Real-time individualized training vectors for experiential learning.

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

Willis, Matt; Tucker, Eilish Marie; Raybourn, Elaine Marie

2011-01-01

Military training utilizing serious games or virtual worlds potentially generate data that can be mined to better understand how trainees learn in experiential exercises. Few data mining approaches for deployed military training games exist. Opportunities exist to collect and analyze these data, as well as to construct a full-history learner model. Outcomes discussed in the present document include results from a quasi-experimental research study on military game-based experiential learning, the deployment of an online game for training evidence collection, and results from a proof-of-concept pilot study on the development of individualized training vectors. This Lab Directed Research & Development (LDRD)more » project leveraged products within projects, such as Titan (Network Grand Challenge), Real-Time Feedback and Evaluation System, (America's Army Adaptive Thinking and Leadership, DARWARS Ambush! NK), and Dynamic Bayesian Networks to investigate whether machine learning capabilities could perform real-time, in-game similarity vectors of learner performance, toward adaptation of content delivery, and quantitative measurement of experiential learning.« less

Using a multifrontal sparse solver in a high performance, finite element code

NASA Technical Reports Server (NTRS)

King, Scott D.; Lucas, Robert; Raefsky, Arthur

1990-01-01

We consider the performance of the finite element method on a vector supercomputer. The computationally intensive parts of the finite element method are typically the individual element forms and the solution of the global stiffness matrix both of which are vectorized in high performance codes. To further increase throughput, new algorithms are needed. We compare a multifrontal sparse solver to a traditional skyline solver in a finite element code on a vector supercomputer. The multifrontal solver uses the Multiple-Minimum Degree reordering heuristic to reduce the number of operations required to factor a sparse matrix and full matrix computational kernels (e.g., BLAS3) to enhance vector performance. The net result in an order-of-magnitude reduction in run time for a finite element application on one processor of a Cray X-MP.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

Agulleiro, J I; Garzón, E M; García, I; Fernández, J J

2010-06-01

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Syngeneic AAV pseudo-vectors potentiates full vector transduction

USDA-ARS?s Scientific Manuscript database

An excessive amount of empty capsids are generated during regular AAV vector production process. These pseudo-vectors often remain in final vectors used for animal studies or clinical trials. The potential effects of these pseudo-vectors on AAV transduction have been a major concern. In the current ...

Early Results from SOLIS

NASA Astrophysics Data System (ADS)

Harvey, J.; Giampapa, M.; Henney, C.; Keller, C.; Jones, H.

2004-05-01

SOLIS (Synoptic Optical Long-Term Investigations of the Sun) is a project that is replacing antiquated synoptic observing equipment at the National Solar Observatory. SOLIS consists of a suite of three instruments on an equatorial mount that will be installed on Kitt Peak in April 2004. The major SOLIS instrument is a vector spectromagnetograph (VSM) that maps magnetic fields across the full solar disk using a slit spectrograph and one arc sec pixels. Limited daily observations started at a temporary site in August, 2003 and include line-of-sight component magnetograms in the photosphere and chromosphere and, for the first time, full-disk vector magnetograms. At a medium scan speed ( ˜ 10 minutes for the full disk) noise is less than 1 Mx/cm2. This low noise, combined with negligible instrumental polarization and well resolved spectral line profiles, yields moderate resolution magnetograms of unprecedented quality. Observations show magnetic flux nearly everywhere in the photosphere from the disk center to the solar limb. Weak, intranetwork fields are now routinely observed and show a tendency to be of opposite polarity to the stronger surrounding fields. Diffuse fields surround decaying active regions and appear to be distinct from canopy fields. Vector magnetograms easily show the radial orientation of network fields, and the diffuse component surrounding decaying active regions. Near the disk center, the transverse magnetic fields of network elements change on a time scale of minutes. Detailed quantitative calibration of the observations is in progress. Good results have been obtained from the other SOLIS instruments: a full-disk filter imager at several narrow wavelengths and a double-pass grating spectrograph that provides high-accuracy line spectra of integrated sunlight. SOLIS data are freely available via the Internet and users are invited to submit observing time requests for special observations. The National Solar Observatory is operated by AURA, Inc. under a cooperative agreement with the National Science Foundation. Additional support for the development of SOLIS from NASA and ONR is gratefully acknowledged.

Hemispheric Patterns in Electric Current Helicity of Solar Magnetic Fields During Solar Cycle 24: Results from SOLIS, SDO and Hinode

NASA Astrophysics Data System (ADS)

Gusain, S.

2017-12-01

We study the hemispheric patterns in electric current helicity distribution on the Sun. Magnetic field vector in the photosphere is now routinely measured by variety of instruments. SOLIS/VSM of NSO observes full disk Stokes spectra in photospheric lines which are used to derive vector magnetograms. Hinode SP is a space based spectropolarimeter which has the same observable as SOLIS albeit with limited field-of-view (FOV) but high spatial resolution. SDO/HMI derives vector magnetograms from full disk Stokes measurements, with rather limited spectral resolution, from space in a different photospheric line. Further, these datasets now exist for several years. SOLIS/VSM from 2003, Hinode SP from 2006, and SDO HMI since 2010. Using these time series of vector magnetograms we compute the electric current density in active regions during solar cycle 24 and study the hemispheric distributions. Many studies show that the helicity parameters and proxies show a strong hemispheric bias, such that Northern hemisphere has preferentially negative and southern positive helicity, respectively. We will confirm these results for cycle 24 from three different datasets and evaluate the statistical significance of the hemispheric bias. Further, we discuss the solar cycle variation in the hemispheric helicity pattern during cycle 24 and discuss its implications in terms of solar dynamo models.

Bias Corrections for Regional Estimates of the Time-averaged Geomagnetic Field

NASA Astrophysics Data System (ADS)

Constable, C.; Johnson, C. L.

2009-05-01

We assess two sources of bias in the time-averaged geomagnetic field (TAF) and paleosecular variation (PSV): inadequate temporal sampling, and the use of unit vectors in deriving temporal averages of the regional geomagnetic field. For the first temporal sampling question we use statistical resampling of existing data sets to minimize and correct for bias arising from uneven temporal sampling in studies of the time- averaged geomagnetic field (TAF) and its paleosecular variation (PSV). The techniques are illustrated using data derived from Hawaiian lava flows for 0-5~Ma: directional observations are an updated version of a previously published compilation of paleomagnetic directional data centered on ± 20° latitude by Lawrence et al./(2006); intensity data are drawn from Tauxe & Yamazaki, (2007). We conclude that poor temporal sampling can produce biased estimates of TAF and PSV, and resampling to appropriate statistical distribution of ages reduces this bias. We suggest that similar resampling should be attempted as a bias correction for all regional paleomagnetic data to be used in TAF and PSV modeling. The second potential source of bias is the use of directional data in place of full vector data to estimate the average field. This is investigated for the full vector subset of the updated Hawaiian data set. Lawrence, K.P., C.G. Constable, and C.L. Johnson, 2006, Geochem. Geophys. Geosyst., 7, Q07007, DOI 10.1029/2005GC001181. Tauxe, L., & Yamazkai, 2007, Treatise on Geophysics,5, Geomagnetism, Elsevier, Amsterdam, Chapter 13,p509

The Method of Fundamental Solutions using the Vector Magnetic Dipoles for Calculation of the Magnetic Fields in the Diagnostic Problems Based on Full-Scale Modelling Experiment

NASA Astrophysics Data System (ADS)

Bakhvalov, Yu A.; Grechikhin, V. V.; Yufanova, A. L.

2016-04-01

The article describes the calculation of the magnetic fields in the problems diagnostic of technical systems based on the full-scale modeling experiment. Use of gridless fundamental solution method and its variants in combination with grid methods (finite differences and finite elements) are allowed to considerably reduce the dimensionality task of the field calculation and hence to reduce calculation time. When implementing the method are used fictitious magnetic charges. In addition, much attention is given to the calculation accuracy. Error occurs when wrong choice of the distance between the charges. The authors are proposing to use vector magnetic dipoles to improve the accuracy of magnetic fields calculation. Examples of this approacharegiven. The article shows the results of research. They are allowed to recommend the use of this approach in the method of fundamental solutions for the full-scale modeling tests of technical systems.

Production of Recombinant Adeno-associated Virus Vectors Using Suspension HEK293 Cells and Continuous Harvest of Vector From the Culture Media for GMP FIX and FLT1 Clinical Vector

PubMed Central

Grieger, Joshua C; Soltys, Stephen M; Samulski, Richard Jude

2016-01-01

Adeno-associated virus (AAV) has shown great promise as a gene therapy vector in multiple aspects of preclinical and clinical applications. Many developments including new serotypes as well as self-complementary vectors are now entering the clinic. With these ongoing vector developments, continued effort has been focused on scalable manufacturing processes that can efficiently generate high-titer, highly pure, and potent quantities of rAAV vectors. Utilizing the relatively simple and efficient transfection system of HEK293 cells as a starting point, we have successfully adapted an adherent HEK293 cell line from a qualified clinical master cell bank to grow in animal component-free suspension conditions in shaker flasks and WAVE bioreactors that allows for rapid and scalable rAAV production. Using the triple transfection method, the suspension HEK293 cell line generates greater than 1 × 105 vector genome containing particles (vg)/cell or greater than 1 × 1014 vg/l of cell culture when harvested 48 hours post-transfection. To achieve these yields, a number of variables were optimized such as selection of a compatible serum-free suspension media that supports both growth and transfection, selection of a transfection reagent, transfection conditions and cell density. A universal purification strategy, based on ion exchange chromatography methods, was also developed that results in high-purity vector preps of AAV serotypes 1–6, 8, 9 and various chimeric capsids tested. This user-friendly process can be completed within 1 week, results in high full to empty particle ratios (>90% full particles), provides postpurification yields (>1 × 1013 vg/l) and purity suitable for clinical applications and is universal with respect to all serotypes and chimeric particles. To date, this scalable manufacturing technology has been utilized to manufacture GMP phase 1 clinical AAV vectors for retinal neovascularization (AAV2), Hemophilia B (scAAV8), giant axonal neuropathy (scAAV9), and retinitis pigmentosa (AAV2), which have been administered into patients. In addition, we report a minimum of a fivefold increase in overall vector production by implementing a perfusion method that entails harvesting rAAV from the culture media at numerous time-points post-transfection. PMID:26437810

CAT-PUMA: CME Arrival Time Prediction Using Machine learning Algorithms

NASA Astrophysics Data System (ADS)

Liu, Jiajia; Ye, Yudong; Shen, Chenglong; Wang, Yuming; Erdélyi, Robert

2018-04-01

CAT-PUMA (CME Arrival Time Prediction Using Machine learning Algorithms) quickly and accurately predicts the arrival of Coronal Mass Ejections (CMEs) of CME arrival time. The software was trained via detailed analysis of CME features and solar wind parameters using 182 previously observed geo-effective partial-/full-halo CMEs and uses algorithms of the Support Vector Machine (SVM) to make its predictions, which can be made within minutes of providing the necessary input parameters of a CME.

An efficient parallel algorithm for matrix-vector multiplication

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

Hendrickson, B.; Leland, R.; Plimpton, S.

The multiplication of a vector by a matrix is the kernel computation of many algorithms in scientific computation. A fast parallel algorithm for this calculation is therefore necessary if one is to make full use of the new generation of parallel supercomputers. This paper presents a high performance, parallel matrix-vector multiplication algorithm that is particularly well suited to hypercube multiprocessors. For an n x n matrix on p processors, the communication cost of this algorithm is O(n/[radical]p + log(p)), independent of the matrix sparsity pattern. The performance of the algorithm is demonstrated by employing it as the kernel in themore » well-known NAS conjugate gradient benchmark, where a run time of 6.09 seconds was observed. This is the best published performance on this benchmark achieved to date using a massively parallel supercomputer.« less

Improved nearest codeword search scheme using a tighter kick-out condition

NASA Astrophysics Data System (ADS)

Hwang, Kuo-Feng; Chang, Chin-Chen

2001-09-01

Using a tighter kick-out condition as a faster approach to nearest codeword searches is proposed. The proposed scheme finds the nearest codeword that is identical to the one found using a full search. However, using our scheme, the search time is much shorter. Our scheme first establishes a tighter kick-out condition. Then, the temporal nearest codeword can be obtained from the codewords that survive the tighter condition. Finally, the temporal nearest codeword cooperatives with the query vector to constitute a better kick-out condition. In other words, more codewords can be excluded without actually computing the distances between the bypassed codewords and the query vector. Comparison to previous work are included to present the benefits of the proposed scheme in relation to search time.

GASP-Galway astronomical Stokes polarimeter

NASA Astrophysics Data System (ADS)

Kyne, G.; Sheehan, B.; Collins, P.; Redfern, M.; Shearer, A.

2010-06-01

The Galway Astronomical Stokes Polarimeter (GASP) is an ultra-high-speed, full Stokes, astronomical imaging polarimeter based upon a Division of Amplitude Polarimeter. It has been developed to resolve extremely rapid stochastic (~ms) variations in objects such as optical pulsars, magnetars and magnetic cataclysmic variables. The polarimeter has no moving parts or modulated components so the complete Stokes vector can be measured from just one exposure - making it unique to astronomy. The time required for the determination of the full Stokes vector is limited only by detector efficiency and photon fluxes. The polarimeter utilizes a modified Fresnel rhomb that acts as a highly achromatic quarter wave plate and a beamsplitter (referred to as an RBS). We present a description of how the DOAP works, some of the optical design for the polarimeter. Calibration is an important and difficult issue with all polarimeters, but particularly in astronomical polarimeters. We give a description of calibration techniques appropriate to this type of polarimeter.

Modeling and control of fuel cell based distributed generation systems

NASA Astrophysics Data System (ADS)

Jung, Jin Woo

This dissertation presents circuit models and control algorithms of fuel cell based distributed generation systems (DGS) for two DGS topologies. In the first topology, each DGS unit utilizes a battery in parallel to the fuel cell in a standalone AC power plant and a grid-interconnection. In the second topology, a Z-source converter, which employs both the L and C passive components and shoot-through zero vectors instead of the conventional DC/DC boost power converter in order to step up the DC-link voltage, is adopted for a standalone AC power supply. In Topology 1, two applications are studied: a standalone power generation (Single DGS Unit and Two DGS Units) and a grid-interconnection. First, dynamic model of the fuel cell is given based on electrochemical process. Second, two full-bridge DC to DC converters are adopted and their controllers are designed: an unidirectional full-bridge DC to DC boost converter for the fuel cell and a bidirectional full-bridge DC to DC buck/boost converter for the battery. Third, for a three-phase DC to AC inverter without or with a Delta/Y transformer, a discrete-time state space circuit model is given and two discrete-time feedback controllers are designed: voltage controller in the outer loop and current controller in the inner loop. And last, for load sharing of two DGS units and power flow control of two DGS units or the DGS connected to the grid, real and reactive power controllers are proposed. Particularly, for the grid-connected DGS application, a synchronization issue between an islanding mode and a paralleling mode to the grid is investigated, and two case studies are performed. To demonstrate the proposed circuit models and control strategies, simulation test-beds using Matlab/Simulink are constructed for each configuration of the fuel cell based DGS with a three-phase AC 120 V (L-N)/60 Hz/50 kVA and various simulation results are presented. In Topology 2, this dissertation presents system modeling, modified space vector PWM implementation (MSVPWM) and design of a closed-loop controller of the Z-source converter which utilizes L and C components and shoot-through zero vectors for the standalone AC power generation. The fuel cell system is modeled by an electrical R-C circuit in order to include slow dynamics of the fuel cells and a voltage-current characteristic of a cell is also considered. A discrete-time state space model is derived to implement digital control and a space vector pulse-width modulation (SVPWM) technique is modified to realize the shoot-through zero vectors that boost the DC-link voltage. Also, three discrete-time feedback controllers are designed: a discrete-time optimal voltage controller, a discrete-time sliding mode current controller, and a discrete-time PI DC-link voltage controller. Furthermore, an asymptotic observer is used to reduce the number of sensors and enhance the reliability of the system. To demonstrate the analyzed circuit model and proposed control strategy, various simulation results using Matlab/Simulink are presented under both light/heavy loads and linear/nonlinear loads for a three-phase AC 208 V (L-L)/60 Hz/10 kVA.

Vector generator scan converter

DOEpatents

Moore, James M.; Leighton, James F.

1990-01-01

High printing speeds for graphics data are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O (input/output) channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardward for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold.

Vector generator scan converter

DOEpatents

Moore, J.M.; Leighton, J.F.

1988-02-05

High printing speeds for graphics data are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold. 7 figs.

Navigation in wood ants Formica japonica: context dependent use of landmarks.

PubMed

Fukushi, Tsukasa; Wehner, Rüdiger

2004-09-01

Wood ants Formica japonica can steer their outbound (foraging) and inbound (homing) courses without using celestial compass information, by relying exclusively on landmark cues. This is shown by training ants to run back and forth between the nest and an artificial feeder, and later displacing the trained ants either from the nest (when starting their foraging runs: outbound full-vector ants) or from the feeder (when starting their home runs: inbound full-vector ants) to various nearby release sites. In addition, ants that have already completed their foraging and homing runs are displaced after arrival either at the feeder (outbound zero-vector ants) or at the nest (inbound zero-vector ants), respectively, to the very same release sites. Upon release, the full-vector ants steer their straight courses by referring to panoramic landmark cues, while the zero-vector ants presented with the very same visual scenery immediately search for local landmark cues defining their final goal. Hence, it depends on the context, in this case on the state of the forager's round-trip cycle, what visual cues are picked out from a given set of landmarks and used for navigation.

Flux-vector splitting algorithm for chain-rule conservation-law form

NASA Technical Reports Server (NTRS)

Shih, T. I.-P.; Nguyen, H. L.; Willis, E. A.; Steinthorsson, E.; Li, Z.

1991-01-01

A flux-vector splitting algorithm with Newton-Raphson iteration was developed for the 'full compressible' Navier-Stokes equations cast in chain-rule conservation-law form. The algorithm is intended for problems with deforming spatial domains and for problems whose governing equations cannot be cast in strong conservation-law form. The usefulness of the algorithm for such problems was demonstrated by applying it to analyze the unsteady, two- and three-dimensional flows inside one combustion chamber of a Wankel engine under nonfiring conditions. Solutions were obtained to examine the algorithm in terms of conservation error, robustness, and ability to handle complex flows on time-dependent grid systems.

Parallel/Vector Integration Methods for Dynamical Astronomy

NASA Astrophysics Data System (ADS)

Fukushima, T.

Progress of parallel/vector computers has driven us to develop suitable numerical integrators utilizing their computational power to the full extent while being independent on the size of system to be integrated. Unfortunately, the parallel version of Runge-Kutta type integrators are known to be not so efficient. Recently we developed a parallel version of the extrapolation method (Ito and Fukushima 1997), which allows variable timesteps and still gives an acceleration factor of 3-4 for general problems. While the vector-mode usage of Picard-Chebyshev method (Fukushima 1997a, 1997b) will lead the acceleration factor of order of 1000 for smooth problems such as planetary/satellites orbit integration. The success of multiple-correction PECE mode of time-symmetric implicit Hermitian integrator (Kokubo 1998) seems to enlighten Milankar's so-called "pipelined predictor corrector method", which is expected to lead an acceleration factor of 3-4. We will review these directions and discuss future prospects.

Development of a new vector using Soybean yellow common mosaic virus for gene function study or heterologous protein expression in soybeans.

PubMed

Lim, Seungmo; Nam, Moon; Kim, Kil Hyun; Lee, Su-Heon; Moon, Jung-Kyung; Lim, Hyoun-Sub; Choung, Myoung-Gun; Kim, Sang-Mok; Moon, Jae Sun

2016-02-01

A new vector using Soybean yellow common mosaic virus (SYCMV) was constructed for gene function study or heterologous protein expression in soybeans. The in vitro transcript with a 5' cap analog m7GpppG from an SYCMV full-length infectious vector driven by a T7 promoter infected soybeans (pSYCMVT7-full). The symptoms observed in the soybeans infected with either the sap from SYCMV-infected leaves or pSYCMVT7-full were indistinguishable, suggesting that the vector exhibits equivalent biological activity as the virus itself. To utilize the vector further, a DNA-based vector driven by the Cauliflower mosaic virus (CaMV) 35S promoter was constructed. The complete sequence of the SYCMV genome was inserted into a binary vector flanked by a CaMV 35S promoter at the 5' terminus of the SYCMV genome and a cis-cleaving ribozyme sequence followed by a nopaline synthase terminator at the 3' terminus of the SYCMV genome (pSYCMV-full). The SYCMV-derived vector was tested for use as a virus-induced gene silencing (VIGS) vector for the functional analysis of soybean genes. VIGS constructs containing either a fragment of the Phytoene desaturase (PDS) gene (pSYCMV-PDS1) or a fragment of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcS) gene (pSYCMV-RbcS2) were constructed. Plants infiltrated with each vector using the Agrobacterium-mediated inoculation method exhibited distinct symptoms, such as photo-bleaching in plants infiltrated with pSYCMV-PDS1 and yellow or pale green coloring in plants infiltrated with pSYCMV-RbcS2. In addition, down-regulation of the transcripts of the two target genes was confirmed via northern blot analysis. Particle bombardment and direct plasmid DNA rubbing were also confirmed as alternative inoculation methods. To determine if the SYCMV vector can be used for the expression of heterologous proteins in soybean plants, the vector encoding amino acids 135-160 of VP1 of Foot-and-mouth disease virus (FMDV) serotype O1 Campos (O1C) was constructed (pSYCMV-FMDV). Plants infiltrated with pSYCMV-FMDV were only detected via western blotting using the O1C antibody. Based on these results, we propose that the SYCMV-derived vector can be used for gene function study or expression of useful heterologous proteins in soybeans. Copyright © 2015 Elsevier B.V. All rights reserved.

Multineuronal vectorization is more efficient than time-segmental vectorization for information extraction from neuronal activities in the inferior temporal cortex.

PubMed

Kaneko, Hidekazu; Tamura, Hiroshi; Tate, Shunta; Kawashima, Takahiro; Suzuki, Shinya S; Fujita, Ichiro

2010-08-01

In order for patients with disabilities to control assistive devices with their own neural activity, multineuronal spike trains must be efficiently decoded because only limited computational resources can be used to generate prosthetic control signals in portable real-time applications. In this study, we compare the abilities of two vectorizing procedures (multineuronal and time-segmental) to extract information from spike trains during the same total neuron-seconds. In the multineuronal vectorizing procedure, we defined a response vector whose components represented the spike counts of one to five neurons. In the time-segmental vectorizing procedure, a response vector consisted of components representing a neuron's spike counts for one to five time-segment(s) of a response period of 1 s. Spike trains were recorded from neurons in the inferior temporal cortex of monkeys presented with visual stimuli. We examined whether the amount of information of the visual stimuli carried by these neurons differed between the two vectorizing procedures. The amount of information calculated with the multineuronal vectorizing procedure, but not the time-segmental vectorizing procedure, significantly increased with the dimensions of the response vector. We conclude that the multineuronal vectorizing procedure is superior to the time-segmental vectorizing procedure in efficiently extracting information from neuronal signals. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Induction of humoral responses to BHV-1 glycoprotein D expressed by HSV-1 amplicon vectors

PubMed Central

Blanc, Andrea Maria; Berois, Mabel Beatriz; Tomé, Lorena Magalí; Epstein, Alberto L.

2012-01-01

Herpes simplex virus type-1 (HSV-1) amplicon vectors are versatile and useful tools for transferring genes into cells that are capable of stimulating a specific immune response to their expressed antigens. In this work, two HSV-1-derived amplicon vectors were generated. One of these expressed the full-length glycoprotein D (gD) of bovine herpesvirus 1 while the second expressed the truncated form of gD (gDtr) which lacked the trans-membrane region. After evaluating gD expression in the infected cells, the ability of both vectors to induce a specific gD immune response was tested in BALB/c mice that were intramuscularly immunized. Specific serum antibody responses were detected in mice inoculated with both vectors, and the response against truncated gD was higher than the response against full-length gD. These results reinforce previous findings that HSV-1 amplicon vectors can potentially deliver antigens to animals and highlight the prospective use of these vectors for treating infectious bovine rhinotracheitis disease. PMID:22437537

Full characterization of dislocations in ion-irradiated polycrystalline UO2

NASA Astrophysics Data System (ADS)

Onofri, C.; Legros, M.; Léchelle, J.; Palancher, H.; Baumier, C.; Bachelet, C.; Sabathier, C.

2017-10-01

In order to fully characterize the dislocation loops and lines features (Burgers vectors, habit/slip planes, interstitial or vacancy type) induced by irradiation in UO2, polycrystalline thin foils were irradiated with 4 MeV Au or 390 keV Xe ions at different temperatures (25, 600 and 800 °C) and fluences (0.5 and 1 × 1015 ions/cm2), and further analyzed using TEM. In all the cases, this study, performed on a large number of dislocation loops (diameter ranging from 10 to 80 nm) and for the first time on several dislocation lines, reveals unfaulted prismatic dislocation loops with an interstitial nature and Burgers vectors only along the <110>-type directions. Almost 60% of the studied loops are purely prismatic type and lie on {110} habit planes perpendicular to the Burgers vector directions. The others lie on the {110} or {111} planes, which are neither perpendicular to the Burgers vectors, nor contain them. About 87% of the dislocation lines, formed by loop overlapping as fluence increases, are edge or mixed type in the <100>{100} slip systems, as those induced under mechanical load.

Calculation of biochemical net reactions and pathways by using matrix operations.

PubMed Central

Alberty, R A

1996-01-01

Pathways for net biochemical reactions can be calculated by using a computer program that solves systems of linear equations. The coefficients in the linear equations are the stoichiometric numbers in the biochemical equations for the system. The solution of the system of linear equations is a vector of the stoichiometric numbers of the reactions in the pathway for the net reaction; this is referred to as the pathway vector. The pathway vector gives the number of times the various reactions have to occur to produce the desired net reaction. Net reactions may involve unknown numbers of ATP, ADP, and Pi molecules. The numbers of ATP, ADP, and Pi in a desired net reaction can be calculated in a two-step process. In the first step, the pathway is calculated by solving the system of linear equations for an abbreviated stoichiometric number matrix without ATP, ADP, Pi, NADred, and NADox. In the second step, the stoichiometric numbers in the desired net reaction, which includes ATP, ADP, Pi, NADred, and NADox, are obtained by multiplying the full stoichiometric number matrix by the calculated pathway vector. PMID:8804633

Habitat suitability and ecological niche profile of major malaria vectors in Cameroon

PubMed Central

2009-01-01

Background Suitability of environmental conditions determines a species distribution in space and time. Understanding and modelling the ecological niche of mosquito disease vectors can, therefore, be a powerful predictor of the risk of exposure to the pathogens they transmit. In Africa, five anophelines are responsible for over 95% of total malaria transmission. However, detailed knowledge of the geographic distribution and ecological requirements of these species is to date still inadequate. Methods Indoor-resting mosquitoes were sampled from 386 villages covering the full range of ecological settings available in Cameroon, Central Africa. Using a predictive species distribution modeling approach based only on presence records, habitat suitability maps were constructed for the five major malaria vectors Anopheles gambiae, Anopheles funestus, Anopheles arabiensis, Anopheles nili and Anopheles moucheti. The influence of 17 climatic, topographic, and land use variables on mosquito geographic distribution was assessed by multivariate regression and ordination techniques. Results Twenty-four anopheline species were collected, of which 17 are known to transmit malaria in Africa. Ecological Niche Factor Analysis, Habitat Suitability modeling and Canonical Correspondence Analysis revealed marked differences among the five major malaria vector species, both in terms of ecological requirements and niche breadth. Eco-geographical variables (EGVs) related to human activity had the highest impact on habitat suitability for the five major malaria vectors, with areas of low population density being of marginal or unsuitable habitat quality. Sunlight exposure, rainfall, evapo-transpiration, relative humidity, and wind speed were among the most discriminative EGVs separating "forest" from "savanna" species. Conclusions The distribution of major malaria vectors in Cameroon is strongly affected by the impact of humans on the environment, with variables related to proximity to human settings being among the best predictors of habitat suitability. The ecologically more tolerant species An. gambiae and An. funestus were recorded in a wide range of eco-climatic settings. The other three major vectors, An. arabiensis, An. moucheti, and An. nili, were more specialized. Ecological niche and species distribution modelling should help improve malaria vector control interventions by targeting places and times where the impact on vector populations and disease transmission can be optimized. PMID:20028559

Habitat suitability and ecological niche profile of major malaria vectors in Cameroon.

PubMed

Ayala, Diego; Costantini, Carlo; Ose, Kenji; Kamdem, Guy C; Antonio-Nkondjio, Christophe; Agbor, Jean-Pierre; Awono-Ambene, Parfait; Fontenille, Didier; Simard, Frédéric

2009-12-23

Suitability of environmental conditions determines a species distribution in space and time. Understanding and modelling the ecological niche of mosquito disease vectors can, therefore, be a powerful predictor of the risk of exposure to the pathogens they transmit. In Africa, five anophelines are responsible for over 95% of total malaria transmission. However, detailed knowledge of the geographic distribution and ecological requirements of these species is to date still inadequate. Indoor-resting mosquitoes were sampled from 386 villages covering the full range of ecological settings available in Cameroon, Central Africa. Using a predictive species distribution modeling approach based only on presence records, habitat suitability maps were constructed for the five major malaria vectors Anopheles gambiae, Anopheles funestus, Anopheles arabiensis, Anopheles nili and Anopheles moucheti. The influence of 17 climatic, topographic, and land use variables on mosquito geographic distribution was assessed by multivariate regression and ordination techniques. Twenty-four anopheline species were collected, of which 17 are known to transmit malaria in Africa. Ecological Niche Factor Analysis, Habitat Suitability modeling and Canonical Correspondence Analysis revealed marked differences among the five major malaria vector species, both in terms of ecological requirements and niche breadth. Eco-geographical variables (EGVs) related to human activity had the highest impact on habitat suitability for the five major malaria vectors, with areas of low population density being of marginal or unsuitable habitat quality. Sunlight exposure, rainfall, evapo-transpiration, relative humidity, and wind speed were among the most discriminative EGVs separating "forest" from "savanna" species. The distribution of major malaria vectors in Cameroon is strongly affected by the impact of humans on the environment, with variables related to proximity to human settings being among the best predictors of habitat suitability. The ecologically more tolerant species An. gambiae and An. funestus were recorded in a wide range of eco-climatic settings. The other three major vectors, An. arabiensis, An. moucheti, and An. nili, were more specialized. Ecological niche and species distribution modelling should help improve malaria vector control interventions by targeting places and times where the impact on vector populations and disease transmission can be optimized.

SOLAR FLARE PREDICTION USING SDO/HMI VECTOR MAGNETIC FIELD DATA WITH A MACHINE-LEARNING ALGORITHM

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

Bobra, M. G.; Couvidat, S., E-mail: couvidat@stanford.edu

2015-01-10

We attempt to forecast M- and X-class solar flares using a machine-learning algorithm, called support vector machine (SVM), and four years of data from the Solar Dynamics Observatory's Helioseismic and Magnetic Imager, the first instrument to continuously map the full-disk photospheric vector magnetic field from space. Most flare forecasting efforts described in the literature use either line-of-sight magnetograms or a relatively small number of ground-based vector magnetograms. This is the first time a large data set of vector magnetograms has been used to forecast solar flares. We build a catalog of flaring and non-flaring active regions sampled from a databasemore » of 2071 active regions, comprised of 1.5 million active region patches of vector magnetic field data, and characterize each active region by 25 parameters. We then train and test the machine-learning algorithm and we estimate its performances using forecast verification metrics with an emphasis on the true skill statistic (TSS). We obtain relatively high TSS scores and overall predictive abilities. We surmise that this is partly due to fine-tuning the SVM for this purpose and also to an advantageous set of features that can only be calculated from vector magnetic field data. We also apply a feature selection algorithm to determine which of our 25 features are useful for discriminating between flaring and non-flaring active regions and conclude that only a handful are needed for good predictive abilities.« less

Wide-angle full-vector beam propagation method based on an alternating direction implicit preconditioner

NASA Astrophysics Data System (ADS)

Chui, Siu Lit; Lu, Ya Yan

2004-03-01

Wide-angle full-vector beam propagation methods (BPMs) for three-dimensional wave-guiding structures can be derived on the basis of rational approximants of a square root operator or its exponential (i.e., the one-way propagator). While the less accurate BPM based on the slowly varying envelope approximation can be efficiently solved by the alternating direction implicit (ADI) method, the wide-angle variants involve linear systems that are more difficult to handle. We present an efficient solver for these linear systems that is based on a Krylov subspace method with an ADI preconditioner. The resulting wide-angle full-vector BPM is used to simulate the propagation of wave fields in a Y branch and a taper.

Wide-angle full-vector beam propagation method based on an alternating direction implicit preconditioner.

PubMed

Chui, Siu Lit; Lu, Ya Yan

2004-03-01

Wide-angle full-vector beam propagation methods (BPMs) for three-dimensional wave-guiding structures can be derived on the basis of rational approximants of a square root operator or its exponential (i.e., the one-way propagator). While the less accurate BPM based on the slowly varying envelope approximation can be efficiently solved by the alternating direction implicit (ADI) method, the wide-angle variants involve linear systems that are more difficult to handle. We present an efficient solver for these linear systems that is based on a Krylov subspace method with an ADI preconditioner. The resulting wide-angle full-vector BPM is used to simulate the propagation of wave fields in a Y branch and a taper.

3G vector-primer plasmid for constructing full-length-enriched cDNA libraries.

PubMed

Zheng, Dong; Zhou, Yanna; Zhang, Zidong; Li, Zaiyu; Liu, Xuedong

2008-09-01

We designed a 3G vector-primer plasmid for the generation of full-length-enriched complementary DNA (cDNA) libraries. By employing the terminal transferase activity of reverse transcriptase and the modified strand replacement method, this plasmid (assembled with a polydT end and a deoxyguanosine [dG] end) combines priming full-length cDNA strand synthesis and directional cDNA cloning. As a result, the number of steps involved in cDNA library preparation is decreased while simplifying downstream gene manipulation, sequencing, and subcloning. The 3G vector-primer plasmid method yields fully represented plasmid primed libraries that are equivalent to those made by the SMART (switching mechanism at 5' end of RNA transcript) approach.

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.

Close range fault tolerant noncontacting position sensor

DOEpatents

Bingham, D.N.; Anderson, A.A.

1996-02-20

A method and system are disclosed for locating the three dimensional coordinates of a moving or stationary object in real time. The three dimensional coordinates of an object in half space or full space are determined based upon the time of arrival or phase of the wave front measured by a plurality of receiver elements and an established vector magnitudes proportional to the measured time of arrival or phase at each receiver element. The coordinates of the object are calculated by solving a matrix equation or a set of closed form algebraic equations. 3 figs.

Sensitivity vector fields in time-delay coordinate embeddings: theory and experiment.

PubMed

Sloboda, A R; Epureanu, B I

2013-02-01

Identifying changes in the parameters of a dynamical system can be vital in many diagnostic and sensing applications. Sensitivity vector fields (SVFs) are one way of identifying such parametric variations by quantifying their effects on the morphology of a dynamical system's attractor. In many cases, SVFs are a more effective means of identification than commonly employed modal methods. Previously, it has only been possible to construct SVFs for a given dynamical system when a full set of state variables is available. This severely restricts SVF applicability because it may be cost prohibitive, or even impossible, to measure the entire state in high-dimensional systems. Thus, the focus of this paper is constructing SVFs with only partial knowledge of the state by using time-delay coordinate embeddings. Local models are employed in which the embedded states of a neighborhood are weighted in a way referred to as embedded point cloud averaging. Application of the presented methodology to both simulated and experimental time series demonstrates its utility and reliability.

Search for the U Boson in the Process e(+e^-) -> mu (+) mu (-) gamma , U -> mu (+mu) (-) with the KLOE Detector

NASA Astrophysics Data System (ADS)

Curciarello, F.

We present a search for a new light vector boson, carrier of a "dark force" between WIMPs, with the KLOE detector at \\DA$\\Phi$NE. We analyzed $e^+ e^- \\to \\mu^+ \\mu^- \\gamma$ ISR events corresponding to an integrated luminosity of $239$ pb$^{-1}$ to find evidence for the $e^+ e^- \\to U\\gamma ,\\,\\, U\\to\\mu^+\\mu^-$ process. We found no $U$ vector boson signal and set a 90% CL upper limit on the ratio of the U boson and photon coupling constants between 1.6$\\times10^{-5}$ to 8.6$\\times10^{-7}$ in the mass region $520

A space-efficient quantum computer simulator suitable for high-speed FPGA implementation

NASA Astrophysics Data System (ADS)

Frank, Michael P.; Oniciuc, Liviu; Meyer-Baese, Uwe H.; Chiorescu, Irinel

2009-05-01

Conventional vector-based simulators for quantum computers are quite limited in the size of the quantum circuits they can handle, due to the worst-case exponential growth of even sparse representations of the full quantum state vector as a function of the number of quantum operations applied. However, this exponential-space requirement can be avoided by using general space-time tradeoffs long known to complexity theorists, which can be appropriately optimized for this particular problem in a way that also illustrates some interesting reformulations of quantum mechanics. In this paper, we describe the design and empirical space/time complexity measurements of a working software prototype of a quantum computer simulator that avoids excessive space requirements. Due to its space-efficiency, this design is well-suited to embedding in single-chip environments, permitting especially fast execution that avoids access latencies to main memory. We plan to prototype our design on a standard FPGA development board.

Effects of OCR Errors on Ranking and Feedback Using the Vector Space Model.

ERIC Educational Resources Information Center

Taghva, Kazem; And Others

1996-01-01

Reports on the performance of the vector space model in the presence of OCR (optical character recognition) errors in information retrieval. Highlights include precision and recall, a full-text test collection, smart vector representation, impact of weighting parameters, ranking variability, and the effect of relevance feedback. (Author/LRW)

Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors

PubMed Central

Giritch, Anatoli; Marillonnet, Sylvestre; Engler, Carola; van Eldik, Gerben; Botterman, Johan; Klimyuk, Victor; Gleba, Yuri

2006-01-01

Plant viral vectors allow expression of heterologous proteins at high yields, but so far, they have been unable to express heterooligomeric proteins efficiently. We describe here a rapid and indefinitely scalable process for high-level expression of functional full-size mAbs of the IgG class in plants. The process relies on synchronous coinfection and coreplication of two viral vectors, each expressing a separate antibody chain. The two vectors are derived from two different plant viruses that were found to be noncompeting. Unlike vectors derived from the same virus, noncompeting vectors effectively coexpress the heavy and light chains in the same cell throughout the plant body, resulting in yields of up to 0.5 g of assembled mAbs per kg of fresh-leaf biomass. This technology allows production of gram quantities of mAbs for research purposes in just several days, and the same protocol can be used on an industrial scale in situations requiring rapid response, such as pandemic or terrorism events. PMID:16973752

TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.

PubMed

Jung, Inuk; Jo, Kyuri; Kang, Hyejin; Ahn, Hongryul; Yu, Youngjae; Kim, Sun

2017-12-01

Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing such data is very high, compared to the already difficult NP-hard two dimensional biclustering algorithms. Because of this challenge, traditional time series clustering algorithms are designed to capture co-expressed genes with similar expression pattern in two sample conditions. We present a triclustering algorithm, TimesVector, specifically designed for clustering three-dimensional time series data to capture distinctively similar or different gene expression patterns between two or more sample conditions. TimesVector identifies clusters with distinctive expression patterns in three steps: (i) dimension reduction and clustering of time-condition concatenated vectors, (ii) post-processing clusters for detecting similar and distinct expression patterns and (iii) rescuing genes from unclassified clusters. Using four sets of time series gene expression data, generated by both microarray and high throughput sequencing platforms, we demonstrated that TimesVector successfully detected biologically meaningful clusters of high quality. TimesVector improved the clustering quality compared to existing triclustering tools and only TimesVector detected clusters with differential expression patterns across conditions successfully. The TimesVector software is available at http://biohealth.snu.ac.kr/software/TimesVector/. sunkim.bioinfo@snu.ac.kr. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Full Vector Wave Calculation of Photonic Band Structures in Face-Centered Cubic Dielectric Media

DTIC Science & Technology

1990-01-01

refractive index ratios90 0(;o8 070 2 were painstakingly machined out of low-loss dk’-tric materials. This very time comsuming approach was necessary to...find that the X-gap goes to zero for f=0.66. This is very close to the experimental value of 0.68. The physical origin of this behavior has been fully

E11, brane dynamics and duality symmetries

NASA Astrophysics Data System (ADS)

West, Peter

2018-05-01

Following arXiv:hep-th/0412336 we use the nonlinear realisation of the semi-direct product of E11 and its vector representation to construct brane dynamics. The brane moves through a space-time which arises in the nonlinear realisation from the vector representation and it contains the usual embedding coordinates as well as the worldvolume fields. The resulting equations of motion are first order in derivatives and can be thought of as duality relations. Each brane carries the full E11 symmetry and so the Cremmer-Julia duality symmetries. We apply this theory to find the dynamics of the IIA and IIB strings, the M2 and M5 branes, the IIB D3 brane as well as the one and two branes in seven dimensions.

Response Mixture Modeling: Accounting for Heterogeneity in Item Characteristics across Response Times.

PubMed

Molenaar, Dylan; de Boeck, Paul

2018-06-01

In item response theory modeling of responses and response times, it is commonly assumed that the item responses have the same characteristics across the response times. However, heterogeneity might arise in the data if subjects resort to different response processes when solving the test items. These differences may be within-subject effects, that is, a subject might use a certain process on some of the items and a different process with different item characteristics on the other items. If the probability of using one process over the other process depends on the subject's response time, within-subject heterogeneity of the item characteristics across the response times arises. In this paper, the method of response mixture modeling is presented to account for such heterogeneity. Contrary to traditional mixture modeling where the full response vectors are classified, response mixture modeling involves classification of the individual elements in the response vector. In a simulation study, the response mixture model is shown to be viable in terms of parameter recovery. In addition, the response mixture model is applied to a real dataset to illustrate its use in investigating within-subject heterogeneity in the item characteristics across response times.

A vector radiative transfer model for coupled atmosphere and ocean systems based on successive order of scattering method.

PubMed

Zhai, Peng-Wang; Hu, Yongxiang; Trepte, Charles R; Lucker, Patricia L

2009-02-16

A vector radiative transfer model has been developed for coupled atmosphere and ocean systems based on the Successive Order of Scattering (SOS) Method. The emphasis of this study is to make the model easy-to-use and computationally efficient. This model provides the full Stokes vector at arbitrary locations which can be conveniently specified by users. The model is capable of tracking and labeling different sources of the photons that are measured, e.g. water leaving radiances and reflected sky lights. This model also has the capability to separate florescence from multi-scattered sunlight. The delta - fit technique has been adopted to reduce computational time associated with the strongly forward-peaked scattering phase matrices. The exponential - linear approximation has been used to reduce the number of discretized vertical layers while maintaining the accuracy. This model is developed to serve the remote sensing community in harvesting physical parameters from multi-platform, multi-sensor measurements that target different components of the atmosphere-oceanic system.

Analysis of vector wind change with respect to time for Cape Kennedy, Florida: Wind aloft profile change vs. time, phase 1

NASA Technical Reports Server (NTRS)

Adelfang, S. I.

1977-01-01

Wind vector change with respect to time at Cape Kennedy, Florida, is examined according to the theory of multivariate normality. The joint distribution of the four variables represented by the components of the wind vector at an initial time and after a specified elapsed time is hypothesized to be quadravariate normal; the fourteen statistics of this distribution, calculated from fifteen years of twice daily Rawinsonde data are presented by monthly reference periods for each month from 0 to 27 km. The hypotheses that the wind component changes with respect to time is univariate normal, the joint distribution of wind component changes is bivariate normal, and the modulus of vector wind change is Rayleigh, has been tested by comparison with observed distributions. Statistics of the conditional bivariate normal distributions of vector wind at a future time given the vector wind at an initial time are derived. Wind changes over time periods from one to five hours, calculated from Jimsphere data, are presented.

Public Health Interventions for Aedes Control in the Time of Zikavirus– A Meta-Review on Effectiveness of Vector Control Strategies

PubMed Central

Bouzid, Maha; Brainard, Julii; Hooper, Lee; Hunter, Paul R.

2016-01-01

Background There is renewed interest in effective measures to control Zika and dengue vectors. A synthesis of published literature with a focus on the quality of evidence is warranted to determine the effectiveness of vector control strategies. Methodology We conducted a meta-review assessing the effectiveness of any Aedes control measure. We searched Scopus and Medline for relevant reviews through to May 2016. Titles, abstracts and full texts were assessed independently for inclusion by two authors. Data extraction was performed in duplicate and validity of the evidence was assessed using GRADE criteria. Findings 13 systematic reviews that investigated the effect of control measures on entomological parameters or disease incidence were included. Biological controls seem to achieve better reduction of entomological indices than chemical controls, while educational campaigns can reduce breeding habitats. Integrated vector control strategies may not always increase effectiveness. The efficacy of any control programme is dependent on local settings, intervention type, resources and study duration, which may partly explain the varying degree of success between studies. Nevertheless, the quality of evidence was mostly low to very low due to poor reporting of study design, observational methodologies, heterogeneity, and indirect outcomes, thus hindering an evidence-based recommendation. Conclusions The evidence for the effectiveness of Aedes control measures is mixed. Chemical control, which is commonly used, does not appear to be associated with sustainable reductions of mosquito populations over time. Indeed, by contributing to a false sense of security, chemical control may reduce the effectiveness of educational interventions aimed at encouraging local people to remove mosquito breeding sites. Better quality studies of the impact of vector control interventions on the incidence of human infections with Dengue or Zika are still needed. PMID:27926934

RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing.

PubMed

Härtl, Katja; Kalinowski, Gregor; Hoffmann, Thomas; Preuss, Anja; Schwab, Wilfried

2017-05-01

RNA interference (RNAi) has been exploited as a reverse genetic tool for functional genomics in the nonmodel species strawberry (Fragaria × ananassa) since 2006. Here, we analysed for the first time different but overlapping nucleotide sections (>200 nt) of two endogenous genes, FaCHS (chalcone synthase) and FaOMT (O-methyltransferase), as inducer sequences and a transitive vector system to compare their gene silencing efficiencies. In total, ten vectors were assembled each containing the nucleotide sequence of one fragment in sense and corresponding antisense orientation separated by an intron (inverted hairpin construct, ihp). All sequence fragments along the full lengths of both target genes resulted in a significant down-regulation of the respective gene expression and related metabolite levels. Quantitative PCR data and successful application of a transitive vector system coinciding with a phenotypic change suggested propagation of the silencing signal. The spreading of the signal in strawberry fruit in the 3' direction was shown for the first time by the detection of secondary small interfering RNAs (siRNAs) outside of the primary targets by deep sequencing. Down-regulation of endogenes by the transitive method was less effective than silencing by ihp constructs probably because the numbers of primary siRNAs exceeded the quantity of secondary siRNAs by three orders of magnitude. Besides, we observed consistent hotspots of primary and secondary siRNA formation along the target sequence which fall within a distance of less than 200 nt. Thus, ihp vectors seem to be superior over the transitive vector system for functional genomics in strawberry fruit. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Cost-Effectiveness of Chagas Disease Vector Control Strategies in Northwestern Argentina

PubMed Central

Vazquez-Prokopec, Gonzalo M.; Spillmann, Cynthia; Zaidenberg, Mario; Kitron, Uriel; Gürtler, Ricardo E.

2009-01-01

Background Control and prevention of Chagas disease rely mostly on residual spraying of insecticides. In Argentina, vector control shifted from a vertical to a fully horizontal strategy based on community participation between 1992 and 2004. The effects of such strategy on Triatoma infestans, the main domestic vector, and on disease transmission have not been assessed. Methods and Findings Based on retrospective (1993–2004) records from the Argentinean Ministry of Health for the Moreno Department, Northwestern Argentina, we performed a cost-effectiveness (CE) analysis and compared the observed CE of the fully horizontal vector control strategy with the expected CE for a vertical or a mixed (i.e., vertical attack phase followed by horizontal surveillance) strategy. Total direct costs (in 2004 US$) of the horizontal and mixed strategies were, respectively, 3.3 and 1.7 times lower than the costs of the vertical strategy, due to reductions in personnel costs. The estimated CE ratios for the vertical, mixed and horizontal strategies were US$132, US$82 and US$45 per averted human case, respectively. When per diems were excluded from the costs (i.e., simulating the decentralization of control activities), the CE of vertical, mixed and horizontal strategies was reduced to US$60, US$42 and US$32 per averted case, respectively. Conclusions and Significance The mixed strategy would have averted between 1.6 and 4.0 times more human cases than the fully horizontal strategy, and would have been the most cost-effective option to interrupt parasite transmission in the Department. In rural and dispersed areas where waning vertical vector programs cannot accomplish full insecticide coverage, alternative strategies need to be developed. If properly implemented, community participation represents not only the most appealing but also the most cost-effective alternative to accomplish such objectives. PMID:19156190

Vector Doppler: spatial sampling analysis and presentation techniques for real-time systems

NASA Astrophysics Data System (ADS)

Capineri, Lorenzo; Scabia, Marco; Masotti, Leonardo F.

2001-05-01

The aim of the vector Doppler (VD) technique is the quantitative reconstruction of a velocity field independently of the ultrasonic probe axis to flow angle. In particular vector Doppler is interesting for studying vascular pathologies related to complex blood flow conditions. Clinical applications require a real-time operating mode and the capability to perform Doppler measurements over a defined volume. The combination of these two characteristics produces a real-time vector velocity map. In previous works the authors investigated the theory of pulsed wave (PW) vector Doppler and developed an experimental system capable of producing off-line 3D vector velocity maps. Afterwards, for producing dynamic velocity vector maps, we realized a new 2D vector Doppler system based on a modified commercial echograph. The measurement and presentation of a vector velocity field requires a correct spatial sampling that must satisfy the Shannon criterion. In this work we tackled this problem, establishing a relationship between sampling steps and scanning system characteristics. Another problem posed by the vector Doppler technique is the data representation in real-time that should be easy to interpret for the physician. With this in mine we attempted a multimedia solution that uses both interpolated images and sound to represent the information of the measured vector velocity map. These presentation techniques were experimented for real-time scanning on flow phantoms and preliminary measurements in vivo on a human carotid artery.

Distribution of AAV8 particles in cell lysates and culture media changes with time and is dependent on the recombinant vector

PubMed Central

Piras, Bryan A; Drury, Jason E; Morton, Christopher L; Spence, Yunyu; Lockey, Timothy D; Nathwani, Amit C; Davidoff, Andrew M; Meagher, Michael M

2016-01-01

With clinical trials ongoing, efficient clinical production of adeno-associated virus (AAV) to treat large numbers of patients remains a challenge. We compared distribution of AAV8 packaged with Factor VIII (FVIII) in cell culture media and lysates on days 3, 5, 6, and 7 post-transfection and found increasing viral production through day 6, with the proportion of viral particles in the media increasing from 76% at day 3 to 94% by day 7. Compared to FVIII, AAV8 packaged with Factor IX and Protective Protein/Cathepsin A vectors demonstrated a greater shift from lysate towards media from day 3 to 6, implying that particle distribution is dependent on recombinant vector. Larger-scale productions showed that the ratio of full-to-empty AAV particles is similar in media and lysate, and that AAV harvested on day 6 post-transfection provides equivalent function in mice compared to AAV harvested on day 3. This demonstrates that AAV8 production can be optimized by prolonging the duration of culture post-transfection, and simplified by allowing harvest of media only, with disposal of cells that contain 10% or less of total vector yield. Additionally, the difference in particle distribution with different expression cassettes implies a recombinant vector-dependent processing mechanism which should be taken into account during process development. PMID:27069949

Attenuated Human Parainfluenza Virus Type 1 Expressing the Respiratory Syncytial Virus (RSV) Fusion (F) Glycoprotein from an Added Gene: Effects of Prefusion Stabilization and Packaging of RSV F

PubMed Central

Liu, Xiang; Liang, Bo; Ngwuta, Joan; Liu, Xueqiao; Surman, Sonja; Lingemann, Matthias; Kwong, Peter D.; Graham, Barney S.; Collins, Peter L.

2017-01-01

ABSTRACT Human respiratory syncytial virus (RSV) is the most prevalent worldwide cause of severe respiratory tract infection in infants and young children. Human parainfluenza virus type 1 (HPIV1) also causes severe pediatric respiratory illness, especially croup. Both viruses lack vaccines. Here, we describe the preclinical development of a bivalent RSV/HPIV1 vaccine based on a recombinant HPIV1 vector, attenuated by a stabilized mutation, that expresses RSV F protein modified for increased stability in the prefusion (pre-F) conformation by previously described disulfide bond (DS) and hydrophobic cavity-filling (Cav1) mutations. RSV F was expressed from the first or second gene position as the full-length protein or as a chimeric protein with its transmembrane and cytoplasmic tail (TMCT) domains substituted with those of HPIV1 F in an effort to direct packaging in the vector particles. All constructs were recovered by reverse genetics. The TMCT versions of RSV F were packaged in the rHPIV1 particles much more efficiently than their full-length counterparts. In hamsters, the presence of the RSV F gene, and in particular the TMCT versions, was attenuating and resulted in reduced immunogenicity. However, the vector expressing full-length RSV F from the pre-N position was immunogenic for RSV and HPIV1. It conferred complement-independent high-quality RSV-neutralizing antibodies at titers similar to those of wild-type RSV and provided protection against RSV challenge. The vectors exhibited stable RSV F expression in vitro and in vivo. In conclusion, an attenuated rHPIV1 vector expressing a pre-F-stabilized form of RSV F demonstrated promising immunogenicity and should be further developed as an intranasal pediatric vaccine. IMPORTANCE RSV and HPIV1 are major viral causes of acute pediatric respiratory illness for which no vaccines or suitable antiviral drugs are available. The RSV F glycoprotein is the major RSV neutralization antigen. We used a rHPIV1 vector, bearing a stabilized attenuating mutation, to express the RSV F glycoprotein bearing amino acid substitutions that increase its stability in the pre-F form, the most immunogenic form that elicits highly functional virus-neutralizing antibodies. RSV F was expressed from the pre-N or N-P gene position of the rHPIV1 vector as a full-length protein or as a chimeric form with its TMCT domain derived from HPIV1 F. TMCT modification greatly increased packaging of RSV F into the vector particles but also increased vector attenuation in vivo, resulting in reduced immunogenicity. In contrast, full-length RSV F expressed from the pre-N position was immunogenic, eliciting complement-independent RSV-neutralizing antibodies and providing protection against RSV challenge. PMID:28835504

Full Gradient Solution to Adaptive Hybrid Control

NASA Technical Reports Server (NTRS)

Bean, Jacob; Schiller, Noah H.; Fuller, Chris

2017-01-01

This paper focuses on the adaptation mechanisms in adaptive hybrid controllers. Most adaptive hybrid controllers update two filters individually according to the filtered reference least mean squares (FxLMS) algorithm. Because this algorithm was derived for feedforward control, it does not take into account the presence of a feedback loop in the gradient calculation. This paper provides a derivation of the proper weight vector gradient for hybrid (or feedback) controllers that takes into account the presence of feedback. In this formulation, a single weight vector is updated rather than two individually. An internal model structure is assumed for the feedback part of the controller. The full gradient is equivalent to that used in the standard FxLMS algorithm with the addition of a recursive term that is a function of the modeling error. Some simulations are provided to highlight the advantages of using the full gradient in the weight vector update rather than the approximation.

Full Gradient Solution to Adaptive Hybrid Control

NASA Technical Reports Server (NTRS)

Bean, Jacob; Schiller, Noah H.; Fuller, Chris

2016-01-01

This paper focuses on the adaptation mechanisms in adaptive hybrid controllers. Most adaptive hybrid controllers update two filters individually according to the filtered-reference least mean squares (FxLMS) algorithm. Because this algorithm was derived for feedforward control, it does not take into account the presence of a feedback loop in the gradient calculation. This paper provides a derivation of the proper weight vector gradient for hybrid (or feedback) controllers that takes into account the presence of feedback. In this formulation, a single weight vector is updated rather than two individually. An internal model structure is assumed for the feedback part of the controller. The full gradient is equivalent to that used in the standard FxLMS algorithm with the addition of a recursive term that is a function of the modeling error. Some simulations are provided to highlight the advantages of using the full gradient in the weight vector update rather than the approximation.

Gravity Field of Venus and Comparison with Earth

NASA Technical Reports Server (NTRS)

Bowin, C.

1985-01-01

The acceleration (gravity) anomaly estimates by spacecraft tracking, determined from Doppler residuals, are components of the gravity field directed along the spacecraft Earth line of sight (LOS). These data constitute a set of vector components of a planet's gravity field, the specific component depending upon where the Earth happened to be at the time of each measurement, and they are at varying altitudes above the planet surface. From this data set the gravity field vector components were derived using the method of harmonic splines which imposes a smoothness criterion to select a gravity model compatible with the LOS data. Given the piecewise model it is now possible to upward and downward continue the field quantities desired with a few parameters unlike some other methods which must return to the full dataset for each desired calculation.

Thrust Vectoring on the NASA F-18 High Alpha Research Vehicle

NASA Technical Reports Server (NTRS)

Bowers, Albion H.; Pahle, Joseph W.

1996-01-01

Investigations into a multiaxis thrust-vectoring system have been conducted on an F-18 configuration. These investigations include ground-based scale-model tests, ground-based full-scale testing, and flight testing. This thrust-vectoring system has been tested on the NASA F-18 High Alpha Research Vehicle (HARV). The system provides thrust vectoring in pitch and yaw axes. Ground-based subscale test data have been gathered as background to the flight phase of the program. Tests investigated aerodynamic interaction and vane control effectiveness. The ground-based full-scale data were gathered from static engine runs with image analysis to determine relative thrust-vectoring effectiveness. Flight tests have been conducted at the NASA Dryden Flight Research Center. Parameter identification input techniques have been developed. Individual vanes were not directly controlled because of a mixer-predictor function built into the flight control laws. Combined effects of the vanes have been measured in flight and compared to combined effects of the vanes as predicted by the cold-jet test data. Very good agreement has been found in the linearized effectiveness derivatives.

