide since 1989, a significant portion of the trials have utilized adenoviral vectors. This review aims to provide a comprehensive overview on the characteristics of adenoviral vectors, including adenoviral biology, approaches to engineering adenoviral vectors, and their applications in clinical and pre-clinical studies with an emphasis in the areas of cancer treatment, vaccination and regenerative medicine. Current challenges and future directions regarding the use of adenoviral vectors are also discussed. It is expected that the continued improvements in adenoviral vectors should provide great opportunities for cell and gene therapies to live up to its enormous potential in personalized medicine. PMID:28944281

Towers of generalized divisible quantum codes

NASA Astrophysics Data System (ADS)

Haah, Jeongwan

2018-04-01

A divisible binary classical code is one in which every code word has weight divisible by a fixed integer. If the divisor is 2ν for a positive integer ν , then one can construct a Calderbank-Shor-Steane (CSS) code, where X -stabilizer space is the divisible classical code, that admits a transversal gate in the ν th level of Clifford hierarchy. We consider a generalization of the divisibility by allowing a coefficient vector of odd integers with which every code word has zero dot product modulo the divisor. In this generalized sense, we construct a CSS code with divisor 2ν +1 and code distance d from any CSS code of code distance d and divisor 2ν where the transversal X is a nontrivial logical operator. The encoding rate of the new code is approximately d times smaller than that of the old code. In particular, for large d and ν ≥2 , our construction yields a CSS code of parameters [[O (dν -1) ,Ω (d ) ,d ] ] admitting a transversal gate at the ν th level of Clifford hierarchy. For our construction we introduce a conversion from magic state distillation protocols based on Clifford measurements to those based on codes with transversal T gates. Our tower contains, as a subclass, generalized triply even CSS codes that have appeared in so-called gauge fixing or code switching methods.

The CMC/3DPNS computer program for prediction of three-dimensional, subsonic, turbulent aerodynamic juncture region flow. Volume 3: Programmers' manual

NASA Technical Reports Server (NTRS)

Orzechowski, J. A.

1982-01-01

The CMC fluid mechanics program system was developed to transmit the theoretical evolution of finite element numerical solution methodology, applied to nonlinear field problems into a versatile computer code for comprehensive flow field analysis. A detailed view of the code from the standpoint of a computer programmer's use is presented. A system macroflow chart and detailed flow charts of several routines necessary to interact with a theoretican/user to modify the operation of this program are presented. All subroutines and details of usage, primarily for input and output routines are described. Integer and real scalars and a cross reference list denoting subroutine usage for these scalars are outlined. Entry points in dynamic storage vector IZ; the lengths of each vector accompanying the scalar definitions are described. A listing of the routines peculiar to the standard test case and a listing of the input deck and printout for this case are included.

Simulating The Prompt Electromagnetic Pulse In 3D Using Vector Spherical Harmonics

NASA Astrophysics Data System (ADS)

Friedman, Alex; Cohen, Bruce I.; Eng, Chester D.; Farmer, William A.; Grote, David P.; Kruger, Hans W.; Larson, David J.

2017-10-01

We describe a new, efficient code for simulating the prompt electromagnetic pulse. In SHEMP (``Spherical Harmonic EMP''), we extend to 3-D the methods pioneered in C. Longmire's CHAP code. The geomagnetic field and air density are consistent with CHAP's assumed spherical symmetry only for narrow domains of influence about the line of sight, limiting validity to very early times. Also, we seek to model inherently 3-D situations. In CHAP and our own CHAP-lite, the independent coordinates are r (the distance from the source) and τ = t-r/c; the pulse varies slowly with r at fixed τ, so a coarse radial grid suffices. We add non-spherically-symmetric physics via a vector spherical harmonic decomposition. For each (l,m) harmonic, the radial equation is similar to that in CHAP and CHAP-lite. We present our methodology and results on model problems. This work was performed under the auspices of the U.S. DOE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Development of Plant Gene Vectors for Tissue-Specific Expression Using GFP as a Reporter Gene

NASA Technical Reports Server (NTRS)

Jackson, Jacquelyn; Egnin, Marceline; Xue, Qi-Han; Prakash, C. S.

1997-01-01

Reporter genes are widely employed in plant molecular biology research to analyze gene expression and to identify promoters. Gus (UidA) is currently the most popular reporter gene but its detection requires a destructive assay. The use of jellyfish green fluorescent protein (GFP) gene from Aequorea Victoria holds promise for noninvasive detection of in vivo gene expression. To study how various plant promoters are expressed in sweet potato (Ipomoea batatas), we are transcriptionally fusing the intron-modified (mGFP) or synthetic (modified for codon-usage) GFP coding regions to these promoters: double cauliflower mosaic virus 35S (CaMV 35S) with AMV translational enhancer, ubiquitin7-intron-ubiquitin coding region (ubi7-intron-UQ) and sporaminA. A few of these vectors have been constructed and introduced into E. coli DH5a and Agrobacterium tumefaciens EHA105. Transient expression studies are underway using protoplast-electroporation and particle bombardment of leaf tissues.

Learning vector quantization neural networks improve accuracy of transcranial color-coded duplex sonography in detection of middle cerebral artery spasm--preliminary report.

PubMed

Swiercz, Miroslaw; Kochanowicz, Jan; Weigele, John; Hurst, Robert; Liebeskind, David S; Mariak, Zenon; Melhem, Elias R; Krejza, Jaroslaw

2008-01-01

To determine the performance of an artificial neural network in transcranial color-coded duplex sonography (TCCS) diagnosis of middle cerebral artery (MCA) spasm. TCCS was prospectively acquired within 2 h prior to routine cerebral angiography in 100 consecutive patients (54M:46F, median age 50 years). Angiographic MCA vasospasm was classified as mild (<25% of vessel caliber reduction), moderate (25-50%), or severe (>50%). A Learning Vector Quantization neural network classified MCA spasm based on TCCS peak-systolic, mean, and end-diastolic velocity data. During a four-class discrimination task, accurate classification by the network ranged from 64.9% to 72.3%, depending on the number of neurons in the Kohonen layer. Accurate classification of vasospasm ranged from 79.6% to 87.6%, with an accuracy of 84.7% to 92.1% for the detection of moderate-to-severe vasospasm. An artificial neural network may increase the accuracy of TCCS in diagnosis of MCA spasm.

[Adeno-associated viral vectors: methods for production and purification for gene therapy applications].

PubMed

Mena-Enriquez, Mayra; Flores-Contreras, Lucia; Armendáriz-Borunda, Juan

2012-01-01

Viral vectors based on adeno-associated virus (AAV) are widely used in gene therapy protocols, because they have characteristics that make them valuable for the treatment of genetic and chronic degenerative diseases. AAV2 serotype had been the best characterized to date. However, the AAV vectors developed from other serotypes is of special interest, since they have organ-specific tropism which increases their potential for transgene delivery to target cells for performing their therapeutic effects. This article summarizes AAV generalities, methods for their production and purification. It also discusses the use of these vectors in vitro, in vivo and their application in gene therapy clinical trials.

Integrated pest management and allocation of control efforts for vector-borne diseases

USGS Publications Warehouse

Ginsberg, H.S.

2001-01-01

Applications of various control methods were evaluated to determine how to integrate methods so as to minimize the number of human cases of vector-borne diseases. These diseases can be controlled by lowering the number of vector-human contacts (e.g., by pesticide applications or use of repellents), or by lowering the proportion of vectors infected with pathogens (e.g., by lowering or vaccinating reservoir host populations). Control methods should be combined in such a way as to most efficiently lower the probability of human encounter with an infected vector. Simulations using a simple probabilistic model of pathogen transmission suggest that the most efficient way to integrate different control methods is to combine methods that have the same effect (e.g., combine treatments that lower the vector population; or combine treatments that lower pathogen prevalence in vectors). Combining techniques that have different effects (e.g., a technique that lowers vector populations with a technique that lowers pathogen prevalence in vectors) will be less efficient than combining two techniques that both lower vector populations or combining two techniques that both lower pathogen prevalence, costs being the same. Costs of alternative control methods generally differ, so the efficiency of various combinations at lowering human contact with infected vectors should be estimated at available funding levels. Data should be collected from initial trials to improve the effects of subsequent interventions on the number of human cases.

Deployment of the OSIRIS EM-PIC code on the Intel Knights Landing architecture

NASA Astrophysics Data System (ADS)

Fonseca, Ricardo

2017-10-01

Electromagnetic particle-in-cell (EM-PIC) codes such as OSIRIS have found widespread use in modelling the highly nonlinear and kinetic processes that occur in several relevant plasma physics scenarios, ranging from astrophysical settings to high-intensity laser plasma interaction. Being computationally intensive, these codes require large scale HPC systems, and a continuous effort in adapting the algorithm to new hardware and computing paradigms. In this work, we report on our efforts on deploying the OSIRIS code on the new Intel Knights Landing (KNL) architecture. Unlike the previous generation (Knights Corner), these boards are standalone systems, and introduce several new features, include the new AVX-512 instructions and on-package MCDRAM. We will focus on the parallelization and vectorization strategies followed, as well as memory management, and present a detailed performance evaluation of code performance in comparison with the CPU code. This work was partially supported by Fundaçã para a Ciência e Tecnologia (FCT), Portugal, through Grant No. PTDC/FIS-PLA/2940/2014.

Extensions and improvements on XTRAN3S

NASA Technical Reports Server (NTRS)

Borland, C. J.

1989-01-01

Improvements to the XTRAN3S computer program are summarized. Work on this code, for steady and unsteady aerodynamic and aeroelastic analysis in the transonic flow regime has concentrated on the following areas: (1) Maintenance of the XTRAN3S code, including correction of errors, enhancement of operational capability, and installation on the Cray X-MP system; (2) Extension of the vectorization concepts in XTRAN3S to include additional areas of the code for improved execution speed; (3) Modification of the XTRAN3S algorithm for improved numerical stability for swept, tapered wing cases and improved computational efficiency; and (4) Extension of the wing-only version of XTRAN3S to include pylon and nacelle or external store capability.

Minimal Increase Network Coding for Dynamic Networks.

PubMed

Zhang, Guoyin; Fan, Xu; Wu, Yanxia

2016-01-01

Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery.