Fast temporal neural learning using teacher forcing

NASA Technical Reports Server (NTRS)

Toomarian, Nikzad (Inventor); Bahren, Jacob (Inventor)

1992-01-01

A neural network is trained to output a time dependent target vector defined over a predetermined time interval in response to a time dependent input vector defined over the same time interval by applying corresponding elements of the error vector, or difference between the target vector and the actual neuron output vector, to the inputs of corresponding output neurons of the network as corrective feedback. This feedback decreases the error and quickens the learning process, so that a much smaller number of training cycles are required to complete the learning process. A conventional gradient descent algorithm is employed to update the neural network parameters at the end of the predetermined time interval. The foregoing process is repeated in repetitive cycles until the actual output vector corresponds to the target vector. In the preferred embodiment, as the overall error of the neural network output decreasing during successive training cycles, the portion of the error fed back to the output neurons is decreased accordingly, allowing the network to learn with greater freedom from teacher forcing as the network parameters converge to their optimum values. The invention may also be used to train a neural network with stationary training and target vectors.

Fast temporal neural learning using teacher forcing

NASA Technical Reports Server (NTRS)

Toomarian, Nikzad (Inventor); Bahren, Jacob (Inventor)

1995-01-01

A neural network is trained to output a time dependent target vector defined over a predetermined time interval in response to a time dependent input vector defined over the same time interval by applying corresponding elements of the error vector, or difference between the target vector and the actual neuron output vector, to the inputs of corresponding output neurons of the network as corrective feedback. This feedback decreases the error and quickens the learning process, so that a much smaller number of training cycles are required to complete the learning process. A conventional gradient descent algorithm is employed to update the neural network parameters at the end of the predetermined time interval. The foregoing process is repeated in repetitive cycles until the actual output vector corresponds to the target vector. In the preferred embodiment, as the overall error of the neural network output decreasing during successive training cycles, the portion of the error fed back to the output neurons is decreased accordingly, allowing the network to learn with greater freedom from teacher forcing as the network parameters converge to their optimum values. The invention may also be used to train a neural network with stationary training and target vectors.

A fast, time-accurate unsteady full potential scheme

NASA Technical Reports Server (NTRS)

Shankar, V.; Ide, H.; Gorski, J.; Osher, S.

1985-01-01

The unsteady form of the full potential equation is solved in conservation form by an implicit method based on approximate factorization. At each time level, internal Newton iterations are performed to achieve time accuracy and computational efficiency. A local time linearization procedure is introduced to provide a good initial guess for the Newton iteration. A novel flux-biasing technique is applied to generate proper forms of the artificial viscosity to treat hyperbolic regions with shocks and sonic lines present. The wake is properly modeled by accounting not only for jumps in phi, but also for jumps in higher derivatives of phi, obtained by imposing the density to be continuous across the wake. The far field is modeled using the Riemann invariants to simulate nonreflecting boundary conditions. The resulting unsteady method performs well which, even at low reduced frequency levels of 0.1 or less, requires fewer than 100 time steps per cycle at transonic Mach numbers. The code is fully vectorized for the CRAY-XMP and the VPS-32 computers.

Generation of an infectious clone of a new Korean isolate of apple chlorotic leaf spot virus (ACLSV) driven by dual 35S and T7 promoters in a versatile binary vector

USDA-ARS?s Scientific Manuscript database

The full-length sequence of a new isolate of Apple chlorotic leaf spot virus (ACLSV) from Korea was divergent, but most closely related to the Japanese isolate A4, at 84% nucleotide identity. The full-length cDNA of the Korean isolate of ACLSV was cloned into a binary vector downstream of the bacter...

A Real-Time Phase Vector Display for EEG Monitoring

NASA Technical Reports Server (NTRS)

Finger, Herbert J.; Anliker, James E.; Rimmer, Tamara

1973-01-01

A real-time, computer-based, phase vector display system has been developed which will output a vector whose phase is equal to the delay between a trigger and the peak of a function which is quasi-coherent with respect to the trigger. The system also contains a sliding averager which enables the operator to average successive trials before calculating the phase vector. Data collection, averaging and display generation are performed on a LINC-8 computer. Output displays appear on several X-Y CRT display units and on a kymograph camera/oscilloscope unit which is used to generate photographs of time-varying phase vectors or contourograms of time-varying averages of input functions.

Towards a comprehensive model of Earth's disk-integrated Stokes vector

NASA Astrophysics Data System (ADS)

García Muñoz, A.

2015-07-01

A significant body of work on simulating the remote appearance of Earth-like exoplanets has been done over the last decade. The research is driven by the prospect of characterizing habitable planets beyond the Solar System in the near future. In this work, I present a method to produce the disk-integrated signature of planets that are described in their three-dimensional complexity, i.e. with both horizontal and vertical variations in the optical properties of their envelopes. The approach is based on Pre-conditioned Backward Monte Carlo integration of the vector Radiative Transport Equation and yields the full Stokes vector for outgoing reflected radiation. The method is demonstrated through selected examples inspired by published work at wavelengths from the visible to the near infrared and terrestrial prescriptions of both cloud and surface albedo maps. I explore the performance of the method in terms of computational time and accuracy. A clear strength of this approach is that its computational cost does not appear to be significantly affected by non-uniformities in the planet optical properties. Earth's simulated appearance is strongly dependent on wavelength; both brightness and polarization undergo diurnal variations arising from changes in the planet cover, but polarization yields a better insight into variations with phase angle. There is partial cancellation of the polarized signal from the northern and southern hemispheres so that the outgoing polarization vector lies preferentially either in the plane parallel or perpendicular to the planet scattering plane, also for non-uniform cloud and albedo properties and various levels of absorption within the atmosphere. The evaluation of circular polarization is challenging; a number of one-photon experiments of 109 or more is needed to resolve hemispherically integrated degrees of circular polarization of a few times 10-5. Last, I introduce brightness curves of Earth obtained with one of the Messenger cameras at three wavelengths (0.48, 0.56 and 0.63 μm) during a flyby in 2005. The light curves show distinct structure associated with the varying aspect of the Earth's visible disk (phases of 98-107°) as the planet undergoes a full 24 h rotation; the structure is reasonably well reproduced with model simulations.

Vector adaptive predictive coder for speech and audio

NASA Technical Reports Server (NTRS)

Chen, Juin-Hwey (Inventor); Gersho, Allen (Inventor)

1990-01-01

A real-time vector adaptive predictive coder which approximates each vector of K speech samples by using each of M fixed vectors in a first codebook to excite a time-varying synthesis filter and picking the vector that minimizes distortion. Predictive analysis for each frame determines parameters used for computing from vectors in the first codebook zero-state response vectors that are stored at the same address (index) in a second codebook. Encoding of input speech vectors s.sub.n is then carried out using the second codebook. When the vector that minimizes distortion is found, its index is transmitted to a decoder which has a codebook identical to the first codebook of the decoder. There the index is used to read out a vector that is used to synthesize an output speech vector s.sub.n. The parameters used in the encoder are quantized, for example by using a table, and the indices are transmitted to the decoder where they are decoded to specify transfer characteristics of filters used in producing the vector s.sub.n from the receiver codebook vector selected by the vector index transmitted.

Detection of a sudden change of the field time series based on the Lorenz system.

PubMed

Da, ChaoJiu; Li, Fang; Shen, BingLu; Yan, PengCheng; Song, Jian; Ma, DeShan

2017-01-01

We conducted an exploratory study of the detection of a sudden change of the field time series based on the numerical solution of the Lorenz system. First, the time when the Lorenz path jumped between the regions on the left and right of the equilibrium point of the Lorenz system was quantitatively marked and the sudden change time of the Lorenz system was obtained. Second, the numerical solution of the Lorenz system was regarded as a vector; thus, this solution could be considered as a vector time series. We transformed the vector time series into a time series using the vector inner product, considering the geometric and topological features of the Lorenz system path. Third, the sudden change of the resulting time series was detected using the sliding t-test method. Comparing the test results with the quantitatively marked time indicated that the method could detect every sudden change of the Lorenz path, thus the method is effective. Finally, we used the method to detect the sudden change of the pressure field time series and temperature field time series, and obtained good results for both series, which indicates that the method can apply to high-dimension vector time series. Mathematically, there is no essential difference between the field time series and vector time series; thus, we provide a new method for the detection of the sudden change of the field time series.

Attenuated Human Parainfluenza Virus Type 1 Expressing the Respiratory Syncytial Virus (RSV) Fusion (F) Glycoprotein from an Added Gene: Effects of Prefusion Stabilization and Packaging of RSV F.

PubMed

Liu, Xiang; Liang, Bo; Ngwuta, Joan; Liu, Xueqiao; Surman, Sonja; Lingemann, Matthias; Kwong, Peter D; Graham, Barney S; Collins, Peter L; Munir, Shirin

2017-11-15

Human respiratory syncytial virus (RSV) is the most prevalent worldwide cause of severe respiratory tract infection in infants and young children. Human parainfluenza virus type 1 (HPIV1) also causes severe pediatric respiratory illness, especially croup. Both viruses lack vaccines. Here, we describe the preclinical development of a bivalent RSV/HPIV1 vaccine based on a recombinant HPIV1 vector, attenuated by a stabilized mutation, that expresses RSV F protein modified for increased stability in the prefusion (pre-F) conformation by previously described disulfide bond (DS) and hydrophobic cavity-filling (Cav1) mutations. RSV F was expressed from the first or second gene position as the full-length protein or as a chimeric protein with its transmembrane and cytoplasmic tail (TMCT) domains substituted with those of HPIV1 F in an effort to direct packaging in the vector particles. All constructs were recovered by reverse genetics. The TMCT versions of RSV F were packaged in the rHPIV1 particles much more efficiently than their full-length counterparts. In hamsters, the presence of the RSV F gene, and in particular the TMCT versions, was attenuating and resulted in reduced immunogenicity. However, the vector expressing full-length RSV F from the pre-N position was immunogenic for RSV and HPIV1. It conferred complement-independent high-quality RSV-neutralizing antibodies at titers similar to those of wild-type RSV and provided protection against RSV challenge. The vectors exhibited stable RSV F expression in vitro and in vivo In conclusion, an attenuated rHPIV1 vector expressing a pre-F-stabilized form of RSV F demonstrated promising immunogenicity and should be further developed as an intranasal pediatric vaccine. IMPORTANCE RSV and HPIV1 are major viral causes of acute pediatric respiratory illness for which no vaccines or suitable antiviral drugs are available. The RSV F glycoprotein is the major RSV neutralization antigen. We used a rHPIV1 vector, bearing a stabilized attenuating mutation, to express the RSV F glycoprotein bearing amino acid substitutions that increase its stability in the pre-F form, the most immunogenic form that elicits highly functional virus-neutralizing antibodies. RSV F was expressed from the pre-N or N-P gene position of the rHPIV1 vector as a full-length protein or as a chimeric form with its TMCT domain derived from HPIV1 F. TMCT modification greatly increased packaging of RSV F into the vector particles but also increased vector attenuation in vivo , resulting in reduced immunogenicity. In contrast, full-length RSV F expressed from the pre-N position was immunogenic, eliciting complement-independent RSV-neutralizing antibodies and providing protection against RSV challenge. Copyright © 2017 American Society for Microbiology.

Extended vector-tensor theories

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

Kimura, Rampei; Naruko, Atsushi; Yoshida, Daisuke, E-mail: rampei@th.phys.titech.ac.jp, E-mail: naruko@th.phys.titech.ac.jp, E-mail: yoshida@th.phys.titech.ac.jp

Recently, several extensions of massive vector theory in curved space-time have been proposed in many literatures. In this paper, we consider the most general vector-tensor theories that contain up to two derivatives with respect to metric and vector field. By imposing a degeneracy condition of the Lagrangian in the context of ADM decomposition of space-time to eliminate an unwanted mode, we construct a new class of massive vector theories where five degrees of freedom can propagate, corresponding to three for massive vector modes and two for massless tensor modes. We find that the generalized Proca and the beyond generalized Procamore » theories up to the quartic Lagrangian, which should be included in this formulation, are degenerate theories even in curved space-time. Finally, introducing new metric and vector field transformations, we investigate the properties of thus obtained theories under such transformations.« less

Models for discrete-time self-similar vector processes with application to network traffic

NASA Astrophysics Data System (ADS)

Lee, Seungsin; Rao, Raghuveer M.; Narasimha, Rajesh

2003-07-01

The paper defines self-similarity for vector processes by employing the discrete-time continuous-dilation operation which has successfully been used previously by the authors to define 1-D discrete-time stochastic self-similar processes. To define self-similarity of vector processes, it is required to consider the cross-correlation functions between different 1-D processes as well as the autocorrelation function of each constituent 1-D process in it. System models to synthesize self-similar vector processes are constructed based on the definition. With these systems, it is possible to generate self-similar vector processes from white noise inputs. An important aspect of the proposed models is that they can be used to synthesize various types of self-similar vector processes by choosing proper parameters. Additionally, the paper presents evidence of vector self-similarity in two-channel wireless LAN data and applies the aforementioned systems to simulate the corresponding network traffic traces.

Attitude Control for an Aero-Vehicle Using Vector Thrusting and Variable Speed Control Moment Gyros

NASA Technical Reports Server (NTRS)

Shin, Jong-Yeob; Lim, K. B.; Moerder, D. D.

2005-01-01

Stabilization of passively unstable thrust-levitated vehicles can require significant control inputs. Although thrust vectoring is a straightforward choice for realizing these inputs, this may lead to difficulties discussed in the paper. This paper examines supplementing thrust vectoring with Variable-Speed Control Moment Gyroscopes (VSCMGs). The paper describes how to allocate VSCMGs and the vectored thrust mechanism for attitude stabilization in frequency domain and also shows trade-off between vectored thrust and VSCMGs. Using an H2 control synthesis methodology in LMI optimization, a feedback control law is designed for a thrust-levitated research vehicle and is simulated with the full nonlinear model. It is demonstrated that VSCMGs can reduce the use of vectored thrust variation for stabilizing the hovering platform in the presence of strong wind gusts.

Estimating residual fault hitting rates by recapture sampling

NASA Technical Reports Server (NTRS)

Lee, Larry; Gupta, Rajan

1988-01-01

For the recapture debugging design introduced by Nayak (1988) the problem of estimating the hitting rates of the faults remaining in the system is considered. In the context of a conditional likelihood, moment estimators are derived and are shown to be asymptotically normal and fully efficient. Fixed sample properties of the moment estimators are compared, through simulation, with those of the conditional maximum likelihood estimators. Properties of the conditional model are investigated such as the asymptotic distribution of linear functions of the fault hitting frequencies and a representation of the full data vector in terms of a sequence of independent random vectors. It is assumed that the residual hitting rates follow a log linear rate model and that the testing process is truncated when the gaps between the detection of new errors exceed a fixed amount of time.

Geometric Corrections for Topographic Distortion from Side Scan Sonar Data Obtained by ANKOU System

NASA Astrophysics Data System (ADS)

Yamamoto, Fujio; Kato, Yukihiro; Ogasawara, Shohei

The ANKOU is a newly developed, full ocean depth, long-range vector side scan sonar system. The system provides real time vector side scan sonar data to produce backscattering images and bathymetric maps for seafloor swaths up to 10 km on either side of ship's centerline. Complete geometric corrections are made using towfish attitude and cross-track distortions known as foreshortening and layover caused by violation of the flat bottom assumption. Foreshortening and layover refers to pixels which have been placed at an incorrect cross-track distance. Our correction of this topographic distortion is accomplished by interpolating a bathymetric profile and ANKOU phase data. We applied these processing techniques to ANKOU backscattering data obtained from off Boso Peninsula, and confirmed their efficiency and utility for making geometric corrections of side scan sonar data.

Comparison of the MPP with other supercomputers for LANDSAT data processing

NASA Technical Reports Server (NTRS)

Ozga, Martin

1987-01-01

The massively parallel processor is compared to the CRAY X-MP and the CYBER-205 for LANDSAT data processing. The maximum likelihood classification algorithm is the basis for comparison since this algorithm is simple to implement and vectorizes very well. The algorithm was implemented on all three machines and tested by classifying the same full scene of LANDSAT multispectral scan data. Timings are compared as well as features of the machines and available software.

Large-scale and Long-duration Simulation of a Multi-stage Eruptive Solar Event

NASA Astrophysics Data System (ADS)

Jiang, chaowei; Hu, Qiang; Wu, S. T.

2015-04-01

We employ a data-driven 3D MHD active region evolution model by using the Conservation Element and Solution Element (CESE) numerical method. This newly developed model retains the full MHD effects, allowing time-dependent boundary conditions and time evolution studies. The time-dependent simulation is driven by measured vector magnetograms and the method of MHD characteristics on the bottom boundary. We have applied the model to investigate the coronal magnetic field evolution of AR11283 which was characterized by a pre-existing sigmoid structure in the core region and multiple eruptions, both in relatively small and large scales. We have succeeded in producing the core magnetic field structure and the subsequent eruptions of flux-rope structures (see https://dl.dropboxusercontent.com/u/96898685/large.mp4 for an animation) as the measured vector magnetograms on the bottom boundary evolve in time with constant flux emergence. The whole process, lasting for about an hour in real time, compares well with the corresponding SDO/AIA and coronagraph imaging observations. From these results, we show the capability of the model, largely data-driven, that is able to simulate complex, topological, and highly dynamic active region evolutions. (We acknowledge partial support of NSF grants AGS 1153323 and AGS 1062050, and data support from SDO/HMI and AIA teams).

On the time-dependent Aharonov-Bohm effect

NASA Astrophysics Data System (ADS)

Jing, Jian; Zhang, Yu-Fei; Wang, Kang; Long, Zheng-Wen; Dong, Shi-Hai

2017-11-01

The Aharonov-Bohm effect in the background of a time-dependent vector potential is re-examined for both non-relativistic and relativistic cases. Based on the solutions to the Schrodinger and Dirac equations which contain the time-dependent magnetic vector potential, we find that contrary to the conclusions in a recent paper (Singleton and Vagenas 2013 [4]), the interference pattern will be altered with respect to time because of the time-dependent vector potential.

Detection of a sudden change of the field time series based on the Lorenz system

PubMed Central

Li, Fang; Shen, BingLu; Yan, PengCheng; Song, Jian; Ma, DeShan

2017-01-01

We conducted an exploratory study of the detection of a sudden change of the field time series based on the numerical solution of the Lorenz system. First, the time when the Lorenz path jumped between the regions on the left and right of the equilibrium point of the Lorenz system was quantitatively marked and the sudden change time of the Lorenz system was obtained. Second, the numerical solution of the Lorenz system was regarded as a vector; thus, this solution could be considered as a vector time series. We transformed the vector time series into a time series using the vector inner product, considering the geometric and topological features of the Lorenz system path. Third, the sudden change of the resulting time series was detected using the sliding t-test method. Comparing the test results with the quantitatively marked time indicated that the method could detect every sudden change of the Lorenz path, thus the method is effective. Finally, we used the method to detect the sudden change of the pressure field time series and temperature field time series, and obtained good results for both series, which indicates that the method can apply to high-dimension vector time series. Mathematically, there is no essential difference between the field time series and vector time series; thus, we provide a new method for the detection of the sudden change of the field time series. PMID:28141832

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

Two-stage continuous operation of recombinant Escherichia coli using the bacteriophage lambda Q- vector.

PubMed

Oh, Jeong Seok; Cho, Daechul; Park, Tai Hyun

2005-11-01

A two-stage continuous culture of Escherichia coli in combination with a bacteriophage lambda system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. A phage lambda vector with a Q(-) mutation was used to enhance the expression of the lambda system. The optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned gene were determined in both batch and continuous cultures. For all culturing modes, the full induction of the cloned gene was observed 4 h after the temperature shift. In the two stage continuous culture, the overproduction reached their maxima at D=0.25 h(-1) with 1.5 S(0) of the medium supply. The maximum productivity of the total beta-galactosidase was 16.3x10(6) U l(-1) h(-1), which was approximately seven times higher than that in the single-copy lysogenic stage. The recombinant cells were stable in the lysogenic state for more than 260 h, while they were stable for 40 h in the lytic state. The instability that developed rapidly in the second tank is believed to be due to the accumulation of lysis proteins as a result of vector leakage during the operation.

Long-term vacuum tests of single-mode vertical cavity surface emitting laser diodes used for a scalar magnetometer

NASA Astrophysics Data System (ADS)

Hagen, C.; Ellmeier, M.; Piris, J.; Lammegger, R.; Jernej, I.; Magnes, W.; Murphy, E.; Pollinger, A.; Erd, C.; Baumjohann, W.

2017-11-01

Scalar magnetometers measure the magnitude of the magnetic field, while vector magnetometers (mostly fluxgate magnetometers) produce three-component outputs proportional to the magnitude and the direction of the magnetic field. While scalar magnetometers have a high accuracy, vector magnetometers suffer from parameter drifts and need to be calibrated during flight. In some cases, full science return can only be achieved by a combination of vector and scalar magnetometers.

Effects of Homology Length in the Repeat Region on Minus-Strand DNA Transfer and Retroviral Replication

PubMed Central

Dang, Que; Hu, Wei-Shau

2001-01-01

Homology between the two repeat (R) regions in the retroviral genome mediates minus-strand DNA transfer during reverse transcription. We sought to define the effects of R homology lengths on minus-strand DNA transfer. We generated five murine leukemia virus (MLV)-based vectors that contained identical sequences but different lengths of the 3′ R (3, 6, 12, 24 and 69 nucleotides [nt]); 69 nt is the full-length MLV R. After one round of replication, viral titers from the vector with a full-length downstream R were compared with viral titers generated from the other four vectors with reduced R lengths. Viral titers generated from vectors with R lengths reduced to one-third (24 nt) or one-sixth (12 nt) that of the wild type were not significantly affected; however, viral titers generated from vectors with only 3- or 6-nt homology in the R region were significantly lower. Because expression and packaging of the RNA were similar among all the vectors, the differences in the viral titers most likely reflected the impact of the homology lengths on the efficiency of minus-strand DNA transfer. The molecular nature of minus-strand DNA transfer was characterized in 63 proviruses. Precise R-to-R transfer was observed in most proviruses generated from vectors with 12-, 24-, or 69-nt homology in R, whereas aberrant transfers were predominantly used to generate proviruses from vectors with 3- or 6-nt homology. Reverse transcription using RNA transcribed from an upstream promoter, termed read-in RNA transcripts, resulted in most of the aberrant transfers. These data demonstrate that minus-strand DNA transfer is homology driven and a minimum homology length is required for accurate and efficient minus-strand DNA transfer. PMID:11134294

Development of iterative techniques for the solution of unsteady compressible viscous flows

NASA Technical Reports Server (NTRS)

Hixon, Duane; Sankar, L. N.

1993-01-01

During the past two decades, there has been significant progress in the field of numerical simulation of unsteady compressible viscous flows. At present, a variety of solution techniques exist such as the transonic small disturbance analyses (TSD), transonic full potential equation-based methods, unsteady Euler solvers, and unsteady Navier-Stokes solvers. These advances have been made possible by developments in three areas: (1) improved numerical algorithms; (2) automation of body-fitted grid generation schemes; and (3) advanced computer architectures with vector processing and massively parallel processing features. In this work, the GMRES scheme has been considered as a candidate for acceleration of a Newton iteration time marching scheme for unsteady 2-D and 3-D compressible viscous flow calculation; from preliminary calculations, this will provide up to a 65 percent reduction in the computer time requirements over the existing class of explicit and implicit time marching schemes. The proposed method has ben tested on structured grids, but is flexible enough for extension to unstructured grids. The described scheme has been tested only on the current generation of vector processor architecture of the Cray Y/MP class, but should be suitable for adaptation to massively parallel machines.

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.

Elucidating the Potential of Plant Rhabdoviruses as Vector Expressions Systems

USDA-ARS?s Scientific Manuscript database

Maize fine streak virus (MFSV) is a member of the genus Nucleorhabdovirus that is transmitted by the leafhopper Graminella nigrifons. The virus replicates in both its maize host and its insect vector. To determine whether Drosophila S2 cells support the production of full-length MFSV proteins, we ...

The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control.

PubMed

Brand, Samuel P C; Rock, Kat S; Keeling, Matt J

2016-04-01

Epidemiological modelling has a vital role to play in policy planning and prediction for the control of vectors, and hence the subsequent control of vector-borne diseases. To decide between competing policies requires models that can generate accurate predictions, which in turn requires accurate knowledge of vector natural histories. Here we highlight the importance of the distribution of times between life-history events, using short-lived midge species as an example. In particular we focus on the distribution of the extrinsic incubation period (EIP) which determines the time between infection and becoming infectious, and the distribution of the length of the gonotrophic cycle which determines the time between successful bites. We show how different assumptions for these periods can radically change the basic reproductive ratio (R0) of an infection and additionally the impact of vector control on the infection. These findings highlight the need for detailed entomological data, based on laboratory experiments and field data, to correctly construct the next-generation of policy-informing models.

Modal loss mechanism of micro-structured VCSELs studied using full vector FDTD method.

PubMed

Jo, Du-Ho; Vu, Ngoc Hai; Kim, Jin-Tae; Hwang, In-Kag

2011-09-12

Modal properties of vertical cavity surface-emitting lasers (VCSELs) with holey structures are studied using a finite difference time domain (FDTD) method. We investigate loss behavior with respect to the variation of structural parameters, and explain the loss mechanism of VCSELs. We also propose an effective method to estimate the modal loss based on mode profiles obtained using FDTD simulation. Our results could provide an important guideline for optimization of the microstructures of high-power single-mode VCSELs.

Full-motion video analysis for improved gender classification

NASA Astrophysics Data System (ADS)

Flora, Jeffrey B.; Lochtefeld, Darrell F.; Iftekharuddin, Khan M.

2014-06-01

The ability of computer systems to perform gender classification using the dynamic motion of the human subject has important applications in medicine, human factors, and human-computer interface systems. Previous works in motion analysis have used data from sensors (including gyroscopes, accelerometers, and force plates), radar signatures, and video. However, full-motion video, motion capture, range data provides a higher resolution time and spatial dataset for the analysis of dynamic motion. Works using motion capture data have been limited by small datasets in a controlled environment. In this paper, we explore machine learning techniques to a new dataset that has a larger number of subjects. Additionally, these subjects move unrestricted through a capture volume, representing a more realistic, less controlled environment. We conclude that existing linear classification methods are insufficient for the gender classification for larger dataset captured in relatively uncontrolled environment. A method based on a nonlinear support vector machine classifier is proposed to obtain gender classification for the larger dataset. In experimental testing with a dataset consisting of 98 trials (49 subjects, 2 trials per subject), classification rates using leave-one-out cross-validation are improved from 73% using linear discriminant analysis to 88% using the nonlinear support vector machine classifier.

Construction of recombinant FGFR1 containing full-length gene and its potential application.

PubMed

Zhou, Yali; Luo, Wenjuan; Zheng, Lei; Li, Miao; Zhang, Yanmin

2010-07-01

FGFR1, one of the four fibroblast growth factor receptors, has been found to be over-expressed in many cancers. In this study, a full-length expression plasmid for FGFR1 was obtained by fragment amplification. The amplified PCR product was then digested and inserted into the pcDNA3.1(+) vector. A recombinant eukaryotic expression vector containing the complete CDS region of FGFR1 was successfully constructed. After it was transfected to Hek293 cell, the expression of the FGFR1 receptor in recombinant Hek293/FGFR1 was 18 times higher than that of Hek293 cell. The biological activities of high expression FGFR1 cell (Hek293/FGFR1) were verified by FCM, immunofluorescent, RT-PCR, western blot and cell cycle analysis. Then, Hek293/FGFR1 was used to screen taspine with cell membrane chromatography (CMC). Finally, we analyzed the effects of taspine on Hek293/FGFR1 cell and MCF-7 cell. In conclusion, Hek293/FGFR1 was successfully constructed. The results demonstrate that taspine can down-regulate phosphorylation of FGFR1 and ERK, and inhibit Hek293/FGFR1 and MCF-7 cell proliferation. Copyright 2010 Elsevier Inc. All rights reserved.

A robust variant of block Jacobi-Davidson for extracting a large number of eigenpairs: Application to grid-based real-space density functional theory

NASA Astrophysics Data System (ADS)

Lee, M.; Leiter, K.; Eisner, C.; Breuer, A.; Wang, X.

2017-09-01

In this work, we investigate a block Jacobi-Davidson (J-D) variant suitable for sparse symmetric eigenproblems where a substantial number of extremal eigenvalues are desired (e.g., ground-state real-space quantum chemistry). Most J-D algorithm variations tend to slow down as the number of desired eigenpairs increases due to frequent orthogonalization against a growing list of solved eigenvectors. In our specification of block J-D, all of the steps of the algorithm are performed in clusters, including the linear solves, which allows us to greatly reduce computational effort with blocked matrix-vector multiplies. In addition, we move orthogonalization against locked eigenvectors and working eigenvectors outside of the inner loop but retain the single Ritz vector projection corresponding to the index of the correction vector. Furthermore, we minimize the computational effort by constraining the working subspace to the current vectors being updated and the latest set of corresponding correction vectors. Finally, we incorporate accuracy thresholds based on the precision required by the Fermi-Dirac distribution. The net result is a significant reduction in the computational effort against most previous block J-D implementations, especially as the number of wanted eigenpairs grows. We compare our approach with another robust implementation of block J-D (JDQMR) and the state-of-the-art Chebyshev filter subspace (CheFSI) method for various real-space density functional theory systems. Versus CheFSI, for first-row elements, our method yields competitive timings for valence-only systems and 4-6× speedups for all-electron systems with up to 10× reduced matrix-vector multiplies. For all-electron calculations on larger elements (e.g., gold) where the wanted spectrum is quite narrow compared to the full spectrum, we observe 60× speedup with 200× fewer matrix-vector multiples vs. CheFSI.

A robust variant of block Jacobi-Davidson for extracting a large number of eigenpairs: Application to grid-based real-space density functional theory.

PubMed

Lee, M; Leiter, K; Eisner, C; Breuer, A; Wang, X

2017-09-21

In this work, we investigate a block Jacobi-Davidson (J-D) variant suitable for sparse symmetric eigenproblems where a substantial number of extremal eigenvalues are desired (e.g., ground-state real-space quantum chemistry). Most J-D algorithm variations tend to slow down as the number of desired eigenpairs increases due to frequent orthogonalization against a growing list of solved eigenvectors. In our specification of block J-D, all of the steps of the algorithm are performed in clusters, including the linear solves, which allows us to greatly reduce computational effort with blocked matrix-vector multiplies. In addition, we move orthogonalization against locked eigenvectors and working eigenvectors outside of the inner loop but retain the single Ritz vector projection corresponding to the index of the correction vector. Furthermore, we minimize the computational effort by constraining the working subspace to the current vectors being updated and the latest set of corresponding correction vectors. Finally, we incorporate accuracy thresholds based on the precision required by the Fermi-Dirac distribution. The net result is a significant reduction in the computational effort against most previous block J-D implementations, especially as the number of wanted eigenpairs grows. We compare our approach with another robust implementation of block J-D (JDQMR) and the state-of-the-art Chebyshev filter subspace (CheFSI) method for various real-space density functional theory systems. Versus CheFSI, for first-row elements, our method yields competitive timings for valence-only systems and 4-6× speedups for all-electron systems with up to 10× reduced matrix-vector multiplies. For all-electron calculations on larger elements (e.g., gold) where the wanted spectrum is quite narrow compared to the full spectrum, we observe 60× speedup with 200× fewer matrix-vector multiples vs. CheFSI.

Hydrologic Process Regularization for Improved Geoelectrical Monitoring of a Lab-Scale Saline Tracer Experiment

NASA Astrophysics Data System (ADS)

Oware, E. K.; Moysey, S. M.

2016-12-01

Regularization stabilizes the geophysical imaging problem resulting from sparse and noisy measurements that render solutions unstable and non-unique. Conventional regularization constraints are, however, independent of the physics of the underlying process and often produce smoothed-out tomograms with mass underestimation. Cascaded time-lapse (CTL) is a widely used reconstruction technique for monitoring wherein a tomogram obtained from the background dataset is employed as starting model for the inversion of subsequent time-lapse datasets. In contrast, a proper orthogonal decomposition (POD)-constrained inversion framework enforces physics-based regularization based upon prior understanding of the expected evolution of state variables. The physics-based constraints are represented in the form of POD basis vectors. The basis vectors are constructed from numerically generated training images (TIs) that mimic the desired process. The target can be reconstructed from a small number of selected basis vectors, hence, there is a reduction in the number of inversion parameters compared to the full dimensional space. The inversion involves finding the optimal combination of the selected basis vectors conditioned on the geophysical measurements. We apply the algorithm to 2-D lab-scale saline transport experiments with electrical resistivity (ER) monitoring. We consider two transport scenarios with one and two mass injection points evolving into unimodal and bimodal plume morphologies, respectively. The unimodal plume is consistent with the assumptions underlying the generation of the TIs, whereas bimodality in plume morphology was not conceptualized. We compare difference tomograms retrieved from POD with those obtained from CTL. Qualitative comparisons of the difference tomograms with images of their corresponding dye plumes suggest that POD recovered more compact plumes in contrast to those of CTL. While mass recovery generally deteriorated with increasing number of time-steps, POD outperformed CTL in terms of mass recovery accuracy rates. POD is computationally superior requiring only 2.5 mins to complete each inversion compared to 3 hours for CTL to do the same.

Determination of key parameters of vector multifractal vector fields

NASA Astrophysics Data System (ADS)

Schertzer, D. J. M.; Tchiguirinskaia, I.

2017-12-01

For too long time, multifractal analyses and simulations have been restricted to scalar-valued fields (Schertzer and Tchiguirinskaia, 2017a,b). For instance, the wind velocity multifractality has been mostly analysed in terms of scalar structure functions and with the scalar energy flux. This restriction has had the unfortunate consequences that multifractals were applicable to their full extent in geophysics, whereas it has inspired them. Indeed a key question in geophysics is the complexity of the interactions between various fields or they components. Nevertheless, sophisticated methods have been developed to determine the key parameters of scalar valued fields. In this communication, we first present the vector extensions of the universal multifractal analysis techniques to multifractals whose generator belong to a Levy-Clifford algebra (Schertzer and Tchiguirinskaia, 2015). We point out further extensions noting the increased complexity. For instance, the (scalar) index of multifractality becomes a matrice. Schertzer, D. and Tchiguirinskaia, I. (2015) `Multifractal vector fields and stochastic Clifford algebra', Chaos: An Interdisciplinary Journal of Nonlinear Science, 25(12), p. 123127. doi: 10.1063/1.4937364. Schertzer, D. and Tchiguirinskaia, I. (2017) `An Introduction to Multifractals and Scale Symmetry Groups', in Ghanbarian, B. and Hunt, A. (eds) Fractals: Concepts and Applications in Geosciences. CRC Press, p. (in press). Schertzer, D. and Tchiguirinskaia, I. (2017b) `Pandora Box of Multifractals: Barely Open ?', in Tsonis, A. A. (ed.) 30 Years of Nonlinear Dynamics in Geophysics. Berlin: Springer, p. (in press).

Application of Bred Vectors To Data Assimilation

NASA Astrophysics Data System (ADS)

Corazza, M.; Kalnay, E.; Patil, Dj

We introduced a statistic, the BV-dimension, to measure the effective local finite-time dimensionality of the atmosphere. We show that this dimension is often quite low, and suggest that this finding has important implications for data assimilation and the accuracy of weather forecasting (Patil et al, 2001). The original database for this study was the forecasts of the NCEP global ensemble forecasting system. The initial differences between the control forecast and the per- turbed forecasts are called bred vectors. The control and perturbed initial conditions valid at time t=n(t are evolved using the forecast model until time t=(n+1) (t. The differences between the perturbed and the control forecasts are scaled down to their initial amplitude, and constitute the bred vectors valid at (n+1) (t. Their growth rate is typically about 1.5/day. The bred vectors are similar by construction to leading Lya- punov vectors except that they have small but finite amplitude, and they are valid at finite times. The original NCEP ensemble data set has 5 independent bred vectors. We define a local bred vector at each grid point by choosing the 5 by 5 grid points centered at the grid point (a region of about 1100km by 1100km), and using the north-south and east- west velocity components at 500mb pressure level to form a 50 dimensional column vector. Since we have k=5 global bred vectors, we also have k local bred vectors at each grid point. We estimate the effective dimensionality of the subspace spanned by the local bred vectors by performing a singular value decomposition (EOF analysis). The k local bred vector columns form a 50xk matrix M. The singular values s(i) of M measure the extent to which the k column unit vectors making up the matrix M point in the direction of v(i). We define the bred vector dimension as BVDIM={Sum[s(i)]}^2/{Sum[s(i)]^2} For example, if 4 out of the 5 vectors lie along v, and one lies along v, the BV- dimension would be BVDIM[sqrt(4), 1, 0,0,0]=1.8, less than 2 because one direction is more dominant than the other in representing the original data. The results (Patil et al, 2001) show that there are large regions where the bred vectors span a subspace of substantially lower dimension than that of the full space. These low dimensionality regions are dominant in the baroclinic extratropics, typically have a lifetime of 3-7 days, have a well-defined horizontal and vertical structure that spans 1 most of the atmosphere, and tend to move eastward. New results with a large number of ensemble members confirm these results and indicate that the low dimensionality regions are quite robust, and depend only on the verification time (i.e., the underlying flow). Corazza et al (2001) have performed experiments with a data assimilation system based on a quasi-geostrophic model and simulated observations (Morss, 1999, Hamill et al, 2000). A 3D-variational data assimilation scheme for a quasi-geostrophic chan- nel model is used to study the structure of the background error and its relationship to the corresponding bred vectors. The "true" evolution of the model atmosphere is defined by an integration of the model and "rawinsonde observations" are simulated by randomly perturbing the true state at fixed locations. It is found that after 3-5 days the bred vectors develop well organized structures which are very similar for the two different norms considered in this paper (potential vorticity norm and streamfunction norm). The results show that the bred vectors do indeed represent well the characteristics of the data assimilation forecast errors, and that the subspace of bred vectors contains most of the forecast error, except in areas where the forecast errors are small. For example, the angle between the 6hr forecast error and the subspace spanned by 10 bred vectors is less than 10o over 90% of the domain, indicating a pattern correlation of more than 98.5% between the forecast error and its projection onto the bred vector subspace. The presence of low-dimensional regions in the perturbations of the basic flow has important implications for data assimilation. At any given time, there is a difference between the true atmospheric state and the model forecast. Assuming that model er- rors are not the dominant source of errors, in a region of low BV-dimensionality the difference between the true state and the forecast should lie substantially in the low dimensional unstable subspace of the few bred vectors that contribute most strongly to the low BV-dimension. This information should yield a substantial improvement in the forecast: the data assimilation algorithm should correct the model state by moving it closer to the observations along the unstable subspace, since this is where the true state most likely lies. Preliminary experiments have been conducted with the quasi-geostrophic data assim- ilation system testing whether it is possible to add "errors of the day" based on bred vectors to the standard (constant) 3D-Var background error covariance in order to capture these important errors. The results are extremely encouraging, indicating a significant reduction (about 40%) in the analysis errors at a very low computational cost. References: 2 Corazza, M., E. Kalnay, DJ Patil, R. Morss, M Cai, I. Szunyogh, BR Hunt, E Ott and JA Yorke, 2001: Use of the breeding technique to estimate the structure of the analysis "errors of the day". Submitted to Nonlinear Processes in Geophysics. Hamill, T.M., Snyder, C., and Morss, R.E., 2000: A Comparison of Probabilistic Fore- casts from Bred, Singular-Vector and Perturbed Observation Ensembles, Mon. Wea. Rev., 128, 1835­1851. Kalnay, E., and Z. Toth, 1994: Removing growing errors in the analysis cycle. Preprints of the Tenth Conference on Numerical Weather Prediction, Amer. Meteor. Soc., 1994, 212-215. Morss, R. E., 1999: Adaptive observations: Idealized sampling strategies for improv- ing numerical weather prediction. PHD thesis, Massachussetts Institute of technology, 225pp. Patil, D. J. S., B. R. Hunt, E. Kalnay, J. A. Yorke, and E. Ott., 2001: Local Low Dimensionality of Atmospheric Dynamics. Phys. Rev. Lett., 86, 5878. 3

Implicit, nonswitching, vector-oriented algorithm for steady transonic flow

NASA Technical Reports Server (NTRS)

Lottati, I.

1983-01-01

A rapid computation of a sequence of transonic flow solutions has to be performed in many areas of aerodynamic technology. The employment of low-cost vector array processors makes the conduction of such calculations economically feasible. However, for a full utilization of the new hardware, the developed algorithms must take advantage of the special characteristics of the vector array processor. The present investigation has the objective to develop an efficient algorithm for solving transonic flow problems governed by mixed partial differential equations on an array processor.

Discrimination of gender-, speed-, and shoe-dependent movement patterns in runners using full-body kinematics.

PubMed

Maurer, Christian; Federolf, Peter; von Tscharner, Vinzenz; Stirling, Lisa; Nigg, Benno M

2012-05-01

Changes in gait kinematics have often been analyzed using pattern recognition methods such as principal component analysis (PCA). It is usually just the first few principal components that are analyzed, because they describe the main variability within a dataset and thus represent the main movement patterns. However, while subtle changes in gait pattern (for instance, due to different footwear) may not change main movement patterns, they may affect movements represented by higher principal components. This study was designed to test two hypotheses: (1) speed and gender differences can be observed in the first principal components, and (2) small interventions such as changing footwear change the gait characteristics of higher principal components. Kinematic changes due to different running conditions (speed - 3.1m/s and 4.9 m/s, gender, and footwear - control shoe and adidas MicroBounce shoe) were investigated by applying PCA and support vector machine (SVM) to a full-body reflective marker setup. Differences in speed changed the basic movement pattern, as was reflected by a change in the time-dependent coefficient derived from the first principal. Gender was differentiated by using the time-dependent coefficient derived from intermediate principal components. (Intermediate principal components are characterized by limb rotations of the thigh and shank.) Different shoe conditions were identified in higher principal components. This study showed that different interventions can be analyzed using a full-body kinematic approach. Within the well-defined vector space spanned by the data of all subjects, higher principal components should also be considered because these components show the differences that result from small interventions such as footwear changes. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Design of thrust vectoring exhaust nozzles for real-time applications using neural networks

NASA Technical Reports Server (NTRS)

Prasanth, Ravi K.; Markin, Robert E.; Whitaker, Kevin W.

1991-01-01

Thrust vectoring continues to be an important issue in military aircraft system designs. A recently developed concept of vectoring aircraft thrust makes use of flexible exhaust nozzles. Subtle modifications in the nozzle wall contours produce a non-uniform flow field containing a complex pattern of shock and expansion waves. The end result, due to the asymmetric velocity and pressure distributions, is vectored thrust. Specification of the nozzle contours required for a desired thrust vector angle (an inverse design problem) has been achieved with genetic algorithms. This approach is computationally intensive and prevents the nozzles from being designed in real-time, which is necessary for an operational aircraft system. An investigation was conducted into using genetic algorithms to train a neural network in an attempt to obtain, in real-time, two-dimensional nozzle contours. Results show that genetic algorithm trained neural networks provide a viable, real-time alternative for designing thrust vectoring nozzles contours. Thrust vector angles up to 20 deg were obtained within an average error of 0.0914 deg. The error surfaces encountered were highly degenerate and thus the robustness of genetic algorithms was well suited for minimizing global errors.

Field site selection: getting it right first time around

PubMed Central

Malcolm, Colin A; El Sayed, Badria; Babiker, Ahmed; Girod, Romain; Fontenille, Didier; Knols, Bart GJ; Nugud, Abdel Hameed; Benedict, Mark Q

2009-01-01

The selection of suitable field sites for integrated control of Anopheles mosquitoes using the sterile insect technique (SIT) requires consideration of the full gamut of factors facing most proposed control strategies, but four criteria identify an ideal site: 1) a single malaria vector, 2) an unstructured, relatively low density target population, 3) isolation of the target population and 4) actual or potential malaria incidence. Such a site can exist in a diverse range of situations or can be created. Two contrasting SIT field sites are examined here: the desert-flanked Dongola Reach of the Nile River in Northern State, Sudan, where malaria is endemic, and the island of La Reunion, where autochthonous malaria is rare but risk is persistent. The single malaria-transmitting vector at both sites is Anopheles arabiensis. In Sudan, the target area is a narrow 500 km corridor stretching from the rocky terrain at the Fourth Cataract - just above the new Merowe Dam, to the northernmost edge of the species range, close to Egypt. Vector distribution and temporal changes in density depend on the Nile level, ambient temperature and human activities. On La Reunion, the An. arabiensis population is coastal, limited and divided into three areas by altitude and exposure to the trade winds on the east coast. Mosquito vectors for other diseases are an issue at both sites, but of primary importance on La Reunion due to the recent chikungunya epidemic. The similarities and differences between these two sites in terms of suitability are discussed in the context of area-wide integrated vector management incorporating the SIT. PMID:19917079

Integrated optic vector-matrix multiplier

DOEpatents

Watts, Michael R [Albuquerque, NM

2011-09-27

A vector-matrix multiplier is disclosed which uses N different wavelengths of light that are modulated with amplitudes representing elements of an N.times.1 vector and combined to form an input wavelength-division multiplexed (WDM) light stream. The input WDM light stream is split into N streamlets from which each wavelength of the light is individually coupled out and modulated for a second time using an input signal representing elements of an M.times.N matrix, and is then coupled into an output waveguide for each streamlet to form an output WDM light stream which is detected to generate a product of the vector and matrix. The vector-matrix multiplier can be formed as an integrated optical circuit using either waveguide amplitude modulators or ring resonator amplitude modulators.

Balancing aggregation and smoothing errors in inverse models

DOE PAGES

Turner, A. J.; Jacob, D. J.

2015-06-30

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function ofmore » state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.« less

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-01-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

Turner, A. J.; Jacob, D. J.

2015-06-01

Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function of state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.

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.

Geometrical pose and structural estimation from a single image for automatic inspection of filter components

NASA Astrophysics Data System (ADS)

Liu, Yonghuai; Rodrigues, Marcos A.

2000-03-01

This paper describes research on the application of machine vision techniques to a real time automatic inspection task of air filter components in a manufacturing line. A novel calibration algorithm is proposed based on a special camera setup where defective items would show a large calibration error. The algorithm makes full use of rigid constraints derived from the analysis of geometrical properties of reflected correspondence vectors which have been synthesized into a single coordinate frame and provides a closed form solution to the estimation of all parameters. For a comparative study of performance, we also developed another algorithm based on this special camera setup using epipolar geometry. A number of experiments using synthetic data have shown that the proposed algorithm is generally more accurate and robust than the epipolar geometry based algorithm and that the geometric properties of reflected correspondence vectors provide effective constraints to the calibration of rigid body transformations.

The F-18 High Alpha Research Vehicle: A High-Angle-of-Attack Testbed Aircraft

NASA Technical Reports Server (NTRS)

Regenie, Victoria; Gatlin, Donald; Kempel, Robert; Matheny, Neil

1992-01-01

The F-18 High Alpha Research Vehicle is the first thrust-vectoring testbed aircraft used to study the aerodynamics and maneuvering available in the poststall flight regime and to provide the data for validating ground prediction techniques. The aircraft includes a flexible research flight control system and full research instrumentation. The capability to control the vehicle at angles of attack up to 70 degrees is also included. This aircraft was modified by adding a pitch and yaw thrust-vectoring system. No significant problems occurred during the envelope expansion phase of the program. This aircraft has demonstrated excellent control in the wing rock region and increased rolling performance at high angles of attack. Initial pilot reports indicate that the increased capability is desirable although some difficulty in judging the size and timing of control inputs was observed. The aircraft, preflight ground testing and envelope expansion flight tests are described.

Enhanced protection against Ebola virus mediated by an improved adenovirus-based vaccine.

PubMed

Richardson, Jason S; Yao, Michel K; Tran, Kaylie N; Croyle, Maria A; Strong, James E; Feldmann, Heinz; Kobinger, Gary P

2009-01-01

The Ebola virus is transmitted by direct contact with bodily fluids of infected individuals, eliciting death rates as high as 90% among infected humans. Currently, replication defective adenovirus-based Ebola vaccine is being studied in a phase I clinical trial. Another Ebola vaccine, based on an attenuated vesicular stomatitis virus has shown efficacy in post-exposure treatment of nonhuman primates to Ebola infection. In this report, we modified the common recombinant adenovirus serotype 5-based Ebola vaccine expressing the wild-type ZEBOV glycoprotein sequence from a CMV promoter (Ad-CMVZGP). The immune response elicited by this improved expression cassette vector (Ad-CAGoptZGP) and its ability to afford protection against lethal ZEBOV challenge in mice was compared to the standard Ad-CMVZGP vector. Ad-CMVZGP was previously shown to protect mice, guinea pigs and nonhuman primates from an otherwise lethal challenge of Zaire ebolavirus. The antigenic expression cassette of this vector was improved through codon optimization, inclusion of a consensus Kozak sequence and reconfiguration of a CAG promoter (Ad-CAGoptZGP). Expression of GP from Ad-CAGoptZGP was substantially higher than from Ad-CMVZGP. Ad-CAGoptZGP significantly improved T and B cell responses at doses 10 to 100-fold lower than that needed with Ad-CMVZGP. Additionally, Ad-CAGoptZGP afforded full protections in mice against lethal challenge at a dose 100 times lower than the dose required for Ad-CMVZGP. Finally, Ad-CAGoptZGP induced full protection to mice when given 30 minutes post-challenge. We describe an improved adenovirus-based Ebola vaccine capable of affording post-exposure protection against lethal challenge in mice. The molecular modifications of the new improved vaccine also translated in the induction of significantly enhanced immune responses and complete protection at a dose 100 times lower than with the previous generation adenovirus-based Ebola vaccine. Understanding and improving the molecular components of adenovirus-based vaccines can produce potent, optimized product, useful for vaccination and post-exposure therapy.

An Efficient Wait-Free Vector

DOE PAGES

Feldman, Steven; Valera-Leon, Carlos; Dechev, Damian

2016-03-01

The vector is a fundamental data structure, which provides constant-time access to a dynamically-resizable range of elements. Currently, there exist no wait-free vectors. The only non-blocking version supports only a subset of the sequential vector API and exhibits significant synchronization overhead caused by supporting opposing operations. Since many applications operate in phases of execution, wherein each phase only a subset of operations are used, this overhead is unnecessary for the majority of the application. To address the limitations of the non-blocking version, we present a new design that is wait-free, supports more of the operations provided by the sequential vector,more » and provides alternative implementations of key operations. These alternatives allow the developer to balance the performance and functionality of the vector as requirements change throughout execution. Compared to the known non-blocking version and the concurrent vector found in Intel’s TBB library, our design outperforms or provides comparable performance in the majority of tested scenarios. Over all tested scenarios, the presented design performs an average of 4.97 times more operations per second than the non-blocking vector and 1.54 more than the TBB vector. In a scenario designed to simulate the filling of a vector, performance improvement increases to 13.38 and 1.16 times. This work presents the first ABA-free non-blocking vector. Finally, unlike the other non-blocking approach, all operations are wait-free and bounds-checked and elements are stored contiguously in memory.« less

An Ecological Assessment of the Pandemic Threat of Zika Virus

PubMed Central

Getz, Wayne

2016-01-01

The current outbreak of Zika virus poses a severe threat to human health. While the range of the virus has been cataloged growing slowly over the last 50 years, the recent explosive expansion in the Americas indicates that the full potential distribution of Zika remains uncertain. Moreover, many studies rely on its similarity to dengue fever, a phylogenetically closely related disease of unknown ecological comparability. Here we compile a comprehensive spatially-explicit occurrence dataset from Zika viral surveillance and serological surveys based in its native range, and construct ecological niche models to test basic hypotheses about its spread and potential establishment. The hypothesis that the outbreak of cases in Mexico and North America are anomalous and outside the native ecological niche of the disease, and may be linked to either genetic shifts between strains, or El Nino or similar climatic events, remains plausible at this time. Comparison of the Zika niche against the known distribution of dengue fever suggests that Zika is more constrained by the seasonality of precipitation and diurnal temperature fluctuations, likely confining autochthonous non-sexual transmission to the tropics without significant evolutionary change. Projecting the range of the diseases in conjunction with three major vector species (Aedes africanus, Ae. aegypti, and Ae. albopictus) that transmit the pathogens, under climate change, suggests that Zika has potential for northward expansion; but, based on current knowledge, our models indicate Zika is unlikely to fill the full range its vectors occupy, and public fear of a vector-borne Zika epidemic in the mainland United States is potentially informed by biased or limited scientific knowledge. With recent sexual transmission of the virus globally, we caution that our results only apply to the vector-borne transmission route of the pathogen, and while the threat of a mosquito-carried Zika pandemic may be overstated in the media, other transmission modes of the virus may emerge and facilitate naturalization worldwide. PMID:27564232

An Ecological Assessment of the Pandemic Threat of Zika Virus.

PubMed

Carlson, Colin J; Dougherty, Eric R; Getz, Wayne

2016-08-01

The current outbreak of Zika virus poses a severe threat to human health. While the range of the virus has been cataloged growing slowly over the last 50 years, the recent explosive expansion in the Americas indicates that the full potential distribution of Zika remains uncertain. Moreover, many studies rely on its similarity to dengue fever, a phylogenetically closely related disease of unknown ecological comparability. Here we compile a comprehensive spatially-explicit occurrence dataset from Zika viral surveillance and serological surveys based in its native range, and construct ecological niche models to test basic hypotheses about its spread and potential establishment. The hypothesis that the outbreak of cases in Mexico and North America are anomalous and outside the native ecological niche of the disease, and may be linked to either genetic shifts between strains, or El Nino or similar climatic events, remains plausible at this time. Comparison of the Zika niche against the known distribution of dengue fever suggests that Zika is more constrained by the seasonality of precipitation and diurnal temperature fluctuations, likely confining autochthonous non-sexual transmission to the tropics without significant evolutionary change. Projecting the range of the diseases in conjunction with three major vector species (Aedes africanus, Ae. aegypti, and Ae. albopictus) that transmit the pathogens, under climate change, suggests that Zika has potential for northward expansion; but, based on current knowledge, our models indicate Zika is unlikely to fill the full range its vectors occupy, and public fear of a vector-borne Zika epidemic in the mainland United States is potentially informed by biased or limited scientific knowledge. With recent sexual transmission of the virus globally, we caution that our results only apply to the vector-borne transmission route of the pathogen, and while the threat of a mosquito-carried Zika pandemic may be overstated in the media, other transmission modes of the virus may emerge and facilitate naturalization worldwide.

Vectorized multigrid Poisson solver for the CDC CYBER 205

NASA Technical Reports Server (NTRS)

Barkai, D.; Brandt, M. A.

1984-01-01

The full multigrid (FMG) method is applied to the two dimensional Poisson equation with Dirichlet boundary conditions. This has been chosen as a relatively simple test case for examining the efficiency of fully vectorizing of the multigrid method. Data structure and programming considerations and techniques are discussed, accompanied by performance details.

Full-field drift Hamiltonian particle orbits in 3D geometry

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Brunner, S.; Isaev, M. Yu

2011-02-01

A Hamiltonian/Lagrangian theory to describe guiding centre orbit drift motion which is canonical in the Boozer coordinate frame has been extended to include full electromagnetic perturbed fields in anisotropic pressure 3D equilibria with nested magnetic flux surfaces. A redefinition of the guiding centre velocity to eliminate the motion due to finite equilibrium radial magnetic fields and the choice of a gauge condition that sets the radial component of the electromagnetic vector potential to zero are invoked to guarantee that the Boozer angular coordinates retain the canonical structure. The canonical momenta are identified and the guiding centre particle radial drift motion and parallel gyroradius evolution are derived. The particle coordinate position is linearly modified by wave-particle interactions. All the nonlinear wave-wave interactions appear explicitly only in the evolution of the parallel gyroradius. The radial variation of the electrostatic potential is related to the binormal component of the displacement vector for MHD-type perturbations. The electromagnetic vector potential projections can then be determined from the electrostatic potential and the radial component of the MHD displacement vector.

Numerical Simulation of Partially-Coherent Broadband Optical Imaging Using the FDTD Method

PubMed Central

Çapoğlu, İlker R.; White, Craig A.; Rogers, Jeremy D.; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

2012-01-01

Rigorous numerical modeling of optical systems has attracted interest in diverse research areas ranging from biophotonics to photolithography. We report the full-vector electromagnetic numerical simulation of a broadband optical imaging system with partially-coherent and unpolarized illumination. The scattering of light from the sample is calculated using the finite-difference time-domain (FDTD) numerical method. Geometrical optics principles are applied to the scattered light to obtain the intensity distribution at the image plane. Multilayered object spaces are also supported by our algorithm. For the first time, numerical FDTD calculations are directly compared to and shown to agree well with broadband experimental microscopy results. PMID:21540939

Cyclen-based double-tailed lipids for DNA delivery: Synthesis and the effect of linking group structures.

PubMed

Zhang, Yi-Mei; Chang, De-Chun; Zhang, Ji; Liu, Yan-Hong; Yu, Xiao-Qi

2015-09-01

The gene transfection efficiency (TE) of cationic lipids is largely influenced by the lipid structure. Six novel 1, 4, 7, 10-tetraazacyclododecane (cyclen)-based cationic lipids L1-L6, which contain double oleyl as hydrophobic tails, were designed and synthesized. The difference between these lipids is their diverse backbone. Liposomes prepared by the lipids and DOPE showed good DNA affinity, and full DNA condensation could be achieved at N/P of 4 to form lipoplexes with proper size and zeta-potentials for gene transfection. Structure-activity relationship of these lipids as non-viral gene delivery vectors was investigated. It was found that minor backbone structural variations, including linking group and the structural symmetry would affect the TE. The diethylenetriamine derived lipid L4 containing amide linking bonds gave the best TE, which was several times higher than commercially available transfection reagent lipofectamine 2000. Besides, these lipids exhibited low cytotoxicity, suggesting their good biocompatibility. Results reveal that such type of cationic lipids might be promising non-viral gene vectors, and also afford us clues for the design of novel vectors with higher TE and biocompatibility. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-view L2-SVM and its multi-view core vector machine.

PubMed

Huang, Chengquan; Chung, Fu-lai; Wang, Shitong

2016-03-01

In this paper, a novel L2-SVM based classifier Multi-view L2-SVM is proposed to address multi-view classification tasks. The proposed Multi-view L2-SVM classifier does not have any bias in its objective function and hence has the flexibility like μ-SVC in the sense that the number of the yielded support vectors can be controlled by a pre-specified parameter. The proposed Multi-view L2-SVM classifier can make full use of the coherence and the difference of different views through imposing the consensus among multiple views to improve the overall classification performance. Besides, based on the generalized core vector machine GCVM, the proposed Multi-view L2-SVM classifier is extended into its GCVM version MvCVM which can realize its fast training on large scale multi-view datasets, with its asymptotic linear time complexity with the sample size and its space complexity independent of the sample size. Our experimental results demonstrated the effectiveness of the proposed Multi-view L2-SVM classifier for small scale multi-view datasets and the proposed MvCVM classifier for large scale multi-view datasets. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of a VLSI vector quantization processor to real-time speech coding

NASA Technical Reports Server (NTRS)

Davidson, G.; Gersho, A.