Minimal Increase Network Coding for Dynamic Networks

PubMed Central

Wu, Yanxia

2016-01-01

Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery. PMID:26867211

Parallelization of Lower-Upper Symmetric Gauss-Seidel Method for Chemically Reacting Flow

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Jost, Gabriele; Chang, Sherry

2005-01-01

Development of technologies for exploration of the solar system has revived an interest in computational simulation of chemically reacting flows since planetary probe vehicles exhibit non-equilibrium phenomena during the atmospheric entry of a planet or a moon as well as the reentry to the Earth. Stability in combustion is essential for new propulsion systems. Numerical solution of real-gas flows often increases computational work by an order-of-magnitude compared to perfect gas flow partly because of the increased complexity of equations to solve. Recently, as part of Project Columbia, NASA has integrated a cluster of interconnected SGI Altix systems to provide a ten-fold increase in current supercomputing capacity that includes an SGI Origin system. Both the new and existing machines are based on cache coherent non-uniform memory access architecture. Lower-Upper Symmetric Gauss-Seidel (LU-SGS) relaxation method has been implemented into both perfect and real gas flow codes including Real-Gas Aerodynamic Simulator (RGAS). However, the vectorized RGAS code runs inefficiently on cache-based shared-memory machines such as SGI system. Parallelization of a Gauss-Seidel method is nontrivial due to its sequential nature. The LU-SGS method has been vectorized on an oblique plane in INS3D-LU code that has been one of the base codes for NAS Parallel benchmarks. The oblique plane has been called a hyperplane by computer scientists. It is straightforward to parallelize a Gauss-Seidel method by partitioning the hyperplanes once they are formed. Another way of parallelization is to schedule processors like a pipeline using software. Both hyperplane and pipeline methods have been implemented using openMP directives. The present paper reports the performance of the parallelized RGAS code on SGI Origin and Altix systems.

Using Intel Xeon Phi to accelerate the WRF TEMF planetary boundary layer scheme

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen

2014-05-01

The Weather Research and Forecasting (WRF) model is designed for numerical weather prediction and atmospheric research. The WRF software infrastructure consists of several components such as dynamic solvers and physics schemes. Numerical models are used to resolve the large-scale flow. However, subgrid-scale parameterizations are for an estimation of small-scale properties (e.g., boundary layer turbulence and convection, clouds, radiation). Those have a significant influence on the resolved scale due to the complex nonlinear nature of the atmosphere. For the cloudy planetary boundary layer (PBL), it is fundamental to parameterize vertical turbulent fluxes and subgrid-scale condensation in a realistic manner. A parameterization based on the Total Energy - Mass Flux (TEMF) that unifies turbulence and moist convection components produces a better result that the other PBL schemes. For that reason, the TEMF scheme is chosen as the PBL scheme we optimized for Intel Many Integrated Core (MIC), which ushers in a new era of supercomputing speed, performance, and compatibility. It allows the developers to run code at trillions of calculations per second using the familiar programming model. In this paper, we present our optimization results for TEMF planetary boundary layer scheme. The optimizations that were performed were quite generic in nature. Those optimizations included vectorization of the code to utilize vector units inside each CPU. Furthermore, memory access was improved by scalarizing some of the intermediate arrays. The results show that the optimization improved MIC performance by 14.8x. Furthermore, the optimizations increased CPU performance by 2.6x compared to the original multi-threaded code on quad core Intel Xeon E5-2603 running at 1.8 GHz. Compared to the optimized code running on a single CPU socket the optimized MIC code is 6.2x faster.

Adenovirus-Vectored Broadly Neutralizing Antibodies Directed Against gp120 Prevent Human Immunodeficiency Virus Type 1 Acquisition in Humanized Mice.

PubMed

Liu, Shan; Jackson, Andrew; Beloor, Jagadish; Kumar, Priti; Sutton, Richard E

2015-09-01

Despite nearly three decades of research, a safe and effective vaccine against human immunodeficiency virus type 1 (HIV-1) has yet to be achieved. More recently, the discovery of highly potent anti-gp160 broadly neutralizing antibodies (bNAbs) has garnered renewed interest in using antibody-based prophylactic and therapeutic approaches. Here, we encoded bNAbs in first-generation adenoviral (ADV) vectors, which have the distinctive features of a large coding capacity and ease of propagation. A single intramuscular injection of ADV-vectorized bNAbs in humanized mice generated high serum levels of bNAbs that provided protection against multiple repeated challenges with a high dose of HIV-1, prevented depletion of peripheral CD4(+) T cells, and reduced plasma viral loads to below detection limits. Our results suggest that ADV vectors may be a viable option for the prophylactic and perhaps therapeutic use of bNAbs in humans.

Medical and Transmission Vector Vocabulary Alignment with Schema.org

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

Smith, William P.; Chappell, Alan R.; Corley, Courtney D.

Available biomedical ontologies and knowledge bases currently lack formal and standards-based interconnections between disease, disease vector, and drug treatment vocabularies. The PNNL Medical Linked Dataset (PNNL-MLD) addresses this gap. This paper describes the PNNL-MLD, which provides a unified vocabulary and dataset of drug, disease, side effect, and vector transmission background information. Currently, the PNNL-MLD combines and curates data from the following research projects: DrugBank, DailyMed, Diseasome, DisGeNet, Wikipedia Infobox, Sider, and PharmGKB. The main outcomes of this effort are a dataset aligned to Schema.org, including a parsing framework, and extensible hooks ready for integration with selected medical ontologies. The PNNL-MLDmore » enables researchers more quickly and easily to query distinct datasets. Future extensions to the PNNL-MLD will include Traditional Chinese Medicine, broader interlinks across genetic structures, a larger thesaurus of synonyms and hypernyms, explicit coding of diseases and drugs across research systems, and incorporating vector-borne transmission vocabularies.« less

The Vector, Signal, and Image Processing Library (VSIPL): an Open Standard for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Kepner, J. V.; Janka, R. S.; Lebak, J.; Richards, M. A.

1999-12-01

The Vector/Signal/Image Processing Library (VSIPL) is a DARPA initiated effort made up of industry, government and academic representatives who have defined an industry standard API for vector, signal, and image processing primitives for real-time signal processing on high performance systems. VSIPL supports a wide range of data types (int, float, complex, ...) and layouts (vectors, matrices and tensors) and is ideal for astronomical data processing. The VSIPL API is intended to serve as an open, vendor-neutral, industry standard interface. The object-based VSIPL API abstracts the memory architecture of the underlying machine by using the concept of memory blocks and views. Early experiments with VSIPL code conversions have been carried out by the High Performance Computing Program team at the UCSD. Commercially, several major vendors of signal processors are actively developing implementations. VSIPL has also been explicitly required as part of a recent Rome Labs teraflop procurement. This poster presents the VSIPL API, its functionality and the status of various implementations.

Enhancing speech recognition using improved particle swarm optimization based hidden Markov model.

PubMed

Selvaraj, Lokesh; Ganesan, Balakrishnan

2014-01-01

Enhancing speech recognition is the primary intention of this work. In this paper a novel speech recognition method based on vector quantization and improved particle swarm optimization (IPSO) is suggested. The suggested methodology contains four stages, namely, (i) denoising, (ii) feature mining (iii), vector quantization, and (iv) IPSO based hidden Markov model (HMM) technique (IP-HMM). At first, the speech signals are denoised using median filter. Next, characteristics such as peak, pitch spectrum, Mel frequency Cepstral coefficients (MFCC), mean, standard deviation, and minimum and maximum of the signal are extorted from the denoised signal. Following that, to accomplish the training process, the extracted characteristics are given to genetic algorithm based codebook generation in vector quantization. The initial populations are created by selecting random code vectors from the training set for the codebooks for the genetic algorithm process and IP-HMM helps in doing the recognition. At this point the creativeness will be done in terms of one of the genetic operation crossovers. The proposed speech recognition technique offers 97.14% accuracy.

Biological Gene Delivery Vehicles: Beyond Viral Vectors

PubMed Central

Seow, Yiqi; Wood, Matthew J

2009-01-01

Gene therapy covers a broad spectrum of applications, from gene replacement and knockdown for genetic or acquired diseases such as cancer, to vaccination, each with different requirements for gene delivery. Viral vectors and synthetic liposomes have emerged as the vehicles of choice for many applications today, but both have limitations and risks, including complexity of production, limited packaging capacity, and unfavorable immunological features, which restrict gene therapy applications and hold back the potential for preventive gene therapy. While continuing to improve these vectors, it is important to investigate other options, particularly nonviral biological agents which include bacteria, bacteriophage, virus-like particles (VLPs), erythrocyte ghosts, and exosomes. Exploiting the natural properties of these biological entities for specific gene delivery applications will expand the repertoire of gene therapy vectors available for clinical use. Here, we review the prospects for nonviral biological delivery vehicles as gene therapy agents with focus on their unique evolved biological properties and respective limitations and potential applications. The potential of these nonviral biological entities to act as clinical gene therapy delivery vehicles has already been shown in clinical trials using bacteria-mediated gene transfer and with sufficient development, these entities will complement the established delivery techniques for gene therapy applications. PMID:19277019

Biological gene delivery vehicles: beyond viral vectors.

PubMed

Seow, Yiqi; Wood, Matthew J

2009-05-01

Gene therapy covers a broad spectrum of applications, from gene replacement and knockdown for genetic or acquired diseases such as cancer, to vaccination, each with different requirements for gene delivery. Viral vectors and synthetic liposomes have emerged as the vehicles of choice for many applications today, but both have limitations and risks, including complexity of production, limited packaging capacity, and unfavorable immunological features, which restrict gene therapy applications and hold back the potential for preventive gene therapy. While continuing to improve these vectors, it is important to investigate other options, particularly nonviral biological agents which include bacteria, bacteriophage, virus-like particles (VLPs), erythrocyte ghosts, and exosomes. Exploiting the natural properties of these biological entities for specific gene delivery applications will expand the repertoire of gene therapy vectors available for clinical use. Here, we review the prospects for nonviral biological delivery vehicles as gene therapy agents with focus on their unique evolved biological properties and respective limitations and potential applications. The potential of these nonviral biological entities to act as clinical gene therapy delivery vehicles has already been shown in clinical trials using bacteria-mediated gene transfer and with sufficient development, these entities will complement the established delivery techniques for gene therapy applications.

Development of nonhuman adenoviruses as vaccine vectors

PubMed Central

Bangari, Dinesh S.; Mittal, Suresh K.

2006-01-01

Human adenoviral (HAd) vectors have demonstrated great potential as vaccine vectors. Preclinical and clinical studies have demonstrated the feasibility of vector design, robust antigen expression and protective immunity using this system. However, clinical use of adenoviral vectors for vaccine purposes is anticipated to be limited by vector immunity that is either preexisting or develops rapidly following the first inoculation with adenoviral vectors. Vector immunity inactivates the vector particles and rapidly removes the transduced cells, thereby limiting the duration of transgene expression. Due to strong vector immunity, subsequent use of the same vector is usually less efficient. In order to circumvent this limitation, nonhuman adenoviral vectors have been proposed as alternative vectors. In addition to eluding HAd immunity, these vectors possess most of the attractive features of HAd vectors. Several replication-competent or replication-defective nonhuman adenoviral vectors have been developed and investigated for their potential as vaccine delivery vectors. Here, we review recent advances in the design and characterization of various nonhuman adenoviral vectors, and discuss their potential applications for human and animal vaccination. PMID:16297508

Accelerating next generation sequencing data analysis with system level optimizations.