1986-01-01

Attention is given to a working vector quantization processor for speech coding that is based on a first-generation VLSI chip which efficiently performs the pattern-matching operation needed for the codebook search process (CPS). Using this chip, the CPS architecture has been successfully incorporated into a compact, single-board Vector PCM implementation operating at 7-18 kbits/sec. A real time Adaptive Vector Predictive Coder system using the CPS has also been implemented.

Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models

DOE PAGES

Carlberg, Kevin T.

2014-11-05

Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less

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

Evaluation of the SPAR thermal analyzer on the CYBER-203 computer

NASA Technical Reports Server (NTRS)

Robinson, J. C.; Riley, K. M.; Haftka, R. T.

1982-01-01

The use of the CYBER 203 vector computer for thermal analysis is investigated. Strengths of the CYBER 203 include the ability to perform, in vector mode using a 64 bit word, 50 million floating point operations per second (MFLOPS) for addition and subtraction, 25 MFLOPS for multiplication and 12.5 MFLOPS for division. The speed of scalar operation is comparable to that of a CDC 7600 and is some 2 to 3 times faster than Langley's CYBER 175s. The CYBER 203 has 1,048,576 64-bit words of real memory with an 80 nanosecond (nsec) access time. Memory is bit addressable and provides single error correction, double error detection (SECDED) capability. The virtual memory capability handles data in either 512 or 65,536 word pages. The machine has 256 registers with a 40 nsec access time. The weaknesses of the CYBER 203 include the amount of vector operation overhead and some data storage limitations. In vector operations there is a considerable amount of time before a single result is produced so that vector calculation speed is slower than scalar operation for short vectors.

Analysis of vector wind change with respect to time for Cape Kennedy, Florida

NASA Technical Reports Server (NTRS)

Adelfang, S. I.

1978-01-01

Multivariate analysis was used to determine the joint distribution of the four variables represented by the components of the wind vector at an initial time and after a specified elapsed time is hypothesized to be quadravariate normal; the fourteen statistics of this distribution, calculated from 15 years of twice-daily rawinsonde data are presented by monthly reference periods for each month from 0 to 27 km. The hypotheses that the wind component changes with respect to time is univariate normal, that the joint distribution of wind component change with respect to time is univariate normal, that the joint distribution of wind component changes is bivariate normal, and that the modulus of vector wind change is Rayleigh are tested by comparison with observed distributions. Statistics of the conditional bivariate normal distributions of vector wind at a future time given the vector wind at an initial time are derived. Wind changes over time periods from 1 to 5 hours, calculated from Jimsphere data, are presented. Extension of the theoretical prediction (based on rawinsonde data) of wind component change standard deviation to time periods of 1 to 5 hours falls (with a few exceptions) within the 95 percentile confidence band of the population estimate obtained from the Jimsphere sample data. The joint distributions of wind change components, conditional wind components, and 1 km vector wind shear change components are illustrated by probability ellipses at the 95 percentile level.

Reversible vector ratchets for skyrmion systems

NASA Astrophysics Data System (ADS)

Ma, X.; Reichhardt, C. J. Olson; Reichhardt, C.

2017-03-01

We show that ac driven skyrmions interacting with an asymmetric substrate provide a realization of a class of ratchet system which we call a vector ratchet that arises due to the effect of the Magnus term on the skyrmion dynamics. In a vector ratchet, the dc motion induced by the ac drive can be described as a vector that can be rotated clockwise or counterclockwise relative to the substrate asymmetry direction. Up to a full 360∘ rotation is possible for varied ac amplitudes or skyrmion densities. In contrast to overdamped systems, in which ratchet motion is always parallel to the substrate asymmetry direction, vector ratchets allow the ratchet motion to be in any direction relative to the substrate asymmetry. It is also possible to obtain a reversal in the direction of rotation of the vector ratchet, permitting the creation of a reversible vector ratchet. We examine vector ratchets for ac drives applied parallel or perpendicular to the substrate asymmetry direction, and show that reverse ratchet motion can be produced by collective effects. No reversals occur for an isolated skyrmion on an asymmetric substrate. Since a vector ratchet can produce motion in any direction, it could represent a method for controlling skyrmion motion for spintronic applications.

C/NOFS Measurements of Magnetic Perturbations in the Low-Latitude Ionosphere During Magnetic Storms

NASA Technical Reports Server (NTRS)

Le, Guan; Burke, William J.; Pfaff, Robert F.; Freudenreich, Henry; Maus, Stefan; Luhr, Hermann

2011-01-01

The Vector Electric Field Investigation suite on the C/NOFS satellite includes a fluxgate magnetometer to monitor the Earth s magnetic fields in the low-latitude ionosphere. Measurements yield full magnetic vectors every second over the range of +/-45,000 nT with a one-bit resolution of 1.37 nT (16 bit A/D) in each component. The sensor s primary responsibility is to support calculations of both V x B and E x B with greater accuracy than can be obtained using standard magnetic field models. The data also contain information about large-scale current systems that, when analyzed in conjunction with electric field measurements, promise to significantly expand understanding of equatorial electrodynamics. We first compare in situ measurements with the POMME (Potsdam Magnetic Model of the Earth) model to establish in-flight sensor "calibrations" and to compute magnetic residuals. At low latitudes the residuals are predominately products of the storm time ring current. Since C/NOFS provides a complete coverage of all local times every 97 min, magnetic field data allow studies of the temporal evolution and local time variations of storm time ring current. The analysis demonstrates the feasibility of using instrumented spacecraft in low-inclination orbits to extract a timely proxy for the provisional Dst index and to specify the ring current s evolution.

Method for enhanced accuracy in predicting peptides using liquid separations or chromatography

DOEpatents

Kangas, Lars J.; Auberry, Kenneth J.; Anderson, Gordon A.; Smith, Richard D.

2006-11-14

A method for predicting the elution time of a peptide in chromatographic and electrophoretic separations by first providing a data set of known elution times of known peptides, then creating a plurality of vectors, each vector having a plurality of dimensions, and each dimension representing the elution time of amino acids present in each of these known peptides from the data set. The elution time of any protein is then be predicted by first creating a vector by assigning dimensional values for the elution time of amino acids of at least one hypothetical peptide and then calculating a predicted elution time for the vector by performing a multivariate regression of the dimensional values of the hypothetical peptide using the dimensional values of the known peptides. Preferably, the multivariate regression is accomplished by the use of an artificial neural network and the elution times are first normalized using a transfer function.

Vectorial nanoscale mapping of optical antenna fields by single molecule dipoles.

PubMed

Singh, Anshuman; Calbris, Gaëtan; van Hulst, Niek F

2014-08-13

Optical nanoantennas confine light on the nanoscale, enabling strong light-matter interactions and ultracompact optical devices. Such confined nanovolumes of light have nonzero field components in all directions (x, y, and z). Unfortunately mapping of the actual nanoscale field vectors has so far remained elusive, though antenna hotspots have been explored by several techniques. In this paper, we present a novel method to probe all three components of the local antenna field. To this end a resonant nanoantenna is fabricated at the vertex of a scanning tip. Next, the nanoantenna is deterministically scanned in close proximity to single fluorescent molecules, whose fixed excitation dipole moment reads out the local field vector. With nanometer molecular resolution, we distinctly map x-, y-, and z-field components of the dipole antenna, i.e. a full vectorial mode map, and show good agreement with full 3D FDTD simulations. Moreover, the fluorescence polarization maps the localized coupling, with emission through the longitudinal antenna mode. Finally, the resonant antenna probe is used for single molecule imaging with 40 nm fwhm response function. The total fluorescence enhancement is 7.6 times, while out-of-plane molecules, almost undetectable in far-field, are made visible by the strong antenna z-field with a fluorescence enhancement up to 100 times. Interestingly, the apparent position of molecules shifts up to 20 nm depending on their orientation. The capability to resolve orientational information on the single molecule level makes the scanning resonant antenna an ideal tool for extreme resolution bioimaging.

Estimation of Discontinuous Displacement Vector Fields with the Minimum Description Length Criterion.

DTIC Science & Technology

1990-10-01

type of approach for finding a dense displacement vector field has a time complexity that allows a real - time implementation when an appropriate control...hardly vector fields as they appear in Stereo or motion. The reason for this is the fact that local displacement vector field ( DVF ) esti- mates bave...2 objects’ motion, but that the quantitative optical flow is not a reliable measure of the real motion [VP87, SU87]. This applies even more to the

INGN 007, an oncolytic adenovirus vector, replicates in Syrian hamsters but not mice: comparison of biodistribution studies.

PubMed

Ying, B; Toth, K; Spencer, J F; Meyer, J; Tollefson, A E; Patra, D; Dhar, D; Shashkova, E V; Kuppuswamy, M; Doronin, K; Thomas, M A; Zumstein, L A; Wold, W S M; Lichtenstein, D L

2009-08-01

Preclinical biodistribution studies with INGN 007, an oncolytic adenovirus (Ad) vector, supporting an early stage clinical trial were conducted in Syrian hamsters, which are permissive for Ad replication, and mice, which are a standard model for assessing toxicity and biodistribution of replication-defective (RD) Ad vectors. Vector dissemination and pharmacokinetics following intravenous administration were examined by real-time PCR in nine tissues and blood at five time points spanning 1 year. Select organs were also examined for the presence of infectious vector/virus. INGN 007 (VRX-007), wild-type Ad5 and AdCMVpA (an RD vector) were compared in the hamster model, whereas only INGN 007 was examined in mice. DNA of all vectors was widely disseminated early after injection, but decayed rapidly in most organs. In the hamster model, DNA of INGN 007 and Ad5 was more abundant than that of the RD vector AdCMVpA at early times after injection, but similar levels were seen later. An increased level of INGN 007 and Ad5 DNA but not AdCMVpA DNA in certain organs early after injection, and the presence of infectious INGN 007 and Ad5 in lung and liver samples at early times after injection, strongly suggests that replication of INGN 007 and Ad5 occurred in several Syrian hamster organs. There was no evidence of INGN 007 replication in mice. In addition to providing important information about INGN 007, the results underscore the utility of the Syrian hamster as a permissive immunocompetent model for Ad5 pathogenesis and oncolytic Ad vectors.

A Shellcode Detection Method Based on Full Native API Sequence and Support Vector Machine

NASA Astrophysics Data System (ADS)

Cheng, Yixuan; Fan, Wenqing; Huang, Wei; An, Jing

2017-09-01

Dynamic monitoring the behavior of a program is widely used to discriminate between benign program and malware. It is usually based on the dynamic characteristics of a program, such as API call sequence or API call frequency to judge. The key innovation of this paper is to consider the full Native API sequence and use the support vector machine to detect the shellcode. We also use the Markov chain to extract and digitize Native API sequence features. Our experimental results show that the method proposed in this paper has high accuracy and low detection rate.

Complete replication-competent adenovirus 11p vectors with E1 or E3 insertions show improved heat stability

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

Mei, Ya-Fang, E-mail: ya-fang.mei@umu.se

2016-10-15

Conventional adenovirus vectors harboring E1 or E3 deletions followed by the insertion of an exogenous gene show considerably reduced virion stability. Here, we report strategies to generate complete replication-competent Ad11p(RCAd11p) vectors that overcome the above disadvantage. A GFP cassette was successfully introduced either upstream of E1A or in the E3A region. The resulting vectors showed high expression levels of the hexon and E1genes and also strongly induced the cytopathic effect in targeted cells. When harboring oversized genomes, the RCAd11pE1 and RCAd11pE3 vectors showed significantly improved heat stability in comparison to Ad11pwt;of the three, RCAd11pE3 was the most tolerant to heatmore » treatment. Electron microscopy showed that RCAd11pE3, RCAd11pE1, Ad11pwt, and Ad11pE1 Delmanifested dominant, moderate, minimum, or no full virus particles after heat treatment at 47 °C for 5 h. Our results demonstrated that both genome size and the insertion site in the viral genome affect virion stability. -- Highlights: •Replicating adenovirus 11p GFP vectors at the E1 or E3 region were generated. •RCAd11pE3 and RCAd11pE1 vectors manifested significantly improved heat stability. •RCAd11pE3 and RCAd11pE1 showed more full viral particles than Ad11pwt after heating. •We demonstrated that both genome size and the insertion site affect virion stability.« less

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.

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

Feldman, Steven; Valera-Leon, Carlos; Dechev, Damian

The vector is a fundamental data structure, which provides constant-time access to a dynamically-resizable range of elements. Currently, there exist no wait-free vectors. The only non-blocking version supports only a subset of the sequential vector API and exhibits significant synchronization overhead caused by supporting opposing operations. Since many applications operate in phases of execution, wherein each phase only a subset of operations are used, this overhead is unnecessary for the majority of the application. To address the limitations of the non-blocking version, we present a new design that is wait-free, supports more of the operations provided by the sequential vector,more » and provides alternative implementations of key operations. These alternatives allow the developer to balance the performance and functionality of the vector as requirements change throughout execution. Compared to the known non-blocking version and the concurrent vector found in Intel’s TBB library, our design outperforms or provides comparable performance in the majority of tested scenarios. Over all tested scenarios, the presented design performs an average of 4.97 times more operations per second than the non-blocking vector and 1.54 more than the TBB vector. In a scenario designed to simulate the filling of a vector, performance improvement increases to 13.38 and 1.16 times. This work presents the first ABA-free non-blocking vector. Finally, unlike the other non-blocking approach, all operations are wait-free and bounds-checked and elements are stored contiguously in memory.« less

First stage of LISA data processing. II. Alternative filtering dynamic models for LISA

NASA Astrophysics Data System (ADS)

Wang, Yan; Heinzel, Gerhard; Danzmann, Karsten

2015-08-01

Space-borne gravitational wave detectors, such as (e)LISA, are designed to operate in the low-frequency band (mHz to Hz), where there is a variety of gravitational wave sources of great scientific value [arXiv:1305.5720 and S. Babak et al., Classical Quantum Gravity 28, 114001 (2011)]. To achieve the extraordinary sensitivity of these detectors, the precise synchronization of the clocks on the separate spacecraft and the accurate determination of the interspacecraft distances are important ingredients. In our previous paper [Y. Wang et al., Phys. Rev. D 90, 064016 (2014)], we have described a hybrid-extend Kalman filter with a full state vector to do this job. In this paper, we explore several different state vectors and their corresponding (phenomenological) dynamic models to reduce the redundancy in the full state vector, to accelerate the algorithm, and to make the algorithm easily extendable to more complicated scenarios.

Suitability of canine herpesvirus as a vector for oral bait vaccination of foxes.

PubMed

Reubel, Gerhard H; Wright, John; Pekin, Jenny; French, Nigel; Strive, Tanja

2006-05-31

Studies were conducted to evaluate the feasibility of using canine herpesvirus (CHV) as a vaccine vector for bait-delivered oral vaccination of wild foxes. To test the viability of CHV in baits, CHV was freeze-dried, incorporated into different baits, stored, and the remaining viral infectivity tested in cell culture after varying periods of time at different storage temperatures. Experimental baits (mouse carcasses) and commercial baits (FOXOFF and PROBAIT) were prepared with either liquid or freeze-dried CHV and tested in two fox trials for their capacity to induce CHV-specific antibodies following oral baiting. Freeze-drying and storage temperatures below 0 degrees C had a stabilizing effect to virus infectivity. When stored at -20 degrees C, freeze-dried CHV retained its full infectivity for up to 3 months in PROBAIT baits, the remaining infectivity in FOXOFF baits was 100-fold less. Oral baiting with CHV induced antiviral serum antibodies in all vaccinated foxes (20/20). None of the vaccinated foxes became ill or shed infectious virus into the environment although viral DNA was detected in body secretions as evaluated by PCR. The results indicate that CHV can be freeze-dried and stored over extended periods of time without loosing much of its infectivity. This is the first report of CHV being used for oral bait vaccination of foxes. It appears that CHV is well suited for use as a recombinant vector for wild canids.

Gauge-invariant expectation values of the energy of a molecule in an electromagnetic field

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

Mandal, Anirban; Hunt, Katharine L. C.

In this paper, we show that the full Hamiltonian for a molecule in an electromagnetic field can be separated into a molecular Hamiltonian and a field Hamiltonian, both with gauge-invariant expectation values. The expectation value of the molecular Hamiltonian gives physically meaningful results for the energy of a molecule in a time-dependent applied field. In contrast, the usual partitioning of the full Hamiltonian into molecular and field terms introduces an arbitrary gauge-dependent potential into the molecular Hamiltonian and leaves a gauge-dependent form of the Hamiltonian for the field. With the usual partitioning of the Hamiltonian, this same problem of gaugemore » dependence arises even in the absence of an applied field, as we show explicitly by considering a gauge transformation from zero applied field and zero external potentials to zero applied field, but non-zero external vector and scalar potentials. We resolve this problem and also remove the gauge dependence from the Hamiltonian for a molecule in a non-zero applied field and from the field Hamiltonian, by repartitioning the full Hamiltonian. It is possible to remove the gauge dependence because the interaction of the molecular charges with the gauge potential cancels identically with a gauge-dependent term in the usual form of the field Hamiltonian. We treat the electromagnetic field classically and treat the molecule quantum mechanically, but nonrelativistically. Our derivation starts from the Lagrangian for a set of charged particles and an electromagnetic field, with the particle coordinates, the vector potential, the scalar potential, and their time derivatives treated as the variables in the Lagrangian. We construct the full Hamiltonian using a Lagrange multiplier method originally suggested by Dirac, partition this Hamiltonian into a molecular term H{sub m} and a field term H{sub f}, and show that both H{sub m} and H{sub f} have gauge-independent expectation values. Any gauge may be chosen for the calculations; but following our partitioning, the expectation values of the molecular Hamiltonian are identical to those obtained directly in the Coulomb gauge. As a corollary of this result, the power absorbed by a molecule from a time-dependent, applied electromagnetic field is equal to the time derivative of the non-adiabatic term in the molecular energy, in any gauge.« less

Optical/Infrared Signatures for Space-Based Remote Sensing

DTIC Science & Technology

2007-11-01

Vanderbilt et al., 1985a, 1985b]. So, first linear polarization was introduced, followed by progress toward a full vector theory of polarization ...radiance profiles taken 30 s apart in a view direction orthogonal to the velocity vector , showing considerable structure due to radiance layers in the...6 Figure 3. The northern polar region and locations of the MSX

A Drosophila melanogaster hobo-white + vector mediates low frequency gene transfer in D. vlrllls with full Interspecific white + complementation

USDA-ARS?s Scientific Manuscript database

Transformation of a Drosophila virilis white mutant host strain was attempted by using a hobo vector containing the D. melanogaster mini-white+ cassette (H[w+, hawN]) and an unmodified or heat shock regulated hobo transposase helper. Two transformant lines were recovered with the unmodified helper (...

Definition of Contravariant Velocity Components

NASA Technical Reports Server (NTRS)

Hung, Ching-Mao; Kwak, Dochan (Technical Monitor)

2002-01-01

This is an old issue in computational fluid dynamics (CFD). What is the so-called contravariant velocity or contravariant velocity component? In the article, we review the basics of tensor analysis and give the contravariant velocity component a rigorous explanation. For a given coordinate system, there exist two uniquely determined sets of base vector systems - one is the covariant and another is the contravariant base vector system. The two base vector systems are reciprocal. The so-called contravariant velocity component is really the contravariant component of a velocity vector for a time-independent coordinate system, or the contravariant component of a relative velocity between fluid and coordinates, for a time-dependent coordinate system. The contravariant velocity components are not physical quantities of the velocity vector. Their magnitudes, dimensions, and associated directions are controlled by their corresponding covariant base vectors. Several 2-D (two-dimensional) linear examples and 2-D mass-conservation equation are used to illustrate the details of expressing a vector with respect to the covariant and contravariant base vector systems, respectively.

Optimized Lentiviral Vector Design Improves Titer and Transgene Expression of Vectors Containing the Chicken β-Globin Locus HS4 Insulator Element

PubMed Central

Hanawa, Hideki; Yamamoto, Motoko; Zhao, Huifen; Shimada, Takashi; Persons, Derek A

2009-01-01

Hematopoietic cell gene therapy using retroviral vectors has achieved success in clinical trials. However, safety issues regarding vector insertional mutagenesis have emerged. In two different trials, vector insertion resulted in the transcriptional activation of proto-oncogenes. One strategy for potentially diminishing vector insertional mutagenesis is through the use of self-inactivating lentiviral vectors containing the 1.2-kb insulator element derived from the chicken β-globin locus. However, use of this element can dramatically decrease both vector titer and transgene expression, thereby compromising its practical use. Here, we studied lentiviral vectors containing either the full-length 1.2-kb insulator or the smaller 0.25-kb core element in both orientations in the partially deleted long-terminal repeat. We show that use of the 0.25-kb core insulator rescued vector titer by alleviating a postentry block to reverse transcription associated with the 1.2-kb element. In addition, in an orientation-dependent manner, the 0.25-kb core element significantly increased transgene expression from an internal promoter due to improved transcriptional termination. This element also demonstrated barrier activity, reducing variability of expression due to position effects. As it is known that the 0.25-kb core insulator has enhancer-blocking activity, this particular insulated lentiviral vector design may be useful for clinical application. PMID:19223867

[Construction and selection of effective mouse Smad6 recombinant lenti-virus interference vectors].

PubMed

Yu, Jing; Qi, Mengchun; Deng, Jiupeng; Liu, Gang; Chen, Huaiqing

2010-10-01

This experiment was designed to construct mouse Smad6 recombinant RNA interference vectors and determine their interference effects on bone marrow mesenchymal stem cells (BMSCs). Three recombinant Smad6 RNA interference vectors were constructed by molecular clone techniques with a lenti-virus vector expressing green fluorescent protein (GFP), and the correctness of recombinant vectors was verified by DNA sequencing. Mouse BMSCs were used for transfection experiments and BMP-2 was in use for osteogenic induction of MSCs. The transfection efficiency of recombinant vectors was examined by Laser confocal scanning microscope and the interference effect of recombinant vectors on Smad6 gene expression was determined by real-time RT-PCR and Western blot, respectively. Three Smad6 recombinant RNA interference vectors were successfully constructed and their correctness was proved by DNA sequencing. After transfection, GFPs were effectively expressed in MSCs and all of three recombinant vectors gained high transfection efficiency (> 95%). Both real-time PCR and Western blot examination indicated that among three recombinant vectors, No. 2 Svector had the best interference effect and the interference effect was nearly 91% at protein level. In conclusion, Mouse recombinant Smad6 RNA interference (RNAi) vector was successfully constructed and it provided an effective tool for further studies on BMP signal pathways.

Validation of SplitVectors Encoding for Quantitative Visualization of Large-Magnitude-Range Vector Fields

PubMed Central

Zhao, Henan; Bryant, Garnett W.; Griffin, Wesley; Terrill, Judith E.; Chen, Jian

2017-01-01

We designed and evaluated SplitVectors, a new vector field display approach to help scientists perform new discrimination tasks on large-magnitude-range scientific data shown in three-dimensional (3D) visualization environments. SplitVectors uses scientific notation to display vector magnitude, thus improving legibility. We present an empirical study comparing the SplitVectors approach with three other approaches - direct linear representation, logarithmic, and text display commonly used in scientific visualizations. Twenty participants performed three domain analysis tasks: reading numerical values (a discrimination task), finding the ratio between values (a discrimination task), and finding the larger of two vectors (a pattern detection task). Participants used both mono and stereo conditions. Our results suggest the following: (1) SplitVectors improve accuracy by about 10 times compared to linear mapping and by four times to logarithmic in discrimination tasks; (2) SplitVectors have no significant differences from the textual display approach, but reduce cluttering in the scene; (3) SplitVectors and textual display are less sensitive to data scale than linear and logarithmic approaches; (4) using logarithmic can be problematic as participants' confidence was as high as directly reading from the textual display, but their accuracy was poor; and (5) Stereoscopy improved performance, especially in more challenging discrimination tasks. PMID:28113469

Validation of SplitVectors Encoding for Quantitative Visualization of Large-Magnitude-Range Vector Fields.

PubMed

Henan Zhao; Bryant, Garnett W; Griffin, Wesley; Terrill, Judith E; Jian Chen

2017-06-01

We designed and evaluated SplitVectors, a new vector field display approach to help scientists perform new discrimination tasks on large-magnitude-range scientific data shown in three-dimensional (3D) visualization environments. SplitVectors uses scientific notation to display vector magnitude, thus improving legibility. We present an empirical study comparing the SplitVectors approach with three other approaches - direct linear representation, logarithmic, and text display commonly used in scientific visualizations. Twenty participants performed three domain analysis tasks: reading numerical values (a discrimination task), finding the ratio between values (a discrimination task), and finding the larger of two vectors (a pattern detection task). Participants used both mono and stereo conditions. Our results suggest the following: (1) SplitVectors improve accuracy by about 10 times compared to linear mapping and by four times to logarithmic in discrimination tasks; (2) SplitVectors have no significant differences from the textual display approach, but reduce cluttering in the scene; (3) SplitVectors and textual display are less sensitive to data scale than linear and logarithmic approaches; (4) using logarithmic can be problematic as participants' confidence was as high as directly reading from the textual display, but their accuracy was poor; and (5) Stereoscopy improved performance, especially in more challenging discrimination tasks.

High-level rapid production of full-size monoclonal antibodies in plants by a single-vector DNA replicon system

PubMed Central

Huang, Zhong; Phoolcharoen, Waranyoo; Lai, Huafang; Piensook, Khanrat; Cardineau, Guy; Zeitlin, Larry; Whaley, Kevin J.; Arntzen, Charles J.

2010-01-01

Plant viral vectors have great potential in rapid production of important pharmaceutical proteins. However, high-yield production of heterooligomeric proteins that require the expression and assembly of two or more protein subunits often suffers problems due to the “competing” nature of viral vectors derived from the same virus. Previously we reported that a bean yellow dwarf virus (BeYDV)-derived, three-component DNA replicon system allows rapid production of single recombinant proteins in plants (Huang et al. 2009). In this article, we report further development of this expression system for its application in high-yield production of oligomeric protein complexes including monoclonal antibodies (mAbs) in plants. We showed that the BeYDV replicon system permits simultaneous efficient replication of two DNA replicons and thus, high-level accumulation of two recombinant proteins in the same plant cell. We also demonstrated that a single vector that contains multiple replicon cassettes was as efficient as the three-component system in driving the expression of two distinct proteins. Using either the non-competing, three-vector system or the multi-replicon single vector, we produced both the heavy and light chain subunits of a protective IgG mAb 6D8 against Ebola virus GP1 (Wilson et al. 2000) at 0.5 mg of mAb per gram leaf fresh weight within 4 days post infiltration of Nicotiana benthamiana leaves. We further demonstrated that full-size tetrameric IgG complex containing two heavy and two light chains was efficiently assembled and readily purified, and retained its functionality in specific binding to inactivated Ebola virus. Thus, our single-vector replicon system provides high-yield production capacity for heterooligomeric proteins, yet eliminates the difficult task of identifying non-competing virus and the need for co-infection of multiple expression modules. The multi-replicon vector represents a significant advance in transient expression technology for antibody production in plants. PMID:20047189

3-D Magnetotelluric Forward Modeling And Inversion Incorporating Topography By Using Vector Finite-Element Method Combined With Divergence Corrections Based On The Magnetic Field (VFEH++)

NASA Astrophysics Data System (ADS)

Shi, X.; Utada, H.; Jiaying, W.

2009-12-01

The vector finite-element method combined with divergence corrections based on the magnetic field H, referred to as VFEH++ method, is developed to simulate the magnetotelluric (MT) responses of 3-D conductivity models. The advantages of the new VFEH++ method are the use of edge-elements to eliminate the vector parasites and the divergence corrections to explicitly guarantee the divergence-free conditions in the whole modeling domain. 3-D MT topographic responses are modeling using the new VFEH++ method, and are compared with those calculated by other numerical methods. The results show that MT responses can be modeled highly accurate using the VFEH+ +method. The VFEH++ algorithm is also employed for the 3-D MT data inversion incorporating topography. The 3-D MT inverse problem is formulated as a minimization problem of the regularized misfit function. In order to avoid the huge memory requirement and very long time for computing the Jacobian sensitivity matrix for Gauss-Newton method, we employ the conjugate gradient (CG) approach to solve the inversion equation. In each iteration of CG algorithm, the cost computation is the product of the Jacobian sensitivity matrix with a model vector x or its transpose with a data vector y, which can be transformed into two pseudo-forwarding modeling. This avoids the full explicitly Jacobian matrix calculation and storage which leads to considerable savings in the memory required by the inversion program in PC computer. The performance of CG algorithm will be illustrated by several typical 3-D models with horizontal earth surface and topographic surfaces. The results show that the VFEH++ and CG algorithms can be effectively employed to 3-D MT field data inversion.

Full-genome dengue virus sequencing in mosquito saliva shows lack of convergent positive selection during transmission by Aedes aegypti

PubMed Central

Cao-Lormeau, Van-Mai; Lambrechts, Louis

2017-01-01

Abstract Like other pathogens with high mutation and replication rates, within-host dengue virus (DENV) populations evolve during infection of their main mosquito vector, Aedes aegypti. Within-host DENV evolution during transmission provides opportunities for adaptation and emergence of novel virus variants. Recent studies of DENV genetic diversity failed to detect convergent evolution of adaptive mutations in mosquito tissues such as midgut and salivary glands, suggesting that convergent positive selection is not a major driver of within-host DENV evolution in the vector. However, it is unknown whether this conclusion extends to the transmitted viral subpopulation because it is technically difficult to sequence DENV genomes in mosquito saliva. Here, we achieved DENV full-genome sequencing by pooling saliva samples collected non-sacrificially from 49 to 163 individual Ae. aegypti mosquitoes previously infected with one of two DENV-1 genotypes. We compared the transmitted viral subpopulations found in the pooled saliva samples collected in time series with the input viral population present in the infectious blood meal. In all pooled saliva samples examined, the full-genome consensus sequence of the input viral population was unchanged. Although the pooling strategy prevents analysis of individual saliva samples, our results demonstrate the lack of strong convergent positive selection during a single round of DENV transmission by Ae. aegypti. This finding reinforces the idea that genetic drift and purifying selection are the dominant evolutionary forces shaping within-host DENV genetic diversity during transmission by mosquitoes. PMID:29497564

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.

Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

PubMed

Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

2015-09-01

Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need to be extracted from single-axis accelerometer data.

C/NOFS Measurements of Stormtime Magnetic Perturbations in the Low-latitude Ionosphere

NASA Technical Reports Server (NTRS)

Le, Guan; Burke, William J.; Pfaff, Robert F.; Freudenreich, Henry; Maus, Stefan; Luehr, Hermann

2012-01-01

The Vector Electric Field Investigation suite on the C/NOFS satellite includes a fluxgate magnetometer to monitor the Earth's magnetic fields in the low-latitude ionosphere. Measurements yield full magnetic vectors every second over the range of +/- 45,000 nT with a one-bit resolution of 1.37 nT (16 bit AID) in each component. The sensor's primary responsibility is to support calculations of both VxB and ExB with greater accuracy than can be obtained using standard magnetic field models. The data also contain information about large-scale current systems, that, when analyzed in conjunction with electric field measurements, promise to significantly expand understanding of equatorial electrodynamics. We first compare in situ measurements with the POMME (POtsdam Magnetic Model of the Earth) model to establish in-flight sensor "calibrations" and to compute magnetic residuals. At low latitudes the residuals are predominately products of the stormtime ring current. Since C/NOFS provides a complete coverage of all local times every 97 minutes, magnetic field data allow studies of the temporal evolution and local-time variations of stormtime ring current. The analysis demonstrates the feasibility of using instrumented spacecraft in low-inclination orbits to extract a timely proxy for the provisional Dst index and to specify the ring current's evolution.

INGN 007, an oncolytic adenovirus vector, replicates in Syrian hamsters but not mice: comparison of biodistribution studies

PubMed Central

Ying, B; Toth, K; Spencer, JF; Meyer, J; Tollefson, AE; Patra, D; Dhar, D; Shashkova, EV; Kuppuswamy, M; Doronin, K; Thomas, MA; Zumstein, LA; Wold, WSM; Lichtenstein, DL

2012-01-01

Preclinical biodistribution studies with INGN 007, an oncolytic adenovirus (Ad) vector, supporting an early stage clinical trial were conducted in Syrian hamsters, which are permissive for Ad replication, and mice, which are a standard model for assessing toxicity and biodistribution of replication-defective (RD) Ad vectors. Vector dissemination and pharmacokinetics following intravenous administration were examined by real-time PCR in nine tissues and blood at five time points spanning 1 year. Select organs were also examined for the presence of infectious vector/virus. INGN 007 (VRX-007), wild-type Ad5 and AdCMVpA (an RD vector) were compared in the hamster model, whereas only INGN 007 was examined in mice. DNA of all vectors was widely disseminated early after injection, but decayed rapidly in most organs. In the hamster model, DNA of INGN 007 and Ad5 was more abundant than that of the RD vector AdCMVpA at early times after injection, but similar levels were seen later. An increased level of INGN 007 and Ad5 DNA but not AdCMVpA DNA in certain organs early after injection, and the presence of infectious INGN 007 and Ad5 in lung and liver samples at early times after injection, strongly suggests that replication of INGN 007 and Ad5 occurred in several Syrian hamster organs. There was no evidence of INGN 007 replication in mice. In addition to providing important information about INGN 007, the results underscore the utility of the Syrian hamster as a permissive immunocompetent model for Ad5 pathogenesis and oncolytic Ad vectors. PMID:19197322

[Preliminary evaluation of the insecticide susceptibility in Anopheles gambiae and Culex quinquefasciatus from Lobito (Angola), using WHO standard assay].

PubMed

Toto, J C; Besnard, P; Le Mire, J; Almeida, D S I; Dos Santos, M A; Fortes, F; Foumane, V; Simard, F; Awono-Ambene, H P; Carnevale, P

2011-10-01

Field collections of the most common urban mosquito vectors Anopheles gambiae and Culex quinquefasciatus were carried out in June 2003, March 2004 and November 2005 to gather preliminary data on the insecticide susceptibility in mosquitoes from Lobito (Angola) using the WHO standard bioassays. Bioassays were performed on F0 adults emerging from the field larval collections and on unfed adults from landing catches on volunteers. Batches of mosquitoes from three selected locations (Alto Liro, San Jao and Bela Vista) were exposed for 1 hour to several insecticides such as DDT 4%, carbosulfan 0.4%, permethrin 1%, deltamethrin 0.05% and cyfluthrin 0.15%, in order to estimate the immediate knockdown times (kdT50 and kdT95) and the mortality rate after exposure. The results revealed that mosquito susceptibility to insecticides varied depending on the insecticide, the site and the period of collection. The main local malaria vector A. gambiae (both M and S forms) was basically resistant to DDT and susceptible to all pyrethoids, regardless of the period and the site of collections. The overall mortality rate due to DDT was 73% in Alto Liro, 89% in San Jao and varied depending on the period in Bela Vista between 95% in March 2004 and 100% in November 2005. The mortality due to pyrethoids was 100% at all locations, with the kdT50 and KdT95 times ranging between 9 and 16 minutes and between 18 and 29 minutes, respectively. Concerning the C. quinquefasciatus, populations from Yard and Caponte were resistant to all insecticides tested; the mortality rate was 40% with deltamethrin and 70% with permethrin, while no lethal effect was observed with DDT or carbosulfan. In conclusion, despite its probable high resistance to DDT, the main local malaria vector A. gambiae remained fully susceptible to pyrethroids. This could forecast a good biological efficacy of the scheduled vector control interventions in Angola, based on a large-scale distribution of long-lasting, insecticide-treated nets and on the implementation of indoor residual spraying. The local vector control programme must include well-adapted IEC campaigns and full participation of the community for better management of the insecticide resistance in targeted mosquitoes and for better control of malaria vector populations.

Recent Developments In Theory Of Balanced Linear Systems

NASA Technical Reports Server (NTRS)

Gawronski, Wodek

1994-01-01

Report presents theoretical study of some issues of controllability and observability of system represented by linear, time-invariant mathematical model of the form. x = Ax + Bu, y = Cx + Du, x(0) = xo where x is n-dimensional vector representing state of system; u is p-dimensional vector representing control input to system; y is q-dimensional vector representing output of system; n,p, and q are integers; x(0) is intial (zero-time) state vector; and set of matrices (A,B,C,D) said to constitute state-space representation of system.

Analysis of Particle Content of Recombinant Adeno-Associated Virus Serotype 8 Vectors by Ion-Exchange Chromatography

PubMed Central

Lock, Martin; Alvira, Mauricio R.

2012-01-01

Abstract Advances in adeno-associated virus (AAV)-mediated gene therapy have brought the possibility of commercial manufacturing of AAV vectors one step closer. To realize this prospect, a parallel effort with the goal of ever-increasing sophistication for AAV vector production technology and supporting assays will be required. Among the important release assays for a clinical gene therapy product, those monitoring potentially hazardous contaminants are most critical for patient safety. A prominent contaminant in many AAV vector preparations is vector particles lacking a genome, which can substantially increase the dose of AAV capsid proteins and lead to possible unwanted immunological consequences. Current methods to determine empty particle content suffer from inconsistency, are adversely affected by contaminants, or are not applicable to all serotypes. Here we describe the development of an ion-exchange chromatography-based assay that permits the rapid separation and relative quantification of AAV8 empty and full vector particles through the application of shallow gradients and a strong anion-exchange monolith chromatography medium. PMID:22428980

Optical cage generated by azimuthal- and radial-variant vector beams.

PubMed

Man, Zhongsheng; Bai, Zhidong; Li, Jinjian; Zhang, Shuoshuo; Li, Xiaoyu; Zhang, Yuquan; Ge, Xiaolu; Fu, Shenggui

2018-05-01

We propose a method to generate an optical cage using azimuthal- and radial-variant vector beams in a high numerical aperture optical system. A new kind of vector beam that has azimuthal- and radial-variant polarization states is proposed and demonstrated theoretically. Then, an integrated analytical model to calculate the electromagnetic field and Poynting vector distributions of the input azimuthal- and radial-variant vector beams is derived and built based on the vector diffraction theory of Richards and Wolf. From calculations, a full polarization-controlled optical cage is obtained by simply tailoring the radial index of the polarization, the uniformity U of which is up to 0.7748, and the cleanness C is zero. Additionally, a perfect optical cage can be achieved with U=1, and C=0 by introducing an amplitude modulation; its magnetic field and energy flow are also demonstrated in detail. Such optical cages may be helpful in applications such as optical trapping and high-resolution imaging.

Improved dual AAV vectors with reduced expression of truncated proteins are safe and effective in the retina of a mouse model of Stargardt disease

PubMed Central

Trapani, Ivana; Toriello, Elisabetta; de Simone, Sonia; Colella, Pasqualina; Iodice, Carolina; Polishchuk, Elena V.; Sommella, Andrea; Colecchi, Linda; Rossi, Settimio; Simonelli, Francesca; Giunti, Massimo; Bacci, Maria L.; Polishchuk, Roman S.; Auricchio, Alberto

2015-01-01

Stargardt disease (STGD1) due to mutations in the large ABCA4 gene is the most common inherited macular degeneration in humans. We have shown that dual adeno-associated viral (AAV) vectors effectively transfer ABCA4 to the retina of Abca4−/− mice. However, they express both lower levels of transgene compared with a single AAV and truncated proteins. To increase productive dual AAV concatemerization, which would overcome these limitations, we have explored the use of either various regions of homology or heterologous inverted terminal repeats (ITR). In addition, we tested the ability of various degradation signals to decrease the expression of truncated proteins. We found the highest levels of transgene expression using regions of homology based on either alkaline phosphatase or the F1 phage (AK). The use of heterologous ITR does not decrease the levels of truncated proteins relative to full-length ABCA4 and impairs AAV vector production. Conversely, the inclusion of the CL1 degradation signal results in the selective degradation of truncated proteins from the 5′-half without affecting full-length protein production. Therefore, we developed dual AAV hybrid ABCA4 vectors including homologous ITR2, the photoreceptor-specific G protein-coupled receptor kinase 1 promoter, the AK region of homology and the CL1 degradation signal. We show that upon subretinal administration these vectors are both safe in pigs and effective in Abca4−/− mice. Our data support the use of improved dual AAV vectors for gene therapy of STGD1. PMID:26420842

Reversible vector ratchets for skyrmion systems

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

Ma, Xiu; Reichhardt, Cynthia Jane Olson; Reichhardt, Charles

In this paper, we show that ac driven skyrmions interacting with an asymmetric substrate provide a realization of a class of ratchet system which we call a vector ratchet that arises due to the effect of the Magnus term on the skyrmion dynamics. In a vector ratchet, the dc motion induced by the ac drive can be described as a vector that can be rotated clockwise or counterclockwise relative to the substrate asymmetry direction. Up to a full 360° rotation is possible for varied ac amplitudes or skyrmion densities. In contrast to overdamped systems, in which ratchet motion is alwaysmore » parallel to the substrate asymmetry direction, vector ratchets allow the ratchet motion to be in any direction relative to the substrate asymmetry. It is also possible to obtain a reversal in the direction of rotation of the vector ratchet, permitting the creation of a reversible vector ratchet. We examine vector ratchets for ac drives applied parallel or perpendicular to the substrate asymmetry direction, and show that reverse ratchet motion can be produced by collective effects. No reversals occur for an isolated skyrmion on an asymmetric substrate. Finally, since a vector ratchet can produce motion in any direction, it could represent a method for controlling skyrmion motion for spintronic applications.« less

PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

PubMed

Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian C; Billker, Oliver

2015-01-01

The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Reversible vector ratchets for skyrmion systems

DOE PAGES

Ma, Xiu; Reichhardt, Cynthia Jane Olson; Reichhardt, Charles

2017-03-03

In this paper, we show that ac driven skyrmions interacting with an asymmetric substrate provide a realization of a class of ratchet system which we call a vector ratchet that arises due to the effect of the Magnus term on the skyrmion dynamics. In a vector ratchet, the dc motion induced by the ac drive can be described as a vector that can be rotated clockwise or counterclockwise relative to the substrate asymmetry direction. Up to a full 360° rotation is possible for varied ac amplitudes or skyrmion densities. In contrast to overdamped systems, in which ratchet motion is alwaysmore » parallel to the substrate asymmetry direction, vector ratchets allow the ratchet motion to be in any direction relative to the substrate asymmetry. It is also possible to obtain a reversal in the direction of rotation of the vector ratchet, permitting the creation of a reversible vector ratchet. We examine vector ratchets for ac drives applied parallel or perpendicular to the substrate asymmetry direction, and show that reverse ratchet motion can be produced by collective effects. No reversals occur for an isolated skyrmion on an asymmetric substrate. Finally, since a vector ratchet can produce motion in any direction, it could represent a method for controlling skyrmion motion for spintronic applications.« less

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.

Unidirectional Wave Vector Manipulation in Two-Dimensional Space with an All Passive Acoustic Parity-Time-Symmetric Metamaterials Crystal

NASA Astrophysics Data System (ADS)

Liu, Tuo; Zhu, Xuefeng; Chen, Fei; Liang, Shanjun; Zhu, Jie

2018-03-01

Exploring the concept of non-Hermitian Hamiltonians respecting parity-time symmetry with classical wave systems is of great interest as it enables the experimental investigation of parity-time-symmetric systems through the quantum-classical analogue. Here, we demonstrate unidirectional wave vector manipulation in two-dimensional space, with an all passive acoustic parity-time-symmetric metamaterials crystal. The metamaterials crystal is constructed through interleaving groove- and holey-structured acoustic metamaterials to provide an intrinsic parity-time-symmetric potential that is two-dimensionally extended and curved, which allows the flexible manipulation of unpaired wave vectors. At the transition point from the unbroken to broken parity-time symmetry phase, the unidirectional sound focusing effect (along with reflectionless acoustic transparency in the opposite direction) is experimentally realized over the spectrum. This demonstration confirms the capability of passive acoustic systems to carry the experimental studies on general parity-time symmetry physics and further reveals the unique functionalities enabled by the judiciously tailored unidirectional wave vectors in space.

Thermofield duality for higher spin Rindler Gravity

DOE PAGES

Jevicki, Antal; Suzuki, Kenta

2016-02-15

In this paper, we study the Thermo-field realization of the duality between the Rindler-AdS higher spin theory and O(N) vector theory. The CFT represents a decoupled pair of free O(N) vector field theories. It is shown how this decoupled domain CFT is capable of generating the connected Rindler-AdS background with the full set of Higher Spin fields.

Wind speed vector restoration algorithm

NASA Astrophysics Data System (ADS)

Baranov, Nikolay; Petrov, Gleb; Shiriaev, Ilia

2018-04-01

Impulse wind lidar (IWL) signal processing software developed by JSC «BANS» recovers full wind speed vector by radial projections and provides wind parameters information up to 2 km distance. Increasing accuracy and speed of wind parameters calculation signal processing technics have been studied in this research. Measurements results of IWL and continuous scanning lidar were compared. Also, IWL data processing modeling results have been analyzed.

Sorting on STAR. [CDC computer algorithm timing comparison

NASA Technical Reports Server (NTRS)

Stone, H. S.

1978-01-01

Timing comparisons are given for three sorting algorithms written for the CDC STAR computer. One algorithm is Hoare's (1962) Quicksort, which is the fastest or nearly the fastest sorting algorithm for most computers. A second algorithm is a vector version of Quicksort that takes advantage of the STAR's vector operations. The third algorithm is an adaptation of Batcher's (1968) sorting algorithm, which makes especially good use of vector operations but has a complexity of N(log N)-squared as compared with a complexity of N log N for the Quicksort algorithms. In spite of its worse complexity, Batcher's sorting algorithm is competitive with the serial version of Quicksort for vectors up to the largest that can be treated by STAR. Vector Quicksort outperforms the other two algorithms and is generally preferred. These results indicate that unusual instruction sets can introduce biases in program execution time that counter results predicted by worst-case asymptotic complexity analysis.

Generation of cylindrically polarized vector vortex beams with digital micromirror device

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

Gong, Lei; Liu, Weiwei; Wang, Meng

We propose a novel technique to directly transform a linearly polarized Gaussian beam into vector-vortex beams with various spatial patterns. Full high-quality control of amplitude and phase is implemented via a Digital Micro-mirror Device (DMD) binary holography for generating Laguerre-Gaussian, Bessel-Gaussian, and helical Mathieu–Gaussian modes, while a radial polarization converter (S-waveplate) is employed to effectively convert the optical vortices into cylindrically polarized vortex beams. Additionally, the generated vector-vortex beams maintain their polarization symmetry after arbitrary polarization manipulation. Due to the high frame rates of DMD, rapid switching among a series of vector modes carrying different orbital angular momenta paves themore » way for optical microscopy, trapping, and communication.« less

Optimal distribution of integration time for intensity measurements in Stokes polarimetry.

PubMed

Li, Xiaobo; Liu, Tiegen; Huang, Bingjing; Song, Zhanjie; Hu, Haofeng

2015-10-19

We consider the typical Stokes polarimetry system, which performs four intensity measurements to estimate a Stokes vector. We show that if the total integration time of intensity measurements is fixed, the variance of the Stokes vector estimator depends on the distribution of the integration time at four intensity measurements. Therefore, by optimizing the distribution of integration time, the variance of the Stokes vector estimator can be decreased. In this paper, we obtain the closed-form solution of the optimal distribution of integration time by employing Lagrange multiplier method. According to the theoretical analysis and real-world experiment, it is shown that the total variance of the Stokes vector estimator can be significantly decreased about 40% in the case discussed in this paper. The method proposed in this paper can effectively decrease the measurement variance and thus statistically improves the measurement accuracy of the polarimetric system.

Small Angle Neutron Scattering Observation of Chain Retraction after a Large Step Deformation

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

Blanchard, A.; Heinrich, M.; Pyckhout-Hintzen, W.

The process of retraction in entangled linear chains after a fast nonlinear stretch was detected from time-resolved but quenched small angle neutron scattering (SANS) experiments on long, well-entangled polyisoprene chains. The statically obtained SANS data cover the relevant time regime for retraction, and they provide a direct, microscopic verification of this nonlinear process as predicted by the tube model. Clear, quantitative agreement is found with recent theories of contour length fluctuations and convective constraint release, using parameters obtained mainly from linear rheology. The theory captures the full range of scattering vectors once the crossover to fluctuations on length scales belowmore » the tube diameter is accounted for.« less

Real time flaw detection and characterization in tube through partial least squares and SVR: Application to eddy current testing

NASA Astrophysics Data System (ADS)

Ahmed, Shamim; Miorelli, Roberto; Calmon, Pierre; Anselmi, Nicola; Salucci, Marco

2018-04-01

This paper describes Learning-By-Examples (LBE) technique for performing quasi real time flaw localization and characterization within a conductive tube based on Eddy Current Testing (ECT) signals. Within the framework of LBE, the combination of full-factorial (i.e., GRID) sampling and Partial Least Squares (PLS) feature extraction (i.e., GRID-PLS) techniques are applied for generating a suitable training set in offine phase. Support Vector Regression (SVR) is utilized for model development and inversion during offine and online phases, respectively. The performance and robustness of the proposed GIRD-PLS/SVR strategy on noisy test set is evaluated and compared with standard GRID/SVR approach.

Direct time integration of Maxwell's equations in linear dispersive media with absorption for scattering and propagation of femtosecond electromagnetic pulses

NASA Technical Reports Server (NTRS)

Joseph, Rose M.; Hagness, Susan C.; Taflove, Allen

1991-01-01

The initial results for femtosecond pulse propagation and scattering interactions for a Lorentz medium obtained by a direct time integration of Maxwell's equations are reported. The computational approach provides reflection coefficients accurate to better than 6 parts in 10,000 over the frequency range of dc to 3 x 10 to the 16th Hz for a single 0.2-fs Gaussian pulse incident upon a Lorentz-medium half-space. New results for Sommerfeld and Brillouin precursors are shown and compared with previous analyses. The present approach is robust and permits 2D and 3D electromagnetic pulse propagation directly from the full-vector Maxwell's equations.

Overcoming preexisting humoral immunity to AAV using capsid decoys.

PubMed

Mingozzi, Federico; Anguela, Xavier M; Pavani, Giulia; Chen, Yifeng; Davidson, Robert J; Hui, Daniel J; Yazicioglu, Mustafa; Elkouby, Liron; Hinderer, Christian J; Faella, Armida; Howard, Carolann; Tai, Alex; Podsakoff, Gregory M; Zhou, Shangzhen; Basner-Tschakarjan, Etiena; Wright, John Fraser; High, Katherine A

2013-07-17

Adeno-associated virus (AAV) vectors delivered through the systemic circulation successfully transduce various target tissues in animal models. However, similar attempts in humans have been hampered by the high prevalence of neutralizing antibodies to AAV, which completely block vector transduction. We show in both mouse and nonhuman primate models that addition of empty capsid to the final vector formulation can, in a dose-dependent manner, adsorb these antibodies, even at high titers, thus overcoming their inhibitory effect. To further enhance the safety of the approach, we mutated the receptor binding site of AAV2 to generate an empty capsid mutant that can adsorb antibodies but cannot enter a target cell. Our work suggests that optimizing the ratio of full/empty capsids in the final formulation of vector, based on a patient's anti-AAV titers, will maximize the efficacy of gene transfer after systemic vector delivery.

Representation and display of vector field topology in fluid flow data sets

NASA Technical Reports Server (NTRS)

Helman, James; Hesselink, Lambertus

1989-01-01

The visualization of physical processes in general and of vector fields in particular is discussed. An approach to visualizing flow topology that is based on the physics and mathematics underlying the physical phenomenon is presented. It involves determining critical points in the flow where the velocity vector vanishes. The critical points, connected by principal lines or planes, determine the topology of the flow. The complexity of the data is reduced without sacrificing the quantitative nature of the data set. By reducing the original vector field to a set of critical points and their connections, a representation of the topology of a two-dimensional vector field that is much smaller than the original data set but retains with full precision the information pertinent to the flow topology is obtained. This representation can be displayed as a set of points and tangent curves or as a graph. Analysis (including algorithms), display, interaction, and implementation aspects are discussed.

Evolution of Lamb Vector as a Vortex Breaking into Turbulence.

NASA Astrophysics Data System (ADS)

Wu, J. Z.; Lu, X. Y.

1996-11-01

In an incompressible flow, either laminar or turbulent, the Lamb vector is solely responsible to nonlinear interactions. While its longitudinal part is balanced by stagnation enthalpy, its transverse part is the unique source (as an external forcing in spectral space) that causes the flow to evolve. Moreover, in Reynolds-averaged flows the turbulent force can be derived exclusively from the Lamb vector instead of the full Reynolds stress tensor. Therefore, studying the evolution of the Lamb vector itself (both longitudinal and transverse parts) is of great interest. We have numerically examined this problem, taking the nonlinear distabilization of a viscous vortex as an example. In the later stage of this evolution we introduced a forcing to keep a statistically steady state, and observed the Lamb vector behavior in the resulting fine turbulence. The result is presented in both physical and spectral spaces.

Overcoming Preexisting Humoral Immunity to AAV Using Capsid Decoys

PubMed Central

Anguela, Xavier M.; Pavani, Giulia; Chen, Yifeng; Davidson, Robert J.; Hui, Daniel J.; Yazicioglu, Mustafa; Elkouby, Liron; Hinderer, Christian J.; Faella, Armida; Howard, Carolann; Tai, Alex; Podsakoff, Gregory M.; Zhou, Shangzhen; Basner-Tschakarjan, Etiena; Wright, John Fraser

2014-01-01

Adeno-associated virus (AAV) vectors delivered through the systemic circulation successfully transduce various target tissues in animal models. However, similar attempts in humans have been hampered by the high prevalence of neutralizing antibodies to AAV, which completely block vector transduction. We show in both mouse and nonhuman primate models that addition of empty capsid to the final vector formulation can, in a dose-dependent manner, adsorb these antibodies, even at high titers, thus overcoming their inhibitory effect. To further enhance the safety of the approach, we mutated the receptor binding site of AAV2 to generate an empty capsid mutant that can adsorb antibodies but cannot enter a target cell. Our work suggests that optimizing the ratio of full/empty capsids in the final formulation of vector, based on a patient's anti-AAV titers, will maximize the efficacy of gene transfer after systemic vector delivery. PMID:23863832

A variational reconstruction method for undersampled dynamic x-ray tomography based on physical motion models

NASA Astrophysics Data System (ADS)

Burger, Martin; Dirks, Hendrik; Frerking, Lena; Hauptmann, Andreas; Helin, Tapio; Siltanen, Samuli

2017-12-01

In this paper we study the reconstruction of moving object densities from undersampled dynamic x-ray tomography in two dimensions. A particular motivation of this study is to use realistic measurement protocols for practical applications, i.e. we do not assume to have a full Radon transform in each time step, but only projections in few angular directions. This restriction enforces a space-time reconstruction, which we perform by incorporating physical motion models and regularization of motion vectors in a variational framework. The methodology of optical flow, which is one of the most common methods to estimate motion between two images, is utilized to formulate a joint variational model for reconstruction and motion estimation. We provide a basic mathematical analysis of the forward model and the variational model for the image reconstruction. Moreover, we discuss the efficient numerical minimization based on alternating minimizations between images and motion vectors. A variety of results are presented for simulated and real measurement data with different sampling strategy. A key observation is that random sampling combined with our model allows reconstructions of similar amount of measurements and quality as a single static reconstruction.

Particle displacement tracking applied to air flows

NASA Technical Reports Server (NTRS)

Wernet, Mark P.

1991-01-01

Electronic Particle Image Velocimeter (PIV) techniques offer many advantages over conventional photographic PIV methods such as fast turn around times and simplified data reduction. A new all electronic PIV technique was developed which can measure high speed gas velocities. The Particle Displacement Tracking (PDT) technique employs a single cw laser, small seed particles (1 micron), and a single intensified, gated CCD array frame camera to provide a simple and fast method of obtaining two-dimensional velocity vector maps with unambiguous direction determination. Use of a single CCD camera eliminates registration difficulties encountered when multiple cameras are used to obtain velocity magnitude and direction information. An 80386 PC equipped with a large memory buffer frame-grabber board provides all of the data acquisition and data reduction operations. No array processors of other numerical processing hardware are required. Full video resolution (640x480 pixel) is maintained in the acquired images, providing high resolution video frames of the recorded particle images. The time between data acquisition to display of the velocity vector map is less than 40 sec. The new electronic PDT technique is demonstrated on an air nozzle flow with velocities less than 150 m/s.

Fast computation of voxel-level brain connectivity maps from resting-state functional MRI using l₁-norm as approximation of Pearson's temporal correlation: proof-of-concept and example vector hardware implementation.

PubMed

Minati, Ludovico; Zacà, Domenico; D'Incerti, Ludovico; Jovicich, Jorge

2014-09-01

An outstanding issue in graph-based analysis of resting-state functional MRI is choice of network nodes. Individual consideration of entire brain voxels may represent a less biased approach than parcellating the cortex according to pre-determined atlases, but entails establishing connectedness for 1(9)-1(11) links, with often prohibitive computational cost. Using a representative Human Connectome Project dataset, we show that, following appropriate time-series normalization, it may be possible to accelerate connectivity determination replacing Pearson correlation with l1-norm. Even though the adjacency matrices derived from correlation coefficients and l1-norms are not identical, their similarity is high. Further, we describe and provide in full an example vector hardware implementation of l1-norm on an array of 4096 zero instruction-set processors. Calculation times <1000 s are attainable, removing the major deterrent to voxel-based resting-sate network mapping and revealing fine-grained node degree heterogeneity. L1-norm should be given consideration as a substitute for correlation in very high-density resting-state functional connectivity analyses. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Angular momentum evolution in dark matter haloes: a study of the Bolshoi and Millennium simulations

NASA Astrophysics Data System (ADS)

Contreras, S.; Padilla, N.; Lagos, C. D. P.

2017-12-01

We use three different cosmological dark matter simulations to study how the orientation of the angular momentum (AM) vector in dark matter haloes evolve with time. We find that haloes in this kind of simulations are constantly affected by a spurious change of mass, which translates into an artificial change in the orientation of the AM. After removing the haloes affected by artificial mass change, we found that the change in the orientation of the AM vector is correlated with time. The change in its angle and direction (i.e. the angle subtended by the AM vector in two consecutive time-steps) that affect the AM vector has a dependence on the change of mass that affects a halo, the time elapsed in which the change of mass occurs and the halo mass. We create a Monte Carlo simulation that reproduces the change of angle and direction of the AM vector. We reproduce the angular separation of the AM vector since a lookback time of 8.5 Gyr to today (α) with an accuracy of approximately 0.05 in cos(α). We are releasing this Monte Carlo simulation together with this publication. We also create a Monte Carlo simulation that reproduces the change of the AM modulus. We find that haloes in denser environments display the most dramatic evolution in their AM direction, as well as haloes with a lower specific AM modulus. These relations could be used to improve the way we follow the AM vector in low-resolution simulations.