PubMed

Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

2017-08-22

Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

Viral and Synthetic RNA Vector Technologies and Applications

PubMed Central

Schott, Juliane W; Morgan, Michael; Galla, Melanie; Schambach, Axel

2016-01-01

Use of RNA is an increasingly popular method to transiently deliver genetic information for cell manipulation in basic research and clinical therapy. In these settings, viral and nonviral RNA platforms are employed for delivery of small interfering RNA and protein-coding mRNA. Technological advances allowing RNA modification for increased stability, improved translation and reduced immunogenicity have led to increased use of nonviral synthetic RNA, which is delivered in naked form or upon formulation. Alternatively, highly efficient viral entry pathways are exploited to transfer genes of interest as RNA incorporated into viral particles. Current viral RNA transfer technologies are derived from Retroviruses, nonsegmented negative-strand RNA viruses or positive-stranded Alpha- and Flaviviruses. In retroviral particles, the genes of interest can either be incorporated directly into the viral RNA genome or as nonviral RNA. Nonsegmented negative-strand virus-, Alpha- and Flavivirus-derived vectors support prolonged expression windows through replication of viral RNA encoding genes of interest. Mixed technologies combining viral and nonviral components are also available. RNA transfer is ideal for all settings that do not require permanent transgene expression and excludes potentially detrimental DNA integration into the target cell genome. Thus, RNA-based technologies are successfully applied for reprogramming, transdifferentiation, gene editing, vaccination, tumor therapy, and gene therapy. PMID:27377044

Deep Learning for Automated Extraction of Primary Sites From Cancer Pathology Reports.

PubMed

Qiu, John X; Yoon, Hong-Jun; Fearn, Paul A; Tourassi, Georgia D

2018-01-01

Pathology reports are a primary source of information for cancer registries which process high volumes of free-text reports annually. Information extraction and coding is a manual, labor-intensive process. In this study, we investigated deep learning and a convolutional neural network (CNN), for extracting ICD-O-3 topographic codes from a corpus of breast and lung cancer pathology reports. We performed two experiments, using a CNN and a more conventional term frequency vector approach, to assess the effects of class prevalence and inter-class transfer learning. The experiments were based on a set of 942 pathology reports with human expert annotations as the gold standard. CNN performance was compared against a more conventional term frequency vector space approach. We observed that the deep learning models consistently outperformed the conventional approaches in the class prevalence experiment, resulting in micro- and macro-F score increases of up to 0.132 and 0.226, respectively, when class labels were well populated. Specifically, the best performing CNN achieved a micro-F score of 0.722 over 12 ICD-O-3 topography codes. Transfer learning provided a consistent but modest performance boost for the deep learning methods but trends were contingent on the CNN method and cancer site. These encouraging results demonstrate the potential of deep learning for automated abstraction of pathology reports.

Towards a next generation open-source video codec

NASA Astrophysics Data System (ADS)

Bankoski, Jim; Bultje, Ronald S.; Grange, Adrian; Gu, Qunshan; Han, Jingning; Koleszar, John; Mukherjee, Debargha; Wilkins, Paul; Xu, Yaowu

2013-02-01

Google has recently been developing a next generation opensource video codec called VP9, as part of the experimental branch of the libvpx repository included in the WebM project (http://www.webmproject.org/). Starting from the VP8 video codec released by Google in 2010 as the baseline, a number of enhancements and new tools have been added to improve the coding efficiency. This paper provides a technical overview of the current status of this project along with comparisons and other stateoftheart video codecs H. 264/AVC and HEVC. The new tools that have been added so far include: larger prediction block sizes up to 64x64, various forms of compound INTER prediction, more modes for INTRA prediction, ⅛pel motion vectors and 8tap switchable subpel interpolation filters, improved motion reference generation and motion vector coding, improved entropy coding and framelevel entropy adaptation for various symbols, improved loop filtering, incorporation of Asymmetric Discrete Sine Transforms and larger 16x16 and 32x32 DCTs, frame level segmentation to group similar areas together, etc. Other tools and various bitstream features are being actively worked on as well. The VP9 bitstream is expected to be finalized by earlyto mid2013. Results show VP9 to be quite competitive in performance with mainstream stateoftheart codecs.

Study of the modifications needed for efficient operation of NASTRAN on the Control Data Corporation STAR-100 computer

NASA Technical Reports Server (NTRS)

1975-01-01

NASA structural analysis (NASTRAN) computer program is operational on three series of third generation computers. The problem and difficulties involved in adapting NASTRAN to a fourth generation computer, namely, the Control Data STAR-100, are discussed. The salient features which distinguish Control Data STAR-100 from third generation computers are hardware vector processing capability and virtual memory. A feasible method is presented for transferring NASTRAN to Control Data STAR-100 system while retaining much of the machine-independent code. Basic matrix operations are noted for optimization for vector processing.

Support vector machine multiuser receiver for DS-CDMA signals in multipath channels.