Classical reconstruction of interference patterns of position-wave-vector-entangled photon pairs by the time-reversal method

NASA Astrophysics Data System (ADS)

Ogawa, Kazuhisa; Kobayashi, Hirokazu; Tomita, Akihisa

2018-02-01

The quantum interference of entangled photons forms a key phenomenon underlying various quantum-optical technologies. It is known that the quantum interference patterns of entangled photon pairs can be reconstructed classically by the time-reversal method; however, the time-reversal method has been applied only to time-frequency-entangled two-photon systems in previous experiments. Here, we apply the time-reversal method to the position-wave-vector-entangled two-photon systems: the two-photon Young interferometer and the two-photon beam focusing system. We experimentally demonstrate that the time-reversed systems classically reconstruct the same interference patterns as the position-wave-vector-entangled two-photon systems.

Ground Operations of the ISS GNC Babb-Mueller Atmospheric Density Model

NASA Technical Reports Server (NTRS)

Brogan, Jonathan

2002-01-01

The ISS GNC system was updated recently with a new software release that provides onboard state determination capability. Prior to this release, only the Russian segment maintained and propagated the onboard state, which was periodically updated through Russian ground tracking. The new software gives the US segment the capability for maintaining the onboard state, and includes new GPS and state vector propagation capabilities. Part of this software package is an atmospheric density model based on the Babb-Mueller algorithm. Babb-Mueller efficiently mimics a full analytical density model, such as the Jacchia model. While lacchia is very robust and is used in the Mission Control Center, it is too computationally intensive for use onboard. Thus, Babb-Mueller was chosen as an alternative. The onboard model depends on a set of calibration coefficients that produce a curve fit to the lacchia model. The ISS GNC system only maintains one set of coefficients onboard, so a new set must be uplinked by controllers when the atmospheric conditions change. The onboard density model provides a real-time density value, which is used to calculate the drag experienced by the ISS. This drag value is then incorporated into the onboard propagation of the state vector. The propagation of the state vector, and therefore operation of the BabbMueller algorithm, will be most critical when GPS updates and secondary state vector sources fail. When GPS is active, the onboard state vector will be updated every ten seconds, so the propagation error is irrelevant. When GPS is inactive, the state vector must be updated at least every 24 hours, based on current protocol. Therefore, the Babb-Mueller coefficients must be accurate enough to fulfill the state vector accuracy requirements for at least one day. A ground operations concept was needed in order to manage both the on board Babb-Mueller density model and the onboard state quality. The Babb-Mueller coefficients can be determined operationally in two ways. The first method is to calibrate the coefficients in real-time, where a set of custom coefficients is generated for the real-time atmospheric conditions. The second approach is to generate pre-canned sets of coefficients that encompass the expected atmospheric conditions over the lifetime of the vehicle. These predetermined sets are known as occurrences. Even though a particular occurrence will not match the true atmospheric conditions, the error will be constrained by limiting the breadth of each occurrence. Both methods were investigated and the advantages and disadvantages of each were considered. The choice between these implementations was a trade-off between the additional accuracy of the real-time calibration and the simpler development for the approach using occurrences. The operations concept for the frequency of updates was also explored, and depends on the deviation in solar flux that still achieves the necessary accuracy of the coefficients. This was determined based on historical solar flux trends. This analysis resulted in an accurate and reliable implementation of the Babb-Mueller coefficients and how flight controllers use them during realtime operations.

Large-scale production of lentiviral vector in a closed system hollow fiber bioreactor

PubMed Central

Sheu, Jonathan; Beltzer, Jim; Fury, Brian; Wilczek, Katarzyna; Tobin, Steve; Falconer, Danny; Nolta, Jan; Bauer, Gerhard

2015-01-01

Lentiviral vectors are widely used in the field of gene therapy as an effective method for permanent gene delivery. While current methods of producing small scale vector batches for research purposes depend largely on culture flasks, the emergence and popularity of lentiviral vectors in translational, preclinical and clinical research has demanded their production on a much larger scale, a task that can be difficult to manage with the numbers of producer cell culture flasks required for large volumes of vector. To generate a large scale, partially closed system method for the manufacturing of clinical grade lentiviral vector suitable for the generation of induced pluripotent stem cells (iPSCs), we developed a method employing a hollow fiber bioreactor traditionally used for cell expansion. We have demonstrated the growth, transfection, and vector-producing capability of 293T producer cells in this system. Vector particle RNA titers after subsequent vector concentration yielded values comparable to lentiviral iPSC induction vector batches produced using traditional culture methods in 225 cm2 flasks (T225s) and in 10-layer cell factories (CF10s), while yielding a volume nearly 145 times larger than the yield from a T225 flask and nearly three times larger than the yield from a CF10. Employing a closed system hollow fiber bioreactor for vector production offers the possibility of manufacturing large quantities of gene therapy vector while minimizing reagent usage, equipment footprint, and open system manipulation. PMID:26151065

On HMI's Mod-L Sequence: Test and Evaluation

NASA Astrophysics Data System (ADS)

Liu, Yang; Baldner, Charles; Bogart, R. S.; Bush, R.; Couvidat, S.; Duvall, Thomas L.; Hoeksema, Jon Todd; Norton, Aimee Ann; Scherrer, Philip H.; Schou, Jesper

2016-05-01

HMI Mod-L sequence can produce full Stokes parameters at a cadence of 90 seconds by combining filtergrams from both cameras, the front camera and the side camera. Within the 90-second, the front camera takes two sets of Left and Right Circular Polarizations (LCP and RCP) at 6 wavelengths; the side camera takes one set of Linear Polarizations (I+/-Q and I+/-U) at 6 wavelengths. By combining two cameras, one can obtain full Stokes parameters of [I,Q,U,V] at 6 wavelengths in 90 seconds. In norminal Mod-C sequence that HMI currently uses, the front camera takes LCP and RCP at a cadence of 45 seconds, while the side camera takes observation of the full Stokes at a cadence of 135 seconds. Mod-L should be better than Mod-C for providing vector magnetic field data because (1) Mod-L increases cadence of full Stokes observation, which leads to higher temporal resolution of vector magnetic field measurement; (2) decreases noise in vector magnetic field data because it uses more filtergrams to produce [I,Q,U,V]. There are two potential issues in Mod-L that need to be addressed: (1) scaling intensity of the two cameras’ filtergrams; and (2) if current polarization calibration model, which is built for each camera separately, works for the combined data from both cameras. This presentation will address these questions, and further place a discussion here.

Output-only modal parameter estimator of linear time-varying structural systems based on vector TAR model and least squares support vector machine

NASA Astrophysics Data System (ADS)

Zhou, Si-Da; Ma, Yuan-Chen; Liu, Li; Kang, Jie; Ma, Zhi-Sai; Yu, Lei

2018-01-01

Identification of time-varying modal parameters contributes to the structural health monitoring, fault detection, vibration control, etc. of the operational time-varying structural systems. However, it is a challenging task because there is not more information for the identification of the time-varying systems than that of the time-invariant systems. This paper presents a vector time-dependent autoregressive model and least squares support vector machine based modal parameter estimator for linear time-varying structural systems in case of output-only measurements. To reduce the computational cost, a Wendland's compactly supported radial basis function is used to achieve the sparsity of the Gram matrix. A Gamma-test-based non-parametric approach of selecting the regularization factor is adapted for the proposed estimator to replace the time-consuming n-fold cross validation. A series of numerical examples have illustrated the advantages of the proposed modal parameter estimator on the suppression of the overestimate and the short data. A laboratory experiment has further validated the proposed estimator.

Video-rate terahertz electric-field vector imaging

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

Takai, Mayuko; Takeda, Masatoshi; Sasaki, Manabu

We present an experimental setup to dramatically reduce a measurement time for obtaining spatial distributions of terahertz electric-field (E-field) vectors. The method utilizes the electro-optic sampling, and we use a charge-coupled device to detect a spatial distribution of the probe beam polarization rotation by the E-field-induced Pockels effect in a 〈110〉-oriented ZnTe crystal. A quick rotation of the ZnTe crystal allows analyzing the terahertz E-field direction at each image position, and the terahertz E-field vector mapping at a fixed position of an optical delay line is achieved within 21 ms. Video-rate mapping of terahertz E-field vectors is likely to bemore » useful for achieving real-time sensing of terahertz vector beams, vector vortices, and surface topography. The method is also useful for a fast polarization analysis of terahertz beams.« less

Limits on the Efficiency of Event-Based Algorithms for Monte Carlo Neutron Transport

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

Romano, Paul K.; Siegel, Andrew R.

The traditional form of parallelism in Monte Carlo particle transport simulations, wherein each individual particle history is considered a unit of work, does not lend itself well to data-level parallelism. Event-based algorithms, which were originally used for simulations on vector processors, may offer a path toward better utilizing data-level parallelism in modern computer architectures. In this study, a simple model is developed for estimating the efficiency of the event-based particle transport algorithm under two sets of assumptions. Data collected from simulations of four reactor problems using OpenMC was then used in conjunction with the models to calculate the speedup duemore » to vectorization as a function of the size of the particle bank and the vector width. When each event type is assumed to have constant execution time, the achievable speedup is directly related to the particle bank size. We observed that the bank size generally needs to be at least 20 times greater than vector size to achieve vector efficiency greater than 90%. Lastly, when the execution times for events are allowed to vary, the vector speedup is also limited by differences in execution time for events being carried out in a single event-iteration.« less

Limits on the Efficiency of Event-Based Algorithms for Monte Carlo Neutron Transport

DOE PAGES

Romano, Paul K.; Siegel, Andrew R.

2017-07-01

The traditional form of parallelism in Monte Carlo particle transport simulations, wherein each individual particle history is considered a unit of work, does not lend itself well to data-level parallelism. Event-based algorithms, which were originally used for simulations on vector processors, may offer a path toward better utilizing data-level parallelism in modern computer architectures. In this study, a simple model is developed for estimating the efficiency of the event-based particle transport algorithm under two sets of assumptions. Data collected from simulations of four reactor problems using OpenMC was then used in conjunction with the models to calculate the speedup duemore » to vectorization as a function of the size of the particle bank and the vector width. When each event type is assumed to have constant execution time, the achievable speedup is directly related to the particle bank size. We observed that the bank size generally needs to be at least 20 times greater than vector size to achieve vector efficiency greater than 90%. Lastly, when the execution times for events are allowed to vary, the vector speedup is also limited by differences in execution time for events being carried out in a single event-iteration.« less

Polarization rotation locking of vector solitons in a fiber ring laser.

PubMed

Zhao, L M; Tang, D Y; Zhang, H; Wu, X

2008-07-07

Polarization rotation of vector solitons in a fiber ring laser was experimentally studied. It was observed that the period of vector soliton polarization rotation could be locked to the cavity roundtrip time or multiple of it. We further show that multiple vector solitons can be formed in a fiber laser, and all the vector solitons have the same group velocity in cavity, however, their instantaneous polarization ellipse orientations could be orthogonal.

Adenovirus-vectored foot-and-mouth disease vaccine confers early and full protection against FMDV O1 Manisa in swine

USDA-ARS?s Scientific Manuscript database

A human adenovirus (Ad5) vectored foot-and-mouth disease virus (FMDV) sero-type O1-Manisa subunit vaccine (Ad5-O1Man) was engineered to deliver FMDV O1-Manisa empty capsids. Swine inoculated with Ad5-O1Man developed an FMDV-specific neutralizing antibody response as compared to animals inoculated wi...

Research on intrusion detection based on Kohonen network and support vector machine

NASA Astrophysics Data System (ADS)

Shuai, Chunyan; Yang, Hengcheng; Gong, Zeweiyi

2018-05-01

In view of the problem of low detection accuracy and the long detection time of support vector machine, which directly applied to the network intrusion detection system. Optimization of SVM parameters can greatly improve the detection accuracy, but it can not be applied to high-speed network because of the long detection time. a method based on Kohonen neural network feature selection is proposed to reduce the optimization time of support vector machine parameters. Firstly, this paper is to calculate the weights of the KDD99 network intrusion data by Kohonen network and select feature by weight. Then, after the feature selection is completed, genetic algorithm (GA) and grid search method are used for parameter optimization to find the appropriate parameters and classify them by support vector machines. By comparing experiments, it is concluded that feature selection can reduce the time of parameter optimization, which has little influence on the accuracy of classification. The experiments suggest that the support vector machine can be used in the network intrusion detection system and reduce the missing rate.

An indirect approach to the extensive calculation of relationship coefficients

PubMed Central

Colleau, Jean-Jacques

2002-01-01

A method was described for calculating population statistics on relationship coefficients without using corresponding individual data. It relied on the structure of the inverse of the numerator relationship matrix between individuals under investigation and ancestors. Computation times were observed on simulated populations and were compared to those incurred with a conventional direct approach. The indirect approach turned out to be very efficient for multiplying the relationship matrix corresponding to planned matings (full design) by any vector. Efficiency was generally still good or very good for calculating statistics on these simulated populations. An extreme implementation of the method is the calculation of inbreeding coefficients themselves. Relative performances of the indirect method were good except when many full-sibs during many generations existed in the population. PMID:12270102

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.

Artificial Potential Field Controllers for Robust Communications in a Network of Swarm Robots

DTIC Science & Technology

2005-05-18

vectors are less than 90◦ apart. Algorithm 1 The Algorithm for generating a feasible set of vectors P ← set of high priority vectors Csum ← [( LOS1 +R1...the 46 C program was finished reading and writing the values to the serial line it would delete the timing file. Only after the timing file had been... deleted would the base station write new values for the wheel velocities. The timing file kept both the Linux PC and the base station synchronized so

Dynamic measurement of local displacements within curing resin-based dental composite using optical coherence elastography

NASA Astrophysics Data System (ADS)

Tomlins, Peter H.; Rahman, Mohammed Wahidur; Donnan, Robert S.

2016-04-01

This study aimed to determine the feasibility of using optical coherence elastography to measure internal displacements during the curing phase of a light-activated, resin-based composite material. Displacement vectors were spatially mapped over time within a commercial dental composite. Measurements revealed that the orientation of cure-induced displacement vectors varied spatially in a complex manner; however, each vector showed a systematic evolution with time. Precision of individual displacements was estimated to be ˜1 to 2 μm, enabling submicrometer time-varying displacements to be detected.

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.

Solar Flare Prediction Model with Three Machine-learning Algorithms using Ultraviolet Brightening and Vector Magnetograms

NASA Astrophysics Data System (ADS)

Nishizuka, N.; Sugiura, K.; Kubo, Y.; Den, M.; Watari, S.; Ishii, M.

2017-02-01

We developed a flare prediction model using machine learning, which is optimized to predict the maximum class of flares occurring in the following 24 hr. Machine learning is used to devise algorithms that can learn from and make decisions on a huge amount of data. We used solar observation data during the period 2010-2015, such as vector magnetograms, ultraviolet (UV) emission, and soft X-ray emission taken by the Solar Dynamics Observatory and the Geostationary Operational Environmental Satellite. We detected active regions (ARs) from the full-disk magnetogram, from which ˜60 features were extracted with their time differentials, including magnetic neutral lines, the current helicity, the UV brightening, and the flare history. After standardizing the feature database, we fully shuffled and randomly separated it into two for training and testing. To investigate which algorithm is best for flare prediction, we compared three machine-learning algorithms: the support vector machine, k-nearest neighbors (k-NN), and extremely randomized trees. The prediction score, the true skill statistic, was higher than 0.9 with a fully shuffled data set, which is higher than that for human forecasts. It was found that k-NN has the highest performance among the three algorithms. The ranking of the feature importance showed that previous flare activity is most effective, followed by the length of magnetic neutral lines, the unsigned magnetic flux, the area of UV brightening, and the time differentials of features over 24 hr, all of which are strongly correlated with the flux emergence dynamics in an AR.

Solar Flare Prediction Model with Three Machine-learning Algorithms using Ultraviolet Brightening and Vector Magnetograms

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

Nishizuka, N.; Kubo, Y.; Den, M.

We developed a flare prediction model using machine learning, which is optimized to predict the maximum class of flares occurring in the following 24 hr. Machine learning is used to devise algorithms that can learn from and make decisions on a huge amount of data. We used solar observation data during the period 2010–2015, such as vector magnetograms, ultraviolet (UV) emission, and soft X-ray emission taken by the Solar Dynamics Observatory and the Geostationary Operational Environmental Satellite . We detected active regions (ARs) from the full-disk magnetogram, from which ∼60 features were extracted with their time differentials, including magnetic neutralmore » lines, the current helicity, the UV brightening, and the flare history. After standardizing the feature database, we fully shuffled and randomly separated it into two for training and testing. To investigate which algorithm is best for flare prediction, we compared three machine-learning algorithms: the support vector machine, k-nearest neighbors (k-NN), and extremely randomized trees. The prediction score, the true skill statistic, was higher than 0.9 with a fully shuffled data set, which is higher than that for human forecasts. It was found that k-NN has the highest performance among the three algorithms. The ranking of the feature importance showed that previous flare activity is most effective, followed by the length of magnetic neutral lines, the unsigned magnetic flux, the area of UV brightening, and the time differentials of features over 24 hr, all of which are strongly correlated with the flux emergence dynamics in an AR.« less

Estimation of attitude sensor timetag biases

NASA Technical Reports Server (NTRS)

Sedlak, J.

1995-01-01

This paper presents an extended Kalman filter for estimating attitude sensor timing errors. Spacecraft attitude is determined by finding the mean rotation from a set of reference vectors in inertial space to the corresponding observed vectors in the body frame. Any timing errors in the observations can lead to attitude errors if either the spacecraft is rotating or the reference vectors themselves vary with time. The state vector here consists of the attitude quaternion, timetag biases, and, optionally, gyro drift rate biases. The filter models the timetags as random walk processes: their expectation values propagate as constants and white noise contributes to their covariance. Thus, this filter is applicable to cases where the true timing errors are constant or slowly varying. The observability of the state vector is studied first through an examination of the algebraic observability condition and then through several examples with simulated star tracker timing errors. The examples use both simulated and actual flight data from the Extreme Ultraviolet Explorer (EUVE). The flight data come from times when EUVE had a constant rotation rate, while the simulated data feature large angle attitude maneuvers. The tests include cases with timetag errors on one or two sensors, both constant and time-varying, and with and without gyro bias errors. Due to EUVE's sensor geometry, the observability of the state vector is severely limited when the spacecraft rotation rate is constant. In the absence of attitude maneuvers, the state elements are highly correlated, and the state estimate is unreliable. The estimates are particularly sensitive to filter mistuning in this case. The EUVE geometry, though, is a degenerate case having coplanar sensors and rotation vector. Observability is much improved and the filter performs well when the rate is either varying or noncoplanar with the sensors, as during a slew. Even with bad geometry and constant rates, if gyro biases are independently known, the timetag error for a single sensor can be accurately estimated as long as its boresight is not too close to the spacecraft rotation axis.

Improved dual AAV vectors with reduced expression of truncated proteins are safe and effective in the retina of a mouse model of Stargardt disease.

PubMed

Trapani, Ivana; Toriello, Elisabetta; de Simone, Sonia; Colella, Pasqualina; Iodice, Carolina; Polishchuk, Elena V; Sommella, Andrea; Colecchi, Linda; Rossi, Settimio; Simonelli, Francesca; Giunti, Massimo; Bacci, Maria L; Polishchuk, Roman S; Auricchio, Alberto

2015-12-01

Stargardt disease (STGD1) due to mutations in the large ABCA4 gene is the most common inherited macular degeneration in humans. We have shown that dual adeno-associated viral (AAV) vectors effectively transfer ABCA4 to the retina of Abca4-/- mice. However, they express both lower levels of transgene compared with a single AAV and truncated proteins. To increase productive dual AAV concatemerization, which would overcome these limitations, we have explored the use of either various regions of homology or heterologous inverted terminal repeats (ITR). In addition, we tested the ability of various degradation signals to decrease the expression of truncated proteins. We found the highest levels of transgene expression using regions of homology based on either alkaline phosphatase or the F1 phage (AK). The use of heterologous ITR does not decrease the levels of truncated proteins relative to full-length ABCA4 and impairs AAV vector production. Conversely, the inclusion of the CL1 degradation signal results in the selective degradation of truncated proteins from the 5'-half without affecting full-length protein production. Therefore, we developed dual AAV hybrid ABCA4 vectors including homologous ITR2, the photoreceptor-specific G protein-coupled receptor kinase 1 promoter, the AK region of homology and the CL1 degradation signal. We show that upon subretinal administration these vectors are both safe in pigs and effective in Abca4-/- mice. Our data support the use of improved dual AAV vectors for gene therapy of STGD1. © The Author 2015. Published by Oxford University Press.

A scalable method for the production of high-titer and high-quality adeno-associated type 9 vectors using the HSV platform

PubMed Central

Adamson-Small, Laura; Potter, Mark; Falk, Darin J; Cleaver, Brian; Byrne, Barry J; Clément, Nathalie

2016-01-01

Recombinant adeno-associated vectors based on serotype 9 (rAAV9) have demonstrated highly effective gene transfer in multiple animal models of muscular dystrophies and other neurological indications. Current limitations in vector production and purification have hampered widespread implementation of clinical candidate vectors, particularly when systemic administration is considered. In this study, we describe a complete herpes simplex virus (HSV)-based production and purification process capable of generating greater than 1 × 1014 rAAV9 vector genomes per 10-layer CellSTACK of HEK 293 producer cells, or greater than 1 × 105 vector genome per cell, in a final, fully purified product. This represents a 5- to 10-fold increase over transfection-based methods. In addition, rAAV vectors produced by this method demonstrated improved biological characteristics when compared to transfection-based production, including increased infectivity as shown by higher transducing unit-to-vector genome ratios and decreased total capsid protein amounts, shown by lower empty-to-full ratios. Together, this data establishes a significant improvement in both rAAV9 yields and vector quality. Further, the method can be readily adapted to large-scale good laboratory practice (GLP) and good manufacturing practice (GMP) production of rAAV9 vectors to enable preclinical and clinical studies and provide a platform to build on toward late-phases and commercial production. PMID:27222839

Search for the standard model Higgs boson decaying to a bb pair in events with no charged leptons and large missing transverse energy using the full CDF data set.

PubMed

Aaltonen, T; Álvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Appel, J A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Auerbach, B; Aurisano, A; Azfar, F; Badgett, W; Bae, T; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauce, M; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Binkley, M E; Bisello, D; Bizjak, I; Bland, K R; Blumenfeld, B; Bocci, A; Bodek, A; Bortoletto, D; Boudreau, J; Boveia, A; Brigliadori, L; Bromberg, C; Brucken, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Calamba, A; Calancha, C; Camarda, S; Campanelli, M; Campbell, M; Canelli, F; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chung, W H; Chung, Y S; Ciocci, M A; Clark, A; Clarke, C; Compostella, G; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Crescioli, F; Cuevas, J; Culbertson, R; Dagenhart, D; d'Ascenzo, N; Datta, M; de Barbaro, P; Dell'Orso, M; Demortier, L; Deninno, M; Devoto, F; d'Errico, M; Di Canto, A; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Dorigo, M; Dorigo, T; Ebina, K; Elagin, A; Eppig, A; Erbacher, R; Errede, S; Ershaidat, N; Eusebi, R; Farrington, S; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Funakoshi, Y; Furic, I; Gallinaro, M; Garcia, J E; Garfinkel, A F; Garosi, P; Gerberich, H; Gerchtein, E; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Ginsburg, C M; Giokaris, N; Giromini, P; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldin, D; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Grinstein, S; Grosso-Pilcher, C; Group, R C; Guimaraes da Costa, J; Hahn, S R; Halkiadakis, E; Hamaguchi, A; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harr, R F; Hatakeyama, K; Hays, C; Heck, M; Heinrich, J; Herndon, M; Hewamanage, S; Hocker, A; Hopkins, W; Horn, D; Hou, S; Hughes, R E; Hurwitz, M; Husemann, U; Hussain, N; Hussein, M; Huston, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kamon, T; Karchin, P E; Kasmi, A; Kato, Y; Ketchum, W; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kim, Y J; Kimura, N; Kirby, M; Klimenko, S; Knoepfel, K; Kondo, K; Kong, D J; Konigsberg, J; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Kruse, M; Krutelyov, V; Kuhr, T; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; LeCompte, T; Lee, E; Lee, H S; Lee, J S; Lee, S W; Leo, S; Leone, S; Lewis, J D; Limosani, A; Lin, C-J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, H; Liu, Q; Liu, T; Lockwitz, S; Loginov, A; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; Madrak, R; Maeshima, K; Maestro, P; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Martínez, M; Mastrandrea, P; Matera, K; Mattson, M E; Mazzacane, A; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Mesropian, C; Miao, T; Mietlicki, D; Mitra, A; Miyake, H; Moed, S; Moggi, N; Mondragon, M N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakano, I; Napier, A; Nett, J; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Noh, S Y; Norniella, O; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Ortolan, L; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Paramonov, A A; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pilot, J; Pitts, K; Plager, C; Pondrom, L; Poprocki, S; Potamianos, K; Prokoshin, F; Pranko, A; Ptohos, F; Punzi, G; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Rescigno, M; Riddick, T; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Ruffini, F; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Sakurai, Y; Santi, L; Sato, K; Saveliev, V; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Seidel, S; Seiya, Y; Semenov, A; Sforza, F; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shochet, M; Shreyber-Tecker, I; Simonenko, A; Sinervo, P; Sliwa, K; Smith, J R; Snider, F D; Soha, A; Sorin, V; Song, H; Squillacioti, P; Stancari, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Sudo, Y; Sukhanov, A; Suslov, I; Takemasa, K; Takeuchi, Y; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thome, J; Thompson, G A; Thomson, E; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Trovato, M; Ukegawa, F; Uozumi, S; Varganov, A; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vila, I; Vilar, R; Vizán, J; Vogel, M; Volpi, G; Wagner, P; Wagner, R L; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Wester, W C; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Wick, F; Williams, H H; Wilson, J S; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, H; Wright, T; Wu, X; Wu, Z; Yamamoto, K; Yamato, D; Yang, T; Yang, U K; Yang, Y C; Yao, W-M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanetti, A; Zeng, Y; Zhou, C; Zucchelli, S

2012-09-14

We report on a search for the standard model Higgs boson produced in association with a vector boson in the full data set of proton-antiproton collisions at sqrt[s]=1.96  TeV recorded by the CDF II detector at the Tevatron, corresponding to an integrated luminosity of 9.45  fb(-1). We consider events having no identified charged lepton, a transverse energy imbalance, and two or three jets, of which at least one is consistent with originating from the decay of a b quark. We place 95% credibility level upper limits on the production cross section times standard model branching fraction for several mass hypotheses between 90 and 150  GeV/c(2). For a Higgs boson mass of 125  GeV/c(2), the observed (expected) limit is 6.7 (3.6) times the standard model prediction.

Numerical study of the effects of icing on viscous flow over wings

NASA Technical Reports Server (NTRS)

Sankar, L. N.

1994-01-01

An improved hybrid method for computing unsteady compressible viscous flows is presented. This method divides the computational domain into two zones. In the outer zone, the unsteady full-potential equation (FPE) is solved. In the inner zone, the Navier-Stokes equations are solved using a diagonal form of an alternating-direction implicit (ADI) approximate factorization procedure. The two zones are tightly coupled so that steady and unsteady flows may be efficiently solved. Characteristic-based viscous/inviscid interface boundary conditions are employed to avoid spurious reflections at that interface. The resulting CPU times are less than 60 percent of that required for a full-blown Navier-Stokes analysis for steady flow applications and about 60 percent of the Navier-Stokes CPU times for unsteady flows in non-vector processing machines. Applications of the method are presented for a rectangular NACA 0012 wing in low subsonic steady flow at moderate and high angles of attack, and for an F-5 wing in steady and unsteady subsonic and transonic flows. Steady surface pressures are in very good agreement with experimental data and are essentially identical to Navier-Stokes predictions. Density contours show that shocks cross the viscous/inviscid interface smoothly, so that the accuracy of full Navier-Stokes equations can be retained with a significant savings in computational time.

Quasiperiodicity in time evolution of the Bloch vector under the thermal Jaynes-Cummings model

NASA Astrophysics Data System (ADS)

Azuma, Hiroo; Ban, Masashi

2014-07-01

We study a quasiperiodic structure in the time evolution of the Bloch vector, whose dynamics is governed by the thermal Jaynes-Cummings model (JCM). Putting the two-level atom into a certain pure state and the cavity field into a mixed state in thermal equilibrium at initial time, we let the whole system evolve according to the JCM Hamiltonian. During this time evolution, motion of the Bloch vector seems to be in disorder. Because of the thermal photon distribution, both a norm and a direction of the Bloch vector change hard at random. In this paper, taking a different viewpoint compared with ones that we have been used to, we investigate quasiperiodicity of the Bloch vector’s trajectories. Introducing the concept of the quasiperiodic motion, we can explain the confused behaviour of the system as an intermediate state between periodic and chaotic motions. More specifically, we discuss the following two facts: (1) If we adjust the time interval Δt properly, figures consisting of plotted dots at the constant time interval acquire scale invariance under replacement of Δt by sΔt, where s(>1) is an arbitrary real but not transcendental number. (2) We can compute values of the time variable t, which let |Sz(t)| (the absolute value of the z-component of the Bloch vector) be very small, with the Diophantine approximation (a rational approximation of an irrational number).

Bayesian Kernel Methods for Non-Gaussian Distributions: Binary and Multi-class Classification Problems

DTIC Science & Technology

2013-05-28

those of the support vector machine and relevance vector machine, and the model runs more quickly than the other algorithms . When one class occurs...incremental support vector machine algorithm for online learning when fewer than 50 data points are available. (a) Papers published in peer-reviewed journals...learning environments, where data processing occurs one observation at a time and the classification algorithm improves over time with new

Adaptive mesh refinement for time-domain electromagnetics using vector finite elements :a feasibility study.

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

Turner, C. David; Kotulski, Joseph Daniel; Pasik, Michael Francis

This report investigates the feasibility of applying Adaptive Mesh Refinement (AMR) techniques to a vector finite element formulation for the wave equation in three dimensions. Possible error estimators are considered first. Next, approaches for refining tetrahedral elements are reviewed. AMR capabilities within the Nevada framework are then evaluated. We summarize our conclusions on the feasibility of AMR for time-domain vector finite elements and identify a path forward.

Real-time optical laboratory solution of parabolic differential equations

NASA Technical Reports Server (NTRS)

Casasent, David; Jackson, James

1988-01-01

An optical laboratory matrix-vector processor is used to solve parabolic differential equations (the transient diffusion equation with two space variables and time) by an explicit algorithm. This includes optical matrix-vector nonbase-2 encoded laboratory data, the combination of nonbase-2 and frequency-multiplexed data on such processors, a high-accuracy optical laboratory solution of a partial differential equation, new data partitioning techniques, and a discussion of a multiprocessor optical matrix-vector architecture.

Single Vector Calibration System for Multi-Axis Load Cells and Method for Calibrating a Multi-Axis Load Cell

NASA Technical Reports Server (NTRS)

Parker, Peter A. (Inventor)

2003-01-01

A single vector calibration system is provided which facilitates the calibration of multi-axis load cells, including wind tunnel force balances. The single vector system provides the capability to calibrate a multi-axis load cell using a single directional load, for example loading solely in the gravitational direction. The system manipulates the load cell in three-dimensional space, while keeping the uni-directional calibration load aligned. The use of a single vector calibration load reduces the set-up time for the multi-axis load combinations needed to generate a complete calibration mathematical model. The system also reduces load application inaccuracies caused by the conventional requirement to generate multiple force vectors. The simplicity of the system reduces calibration time and cost, while simultaneously increasing calibration accuracy.

Vector analysis of postcardiotomy behavioral phenomena.

PubMed

Caston, J C; Miller, W C; Felber, W J

1975-04-01

The classification of postcardiotomy behavioral phenomena in Figure 1 is proposed for use as a clinical instrument to analyze etiological determinants. The utilization of a vector analysis analogy inherently denies absolutism. Classifications A-P are presented as prototypes of certain ratio imbalances of the metabolic, hemodynamic, environmental, and psychic vectors. Such a system allows for change from one type to another according to the individuality of the patient and the highly specific changes in his clinical presentation. A vector analysis also allows for infinite intermediary ratio imbalances between classification types as a function of time. Thus, postcardiotomy behavioral phenomena could be viewed as the vector summation of hemodynamic, metabolic, environmental, and psychic processes at a given point in time. Elaboration of unknown determinants in this complex syndrome appears to be task for the future.

Field Worker Evaluation of Dengue Vector Surveillance Methods: Factors That Determine Perceived Ease, Difficulty, Value, and Time Effectiveness in Australia and Malaysia.

PubMed

Azil, Aishah H; Ritchie, Scott A; Williams, Craig R

2015-10-01

This qualitative study aimed to describe field worker perceptions, evaluations of worth, and time costs of routine dengue vector surveillance methods in Cairns (Australia), Kuala Lumpur and Petaling District (Malaysia). In Cairns, the BG-Sentinel trap is a favored method for field workers because of its user-friendliness, but is not as cost-efficient as the sticky ovitrap. In Kuala Lumpur, the Mosquito Larvae Trapping Device is perceived as a solution for the inaccessibility of premises to larval surveys. Nonetheless, the larval survey method is retained in Malaysia for prompt detection of dengue vectors. For dengue vector surveillance to be successful, there needs to be not only technical, quantitative evaluations of method performance but also an appreciation of how amenable field workers are to using particular methods. Here, we report novel field worker perceptions of dengue vector surveillance methods in addition to time analysis for each method. © 2014 APJPH.

Semiflexible polymer dynamics with a bead-spring model

NASA Astrophysics Data System (ADS)

Barkema, Gerard T.; Panja, Debabrata; van Leeuwen, J. M. J.

2014-11-01

We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA (dsDNA). The two parameters of the model, T* and ν, are chosen to match its experimental force-extension curve. In comparison to its groundstate value, the bead-spring Hamiltonian is approximated in the first order by the Hessian that is quadratic in the bead positions. The eigenmodes of the Hessian provide the longitudinal (stretching) and transverse (bending) eigenmodes of the polymer, and the corresponding eigenvalues match well with the established phenomenology of semiflexible polymers. At the Hessian approximation of the Hamiltonian, the polymer dynamics is linear. Using the longitudinal and transverse eigenmodes, for the linearized problem, we obtain analytical expressions of (i) the autocorrelation function of the end-to-end vector, (ii) the autocorrelation function of a bond (i.e. a spring, or a tangent) vector at the middle of the chain, and (iii) the mean-square displacement of a tagged bead in the middle of the chain, as the sum over the contributions from the modes—the so-called ‘mode sums’. We also perform simulations with the full dynamics of the model. The simulations yield numerical values of the correlations functions (i-iii) that agree very well with the analytical expressions for the linearized dynamics. This does not however mean that the nonlinearities are not present. In fact, we also study the mean-square displacement of the longitudinal component of the end-to-end vector that showcases strong nonlinear effects in the polymer dynamics, and we identify at least an effective t7/8 power-law regime in its time-dependence. Nevertheless, in comparison to the full mean-square displacement of the end-to-end vector the nonlinear effects remain small at all times—it is in this sense we state that our results demonstrate that the linearized dynamics suffices for dsDNA fragments that are shorter than or comparable to the persistence length. Our results are consistent with those of the wormlike chain (WLC) model, the commonly used descriptive tool of semiflexible polymers.

Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases.

PubMed

Okamoto, Kenichi W; Gould, Fred; Lloyd, Alun L

2016-03-01

Many vector-borne diseases lack effective vaccines and medications, and the limitations of traditional vector control have inspired novel approaches based on using genetic engineering to manipulate vector populations and thereby reduce transmission. Yet both the short- and long-term epidemiological effects of these transgenic strategies are highly uncertain. If neither vaccines, medications, nor transgenic strategies can by themselves suffice for managing vector-borne diseases, integrating these approaches becomes key. Here we develop a framework to evaluate how clinical interventions (i.e., vaccination and medication) can be integrated with transgenic vector manipulation strategies to prevent disease invasion and reduce disease incidence. We show that the ability of clinical interventions to accelerate disease suppression can depend on the nature of the transgenic manipulation deployed (e.g., whether vector population reduction or replacement is attempted). We find that making a specific, individual strategy highly effective may not be necessary for attaining public-health objectives, provided suitable combinations can be adopted. However, we show how combining only partially effective antimicrobial drugs or vaccination with transgenic vector manipulations that merely temporarily lower vector competence can amplify disease resurgence following transient suppression. Thus, transgenic vector manipulation that cannot be sustained can have adverse consequences-consequences which ineffective clinical interventions can at best only mitigate, and at worst temporarily exacerbate. This result, which arises from differences between the time scale on which the interventions affect disease dynamics and the time scale of host population dynamics, highlights the importance of accounting for the potential delay in the effects of deploying public health strategies on long-term disease incidence. We find that for systems at the disease-endemic equilibrium, even modest perturbations induced by weak interventions can exhibit strong, albeit transient, epidemiological effects. This, together with our finding that under some conditions combining strategies could have transient adverse epidemiological effects suggests that a relatively long time horizon may be necessary to discern the efficacy of alternative intervention strategies.

Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases

PubMed Central

Okamoto, Kenichi W.; Gould, Fred; Lloyd, Alun L.

2016-01-01

Many vector-borne diseases lack effective vaccines and medications, and the limitations of traditional vector control have inspired novel approaches based on using genetic engineering to manipulate vector populations and thereby reduce transmission. Yet both the short- and long-term epidemiological effects of these transgenic strategies are highly uncertain. If neither vaccines, medications, nor transgenic strategies can by themselves suffice for managing vector-borne diseases, integrating these approaches becomes key. Here we develop a framework to evaluate how clinical interventions (i.e., vaccination and medication) can be integrated with transgenic vector manipulation strategies to prevent disease invasion and reduce disease incidence. We show that the ability of clinical interventions to accelerate disease suppression can depend on the nature of the transgenic manipulation deployed (e.g., whether vector population reduction or replacement is attempted). We find that making a specific, individual strategy highly effective may not be necessary for attaining public-health objectives, provided suitable combinations can be adopted. However, we show how combining only partially effective antimicrobial drugs or vaccination with transgenic vector manipulations that merely temporarily lower vector competence can amplify disease resurgence following transient suppression. Thus, transgenic vector manipulation that cannot be sustained can have adverse consequences—consequences which ineffective clinical interventions can at best only mitigate, and at worst temporarily exacerbate. This result, which arises from differences between the time scale on which the interventions affect disease dynamics and the time scale of host population dynamics, highlights the importance of accounting for the potential delay in the effects of deploying public health strategies on long-term disease incidence. We find that for systems at the disease-endemic equilibrium, even modest perturbations induced by weak interventions can exhibit strong, albeit transient, epidemiological effects. This, together with our finding that under some conditions combining strategies could have transient adverse epidemiological effects suggests that a relatively long time horizon may be necessary to discern the efficacy of alternative intervention strategies. PMID:26962871

Influence of vectors' risk-spreading strategies and environmental stochasticity on the epidemiology and evolution of vector-borne diseases: the example of Chagas' disease.

PubMed

Pelosse, Perrine; Kribs-Zaleta, Christopher M; Ginoux, Marine; Rabinovich, Jorge E; Gourbière, Sébastien; Menu, Frédéric

2013-01-01

Insects are known to display strategies that spread the risk of encountering unfavorable conditions, thereby decreasing the extinction probability of genetic lineages in unpredictable environments. To what extent these strategies influence the epidemiology and evolution of vector-borne diseases in stochastic environments is largely unknown. In triatomines, the vectors of the parasite Trypanosoma cruzi, the etiological agent of Chagas' disease, juvenile development time varies between individuals and such variation most likely decreases the extinction risk of vector populations in stochastic environments. We developed a simplified multi-stage vector-borne SI epidemiological model to investigate how vector risk-spreading strategies and environmental stochasticity influence the prevalence and evolution of a parasite. This model is based on available knowledge on triatomine biodemography, but its conceptual outcomes apply, to a certain extent, to other vector-borne diseases. Model comparisons between deterministic and stochastic settings led to the conclusion that environmental stochasticity, vector risk-spreading strategies (in particular an increase in the length and variability of development time) and their interaction have drastic consequences on vector population dynamics, disease prevalence, and the relative short-term evolution of parasite virulence. Our work shows that stochastic environments and associated risk-spreading strategies can increase the prevalence of vector-borne diseases and favor the invasion of more virulent parasite strains on relatively short evolutionary timescales. This study raises new questions and challenges in a context of increasingly unpredictable environmental variations as a result of global climate change and human interventions such as habitat destruction or vector control.

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

Comparative field efficacy of newly developed formulations of larvicides against Aedes aegypti (L.) (Diptera: Culicidae).

PubMed

Thavara, Usavadee; Tawatsin, Apiwat; Chompoosri, Jakkrawarn; Bhakdeenuan, Payu; Khamsawads, Chayada; Sangkitporn, Somchai; Siriyasatien, Padet; Asavadachanukorn, Preecha; Boonmuen, Saibua; Mulla, Mir S

2013-09-01

Aedes aegypti (L.) is known as vector of dengue and chikungunya fever. Larvicides are used to control this vector. We evaluated the efficacy of newly developed formulations of larvicides to control Ae. aegypti under field conditions for 24 weeks post single application. Mosdop P and Mosdop TB containing diflubenzuron (2% and 40 mg/tablet, respectively) as the active ingredient, were applied at a dosage of 0.1 mg a.i./1 and Mosquit TB10, Mosquit TB100 and Temecal containing temephos (1%, 10% and 1%, respectively) as the active ingredient were applied at a dosage of 1 mg active ingredent (a.i.) to 200 liter water storage jars. Two water regimens were used in the jars: in one regimen the jar was kept full of water all the time and in the other regimen a full jar had half the volume removed and refilled weekly. The larvicidal efficacy was reported as the level of inhibition of emergence (IE%) calculated based on the pupal skins in the jars versus the original number of larvae added. Mosdop P, Mosdop TB, Mosquit TB10, Mosquit TB100 and Temecal showed complete larvicidal efficacy (100% IE) in the constantly full jars for 16, 17, 14, 20 and 13 weeks posttreatment, respectively; in the jars where half the volum of water was replaced weekly, the larvicides had complete larvicidal efficacy (100% IE) for 19, 20, 17, 24 and 15 weeks post-treatment, respectively. The five larvicide regimens evaluated in this study are effective for controlling Ae. aegypti larvae.

ML 3.1 developer's guide.

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

Sala, Marzio; Hu, Jonathan Joseph; Tuminaro, Raymond Stephen

2004-05-01

ML development was started in 1997 by Ray Tuminaro and Charles Tong. Currently, there are several full- and part-time developers. The kernel of ML is written in ANSI C, and there is a rich C++ interface for Trilinos users and developers. ML can be customized to run geometric and algebraic multigrid; it can solve a scalar or a vector equation (with constant number of equations per grid node), and it can solve a form of Maxwell's equations. For a general introduction to ML and its applications, we refer to the Users Guide [SHT04], and to the ML web site, http://software.sandia.gov/ml.

Small Sample Properties of Bayesian Multivariate Autoregressive Time Series Models

ERIC Educational Resources Information Center

Price, Larry R.

2012-01-01

The aim of this study was to compare the small sample (N = 1, 3, 5, 10, 15) performance of a Bayesian multivariate vector autoregressive (BVAR-SEM) time series model relative to frequentist power and parameter estimation bias. A multivariate autoregressive model was developed based on correlated autoregressive time series vectors of varying…

Limits on the Efficiency of Event-Based Algorithms for Monte Carlo Neutron Transport

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

Romano, Paul K.; Siegel, Andrew R.

The traditional form of parallelism in Monte Carlo particle transport simulations, wherein each individual particle history is considered a unit of work, does not lend itself well to data-level parallelism. Event-based algorithms, which were originally used for simulations on vector processors, may offer a path toward better utilizing data-level parallelism in modern computer architectures. In this study, a simple model is developed for estimating the efficiency of the event-based particle transport algorithm under two sets of assumptions. Data collected from simulations of four reactor problems using OpenMC was then used in conjunction with the models to calculate the speedup duemore » to vectorization as a function of two parameters: the size of the particle bank and the vector width. When each event type is assumed to have constant execution time, the achievable speedup is directly related to the particle bank size. We observed that the bank size generally needs to be at least 20 times greater than vector size in order to achieve vector efficiency greater than 90%. When the execution times for events are allowed to vary, however, the vector speedup is also limited by differences in execution time for events being carried out in a single event-iteration. For some problems, this implies that vector effciencies over 50% may not be attainable. While there are many factors impacting performance of an event-based algorithm that are not captured by our model, it nevertheless provides insights into factors that may be limiting in a real implementation.« less

Method for network analyzation and apparatus

DOEpatents

Bracht, Roger B.; Pasquale, Regina V.

2001-01-01

A portable network analyzer and method having multiple channel transmit and receive capability for real-time monitoring of processes which maintains phase integrity, requires low power, is adapted to provide full vector analysis, provides output frequencies of up to 62.5 MHz and provides fine sensitivity frequency resolution. The present invention includes a multi-channel means for transmitting and a multi-channel means for receiving, both in electrical communication with a software means for controlling. The means for controlling is programmed to provide a signal to a system under investigation which steps consecutively over a range of predetermined frequencies. The resulting received signal from the system provides complete time domain response information by executing a frequency transform of the magnitude and phase information acquired at each frequency step.

A comparative study of surface EMG classification by fuzzy relevance vector machine and fuzzy support vector machine.

PubMed

Xie, Hong-Bo; Huang, Hu; Wu, Jianhua; Liu, Lei

2015-02-01

We present a multiclass fuzzy relevance vector machine (FRVM) learning mechanism and evaluate its performance to classify multiple hand motions using surface electromyographic (sEMG) signals. The relevance vector machine (RVM) is a sparse Bayesian kernel method which avoids some limitations of the support vector machine (SVM). However, RVM still suffers the difficulty of possible unclassifiable regions in multiclass problems. We propose two fuzzy membership function-based FRVM algorithms to solve such problems, based on experiments conducted on seven healthy subjects and two amputees with six hand motions. Two feature sets, namely, AR model coefficients and room mean square value (AR-RMS), and wavelet transform (WT) features, are extracted from the recorded sEMG signals. Fuzzy support vector machine (FSVM) analysis was also conducted for wide comparison in terms of accuracy, sparsity, training and testing time, as well as the effect of training sample sizes. FRVM yielded comparable classification accuracy with dramatically fewer support vectors in comparison with FSVM. Furthermore, the processing delay of FRVM was much less than that of FSVM, whilst training time of FSVM much faster than FRVM. The results indicate that FRVM classifier trained using sufficient samples can achieve comparable generalization capability as FSVM with significant sparsity in multi-channel sEMG classification, which is more suitable for sEMG-based real-time control applications.

Double-stranded RNA innate immune response activation from long-term adeno-associated virus vector transduction.

PubMed

Shao, Wenwei; Earley, Lauriel F; Chai, Zheng; Chen, Xiaojing; Sun, Junjiang; He, Ting; Deng, Meng; Hirsch, Matthew L; Ting, Jenny; Samulski, R Jude; Li, Chengwen

2018-06-21

Data from clinical trials for hemophilia B using adeno-associated virus (AAV) vectors have demonstrated decreased transgenic coagulation factor IX (hFIX) expression 6-10 weeks after administration of a high vector dose. While it is likely that capsid-specific cytotoxic T lymphocytes eliminate vector-transduced hepatocytes, thereby resulting in decreased hFIX, this observation is not intuitively consistent with restored hFIX levels following prednisone application. Although the innate immune response is immediately activated following AAV vector infection via TLR pathways, no studies exist regarding the role of the innate immune response at later time points after AAV vector transduction. Herein, activation of the innate immune response in cell lines, primary human hepatocytes, and hepatocytes in a human chimeric mouse model was observed at later time points following AAV vector transduction. Mechanistic analysis demonstrated that the double-stranded RNA (dsRNA) sensor MDA5 was necessary for innate immune response activation and that transient knockdown of MDA5, or MAVS, decreased IFN-β expression while increasing transgene production in AAV-transduced cells. These results both highlight the role of the dsRNA-triggered innate immune response in therapeutic transgene expression at later time points following AAV transduction and facilitate the execution of effective strategies to block the dsRNA innate immune response in future clinical trials.

The parallel-antiparallel signal difference in double-wave-vector diffusion-weighted MR at short mixing times: A phase evolution perspective

NASA Astrophysics Data System (ADS)

Finsterbusch, Jürgen

2011-01-01

Experiments with two diffusion weightings applied in direct succession in a single acquisition, so-called double- or two-wave-vector diffusion-weighting (DWV) experiments at short mixing times, have been shown to be a promising tool to estimate cell or compartment sizes, e.g. in living tissue. The basic theory for such experiments predicts that the signal decays for parallel and antiparallel wave vector orientations differ by a factor of three for small wave vectors. This seems to be surprising because in standard, single-wave-vector experiments the polarity of the diffusion weighting has no influence on the signal attenuation. Thus, the question how this difference can be understood more pictorially is often raised. In this rather educational manuscript, the phase evolution during a DWV experiment for simple geometries, e.g. diffusion between parallel, impermeable planes oriented perpendicular to the wave vectors, is considered step-by-step and demonstrates how the signal difference develops. Considering the populations of the phase distributions obtained, the factor of three between the signal decays which is predicted by the theory can be reproduced. Furthermore, the intermediate signal decay for orthogonal wave vector orientations can be derived when investigating diffusion in a box. Thus, the presented “phase gymnastics” approach may help to understand the signal modulation observed in DWV experiments at short mixing times.

Reconstruction of fetal vector electrocardiogram from maternal abdominal signals under fetus body rotations.

PubMed

Nabeshima, Yuji; Kimura, Yoshitaka; Ito, Takuro; Ohwada, Kazunari; Karashima, Akihiro; Katayama, Norihiro; Nakao, Mitsuyuki

2013-01-01

Fetal electrocardiogram (fECG) and its vector form (fVECG) could provide significant clinical information concerning physiological conditions of a fetus. So far various independent component analysis (ICA)-based methods for extracting fECG from maternal abdominal signals have been proposed. Because full extraction of component waves such as P, Q, R, S, and T, is difficult to be realized under noisy and nonstationary situations, the fVECG is further hard to be reconstructed, where different projections of the fetal heart vector are required. In order to reconstruct fVECG, we proposed a novel method for synthesizing different projections of the heart vector, making good use of the fetus movement. This method consists of ICA, estimation of rotation angles of fetus, and synthesis of projections of the heart vector. Through applications to the synthetic and actual data, our method is shown to precisely estimate rotation angle of the fetus and to successfully reconstruct the fVECG.

A Self-Organizing Map-Based Approach to Generating Reduced-Size, Statistically Similar Climate Datasets

NASA Astrophysics Data System (ADS)

Cabell, R.; Delle Monache, L.; Alessandrini, S.; Rodriguez, L.

2015-12-01

Climate-based studies require large amounts of data in order to produce accurate and reliable results. Many of these studies have used 30-plus year data sets in order to produce stable and high-quality results, and as a result, many such data sets are available, generally in the form of global reanalyses. While the analysis of these data lead to high-fidelity results, its processing can be very computationally expensive. This computational burden prevents the utilization of these data sets for certain applications, e.g., when rapid response is needed in crisis management and disaster planning scenarios resulting from release of toxic material in the atmosphere. We have developed a methodology to reduce large climate datasets to more manageable sizes while retaining statistically similar results when used to produce ensembles of possible outcomes. We do this by employing a Self-Organizing Map (SOM) algorithm to analyze general patterns of meteorological fields over a regional domain of interest to produce a small set of "typical days" with which to generate the model ensemble. The SOM algorithm takes as input a set of vectors and generates a 2D map of representative vectors deemed most similar to the input set and to each other. Input predictors are selected that are correlated with the model output, which in our case is an Atmospheric Transport and Dispersion (T&D) model that is highly dependent on surface winds and boundary layer depth. To choose a subset of "typical days," each input day is assigned to its closest SOM map node vector and then ranked by distance. Each node vector is treated as a distribution and days are sampled from them by percentile. Using a 30-node SOM, with sampling every 20th percentile, we have been able to reduce 30 years of the Climate Forecast System Reanalysis (CFSR) data for the month of October to 150 "typical days." To estimate the skill of this approach, the "Measure of Effectiveness" (MOE) metric is used to compare area and overlap of statistical exceedance between the reduced data set and the full 30-year CFSR dataset. Using the MOE, we find that our SOM-derived climate subset produces statistics that fall within 85-90% overlap with the full set while using only 15% of the total data length, and consequently, 15% of the computational time required to run the T&D model for the full period.

Quantum and electromagnetic propagation with the conjugate symmetric Lanczos method.

PubMed

Acevedo, Ramiro; Lombardini, Richard; Turner, Matthew A; Kinsey, James L; Johnson, Bruce R

2008-02-14

The conjugate symmetric Lanczos (CSL) method is introduced for the solution of the time-dependent Schrodinger equation. This remarkably simple and efficient time-domain algorithm is a low-order polynomial expansion of the quantum propagator for time-independent Hamiltonians and derives from the time-reversal symmetry of the Schrodinger equation. The CSL algorithm gives forward solutions by simply complex conjugating backward polynomial expansion coefficients. Interestingly, the expansion coefficients are the same for each uniform time step, a fact that is only spoiled by basis incompleteness and finite precision. This is true for the Krylov basis and, with further investigation, is also found to be true for the Lanczos basis, important for efficient orthogonal projection-based algorithms. The CSL method errors roughly track those of the short iterative Lanczos method while requiring fewer matrix-vector products than the Chebyshev method. With the CSL method, only a few vectors need to be stored at a time, there is no need to estimate the Hamiltonian spectral range, and only matrix-vector and vector-vector products are required. Applications using localized wavelet bases are made to harmonic oscillator and anharmonic Morse oscillator systems as well as electrodynamic pulse propagation using the Hamiltonian form of Maxwell's equations. For gold with a Drude dielectric function, the latter is non-Hermitian, requiring consideration of corrections to the CSL algorithm.

A Search for Vector Magnetic Field Variations Associated with the M-Class Flares of 1991 June 10 in AR 6659

NASA Technical Reports Server (NTRS)

Hagyard, Mona J.; Stark, B. A.; Venkatakrishnan, P.

1998-01-01

A careful analysis of a 6-hour time sequence of vector magnetograms of AR 6659, observed on 1991 June 10 with the MSFC vector magnetograph, has revealed only minor changes in the vector magnetic field azimuths in the vicinity of two M-class flares, and the association of these changes with the flares is not unambiguous. In this paper we present our analysis of the data which includes comparison of vector magnetograms prior to and during the flares, calculation of distributions of the rms variation of the azimuth at each pixel in the field of view of the active region, and examination of the variation with time of the azimuths at every pixel covered by the main flare emissions as observed with the H-alpha telescope coaligned with the vector magnetograph. We also present results of an analysis of evolutionary changes in the azimuth over the field of view of the active region.

A Study on Aircraft Engine Control Systems for Integrated Flight and Propulsion Control

NASA Astrophysics Data System (ADS)

Yamane, Hideaki; Matsunaga, Yasushi; Kusakawa, Takeshi; Yasui, Hisako

The Integrated Flight and Propulsion Control (IFPC) for a highly maneuverable aircraft and a fighter-class engine with pitch/yaw thrust vectoring is described. Of the two IFPC functions the aircraft maneuver control utilizes the thrust vectoring based on aerodynamic control surfaces/thrust vectoring control allocation specified by the Integrated Control Unit (ICU) of a FADEC (Full Authority Digital Electronic Control) system. On the other hand in the Performance Seeking Control (PSC) the ICU identifies engine's various characteristic changes, optimizes manipulated variables and finally adjusts engine control parameters in cooperation with the Engine Control Unit (ECU). It is shown by hardware-in-the-loop simulation that the thrust vectoring can enhance aircraft maneuverability/agility and that the PSC can improve engine performance parameters such as SFC (specific fuel consumption), thrust and gas temperature.

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

PubMed Central

Deng, Shunzhou; Martin, Carly; Patil, Rasika; Zhu, Felix; Zhao, Bin; Xiang, Zuoshuang; He, Yongqun

2015-01-01

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development. PMID:26403370

A Parallel Framework with Block Matrices of a Discrete Fourier Transform for Vector-Valued Discrete-Time Signals.

PubMed

Soto-Quiros, Pablo

2015-01-01

This paper presents a parallel implementation of a kind of discrete Fourier transform (DFT): the vector-valued DFT. The vector-valued DFT is a novel tool to analyze the spectra of vector-valued discrete-time signals. This parallel implementation is developed in terms of a mathematical framework with a set of block matrix operations. These block matrix operations contribute to analysis, design, and implementation of parallel algorithms in multicore processors. In this work, an implementation and experimental investigation of the mathematical framework are performed using MATLAB with the Parallel Computing Toolbox. We found that there is advantage to use multicore processors and a parallel computing environment to minimize the high execution time. Additionally, speedup increases when the number of logical processors and length of the signal increase.

Understanding the effect of vector dynamics in epidemic models using center manifold analysis

NASA Astrophysics Data System (ADS)

Rocha, Filipe; Aguiar, Maíra; Souza, Max; Stollenwerk, Nico

2012-09-01

In vector borne diseases the human hosts' epidemiology often acts on a much slower time scales than the one of the mosquitos which transmit the disease as a vector from human to human, due to their vastly different life cycles. We investigate in a model with susceptible (S), infected (I) and recovered (R) humans and susceptible (U) and infected (V) mosquitoes in how far the fast time scale of the mosquito epidemiology can be slaved by the slower human epidemiology, so that for the understanding of human disease data mainly the dynamics of the human time scale is essential and only slightly perturbed by the mosquito dynamics. This analysis of the SIRUV model is qualitatively in agreement with a previously investigated simpler SISUV model, hence a feature of vector-borne diseases in general.

Influence of Vectors’ Risk-Spreading Strategies and Environmental Stochasticity on the Epidemiology and Evolution of Vector-Borne Diseases: The Example of Chagas’ Disease

PubMed Central

Pelosse, Perrine; Kribs-Zaleta, Christopher M.; Ginoux, Marine; Rabinovich, Jorge E.; Gourbière, Sébastien; Menu, Frédéric

2013-01-01

Insects are known to display strategies that spread the risk of encountering unfavorable conditions, thereby decreasing the extinction probability of genetic lineages in unpredictable environments. To what extent these strategies influence the epidemiology and evolution of vector-borne diseases in stochastic environments is largely unknown. In triatomines, the vectors of the parasite Trypanosoma cruzi, the etiological agent of Chagas’ disease, juvenile development time varies between individuals and such variation most likely decreases the extinction risk of vector populations in stochastic environments. We developed a simplified multi-stage vector-borne SI epidemiological model to investigate how vector risk-spreading strategies and environmental stochasticity influence the prevalence and evolution of a parasite. This model is based on available knowledge on triatomine biodemography, but its conceptual outcomes apply, to a certain extent, to other vector-borne diseases. Model comparisons between deterministic and stochastic settings led to the conclusion that environmental stochasticity, vector risk-spreading strategies (in particular an increase in the length and variability of development time) and their interaction have drastic consequences on vector population dynamics, disease prevalence, and the relative short-term evolution of parasite virulence. Our work shows that stochastic environments and associated risk-spreading strategies can increase the prevalence of vector-borne diseases and favor the invasion of more virulent parasite strains on relatively short evolutionary timescales. This study raises new questions and challenges in a context of increasingly unpredictable environmental variations as a result of global climate change and human interventions such as habitat destruction or vector control. PMID:23951018

Inhalation of Nebulized Perfluorochemical Enhances Recombinant Adenovirus and Adeno-Associated Virus-Mediated Gene Expression in Lung Epithelium

PubMed Central

Beckett, Travis; Bonneau, Laura; Howard, Alan; Blanchard, James; Borda, Juan; Weiner, Daniel J.; Wang, Lili; Gao, Guang Ping; Kolls, Jay K.; Bohm, Rudolf; Liggitt, Denny

2012-01-01

Abstract Use of perfluorochemical liquids during intratracheal vector administration enhances recombinant adenovirus and adeno-associated virus (AAV)-mediated lung epithelial gene expression. We hypothesized that inhalation of nebulized perfluorochemical vapor would also enhance epithelial gene expression after subsequent intratracheal vector administration. Freely breathing adult C57BL/6 mice were exposed for selected times to nebulized perflubron or sterile saline in a sealed Plexiglas chamber. Recombinant adenoviral vector was administered by transtracheal puncture at selected times afterward and mice were killed 3 days after vector administration to assess transgene expression. Mice tolerated the nebulized perflubron without obvious ill effects. Vector administration 6 hr after nebulized perflubron exposure resulted in an average 540% increase in gene expression in airway and alveolar epithelium, compared with that with vector alone or saline plus vector control (p<0.05). However, vector administration 1 hr, 1 day, or 3 days after perflubron exposure was not different from either nebulized saline with vector or vector alone and a 60-min exposure to nebulized perflubron is required. In parallel pilot studies in macaques, inhalation of nebulized perflubron enhanced recombinant AAV2/5 vector expression throughout the lung. Serial chest radiographs, bronchoalveolar lavages, and results of complete blood counts and serum biochemistries demonstrated no obvious adverse effects of nebulized perflubron. Further, one macaque receiving nebulized perflubron only was monitored for 1 year with no obvious adverse effects of exposure. These results demonstrate that inhalation of nebulized perflubron, a simple, clinically more feasible technique than intratracheal administration of liquid perflubron, safely enhances lung gene expression. PMID:22568624

Biosensor method and system based on feature vector extraction

DOEpatents

Greenbaum, Elias; Rodriguez, Jr., Miguel; Qi, Hairong; Wang, Xiaoling

2013-07-02

A system for biosensor-based detection of toxins includes providing at least one time-dependent control signal generated by a biosensor in a gas or liquid medium, and obtaining a time-dependent biosensor signal from the biosensor in the gas or liquid medium to be monitored or analyzed for the presence of one or more toxins selected from chemical, biological or radiological agents. The time-dependent biosensor signal is processed to obtain a plurality of feature vectors using at least one of amplitude statistics and a time-frequency analysis. At least one parameter relating to toxicity of the gas or liquid medium is then determined from the feature vectors based on reference to the control signal.

Large-scale Clinical-grade Retroviral Vector Production in a Fixed-Bed Bioreactor

PubMed Central

Wang, Xiuyan; Olszewska, Malgorzata; Qu, Jinrong; Wasielewska, Teresa; Bartido, Shirley; Hermetet, Gregory; Sadelain, Michel

2015-01-01

The successful genetic engineering of patient T cells with γ-retroviral vectors expressing chimeric antigen receptors or T-cell receptors for phase II clinical trials and beyond requires the large-scale manufacture of high-titer vector stocks. The production of retroviral vectors from stable packaging cell lines using roller bottles or 10- to 40-layer cell factories is limited by a narrow harvest window, labor intensity, open-system operations, and the requirement for significant incubator space. To circumvent these shortcomings, we optimized the production of vector stocks in a disposable fixed-bed bioreactor using good manufacturing practice–grade packaging cell lines. High-titer vector stocks were harvested over 10 days, representing a much broader harvest window than the 3-day harvest afforded by cell factories. For PG13 and 293Vec packaging cells, the average vector titer and the vector stocks’ yield in the bioreactor were higher by 3.2- to 7.3-fold, and 5.6- to 13.1-fold, respectively, than those obtained in cell factories. The vector production was 10.4 and 18.6 times more efficient than in cell factories for PG13 and 293Vec cells, respectively. Furthermore, the vectors produced from the fixed-bed bioreactors passed the release test assays for clinical applications. Therefore, a single vector lot derived from 293Vec is suitable to transduce up to 500 patients cell doses in the context of large clinical trials using chimeric antigen receptors or T-cell receptors. These findings demonstrate for the first time that a robust fixed-bed bioreactor process can be used to produce γ-retroviral vector stocks scalable up to the commercialization phase. PMID:25751502

Chaos and Forecasting - Proceedings of the Royal Society Discussion Meeting

NASA Astrophysics Data System (ADS)

Tong, Howell

1995-04-01

The Table of Contents for the full book PDF is as follows: * Preface * Orthogonal Projection, Embedding Dimension and Sample Size in Chaotic Time Series from a Statistical Perspective * A Theory of Correlation Dimension for Stationary Time Series * On Prediction and Chaos in Stochastic Systems * Locally Optimized Prediction of Nonlinear Systems: Stochastic and Deterministic * A Poisson Distribution for the BDS Test Statistic for Independence in a Time Series * Chaos and Nonlinear Forecastability in Economics and Finance * Paradigm Change in Prediction * Predicting Nonuniform Chaotic Attractors in an Enzyme Reaction * Chaos in Geophysical Fluids * Chaotic Modulation of the Solar Cycle * Fractal Nature in Earthquake Phenomena and its Simple Models * Singular Vectors and the Predictability of Weather and Climate * Prediction as a Criterion for Classifying Natural Time Series * Measuring and Characterising Spatial Patterns, Dynamics and Chaos in Spatially-Extended Dynamical Systems and Ecologies * Non-Linear Forecasting and Chaos in Ecology and Epidemiology: Measles as a Case Study

A novel salt-inducible gene SbSI-1 from Salicornia brachiata confers salt and desiccation tolerance in E. coli.

PubMed

Yadav, Narendra Singh; Rashmi, Deo; Singh, Dinkar; Agarwal, Pradeep K; Jha, Bhavanath

2012-02-01

Salicornia brachiata is one of the extreme salt tolerant plants and grows luxuriantly in coastal areas. Previously we have reported isolation and characterization of ESTs from S. brachiata with large number of unknown gene sequences. Reverse Northern analysis showed upregulation and downregulation of few unknown genes in response to salinity. Some of these unknown genes were made full length and their functional analysis is being tested. In this study, we have selected a novel unknown salt inducible gene SbSI-1 (Salicornia brachiata salt inducible-1) for the functional validation. The SbSI-1 (Gen-Bank accession number JF 965339) was made full length and characterized in detail for its functional validation under desiccation and salinity. The SbSI-1 gene is 917 bp long, and contained 437 bp 3' UTR, and 480 bp ORF region encoding 159 amino acids protein with estimated molecular mass of 18.39 kDa and pI 8.58. The real time PCR analysis revealed high transcript expression in salt, desiccation, cold and heat stresses. However, the maximum expression was obtained by desiccation. The ORF region of SbSI-1 was cloned in pET28a vector and transformed in BL21 (DE3) E. coli cells. The SbSI-1 recombinant E. coli cells showed tolerance to desiccation and salinity stress compared to only vector in the presence of stress.

Magnetic Rotational Spectroscopy with Nanorods to Probe Time-Dependent Rheology of Microdroplets (Postprint)

DTIC Science & Technology

2012-05-10

this angle depends linearly on time, α = 2πf t, where f is the frequency of the rotating magnetic field. We assume that the magnetization vector M is... vector B (Figure 1). In order to derive an equation governing the nanorod rotation, it is convenient to count its revolutions with respect to the fixed... vector directed perpendicularly to the plane of the nanorod rotation.27,28 Substituting the definition of angle φ(t) through the angles α(t) and θ(t

Aspects of mutually unbiased bases in odd-prime-power dimensions

NASA Astrophysics Data System (ADS)

Chaturvedi, S.

2002-04-01

We rephrase the Wootters-Fields construction [W. K. Wootters and B. C. Fields, Ann. Phys. 191, 363 (1989)] of a full set of mutually unbiased bases in a complex vector space of dimensions N=pr, where p is an odd prime, in terms of the character vectors of the cyclic group G of order p. This form may be useful in explicitly writing down mutually unbiased bases for N=pr.

Time-varying behavior of motion vectors in vection-induced images in relation to autonomic regulation.

PubMed

Kiryu, Tohru; Yamada, Hiroshi; Jimbo, Masahiro; Bando, Takehiko

2004-01-01

Virtual reality (VR) is a promising technology in biomedical engineering, but at the same time enlarges another problem called cybersickness. Aiming at suppression of cybersicknes, we are investigating the influences of vection-induced images on the autonomic regulation quantitatively. We used the motion vectors to quantify image scenes and measured electrocardiogram, blood pressure, and respiration for evaluating the autonomic regulation. Using the estimated motion vectors, we further synthesized random-dot pattern images to survey which component of the global motion vectors seriously affected the autonomic regulation. The results showed that the zoom component with a specific frequency band (0.1-3.0 Hz) would induce sickness.

Euclidean supergravity

NASA Astrophysics Data System (ADS)

de Wit, Bernard; Reys, Valentin

2017-12-01

Supergravity with eight supercharges in a four-dimensional Euclidean space is constructed at the full non-linear level by performing an off-shell time-like reduction of five-dimensional supergravity. The resulting four-dimensional theory is realized off-shell with the Weyl, vector and tensor supermultiplets and a corresponding multiplet calculus. Hypermultiplets are included as well, but they are themselves only realized with on-shell supersymmetry. We also briefly discuss the non-linear supermultiplet. The off-shell reduction leads to a full understanding of the Euclidean theory. A complete multiplet calculus is presented along the lines of the Minkowskian theory. Unlike in Minkowski space, chiral and anti-chiral multiplets are real and supersymmetric actions are generally unbounded from below. Precisely as in the Minkowski case, where one has different formulations of Poincaré supergravity upon introducing different compensating supermultiplets, one can also obtain different versions of Euclidean supergravity.

Bayesian data assimilation provides rapid decision support for vector-borne diseases.

PubMed

Jewell, Chris P; Brown, Richard G

2015-07-06

Predicting the spread of vector-borne diseases in response to incursions requires knowledge of both host and vector demographics in advance of an outbreak. Although host population data are typically available, for novel disease introductions there is a high chance of the pathogen using a vector for which data are unavailable. This presents a barrier to estimating the parameters of dynamical models representing host-vector-pathogen interaction, and hence limits their ability to provide quantitative risk forecasts. The Theileria orientalis (Ikeda) outbreak in New Zealand cattle demonstrates this problem: even though the vector has received extensive laboratory study, a high degree of uncertainty persists over its national demographic distribution. Addressing this, we develop a Bayesian data assimilation approach whereby indirect observations of vector activity inform a seasonal spatio-temporal risk surface within a stochastic epidemic model. We provide quantitative predictions for the future spread of the epidemic, quantifying uncertainty in the model parameters, case infection times and the disease status of undetected infections. Importantly, we demonstrate how our model learns sequentially as the epidemic unfolds and provide evidence for changing epidemic dynamics through time. Our approach therefore provides a significant advance in rapid decision support for novel vector-borne disease outbreaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Full Angular Profile of the Coherent Polarization Opposition Effect

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Luck, Jean-Marc; Nieuwenhuizen, Theo M.

1999-01-01

We use the rigorous vector theory of weak photon localization for a semi-infinite medium composed of nonabsorbing Rayleigh scatterers to compute the full angular profile of the polarization opposition effect. The latter is caused by coherent backscattering of unpolarized incident light and accompanies the renowned backscattering intensity peak.

Evaluation of the impacts of climate change on disease vectors through ecological niche modelling.

PubMed

Carvalho, B M; Rangel, E F; Vale, M M

2017-08-01

Vector-borne diseases are exceptionally sensitive to climate change. Predicting vector occurrence in specific regions is a challenge that disease control programs must meet in order to plan and execute control interventions and climate change adaptation measures. Recently, an increasing number of scientific articles have applied ecological niche modelling (ENM) to study medically important insects and ticks. With a myriad of available methods, it is challenging to interpret their results. Here we review the future projections of disease vectors produced by ENM, and assess their trends and limitations. Tropical regions are currently occupied by many vector species; but future projections indicate poleward expansions of suitable climates for their occurrence and, therefore, entomological surveillance must be continuously done in areas projected to become suitable. The most commonly applied methods were the maximum entropy algorithm, generalized linear models, the genetic algorithm for rule set prediction, and discriminant analysis. Lack of consideration of the full-known current distribution of the target species on models with future projections has led to questionable predictions. We conclude that there is no ideal 'gold standard' method to model vector distributions; researchers are encouraged to test different methods for the same data. Such practice is becoming common in the field of ENM, but still lags behind in studies of disease vectors.

An algorithm for fast elastic wave simulation using a vectorized finite difference operator

NASA Astrophysics Data System (ADS)

Malkoti, Ajay; Vedanti, Nimisha; Tiwari, Ram Krishna

2018-07-01

Modern geophysical imaging techniques exploit the full wavefield information which can be simulated numerically. These numerical simulations are computationally expensive due to several factors, such as a large number of time steps and nodes, big size of the derivative stencil and huge model size. Besides these constraints, it is also important to reformulate the numerical derivative operator for improved efficiency. In this paper, we have introduced a vectorized derivative operator over the staggered grid with shifted coordinate systems. The operator increases the efficiency of simulation by exploiting the fact that each variable can be represented in the form of a matrix. This operator allows updating all nodes of a variable defined on the staggered grid, in a manner similar to the collocated grid scheme and thereby reducing the computational run-time considerably. Here we demonstrate an application of this operator to simulate the seismic wave propagation in elastic media (Marmousi model), by discretizing the equations on a staggered grid. We have compared the performance of this operator on three programming languages, which reveals that it can increase the execution speed by a factor of at least 2-3 times for FORTRAN and MATLAB; and nearly 100 times for Python. We have further carried out various tests in MATLAB to analyze the effect of model size and the number of time steps on total simulation run-time. We find that there is an additional, though small, computational overhead for each step and it depends on total number of time steps used in the simulation. A MATLAB code package, 'FDwave', for the proposed simulation scheme is available upon request.

Video data compression using artificial neural network differential vector quantization

NASA Technical Reports Server (NTRS)

Krishnamurthy, Ashok K.; Bibyk, Steven B.; Ahalt, Stanley C.

1991-01-01

An artificial neural network vector quantizer is developed for use in data compression applications such as Digital Video. Differential Vector Quantization is used to preserve edge features, and a new adaptive algorithm, known as Frequency-Sensitive Competitive Learning, is used to develop the vector quantizer codebook. To develop real time performance, a custom Very Large Scale Integration Application Specific Integrated Circuit (VLSI ASIC) is being developed to realize the associative memory functions needed in the vector quantization algorithm. By using vector quantization, the need for Huffman coding can be eliminated, resulting in superior performance against channel bit errors than methods that use variable length codes.

Vector-borne diseases models with residence times - A Lagrangian perspective.

PubMed

Bichara, Derdei; Castillo-Chavez, Carlos

2016-11-01

A multi-patch and multi-group modeling framework describing the dynamics of a class of diseases driven by the interactions between vectors and hosts structured by groups is formulated. Hosts' dispersal is modeled in terms of patch-residence times with the nonlinear dynamics taking into account the effective patch-host size. The residence times basic reproduction number R 0 is computed and shown to depend on the relative environmental risk of infection. The model is robust, that is, the disease free equilibrium is globally asymptotically stable (GAS) if R 0 ≤1 and a unique interior endemic equilibrium is shown to exist that is GAS whenever R 0 >1 whenever the configuration of host-vector interactions is irreducible. The effects of patchiness and groupness, a measure of host-vector heterogeneous structure, on the basic reproduction number R 0 , are explored. Numerical simulations are carried out to highlight the effects of residence times on disease prevalence. Copyright © 2016 Elsevier Inc. All rights reserved.

Full-text automated detection of surgical site infections secondary to neurosurgery in Rennes, France.

PubMed

Campillo-Gimenez, Boris; Garcelon, Nicolas; Jarno, Pascal; Chapplain, Jean Marc; Cuggia, Marc

2013-01-01

The surveillance of Surgical Site Infections (SSI) contributes to the management of risk in French hospitals. Manual identification of infections is costly, time-consuming and limits the promotion of preventive procedures by the dedicated teams. The introduction of alternative methods using automated detection strategies is promising to improve this surveillance. The present study describes an automated detection strategy for SSI in neurosurgery, based on textual analysis of medical reports stored in a clinical data warehouse. The method consists firstly, of enrichment and concept extraction from full-text reports using NOMINDEX, and secondly, text similarity measurement using a vector space model. The text detection was compared to the conventional strategy based on self-declaration and to the automated detection using the diagnosis-related group database. The text-mining approach showed the best detection accuracy, with recall and precision equal to 92% and 40% respectively, and confirmed the interest of reusing full-text medical reports to perform automated detection of SSI.

On sufficient statistics of least-squares superposition of vector sets.

PubMed

Konagurthu, Arun S; Kasarapu, Parthan; Allison, Lloyd; Collier, James H; Lesk, Arthur M

2015-06-01

The problem of superposition of two corresponding vector sets by minimizing their sum-of-squares error under orthogonal transformation is a fundamental task in many areas of science, notably structural molecular biology. This problem can be solved exactly using an algorithm whose time complexity grows linearly with the number of correspondences. This efficient solution has facilitated the widespread use of the superposition task, particularly in studies involving macromolecular structures. This article formally derives a set of sufficient statistics for the least-squares superposition problem. These statistics are additive. This permits a highly efficient (constant time) computation of superpositions (and sufficient statistics) of vector sets that are composed from its constituent vector sets under addition or deletion operation, where the sufficient statistics of the constituent sets are already known (that is, the constituent vector sets have been previously superposed). This results in a drastic improvement in the run time of the methods that commonly superpose vector sets under addition or deletion operations, where previously these operations were carried out ab initio (ignoring the sufficient statistics). We experimentally demonstrate the improvement our work offers in the context of protein structural alignment programs that assemble a reliable structural alignment from well-fitting (substructural) fragment pairs. A C++ library for this task is available online under an open-source license.

Serological and molecular prevalence of canine vector-borne diseases (CVBDs) in Korea.

PubMed

Suh, Guk-Hyun; Ahn, Kyu-Sung; Ahn, Jong-Ho; Kim, Ha-Jung; Leutenegger, Christian; Shin, SungShik

2017-03-16

Previous surveys in dogs from Korea indicated that dogs are exposed to a variety of vector- borne pathogens, but perception for a nation-wide canine vector-borne disease (CVBD) occurrence has been missing. We report here results of both serological and molecular prevalence studies for major CVBDs of dogs from all over the South Korean Peninsula except for Jeju Island. Serological survey of 532 outdoor dogs revealed the highest prevalence for Dirofilaria immitis (25.2%), followed by Anaplasma phagocytophilum (15.6%), Ehrlichia canis (4.7%) whereas Borrelia burgdorferi showed the lowest prevalence (1.1%). The number of serologically positive dogs for any of the four pathogens was 216 (40.6%). Concurrent real-time PCR assay of 440 dogs in the study indicated that DNA of "Candidatus M. haematoparvum", Mycoplasma haemocanis, Babesia gibsoni, A. phagocytophilum, and Hepatozoon canis was identified in 190 (43.2%), 168 (38.2%), 23 (5.2%), 10 (2.3%) and 1 (0.2%) dogs, respectively. DNA of Bartonella spp., Ehrlichia spp., Leishmania spp., Rickettsia spp. and Neorickettsia risticii was not identified. Analysis of questionnaires collected from owners of 440 dogs showed that the number of dogs with heartworm preventive medication was 348 (79.1%) among which dogs still positive to D. immitis infection were 60 (17.2%), probably due to the mean months of heartworm preventive medication being only 6.5. The high prevalence rates of both "Ca. M. haematoparvum" and Mycoplasma haemocanis in dogs from Korea indicate that these organisms may be transmitted by vectors other than Rhipicephalus sanguineus because this tick species has rarely been found in Korea. This is the first nationwide survey for canine haemotropic mycoplasma infections in Korea. This study showed that the risk of exposure to major vector-borne diseases in dogs is quite high throughout all areas of South Korean Peninsula. Since achieving full elimination of many pathogens causing CVBDs from infected animals is often impossible even when they are clinically cured, dogs once exposed to CVBDs can remain as lifetime reservoirs of disease for both other animals and humans in the close vicinity, and should therefore be treated with preventative medications to minimise the risk of pathogen transmission by the competent vectors.

Bayesian data assimilation provides rapid decision support for vector-borne diseases

PubMed Central

Jewell, Chris P.; Brown, Richard G.

2015-01-01

Predicting the spread of vector-borne diseases in response to incursions requires knowledge of both host and vector demographics in advance of an outbreak. Although host population data are typically available, for novel disease introductions there is a high chance of the pathogen using a vector for which data are unavailable. This presents a barrier to estimating the parameters of dynamical models representing host–vector–pathogen interaction, and hence limits their ability to provide quantitative risk forecasts. The Theileria orientalis (Ikeda) outbreak in New Zealand cattle demonstrates this problem: even though the vector has received extensive laboratory study, a high degree of uncertainty persists over its national demographic distribution. Addressing this, we develop a Bayesian data assimilation approach whereby indirect observations of vector activity inform a seasonal spatio-temporal risk surface within a stochastic epidemic model. We provide quantitative predictions for the future spread of the epidemic, quantifying uncertainty in the model parameters, case infection times and the disease status of undetected infections. Importantly, we demonstrate how our model learns sequentially as the epidemic unfolds and provide evidence for changing epidemic dynamics through time. Our approach therefore provides a significant advance in rapid decision support for novel vector-borne disease outbreaks. PMID:26136225

Design Spectrum Analysis in NASTRAN

NASA Technical Reports Server (NTRS)

Butler, T. G.

1984-01-01

The utility of Design Spectrum Analysis is to give a mode by mode characterization of the behavior of a design under a given loading. The theory of design spectrum is discussed after operations are explained. User instructions are taken up here in three parts: Transient Preface, Maximum Envelope Spectrum, and RMS Average Spectrum followed by a Summary Table. A single DMAP ALTER packet will provide for all parts of the design spectrum operations. The starting point for getting a modal break-down of the response to acceleration loading is the Modal Transient rigid format. After eigenvalue extraction, modal vectors need to be isolated in the full set of physical coordinates (P-sized as opposed to the D-sized vectors in RF 12). After integration for transient response the results are scanned over the solution time interval for the peak values and for the times that they occur. A module called SCAN was written to do this job, that organizes these maxima into a diagonal output matrix. The maximum amplifier in each mode is applied to the eigenvector of each mode which then reveals the maximum displacements, stresses, forces and boundary reactions that the structure will experience for a load history, mode by mode. The standard NASTRAN output processors have been modified for this task. It is required that modes be normalized to mass.

A Multi-Index Integrated Change detection method for updating the National Land Cover Database

USGS Publications Warehouse

Jin, Suming; Yang, Limin; Xian, George Z.; Danielson, Patrick; Homer, Collin G.

2010-01-01

Land cover change is typically captured by comparing two or more dates of imagery and associating spectral change with true thematic change. A new change detection method, Multi-Index Integrated Change (MIIC), has been developed to capture a full range of land cover disturbance patterns for updating the National Land Cover Database (NLCD). Specific indices typically specialize in identifying only certain types of disturbances; for example, the Normalized Burn Ratio (NBR) has been widely used for monitoring fire disturbance. Recognizing the potential complementary nature of multiple indices, we integrated four indices into one model to more accurately detect true change between two NLCD time periods. The four indices are NBR, Normalized Difference Vegetation Index (NDVI), Change Vector (CV), and a newly developed index called the Relative Change Vector (RCV). The model is designed to provide both change location and change direction (e.g. biomass increase or biomass decrease). The integrated change model has been tested on five image pairs from different regions exhibiting a variety of disturbance types. Compared with a simple change vector method, MIIC can better capture the desired change without introducing additional commission errors. The model is particularly accurate at detecting forest disturbances, such as forest harvest, forest fire, and forest regeneration. Agreement between the initial change map areas derived from MIIC and the retained final land cover type change areas will be showcased from the pilot test sites.

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.

PubMed

Gaj, Thomas; Staahl, Brett T; Rodrigues, Gonçalo M C; Limsirichai, Prajit; Ekman, Freja K; Doudna, Jennifer A; Schaffer, David V

2017-06-20

Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology-directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Understanding Solar Eruptions with SDO/HMI Measuring Photospheric Flows, Testing Models, and Steps Towards Forecasting Solar Eruptions

NASA Technical Reports Server (NTRS)

Schuck, Peter W.; Linton, Mark; Muglach, Karin; Welsch, Brian; Hageman, Jacob

2010-01-01

The imminent launch of Solar Dynamics Observatory (SDO) will carry the first full-disk imaging vector magnetograph, the Helioseismic and Magnetic Imager (HMI), into an inclined geosynchronous orbit. This magnetograph will provide nearly continuous measurements of photospheric vector magnetic fields at cadences of 90 seconds to 12 minutes with I" resolution, precise pointing, and unfettered by atmospheric seeing. The enormous data stream of 1.5 Terabytes per day from SDO will provide an unprecedented opportunity to understand the mysteries of solar eruptions. These ground-breaking observations will permit the application of a new technique, the differential affine velocity estimator for vector magnetograms (DAVE4VM), to measure photospheric plasma flows in active regions. These measurements will permit, for the first time, accurate assessments of the coronal free energy available for driving CMEs and flares. The details of photospheric plasma flows, particularly along magnetic neutral-lines, are critical to testing models for initiating coronal mass ejections (CMEs) and flares. Assimilating flows and fields into state-of-the art 3D MHD simulations that model the highly stratified solar atmosphere from the convection zone to the corona represents the next step towards achieving NASA's Living with a Star forecasting goals of predicting "when a solar eruption leading to a CME will occur." This talk will describe these major science and predictive advances that will be delivered by SDO /HMI.

Understanding Solar Eruptions with SDO/HMI Measuring Photospheric Flows, Testing Models, and Steps Towards Forecasting Solar Eruptions

NASA Technical Reports Server (NTRS)

Schuck, Peter W.; Linton, M.; Muglach, K.; Hoeksema, T.

2010-01-01

The Solar Dynamics Observatory (SDO) is carrying the first full-disk imaging vector magnetograph, the Helioseismic and Magnetic Imager (HMI), into an inclined geosynchronous orbit. This magnetograph will provide nearly continuous measurements of photospheric vector magnetic fields at cadences of 90 seconds to 12 minutes with 1" resolution, precise pointing, and unfettered by atmospheric seeing. The enormous data stream of 1.5 Terabytes per day from SAO will provide an unprecedented opportunity to understand the mysteries of solar eruptions. These ground-breaking observations will permit the application of a new technique, the differential affine velocity estimator for vector magnetograms (DAVE4VM), to measure photospheric plasma flows in active regions. These measurements will permit, for the first time, accurate assessments of the coronal free energy available for driving CMEs and flares. The details of photospheric plasma flows, particularly along magnetic neutral-lines, are critical to testing models for initiating coronal mass ejections (CMEs) and flares. Assimilating flows and fields into state-of-the art 3D MHD simulations that model the highly stratified solar atmosphere from the convection zone to the corona represents the next step towards achieving NASA's Living with a Star forecasting goals of predicting "when a solar eruption leading to a CME will occur." Our presentation will describe these major science and predictive advances that will be delivered by SDO/HMI.

A new parallel-vector finite element analysis software on distributed-memory computers

NASA Technical Reports Server (NTRS)

Qin, Jiangning; Nguyen, Duc T.

1993-01-01

A new parallel-vector finite element analysis software package MPFEA (Massively Parallel-vector Finite Element Analysis) is developed for large-scale structural analysis on massively parallel computers with distributed-memory. MPFEA is designed for parallel generation and assembly of the global finite element stiffness matrices as well as parallel solution of the simultaneous linear equations, since these are often the major time-consuming parts of a finite element analysis. Block-skyline storage scheme along with vector-unrolling techniques are used to enhance the vector performance. Communications among processors are carried out concurrently with arithmetic operations to reduce the total execution time. Numerical results on the Intel iPSC/860 computers (such as the Intel Gamma with 128 processors and the Intel Touchstone Delta with 512 processors) are presented, including an aircraft structure and some very large truss structures, to demonstrate the efficiency and accuracy of MPFEA.

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis.

PubMed

Deng, Shunzhou; Martin, Carly; Patil, Rasika; Zhu, Felix; Zhao, Bin; Xiang, Zuoshuang; He, Yongqun

2015-11-27

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development. Copyright © 2015 Elsevier Ltd. All rights reserved.

Vector-model-supported optimization in volumetric-modulated arc stereotactic radiotherapy planning for brain metastasis

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

Liu, Eva Sau Fan; Department of Health Technology and Informatics, The Hong Kong Polytechnic University; Wu, Vincent Wing Cheung

Long planning time in volumetric-modulated arc stereotactic radiotherapy (VMA-SRT) cases can limit its clinical efficiency and use. A vector model could retrieve previously successful radiotherapy cases that share various common anatomic features with the current case. The prsent study aimed to develop a vector model that could reduce planning time by applying the optimization parameters from those retrieved reference cases. Thirty-six VMA-SRT cases of brain metastasis (gender, male [n = 23], female [n = 13]; age range, 32 to 81 years old) were collected and used as a reference database. Another 10 VMA-SRT cases were planned with both conventional optimization and vector-model-supported optimization, followingmore » the oncologists' clinical dose prescriptions. Planning time and plan quality measures were compared using the 2-sided paired Wilcoxon signed rank test with a significance level of 0.05, with positive false discovery rate (pFDR) of less than 0.05. With vector-model-supported optimization, there was a significant reduction in the median planning time, a 40% reduction from 3.7 to 2.2 hours (p = 0.002, pFDR = 0.032), and for the number of iterations, a 30% reduction from 8.5 to 6.0 (p = 0.006, pFDR = 0.047). The quality of plans from both approaches was comparable. From these preliminary results, vector-model-supported optimization can expedite the optimization of VMA-SRT for brain metastasis while maintaining plan quality.« less

Modulating ectopic gene expression levels by using retroviral vectors equipped with synthetic promoters.

PubMed

Ferreira, Joshua P; Peacock, Ryan W S; Lawhorn, Ingrid E B; Wang, Clifford L

2011-12-01

The human cytomegalovirus and elongation factor 1α promoters are constitutive promoters commonly employed by mammalian expression vectors. These promoters generally produce high levels of expression in many types of cells and tissues. To generate a library of synthetic promoters capable of generating a range of low, intermediate, and high expression levels, the TATA and CAAT box elements of these promoters were mutated. Other promoter variants were also generated by random mutagenesis. Evaluation using plasmid vectors integrated at a single site in the genome revealed that these various synthetic promoters were capable of expression levels spanning a 40-fold range. Retroviral vectors were equipped with the synthetic promoters and evaluated for their ability to reproduce the graded expression demonstrated by plasmid integration. A vector with a self-inactivating long terminal repeat could neither reproduce the full range of expression levels nor produce stable expression. Using a second vector design, the different synthetic promoters enabled stable expression over a broad range of expression levels in different cell lines. The online version of this article (doi:10.1007/s11693-011-9089-0) contains supplementary material, which is available to authorized users.

Enhanced green fluorescent protein (egfp) gene expression in Tetraselmis subcordiformis chloroplast with endogenous regulators.

PubMed

Cui, Yulin; Zhao, Jialin; Hou, Shichang; Qin, Song

2016-05-01

On the basis of fundamental genetic transformation technologies, the goal of this study was to optimize Tetraselmis subcordiformis chloroplast transformation through the use of endogenous regulators. The genes rrn16S, rbcL, psbA, and psbC are commonly highly expressed in chloroplasts, and the regulators of these genes are often used in chloroplast transformation. For lack of a known chloroplast genome sequence, the genome-walking method was used here to obtain full sequences of T. subcordiformis endogenous regulators. The resulting regulators, including three promoters, two terminators, and a ribosome combination sequence, were inserted into the previously constructed plasmid pPSC-R, with the egfp gene included as a reporter gene, and five chloroplast expression vectors prepared. These vectors were successfully transformed into T. subcordiformis by particle bombardment and the efficiency of each vector tested by assessing EGFP fluorescence via microscopy. The results showed that these vectors exhibited higher efficiency than the former vector pPSC-G carrying exogenous regulators, and the vector pRFA with Prrn, psbA-5'RE, and TpsbA showed the highest efficiency. This research provides a set of effective endogenous regulators for T. subcordiformis and will facilitate future fundamental studies of this alga.

Research on bearing fault diagnosis of large machinery based on mathematical morphology

NASA Astrophysics Data System (ADS)

Wang, Yu

2018-04-01

To study the automatic diagnosis of large machinery fault based on support vector machine, combining the four common faults of the large machinery, the support vector machine is used to classify and identify the fault. The extracted feature vectors are entered. The feature vector is trained and identified by multi - classification method. The optimal parameters of the support vector machine are searched by trial and error method and cross validation method. Then, the support vector machine is compared with BP neural network. The results show that the support vector machines are short in time and high in classification accuracy. It is more suitable for the research of fault diagnosis in large machinery. Therefore, it can be concluded that the training speed of support vector machines (SVM) is fast and the performance is good.

Mission Capability Gains from Multi-Mode Propulsion Thrust Profile Variations for a Plane Change Maneuver

DTIC Science & Technology

2010-12-29

propellant mass [kg] msc = mass of the spacecraft [kg] MMP = multi-mode propulsion   = position in the Geocentric Equatorial Reference...thrust burn time [s] Tsc = thrust of the spacecraft [N] = vector between current and final velocity vector   = velocity vector in the Geocentric ...Equatorial Reference Frame of spacecraft in intended orbit [km/s]   = velocity vector in the Geocentric Equatorial Reference Frame of spacecraft in

Triatomine Infestation in Guatemala: Spatial Assessment after Two Rounds of Vector Control

PubMed Central

Manne, Jennifer; Nakagawa, Jun; Yamagata, Yoichi; Goehler, Alexander; Brownstein, John S.; Castro, Marcia C.

2012-01-01

In 2000, the Guatemalan Ministry of Health initiated a Chagas disease program to control Rhodnius prolixus and Triatoma dimidiata by periodic house spraying with pyrethroid insecticides to characterize infestation patterns and analyze the contribution of programmatic practices to these patterns. Spatial infestation patterns at three time points were identified using the Getis-Ord Gi*(d) test. Logistic regression was used to assess predictors of reinfestation after pyrethroid insecticide administration. Spatial analysis showed high and low clusters of infestation at three time points. After two rounds of spray, 178 communities persistently fell in high infestation clusters. A time lapse between rounds of vector control greater than 6 months was associated with 1.54 (95% confidence interval = 1.07–2.23) times increased odds of reinfestation after first spray, whereas a time lapse of greater than 1 year was associated with 2.66 (95% confidence interval = 1.85–3.83) times increased odds of reinfestation after first spray compared with localities where the time lapse was less than 180 days. The time lapse between rounds of vector control should remain under 1 year. Spatial analysis can guide targeted vector control efforts by enabling tracking of reinfestation hotspots and improved targeting of resources. PMID:22403315

nu-Anomica: A Fast Support Vector Based Novelty Detection Technique

NASA Technical Reports Server (NTRS)

Das, Santanu; Bhaduri, Kanishka; Oza, Nikunj C.; Srivastava, Ashok N.

2009-01-01

In this paper we propose nu-Anomica, a novel anomaly detection technique that can be trained on huge data sets with much reduced running time compared to the benchmark one-class Support Vector Machines algorithm. In -Anomica, the idea is to train the machine such that it can provide a close approximation to the exact decision plane using fewer training points and without losing much of the generalization performance of the classical approach. We have tested the proposed algorithm on a variety of continuous data sets under different conditions. We show that under all test conditions the developed procedure closely preserves the accuracy of standard one-class Support Vector Machines while reducing both the training time and the test time by 5 - 20 times.

Biosensor method and system based on feature vector extraction

DOEpatents

Greenbaum, Elias [Knoxville, TN; Rodriguez, Jr., Miguel; Qi, Hairong [Knoxville, TN; Wang, Xiaoling [San Jose, CA

2012-04-17

A method of biosensor-based detection of toxins comprises the steps of providing at least one time-dependent control signal generated by a biosensor in a gas or liquid medium, and obtaining a time-dependent biosensor signal from the biosensor in the gas or liquid medium to be monitored or analyzed for the presence of one or more toxins selected from chemical, biological or radiological agents. The time-dependent biosensor signal is processed to obtain a plurality of feature vectors using at least one of amplitude statistics and a time-frequency analysis. At least one parameter relating to toxicity of the gas or liquid medium is then determined from the feature vectors based on reference to the control signal.

Higher-dimensional generalizations of the Watanabe–Strogatz transform for vector models of synchronization

NASA Astrophysics Data System (ADS)

Lohe, M. A.

2018-06-01

We generalize the Watanabe–Strogatz (WS) transform, which acts on the Kuramoto model in d  =  2 dimensions, to a higher-dimensional vector transform which operates on vector oscillator models of synchronization in any dimension , for the case of identical frequency matrices. These models have conserved quantities constructed from the cross ratios of inner products of the vector variables, which are invariant under the vector transform, and have trajectories which lie on the unit sphere S d‑1. Application of the vector transform leads to a partial integration of the equations of motion, leaving independent equations to be solved, for any number of nodes N. We discuss properties of complete synchronization and use the reduced equations to derive a stability condition for completely synchronized trajectories on S d‑1. We further generalize the vector transform to a mapping which acts in and in particular preserves the unit ball , and leaves invariant the cross ratios constructed from inner products of vectors in . This mapping can be used to partially integrate a system of vector oscillators with trajectories in , and for d  =  2 leads to an extension of the Kuramoto system to a system of oscillators with time-dependent amplitudes and trajectories in the unit disk. We find an inequivalent generalization of the Möbius map which also preserves but leaves invariant a different set of cross ratios, this time constructed from the vector norms. This leads to a different extension of the Kuramoto model with trajectories in the complex plane that can be partially integrated by means of fractional linear transformations.

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.

Fast support vector data descriptions for novelty detection.

PubMed

Liu, Yi-Hung; Liu, Yan-Chen; Chen, Yen-Jen

2010-08-01

Support vector data description (SVDD) has become a very attractive kernel method due to its good results in many novelty detection problems. However, the decision function of SVDD is expressed in terms of the kernel expansion, which results in a run-time complexity linear in the number of support vectors. For applications where fast real-time response is needed, how to speed up the decision function is crucial. This paper aims at dealing with the issue of reducing the testing time complexity of SVDD. A method called fast SVDD (F-SVDD) is proposed. Unlike the traditional methods which all try to compress a kernel expansion into one with fewer terms, the proposed F-SVDD directly finds the preimage of a feature vector, and then uses a simple relationship between this feature vector and the SVDD sphere center to re-express the center with a single vector. The decision function of F-SVDD contains only one kernel term, and thus the decision boundary of F-SVDD is only spherical in the original space. Hence, the run-time complexity of the F-SVDD decision function is no longer linear in the support vectors, but is a constant, no matter how large the training set size is. In this paper, we also propose a novel direct preimage-finding method, which is noniterative and involves no free parameters. The unique preimage can be obtained in real time by the proposed direct method without taking trial-and-error. For demonstration, several real-world data sets and a large-scale data set, the extended MIT face data set, are used in experiments. In addition, a practical industry example regarding liquid crystal display micro-defect inspection is also used to compare the applicability of SVDD and our proposed F-SVDD when faced with mass data input. The results are very encouraging.

Time Safety Margin: Theory and Practice

DTIC Science & Technology

2016-09-01

Basic Dive Recovery Terminology The Simplest Definition of TSM: Time Safety Margin is the time to directly travel from the worst-case vector to an...Safety Margin (TSM). TSM is defined as the time in seconds to directly travel from the worst case vector (i.e. worst case combination of parameters...invoked by this AFI, base recovery planning and risk management upon the calculated TSM. TSM is the time in seconds to di- rectly travel from the worst case

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.

Gene transfer to the cerebellum.

PubMed

Louboutin, Jean-Pierre; Reyes, Beverly A S; Van Bockstaele, Elisabeth J; Strayer, David S

2010-12-01

There are several diseases for which gene transfer therapy to the cerebellum might be practicable. In these studies, we used recombinant Tag-deleted SV40-derived vectors (rSV40s) to study gene delivery targeting the cerebellum. These vectors transduce neurons and microglia very effectively in vitro and in vivo, and so we tested them to evaluate gene transfer to the cerebellum in vivo. Using a rSV40 vector carrying human immunodeficiency virus (HIV)-Nef with a C-terminal FLAG epitope, we characterized the distribution, duration, and cell types transduced. Rats received test and control vectors by stereotaxic injection into the cerebellum. Transgene expression was assessed 1, 2, and 4 weeks later by immunostaining of serial brain sections. FLAG epitope-expressing cells were seen, at all times after vector administration, principally detected in the Purkinje cells of the cerebellum, identified as immunopositive for calbindin. Occasional microglial cells were tranduced; transgene expression was not detected in astrocytes or oligodendrocytes. No inflammatory or other reaction was detected at any time. Thus, SV40-derived vectors can deliver effective, safe, and durable transgene expression to the cerebellum.

Rotational polarities of sudden impulses in the magnetotail lobe

NASA Technical Reports Server (NTRS)

Kawano, H.; Yamamoto, T.; Kokubun, S.; Lepping, R. P.

1992-01-01

A sudden impulse (SI) is a sudden change in the magnetic field strength which is caused by a change in the solar wind pressure and is observed throughout the magnetosphere. In this report we have examined the rotations of the magnetic field vectors at times of SIs in the magnetotail lobe, by using IMP 6, 7, and 8 magnetometer data. The following properties have been found: (1) at the time of SI the arrowhead of the magnetic vector tends to rotate in one plane; (2) the plane of rotation tends to include the unperturbed magnetic field vector; (3) the plane of rotation tends to be aligned with the radial direction from the magnetotail axis; and (4) the magnetic vectors have a particular rotational polarity: when the plane of rotation is viewed so that the Sun is to the right of the viewed plane and the magnetotail axis is to the bottom, the arrowhead of the vector tends to rotate counterclockwise in this plane. These magnetic vector properties are consistent with those expected when part of an increase in solar wind lateral pressure squeezes the magnetotail axisymmetrically while moving tailward.

Successes and failures of sixty years of vector control in French Guiana: what is the next step?

PubMed

Epelboin, Yanouk; Chaney, Sarah C; Guidez, Amandine; Habchi-Hanriot, Nausicaa; Talaga, Stanislas; Wang, Lanjiao; Dusfour, Isabelle

2018-03-12

Since the 1940s, French Guiana has implemented vector control to contain or eliminate malaria, yellow fever, and, recently, dengue, chikungunya, and Zika. Over time, strategies have evolved depending on the location, efficacy of the methods, development of insecticide resistance, and advances in vector control techniques. This review summarises the history of vector control in French Guiana by reporting the records found in the private archives of the Institute Pasteur in French Guiana and those accessible in libraries worldwide. This publication highlights successes and failures in vector control and identifies the constraints and expectations for vector control in this French overseas territory in the Americas.

Shape and 3D acoustically induced vibrations of the human eardrum characterized by digital holography

NASA Astrophysics Data System (ADS)

Khaleghi, Morteza; Furlong, Cosme; Cheng, Jeffrey Tao; Rosowski, John J.

2014-07-01

The eardrum or Tympanic Membrane (TM) transfers acoustic energy from the ear canal (at the external ear) into mechanical motions of the ossicles (at the middle ear). The acousto-mechanical-transformer behavior of the TM is determined by its shape and mechanical properties. For a better understanding of hearing mysteries, full-field-of-view techniques are required to quantify shape, nanometer-scale sound-induced displacement, and mechanical properties of the TM in 3D. In this paper, full-field-of-view, three-dimensional shape and sound-induced displacement of the surface of the TM are obtained by the methods of multiple wavelengths and multiple sensitivity vectors with lensless digital holography. Using our developed digital holographic systems, unique 3D information such as, shape (with micrometer resolution), 3D acoustically-induced displacement (with nanometer resolution), full strain tensor (with nano-strain resolution), 3D phase of motion, and 3D directional cosines of the displacement vectors can be obtained in full-field-ofview with a spatial resolution of about 3 million points on the surface of the TM and a temporal resolution of 15 Hz.

Evaluation of vector-primed cDNA library production from microgram quantities of total RNA.

PubMed

Kuo, Jonathan; Inman, Jason; Brownstein, Michael; Usdin, Ted B

2004-12-15

cDNA sequences are important for defining the coding region of genes, and full-length cDNA clones have proven to be useful for investigation of the function of gene products. We produced cDNA libraries containing 3.5-5 x 10(5) primary transformants, starting with 5 mug of total RNA prepared from mouse pituitary, adrenal, thymus, and pineal tissue, using a vector-primed cDNA synthesis method. Of approximately 1000 clones sequenced, approximately 20% contained the full open reading frames (ORFs) of known transcripts, based on the presence of the initiating methionine residue codon. The libraries were complex, with 94, 91, 83 and 55% of the clones from the thymus, adrenal, pineal and pituitary libraries, respectively, represented only once. Twenty-five full-length clones, not yet represented in the Mammalian Gene Collection, were identified. Thus, we have produced useful cDNA libraries for the isolation of full-length cDNA clones that are not yet available in the public domain, and demonstrated the utility of a simple method for making high-quality libraries from small amounts of starting material.

Dispersion curve estimation via a spatial covariance method with ultrasonic wavefield imaging.

PubMed

Chong, See Yenn; Todd, Michael D

2018-05-01

Numerous Lamb wave dispersion curve estimation methods have been developed to support damage detection and localization strategies in non-destructive evaluation/structural health monitoring (NDE/SHM) applications. In this paper, the covariance matrix is used to extract features from an ultrasonic wavefield imaging (UWI) scan in order to estimate the phase and group velocities of S0 and A0 modes. A laser ultrasonic interrogation method based on a Q-switched laser scanning system was used to interrogate full-field ultrasonic signals in a 2-mm aluminum plate at five different frequencies. These full-field ultrasonic signals were processed in three-dimensional space-time domain. Then, the time-dependent covariance matrices of the UWI were obtained based on the vector variables in Cartesian and polar coordinate spaces for all time samples. A spatial covariance map was constructed to show spatial correlations within the full wavefield. It was observed that the variances may be used as a feature for S0 and A0 mode properties. The phase velocity and the group velocity were found using a variance map and an enveloped variance map, respectively, at five different frequencies. This facilitated the estimation of Lamb wave dispersion curves. The estimated dispersion curves of the S0 and A0 modes showed good agreement with the theoretical dispersion curves. Copyright © 2018 Elsevier B.V. All rights reserved.

Dengue Fever Occurrence and Vector Detection by Larval Survey, Ovitrap and MosquiTRAP: A Space-Time Clusters Analysis

PubMed Central

de Melo, Diogo Portella Ornelas; Scherrer, Luciano Rios; Eiras, Álvaro Eduardo

2012-01-01

The use of vector surveillance tools for preventing dengue disease requires fine assessment of risk, in order to improve vector control activities. Nevertheless, the thresholds between vector detection and dengue fever occurrence are currently not well established. In Belo Horizonte (Minas Gerais, Brazil), dengue has been endemic for several years. From January 2007 to June 2008, the dengue vector Aedes (Stegomyia) aegypti was monitored by ovitrap, the sticky-trap MosquiTRAP™ and larval surveys in an study area in Belo Horizonte. Using a space-time scan for clusters detection implemented in SaTScan software, the vector presence recorded by the different monitoring methods was evaluated. Clusters of vectors and dengue fever were detected. It was verified that ovitrap and MosquiTRAP vector detection methods predicted dengue occurrence better than larval survey, both spatially and temporally. MosquiTRAP and ovitrap presented similar results of space-time intersections to dengue fever clusters. Nevertheless ovitrap clusters presented longer duration periods than MosquiTRAP ones, less acuratelly signalizing the dengue risk areas, since the detection of vector clusters during most of the study period was not necessarily correlated to dengue fever occurrence. It was verified that ovitrap clusters occurred more than 200 days (values ranged from 97.0±35.35 to 283.0±168.4 days) before dengue fever clusters, whereas MosquiTRAP clusters preceded dengue fever clusters by approximately 80 days (values ranged from 65.5±58.7 to 94.0±14. 3 days), the former showing to be more temporally precise. Thus, in the present cluster analysis study MosquiTRAP presented superior results for signaling dengue transmission risks both geographically and temporally. Since early detection is crucial for planning and deploying effective preventions, MosquiTRAP showed to be a reliable tool and this method provides groundwork for the development of even more precise tools. PMID:22848729

Longevity of rAAV vector and plasmid DNA in blood after intramuscular injection in nonhuman primates: implications for gene doping.

PubMed

Ni, W; Le Guiner, C; Gernoux, G; Penaud-Budloo, M; Moullier, P; Snyder, R O

2011-07-01

Legitimate uses of gene transfer technology can benefit from sensitive detection methods to determine vector biodistribution in pre-clinical studies and in human clinical trials, and similar methods can detect illegitimate gene transfer to provide sports-governing bodies with the ability to maintain fairness. Real-time PCR assays were developed to detect a performance-enhancing transgene (erythropoietin, EPO) and backbone sequences in the presence of endogenous cellular sequences. In addition to developing real-time PCR assays, the steps involved in DNA extraction, storage and transport were investigated. By real-time PCR, the vector transgene is distinguishable from the genomic DNA sequence because of the absence of introns, and the vector backbone can be identified by heterologous gene expression control elements. After performance of the assays was optimized, cynomolgus macaques received a single dose by intramuscular (IM) injection of plasmid DNA, a recombinant adeno-associated viral vector serotype 1 (rAAV1) or a rAAV8 vector expressing cynomolgus macaque EPO. Macaques received a high plasmid dose intended to achieve a significant, but not life-threatening, increase in hematocrit. rAAV vectors were used at low doses to achieve a small increase in hematocrit and to determine the limit of sensitivity for detecting rAAV sequences by single-step PCR. DNA extracted from white blood cells (WBCs) was tested to determine whether WBCs can be collaterally transfected by plasmid or transduced by rAAV vectors in this context, and can be used as a surrogate marker for gene doping. We demonstrate that IM injection of a conventional plasmid and rAAV vectors results in the presence of DNA that can be detected at high levels in blood before rapid elimination, and that rAAV genomes can persist for several months in WBCs.

Efficient assembly of full-length infectious clone of Brazilian IBDV isolate by homologous recombination in yeast

PubMed Central

Silva, J.V.J.; Arenhart, S.; Santos, H.F.; Almeida-Queiroz, S.R.; Silva, A.N.M.R.; Trevisol, I.M.; Bertani, G.R.; Gil, L.H.V.G.

2014-01-01

The Infectious Bursal Disease Virus (IBDV) causes immunosuppression in young chickens. Advances in molecular virology and vaccines for IBDV have been achieved by viral reverse genetics (VRG). VRG for IBDV has undergone changes over time, however all strategies used to generate particles of IBDV involves multiple rounds of amplification and need of in vitro ligation and restriction sites. The aim of this research was to build the world’s first VRG for IBDV by yeast-based homologous recombination; a more efficient, robust and simple process than cloning by in vitro ligation. The wild type IBDV (Wt-IBDV-Br) was isolated in Brazil and had its genome cloned in pJG-CMV-HDR vector by yeast-based homologous recombination. The clones were transfected into chicken embryo fibroblasts and the recovered virus (IC-IBDV-Br) showed genetic stability and similar phenotype to Wt-IBDV-Br, which were observed by nucleotide sequence, focus size/morphology and replication kinetics, respectively. Thus, IBDV reverse genetics by yeast-based homologous recombination provides tools to IBDV understanding and vaccines/viral vectors development. PMID:25763067

Dengue and dengue haemorrhagic fever: Indian perspective.

PubMed

Chaturvedi, U C; Nagar, Rachna

2008-11-01

The relationship of this country with dengue has been long and intense. The ?rst recorded epidemic of clinically dengue-like illness occurred at Madras in 1780 and the dengue virus was isolated for the ?rst time almost simultaneously in Japan and Calcutta in 1943-1944. After the ?rst virologically proved epidemic of dengue fever along the East Coast of India in 1963-1964, it spread to allover the country.The ?rst full-blown epidemic of the severe form of the illness,the dengue haemorrhagic fever/dengue shock syndrome occurred in North India in 1996. Aedes aegypti is the vector for transmission of the disease. Vaccines or antiviral drugs are not available for dengue viruses; the only effective way to prevent epidemic degure fever/dengue haemorrhagic fever (DF/DHF) is to control the mosquito vector, Aedes aegypti and prevent its bite. This country has few virus laboratories and some of them have done excellent work in the area of molecular epidemiology,immunopathology and vaccine development. Selected work done in this country on the problems of dengue is presented here.

Genetic modification of hematopoietic cells using retroviral and lentiviral vectors: safety considerations for vector design and delivery into target cells.

PubMed

Dropulic, Boro

2005-07-01

The recent development of leukemia in three patients following retroviral vector gene transfer in hematopoietic stem cells, resulting in the death of one patient, has raised safety concerns for the use of integrating gene transfer vectors for human gene therapy. This review discusses these serious adverse events from the perspective of whether restrictions on vector design and vector-modified target cells are warranted at this time. A case is made against presently establishing specific restrictions for vector design and transduced cells; rather, their safety should be ascertained by empiric evaluation in appropriate preclinical models on a case-by-case basis. Such preclinical data, coupled with proper informed patient consent and a risk-benefit ratio analysis, provide the best available prospective evaluation of gene transfer vectors prior to their translation into the clinic.

Enhanced Central Nervous System Transduction with Lentiviral Vectors Pseudotyped with RVG/HIV-1gp41 Chimeric Envelope Glycoproteins

PubMed Central

Trabalza, Antonio; Eleftheriadou, Ioanna; Sgourou, Argyro; Liao, Ting-Yi; Patsali, Petros; Lee, Heyne

2014-01-01

ABSTRACT To investigate the potential benefits which may arise from pseudotyping the HIV-1 lentiviral vector with its homologous gp41 envelope glycoprotein (GP) cytoplasmic tail (CT), we created chimeric RVG/HIV-1gp41 GPs composed of the extracellular and transmembrane sequences of RVG and either the full-length gp41 CT or C terminus gp41 truncations sequentially removing existing conserved motifs. Lentiviruses (LVs) pseudotyped with the chimeric GPs were evaluated in terms of particle release (physical titer), biological titers, infectivity, and in vivo central nervous system (CNS) transduction. We report here that LVs carrying shorter CTs expressed higher levels of envelope GP and showed a higher average infectivity than those bearing full-length GPs. Interestingly, complete removal of GP CT led to vectors with the highest transduction efficiency. Removal of all C-terminal gp41 CT conserved motifs, leaving just 17 amino acids (aa), appeared to preserve infectivity and resulted in a significantly increased physical titer. Furthermore, incorporation of these 17 aa in the RVG CT notably enhanced the physical titer. In vivo stereotaxic delivery of LV vectors exhibiting the best in vitro titers into rodent striatum facilitated efficient transduction of the CNS at the site of injection. A particular observation was the improved retrograde transduction of neurons in connected distal sites that resulted from the chimeric envelope R5 which included the “Kennedy” sequence (Ken) and lentivirus lytic peptide 2 (LLP2) conserved motifs in the CT, and although it did not exhibit a comparable high titer upon pseudotyping, it led to a significant increase in distal retrograde transduction of neurons. IMPORTANCE In this study, we have produced novel chimeric envelopes bearing the extracellular domain of rabies fused to the cytoplasmic tail (CT) of gp41 and pseudotyped lentiviral vectors with them. Here we report novel effects on the transduction efficiency and physical titer of these vectors, depending on CT length and context. We also managed to achieve increased neuronal transduction in vivo in the rodent CNS, thus demonstrating that the efficiency of these vectors can be enhanced following merely CT manipulation. We believe that this paper is a novel contribution to the field and opens the way for further attempts to surface engineer lentiviral vectors and make them more amenable for applications in human disease. PMID:24371049

The role of Coulomb collisions in limiting differential flow and temperature differences in the solar wind

NASA Technical Reports Server (NTRS)

Neugebauer, M.

1976-01-01

Data obtained by OGO 5 are used to confirm IMP 6 observations of an inverse dependence of the helium-to-hydrogen temperature ratio in the solar wind on the ratio of solar-wind expansion time to the Coulomb-collision equipartition time. The analysis is then extended to determine the relation of the difference between the hydrogen and helium bulk velocities (the differential flow vector) with the ratio between the solar-wind expansion time and the time required for Coulomb collisions to slow down a beam of ions passing through a plasma. It is found that the magnitude of the differential flow vector varies inversely with the time ratio when the latter is small and approaches zero when it is large. These results are shown to suggest a model of continuous preferential heating and acceleration of helium (or cooling and deceleration of hydrogen), which is cancelled or limited by Coulomb collisions by the time the plasma has reached 1 AU. Since the average dependence of the differential flow vector on the time ratio cannot explain all the systematic variations of the vector observed in corotating high-velocity streams, it is concluded that additional helium acceleration probably occurs on the leading edge of such streams.

Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors.

PubMed

Kutner, Robert H; Zhang, Xian-Yang; Reiser, Jakob

2009-01-01

Over the past decade, lentiviral vectors have emerged as powerful tools for transgene delivery. The use of lentiviral vectors has become commonplace and applications in the fields of neuroscience, hematology, developmental biology, stem cell biology and transgenesis are rapidly emerging. Also, lentiviral vectors are at present being explored in the context of human clinical trials. Here we describe improved protocols to generate highly concentrated lentiviral vector pseudotypes involving different envelope glycoproteins. In this protocol, vector stocks are prepared by transient transfection using standard cell culture media or serum-free media. Such stocks are then concentrated by ultracentrifugation and/or ion exchange chromatography, or by precipitation using polyethylene glycol 6000, resulting in vector titers of up to 10(10) transducing units per milliliter and above. We also provide reliable real-time PCR protocols to titrate lentiviral vectors based on proviral DNA copies present in genomic DNA extracted from transduced cells or on vector RNA. These production/concentration methods result in high-titer vector preparations that show reduced toxicity compared with lentiviral vectors produced using standard protocols involving ultracentrifugation-based methods. The vector production and titration protocol described here can be completed within 8 d.