PubMed

Chen, S; Samingan, A K; Hanzo, L

2001-01-01

The problem of constructing an adaptive multiuser detector (MUD) is considered for direct sequence code division multiple access (DS-CDMA) signals transmitted through multipath channels. The emerging learning technique, called support vector machines (SVM), is proposed as a method of obtaining a nonlinear MUD from a relatively small training data block. Computer simulation is used to study this SVM MUD, and the results show that it can closely match the performance of the optimal Bayesian one-shot detector. Comparisons with an adaptive radial basis function (RBF) MUD trained by an unsupervised clustering algorithm are discussed.

A Study of Shaped-Charge Collapse and Jet Formation Using the HEMP (hydrodynamic, Elastic, Magneto, and Plastic) Code and a Comparison with Experimental Observations

DTIC Science & Technology

1984-12-01

Octol** explosive. The experimental charges were lightly confined with aluminum bodies and had cone diameters of 84mm. The charges modelled using HEMP...solved using the following relationships: .Final Final V 0 1 IV sin 9, where Voz aj i teailcmpnn fj~Fnl n Final F where V is the adial component of Fnan h...velocity vector is equal to the vector addition of the flow and 8. MMiles L. Lampson, "The Influence of Convergence - Velocity Gradients on the Formation

Ultra-low background DNA cloning system.

PubMed

Goto, Kenta; Nagano, Yukio

2013-01-01

Yeast-based in vivo cloning is useful for cloning DNA fragments into plasmid vectors and is based on the ability of yeast to recombine the DNA fragments by homologous recombination. Although this method is efficient, it produces some by-products. We have developed an "ultra-low background DNA cloning system" on the basis of yeast-based in vivo cloning, by almost completely eliminating the generation of by-products and applying the method to commonly used Escherichia coli vectors, particularly those lacking yeast replication origins and carrying an ampicillin resistance gene (Amp(r)). First, we constructed a conversion cassette containing the DNA sequences in the following order: an Amp(r) 5' UTR (untranslated region) and coding region, an autonomous replication sequence and a centromere sequence from yeast, a TRP1 yeast selectable marker, and an Amp(r) 3' UTR. This cassette allowed conversion of the Amp(r)-containing vector into the yeast/E. coli shuttle vector through use of the Amp(r) sequence by homologous recombination. Furthermore, simultaneous transformation of the desired DNA fragment into yeast allowed cloning of this DNA fragment into the same vector. We rescued the plasmid vectors from all yeast transformants, and by-products containing the E. coli replication origin disappeared. Next, the rescued vectors were transformed into E. coli and the by-products containing the yeast replication origin disappeared. Thus, our method used yeast- and E. coli-specific "origins of replication" to eliminate the generation of by-products. Finally, we successfully cloned the DNA fragment into the vector with almost 100% efficiency.

Studying an Eulerian Computer Model on Different High-performance Computer Platforms and Some Applications

NASA Astrophysics Data System (ADS)

Georgiev, K.; Zlatev, Z.

2010-11-01

The Danish Eulerian Model (DEM) is an Eulerian model for studying the transport of air pollutants on large scale. Originally, the model was developed at the National Environmental Research Institute of Denmark. The model computational domain covers Europe and some neighbour parts belong to the Atlantic Ocean, Asia and Africa. If DEM model is to be applied by using fine grids, then its discretization leads to a huge computational problem. This implies that such a model as DEM must be run only on high-performance computer architectures. The implementation and tuning of such a complex large-scale model on each different computer is a non-trivial task. Here, some comparison results of running of this model on different kind of vector (CRAY C92A, Fujitsu, etc.), parallel computers with distributed memory (IBM SP, CRAY T3E, Beowulf clusters, Macintosh G4 clusters, etc.), parallel computers with shared memory (SGI Origin, SUN, etc.) and parallel computers with two levels of parallelism (IBM SMP, IBM BlueGene/P, clusters of multiprocessor nodes, etc.) will be presented. The main idea in the parallel version of DEM is domain partitioning approach. Discussions according to the effective use of the cache and hierarchical memories of the modern computers as well as the performance, speed-ups and efficiency achieved will be done. The parallel code of DEM, created by using MPI standard library, appears to be highly portable and shows good efficiency and scalability on different kind of vector and parallel computers. Some important applications of the computer model output are presented in short.

A novel protocol for the production of recombinant LL-37 expressed as a thioredoxin fusion protein.

PubMed

Li, Yifeng

2012-02-01

LL-37 is the only cathelicidin-derived antimicrobial peptide found in humans and it has a multifunctional role in host defense. The peptide has been shown to possess immunomodulatory functions in addition to antimicrobial activity. To provide sufficient material for biological and structural characterization of this important peptide, various systems were developed to produce recombinant LL-37 in Escherichia coli. In one previous approach, LL-37 coding sequence was cloned into vector pET-32a, allowing the peptide to be expressed as a thioredoxin fusion. The fusion protein contains two thrombin cleavage sites: a vector-encoded one that is 30-residue upstream of the insert and an engineered one that is immediately adjacent to LL-37. Cleavage at these two sites shall generate three fragments, one of which is the target peptide. However, when the fusion protein was treated with thrombin, cleavage only occurred at the remote upstream site. A plausible explanation is that the thrombin site adjacent to LL-37 is less accessible due to the peptide's aggregation tendency and cleavage at the remote site generates a fragment, which forms a large aggregate that buries the intended site. In this study, I deleted the vector-encoded thrombin site and S tag in pET-32a, and then inserted the coding sequence for LL-37 plus a thrombin site into the modified vector. Although removing the S tag did not change the oligomeric state of the fusion protein, deletion of the vector-encoded thrombin site allowed the fusion to be cleaved at the engineered site to release LL-37. The released peptide was separated from the carrier and cleavage enzyme by size-exclusion chromatography. This new approach enables a quick production of high quality active LL-37 with a decent amount. Copyright © 2011 Elsevier Inc. All rights reserved.