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.

Equivalent magnetic vector potential model for low-frequency magnetic exposure assessment

NASA Astrophysics Data System (ADS)

Diao, Y. L.; Sun, W. N.; He, Y. Q.; Leung, S. W.; Siu, Y. M.

2017-10-01

In this paper, a novel source model based on a magnetic vector potential for the assessment of induced electric field strength in a human body exposed to the low-frequency (LF) magnetic field of an electrical appliance is presented. The construction of the vector potential model requires only a single-component magnetic field to be measured close to the appliance under test, hence relieving considerable practical measurement effort—the radial basis functions (RBFs) are adopted for the interpolation of discrete measurements; the magnetic vector potential model can then be directly constructed by summing a set of simple algebraic functions of RBF parameters. The vector potentials are then incorporated into numerical calculations as the equivalent source for evaluations of the induced electric field in the human body model. The accuracy and effectiveness of the proposed model are demonstrated by comparing the induced electric field in a human model to that of the full-wave simulation. This study presents a simple and effective approach for modelling the LF magnetic source. The result of this study could simplify the compliance test procedure for assessing an electrical appliance regarding LF magnetic exposure.

Equivalent magnetic vector potential model for low-frequency magnetic exposure assessment.

PubMed

Diao, Y L; Sun, W N; He, Y Q; Leung, S W; Siu, Y M

2017-09-21

In this paper, a novel source model based on a magnetic vector potential for the assessment of induced electric field strength in a human body exposed to the low-frequency (LF) magnetic field of an electrical appliance is presented. The construction of the vector potential model requires only a single-component magnetic field to be measured close to the appliance under test, hence relieving considerable practical measurement effort-the radial basis functions (RBFs) are adopted for the interpolation of discrete measurements; the magnetic vector potential model can then be directly constructed by summing a set of simple algebraic functions of RBF parameters. The vector potentials are then incorporated into numerical calculations as the equivalent source for evaluations of the induced electric field in the human body model. The accuracy and effectiveness of the proposed model are demonstrated by comparing the induced electric field in a human model to that of the full-wave simulation. This study presents a simple and effective approach for modelling the LF magnetic source. The result of this study could simplify the compliance test procedure for assessing an electrical appliance regarding LF magnetic exposure.

The method for froth floatation condition recognition based on adaptive feature weighted

NASA Astrophysics Data System (ADS)

Wang, Jieran; Zhang, Jun; Tian, Jinwen; Zhang, Daimeng; Liu, Xiaomao

2018-03-01

The fusion of foam characteristics can play a complementary role in expressing the content of foam image. The weight of foam characteristics is the key to make full use of the relationship between the different features. In this paper, an Adaptive Feature Weighted Method For Froth Floatation Condition Recognition is proposed. Foam features without and with weights are both classified by using support vector machine (SVM).The classification accuracy and optimal equaling algorithm under the each ore grade are regarded as the result of the adaptive feature weighting algorithm. At the same time the effectiveness of adaptive weighted method is demonstrated.

Supersonic quasi-axisymmetric vortex breakdown

NASA Technical Reports Server (NTRS)

Kandil, Osama A.; Kandil, Hamdy A.; Liu, C. H.

1991-01-01

An extensive computational study of supersonic quasi-axisymmetric vortex breakdown in a configured circular duct is presented. The unsteady, compressible, full Navier-Stokes (NS) equations are used. The NS equations are solved for the quasi-axisymmetric flows using an implicit, upwind, flux difference splitting, finite volume scheme. The quasi-axisymmetric solutions are time accurate and are obtained by forcing the components of the flowfield vector to be equal on two axial planes, which are in close proximity of each other. The effect of Reynolds number, for laminar flows, on the evolution and persistence of vortex breakdown, is studied. Finally, the effect of swirl ration at the duct inlet is investigated.

Recombination of polynucleotide sequences using random or defined primers

DOEpatents

Arnold, Frances H.; Shao, Zhixin; Affholter, Joseph A.; Zhao, Huimin H; Giver, Lorraine J.

2000-01-01

A method for in vitro mutagenesis and recombination of polynucleotide sequences based on polymerase-catalyzed extension of primer oligonucleotides is disclosed. The method involves priming template polynucleotide(s) with random-sequences or defined-sequence primers to generate a pool of short DNA fragments with a low level of point mutations. The DNA fragments are subjected to denaturization followed by annealing and further enzyme-catalyzed DNA polymerization. This procedure is repeated a sufficient number of times to produce full-length genes which comprise mutants of the original template polynucleotides. These genes can be further amplified by the polymerase chain reaction and cloned into a vector for expression of the encoded proteins.

ECB deacylase mutants

DOEpatents

Arnold, Frances H.; Shao, Zhixin; Zhao, Huimin; Giver, Lorraine J.

2002-01-01

A method for in vitro mutagenesis and recombination of polynucleotide sequences based on polymerase-catalyzed extension of primer oligonucleotides is disclosed. The method involves priming template polynucleotide(s) with random-sequences or defined-sequence primers to generate a pool of short DNA fragments with a low level of point mutations. The DNA fragments are subjected to denaturization followed by annealing and further enzyme-catalyzed DNA polymerization. This procedure is repeated a sufficient number of times to produce full-length genes which comprise mutants of the original template polynucleotides. These genes can be further amplified by the polymerase chain reaction and cloned into a vector for expression of the encoded proteins.

Recombination of polynucleotide sequences using random or defined primers

DOEpatents

Arnold, Frances H.; Shao, Zhixin; Affholter, Joseph A.; Zhao, Huimin; Giver, Lorraine J.

2001-01-01

A method for in vitro mutagenesis and recombination of polynucleotide sequences based on polymerase-catalyzed extension of primer oligonucleotides is disclosed. The method involves priming template polynucleotide(s) with random-sequences or defined-sequence primers to generate a pool of short DNA fragments with a low level of point mutations. The DNA fragments are subjected to denaturization followed by annealing and further enzyme-catalyzed DNA polymerization. This procedure is repeated a sufficient number of times to produce full-length genes which comprise mutants of the original template polynucleotides. These genes can be further amplified by the polymerase chain reaction and cloned into a vector for expression of the encoded proteins.

Current vector control challenges in the fight against malaria.

PubMed

Benelli, Giovanni; Beier, John C

2017-10-01

The effective and eco-friendly control of Anopheles vectors plays a key role in any malaria management program. Integrated Vector Management (IVM) suggests making use of the full range of vector control tools available. The strategies for IVM require novel technologies to control outdoor transmission of malaria. Despite the wide number of promising control tools tested against mosquitoes, current strategies for malaria vector control used in most African countries are not sufficient to achieve successful malaria control. The majority of National Malaria Control Programs in Africa still rely on indoor residual spraying (IRS) and long-lasting insecticidal nets (LLINs). These methods reduce malaria incidence but generally have little impact on malaria prevalence. In addition to outdoor transmission, growing levels of insecticide resistance in targeted vectors threaten the efficacy of LLINs and IRS. Larvicidal treatments can be useful, but are not recommended for rural areas. The research needed to improve the quality and delivery of mosquito vector control should focus on (i) optimization of processes and methods for vector control delivery; (ii) monitoring of vector populations and biting activity with reliable techniques; (iii) the development of effective and eco-friendly tools to reduce the burden or locally eliminate malaria and other mosquito-borne diseases; (iv) the careful evaluation of field suitability and efficacy of new mosquito control tools to prove their epidemiological impact; (v) the continuous monitoring of environmental changes which potentially affect malaria vector populations; (vi) the cooperation among different disciplines, with main emphasis on parasitology, tropical medicine, ecology, entomology, and ecotoxicology. A better understanding of behavioral ecology of malaria vectors is required. Key ecological obstacles that limit the effectiveness of vector control include the variation in mosquito behavior, development of insecticide resistance, presence of behavioral avoidance, high vector biodiversity, competitive and food web interactions, lack of insights on mosquito dispersal and mating behavior, and the impact of environmental changes on mosquito ecological traits. Overall, the trans-disciplinary cooperation among parasitologists and entomologists is crucial to ensure proper evaluation of the epidemiological impact triggered by novel mosquito vector control strategies. Copyright © 2017 Elsevier B.V. All rights reserved.

GRASS GIS: The first Open Source Temporal GIS

NASA Astrophysics Data System (ADS)

Gebbert, Sören; Leppelt, Thomas

2015-04-01

GRASS GIS is a full featured, general purpose Open Source geographic information system (GIS) with raster, 3D raster and vector processing support[1]. Recently, time was introduced as a new dimension that transformed GRASS GIS into the first Open Source temporal GIS with comprehensive spatio-temporal analysis, processing and visualization capabilities[2]. New spatio-temporal data types were introduced in GRASS GIS version 7, to manage raster, 3D raster and vector time series. These new data types are called space time datasets. They are designed to efficiently handle hundreds of thousands of time stamped raster, 3D raster and vector map layers of any size. Time stamps can be defined as time intervals or time instances in Gregorian calendar time or relative time. Space time datasets are simplifying the processing and analysis of large time series in GRASS GIS, since these new data types are used as input and output parameter in temporal modules. The handling of space time datasets is therefore equal to the handling of raster, 3D raster and vector map layers in GRASS GIS. A new dedicated Python library, the GRASS GIS Temporal Framework, was designed to implement the spatio-temporal data types and their management. The framework provides the functionality to efficiently handle hundreds of thousands of time stamped map layers and their spatio-temporal topological relations. The framework supports reasoning based on the temporal granularity of space time datasets as well as their temporal topology. It was designed in conjunction with the PyGRASS [3] library to support parallel processing of large datasets, that has a long tradition in GRASS GIS [4,5]. We will present a subset of more than 40 temporal modules that were implemented based on the GRASS GIS Temporal Framework, PyGRASS and the GRASS GIS Python scripting library. These modules provide a comprehensive temporal GIS tool set. The functionality range from space time dataset and time stamped map layer management over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus

PubMed Central

Matassov, Demetrius; Marzi, Andrea; Latham, Terri; Xu, Rong; Ota-Setlik, Ayuko; Feldmann, Friederike; Geisbert, Joan B.; Mire, Chad E.; Hamm, Stefan; Nowak, Becky; Egan, Michael A.; Geisbert, Thomas W.; Eldridge, John H.; Feldmann, Heinz; Clarke, David K.

2015-01-01

Previously, recombinant vesicular stomatitis virus (rVSV) pseudotypes expressing Ebolavirus glycoproteins (GPs) in place of the VSV G protein demonstrated protection of nonhuman primates from lethal homologous Ebolavirus challenge. Those pseudotype vectors contained no additional attenuating mutations in the rVSV genome. Here we describe rVSV vectors containing a full complement of VSV genes and expressing the Ebola virus (EBOV) GP from an additional transcription unit. These rVSV vectors contain the same combination of attenuating mutations used previously in the clinical development pathway of an rVSV/human immunodeficiency virus type 1 vaccine. One of these rVSV vectors (N4CT1-EBOVGP1), which expresses membrane-anchored EBOV GP from the first position in the genome (GP1), elicited a balanced cellular and humoral GP-specific immune response in mice. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7–9 days. Subsequently, N4CT1-EBOVGP1 demonstrated complete, single-dose protection of 2 macaques following lethal EBOV challenge. A single sham-vaccinated macaque died from disease due to EBOV infection. These results demonstrate that highly attenuated rVSV vectors expressing EBOV GP may provide safer alternatives to current EBOV vaccines. PMID:26109675

Does ITV vaginal procedure ensure dosimetric coverage during IMRT of post-operative gynaecological tumours without instructions concerning rectal filling?

PubMed

Verges, Ramona; Giraldo, Alexandra; Seoane, Alejandro; Toral, Elisabet; Ruiz, M Carmen; Pons, Ariadna; Giralt, Jordi

2018-01-01

To find out whether the internal target volume (ITV) vaginal procedure ensures dosimetric coverage during intensity-modulated radiation therapy (IMRT) of post-operative gynaecological tumours without instructions on rectal filling. The ITV vaginal procedure does not necessarily include all movements of the bladder, and does not include changes in the rectal volume. We should know if the vaginal ITV is a useful tool in maintaining CTV coverage during treatment. A retrospective analysis of 24 patients treated between July 2012 and July 2014 with adjuvant IMRT for gynaecological cancer. All patients underwent empty and full bladder CT on simulation (CT-planning) and three weeks later (CT-control). ITV displacement was measured and the 3D vector was calculated. ITV coverage was then evaluated by comparing the volume covered by the prescription isodose on both CT's. Patients were asked to have full bladder but they did not follow recommendations for the rectum. The mean 3D vector was 0.64 ± 0.32 cm (0.09-1.30). The mean ITV coverage loss was 5.8 ± 5.7% (0-20.2). We found a significant positive correlation between the 3D vector and the loss of coverage (Pearson correlation, r  = 0.493, 95% CI: 0.111-0.748, p  = 0.0144). We did not find any significant correlation between the bladder and rectal parameters with the 3D vector and loss of dosimetric coverage. We found a trend between the maximum rectal diameter in CT-planning and 3D vector ( r  = 0.400, 95% CI: -0.004 to 0.692, p  = 0.0529). ITV vaginal procedure contributed to ensuring a good dose coverage without instructions on rectal filling.

Application of wavelet-based multi-model Kalman filters to real-time flood forecasting

NASA Astrophysics Data System (ADS)

Chou, Chien-Ming; Wang, Ru-Yih

2004-04-01

This paper presents the application of a multimodel method using a wavelet-based Kalman filter (WKF) bank to simultaneously estimate decomposed state variables and unknown parameters for real-time flood forecasting. Applying the Haar wavelet transform alters the state vector and input vector of the state space. In this way, an overall detail plus approximation describes each new state vector and input vector, which allows the WKF to simultaneously estimate and decompose state variables. The wavelet-based multimodel Kalman filter (WMKF) is a multimodel Kalman filter (MKF), in which the Kalman filter has been substituted for a WKF. The WMKF then obtains M estimated state vectors. Next, the M state-estimates, each of which is weighted by its possibility that is also determined on-line, are combined to form an optimal estimate. Validations conducted for the Wu-Tu watershed, a small watershed in Taiwan, have demonstrated that the method is effective because of the decomposition of wavelet transform, the adaptation of the time-varying Kalman filter and the characteristics of the multimodel method. Validation results also reveal that the resulting method enhances the accuracy of the runoff prediction of the rainfall-runoff process in the Wu-Tu watershed.

Adjustable vector Airy light-sheet single optical tweezers: negative radiation forces on a subwavelength spheroid and spin torque reversal

NASA Astrophysics Data System (ADS)

Mitri, Farid G.

2018-01-01

Generalized solutions of vector Airy light-sheets, adjustable per their derivative order m, are introduced stemming from the Lorenz gauge condition and Maxwell's equations using the angular spectrum decomposition method. The Cartesian components of the incident radiated electric, magnetic and time-averaged Poynting vector fields in free space (excluding evanescent waves) are determined and computed with particular emphasis on the derivative order of the Airy light-sheet and the polarization on the magnetic vector potential forming the beam. Negative transverse time-averaged Poynting vector components can arise, while the longitudinal counterparts are always positive. Moreover, the analysis is extended to compute the optical radiation force and spin torque vector components on a lossless dielectric prolate subwavelength spheroid in the framework of the electric dipole approximation. The results show that negative forces and spin torques sign reversal arise depending on the derivative order of the beam, the polarization of the magnetic vector potential, and the orientation of the subwavelength prolate spheroid in space. The spin torque sign reversal suggests that counter-clockwise or clockwise rotations around the center of mass of the subwavelength spheroid can occur. The results find useful applications in single Airy light-sheet tweezers, particle manipulation, handling, and rotation applications to name a few examples.

Vector-control response in a post-flood disaster setting, Honiara, Solomon Islands, 2014.

PubMed

Shortus, Matthew; Musto, Jennie; Bugoro, Hugo; Butafa, Charles; Sio, Alison; Joshua, Cynthia

2016-01-01

The close quartering and exposed living conditions in evacuation centres and the potential increase in vector density after flooding in Solomon Islands resulted in an increased risk of exposure for the occupants to vectorborne diseases. In April 2014, Solomon Islands experienced a flash flooding event that affected many areas and displaced a large number of people. In the capital, Honiara, nearly 10 000 people were housed in emergency evacuation centres at the peak of the post-flood emergency. At the time of the floods, the number of dengue cases was increasing, following a record outbreak in 2013. The National Vector Borne Disease Control Programme with the assistance of the World Health Organization implemented an emergency vector-control response plan to provide protection to the at-risk populations in the evacuation centres. The National Surveillance Unit also activated an early warning disease surveillance system to monitor communicable diseases, including dengue and malaria. Timely and strategic application of the emergency interventions probably prevented an increase in dengue and malaria cases in the affected areas. Rapid and appropriate precautionary vector-control measures applied in a post-natural disaster setting can prevent and mitigate vectorborne disease incidences. Collecting vector surveillance data allows better analysis of vector-control operations' effectiveness.

Vector-control response in a post-flood disaster setting, Honiara, Solomon Islands, 2014

PubMed Central

Musto, Jennie; Bugoro, Hugo; Butafa, Charles; Sio, Alison; Joshua, Cynthia

2016-01-01

Problem The close quartering and exposed living conditions in evacuation centres and the potential increase in vector density after flooding in Solomon Islands resulted in an increased risk of exposure for the occupants to vectorborne diseases. Context In April 2014, Solomon Islands experienced a flash flooding event that affected many areas and displaced a large number of people. In the capital, Honiara, nearly 10 000 people were housed in emergency evacuation centres at the peak of the post-flood emergency. At the time of the floods, the number of dengue cases was increasing, following a record outbreak in 2013. Action The National Vector Borne Disease Control Programme with the assistance of the World Health Organization implemented an emergency vector-control response plan to provide protection to the at-risk populations in the evacuation centres. The National Surveillance Unit also activated an early warning disease surveillance system to monitor communicable diseases, including dengue and malaria. Outcome Timely and strategic application of the emergency interventions probably prevented an increase in dengue and malaria cases in the affected areas. Discussion Rapid and appropriate precautionary vector-control measures applied in a post-natural disaster setting can prevent and mitigate vectorborne disease incidences. Collecting vector surveillance data allows better analysis of vector-control operations’ effectiveness. PMID:27757255

Computer simulations and real-time control of ELT AO systems using graphical processing units

NASA Astrophysics Data System (ADS)

Wang, Lianqi; Ellerbroek, Brent

2012-07-01

The adaptive optics (AO) simulations at the Thirty Meter Telescope (TMT) have been carried out using the efficient, C based multi-threaded adaptive optics simulator (MAOS, http://github.com/lianqiw/maos). By porting time-critical parts of MAOS to graphical processing units (GPU) using NVIDIA CUDA technology, we achieved a 10 fold speed up for each GTX 580 GPU used compared to a modern quad core CPU. Each time step of full scale end to end simulation for the TMT narrow field infrared AO system (NFIRAOS) takes only 0.11 second in a desktop with two GTX 580s. We also demonstrate that the TMT minimum variance reconstructor can be assembled in matrix vector multiply (MVM) format in 8 seconds with 8 GTX 580 GPUs, meeting the TMT requirement for updating the reconstructor. Analysis show that it is also possible to apply the MVM using 8 GTX 580s within the required latency.

Selected Aspects of Markovian and Non-Markovian Quantum Master Equations

NASA Astrophysics Data System (ADS)

Lendi, K.

A few particular marked properties of quantum dynamical equations accounting for general relaxation and dissipation are selected and summarized in brief. Most results derive from the universal concept of complete positivity. The considerations mainly regard genuinely irreversible processes as characterized by a unique asymptotically stationary final state for arbitrary initial conditions. From ordinary Markovian master equations and associated quantum dynamical semigroup time-evolution, derivations of higher order Onsager coefficients and related entropy production are discussed. For general processes including non-faithful states a regularized version of quantum relative entropy is introduced. Further considerations extend to time-dependent infinitesimal generators of time-evolution and to a possible description of propagation of initial states entangled between open system and environment. In the coherence-vector representation of the full non-Markovian equations including entangled initial states, first results are outlined towards identifying mathematical properties of a restricted class of trial integral-kernel functions suited to phenomenological applications.

Spin Flips versus Spin Transport in Nonthermal Electrons Excited by Ultrashort Optical Pulses in Transition Metals

NASA Astrophysics Data System (ADS)

Shokeen, V.; Sanchez Piaia, M.; Bigot, J.-Y.; Müller, T.; Elliott, P.; Dewhurst, J. K.; Sharma, S.; Gross, E. K. U.

2017-09-01

A joint theoretical and experimental investigation is performed to understand the underlying physics of laser-induced demagnetization in Ni and Co films with varying thicknesses excited by 10 fs optical pulses. Experimentally, the dynamics of spins is studied by determining the time-dependent amplitude of the Voigt vector, retrieved from a full set of magnetic and nonmagnetic quantities performed on both sides of films, with absolute time reference. Theoretically, ab initio calculations are performed using time-dependent density functional theory. Overall, we demonstrate that spin-orbit induced spin flips are the most significant contributors with superdiffusive spin transport, which assumes only that the transport of majority spins without spin flips induced by scattering does not apply in Ni. In Co it plays a significant role during the first ˜20 fs only. Our study highlights the material dependent nature of the demagnetization during the process of thermalization of nonequilibrium spins.

Embedding of multidimensional time-dependent observations.

PubMed

Barnard, J P; Aldrich, C; Gerber, M

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

Embedding of multidimensional time-dependent observations

NASA Astrophysics Data System (ADS)

Barnard, Jakobus P.; Aldrich, Chris; Gerber, Marius

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

Comparison of algorithms for computing the two-dimensional discrete Hartley transform

NASA Technical Reports Server (NTRS)

Reichenbach, Stephen E.; Burton, John C.; Miller, Keith W.

1989-01-01

Three methods have been described for computing the two-dimensional discrete Hartley transform. Two of these employ a separable transform, the third method, the vector-radix algorithm, does not require separability. In-place computation of the vector-radix method is described. Operation counts and execution times indicate that the vector-radix method is fastest.

Equivalent Vectors

ERIC Educational Resources Information Center

Levine, Robert

2004-01-01

The cross-product is a mathematical operation that is performed between two 3-dimensional vectors. The result is a vector that is orthogonal or perpendicular to both of them. Learning about this for the first time while taking Calculus-III, the class was taught that if AxB = AxC, it does not necessarily follow that B = C. This seemed baffling. The…

Multigrid Equation Solvers for Large Scale Nonlinear Finite Element Simulations

DTIC Science & Technology

1999-01-01

purpose of the second partitioning phase , on each SMP, is to minimize the communication within the SMP; even if a multi - threaded matrix vector product...8.7 Comparison of model with experimental data for send phase of matrix vector product on ne grid...140 8.4 Matrix vector product phase times : : : : : : : : : : : : : : : : : : : : : : : 145 9.1 Flat and

Quantum speed limit time in a magnetic resonance

NASA Astrophysics Data System (ADS)

Ivanchenko, E. A.

2017-12-01

A visualization for dynamics of a qudit spin vector in a time-dependent magnetic field is realized by means of mapping a solution for a spin vector on the three-dimensional spherical curve (vector hodograph). The obtained results obviously display the quantum interference of precessional and nutational effects on the spin vector in the magnetic resonance. For any spin the bottom bounds of the quantum speed limit time (QSL) are found. It is shown that the bottom bound goes down when using multilevel spin systems. Under certain conditions the non-nil minimal time, which is necessary to achieve the orthogonal state from the initial one, is attained at spin S = 2. An estimation of the product of two and three standard deviations of the spin components are presented. We discuss the dynamics of the mutual uncertainty, conditional uncertainty and conditional variance in terms of spin standard deviations. The study can find practical applications in the magnetic resonance, 3D visualization of computational data and in designing of optimized information processing devices for quantum computation and communication.

Tagged fast neutron beams En > 6 MeV

NASA Astrophysics Data System (ADS)

Favela, F.; Huerta, A.; Santa Rita, P.; Ramos, A. T.; de Lucio, O.; Andrade, E.; Acosta, L.; Ortiz, M. E.; Araujo, V.; Murillo, G.; Policroniades, R.; Varela, A.; Chávez, E.

2015-07-01

Controlled flux of neutrons are produced through the 14N(d,n)15O nuclear reaction. Deuteron beams (2-4 MeV) are delivered by the CN-Van de Graaff accelerator and directed with full intensity to our Nitrogen target at SUGAR (SUpersonic GAs jet taRget). Each neutron is electronically tagged by the detection of the associated15O. Its energy and direction are known and "beams" of fast monochromatic tagged neutrons (En> 6 MeV) are available for basic research and applied work. MONDE is a large area (158 × 63 cm2) plastic scintillating slab (5 cm thick), viewed by 16 PMTs from the sides. Fast neutrons (MeV) entering the detector will produce a recoiling proton that induces a light spark at the spot. Signals from the 16 detectors are processed to deduce the position of the spark. Time logic signals from both the 15O detector and MONDE are combined to deduce a time of flight (TOF) signal. Finally, the position information together with the TOF yields the full momentum vector of each detected neutron.

The Age of Saturn's Rings Constrained by the Meteoroid Flux Into the System

NASA Astrophysics Data System (ADS)

Kempf, S.; Altobelli, N.; Srama, R.; Cuzzi, J. N.; Estrada, P. R.

2017-12-01

The origin of Saturn's ring is still not known. There is an ongoing argument whether Saturn's ring are rather young or have been formed shortly after Saturn together with its satellites. The water-ice rings contain about 5% rocky material resulting from continuous meteoroid bombardment of the ring material with interplanetary micrometeoroids. Knowledge of the incoming mass flux would allow to estimate the ring's exposure time. Model calculations suggest exposure times of 108 years implying a late ring formation. This scenario is problematic because the tidal disruption of a Mimas-sized moon or of a comet within the planet's Roche zone would lead to a much larger rock content as observed today. Here we report on the measurement of the meteoroid mass flux into the Saturnian system obtained by the charge-sensitive entrance grid system (QP) of the Cosmic Dust Analyser (CDA) on the Cassini spacecraft. Interplanetary dust particles (IDPs) entering Saturn's sphere of gravitational influence are identified through the measurements of their speed vectors. We analyzed the full CDA data set acquired after Cassini's arrival at Saturn in 2004, identified the impact speed vectors of 128 extrinsic micrometeoroids ≥ 2 μm, and determined their orbital elements. On the basis of these measurements we determined the mass flux into the Saturnian system. Our preliminary findings are in support of an old ring. The knowledge of the meteoroids orbital elements allows us for the first time to characterize the meteoroid environment in the outer solar system based on direct measurements.

Optimized scalable network switch

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton On Hudson, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Steinmacher-Burow, Burkhard D [Mount Kisco, NY; Takken, Todd E [Mount Kisco, NY; Vranas, Pavlos M [Bedford Hills, NY

2007-12-04

In a massively parallel computing system having a plurality of nodes configured in m multi-dimensions, each node including a computing device, a method for routing packets towards their destination nodes is provided which includes generating at least one of a 2m plurality of compact bit vectors containing information derived from downstream nodes. A multilevel arbitration process in which downstream information stored in the compact vectors, such as link status information and fullness of downstream buffers, is used to determine a preferred direction and virtual channel for packet transmission. Preferred direction ranges are encoded and virtual channels are selected by examining the plurality of compact bit vectors. This dynamic routing method eliminates the necessity of routing tables, thus enhancing scalability of the switch.

Optimized scalable network switch

DOEpatents

Blumrich, Matthias A.; Chen, Dong; Coteus, Paul W.

2010-02-23

In a massively parallel computing system having a plurality of nodes configured in m multi-dimensions, each node including a computing device, a method for routing packets towards their destination nodes is provided which includes generating at least one of a 2m plurality of compact bit vectors containing information derived from downstream nodes. A multilevel arbitration process in which downstream information stored in the compact vectors, such as link status information and fullness of downstream buffers, is used to determine a preferred direction and virtual channel for packet transmission. Preferred direction ranges are encoded and virtual channels are selected by examining the plurality of compact bit vectors. This dynamic routing method eliminates the necessity of routing tables, thus enhancing scalability of the switch.

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

The effect of transverse wave vector and magnetic fields on resonant tunneling times in double-barrier structures

NASA Astrophysics Data System (ADS)

Wang, Hongmei; Zhang, Yafei; Xu, Huaizhe

2007-01-01

The effect of transverse wave vector and magnetic fields on resonant tunneling times in double-barrier structures, which is significant but has been frequently omitted in previous theoretical methods, has been reported in this paper. The analytical expressions of the longitudinal energies of quasibound levels (LEQBL) and the lifetimes of quasibound levels (LQBL) in symmetrical double-barrier (SDB) structures have been derived as a function of transverse wave vector and longitudinal magnetic fields perpendicular to interfaces. Based on our derived analytical expressions, the LEQBL and LQBL dependence upon transverse wave vector and longitudinal magnetic fields has been explored numerically for a SDB structure. Model calculations show that the LEQBL decrease monotonically and the LQBL shorten with increasing transverse wave vector, and each original LEQBL splits to a series of sub-LEQBL which shift nearly linearly toward the well bottom and the lifetimes of quasibound level series (LQBLS) shorten with increasing Landau-level indices and magnetic fields.

Efficient transduction of equine adipose-derived mesenchymal stem cells by VSV-G pseudotyped lentiviral vectors.

PubMed

Petersen, Gayle F; Hilbert, Bryan; Trope, Gareth; Kalle, Wouter; Strappe, Padraig

2014-12-01

Equine adipose-derived mesenchymal stem cells (EADMSC) provide a unique cell-based approach for treatment of a variety of equine musculoskeletal injuries, via regeneration of diseased or damaged tissue, or the secretion of immunomodulatory molecules. These capabilities can be further enhanced by genetic modification using lentiviral vectors, which provide a safe and efficient method of gene delivery. We investigated the suitability of lentiviral vector technology for gene delivery into EADMSC, using GFP expressing lentiviral vectors pseudotyped with the G glycoprotein from the vesicular stomatitis virus (V-GFP) or, for the first time, the baculovirus gp64 envelope protein (G-GFP). In this study, we produced similarly high titre V-GFP and G-GFP lentiviral vectors. Flow cytometric analysis showed efficient transduction using V-GFP; however G-GFP exhibited a poor ability to transduce EADMSC. Transduction resulted in sustained GFP expression over four passages, with minimal effects on cell viability and doubling time, and an unaltered chondrogenic differentiation potential. Copyright © 2014 Elsevier Ltd. All rights reserved.

Elastic and acoustic wavefield decompositions and application to reverse time migrations

NASA Astrophysics Data System (ADS)

Wang, Wenlong

P- and S-waves coexist in elastic wavefields, and separation between them is an essential step in elastic reverse-time migrations (RTMs). Unlike the traditional separation methods that use curl and divergence operators, which do not preserve the wavefield vector component information, we propose and compare two vector decomposition methods, which preserve the same vector components that exist in the input elastic wavefield. The amplitude and phase information is automatically preserved, so no amplitude or phase corrections are required. The decoupled propagation method is extended from elastic to viscoelastic wavefields. To use the decomposed P and S vector wavefields and generate PP and PS images, we create a new 2D migration context for isotropic, elastic RTM which includes PS vector decomposition; the propagation directions of both incident and reflected P- and S-waves are calculated directly from the stress and particle velocity definitions of the decomposed P- and S-wave Poynting vectors. Then an excitation-amplitude image condition that scales the receiver wavelet by the source vector magnitude produces angle-dependent images of PP and PS reflection coefficients with the correct polarities, polarization, and amplitudes. It thus simplifies the process of obtaining PP and PS angle-domain common-image gathers (ADCIGs); it is less effort to generate ADCIGs from vector data than from scalar data. Besides P- and S-waves decomposition, separations of up- and down-going waves are also a part of processing of multi-component recorded data and propagating wavefields. A complex trace based up/down separation approach is extended from acoustic to elastic, and combined with P- and S-wave decomposition by decoupled propagation. This eliminates the need for a Fourier transform over time, thereby significantly reducing the storage cost and improving computational efficiency. Wavefield decomposition is applied to both synthetic elastic VSP data and propagating wavefield snapshots. Poynting vectors obtained from the particle-velocity and stress fields after P/S and up/down decompositions are much more accurate than those without. The up/down separation algorithm is also applicable in acoustic RTMs, where both (forward-time extrapolated) source and (reverse-time extrapolated) receiver wavefields are decomposed into up-going and down-going parts. Together with the crosscorrelation imaging condition, four images (down-up, up-down, up-up and down-down) are generated, which facilitate the analysis of artifacts and the imaging ability of the four images. Artifacts may exist in all the decomposed images, but their positions and types are different. The causes of artifacts in different images are explained and illustrated with sketches and numerical tests.

An Energy Scaled and Expanded Vector-Based Forwarding Scheme for Industrial Underwater Acoustic Sensor Networks with Sink Mobility.

PubMed

Wadud, Zahid; Hussain, Sajjad; Javaid, Nadeem; Bouk, Safdar Hussain; Alrajeh, Nabil; Alabed, Mohamad Souheil; Guizani, Nadra

2017-09-30

Industrial Underwater Acoustic Sensor Networks (IUASNs) come with intrinsic challenges like long propagation delay, small bandwidth, large energy consumption, three-dimensional deployment, and high deployment and battery replacement cost. Any routing strategy proposed for IUASN must take into account these constraints. The vector based forwarding schemes in literature forward data packets to sink using holding time and location information of the sender, forwarder, and sink nodes. Holding time suppresses data broadcasts; however, it fails to keep energy and delay fairness in the network. To achieve this, we propose an Energy Scaled and Expanded Vector-Based Forwarding (ESEVBF) scheme. ESEVBF uses the residual energy of the node to scale and vector pipeline distance ratio to expand the holding time. Resulting scaled and expanded holding time of all forwarding nodes has a significant difference to avoid multiple forwarding, which reduces energy consumption and energy balancing in the network. If a node has a minimum holding time among its neighbors, it shrinks the holding time and quickly forwards the data packets upstream. The performance of ESEVBF is analyzed through in network scenario with and without node mobility to ensure its effectiveness. Simulation results show that ESEVBF has low energy consumption, reduces forwarded data copies, and less end-to-end delay.

Development and test of electromechanical actuators for thrust vector control

NASA Technical Reports Server (NTRS)

Weir, Rae A.; Cowan, John R.

1993-01-01

A road map of milestones toward the goal of a full scale Redesigned Solid Rocket Motor/Flight Support Motor (RSRM/FSM) hot fire test is discussed. These milestones include: component feasibility, full power system demonstration, SSME hot fire tests, and RSRM hot fire tests. The participation of the Marshall Space Flight Center is emphasized.

Full-Physics Inverse Learning Machine for Satellite Remote Sensing Retrievals

NASA Astrophysics Data System (ADS)

Loyola, D. G.

2017-12-01

The satellite remote sensing retrievals are usually ill-posed inverse problems that are typically solved by finding a state vector that minimizes the residual between simulated data and real measurements. The classical inversion methods are very time-consuming as they require iterative calls to complex radiative-transfer forward models to simulate radiances and Jacobians, and subsequent inversion of relatively large matrices. In this work we present a novel and extremely fast algorithm for solving inverse problems called full-physics inverse learning machine (FP-ILM). The FP-ILM algorithm consists of a training phase in which machine learning techniques are used to derive an inversion operator based on synthetic data generated using a radiative transfer model (which expresses the "full-physics" component) and the smart sampling technique, and an operational phase in which the inversion operator is applied to real measurements. FP-ILM has been successfully applied to the retrieval of the SO2 plume height during volcanic eruptions and to the retrieval of ozone profile shapes from UV/VIS satellite sensors. Furthermore, FP-ILM will be used for the near-real-time processing of the upcoming generation of European Sentinel sensors with their unprecedented spectral and spatial resolution and associated large increases in the amount of data.

On the use of finite difference matrix-vector products in Newton-Krylov solvers for implicit climate dynamics with spectral elements

DOE PAGES

Woodward, Carol S.; Gardner, David J.; Evans, Katherine J.

2015-01-01

Efficient solutions of global climate models require effectively handling disparate length and time scales. Implicit solution approaches allow time integration of the physical system with a step size governed by accuracy of the processes of interest rather than by stability of the fastest time scales present. Implicit approaches, however, require the solution of nonlinear systems within each time step. Usually, a Newton's method is applied to solve these systems. Each iteration of the Newton's method, in turn, requires the solution of a linear model of the nonlinear system. This model employs the Jacobian of the problem-defining nonlinear residual, but thismore » Jacobian can be costly to form. If a Krylov linear solver is used for the solution of the linear system, the action of the Jacobian matrix on a given vector is required. In the case of spectral element methods, the Jacobian is not calculated but only implemented through matrix-vector products. The matrix-vector multiply can also be approximated by a finite difference approximation which may introduce inaccuracy in the overall nonlinear solver. In this paper, we review the advantages and disadvantages of finite difference approximations of these matrix-vector products for climate dynamics within the spectral element shallow water dynamical core of the Community Atmosphere Model.« less

Lentiviral Vector Induced Insertional Haploinsufficiency of Ebf1 Causes Murine Leukemia

PubMed Central

Heckl, Dirk; Schwarzer, Adrian; Haemmerle, Reinhard; Steinemann, Doris; Rudolph, Cornelia; Skawran, Britta; Knoess, Sabine; Krause, Johanna; Li, Zhixiong; Schlegelberger, Brigitte; Baum, Christopher; Modlich, Ute

2012-01-01

Integrating vectors developed on the basis of various retroviruses have demonstrated therapeutic potential following genetic modification of long-lived hematopoietic stem and progenitor cells. Lentiviral vectors (LV) are assumed to circumvent genotoxic events previously observed with γ-retroviral vectors, due to their integration bias to transcription units in comparison to the γ-retroviral preference for promoter regions and CpG islands. However, recently several studies have revealed the potential for gene activation by LV insertions. Here, we report a murine acute B-lymphoblastic leukemia (B-ALL) triggered by insertional gene inactivation. LV integration occurred into the 8th intron of Ebf1, a major regulator of B-lymphopoiesis. Various aberrant splice variants could be detected that involved splice donor and acceptor sites of the lentiviral construct, inducing downregulation of Ebf1 full-length message. The transcriptome signature was compatible with loss of this major determinant of B-cell differentiation, with partial acquisition of myeloid markers, including Csf1r (macrophage colony-stimulating factor (M-CSF) receptor). This was accompanied by receptor phosphorylation and STAT5 activation, both most likely contributing to leukemic progression. Our results highlight the risk of intragenic vector integration to initiate leukemia by inducing haploinsufficiency of a tumor suppressor gene. We propose to address this risk in future vector design. PMID:22472950

750 GeV diphotons: implications for supersymmetric unification II

DOE PAGES

Hall, Lawrence J.; Harigaya, Keisuke; Nomura, Yasunori

2016-07-29

Perturbative supersymmetric gauge coupling unification is possible in six theories where complete SU (5) TeV-scale multiplets of vector matter account for the size of the reported 750 GeV diphoton resonance, interpreted as a singlet multiplet S=(s+ia)/√2. One of these has a full generation of vector matter and a unified gauge coupling αG ~ 1. The diphoton signal rate is enhanced by loops of vector squarks and sleptons, especially when the trilinear A couplings are large. If the SH uH d coupling is absent, both s and a can contribute to the resonance, which may then have a large apparent widthmore » if the mass splitting from s and a arises from loops of vector matter. The width depends sensitively on A parameters and phases of the vector squark and slepton masses. Vector quarks and/or squarks are expected to be in reach of the LHC. If the SH uH d coupling is present, a leads to a narrow diphoton resonance, while a second resonance with decays s → hh, W +W – , ZZ is likely to be discovered at future LHC runs. In some of the theories a non-standard origin or running of the soft parameters is required, for example involving conformal hidden sector interactions.« less

Adenoviral vectors elicit humoral immunity against variable loop 2 of clade C HIV-1 gp120 via "Antigen Capsid-Incorporation" strategy.

PubMed

Gu, Linlin; Krendelchtchikova, Valentina; Krendelchtchikov, Alexandre; Farrow, Anitra L; Derdeyn, Cynthia A; Matthews, Qiana L

2016-01-01

Adenoviral (Ad) vectors in combination with the "Antigen Capsid-Incorporation" strategy have been applied in developing HIV-1 vaccines, due to the vectors׳ abilities in incorporating and inducing immunity of capsid-incorporated antigens. Variable loop 2 (V2)-specific antibodies were suggested in the RV144 trial to correlate with reduced HIV-1 acquisition, which highlights the importance of developing novel HIV-1 vaccines by targeting the V2 loop. Therefore, the V2 loop of HIV-1 has been incorporated into the Ad capsid protein. We generated adenovirus serotype 5 (Ad5) vectors displaying variable loop 2 (V2) of HIV-1 gp120, with the "Antigen Capsid-Incorporation" strategy. To assess the incorporation capabilities on hexon hypervariable region1 (HVR1) and protein IX (pIX), 20aa or full length (43aa) of V2 and V1V2 (67aa) were incorporated, respectively. Immunizations with the recombinant vectors significantly generated antibodies against both linear and discontinuous V2 epitopes. The immunizations generated durable humoral immunity against V2. This study will lead to more stringent development of various serotypes of adenovirus-vectored V2 vaccine candidates, based on breakthroughs regarding the immunogenicity of V2. Copyright © 2015. Published by Elsevier Inc.

Vectorization efforts to increase Gram-negative intracellular drug concentration: a case study on HldE-K inhibitors.

PubMed

Atamanyuk, Dmytro; Faivre, Fabien; Oxoby, Mayalen; Ledoussal, Benoit; Drocourt, Elodie; Moreau, François; Gerusz, Vincent

2013-03-14

In this paper, we present different strategies to vectorize HldE kinase inhibitors with the goal to improve their gram-negative intracellular concentration. Syntheses and biological effects of siderophoric, aminoglycosidic, amphoteric, and polycationic vectors are discussed. While siderophoric and amphoteric vectorization efforts proved to be disappointing in this series, aminoglycosidic and polycationic vectors were able for the first time to achieve synergistic effects of our inhibitors with erythromycin. Although these effects proved to be nonspecific, this study provides information about the required stereoelectronic arrangement of the polycationic amines and their basicity requirements to fulfill outer membrane destabilization resulting in better erythromycin synergies.

[A research on real-time ventricular QRS classification methods for single-chip-microcomputers].

PubMed

Peng, L; Yang, Z; Li, L; Chen, H; Chen, E; Lin, J

1997-05-01

Ventricular QRS classification is key technique of ventricular arrhythmias detection in single-chip-microcomputer based dynamic electrocardiogram real-time analyser. This paper adopts morphological feature vector including QRS amplitude, interval information to reveal QRS morphology. After studying the distribution of QRS morphology feature vector of MIT/BIH DB ventricular arrhythmia files, we use morphological feature vector cluster to classify multi-morphology QRS. Based on the method, morphological feature parameters changing method which is suitable to catch occasional ventricular arrhythmias is presented. Clinical experiments verify missed ventricular arrhythmia is less than 1% by this method.

A Field Trial of Alternative Targeted Screening Strategies for Chagas Disease in Arequipa, Peru

PubMed Central

Hunter, Gabrielle C.; Borrini-Mayorí, Katty; Ancca Juárez, Jenny; Castillo Neyra, Ricardo; Verastegui, Manuela R.; Malaga Chavez, Fernando S.; Cornejo del Carpio, Juan Geny; Córdova Benzaquen, Eleazar; Náquira, César; Gilman, Robert H.; Bern, Caryn; Levy, Michael Z.

2012-01-01

Background Chagas disease is endemic in the rural areas of southern Peru and a growing urban problem in the regional capital of Arequipa, population ∼860,000. It is unclear how to implement cost-effective screening programs across a large urban and periurban environment. Methods We compared four alternative screening strategies in 18 periurban communities, testing individuals in houses with 1) infected vectors; 2) high vector densities; 3) low vector densities; and 4) no vectors. Vector data were obtained from routine Ministry of Health insecticide application campaigns. We performed ring case detection (radius of 15 m) around seropositive individuals, and collected data on costs of implementation for each strategy. Results Infection was detected in 21 of 923 (2.28%) participants. Cases had lived more time on average in rural places than non-cases (7.20 years versus 3.31 years, respectively). Significant risk factors on univariate logistic regression for infection were age (OR 1.02; p = 0.041), time lived in a rural location (OR 1.04; p = 0.022), and time lived in an infested area (OR 1.04; p = 0.008). No multivariate model with these variables fit the data better than a simple model including only the time lived in an area with triatomine bugs. There was no significant difference in prevalence across the screening strategies; however a self-assessment of disease risk may have biased participation, inflating prevalence among residents of houses where no infestation was detected. Testing houses with infected-vectors was least expensive. Ring case detection yielded four secondary cases in only one community, possibly due to vector-borne transmission in this community, apparently absent in the others. Conclusions Targeted screening for urban Chagas disease is promising in areas with ongoing vector-borne transmission; however, these pockets of epidemic transmission remain difficult to detect a priori. The flexibility to adapt to the epidemiology that emerges during screening is key to an efficient case detection intervention. In heterogeneous urban environments, self-assessments of risk and simple residence history questionnaires may be useful to identify those at highest risk for Chagas disease to guide diagnostic efforts. PMID:22253939

A field trial of alternative targeted screening strategies for Chagas disease in Arequipa, Peru.

PubMed

Hunter, Gabrielle C; Borrini-Mayorí, Katty; Ancca Juárez, Jenny; Castillo Neyra, Ricardo; Verastegui, Manuela R; Malaga Chavez, Fernando S; Cornejo del Carpio, Juan Geny; Córdova Benzaquen, Eleazar; Náquira, César; Gilman, Robert H; Bern, Caryn; Levy, Michael Z

2012-01-01

Chagas disease is endemic in the rural areas of southern Peru and a growing urban problem in the regional capital of Arequipa, population ∼860,000. It is unclear how to implement cost-effective screening programs across a large urban and periurban environment. We compared four alternative screening strategies in 18 periurban communities, testing individuals in houses with 1) infected vectors; 2) high vector densities; 3) low vector densities; and 4) no vectors. Vector data were obtained from routine Ministry of Health insecticide application campaigns. We performed ring case detection (radius of 15 m) around seropositive individuals, and collected data on costs of implementation for each strategy. Infection was detected in 21 of 923 (2.28%) participants. Cases had lived more time on average in rural places than non-cases (7.20 years versus 3.31 years, respectively). Significant risk factors on univariate logistic regression for infection were age (OR 1.02; p = 0.041), time lived in a rural location (OR 1.04; p = 0.022), and time lived in an infested area (OR 1.04; p = 0.008). No multivariate model with these variables fit the data better than a simple model including only the time lived in an area with triatomine bugs. There was no significant difference in prevalence across the screening strategies; however a self-assessment of disease risk may have biased participation, inflating prevalence among residents of houses where no infestation was detected. Testing houses with infected-vectors was least expensive. Ring case detection yielded four secondary cases in only one community, possibly due to vector-borne transmission in this community, apparently absent in the others. Targeted screening for urban Chagas disease is promising in areas with ongoing vector-borne transmission; however, these pockets of epidemic transmission remain difficult to detect a priori. The flexibility to adapt to the epidemiology that emerges during screening is key to an efficient case detection intervention. In heterogeneous urban environments, self-assessments of risk and simple residence history questionnaires may be useful to identify those at highest risk for Chagas disease to guide diagnostic efforts.

Multipole Vectors: Decomposing Functions on a Sphere

NASA Astrophysics Data System (ADS)

Copi, C. J.; Huterer, D.; Starkman, G. D.

2011-09-01

We propose a novel representation of cosmic microwave anisotropy maps, where each multipole order l is represented by l unit vectors pointing in directions on the sky and an overall magnitude. These "multipole vectors and scalars" transform as vectors under rotations. Like the usual spherical harmonics, multipole vectors form an irreducible representation of the proper rotation group SO(3). However, they are related to the familiar spherical harmonic coefficients, alm, in a nonlinear way, and are therefore sensitive to different aspects of the CMB anisotropy. Nevertheless, it is straightforward to determine the multipole vectors for a given CMB map and we present an algorithm to compute them. Using the WMAP full-sky maps, we perform several tests of the hypothesis that the CMB anisotropy is statistically isotropic and Gaussian random. We find that the result from comparing the oriented area of planes defined by these vectors between multipole pairs 2<=l1!=l2<=8 is inconsistent with the isotropic Gaussian hypothesis at the 99.4% level for the ILC map and at 98.9% level for the cleaned map of Tegmark et al. A particular correlation is suggested between the l=3 and l=8 multipoles, as well as several other pairs. This effect is entirely different from the now familiar planarity and alignment of the quadrupole and octupole: while the aforementioned is fairly unlikely, the multipole vectors indicate correlations not expected in Gaussian random skies that make them unusually likely. The result persists after accounting for pixel noise and after assuming a residual 10% dust contamination in the cleaned WMAP map. While the definitive analysis of these results will require more work, we hope that multipole vectors will become a valuable tool for various cosmological tests, in particular those of cosmic isotropy.

A force vector and surface orientation sensor for intelligent grasping

NASA Technical Reports Server (NTRS)

Mcglasson, W. D.; Lorenz, R. D.; Duffie, N. A.; Gale, K. L.

1991-01-01

The paper discusses a force vector and surface orientation sensor suitable for intelligent grasping. The use of a novel four degree-of-freedom force vector robotic fingertip sensor allows efficient, real time intelligent grasping operations. The basis of sensing for intelligent grasping operations is presented and experimental results demonstrate the accuracy and ease of implementation of this approach.

Superinfection exclusion of the ruminant pathogen anaplasma marginale in the tick vector is dependent on time between exposures to the strains

USDA-ARS?s Scientific Manuscript database

The remarkable genetic diversity of vector-borne pathogens allows for the establishment of superinfection in the mammalian host. To have a long-term impact on population strain structure, the introduced strains must also be transmitted by a vector population that has been exposed to the existing pri...

Temporal Variation in the Abundance and Timing of Daily Activity of Chagas Disease Vector Triatoma gerstaeckeri (Stål, 1859) in a Natural Habitat in the Lower Rio Grande Valley, South Texas.

PubMed

Flores, A; Vitek, C; Feria-Arroyo, T P; Fredensborg, B L

2017-10-01

Chagas disease caused by Trypanosoma cruzi is a burden to millions of people in South and Central America. A sylvatic life cycle of the parasite exists in the Southern United States, but recent studies indicate an active peri-domestic life cycle of T. cruzi in Texas. The United States-Mexico border region in Texas displays areas of high poverty and sub-standard housing conditions which are important risk factors for a potential spill-over transmission to a domestic life cycle including humans. The objectives of the study were to examine short- and long-term temporal variation in vector activity and to evaluate the effect of different combinations of attractants on the capture of potential triatomine vectors. We collected local triatomine vectors (all of them identified as Triatoma gerstaeckeri) from a natural habitat in South Texas during the course of a year. The exact time of collection was recorded to examine the timing of flight activity of the triatomine vector. We also conducted a comparative study of the efficiency of 2 commonly used attractants (light and CO 2 ) and the combination of those on the capture rate of Tr. gerstaeckeri. Our study indicates a short season of dispersal of Tr. gerstaeckeri (April/May) and it suggests a unimodal distribution of activity peaking between 2 and 3 hr after sunset. Ultra-violet light served as the main attractant of Tr. gerstaeckeri while CO 2 from dry ice did not significantly contribute to the collection of vectors. The pronounced timing of activity in Tr. gerstaeckeri reported in this study contributes to our understanding of the epidemiology of T. cruzi in wildlife and its potential as a Chagas disease vector to humans in the Rio Grande Valley, South Texas.

Vector-model-supported approach in prostate plan optimization

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

Liu, Eva Sau Fan; Department of Health Technology and Informatics, The Hong Kong Polytechnic University; Wu, Vincent Wing Cheung

Lengthy time consumed in traditional manual plan optimization can limit the use of step-and-shoot intensity-modulated radiotherapy/volumetric-modulated radiotherapy (S&S IMRT/VMAT). A vector model base, retrieving similar radiotherapy cases, was developed with respect to the structural and physiologic features extracted from the Digital Imaging and Communications in Medicine (DICOM) files. Planning parameters were retrieved from the selected similar reference case and applied to the test case to bypass the gradual adjustment of planning parameters. Therefore, the planning time spent on the traditional trial-and-error manual optimization approach in the beginning of optimization could be reduced. Each S&S IMRT/VMAT prostate reference database comprised 100more » previously treated cases. Prostate cases were replanned with both traditional optimization and vector-model-supported optimization based on the oncologists' clinical dose prescriptions. A total of 360 plans, which consisted of 30 cases of S&S IMRT, 30 cases of 1-arc VMAT, and 30 cases of 2-arc VMAT plans including first optimization and final optimization with/without vector-model-supported optimization, were compared using the 2-sided t-test and paired Wilcoxon signed rank test, with a significance level of 0.05 and a false discovery rate of less than 0.05. For S&S IMRT, 1-arc VMAT, and 2-arc VMAT prostate plans, there was a significant reduction in the planning time and iteration with vector-model-supported optimization by almost 50%. When the first optimization plans were compared, 2-arc VMAT prostate plans had better plan quality than 1-arc VMAT plans. The volume receiving 35 Gy in the femoral head for 2-arc VMAT plans was reduced with the vector-model-supported optimization compared with the traditional manual optimization approach. Otherwise, the quality of plans from both approaches was comparable. Vector-model-supported optimization was shown to offer much shortened planning time and iteration number without compromising the plan quality.« less

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.

Space Object Classification Using Fused Features of Time Series Data

NASA Astrophysics Data System (ADS)

Jia, B.; Pham, K. D.; Blasch, E.; Shen, D.; Wang, Z.; Chen, G.

In this paper, a fused feature vector consisting of raw time series and texture feature information is proposed for space object classification. The time series data includes historical orbit trajectories and asteroid light curves. The texture feature is derived from recurrence plots using Gabor filters for both unsupervised learning and supervised learning algorithms. The simulation results show that the classification algorithms using the fused feature vector achieve better performance than those using raw time series or texture features only.

A simple method of equine limb force vector analysis and its potential applications.

PubMed

Hobbs, Sarah Jane; Robinson, Mark A; Clayton, Hilary M

2018-01-01

Ground reaction forces (GRF) measured during equine gait analysis are typically evaluated by analyzing discrete values obtained from continuous force-time data for the vertical, longitudinal and transverse GRF components. This paper describes a simple, temporo-spatial method of displaying and analyzing sagittal plane GRF vectors. In addition, the application of statistical parametric mapping (SPM) is introduced to analyse differences between contra-lateral fore and hindlimb force-time curves throughout the stance phase. The overall aim of the study was to demonstrate alternative methods of evaluating functional (a)symmetry within horses. GRF and kinematic data were collected from 10 horses trotting over a series of four force plates (120 Hz). The kinematic data were used to determine clean hoof contacts. The stance phase of each hoof was determined using a 50 N threshold. Vertical and longitudinal GRF for each stance phase were plotted both as force-time curves and as force vector diagrams in which vectors originating at the centre of pressure on the force plate were drawn at intervals of 8.3 ms for the duration of stance. Visual evaluation was facilitated by overlay of the vector diagrams for different limbs. Summary vectors representing the magnitude (VecMag) and direction (VecAng) of the mean force over the entire stance phase were superimposed on the force vector diagram. Typical measurements extracted from the force-time curves (peak forces, impulses) were compared with VecMag and VecAng using partial correlation (controlling for speed). Paired samples t -tests (left v. right diagonal pair comparison and high v. low vertical force diagonal pair comparison) were performed on discrete and vector variables using traditional methods and Hotelling's T 2 tests on normalized stance phase data using SPM. Evidence from traditional statistical tests suggested that VecMag is more influenced by the vertical force and impulse, whereas VecAng is more influenced by the longitudinal force and impulse. When used to evaluate mean data from the group of ten sound horses, SPM did not identify differences between the left and right contralateral limb pairs or between limb pairs classified according to directional asymmetry. When evaluating a single horse, three periods were identified during which differences in the forces between the left and right forelimbs exceeded the critical threshold ( p  < .01). Traditional statistical analysis of 2D GRF peak values, summary vector variables and visual evaluation of force vector diagrams gave harmonious results and both methods identified the same inter-limb asymmetries. As alpha was more tightly controlled using SPM, significance was only found in the individual horse although T 2 plots followed the same trends as discrete analysis for the group. The techniques of force vector analysis and SPM hold promise for investigations of sidedness and asymmetry in horses.

A new technique for the measurement of surface shear stress vectors using liquid crystal coatings

NASA Technical Reports Server (NTRS)

Reda, Daniel C.; Muratore, J. J., Jr.

1994-01-01

Research has recently shown that liquid crystal coating (LCC) color-change response to shear depends on both shear stress magnitude and direction. Additional research was thus conducted to extend the LCC method from a flow-visualization tool to a surface shear stress vector measurement technique. A shear-sensitive LCC was applied to a planar test surface and illuminated by white light from the normal direction. A fiber optic probe was used to capture light scattered by the LCC from a point on the centerline of a turbulent, tangential-jet flow. Both the relative shear stress magnitude and the relative in-plane view angle between the sensor and the centerline shear vector were systematically varied. A spectrophotometer was used to obtain scattered-light spectra which were used to quantify the LCC color (dominant wavelength) as a function of shear stress magnitude and direction. At any fixed shear stress magnitude, the minimum dominant wavelength was measured when the shear vector was aligned with and directed away from the observer; changes in the relative in-plane view angle to either side of this vector/observer aligned position resulted in symmetric Gaussian increases in measured dominant wavelength. Based on these results, a vector measurement methodology, involving multiple oblique-view observations of the test surface, was formulated. Under present test conditions, the measurement resolution of this technique was found to be +/- 1 deg for vector orientations and +/- 5% for vector magnitudes. An approach t o extend the present methodology to full-surface applications is proposed.

The myeloid-binding peptide adenoviral vector enables multi-organ vascular endothelial gene targeting.

PubMed

Lu, Zhi Hong; Kaliberov, Sergey; Zhang, Jingzhu; Muz, Barbara; Azab, Abdel K; Sohn, Rebecca E; Kaliberova, Lyudmila; Du, Yingqiu; Curiel, David T; Arbeit, Jeffrey M

2014-08-01

Vascular endothelial cells (ECs) are ideal gene therapy targets as they provide widespread tissue access and are the first contact surfaces following intravenous vector administration. Human recombinant adenovirus serotype 5 (Ad5) is the most frequently used gene transfer system because of its appreciable transgene payload capacity and lack of somatic mutation risk. However, standard Ad5 vectors predominantly transduce liver but not the vasculature following intravenous administration. We recently developed an Ad5 vector with a myeloid cell-binding peptide (MBP) incorporated into the knob-deleted, T4 fibritin chimeric fiber (Ad.MBP). This vector was shown to transduce pulmonary ECs presumably via a vector handoff mechanism. Here we tested the body-wide tropism of the Ad.MBP vector, its myeloid cell necessity, and vector-EC expression dose response. Using comprehensive multi-organ co-immunofluorescence analysis, we discovered that Ad.MBP produced widespread EC transduction in the lung, heart, kidney, skeletal muscle, pancreas, small bowel, and brain. Surprisingly, Ad.MBP retained hepatocyte tropism albeit at a reduced frequency compared with the standard Ad5. While binding specifically to myeloid cells ex vivo, multi-organ Ad.MBP expression was not dependent on circulating monocytes or macrophages. Ad.MBP dose de-escalation maintained full lung-targeting capacity but drastically reduced transgene expression in other organs. Swapping the EC-specific ROBO4 for the CMV promoter/enhancer abrogated hepatocyte expression but also reduced gene expression in other organs. Collectively, our multilevel targeting strategy could enable therapeutic biological production in previously inaccessible organs that pertain to the most debilitating or lethal human diseases.

Implementation theory of distortion-invariant pattern recognition for optical and digital signal processing systems

NASA Astrophysics Data System (ADS)

Lhamon, Michael Earl

A pattern recognition system which uses complex correlation filter banks requires proportionally more computational effort than single-real valued filters. This introduces increased computation burden but also introduces a higher level of parallelism, that common computing platforms fail to identify. As a result, we consider algorithm mapping to both optical and digital processors. For digital implementation, we develop computationally efficient pattern recognition algorithms, referred to as, vector inner product operators that require less computational effort than traditional fast Fourier methods. These algorithms do not need correlation and they map readily onto parallel digital architectures, which imply new architectures for optical processors. These filters exploit circulant-symmetric matrix structures of the training set data representing a variety of distortions. By using the same mathematical basis as with the vector inner product operations, we are able to extend the capabilities of more traditional correlation filtering to what we refer to as "Super Images". These "Super Images" are used to morphologically transform a complicated input scene into a predetermined dot pattern. The orientation of the dot pattern is related to the rotational distortion of the object of interest. The optical implementation of "Super Images" yields feature reduction necessary for using other techniques, such as artificial neural networks. We propose a parallel digital signal processor architecture based on specific pattern recognition algorithms but general enough to be applicable to other similar problems. Such an architecture is classified as a data flow architecture. Instead of mapping an algorithm to an architecture, we propose mapping the DSP architecture to a class of pattern recognition algorithms. Today's optical processing systems have difficulties implementing full complex filter structures. Typically, optical systems (like the 4f correlators) are limited to phase-only implementation with lower detection performance than full complex electronic systems. Our study includes pseudo-random pixel encoding techniques for approximating full complex filtering. Optical filter bank implementation is possible and they have the advantage of time averaging the entire filter bank at real time rates. Time-averaged optical filtering is computational comparable to billions of digital operations-per-second. For this reason, we believe future trends in high speed pattern recognition will involve hybrid architectures of both optical and DSP elements.

The simulation on diode-clamped five-level converters common-mode voltage suppression with zero-vector PWM strategy

NASA Astrophysics Data System (ADS)

Zhang, Yonggao; Gao, Yanli; Long, Lizhong

2012-04-01

More and more researchers have great concern on the issue of Common-mode voltage (CMV) in high voltage large power converter. A novel common-mode voltage suppression scheme based on zero-vector PWM strategy (ZVPWM) is present in this paper. Taking a diode-clamped five-level converter as example, the principle of zero vector PWM common-mode voltage (ZCMVPWM) suppression method is studied in detail. ZCMVPWM suppression strategy is including four important parts, which are locating the sector of reference voltage vector, locating the small triangular sub-sector of reference voltage vector, reference vector synthesis, and calculating the operating time of vector. The principles of four important pars are illustrated in detail and the corresponding MATLAB models are established. System simulation and experimental results are provided. It gives some consultation value for the development and research of multi-level converters.

The evolution of adenoviral vectors through genetic and chemical surface modifications.

PubMed

Capasso, Cristian; Garofalo, Mariangela; Hirvinen, Mari; Cerullo, Vincenzo

2014-02-17

A long time has passed since the first clinical trial with adenoviral (Ad) vectors. Despite being very promising, Ad vectors soon revealed their limitations in human clinical trials. The pre-existing immunity, the marked liver tropism and the high toxicity of first generation Ad (FG-Ad) vectors have been the main challenges for the development of new approaches. Significant effort toward the development of genetically and chemically modified adenoviral vectors has enabled researchers to create more sophisticated vectors for gene therapy, with an improved safety profile and a higher transduction ability of different tissues. In this review, we will describe the latest findings in the high-speed, evolving field of genetic and chemical modifications of adenoviral vectors, a field in which different disciplines, such as biomaterial research, virology and immunology, co-operate synergistically to create better gene therapy tools for modern challenges.

Vectoring of parallel synthetic jets

NASA Astrophysics Data System (ADS)

Berk, Tim; Ganapathisubramani, Bharathram; Gomit, Guillaume

2015-11-01

A pair of parallel synthetic jets can be vectored by applying a phase difference between the two driving signals. The resulting jet can be merged or bifurcated and either vectored towards the actuator leading in phase or the actuator lagging in phase. In the present study, the influence of phase difference and Strouhal number on the vectoring behaviour is examined experimentally. Phase-locked vorticity fields, measured using Particle Image Velocimetry (PIV), are used to track vortex pairs. The physical mechanisms that explain the diversity in vectoring behaviour are observed based on the vortex trajectories. For a fixed phase difference, the vectoring behaviour is shown to be primarily influenced by pinch-off time of vortex rings generated by the synthetic jets. Beyond a certain formation number, the pinch-off timescale becomes invariant. In this region, the vectoring behaviour is determined by the distance between subsequent vortex rings. We acknowledge the financial support from the European Research Council (ERC grant agreement no. 277472).

Acceleration of GPU-based Krylov solvers via data transfer reduction

DOE PAGES

Anzt, Hartwig; Tomov, Stanimire; Luszczek, Piotr; ...

2015-04-08

Krylov subspace iterative solvers are often the method of choice when solving large sparse linear systems. At the same time, hardware accelerators such as graphics processing units continue to offer significant floating point performance gains for matrix and vector computations through easy-to-use libraries of computational kernels. However, as these libraries are usually composed of a well optimized but limited set of linear algebra operations, applications that use them often fail to reduce certain data communications, and hence fail to leverage the full potential of the accelerator. In this study, we target the acceleration of Krylov subspace iterative methods for graphicsmore » processing units, and in particular the Biconjugate Gradient Stabilized solver that significant improvement can be achieved by reformulating the method to reduce data-communications through application-specific kernels instead of using the generic BLAS kernels, e.g. as provided by NVIDIA’s cuBLAS library, and by designing a graphics processing unit specific sparse matrix-vector product kernel that is able to more efficiently use the graphics processing unit’s computing power. Furthermore, we derive a model estimating the performance improvement, and use experimental data to validate the expected runtime savings. Finally, considering that the derived implementation achieves significantly higher performance, we assert that similar optimizations addressing algorithm structure, as well as sparse matrix-vector, are crucial for the subsequent development of high-performance graphics processing units accelerated Krylov subspace iterative methods.« less

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.

How well does the Rayleigh model describe the E-vector distribution of skylight in clear and cloudy conditions? A full-sky polarimetric study.

PubMed

Suhai, Bence; Horváth, Gábor

2004-09-01

We present the first high-resolution maps of Rayleigh behavior in clear and cloudy sky conditions measured by full-sky imaging polarimetry at the wavelengths of 650 nm (red), 550 nm (green), and 450 nm (blue) versus the solar elevation angle thetas. Our maps display those celestial areas at which the deviation deltaalpha = /alphameas - alphaRyleigh/ is below the threshold alphathres = 5 degrees, where alphameas is the angle of polarization of skylight measured by full-sky imaging polarimetry, and alphaRayleigh is the celestial angle of polarization calculated on the basis of the single-scattering Rayleigh model. From these maps we derived the proportion r of the full sky for which the single-scattering Rayleigh model describes well (with an accuracy of deltaalpha = 5 degrees) the E-vector alignment of skylight. Depending on thetas, r is high for clear skies, especially for low solar elevations (40% < r < 70% for thetas < or = 13 degrees). Depending on the cloud cover and the solar illumination, r decreases more or less under cloudy conditions, but sometimes its value remains remarkably high, especially at low solar elevations (rmax = 69% for thetas = 0 degrees). The proportion r of the sky that follows the Rayleigh model is usually higher for shorter wavelengths under clear as well as cloudy sky conditions. This partly explains why the shorter wavelengths are generally preferred by animals navigating by means of the celestial polarization. We found that the celestial E-vector pattern generally follows the Rayleigh pattern well, which is a fundamental hypothesis in the studies of animal orientation and human navigation (e.g., in aircraft flying near the geomagnetic poles and using a polarization sky compass) with the use of the celestial alpha pattern.

Object recognition of real targets using modelled SAR images

NASA Astrophysics Data System (ADS)

Zherdev, D. A.

2017-12-01

In this work the problem of recognition is studied using SAR images. The algorithm of recognition is based on the computation of conjugation indices with vectors of class. The support subspaces for each class are constructed by exception of the most and the less correlated vectors in a class. In the study we examine the ability of a significant feature vector size reduce that leads to recognition time decrease. The images of targets form the feature vectors that are transformed using pre-trained convolutional neural network (CNN).

Characterization and expression analysis of gene encoding heme peroxidase HPX15 in major Indian malaria vector Anopheles stephensi (Diptera: Culicidae).

PubMed

Kajla, Mithilesh; Kakani, Parik; Choudhury, Tania Pal; Gupta, Kuldeep; Gupta, Lalita; Kumar, Sanjeev

2016-06-01

The interaction of mosquito immune system with Plasmodium is critical in determining the vector competence. Thus, blocking the crucial mosquito molecules that regulate parasite development might be effective in controlling the disease transmission. In this study, we characterized a full-length AsHPX15 gene from the major Indian malaria vector Anopheles stephensi. This gene is true ortholog of Anopheles gambiae heme peroxidase AgHPX15 (AGAP013327), which modulates midgut immunity and regulates Plasmodium falciparum development. We found that AsHPX15 is highly induced in mosquito developmental stages and blood fed midguts. In addition, this is a lineage-specific gene that has identical features and 65-99% amino acids identity with other HPX15 genes present in eighteen worldwide-distributed anophelines. We discuss that the conserved HPX15 gene might serve as a common target to manipulate mosquito immunity and arresting Plasmodium development inside the vector host. Copyright © 2016 Elsevier B.V. All rights reserved.

Flanking sequence determination and specific PCR identification of transgenic wheat B102-1-2.

PubMed

Cao, Jijuan; Xu, Junyi; Zhao, Tongtong; Cao, Dongmei; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

2014-01-01

The exogenous fragment sequence and flanking sequence between the exogenous fragment and recombinant chromosome of transgenic wheat B102-1-2 were successfully acquired using genome walking technology. The newly acquired exogenous fragment encoded the full-length sequence of transformed genes with transformed plasmid and corresponding functional genes including ubi, vector pBANF-bar, vector pUbiGUSPlus, vector HSP, reporter vector pUbiGUSPlus, promoter ubiquitin, and coli DH1. A specific polymerase chain reaction (PCR) identification method for transgenic wheat B102-1-2 was established on the basis of designed primers according to flanking sequence. This established specific PCR strategy was validated by using transgenic wheat, transgenic corn, transgenic soybean, transgenic rice, and non-transgenic wheat. A specifically amplified target band was observed only in transgenic wheat B102-1-2. Therefore, this method is characterized by high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of transgenic wheat B102-1-2.

Enhancing and targeting nucleic acid delivery by magnetic force.

PubMed

Plank, Christian; Anton, Martina; Rudolph, Carsten; Rosenecker, Joseph; Krötz, Florian

2003-08-01

Insufficient contact of inherently highly active nucleic acid delivery systems with target cells is a primary reason for their often observed limited efficacy. Physical methods of targeting can overcome this limitation and reduce the risk of undesired side effects due to non-target site delivery. The authors and others have developed a novel means of physical targeting, exploiting magnetic force acting on nucleic acid vectors associated with magnetic particles in order to mediate the rapid contact of vectors with target cells. Here, the principles of magnetic drug and nucleic acid delivery are reviewed, and the facts and potentials of the technique for research and therapeutic applications are discussed. Magnetically enhanced nucleic acid delivery - magnetofection - is universally applicable to viral and non-viral vectors, is extraordinarily rapid, simple and yields saturation level transfection at low dose in vitro. The method is useful for site-specific vector targeting in vivo. Exploiting the full potential of the technique requires an interdisciplinary research effort in magnetic field physics, magnetic particle chemistry, pharmaceutical formulation and medical application.

LCD denoise and the vector mutual information method in the application of the gear fault diagnosis under different working conditions

NASA Astrophysics Data System (ADS)

Xiangfeng, Zhang; Hong, Jiang

2018-03-01

In this paper, the full vector LCD method is proposed to solve the misjudgment problem caused by the change of the working condition. First, the signal from different working condition is decomposed by LCD, to obtain the Intrinsic Scale Component (ISC)whose instantaneous frequency with physical significance. Then, calculate of the cross correlation coefficient between ISC and the original signal, signal denoising based on the principle of mutual information minimum. At last, calculate the sum of absolute Vector mutual information of the sample under different working condition and the denoised ISC as the characteristics to classify by use of Support vector machine (SVM). The wind turbines vibration platform gear box experiment proves that this method can identify fault characteristics under different working conditions. The advantage of this method is that it reduce dependence of man’s subjective experience, identify fault directly from the original data of vibration signal. It will has high engineering value.

Design and experimental verification for optical module of optical vector-matrix multiplier.

PubMed

Zhu, Weiwei; Zhang, Lei; Lu, Yangyang; Zhou, Ping; Yang, Lin

2013-06-20

Optical computing is a new method to implement signal processing functions. The multiplication between a vector and a matrix is an important arithmetic algorithm in the signal processing domain. The optical vector-matrix multiplier (OVMM) is an optoelectronic system to carry out this operation, which consists of an electronic module and an optical module. In this paper, we propose an optical module for OVMM. To eliminate the cross talk and make full use of the optical elements, an elaborately designed structure that involves spherical lenses and cylindrical lenses is utilized in this optical system. The optical design software package ZEMAX is used to optimize the parameters and simulate the whole system. Finally, experimental data is obtained through experiments to evaluate the overall performance of the system. The results of both simulation and experiment indicate that the system constructed can implement the multiplication between a matrix with dimensions of 16 by 16 and a vector with a dimension of 16 successfully.

The synoptic maps of Br from HMI observations

NASA Astrophysics Data System (ADS)

Hayashi, Keiji; Hoeksema, J. Todd; Liu, Sun; Yang, Xudong; Centeno, Rebecca; Leka, K. D.; Barnes, Graham

2012-03-01

The vector magnetic field measurement can, in principal, give the "true" radial component of the magnetic field. We prepare 4 types of synoptic maps of the radial photospheric magnetic field, from the vector magnetic field data disambiguated by means of the minimum energy method developed at NWRA/CoRA, the vector data determined under the potential-field acute assumption, and the vector data determined under the radial-acute assumption, and the standard line-of-sight magnetogram. The models of the global corona, the MHD and the PFSS, are applied to different types of maps. Although the three-dimensional structures of the global coronal magnetic field with different maps are similar and overall agreeing well the AIA full-disk images, noticeable differences among the model outputs are found especially in the high latitude regions. We will show details of these test maps and discuss the issues in determining the radial component of the photospheric magnetic field near the poles and limb.

Using a new discretization approach to design a delayed LQG controller

NASA Astrophysics Data System (ADS)

Haraguchi, M.; Hu, H. Y.

2008-07-01

In general, discrete-time controls have become more and more preferable in engineering because of their easy implementation and simple computations. However, the available discretization approaches for the systems having time delays increase the system dimensions and have a high computational cost. This paper presents an effective discretization approach for the continuous-time systems with an input delay. The approach enables one to transform the input-delay system into a delay-free system, but retain the system dimensions unchanged in the state transformation. To demonstrate an application of the approach, this paper presents the design of an LQ regulator for continuous-time systems with an input delay and gives a state observer with a Kalman filter for estimating the full-state vector from some measurements of the system as well. The case studies in the paper well support the efficacy and efficiency of the proposed approach applied to the vibration control of a three-story structure model with the actuator delay taken into account.

Quantum dot coating of baculoviral vectors enables visualization of transduced cells and tissues

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

Zhao, Ying; Lo, Seong Loong; Zheng, Yuangang

2013-04-26

Highlights: •The use of quantum dot (QD)-labeled viral vectors for in vivo imaging is not well investigated. •A new method to label enveloped baculovirus with glutathione-capped CdTe QDs is developed. •The labeling enables the identification of transduced, cultured cells based on fluorescence. •The labeling also allows evaluation of viral transduction in a real-time manner in living mice. •The method has the potential to assess viral vector-based gene therapy protocols in future. -- Abstract: Imaging of transduced cells and tissues is valuable in developing gene transfer vectors and evaluating gene therapy efficacy. We report here a simple method to use brightmore » and photostable quantum dots to label baculovirus, an emerging gene therapy vector. The labeling was achieved through the non-covalent interaction of glutathione-capped CdTe quantum dots with the virus envelope, without the use of chemical conjugation. The quantum dot labeling was nondestructive to viral transduction function and enabled the identification of baculoviral vector-transduced, living cells based on red fluorescence. When the labeled baculoviral vectors were injected intravenously or intraventricularly for in vivo delivery of a transgene into mice, quantum dot fluorescence signals allow us monitor whether or not the injected tissues were transduced. More importantly, using a dual-color whole-body imaging technology, we demonstrated that in vivo viral transduction could be evaluated in a real-time manner in living mice. Thus, our method of labeling a read-to-use gene delivery vector with quantum dots could be useful towards the improvement of vector design and will have the potential to assess baculovirus-based gene therapy protocols in future.« less

SIC-POVMS and MUBS: Geometrical Relationships in Prime Dimension

NASA Astrophysics Data System (ADS)

Appleby, D. M.

2009-03-01

The paper concerns Weyl-Heisenberg covariant SIC-POVMs (symmetric informationally complete positive operator valued measures) and full sets of MUBs (mutually unbiased bases) in prime dimension. When represented as vectors in generalized Bloch space a SIC-POVM forms a d2-1 dimensional regular simplex (d being the Hilbert space dimension). By contrast, the generalized Bloch vectors representing a full set of MUBs form d+1 mutually orthogonal d-1 dimensional regular simplices. In this paper we show that, in the Weyl-Heisenberg case, there are some simple geometrical relationships between the single SIC-POVM simplex and the d+1 MUB simplices. We go on to give geometrical interpretations of the minimum uncertainty states introduced by Wootters and Sussman, and by Appleby, Dang and Fuchs, and of the fiduciality condition given by Appleby, Dang and Fuchs.

Quasi-steady-state analysis of coupled flashing ratchets.

PubMed

Levien, Ethan; Bressloff, Paul C

2015-10-01

We perform a quasi-steady-state (QSS) reduction of a flashing ratchet to obtain a Brownian particle in an effective potential. The resulting system is analytically tractable and yet preserves essential dynamical features of the full model. We first use the QSS reduction to derive an explicit expression for the velocity of a simple two-state flashing ratchet. In particular, we determine the relationship between perturbations from detailed balance, which are encoded in the transitions rates of the flashing ratchet, and a tilted-periodic potential. We then perform a QSS analysis of a pair of elastically coupled flashing ratchets, which reduces to a Brownian particle moving in a two-dimensional vector field. We suggest that the fixed points of this vector field accurately approximate the metastable spatial locations of the coupled ratchets, which are, in general, impossible to identify from the full system.

Fuzzy Relational Compression Applied on Feature Vectors for Infant Cry Recognition

NASA Astrophysics Data System (ADS)

Reyes-Galaviz, Orion Fausto; Reyes-García, Carlos Alberto

Data compression is always advisable when it comes to handling and processing information quickly and efficiently. There are two main problems that need to be solved when it comes to handling data; store information in smaller spaces and processes it in the shortest possible time. When it comes to infant cry analysis (ICA), there is always the need to construct large sound repositories from crying babies. Samples that have to be analyzed and be used to train and test pattern recognition algorithms; making this a time consuming task when working with uncompressed feature vectors. In this work, we show a simple, but efficient, method that uses Fuzzy Relational Product (FRP) to compresses the information inside a feature vector, building with this a compressed matrix that will help us recognize two kinds of pathologies in infants; Asphyxia and Deafness. We describe the sound analysis, which consists on the extraction of Mel Frequency Cepstral Coefficients that generate vectors which will later be compressed by using FRP. There is also a description of the infant cry database used in this work, along with the training and testing of a Time Delay Neural Network with the compressed features, which shows a performance of 96.44% with our proposed feature vector compression.

Application of information-retrieval methods to the classification of physical data

NASA Technical Reports Server (NTRS)

Mamotko, Z. N.; Khorolskaya, S. K.; Shatrovskiy, L. I.

1975-01-01

Scientific data received from satellites are characterized as a multi-dimensional time series, whose terms are vector functions of a vector of measurement conditions. Information retrieval methods are used to construct lower dimensional samples on the basis of the condition vector, in order to obtain these data and to construct partial relations. The methods are applied to the joint Soviet-French Arkad project.

Explicit time integration of finite element models on a vectorized, concurrent computer with shared memory

NASA Technical Reports Server (NTRS)

Gilbertsen, Noreen D.; Belytschko, Ted

1990-01-01

The implementation of a nonlinear explicit program on a vectorized, concurrent computer with shared memory is described and studied. The conflict between vectorization and concurrency is described and some guidelines are given for optimal block sizes. Several example problems are summarized to illustrate the types of speed-ups which can be achieved by reprogramming as compared to compiler optimization.

Visualization and Analysis of Geology Word Vectors for Efficient Information Extraction

NASA Astrophysics Data System (ADS)

Floyd, J. S.

2016-12-01

When a scientist begins studying a new geographic region of the Earth, they frequently begin by gathering relevant scientific literature in order to understand what is known, for example, about the region's geologic setting, structure, stratigraphy, and tectonic and environmental history. Experienced scientists typically know what keywords to seek and understand that if a document contains one important keyword, then other words in the document may be important as well. Word relationships in a document give rise to what is known in linguistics as the context-dependent nature of meaning. For example, the meaning of the word `strike' in geology, as in the strike of a fault, is quite different from its popular meaning in baseball. In addition, word order, such as in the phrase `Cretaceous-Tertiary boundary,' often corresponds to the order of sequences in time or space. The context of words and the relevance of words to each other can be derived quantitatively by machine learning vector representations of words. Here we show the results of training a neural network to create word vectors from scientific research papers from selected rift basins and mid-ocean ridges: the Woodlark Basin of Papua New Guinea, the Hess Deep rift, and the Gulf of Mexico basin. The word vectors are statistically defined by surrounding words within a given window, limited by the length of each sentence. The word vectors are analyzed by their cosine distance to related words (e.g., `axial' and `magma'), classified by high dimensional clustering, and visualized by reducing the vector dimensions and plotting the vectors on a two- or three-dimensional graph. Similarity analysis of `Triassic' and `Cretaceous' returns `Jurassic' as the nearest word vector, suggesting that the model is capable of learning the geologic time scale. Similarity analysis of `basalt' and `minerals' automatically returns mineral names such as `chlorite', `plagioclase,' and `olivine.' Word vector analysis and visualization allow one to extract information from hundreds of papers or more and find relationships in less time than it would take to read all of the papers. As machine learning tools become more commonly available, more and more scientists will be able to use and refine these tools for their individual needs.

The role of remote sensing and GIS for spatial prediction of vector-borne diseases transmission: a systematic review.

PubMed

Palaniyandi, M

2012-12-01

There have been several attempts made to the appreciation of remote sensing and GIS for the study of vectors, biodiversity, vector presence, vector abundance and the vector-borne diseases with respect to space and time. This study was made for reviewing and appraising the potential use of remote sensing and GIS applications for spatial prediction of vector-borne diseases transmission. The nature of the presence and the abundance of vectors and vector-borne diseases, disease infection and the disease transmission are not ubiquitous and are confined with geographical, environmental and climatic factors, and are localized. The presence of vectors and vector-borne diseases is most complex in nature, however, it is confined and fueled by the geographical, climatic and environmental factors including man-made factors. The usefulness of the present day availability of the information derived from the satellite data including vegetation indices of canopy cover and its density, soil types, soil moisture, soil texture, soil depth, etc. is integrating the information in the expert GIS engine for the spatial analysis of other geoclimatic and geoenvironmental variables. The present study gives the detailed information on the classical studies of the past and present, and the future role of remote sensing and GIS for the vector-borne diseases control. The ecological modeling directly gives us the relevant information to understand the spatial variation of the vector biodiversity, vector presence, vector abundance and the vector-borne diseases in association with geoclimatic and the environmental variables. The probability map of the geographical distribution and seasonal variations of horizontal and vertical distribution of vector abundance and its association with vector -borne diseases can be obtained with low cost remote sensing and GIS tool with reliable data and speed.

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.

Evidence that implicit assumptions of ‘no evolution’ of disease vectors in changing environments can be violated on a rapid timescale

PubMed Central

Egizi, Andrea; Fefferman, Nina H.; Fonseca, Dina M.

2015-01-01

Projected impacts of climate change on vector-borne disease dynamics must consider many variables relevant to hosts, vectors and pathogens, including how altered environmental characteristics might affect the spatial distributions of vector species. However, many predictive models for vector distributions consider their habitat requirements to be fixed over relevant time-scales, when they may actually be capable of rapid evolutionary change and even adaptation. We examine the genetic signature of a spatial expansion by an invasive vector into locations with novel temperature conditions compared to its native range as a proxy for how existing vector populations may respond to temporally changing habitat. Specifically, we compare invasions into different climate ranges and characterize the importance of selection from the invaded habitat. We demonstrate that vector species can exhibit evolutionary responses (altered allelic frequencies) to a temperature gradient in as little as 7–10 years even in the presence of high gene flow, and further, that this response varies depending on the strength of selection. We interpret these findings in the context of climate change predictions for vector populations and emphasize the importance of incorporating vector evolution into models of future vector-borne disease dynamics. PMID:25688024

Overcoming Challenges in Kinetic Modeling of Magnetized Plasmas and Vacuum Electronic Devices

NASA Astrophysics Data System (ADS)

Omelchenko, Yuri; Na, Dong-Yeop; Teixeira, Fernando

2017-10-01

We transform the state-of-the art of plasma modeling by taking advantage of novel computational techniques for fast and robust integration of multiscale hybrid (full particle ions, fluid electrons, no displacement current) and full-PIC models. These models are implemented in 3D HYPERS and axisymmetric full-PIC CONPIC codes. HYPERS is a massively parallel, asynchronous code. The HYPERS solver does not step fields and particles synchronously in time but instead executes local variable updates (events) at their self-adaptive rates while preserving fundamental conservation laws. The charge-conserving CONPIC code has a matrix-free explicit finite-element (FE) solver based on a sparse-approximate inverse (SPAI) algorithm. This explicit solver approximates the inverse FE system matrix (``mass'' matrix) using successive sparsity pattern orders of the original matrix. It does not reduce the set of Maxwell's equations to a vector-wave (curl-curl) equation of second order but instead utilizes the standard coupled first-order Maxwell's system. We discuss the ability of our codes to accurately and efficiently account for multiscale physical phenomena in 3D magnetized space and laboratory plasmas and axisymmetric vacuum electronic devices.

Full field gas phase velocity measurements in microgravity

NASA Technical Reports Server (NTRS)

Griffin, Devon W.; Yanis, William

1995-01-01

Measurement of full-field velocities via Particle Imaging Velocimetry (PIV) is common in research efforts involving fluid motion. While such measurements have been successfully performed in the liquid phase in a microgravity environment, gas-phase measurements have been beset by difficulties with seeding and laser strength. A synthesis of techniques developed at NASA LeRC exhibits promise in overcoming these difficulties. Typical implementation of PIV involves forming the light from a pulsed laser into a sheet that is some fraction of a millimeter thick and 50 or more millimeters wide. When a particle enters this sheet during a pulse, light scattered from the particle is recorded by a detector, which may be a film plane or a CCD array. Assuming that the particle remains within the boundaries of the sheet for the second pulse and can be distinguished from neighboring particles, comparison of the two images produces an average velocity vector for the time between the pulses. If the concentration of particles in the sampling volume is sufficiently large but the particles remain discrete, a full field map may be generated.

Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates

NASA Astrophysics Data System (ADS)

den Otter, W. K.

2000-05-01

A generalized formulation of the thermodynamic integration (TI) method for calculating the free energy along a reaction coordinate is derived. Molecular dynamics simulations with a constrained reaction coordinate are used to sample conformations. These are then projected onto conformations with a higher value of the reaction coordinate by means of a vector field. The accompanying change in potential energy plus the divergence of the vector field constitute the derivative of the free energy. Any vector field meeting some simple requirements can be used as the basis of this TI expression. Two classes of vector fields are of particular interest here. The first recovers the conventional TI expression, with its cumbersome dependence on a full set of generalized coordinates. As the free energy is a function of the reaction coordinate only, it should in principle be possible to derive an expression depending exclusively on the definition of the reaction coordinate. This objective is met by the second class of vector fields to be discussed. The potential of mean constraint force (PMCF) method, after averaging over the unconstrained momenta, falls in this second class. The new method is illustrated by calculations on the isomerization of n-butane, and is compared with existing methods.

Cre-lox Univector acceptor vectors for functional screening in protoplasts: analysis of Arabidopsis donor cDNAs encoding ABSCISIC ACID INSENSITIVE1-Like protein phosphatases

PubMed Central

Jia, Fan; Gampala, Srinivas S.L.; Mittal, Amandeep; Luo, Qingjun; Rock, Christopher D.

2009-01-01

The 14,200 available full length Arabidopsis thaliana cDNAs in the Universal Plasmid System (UPS) donor vector pUNI51 should be applied broadly and efficiently to leverage a “functional map-space” of homologous plant genes. We have engineered Cre-lox UPS host acceptor vectors (pCR701- 705) with N-terminal epitope tags in frame with the loxH site and downstream from the maize Ubiquitin promoter for use in transient protoplast expression assays and particle bombardment transformation of monocots. As an example of the utility of these vectors, we recombined them with several Arabidopsis cDNAs encoding Ser/Thr protein phosphatase type 2C (PP2Cs) known from genetic studies or predicted by hierarchical clustering meta-analysis to be involved in ABA and stress responses. Our functional results in Zea mays mesophyll protoplasts on ABA-inducible expression effects on the Late Embryogenesis Abundant promoter ProEm:GUS reporter were consistent with predictions and resulted in identification of novel activities of some PP2Cs. Deployment of these vectors can facilitate functional genomics and proteomics and identification of novel gene activities. PMID:19499346

Optimized Pan-species and Speciation Duplex Real-time PCR Assays for Plasmodium Parasites Detection in Malaria Vectors

PubMed Central

Sandeu, Maurice Marcel; Moussiliou, Azizath; Moiroux, Nicolas; Padonou, Gilles G.; Massougbodji, Achille; Corbel, Vincent; Tuikue Ndam, Nicaise

2012-01-01

Background An accurate method for detecting malaria parasites in the mosquito’s vector remains an essential component in the vector control. The Enzyme linked immunosorbent assay specific for circumsporozoite protein (ELISA-CSP) is the gold standard method for the detection of malaria parasites in the vector even if it presents some limitations. Here, we optimized multiplex real-time PCR assays to accurately detect minor populations in mixed infection with multiple Plasmodium species in the African malaria vectors Anopheles gambiae and Anopheles funestus. Methods Complementary TaqMan-based real-time PCR assays that detect Plasmodium species using specific primers and probes were first evaluated on artificial mixtures of different targets inserted in plasmid constructs. The assays were further validated in comparison with the ELISA-CSP on 200 field caught Anopheles gambiae and Anopheles funestus mosquitoes collected in two localities in southern Benin. Results The validation of the duplex real-time PCR assays on the plasmid mixtures demonstrated robust specificity and sensitivity for detecting distinct targets. Using a panel of mosquito specimen, the real-time PCR showed a relatively high sensitivity (88.6%) and specificity (98%), compared to ELISA-CSP as the referent standard. The agreement between both methods was “excellent” (κ = 0.8, P<0.05). The relative quantification of Plasmodium DNA between the two Anopheles species analyzed showed no significant difference (P = 0, 2). All infected mosquito samples contained Plasmodium falciparum DNA and mixed infections with P. malariae and/or P. ovale were observed in 18.6% and 13.6% of An. gambiae and An. funestus respectively. Plasmodium vivax was found in none of the mosquito samples analyzed. Conclusion This study presents an optimized method for detecting the four Plasmodium species in the African malaria vectors. The study highlights substantial discordance with traditional ELISA-CSP pointing out the utility of employing an accurate molecular diagnostic tool for detecting malaria parasites in field mosquito populations. PMID:23285168

The Weighted Burgers Vector: a new quantity for constraining dislocation densities and types using electron backscatter diffraction on 2D sections through crystalline materials.

PubMed

Wheeler, J; Mariani, E; Piazolo, S; Prior, D J; Trimby, P; Drury, M R

2009-03-01

The Weighted Burgers Vector (WBV) is defined here as the sum, over all types of dislocations, of [(density of intersections of dislocation lines with a map) x (Burgers vector)]. Here we show that it can be calculated, for any crystal system, solely from orientation gradients in a map view, unlike the full dislocation density tensor, which requires gradients in the third dimension. No assumption is made about gradients in the third dimension and they may be non-zero. The only assumption involved is that elastic strains are small so the lattice distortion is entirely due to dislocations. Orientation gradients can be estimated from gridded orientation measurements obtained by EBSD mapping, so the WBV can be calculated as a vector field on an EBSD map. The magnitude of the WBV gives a lower bound on the magnitude of the dislocation density tensor when that magnitude is defined in a coordinate invariant way. The direction of the WBV can constrain the types of Burgers vectors of geometrically necessary dislocations present in the microstructure, most clearly when it is broken down in terms of lattice vectors. The WBV has three advantages over other measures of local lattice distortion: it is a vector and hence carries more information than a scalar quantity, it has an explicit mathematical link to the individual Burgers vectors of dislocations and, since it is derived via tensor calculus, it is not dependent on the map coordinate system. If a sub-grain wall is included in the WBV calculation, the magnitude of the WBV becomes dependent on the step size but its direction still carries information on the Burgers vectors in the wall. The net Burgers vector content of dislocations intersecting an area of a map can be simply calculated by an integration round the edge of that area, a method which is fast and complements point-by-point WBV calculations.

Linear Magnetochiral effect in Weyl Semimetals

NASA Astrophysics Data System (ADS)

Cortijo, Alberto

We describe the presence of a linear magnetochiral effect in time reversal breaking Weyl semimetals. The magnetochiral effect consists in a simultaneous linear dependence of the magnetotransport coefficients with the magnetic field and a momentum vector. This simultaneous dependence is allowed by the Onsager reciprocity relations, being the separation vector between the Weyl nodes the vector that plays such role. This linear magnetochiral effect constitutes a new transport effect associated to the topological structures linked to time reversal breaking Weyl semimetals. European Union structural funds and the Comunidad de Madrid MAD2D-CM Program (S2013/MIT-3007) and MINECO (Spain) Grant No. FIS2015-73454-JIN.

Characterization of a 300-GHz Transmission System for Digital Communications

NASA Astrophysics Data System (ADS)

Hudlička, Martin; Salhi, Mohammed; Kleine-Ostmann, Thomas; Schrader, Thorsten

2017-08-01

The paper presents the characterization of a 300-GHz transmission system for modern digital communications. The quality of the modulated signal at the output of the system (error vector magnitude, EVM) is measured using a vector signal analyzer. A method using a digital real-time oscilloscope and consecutive mathematical processing in a computer is shown for analysis of signals with bandwidths exceeding that of state-of-the-art vector signal analyzers. The uncertainty of EVM measured using the real-time oscilloscope is open to analysis. Behaviour of the 300-GHz transmission system is studied with respect to various modulation schemes and different signal symbol rates.

The MAGSAT vector magnetometer: A precision fluxgate magnetometer for the measurement of the geomagnetic field

NASA Technical Reports Server (NTRS)

Acuna, M. H.; Scearce, C. S.; Seek, J.; Scheifele, J.

1978-01-01

A description of the precision triaxial fluxgate magnetometer to be flown aboard the MAGSAT spacecraft is presented. The instrument covers the range of + or - 64,000 nT with a resolution of + or - 0.5 nT, an intrinsic accuracy of + or - 0.001% of full scale and an angular alignment stability of the order of 2 seconds of arc. It was developed at NASA's Goddard Space Flight Center and represents the state-of-the-art in precision vector magnetometers developed for spaceflight use.

Progressive Vector Quantization on a massively parallel SIMD machine with application to multispectral image data

NASA Technical Reports Server (NTRS)

Manohar, Mareboyana; Tilton, James C.

1994-01-01

A progressive vector quantization (VQ) compression approach is discussed which decomposes image data into a number of levels using full search VQ. The final level is losslessly compressed, enabling lossless reconstruction. The computational difficulties are addressed by implementation on a massively parallel SIMD machine. We demonstrate progressive VQ on multispectral imagery obtained from the Advanced Very High Resolution Radiometer instrument and other Earth observation image data, and investigate the trade-offs in selecting the number of decomposition levels and codebook training method.

Monte Carlo simulation of a dynamical fermion problem: The light q sup 2 q sup 2 system

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

Grondin, G.

1991-01-01

We present results from a Guided Random Walk Monte Carlo simulation of the light q{sup 2}{bar q}{sup 2} system in a Coulomb-plus-linear quark potential model using an Intel iPSC/860 hypercube. A solvable model problem is first considered, after which we study the full q{sup 2}{bar q}{sup 2} system in (J,I) = (2,2) and (2,0) sectors. We find evidence for no bound states below the vector-vector threshold in these systems. 17 refs., 6 figs.

Effective genetic modification and differentiation of hMSCs upon controlled release of rAAV vectors using alginate/poloxamer composite systems.

PubMed

Díaz-Rodríguez, P; Rey-Rico, A; Madry, H; Landin, M; Cucchiarini, M

2015-12-30

Viral vectors are common tools in gene therapy to deliver foreign therapeutic sequences in a specific target population via their natural cellular entry mechanisms. Incorporating such vectors in implantable systems may provide strong alternatives to conventional gene transfer procedures. The goal of the present study was to generate different hydrogel structures based on alginate (AlgPH155) and poloxamer PF127 as new systems to encapsulate and release recombinant adeno-associated viral (rAAV) vectors. Inclusion of rAAV in such polymeric capsules revealed an influence of the hydrogel composition and crosslinking temperature upon the vector release profiles, with alginate (AlgPH155) structures showing the fastest release profiles early on while over time vector release was more effective from AlgPH155+PF127 [H] capsules crosslinked at a high temperature (50°C). Systems prepared at room temperature (AlgPH155+PF127 [C]) allowed instead to achieve a more controlled release profile. When tested for their ability to target human mesenchymal stem cells, the different systems led to high transduction efficiencies over time and to gene expression levels in the range of those achieved upon direct vector application, especially when using AlgPH155+PF127 [H]. No detrimental effects were reported on either cell viability or on the potential for chondrogenic differentiation. Inclusion of PF127 in the capsules was also capable of delaying undesirable hypertrophic cell differentiation. These findings are of promising value for the further development of viral vector controlled release strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

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

A straightforward characterization of non-modal effects from the evolution of linear dynamical systems

NASA Astrophysics Data System (ADS)

Arratia, Cristobal

2014-11-01

A simple construction will be shown, which reveals a general property satisfied by the evolution in time of a state vector composed by a superposition of orthogonal eigenmodes of a linear dynamical system. This property results from the conservation of the inner product between such state vectors evolving forward and backwards in time, and it can be simply evaluated from the state vector and its first and second time derivatives. This provides an efficient way to characterize, instantaneously along any specific phase-space trajectory of the linear system, the relevance of the non-normality of the linearized Navier-Stokes operator on the energy (or any other norm) gain or decay of small perturbations. Examples of this characterization applied to stationary or time dependent base flows will be shown. CONICYT, Concurso de Apoyo al Retorno de Investigadores del Extranjero, folio 821320055.

MGRA: Motion Gesture Recognition via Accelerometer.

PubMed

Hong, Feng; You, Shujuan; Wei, Meiyu; Zhang, Yongtuo; Guo, Zhongwen

2016-04-13

Accelerometers have been widely embedded in most current mobile devices, enabling easy and intuitive operations. This paper proposes a Motion Gesture Recognition system (MGRA) based on accelerometer data only, which is entirely implemented on mobile devices and can provide users with real-time interactions. A robust and unique feature set is enumerated through the time domain, the frequency domain and singular value decomposition analysis using our motion gesture set containing 11,110 traces. The best feature vector for classification is selected, taking both static and mobile scenarios into consideration. MGRA exploits support vector machine as the classifier with the best feature vector. Evaluations confirm that MGRA can accommodate a broad set of gesture variations within each class, including execution time, amplitude and non-gestural movement. Extensive evaluations confirm that MGRA achieves higher accuracy under both static and mobile scenarios and costs less computation time and energy on an LG Nexus 5 than previous methods.

Image segmentation of pyramid style identifier based on Support Vector Machine for colorectal endoscopic images.

PubMed

Okamoto, Takumi; Koide, Tetsushi; Sugi, Koki; Shimizu, Tatsuya; Anh-Tuan Hoang; Tamaki, Toru; Raytchev, Bisser; Kaneda, Kazufumi; Kominami, Yoko; Yoshida, Shigeto; Mieno, Hiroshi; Tanaka, Shinji

2015-08-01

With the increase of colorectal cancer patients in recent years, the needs of quantitative evaluation of colorectal cancer are increased, and the computer-aided diagnosis (CAD) system which supports doctor's diagnosis is essential. In this paper, a hardware design of type identification module in CAD system for colorectal endoscopic images with narrow band imaging (NBI) magnification is proposed for real-time processing of full high definition image (1920 × 1080 pixel). A pyramid style image segmentation with SVMs for multi-size scan windows, which can be implemented on an FPGA with small circuit area and achieve high accuracy, is proposed for actual complex colorectal endoscopic images.

A summary of the results from the UCLA OGO-5 fluxgate magnetometer

NASA Technical Reports Server (NTRS)

Coleman, P. J., Jr.; Russell, C. T.

1973-01-01

The OGO-5 fluxgate magnetometer experiment (E-14) was designed to measure the vector magnetic field over the full range of the OGO-5 orbit. Thus, it had a dynamic range of + or - 64,000 gamma yet it maintained a precision of + or - 1/16 gamma at all times. This enabled a broad spectrum of problems to be attached. Studies of the magnetospheric waves, currents, waves-particle interactions, pitch angle distributions and wave normal directions were made. The structure of the magnetopause, the magnetotail, and bow shock were probed, waves and discontinuities in the solar wind were examined and the various phases of substorms were examined in depth.

Transient radiative transfer in a scattering slab considering polarization.

PubMed

Yi, Hongliang; Ben, Xun; Tan, Heping

2013-11-04

The characteristics of the transient and polarization must be considered for a complete and correct description of short-pulse laser transfer in a scattering medium. A Monte Carlo (MC) method combined with a time shift and superposition principle is developed to simulate transient vector (polarized) radiative transfer in a scattering medium. The transient vector radiative transfer matrix (TVRTM) is defined to describe the transient polarization behavior of short-pulse laser propagating in the scattering medium. According to the definition of reflectivity, a new criterion of reflection at Fresnel surface is presented. In order to improve the computational efficiency and accuracy, a time shift and superposition principle is applied to the MC model for transient vector radiative transfer. The results for transient scalar radiative transfer and steady-state vector radiative transfer are compared with those in published literatures, respectively, and an excellent agreement between them is observed, which validates the correctness of the present model. Finally, transient radiative transfer is simulated considering the polarization effect of short-pulse laser in a scattering medium, and the distributions of Stokes vector in angular and temporal space are presented.

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.

Predictive modeling of mosquito abundance and dengue transmission in Kenya

NASA Astrophysics Data System (ADS)

Caldwell, J.; Krystosik, A.; Mutuku, F.; Ndenga, B.; LaBeaud, D.; Mordecai, E.

2017-12-01

Approximately 390 million people are exposed to dengue virus every year, and with no widely available treatments or vaccines, predictive models of disease risk are valuable tools for vector control and disease prevention. The aim of this study was to modify and improve climate-driven predictive models of dengue vector abundance (Aedes spp. mosquitoes) and viral transmission to people in Kenya. We simulated disease transmission using a temperature-driven mechanistic model and compared model predictions with vector trap data for larvae, pupae, and adult mosquitoes collected between 2014 and 2017 at four sites across urban and rural villages in Kenya. We tested predictive capacity of our models using four temperature measurements (minimum, maximum, range, and anomalies) across daily, weekly, and monthly time scales. Our results indicate seasonal temperature variation is a key driving factor of Aedes mosquito abundance and disease transmission. These models can help vector control programs target specific locations and times when vectors are likely to be present, and can be modified for other Aedes-transmitted diseases and arboviral endemic regions around the world.

Vectorcardiographic diagnostic & prognostic information derived from the 12-lead electrocardiogram: Historical review and clinical perspective.

PubMed

Man, Sumche; Maan, Arie C; Schalij, Martin J; Swenne, Cees A

2015-01-01

In the course of time, electrocardiography has assumed several modalities with varying electrode numbers, electrode positions and lead systems. 12-lead electrocardiography and 3-lead vectorcardiography have become particularly popular. These modalities developed in parallel through the mid-twentieth century. In the same time interval, the physical concepts underlying electrocardiography were defined and worked out. In particular, the vector concept (heart vector, lead vector, volume conductor) appeared to be essential to understanding the manifestations of electrical heart activity, both in the 12-lead electrocardiogram (ECG) and in the 3-lead vectorcardiogram (VCG). Not universally appreciated in the clinic, the vectorcardiogram, and with it the vector concept, went out of use. A revival of vectorcardiography started in the 90's, when VCGs were mathematically synthesized from standard 12-lead ECGs. This facilitated combined electrocardiography and vectorcardiography without the need for a special recording system. This paper gives an overview of these historical developments, elaborates on the vector concept and seeks to define where VCG analysis/interpretation can add diagnostic/prognostic value to conventional 12-lead ECG analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

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

Liu, Hualan; Price, Morgan N.; Waters, Robert Jordan

Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools.” Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. Tomore » identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylumBacteroidetes. IMPORTANCEMolecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA “parts,” we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.« less

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

DOE PAGES

Liu, Hualan; Price, Morgan N.; Waters, Robert Jordan; ...

2018-01-16

Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools.” Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. Tomore » identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylumBacteroidetes. IMPORTANCEMolecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The efficacy of each vector in a magic pool is monitored in parallel using a unique DNA barcode that is introduced into each vector design. Using archived DNA “parts,” we next reassemble an effective vector for making a whole-genome transposon mutant library that is suitable for large-scale interrogation of gene function using competitive growth assays. Here, we demonstrate the utility of the magic pool system to make mutant libraries in five genera of bacteria.« less

Predators indirectly reduce the prevalence of an insect-vectored plant pathogen independent of predator diversity.

PubMed

Long, Elizabeth Y; Finke, Deborah L

2015-04-01

A widely cited benefit of predator diversity is greater suppression of insect herbivores, with corresponding increases in plant biomass. In the context of a vector-borne pathogen system, predator species richness may also influence plant disease risk via the direct effects of predators on the abundance and behavior of herbivores that also act as pathogen vectors. Using an assemblage of generalist insect predators, we examined the relationship between predator species richness and the prevalence of the aphid-vectored cereal yellow dwarf virus in wheat. We found that increasing predator richness enhanced suppression of the vector population and that pathogen prevalence was reduced when predators were present, but the reduction in prevalence was independent of predator species richness. To determine the mechanism(s) by which predator species richness contributes to vector suppression, but not pathogen prevalence, we evaluated vector movement and host plant occupancy in response to predator treatments. We found that pathogen prevalence was unrelated to vector suppression because host plant occupancy by vectors did not vary as a function of vector abundance. However, the presence of predators reduced pathogen prevalence because predators stimulated greater plant-to-plant movement by vectors, which likely diminished vector feeding time and reduced the transmission efficiency of this persistent pathogen. We conclude that community structure (i.e., the presence of predators), but not predator diversity, is a potential factor influencing local plant infection by this insect-vectored pathogen.

Derivation of the Lorentz force law, the magnetic field concept and the Faraday Lenz and magnetic Gauss laws using an invariant formulation of the Lorentz transformation

NASA Astrophysics Data System (ADS)

Field, J. H.

2006-06-01

It is demonstrated how the right-hand sides of the Lorentz transformation equations may be written, in a Lorentz-invariant manner, as 4-vector scalar products. This implies the existence of invariant length intervals analogous to invariant proper time intervals. An important distinction between the physical meanings of the space time and energy momentum 4-vectors is pointed out. The formalism is shown to provide a short derivation of the Lorentz force law of classical electrodynamics, and the conventional definition of the magnetic field, in terms of spatial derivatives of the 4-vector potential, as well as the Faraday Lenz law and the Gauss law for magnetic fields. The connection between the Gauss law for the electric field and the electrodynamic Ampère law, due to the 4-vector character of the electromagnetic potential, is also pointed out.

The International Conference on Vector and Parallel Computing (2nd)

DTIC Science & Technology

1989-01-17

Computation of the SVD of Bidiagonal Matrices" ...................................... 11 " Lattice QCD -As a Large Scale Scientific Computation...vectorizcd for the IBM 3090 Vector Facility. In addition, elapsed times " Lattice QCD -As a Large Scale Scientific have been reduced by using 3090...benchmarked Lattice QCD on a large number ofcompu- come from the wavefront solver routine. This was exten- ters: CrayX-MP and Cray 2 (vector

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 dual host vector for Fab phage display and expression of native IgG in mammalian cells.

PubMed

Tesar, Devin; Hötzel, Isidro

2013-10-01

A significant bottleneck in antibody discovery by phage display is the transfer of immunoglobulin variable regions from phage clones to vectors that express immunoglobulin G (IgG) in mammalian cells for screening. Here, we describe a novel phagemid vector for Fab phage display that allows expression of native IgG in mammalian cells without sub-cloning. The vector uses an optimized mammalian signal sequence that drives robust expression of Fab fragments fused to an M13 phage coat protein in Escherichia coli and IgG expression in mammalian cells. To allow the expression of Fab fragments fused to a phage coat protein in E.coli and full-length IgG in mammalian cells from the same vector without sub-cloning, the sequence encoding the phage coat protein was embedded in an optimized synthetic intron within the immunoglobulin heavy chain gene. This intron is removed from transcripts in mammalian cells by RNA splicing. Using this vector, we constructed a synthetic Fab phage display library with diversity in the heavy chain only and selected for clones binding different antigens. Co-transfection of mammalian cells with DNA from individual phage clones and a plasmid expressing the invariant light chain resulted in the expression of native IgG that was used to assay affinity, ligand blocking activity and specificity.

HMM for hyperspectral spectrum representation and classification with endmember entropy vectors

NASA Astrophysics Data System (ADS)

Arabi, Samir Y. W.; Fernandes, David; Pizarro, Marco A.

2015-10-01

The Hyperspectral images due to its good spectral resolution are extensively used for classification, but its high number of bands requires a higher bandwidth in the transmission data, a higher data storage capability and a higher computational capability in processing systems. This work presents a new methodology for hyperspectral data classification that can work with a reduced number of spectral bands and achieve good results, comparable with processing methods that require all hyperspectral bands. The proposed method for hyperspectral spectra classification is based on the Hidden Markov Model (HMM) associated to each Endmember (EM) of a scene and the conditional probabilities of each EM belongs to each other EM. The EM conditional probability is transformed in EM vector entropy and those vectors are used as reference vectors for the classes in the scene. The conditional probability of a spectrum that will be classified is also transformed in a spectrum entropy vector, which is classified in a given class by the minimum ED (Euclidian Distance) among it and the EM entropy vectors. The methodology was tested with good results using AVIRIS spectra of a scene with 13 EM considering the full 209 bands and the reduced spectral bands of 128, 64 and 32. For the test area its show that can be used only 32 spectral bands instead of the original 209 bands, without significant loss in the classification process.

Use of Mapping and Spatial and Space-Time Modeling Approaches in Operational Control of Aedes aegypti and Dengue

PubMed Central

Eisen, Lars; Lozano-Fuentes, Saul

2009-01-01

The aims of this review paper are to 1) provide an overview of how mapping and spatial and space-time modeling approaches have been used to date to visualize and analyze mosquito vector and epidemiologic data for dengue; and 2) discuss the potential for these approaches to be included as routine activities in operational vector and dengue control programs. Geographical information system (GIS) software are becoming more user-friendly and now are complemented by free mapping software that provide access to satellite imagery and basic feature-making tools and have the capacity to generate static maps as well as dynamic time-series maps. Our challenge is now to move beyond the research arena by transferring mapping and GIS technologies and spatial statistical analysis techniques in user-friendly packages to operational vector and dengue control programs. This will enable control programs to, for example, generate risk maps for exposure to dengue virus, develop Priority Area Classifications for vector control, and explore socioeconomic associations with dengue risk. PMID:19399163

Vector Analysis of Ionic Collision on CaCO3 Precipitation Based on Vibration Time History

NASA Astrophysics Data System (ADS)

Mangestiyono, W.; Muryanto, S.; Jamari, J.; Bayuseno, A. P.

2017-05-01

Vibration effects on the piping system can result from the internal factor of fluid or the external factor of the mechanical equipment operation. As the pipe vibrated, the precipitation process of CaCO3 on the inner pipe could be affected. In the previous research, the effect of vibration on CaCO3 precipitation in piping system was clearly verified. This increased the deposition rate and decreased the induction time. However, the mechanism of vibration control in CaCO3 precipitation process as the presence of vibration has not been recognized yet. In the present research, the mechanism of vibration affecting the CaCO3 precipitation was investigated through vector analysis of ionic collision. The ionic vector force was calculated based on the amount of the activation energy and the vibration force was calculated based on the vibration sensor data. The vector resultant of ionic collision based on the vibration time history was analyzed to prove that vibration brings ionic collision randomly to the planar horizontal direction and its collision model was suspected as the cause of the increasing deposition rate.

Prediction of hourly PM2.5 using a space-time support vector regression model

NASA Astrophysics Data System (ADS)

Yang, Wentao; Deng, Min; Xu, Feng; Wang, Hang

2018-05-01

Real-time air quality prediction has been an active field of research in atmospheric environmental science. The existing methods of machine learning are widely used to predict pollutant concentrations because of their enhanced ability to handle complex non-linear relationships. However, because pollutant concentration data, as typical geospatial data, also exhibit spatial heterogeneity and spatial dependence, they may violate the assumptions of independent and identically distributed random variables in most of the machine learning methods. As a result, a space-time support vector regression model is proposed to predict hourly PM2.5 concentrations. First, to address spatial heterogeneity, spatial clustering is executed to divide the study area into several homogeneous or quasi-homogeneous subareas. To handle spatial dependence, a Gauss vector weight function is then developed to determine spatial autocorrelation variables as part of the input features. Finally, a local support vector regression model with spatial autocorrelation variables is established for each subarea. Experimental data on PM2.5 concentrations in Beijing are used to verify whether the results of the proposed model are superior to those of other methods.

Gallid herpesvirus 3 SB-1 strain as a recombinant viral vector for poultry vaccination.

PubMed

Sadigh, Yashar; Powers, Claire; Spiro, Simon; Pedrera, Miriam; Broadbent, Andrew; Nair, Venugopal

2018-01-01

Live herpesvirus-vectored vaccines are widely used in veterinary medicine to protect against many infectious diseases. In poultry, three strains of herpesvirus vaccines are used against Marek's disease (MD). However, of these, only the herpesvirus of turkeys (HVT) has been successfully developed and used as a recombinant vaccine vector to induce protection against other avian viral diseases such as infectious bursal disease (IBD), Newcastle disease (ND) or avian influenza (AI). Although effective when administered individually, recombinant HVT vectors have limitations when combined in multivalent vaccines. Thus there is a need for developing additional viral vectors that could be combined with HVT in inducing protection against multiple avian diseases in multivalent vaccines. Gallid herpesvirus 3 (GaHV3) strain SB-1 is widely used by the poultry industry as bivalent vaccine in combination with HVT to exploit synergistic effects against MD. Here, we report the development and application of SB-1 as a vaccine vector to express the VP2 capsid antigen of IBD virus. A VP2 expression cassette was introduced into the SB-1 genome at three intergenic locations (UL3/UL4, UL10/UL11 and UL21/UL22) using recombineering methods on the full-length pSB-1 infectious clone of the virus. We show that the recombinant SB-1 vectors expressing VP2 induced neutralising antibody responses at levels comparable to that of commercial HVT-based VAXXITEK HVT+IBD vaccine. Birds vaccinated with the experimental recombinant SB-1 vaccine were protected against clinical disease after challenge with the very virulent UK661 IBDV isolate, demonstrating its value as an efficient viral vector for developing multivalent vaccines against avian diseases.

Spatiotemporal image correlation spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells.

PubMed

Hebert, Benedict; Costantino, Santiago; Wiseman, Paul W

2005-05-01

We introduce a new extension of image correlation spectroscopy (ICS) and image cross-correlation spectroscopy (ICCS) that relies on complete analysis of both the temporal and spatial correlation lags for intensity fluctuations from a laser-scanning microscopy image series. This new approach allows measurement of both diffusion coefficients and velocity vectors (magnitude and direction) for fluorescently labeled membrane proteins in living cells through monitoring of the time evolution of the full space-time correlation function. By using filtering in Fourier space to remove frequencies associated with immobile components, we are able to measure the protein transport even in the presence of a large fraction (>90%) of immobile species. We present the background theory, computer simulations, and analysis of measurements on fluorescent microspheres to demonstrate proof of principle, capabilities, and limitations of the method. We demonstrate mapping of flow vectors for mixed samples containing fluorescent microspheres with different emission wavelengths using space time image cross-correlation. We also present results from two-photon laser-scanning microscopy studies of alpha-actinin/enhanced green fluorescent protein fusion constructs at the basal membrane of living CHO cells. Using space-time image correlation spectroscopy (STICS), we are able to measure protein fluxes with magnitudes of mum/min from retracting lamellar regions and protrusions for adherent cells. We also demonstrate the measurement of correlated directed flows (magnitudes of mum/min) and diffusion of interacting alpha5 integrin/enhanced cyan fluorescent protein and alpha-actinin/enhanced yellow fluorescent protein within living CHO cells. The STICS method permits us to generate complete transport maps of proteins within subregions of the basal membrane even if the protein concentration is too high to perform single particle tracking measurements.