The Monkey and the Hunter.

ERIC Educational Resources Information Center

Rogowski, Steve

1982-01-01

A problem is detailed which has a solution that embodies geometry, trigonometry, ballistics, projectile mechanics, vector analysis, and elementary computer graphics. It is felt that the information and sample computer programs can be a useful starting point for a user written code that involves missiles and other projectiles. (MP)

Bayesian Analogy with Relational Transformations

ERIC Educational Resources Information Center

Lu, Hongjing; Chen, Dawn; Holyoak, Keith J.

2012-01-01

How can humans acquire relational representations that enable analogical inference and other forms of high-level reasoning? Using comparative relations as a model domain, we explore the possibility that bottom-up learning mechanisms applied to objects coded as feature vectors can yield representations of relations sufficient to solve analogy…

A spectral-structural bag-of-features scene classifier for very high spatial resolution remote sensing imagery

NASA Astrophysics Data System (ADS)

Zhao, Bei; Zhong, Yanfei; Zhang, Liangpei

2016-06-01

Land-use classification of very high spatial resolution remote sensing (VHSR) imagery is one of the most challenging tasks in the field of remote sensing image processing. However, the land-use classification is hard to be addressed by the land-cover classification techniques, due to the complexity of the land-use scenes. Scene classification is considered to be one of the expected ways to address the land-use classification issue. The commonly used scene classification methods of VHSR imagery are all derived from the computer vision community that mainly deal with terrestrial image recognition. Differing from terrestrial images, VHSR images are taken by looking down with airborne and spaceborne sensors, which leads to the distinct light conditions and spatial configuration of land cover in VHSR imagery. Considering the distinct characteristics, two questions should be answered: (1) Which type or combination of information is suitable for the VHSR imagery scene classification? (2) Which scene classification algorithm is best for VHSR imagery? In this paper, an efficient spectral-structural bag-of-features scene classifier (SSBFC) is proposed to combine the spectral and structural information of VHSR imagery. SSBFC utilizes the first- and second-order statistics (the mean and standard deviation values, MeanStd) as the statistical spectral descriptor for the spectral information of the VHSR imagery, and uses dense scale-invariant feature transform (SIFT) as the structural feature descriptor. From the experimental results, the spectral information works better than the structural information, while the combination of the spectral and structural information is better than any single type of information. Taking the characteristic of the spatial configuration into consideration, SSBFC uses the whole image scene as the scope of the pooling operator, instead of the scope generated by a spatial pyramid (SP) commonly used in terrestrial image classification. The experimental results show that the whole image as the scope of the pooling operator performs better than the scope generated by SP. In addition, SSBFC codes and pools the spectral and structural features separately to avoid mutual interruption between the spectral and structural features. The coding vectors of spectral and structural features are then concatenated into a final coding vector. Finally, SSBFC classifies the final coding vector by support vector machine (SVM) with a histogram intersection kernel (HIK). Compared with the latest scene classification methods, the experimental results with three VHSR datasets demonstrate that the proposed SSBFC performs better than the other classification methods for VHSR image scenes.

A Semi-Vectorization Algorithm to Synthesis of Gravitational Anomaly Quantities on the Earth

NASA Astrophysics Data System (ADS)

Abdollahzadeh, M.; Eshagh, M.; Najafi Alamdari, M.

2009-04-01

The Earth's gravitational potential can be expressed by the well-known spherical harmonic expansion. The computational time of summing up this expansion is an important practical issue which can be reduced by an efficient numerical algorithm. This paper proposes such a method for block-wise synthesizing the anomaly quantities on the Earth surface using vectorization. Fully-vectorization means transformation of the summations to the simple matrix and vector products. It is not a practical for the matrices with large dimensions. Here a semi-vectorization algorithm is proposed to avoid working with large vectors and matrices. It speeds up the computations by using one loop for the summation either on degrees or on orders. The former is a good option to synthesize the anomaly quantities on the Earth surface considering a digital elevation model (DEM). This approach is more efficient than the two-step method which computes the quantities on the reference ellipsoid and continues them upward to the Earth surface. The algorithm has been coded in MATLAB which synthesizes a global grid of 5′Ã- 5′ (corresponding 9 million points) of gravity anomaly or geoid height using a geopotential model to degree 360 in 10000 seconds by an ordinary computer with 2G RAM.

Navier-Stokes calculations for DFVLR F5-wing in wind tunnel using Runge-Kutta time-stepping scheme

NASA Technical Reports Server (NTRS)

Vatsa, V. N.; Wedan, B. W.

1988-01-01

A three-dimensional Navier-Stokes code using an explicit multistage Runge-Kutta type of time-stepping scheme is used for solving the transonic flow past a finite wing mounted inside a wind tunnel. Flow past the same wing in free air was also computed to assess the effect of wind-tunnel walls on such flows. Numerical efficiency is enhanced through vectorization of the computer code. A Cyber 205 computer with 32 million words of internal memory was used for these computations.

A computer program for estimation from incomplete multinomial data

NASA Technical Reports Server (NTRS)

Credeur, K. R.

1978-01-01

Coding is given for maximum likelihood and Bayesian estimation of the vector p of multinomial cell probabilities from incomplete data. Also included is coding to calculate and approximate elements of the posterior mean and covariance matrices. The program is written in FORTRAN 4 language for the Control Data CYBER 170 series digital computer system with network operating system (NOS) 1.1. The program requires approximately 44000 octal locations of core storage. A typical case requires from 72 seconds to 92 seconds on CYBER 175 depending on the value of the prior parameter.

Additional development of the XTRAN3S computer program

NASA Technical Reports Server (NTRS)

Borland, C. J.

1989-01-01

Additional developments and enhancements to the XTRAN3S computer program, a code for calculation of steady and unsteady aerodynamics, and associated aeroelastic solutions, for 3-D wings in the transonic flow regime are described. Algorithm improvements for the XTRAN3S program were provided including an implicit finite difference scheme to enhance the allowable time step and vectorization for improved computational efficiency. The code was modified to treat configurations with a fuselage, multiple stores/nacelles/pylons, and winglets. Computer program changes (updates) for error corrections and updates for version control are provided.

A vectorized code for calculating laminar and turbulent hypersonic flows about blunt axisymmetric bodies at zero and small angles of attack

NASA Technical Reports Server (NTRS)

Kumar, A.; Graves, R. A., Jr.

1980-01-01

A user's guide is provided for a computer code which calculates the laminar and turbulent hypersonic flows about blunt axisymmetric bodies, such as spherically blunted cones, hyperboloids, etc., at zero and small angles of attack. The code is written in STAR FORTRAN language for the CDC-STAR-100 computer. Time-dependent, viscous-shock-layer-type equations are used to describe the flow field. These equations are solved by an explicit, two-step, time asymptotic, finite-difference method. For the turbulent flow, a two-layer, eddy-viscosity model is used. The code provides complete flow-field properties including shock location, surface pressure distribution, surface heating rates, and skin-friction coefficients. This report contains descriptions of the input and output, the listing of the program, and a sample flow-field solution.

Comparison of deterministic and stochastic approaches for isotopic concentration and decay heat uncertainty quantification on elementary fission pulse

NASA Astrophysics Data System (ADS)

Lahaye, S.; Huynh, T. D.; Tsilanizara, A.

2016-03-01

Uncertainty quantification of interest outputs in nuclear fuel cycle is an important issue for nuclear safety, from nuclear facilities to long term deposits. Most of those outputs are functions of the isotopic vector density which is estimated by fuel cycle codes, such as DARWIN/PEPIN2, MENDEL, ORIGEN or FISPACT. CEA code systems DARWIN/PEPIN2 and MENDEL propagate by two different methods the uncertainty from nuclear data inputs to isotopic concentrations and decay heat. This paper shows comparisons between those two codes on a Uranium-235 thermal fission pulse. Effects of nuclear data evaluation's choice (ENDF/B-VII.1, JEFF-3.1.1 and JENDL-2011) is inspected in this paper. All results show good agreement between both codes and methods, ensuring the reliability of both approaches for a given evaluation.

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

Ontology Sparse Vector Learning Algorithm for Ontology Similarity Measuring and Ontology Mapping via ADAL Technology

NASA Astrophysics Data System (ADS)

Gao, Wei; Zhu, Linli; Wang, Kaiyun

2015-12-01

Ontology, a model of knowledge representation and storage, has had extensive applications in pharmaceutics, social science, chemistry and biology. In the age of “big data”, the constructed concepts are often represented as higher-dimensional data by scholars, and thus the sparse learning techniques are introduced into ontology algorithms. In this paper, based on the alternating direction augmented Lagrangian method, we present an ontology optimization algorithm for ontological sparse vector learning, and a fast version of such ontology technologies. The optimal sparse vector is obtained by an iterative procedure, and the ontology function is then obtained from the sparse vector. Four simulation experiments show that our ontological sparse vector learning model has a higher precision ratio on plant ontology, humanoid robotics ontology, biology ontology and physics education ontology data for similarity measuring and ontology mapping applications.

Application of optical correlation techniques to particle imaging velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1988-01-01

Pulsed laser sheet velocimetry yields nonintrusive measurements of velocity vectors across an extended 2-dimensional region of the flow field. The application of optical correlation techniques to the analysis of multiple exposure laser light sheet photographs can reduce and/or simplify the data reduction time and hardware. Here, Matched Spatial Filters (MSF) are used in a pattern recognition system. Usually MSFs are used to identify the assembly line parts. In this application, the MSFs are used to identify the iso-velocity vector contours in the flow. The patterns to be recognized are the recorded particle images in a pulsed laser light sheet photograph. Measurement of the direction of the partical image displacements between exposures yields the velocity vector. The particle image exposure sequence is designed such that the velocity vector direction is determined unambiguously. A global analysis technique is used in comparison to the more common particle tracking algorithms and Young's fringe analysis technique.

WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

NASA Technical Reports Server (NTRS)

Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

1998-01-01

This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves vectorization of the code on uni-processor hardware and enables straightforward parallel-vector processing of element blocks on multi-processor hardware.