A simple method of equine limb force vector analysis and its potential applications

PubMed Central

Robinson, Mark A.; Clayton, Hilary M.

2018-01-01

Background Ground reaction forces (GRF) measured during equine gait analysis are typically evaluated by analyzing discrete values obtained from continuous force-time data for the vertical, longitudinal and transverse GRF components. This paper describes a simple, temporo-spatial method of displaying and analyzing sagittal plane GRF vectors. In addition, the application of statistical parametric mapping (SPM) is introduced to analyse differences between contra-lateral fore and hindlimb force-time curves throughout the stance phase. The overall aim of the study was to demonstrate alternative methods of evaluating functional (a)symmetry within horses. Methods GRF and kinematic data were collected from 10 horses trotting over a series of four force plates (120 Hz). The kinematic data were used to determine clean hoof contacts. The stance phase of each hoof was determined using a 50 N threshold. Vertical and longitudinal GRF for each stance phase were plotted both as force-time curves and as force vector diagrams in which vectors originating at the centre of pressure on the force plate were drawn at intervals of 8.3 ms for the duration of stance. Visual evaluation was facilitated by overlay of the vector diagrams for different limbs. Summary vectors representing the magnitude (VecMag) and direction (VecAng) of the mean force over the entire stance phase were superimposed on the force vector diagram. Typical measurements extracted from the force-time curves (peak forces, impulses) were compared with VecMag and VecAng using partial correlation (controlling for speed). Paired samples t-tests (left v. right diagonal pair comparison and high v. low vertical force diagonal pair comparison) were performed on discrete and vector variables using traditional methods and Hotelling’s T2 tests on normalized stance phase data using SPM. Results Evidence from traditional statistical tests suggested that VecMag is more influenced by the vertical force and impulse, whereas VecAng is more influenced by the longitudinal force and impulse. When used to evaluate mean data from the group of ten sound horses, SPM did not identify differences between the left and right contralateral limb pairs or between limb pairs classified according to directional asymmetry. When evaluating a single horse, three periods were identified during which differences in the forces between the left and right forelimbs exceeded the critical threshold (p < .01). Discussion Traditional statistical analysis of 2D GRF peak values, summary vector variables and visual evaluation of force vector diagrams gave harmonious results and both methods identified the same inter-limb asymmetries. As alpha was more tightly controlled using SPM, significance was only found in the individual horse although T2 plots followed the same trends as discrete analysis for the group. Conclusions The techniques of force vector analysis and SPM hold promise for investigations of sidedness and asymmetry in horses. PMID:29492341

Transcriptional Enhancers Induce Insertional Gene Deregulation Independently From the Vector Type and Design

PubMed Central

Maruggi, Giulietta; Porcellini, Simona; Facchini, Giulia; Perna, Serena K; Cattoglio, Claudia; Sartori, Daniela; Ambrosi, Alessandro; Schambach, Axel; Baum, Christopher; Bonini, Chiara; Bovolenta, Chiara; Mavilio, Fulvio; Recchia, Alessandra

2009-01-01

The integration characteristics of retroviral (RV) vectors increase the probability of interfering with the regulation of cellular genes, and account for a tangible risk of insertional mutagenesis in treated patients. To assess the potential genotoxic risk of conventional or self-inactivating (SIN) γ-RV and lentiviral (LV) vectors independently from the biological consequences of the insertion event, we developed a quantitative assay based on real-time reverse transcriptase—PCR on low-density arrays to evaluate alterations of gene expression in individual primary T-cell clones. We show that the Moloney leukemia virus long terminal repeat (LTR) enhancer has the strongest activity in both a γ-RV and a LV vector context, while an internal cellular promoter induces deregulation of gene expression less frequently, at a shorter range and to a lower extent in both vector types. Downregulation of gene expression was observed only in the context of LV vectors. This study indicates that insertional gene activation is determined by the characteristics of the transcriptional regulatory elements carried by the vector, and is largely independent from the vector type or design. PMID:19293778

Borrelia miyamotoi, Other Vector-Borne Agents in Cat Blood and Ticks in Eastern Maryland.

PubMed

Shannon, Avery B; Rucinsky, Renee; Gaff, Holly D; Brinkerhoff, R Jory

2017-12-01

We collected blood and tick samples in eastern Maryland to quantify vector-borne pathogen exposure and infection in healthy cats and to assess occupational disease risk to veterinary professionals and others who regularly interact with household pets. Thirty-six percent of healthy cats parasitized by ticks at time of examination (9/25) were exposed to, and 14% of bloods (7/49) tested PCR-positive for, at least one vector-borne pathogen including several bloods and ticks with Borrelia miyamotoi, a recently recognized tick-borne zoonotic bacterium. There was no indication that high tick burdens were associated with exposure to vector-borne pathogens. Our results underscore the potential importance of cats to human vector-borne disease risk.

Viral vector-based influenza vaccines

PubMed Central

de Vries, Rory D.; Rimmelzwaan, Guus F.

2016-01-01

ABSTRACT Antigenic drift of seasonal influenza viruses and the occasional introduction of influenza viruses of novel subtypes into the human population complicate the timely production of effective vaccines that antigenically match the virus strains that cause epidemic or pandemic outbreaks. The development of game-changing vaccines that induce broadly protective immunity against a wide variety of influenza viruses is an unmet need, in which recombinant viral vectors may provide. Use of viral vectors allows the delivery of any influenza virus antigen, or derivative thereof, to the immune system, resulting in the optimal induction of virus-specific B- and T-cell responses against this antigen of choice. This systematic review discusses results obtained with vectored influenza virus vaccines and advantages and disadvantages of the currently available viral vectors. PMID:27455345

Viral vector-based influenza vaccines.

PubMed

de Vries, Rory D; Rimmelzwaan, Guus F

2016-11-01

Antigenic drift of seasonal influenza viruses and the occasional introduction of influenza viruses of novel subtypes into the human population complicate the timely production of effective vaccines that antigenically match the virus strains that cause epidemic or pandemic outbreaks. The development of game-changing vaccines that induce broadly protective immunity against a wide variety of influenza viruses is an unmet need, in which recombinant viral vectors may provide. Use of viral vectors allows the delivery of any influenza virus antigen, or derivative thereof, to the immune system, resulting in the optimal induction of virus-specific B- and T-cell responses against this antigen of choice. This systematic review discusses results obtained with vectored influenza virus vaccines and advantages and disadvantages of the currently available viral vectors.

Local Gram-Schmidt and covariant Lyapunov vectors and exponents for three harmonic oscillator problems

NASA Astrophysics Data System (ADS)

Hoover, Wm. G.; Hoover, Carol G.

2012-02-01

We compare the Gram-Schmidt and covariant phase-space-basis-vector descriptions for three time-reversible harmonic oscillator problems, in two, three, and four phase-space dimensions respectively. The two-dimensional problem can be solved analytically. The three-dimensional and four-dimensional problems studied here are simultaneously chaotic, time-reversible, and dissipative. Our treatment is intended to be pedagogical, for use in an updated version of our book on Time Reversibility, Computer Simulation, and Chaos. Comments are very welcome.

Black hole superradiance signatures of ultralight vectors

NASA Astrophysics Data System (ADS)

Baryakhtar, Masha; Lasenby, Robert; Teo, Mae

2017-08-01

The process of superradiance can extract angular momentum and energy from astrophysical black holes (BHs) to populate gravitationally bound states with an exponentially large number of light bosons. We analytically calculate superradiant growth rates for vectors around rotating BHs in the regime where the vector Compton wavelength is much larger than the BH size. Spin-1 bound states have superradiance times as short as a second around stellar BHs, growing up to a thousand times faster than their spin-0 counterparts. The fast rates allow us to use measurements of rapidly spinning BHs in x-ray binaries to exclude a wide range of masses for weakly coupled spin-1 particles, 5 ×10-14-2 ×10-11 eV ; lighter masses in the range 6 ×10-20-2 ×10-17 eV start to be constrained by supermassive BH spin measurements at a lower level of confidence. We also explore routes to detection of new vector particles possible with the advent of gravitational wave (GW) astronomy. The LIGO-Virgo Collaboration could discover hints of a new light vector particle in statistical analyses of masses and spins of merging BHs. Vector annihilations source continuous monochromatic gravitational radiation which could be observed by current GW observatories. At design sensitivity, Advanced LIGO may measure up to thousands of annihilation signals from within the Milky Way, while hundreds of BHs born in binary mergers across the observable Universe may superradiate vector bound states and become new beacons of monochromatic gravitational waves.

Generation of vector dissipative and conventional solitons in large normal dispersion regime.

PubMed

Yun, Ling

2017-08-07

We report the generation of both polarization-locked vector dissipative soliton and group velocity-locked vector conventional soliton in a nanotube-mode-locked fiber ring laser with large normal dispersion, for the first time to our best knowledge. Depending on the polarization-depended extinction ratio of the fiber-based Lyot filter, the two types of vector solitons can be switched by simply tuning the polarization controller. In the case of low filter extinction ratio, the output vector dissipative soliton exhibits steep spectral edges and strong frequency chirp, which presents a typical pulse duration of ~23.4 ps, and can be further compressed to ~0.9 ps. In the contrastive case of high filter extinction ratio, the vector conventional soliton has clear Kelly sidebands with transform-limited pulse duration of ~1.8 ps. Our study provides a new and simple method to achieve two different vector soliton sources, which is attractive for potential applications requiring different pulse profiles.

Can antibodies against flies alter malaria transmission in birds by changing vector behavior?

PubMed

Ghosh, Suma; Waite, Jessica L; Clayton, Dale H; Adler, Frederick R

2014-10-07

Transmission of insect-borne diseases is shaped by the interactions among parasites, vectors, and hosts. Any factor that alters movement of infected vectors from infected to uninfeced hosts will in turn alter pathogen spread. In this paper, we study one such pathogen-vector-host system, avian malaria in pigeons transmitted by fly ectoparasites, where both two-way and three-way interactions play a key role in shaping disease spread. Bird immune defenses against flies can decrease malaria prevalence by reducing fly residence time on infected birds or increase disease prevalence by enhancing fly movement and thus infection transmission. We develop a mathematical model that illustrates how these changes in vector behavior influence pathogen transmission and show that malaria prevalence is maximized at an intermediate level of defense avoidance by the flies. Understanding how host immune defenses indirectly alter disease transmission by influencing vector behavior has implications for reducing the transmission of human malaria and other vectored pathogens. Published by Elsevier Ltd.

Pushing Memory Bandwidth Limitations Through Efficient Implementations of Block-Krylov Space Solvers on GPUs

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

Clark, M. A.; Strelchenko, Alexei; Vaquero, Alejandro

Lattice quantum chromodynamics simulations in nuclear physics have benefited from a tremendous number of algorithmic advances such as multigrid and eigenvector deflation. These improve the time to solution but do not alleviate the intrinsic memory-bandwidth constraints of the matrix-vector operation dominating iterative solvers. Batching this operation for multiple vectors and exploiting cache and register blocking can yield a super-linear speed up. Block-Krylov solvers can naturally take advantage of such batched matrix-vector operations, further reducing the iterations to solution by sharing the Krylov space between solves. However, practical implementations typically suffer from the quadratic scaling in the number of vector-vector operations.more » Using the QUDA library, we present an implementation of a block-CG solver on NVIDIA GPUs which reduces the memory-bandwidth complexity of vector-vector operations from quadratic to linear. We present results for the HISQ discretization, showing a 5x speedup compared to highly-optimized independent Krylov solves on NVIDIA's SaturnV cluster.« less

Biological Response to the Dynamic Spectral-Polarized Underwater Light Field

DTIC Science & Technology

2012-09-30

deployment of a comprehensive optical suite including underwater video- polarimetry (full Stokes vector video-imaging camera custom-built Cummings; and...During field operations, we couple polarimetry measurements of live, free-swimming animals in their environments with a full suite of optical...Seibel, Ahmed). We also restrain live, awake animals to take polarimetry measurements (in the field and laboratory) under a complete set of

Giardia canis: ultrastructural analysis of G. canis trophozoites transfected with full length G. canis virus cDNA transcripts

USDA-ARS?s Scientific Manuscript database

Giardia canis virus (GCV) is a double-stranded RNA (dsRNA) virus of the family Totiviridae. In this study, the full-length cDNA of the G. canis virus was constructed in pPoly2/sfinot vector and RNA was transcribed in vitro. Virus-free G. canis trophozoites were transfected with in vitro transcribed ...

Multivariate analysis of fMRI time series: classification and regression of brain responses using machine learning.

PubMed

Formisano, Elia; De Martino, Federico; Valente, Giancarlo

2008-09-01

Machine learning and pattern recognition techniques are being increasingly employed in functional magnetic resonance imaging (fMRI) data analysis. By taking into account the full spatial pattern of brain activity measured simultaneously at many locations, these methods allow detecting subtle, non-strictly localized effects that may remain invisible to the conventional analysis with univariate statistical methods. In typical fMRI applications, pattern recognition algorithms "learn" a functional relationship between brain response patterns and a perceptual, cognitive or behavioral state of a subject expressed in terms of a label, which may assume discrete (classification) or continuous (regression) values. This learned functional relationship is then used to predict the unseen labels from a new data set ("brain reading"). In this article, we describe the mathematical foundations of machine learning applications in fMRI. We focus on two methods, support vector machines and relevance vector machines, which are respectively suited for the classification and regression of fMRI patterns. Furthermore, by means of several examples and applications, we illustrate and discuss the methodological challenges of using machine learning algorithms in the context of fMRI data analysis.

Analysis of nonlocal phonon thermal conductivity simulations showing the ballistic to diffusive crossover

NASA Astrophysics Data System (ADS)

Allen, Philip B.

2018-04-01

Simulations [e.g., X. W. Zhou et al., Phys. Rev. B 79, 115201 (2009), 10.1103/PhysRevB.79.115201] show nonlocal effects of the ballistic/diffusive crossover. The local temperature has nonlinear spatial variation not contained in the local Fourier law j ⃗(r ⃗) =-κ ∇ ⃗T (r ⃗) . The heat current j ⃗(r ⃗) depends not just on the local temperature gradient ∇ ⃗T (r ⃗) but also on temperatures at points r⃗' within phonon mean free paths, which can be micrometers long. This paper uses the Peierls-Boltzmann transport theory in nonlocal form to analyze the spatial variation Δ T (r ⃗) . The relaxation-time approximation (RTA) is used because the full solution is very challenging. Improved methods of extrapolation to obtain the bulk thermal conductivity κ are proposed. Callaway invented an approximate method of correcting RTA for the q ⃗ (phonon wave vector or crystal momentum) conservation of N (Normal as opposed to Umklapp) anharmonic collisions. This method is generalized to the nonlocal case where κ (k ⃗) depends on the wave vector of the current j ⃗(k ⃗) and temperature gradient i k ⃗Δ T (k ⃗) .

Odorant receptor-based discovery of natural repellents of human lice.

PubMed

Pelletier, Julien; Xu, Pingxi; Yoon, Kyong S; Clark, John M; Leal, Walter S

2015-11-01

The body louse, Pediculus humanus humanus, is an obligate blood-feeding ectoparasite and an important insect vector that mediates the transmission of diseases to humans. The analysis of the body louse genome revealed a drastic reduction of the chemosensory gene repertoires when compared to other insects, suggesting specific olfactory adaptations to host specialization and permanent parasitic lifestyle. Here, we present for the first time functional evidence for the role of odorant receptors (ORs) in this insect, with the objective to gain insight into the chemical ecology of this vector. We identified seven putative full-length ORs, in addition to the odorant receptor co-receptor (Orco), and expressed four of them in the Xenopus laevis oocytes system. When screened with a panel of ecologically-relevant odorants, PhumOR2 responded to a narrow set of compounds. At the behavior level, both head and body lice were repelled by the physiologically-active chemicals. This study presents the first evidence of the OR pathway being functional in lice and identifies PhumOR2 as a sensitive receptor of natural repellents that could be used to develop novel efficient molecules to control these insects. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Efficient combination of a 3D Quasi-Newton inversion algorithm and a vector dual-primal finite element tearing and interconnecting method

NASA Astrophysics Data System (ADS)

Voznyuk, I.; Litman, A.; Tortel, H.

2015-08-01

A Quasi-Newton method for reconstructing the constitutive parameters of three-dimensional (3D) penetrable scatterers from scattered field measurements is presented. This method is adapted for handling large-scale electromagnetic problems while keeping the memory requirement and the time flexibility as low as possible. The forward scattering problem is solved by applying the finite-element tearing and interconnecting full-dual-primal (FETI-FDP2) method which shares the same spirit as the domain decomposition methods for finite element methods. The idea is to split the computational domain into smaller non-overlapping sub-domains in order to simultaneously solve local sub-problems. Various strategies are proposed in order to efficiently couple the inversion algorithm with the FETI-FDP2 method: a separation into permanent and non-permanent subdomains is performed, iterative solvers are favorized for resolving the interface problem and a marching-on-in-anything initial guess selection further accelerates the process. The computational burden is also reduced by applying the adjoint state vector methodology. Finally, the inversion algorithm is confronted to measurements extracted from the 3D Fresnel database.

Social acceptability and durability of two different house screening interventions against exposure to malaria vectors, Plasmodium falciparum infection, and anemia in children in the Gambia, West Africa.

PubMed

Kirby, Matthew J; Bah, Pateh; Jones, Caroline O H; Kelly, Ann H; Jasseh, Momodou; Lindsay, Steve W

2010-11-01

The social acceptability and durability of two house screening interventions were addressed using focus group discussions, questionnaires, indoor climate measurements, and durability surveys. Participants recognized that screening stopped mosquitoes (79-96%) and other insects (86-98%) entering their houses. These and other benefits were appreciated by significantly more recipients of full screening than users of screened ceilings. Full screened houses were 0.26°C hotter at night (P = 0.05) than houses with screened ceilings and 0.51°C (P < 0.001) hotter than houses with no screening (28.43°C), though only 9% of full screened house users and 17% of screened ceiling users complained about the heat. Although 71% of screened doors and 85% of ceilings had suffered some damage after 12 months, the average number of holes of any size was < 5 for doors and < 7 for ceilings. In conclusion, house screening is a well-appreciated and durable vector control tool.

Social Acceptability and Durability of Two Different House Screening Interventions against Exposure to Malaria Vectors, Plasmodium falciparum Infection, and Anemia in Children in The Gambia, West Africa

PubMed Central

Kirby, Matthew J.; Bah, Pateh; Jones, Caroline O. H.; Kelly, Ann H.; Jasseh, Momodou; Lindsay, Steve W.

2010-01-01

The social acceptability and durability of two house screening interventions were addressed using focus group discussions, questionnaires, indoor climate measurements, and durability surveys. Participants recognized that screening stopped mosquitoes (79–96%) and other insects (86–98%) entering their houses. These and other benefits were appreciated by significantly more recipients of full screening than users of screened ceilings. Full screened houses were 0.26°C hotter at night (P = 0.05) than houses with screened ceilings and 0.51°C (P < 0.001) hotter than houses with no screening (28.43°C), though only 9% of full screened house users and 17% of screened ceiling users complained about the heat. Although 71% of screened doors and 85% of ceilings had suffered some damage after 12 months, the average number of holes of any size was < 5 for doors and < 7 for ceilings. In conclusion, house screening is a well-appreciated and durable vector control tool. PMID:21036822

Viral Vectors for in Vivo Gene Transfer

NASA Astrophysics Data System (ADS)

Thévenot, E.; Dufour, N.; Déglon, N.

The transfer of DNA into the nucleus of a eukaryotic cell (gene transfer) is a central theme of modern biology. The transfer is said to be somatic when it refers to non-germline organs of a developed individual, and germline when it concerns gametes or the fertilised egg of an animal, with the aim of transmitting the relevant genetic modification to its descendents [1]. The efficient introduction of genetic material into a somatic or germline cell and the control of its expression over time have led to major advances in understanding how genes work in vivo, i.e., in living organisms (functional genomics), but also to the development of innovative therapeutic methods (gene therapy). The efficiency of gene transfer is conditioned by the vehicle used, called the vector. Desirable features for a vector are as follows: Easy to produce high titer stocks of the vector in a reproducible way. Absence of toxicity related to transduction (transfer of genetic material into the target cell, and its expression there) and no immune reaction of the organism against the vector and/or therapeutic protein. Stability in the expression of the relevant gene over time, and the possibility of regulation, e.g., to control expression of the therapeutic protein on the physiological level, or to end expression at the end of treatment. Transduction of quiescent cells should be as efficient as transduction of dividing cells. Vectors currently used fall into two categories: non-viral and viral vectors. In non-viral vectors, the DNA is complexed with polymers, lipids, or cationic detergents (described in Chap. 3). These vectors have a low risk of toxicity and immune reaction. However, they are less efficient in vivo than viral vectors when it comes to the number of cells transduced and long-term transgene expression. (Naked DNA transfer or electroporation is rather inefficient in the organism. This type of gene transfer will not be discussed here, and the interested reader is referred to the review [2].) For this reason, it is mainly viral vectors that are used for gene transfer in animals and humans.

Measuring and Modeling Shared Visual Attention

NASA Technical Reports Server (NTRS)

Mulligan, Jeffrey B.; Gontar, Patrick

2016-01-01

Multi-person teams are sometimes responsible for critical tasks, such as flying an airliner. Here we present a method using gaze tracking data to assess shared visual attention, a term we use to describe the situation where team members are attending to a common set of elements in the environment. Gaze data are quantized with respect to a set of N areas of interest (AOIs); these are then used to construct a time series of N dimensional vectors, with each vector component representing one of the AOIs, all set to 0 except for the component corresponding to the currently fixated AOI, which is set to 1. The resulting sequence of vectors can be averaged in time, with the result that each vector component represents the proportion of time that the corresponding AOI was fixated within the given time interval. We present two methods for comparing sequences of this sort, one based on computing the time-varying correlation of the averaged vectors, and another based on a chi-square test testing the hypothesis that the observed gaze proportions are drawn from identical probability distributions. We have evaluated the method using synthetic data sets, in which the behavior was modeled as a series of "activities," each of which was modeled as a first-order Markov process. By tabulating distributions for pairs of identical and disparate activities, we are able to perform a receiver operating characteristic (ROC) analysis, allowing us to choose appropriate criteria and estimate error rates. We have applied the methods to data from airline crews, collected in a high-fidelity flight simulator (Haslbeck, Gontar & Schubert, 2014). We conclude by considering the problem of automatic (blind) discovery of activities, using methods developed for text analysis.

The abundance of the Lyme disease pathogen Borrelia afzelii declines over time in the tick vector Ixodes ricinus.

PubMed

Jacquet, Maxime; Genné, Dolores; Belli, Alessandro; Maluenda, Elodie; Sarr, Anouk; Voordouw, Maarten J

2017-05-25

The population dynamics of vector-borne pathogens inside the arthropod vector can have important consequences for vector-to-host transmission. Tick-borne spirochete bacteria of the Borrelia burgdorferi (sensu lato) species complex cause Lyme borreliosis in humans and spend long periods of time (>12 months) in their Ixodes tick vectors. To date, few studies have investigated the dynamics of Borrelia spirochete populations in unfed Ixodes nymphal ticks. Larval ticks from our laboratory colony of I. ricinus were experimentally infected with B. afzelii, and killed at 1 month and 4 months after the larva-to-nymph moult. The spirochete load was also compared between engorged larval ticks and unfed nymphs (from the same cohort) and between unfed nymphs and unfed adult ticks (from the same cohort). The spirochete load of B. afzelii in each tick was estimated using qPCR. The mean spirochete load in the 1-month-old nymphs (~14,000 spirochetes) was seven times higher than the 4-month-old nymphs (~2000 spirochetes). Thus, the nymphal spirochete load declined by 80% over a period of 3 months. An engorged larval tick acquired ~100 spirochetes, and this population was 20 times larger in a young, unfed nymph. The spirochete load also appeared to decline in adult ticks. Comparison between wild and laboratory populations found that lab ticks were more susceptible to acquiring B. afzelii. The spirochete load of B. afzelii declines dramatically over time in domesticated I. ricinus nymphs under laboratory conditions. Future studies should investigate whether temporal declines in spirochete load occur in wild Ixodes ticks under natural conditions and whether these declines influence the tick-to-host transmission of Borrelia.

Measuring and Modeling Shared Visual Attention

NASA Technical Reports Server (NTRS)

Mulligan, Jeffrey B.

2016-01-01

Multi-person teams are sometimes responsible for critical tasks, such as flying an airliner. Here we present a method using gaze tracking data to assess shared visual attention, a term we use to describe the situation where team members are attending to a common set of elements in the environment. Gaze data are quantized with respect to a set of N areas of interest (AOIs); these are then used to construct a time series of N dimensional vectors, with each vector component representing one of the AOIs, all set to 0 except for the component corresponding to the currently fixated AOI, which is set to 1. The resulting sequence of vectors can be averaged in time, with the result that each vector component represents the proportion of time that the corresponding AOI was fixated within the given time interval. We present two methods for comparing sequences of this sort, one based on computing the time-varying correlation of the averaged vectors, and another based on a chi-square test testing the hypothesis that the observed gaze proportions are drawn from identical probability distributions.We have evaluated the method using synthetic data sets, in which the behavior was modeled as a series of activities, each of which was modeled as a first-order Markov process. By tabulating distributions for pairs of identical and disparate activities, we are able to perform a receiver operating characteristic (ROC) analysis, allowing us to choose appropriate criteria and estimate error rates.We have applied the methods to data from airline crews, collected in a high-fidelity flight simulator (Haslbeck, Gontar Schubert, 2014). We conclude by considering the problem of automatic (blind) discovery of activities, using methods developed for text analysis.

Associated production of a Higgs boson decaying into bottom quarks at the LHC in full NNLO QCD

NASA Astrophysics Data System (ADS)

Ferrera, Giancarlo; Somogyi, Gábor; Tramontano, Francesco

2018-05-01

We consider the production of a Standard Model Higgs boson decaying to bottom quarks in association with a vector boson W± / Z in hadron collisions. We present a fully exclusive calculation of QCD radiative corrections both for the production cross section and for the Higgs boson decay rate up to next-to-next-to-leading order (NNLO) accuracy. Our calculation also includes the leptonic decay of the vector boson with finite-width effects and spin correlations. We consider typical kinematical cuts applied in the experimental analyses at the Large Hadron Collider (LHC) and we find that the full NNLO QCD corrections significantly decrease the accepted cross section and have a substantial impact on the shape of distributions. We point out that these additional effects are essential to obtain precise theoretical predictions to be compared with the LHC data.

Ultrabroadband polarization splitter based on three-core photonic crystal fiber with a modulation core.

PubMed

Zhao, Tongtong; Lou, Shuqin; Wang, Xin; Zhou, Min; Lian, Zhenggang

2016-08-10

We design an ultrabroadband polarization splitter based on three-core photonic crystal fiber (PCF). A modulation core and two fluorine-doped cores are introduced to achieve an ultrawide bandwidth. The properties of three-core PCF are modeled by using the full-vector finite element method along with the full-vector beam propagation method. Numerical results demonstrate that an ultrabroadband splitter with 320 nm bandwidth with an extinction ratio as low as -20  dB can be achieved by using 52.8 mm long three-core PCF. This splitter also has high compatibility with standard single-mode fibers as the input and output ports due to low splicing loss of 0.02 dB. All the air holes in the proposed structure are circular holes and arranged in a triangular lattice that makes it easy to fabricate.

Spatial aliasing for efficient direction-of-arrival estimation based on steering vector reconstruction

NASA Astrophysics Data System (ADS)

Yan, Feng-Gang; Cao, Bin; Rong, Jia-Jia; Shen, Yi; Jin, Ming

2016-12-01

A new technique is proposed to reduce the computational complexity of the multiple signal classification (MUSIC) algorithm for direction-of-arrival (DOA) estimate using a uniform linear array (ULA). The steering vector of the ULA is reconstructed as the Kronecker product of two other steering vectors, and a new cost function with spatial aliasing at hand is derived. Thanks to the estimation ambiguity of this spatial aliasing, mirror angles mathematically relating to the true DOAs are generated, based on which the full spectral search involved in the MUSIC algorithm is highly compressed into a limited angular sector accordingly. Further complexity analysis and performance studies are conducted by computer simulations, which demonstrate that the proposed estimator requires an extremely reduced computational burden while it shows a similar accuracy to the standard MUSIC.

[Lymphoscintigrams with anatomical landmarks obtained with vector graphics].

PubMed

Rubini, Giuseppe; Antonica, Filippo; Renna, Maria Antonia; Ferrari, Cristina; Iuele, Francesca; Stabile Ianora, Antonio Amato; Losco, Matteo; Niccoli Asabella, Artor

2012-11-01

Nuclear medicine images are difficult to interpret because they do not include anatomical details. The aim of this study was to obtain lymphoscintigrams with anatomical landmarks that could be easily interpreted by General Physicians. Traditional lymphoscintigrams were processed with Adobe© Photoshop® CS6 and converted into vector images created by Illustrator®. The combination with a silhouette vector improved image interpretation, without resulting in longer radiation exposure or acquisition times.

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.

Effective gravitational couplings for cosmological perturbations in generalized Proca theories

NASA Astrophysics Data System (ADS)

De Felice, Antonio; Heisenberg, Lavinia; Kase, Ryotaro; Mukohyama, Shinji; Tsujikawa, Shinji; Zhang, Ying-li

2016-08-01

We consider the finite interactions of the generalized Proca theory including the sixth-order Lagrangian and derive the full linear perturbation equations of motion on the flat Friedmann-Lemaître-Robertson-Walker background in the presence of a matter perfect fluid. By construction, the propagating degrees of freedom (besides the matter perfect fluid) are two transverse vector perturbations, one longitudinal scalar, and two tensor polarizations. The Lagrangians associated with intrinsic vector modes neither affect the background equations of motion nor the second-order action of tensor perturbations, but they do give rise to nontrivial modifications to the no-ghost condition of vector perturbations and to the propagation speeds of vector and scalar perturbations. We derive the effective gravitational coupling Geff with matter density perturbations under a quasistatic approximation on scales deep inside the sound horizon. We find that the existence of intrinsic vector modes allows a possibility for reducing Geff. In fact, within the parameter space, Geff can be even smaller than the Newton gravitational constant G at the late cosmological epoch, with a peculiar phantom dark energy equation of state (without ghosts). The modifications to the slip parameter η and the evolution of the growth rate f σ8 are discussed as well. Thus, dark energy models in the framework of generalized Proca theories can be observationally distinguished from the Λ CDM model according to both cosmic growth and expansion history. Furthermore, we study the evolution of vector perturbations and show that outside the vector sound horizon the perturbations are nearly frozen and start to decay with oscillations after the horizon entry.

Vaccination with Replication Deficient Adenovectors Encoding YF-17D Antigens Induces Long-Lasting Protection from Severe Yellow Fever Virus Infection in Mice.

PubMed

Bassi, Maria R; Larsen, Mads A B; Kongsgaard, Michael; Rasmussen, Michael; Buus, Søren; Stryhn, Anette; Thomsen, Allan R; Christensen, Jan P

2016-02-01

The live attenuated yellow fever vaccine (YF-17D) has been successfully used for more than 70 years. It is generally considered a safe vaccine, however, recent reports of serious adverse events following vaccination have raised concerns and led to suggestions that even safer YF vaccines should be developed. Replication deficient adenoviruses (Ad) have been widely evaluated as recombinant vectors, particularly in the context of prophylactic vaccination against viral infections in which induction of CD8+ T-cell mediated immunity is crucial, but potent antibody responses may also be elicited using these vectors. In this study, we present two adenobased vectors targeting non-structural and structural YF antigens and characterize their immunological properties. We report that a single immunization with an Ad-vector encoding the non-structural protein 3 from YF-17D could elicit a strong CD8+ T-cell response, which afforded a high degree of protection from subsequent intracranial challenge of vaccinated mice. However, full protection was only observed using a vector encoding the structural proteins from YF-17D. This vector elicited virus-specific CD8+ T cells as well as neutralizing antibodies, and both components were shown to be important for protection thus mimicking the situation recently uncovered in YF-17D vaccinated mice. Considering that Ad-vectors are very safe, easy to produce and highly immunogenic in humans, our data indicate that a replication deficient adenovector-based YF vaccine may represent a safe and efficient alternative to the classical live attenuated YF vaccine and should be further tested.

Iterative-method performance evaluation for multiple vectors associated with a large-scale sparse matrix

NASA Astrophysics Data System (ADS)

Imamura, Seigo; Ono, Kenji; Yokokawa, Mitsuo

2016-07-01

Ensemble computing, which is an instance of capacity computing, is an effective computing scenario for exascale parallel supercomputers. In ensemble computing, there are multiple linear systems associated with a common coefficient matrix. We improve the performance of iterative solvers for multiple vectors by solving them at the same time, that is, by solving for the product of the matrices. We implemented several iterative methods and compared their performance. The maximum performance on Sparc VIIIfx was 7.6 times higher than that of a naïve implementation. Finally, to deal with the different convergence processes of linear systems, we introduced a control method to eliminate the calculation of already converged vectors.

[Cloning of Chinese Banna minipig inbred-line alpha1,3-galactosyltransferase gene and construction of its recombinant eukaryotic expression vector].

PubMed

Zhu, Shengming; Wang, Yanping; Zheng, Hong; Cheng, Jingqiu; Lu, Yanrong; Zeng, Yangzhi; Wang, Yu; Wang, Zhu

2009-04-01

This study sought to clone Chinese Banna minipig inbred-line (BMI) alpha1,3-galactosyltransferase (alpha1,3-GT) gene and construct its recombinant eukaryotic expression vector. Total RNA was isolated from BMI liver. Full length cDNA of alpha1,3-GT gene was amplified by RT-PCR and cloned into pMD18-T vector to sequence. Subsequently, alpha1,3-GT gene was inserted into pEGFP-N1 to construct eukaryotic expression vector pEGFP-N1-GT. Then the reconstructed plasmid pEGFP-N1-GT was transiently transfected into human lung cancer cell line A549. The expression of alpha1,3-GT mRNA in transfected cells was detected by RT-PCR. FITC-BS-IB4 lectin was used in the direct immunofluorescence method, which was performed to observe the alpha-Gal synthesis function of BMI alpha1,3-GT in transfected cells. The results showed that full length of BMI alpha1,3-GT cDNA was 1116 bp. BMI alpha1,3-GT cDNA sequence was highly homogenous with those of mouse and bovine, and was exactly the same as the complete sequence of those of swine, pEGFP-N1-GT was confirmed by enzyme digestion and PCR. The expression of alpha1,3-GT mRNA was detected in A549 cells transfected by pEGFP-N1-GT. The expression of alpha-Gal was observed on the membrane of A549 cells transfected by pEGFP-N1-GT. Successful cloning of BMI alpha1,3-GT cDNA and construction of its eukaryotic expression vector have established a foundation for further research and application of BMI alpha1,3-GT in the fields of xenotransplantation and immunological therapy of cancer.

Tsetse Control and Gambian Sleeping Sickness; Implications for Control Strategy.

PubMed

Tirados, Inaki; Esterhuizen, Johan; Kovacic, Vanja; Mangwiro, T N Clement; Vale, Glyn A; Hastings, Ian; Solano, Philippe; Lehane, Michael J; Torr, Steve J

2015-01-01

Gambian sleeping sickness (human African trypanosomiasis, HAT) outbreaks are brought under control by case detection and treatment although it is recognised that this typically only reaches about 75% of the population. Vector control is capable of completely interrupting HAT transmission but is not used because it is considered too expensive and difficult to organise in resource-poor settings. We conducted a full scale field trial of a refined vector control technology to determine its utility in control of Gambian HAT. The major vector of Gambian HAT is the tsetse fly Glossina fuscipes which lives in the humid zone immediately adjacent to water bodies. From a series of preliminary trials we determined the number of tiny targets required to reduce G. fuscipes populations by more than 90%. Using these data for model calibration we predicted we needed a target density of 20 per linear km of river in riverine savannah to achieve >90% tsetse control. We then carried out a full scale, 500 km2 field trial covering two HAT foci in Northern Uganda to determine the efficacy of tiny targets (overall target density 5.7/km2). In 12 months, tsetse populations declined by more than 90%. As a guide we used a published HAT transmission model and calculated that a 72% reduction in tsetse population is required to stop transmission in those settings. The Ugandan census suggests population density in the HAT foci is approximately 500 per km2. The estimated cost for a single round of active case detection (excluding treatment), covering 80% of the population, is US$433,333 (WHO figures). One year of vector control organised within the country, which can completely stop HAT transmission, would cost US$42,700. The case for adding this method of vector control to case detection and treatment is strong. We outline how such a component could be organised.

Tsetse Control and Gambian Sleeping Sickness; Implications for Control Strategy

PubMed Central

Kovacic, Vanja; Mangwiro, T. N. Clement; Vale, Glyn A.; Hastings, Ian; Solano, Philippe; Lehane, Michael J.; Torr, Steve J.

2015-01-01

Background Gambian sleeping sickness (human African trypanosomiasis, HAT) outbreaks are brought under control by case detection and treatment although it is recognised that this typically only reaches about 75% of the population. Vector control is capable of completely interrupting HAT transmission but is not used because it is considered too expensive and difficult to organise in resource-poor settings. We conducted a full scale field trial of a refined vector control technology to determine its utility in control of Gambian HAT. Methods and Findings The major vector of Gambian HAT is the tsetse fly Glossina fuscipes which lives in the humid zone immediately adjacent to water bodies. From a series of preliminary trials we determined the number of tiny targets required to reduce G. fuscipes populations by more than 90%. Using these data for model calibration we predicted we needed a target density of 20 per linear km of river in riverine savannah to achieve >90% tsetse control. We then carried out a full scale, 500 km2 field trial covering two HAT foci in Northern Uganda to determine the efficacy of tiny targets (overall target density 5.7/km2). In 12 months, tsetse populations declined by more than 90%. As a guide we used a published HAT transmission model and calculated that a 72% reduction in tsetse population is required to stop transmission in those settings. Interpretation The Ugandan census suggests population density in the HAT foci is approximately 500 per km2. The estimated cost for a single round of active case detection (excluding treatment), covering 80% of the population, is US$433,333 (WHO figures). One year of vector control organised within the country, which can completely stop HAT transmission, would cost US$42,700. The case for adding this method of vector control to case detection and treatment is strong. We outline how such a component could be organised. PMID:26267814

Comparative evaluation of the Ifakara tent trap-B, the standardized resting boxes and the human landing catch for sampling malaria vectors and other mosquitoes in urban Dar es Salaam, Tanzania

PubMed Central

Sikulu, Maggy; Govella, Nicodem J; Ogoma, Sheila B; Mpangile, John; Kambi, Said H; Kannady, Khadija; Chaki, Prosper C; Mukabana, Wolfgang R; Killeen, Gerry F

2009-01-01

Background Frequent, sensitive and accurate sampling of Anopheles mosquitoes is a prerequisite for effective management of malaria vector control programmes. The most reliable existing means to measure mosquito density is the human landing catch (HLC). However, the HLC technique raises major ethical concerns because of the necessity to expose humans to vectors of malaria and a variety of other pathogens. Furthermore, it is a very arduous undertaking that requires intense supervision, which is severely limiting in terms of affordability and sustainability. Methods A community-based, mosquito sampling protocol, using the Ifakara tent trap-B (ITT-B) and standardized resting boxes (SRB), was developed and evaluated in terms of the number and sample composition of mosquitoes caught by each, compared to rigorously controlled HLC. Mosquitoes were collected once and three times every week by the HLC and the alternative methods, respectively, in the same time and location. Results Overall, the three traps caught 44,848 mosquitoes. The ITT-B, HLC and SRB caught 168, 143 and 46 Anopheles gambiae s.l. as well as 26,315, 13,258 and 4,791 Culex species respectively. The ITT-B was three- and five-times cheaper than the HLC per mosquito caught for An. gambiae and Cx. Species, respectively. Significant correlations between the numbers caught by HLC and ITT-B were observed for both An. gambiae s.l. (P < 0.001) and Cx. species (P = 0.003). Correlation between the catches with HLC and SRB were observed for Cx. species (P < 0.001) but not An. gambiae s.l. (P = 0.195), presumably because of the low density of the latter. Neither ITT-B nor SRB exhibited any obvious density dependence for sampling the two species. Conclusion SRBs exhibited poor sensitivity for both mosquito taxa and are not recommended in this setting. However, this protocol is affordable and effective for routine use of the ITT-B under programmatic conditions. Nevertheless, it is recommended that the trap and the protocol be evaluated further at full programmatic scales to establish effectiveness under fully representative conditions of routine practice. PMID:19674477

Automated innovative diagnostic, data management and communication tool, for improving malaria vector control in endemic settings.

PubMed

Vontas, John; Mitsakakis, Konstantinos; Zengerle, Roland; Yewhalaw, Delenasaw; Sikaala, Chadwick Haadezu; Etang, Josiane; Fallani, Matteo; Carman, Bill; Müller, Pie; Chouaïbou, Mouhamadou; Coleman, Marlize; Coleman, Michael

2016-01-01

Malaria is a life-threatening disease that caused more than 400,000 deaths in sub-Saharan Africa in 2015. Mass prevention of the disease is best achieved by vector control which heavily relies on the use of insecticides. Monitoring mosquito vector populations is an integral component of control programs and a prerequisite for effective interventions. Several individual methods are used for this task; however, there are obstacles to their uptake, as well as challenges in organizing, interpreting and communicating vector population data. The Horizon 2020 project "DMC-MALVEC" consortium will develop a fully integrated and automated multiplex vector-diagnostic platform (LabDisk) for characterizing mosquito populations in terms of species composition, Plasmodium infections and biochemical insecticide resistance markers. The LabDisk will be interfaced with a Disease Data Management System (DDMS), a custom made data management software which will collate and manage data from routine entomological monitoring activities providing information in a timely fashion based on user needs and in a standardized way. The ResistanceSim, a serious game, a modern ICT platform that uses interactive ways of communicating guidelines and exemplifying good practices of optimal use of interventions in the health sector will also be a key element. The use of the tool will teach operational end users the value of quality data (relevant, timely and accurate) to make informed decisions. The integrated system (LabDisk, DDMS & ResistanceSim) will be evaluated in four malaria endemic countries, representative of the vector control challenges in sub-Saharan Africa, (Cameroon, Ivory Coast, Ethiopia and Zambia), highly representative of malaria settings with different levels of endemicity and vector control challenges, to support informed decision-making in vector control and disease management.

A Nearest Neighbor Classifier Employing Critical Boundary Vectors for Efficient On-Chip Template Reduction.

PubMed

Xia, Wenjun; Mita, Yoshio; Shibata, Tadashi

2016-05-01

Aiming at efficient data condensation and improving accuracy, this paper presents a hardware-friendly template reduction (TR) method for the nearest neighbor (NN) classifiers by introducing the concept of critical boundary vectors. A hardware system is also implemented to demonstrate the feasibility of using an field-programmable gate array (FPGA) to accelerate the proposed method. Initially, k -means centers are used as substitutes for the entire template set. Then, to enhance the classification performance, critical boundary vectors are selected by a novel learning algorithm, which is completed within a single iteration. Moreover, to remove noisy boundary vectors that can mislead the classification in a generalized manner, a global categorization scheme has been explored and applied to the algorithm. The global characterization automatically categorizes each classification problem and rapidly selects the boundary vectors according to the nature of the problem. Finally, only critical boundary vectors and k -means centers are used as the new template set for classification. Experimental results for 24 data sets show that the proposed algorithm can effectively reduce the number of template vectors for classification with a high learning speed. At the same time, it improves the accuracy by an average of 2.17% compared with the traditional NN classifiers and also shows greater accuracy than seven other TR methods. We have shown the feasibility of using a proof-of-concept FPGA system of 256 64-D vectors to accelerate the proposed method on hardware. At a 50-MHz clock frequency, the proposed system achieves a 3.86 times higher learning speed than on a 3.4-GHz PC, while consuming only 1% of the power of that used by the PC.

A Comprehensive Optimization Strategy for Real-time Spatial Feature Sharing and Visual Analytics in Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Li, W.; Shao, H.

2017-12-01

For geospatial cyberinfrastructure enabled web services, the ability of rapidly transmitting and sharing spatial data over the Internet plays a critical role to meet the demands of real-time change detection, response and decision-making. Especially for the vector datasets which serve as irreplaceable and concrete material in data-driven geospatial applications, their rich geometry and property information facilitates the development of interactive, efficient and intelligent data analysis and visualization applications. However, the big-data issues of vector datasets have hindered their wide adoption in web services. In this research, we propose a comprehensive optimization strategy to enhance the performance of vector data transmitting and processing. This strategy combines: 1) pre- and on-the-fly generalization, which automatically determines proper simplification level through the introduction of appropriate distance tolerance (ADT) to meet various visualization requirements, and at the same time speed up simplification efficiency; 2) a progressive attribute transmission method to reduce data size and therefore the service response time; 3) compressed data transmission and dynamic adoption of a compression method to maximize the service efficiency under different computing and network environments. A cyberinfrastructure web portal was developed for implementing the proposed technologies. After applying our optimization strategies, substantial performance enhancement is achieved. We expect this work to widen the use of web service providing vector data to support real-time spatial feature sharing, visual analytics and decision-making.

[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.

Expressing Transgenes That Exceed the Packaging Capacity of Adeno-Associated Virus Capsids

PubMed Central

Chamberlain, Kyle; Riyad, Jalish Mahmud; Weber, Thomas

2016-01-01

Recombinant adeno-associated virus vectors (rAAV) are being explored as gene delivery vehicles for the treatment of various inherited and acquired disorders. rAAVs are attractive vectors for several reasons: wild-type AAVs are nonpathogenic, and rAAVs can trigger long-term transgene expression even in the absence of genome integration—at least in postmitotic tissues. Moreover, rAAVs have a low immunogenic profile, and the various AAV serotypes and variants display broad but distinct tropisms. One limitation of rAAVs is that their genome-packaging capacity is only ∼5 kb. For most applications this is not of major concern because the median human protein size is 375 amino acids. Excluding the ITRs, for a protein of typical length, this allows the incorporation of ∼3.5 kb of DNA for the promoter, polyadenylation sequence, and other regulatory elements into a single AAV vector. Nonetheless, for certain diseases the packaging limit of AAV does not allow the delivery of a full-length therapeutic protein by a single AAV vector. Hence, approaches to overcome this limitation have become an important area of research for AAV gene therapy. Among the most promising approaches to overcome the limitation imposed by the packaging capacity of AAV is the use of dual-vector approaches, whereby a transgene is split across two separate AAV vectors. Coinfection of a cell with these two rAAVs will then—through a variety of mechanisms—result in the transcription of an assembled mRNA that could not be encoded by a single AAV vector because of the DNA packaging limits of AAV. The main purpose of this review is to assess the current literature with respect to dual-AAV-vector design, to highlight the effectiveness of the different methodologies and to briefly discuss future areas of research to improve the efficiency of dual-AAV-vector transduction. PMID:26757051

High-quality and interactive animations of 3D time-varying vector fields.

PubMed

Helgeland, Anders; Elboth, Thomas

2006-01-01

In this paper, we present an interactive texture-based method for visualizing three-dimensional unsteady vector fields. The visualization method uses a sparse and global representation of the flow, such that it does not suffer from the same perceptual issues as is the case for visualizing dense representations. The animation is made by injecting a collection of particles evenly distributed throughout the physical domain. These particles are then tracked along their path lines. At each time step, these particles are used as seed points to generate field lines using any vector field such as the velocity field or vorticity field. In this way, the animation shows the advection of particles while each frame in the animation shows the instantaneous vector field. In order to maintain a coherent particle density and to avoid clustering as time passes, we have developed a novel particle advection strategy which produces approximately evenly-spaced field lines at each time step. To improve rendering performance, we decouple the rendering stage from the preceding stages of the visualization method. This allows interactive exploration of multiple fields simultaneously, which sets the stage for a more complete analysis of the flow field. The final display is rendered using texture-based direct volume rendering.

Numerical simulations of short-mixing-time double-wave-vector diffusion-weighting experiments with multiple concatenations on whole-body MR systems

NASA Astrophysics Data System (ADS)

Finsterbusch, Jürgen

2010-12-01

Double- or two-wave-vector diffusion-weighting experiments with short mixing times in which two diffusion-weighting periods are applied in direct succession, are a promising tool to estimate cell sizes in the living tissue. However, the underlying effect, a signal difference between parallel and antiparallel wave vector orientations, is considerably reduced for the long gradient pulses required on whole-body MR systems. Recently, it has been shown that multiple concatenations of the two wave vectors in a single acquisition can double the modulation amplitude if short gradient pulses are used. In this study, numerical simulations of such experiments were performed with parameters achievable with whole-body MR systems. It is shown that the theoretical model yields a good approximation of the signal behavior if an additional term describing free diffusion is included. More importantly, it is demonstrated that the shorter gradient pulses sufficient to achieve the desired diffusion weighting for multiple concatenations, increase the signal modulation considerably, e.g. by a factor of about five for five concatenations. Even at identical echo times, achieved by a shortened diffusion time, a moderate number of concatenations significantly improves the signal modulation. Thus, experiments on whole-body MR systems may benefit from multiple concatenations.

Programmable lithography engine (ProLE) grid-type supercomputer and its applications

NASA Astrophysics Data System (ADS)

Petersen, John S.; Maslow, Mark J.; Gerold, David J.; Greenway, Robert T.

2003-06-01

There are many variables that can affect lithographic dependent device yield. Because of this, it is not enough to make optical proximity corrections (OPC) based on the mask type, wavelength, lens, illumination-type and coherence. Resist chemistry and physics along with substrate, exposure, and all post-exposure processing must be considered too. Only a holistic approach to finding imaging solutions will accelerate yield and maximize performance. Since experiments are too costly in both time and money, accomplishing this takes massive amounts of accurate simulation capability. Our solution is to create a workbench that has a set of advanced user applications that utilize best-in-class simulator engines for solving litho-related DFM problems using distributive computing. Our product, ProLE (Programmable Lithography Engine), is an integrated system that combines Petersen Advanced Lithography Inc."s (PAL"s) proprietary applications and cluster management software wrapped around commercial software engines, along with optional commercial hardware and software. It uses the most rigorous lithography simulation engines to solve deep sub-wavelength imaging problems accurately and at speeds that are several orders of magnitude faster than current methods. Specifically, ProLE uses full vector thin-mask aerial image models or when needed, full across source 3D electromagnetic field simulation to make accurate aerial image predictions along with calibrated resist models;. The ProLE workstation from Petersen Advanced Lithography, Inc., is the first commercial product that makes it possible to do these intensive calculations at a fraction of a time previously available thus significantly reducing time to market for advance technology devices. In this work, ProLE is introduced, through model comparison to show why vector imaging and rigorous resist models work better than other less rigorous models, then some applications of that use our distributive computing solution are shown. Topics covered describe why ProLE solutions are needed from an economic and technical aspect, a high level discussion of how the distributive system works, speed benchmarking, and finally, a brief survey of applications including advanced aberrations for lens sensitivity and flare studies, optical-proximity-correction for a bitcell and an application that will allow evaluation of the potential of a design to have systematic failures during fabrication.

Recovery of infectious virus from full-length cowpox virus (CPXV) DNA cloned as a bacterial artificial chromosome (BAC)

PubMed Central

2011-01-01

Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV). We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR) as a bacterial artificial chromosome (BAC) in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows maintenance of large circular DNA in E. coli, into the thymidine kinase locus of CPXV by homologous recombination. Circular replication intermediates were then electroporated into E. coli DH10B cells. Upon successful establishment of the infectious BR clone, we modified the full-length clone such that recombination-mediated excision of bacterial sequences can occur upon transfection in eukaryotic cells. This self-excision of the bacterial replicon is made possible by a sequence duplication within mini-F sequences and allows recovery of recombinant virus progeny without remaining marker or vector sequences. The in vitro growth properties of viruses derived from both BAC clones were determined and found to be virtually indistinguishable from those of parental, wild-type BR. Finally, the complete genomic sequence of the infectious clone was determined and the cloned viral genome was shown to be identical to that of the parental virus. In summary, the generated infectious clone will greatly facilitate studies on individual genes and pathogenesis of CPXV. Moreover, the vector potential of CPXV can now be more systematically explored using this newly generated tool. PMID:21314965

Constrains on the South Atlantic Anomaly from Réunion Island

NASA Astrophysics Data System (ADS)

Béguin, A.; de Groot, L. V.

2017-12-01

The South Atlantic Anomaly (SAA) is a region where the geomagnetic field intensity is about half as strong as would be expected from the current geomagnetic dipole moment that arises from geomagnetic field models. Those field models predict a westward movement of the SAA and predicts its origin East of Africa around 1500 AD. The onset and evolution of the SAA, however, are poorly constrained due to a lack of full-vector paleomagnetic data from Africa and the Indian Ocean for the past centuries. Here we present a full-vector paleosecular variation (PSV) curve for Réunion Island (21°S, 55°E) located East the African continent, in the region that currently shows the fastest increase in geomagnetic field strength in contrast to the average global decay. We sampled 27 sites covering the last 700 years, and subjected them to a directional and multi-method paleointensity study. The obtained directional records reveal shallower inclinations and less variation in the declination compared to current geomagnetic field model predictions. Scrutinizing the IZZI-Thellier, Multispecimen, and calibrated pseudo-Thellier results produces a coherent paleointensity record. The predicted intensity trend from the geomagnetic field models generally agrees with the trend in our data, however, the high paleointensities are higher than the models predict, and the low paleointensities are lower than the models. This illustrates the inevitable smoothing inherent to geomagnetic field modelling. We will discuss the constraints on the onset of the SAA that arise from the new full-vector PSV curve for Réunion that we present and the implications for the past and future evolution of this geomagnetic phenomenon.

Anti-hIgE gene therapy of peanut-induced anaphylaxis in a humanized murine model of peanut allergy.

PubMed

Pagovich, Odelya E; Wang, Bo; Chiuchiolo, Maria J; Kaminsky, Stephen M; Sondhi, Dolan; Jose, Clarisse L; Price, Christina C; Brooks, Sarah F; Mezey, Jason G; Crystal, Ronald G

2016-12-01

Peanuts are the most common food to provoke fatal or near-fatal anaphylactic reactions. Treatment with an anti-hIgE mAb is efficacious but requires frequent parenteral administration. Based on the knowledge that peanut allergy is mediated by peanut-specific IgE, we hypothesized that a single administration of an adeno-associated virus (AAV) gene transfer vector encoding for anti-hIgE would protect against repeated peanut exposure in the host with peanut allergy. We developed a novel humanized murine model of peanut allergy that recapitulates the human anaphylactic response to peanuts in NOD-scid IL2Rgamma null mice transferred with blood mononuclear cells from donors with peanut allergy and then sensitized with peanut extract. As therapy, we constructed an adeno-associated rh.10 serotype vector coding for a full-length, high-affinity, anti-hIgE antibody derived from the Fab fragment of the anti-hIgE mAb omalizumab (AAVrh.10anti-hIgE). In the reconstituted mice peanut-specific IgE was induced by peanut sensitization and hypersensitivity, and reactions were provoked by feeding peanuts to mice with symptoms similar to those of human subjects with peanut allergy. A single administration of AAVrh.10anti-hIgE vector expressed persistent levels of anti-hIgE. The anti-hIgE vector, administered either before sensitization or after peanut sensitization and manifestation of the peanut-induced phenotype, blocked IgE-mediated alterations in peanut-induced histamine release, anaphylaxis scores, locomotor activity, and free IgE levels and protected animals from death caused by anaphylaxis. If this degree of persistent efficacy translates to human subjects, AAVrh.10anti-hIgE could be an effective 1-time preventative therapy for peanut allergy and possibly other severe, IgE-mediated allergies. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential

PubMed Central

2017-01-01

ABSTRACT Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in “enhancerless” self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the LMO2 gene and then measuring LMO2 expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, LMO2 expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required. IMPORTANCE Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene therapy. Self-inactivating vectors devoid of viral long-terminal-repeat enhancers have proven safe; however, transgene expression from cellular promoters is often insufficient for full phenotypic correction. Foamy virus is an attractive vector for gene therapy. We found foamy virus vectors to be remarkably less genotoxic, well below what was expected from their integration site preferences. We demonstrate that the foamy virus long terminal repeats contain an insulator element that binds CCCTC-binding factor and reduces its insertional genotoxicity. Our study elucidates a mechanism behind the low genotoxic potential of foamy virus, identifies a unique insulator, and supports the use of foamy virus as a vector for gene therapy. PMID:29046446

Optimal four-impulse rendezvous between coplanar elliptical orbits

NASA Astrophysics Data System (ADS)

Wang, JianXia; Baoyin, HeXi; Li, JunFeng; Sun, FuChun

2011-04-01

Rendezvous in circular or near circular orbits has been investigated in great detail, while rendezvous in arbitrary eccentricity elliptical orbits is not sufficiently explored. Among the various optimization methods proposed for fuel optimal orbital rendezvous, Lawden's primer vector theory is favored by many researchers with its clear physical concept and simplicity in solution. Prussing has applied the primer vector optimization theory to minimum-fuel, multiple-impulse, time-fixed orbital rendezvous in a near circular orbit and achieved great success. Extending Prussing's work, this paper will employ the primer vector theory to study trajectory optimization problems of arbitrary eccentricity elliptical orbit rendezvous. Based on linearized equations of relative motion on elliptical reference orbit (referred to as T-H equations), the primer vector theory is used to deal with time-fixed multiple-impulse optimal rendezvous between two coplanar, coaxial elliptical orbits with arbitrary large eccentricity. A parameter adjustment method is developed for the prime vector to satisfy the Lawden's necessary condition for the optimal solution. Finally, the optimal multiple-impulse rendezvous solution including the time, direction and magnitudes of the impulse is obtained by solving the two-point boundary value problem. The rendezvous error of the linearized equation is also analyzed. The simulation results confirmed the analyzed results that the rendezvous error is small for the small eccentricity case and is large for the higher eccentricity. For better rendezvous accuracy of high eccentricity orbits, a combined method of multiplier penalty function with the simplex search method is used for local optimization. The simplex search method is sensitive to the initial values of optimization variables, but the simulation results show that initial values with the primer vector theory, and the local optimization algorithm can improve the rendezvous accuracy effectively with fast convergence, because the optimal results obtained by the primer vector theory are already very close to the actual optimal solution. If the initial values are taken randomly, it is difficult to converge to the optimal solution.

Attitude estimation from magnetometer and earth-albedo-corrected coarse sun sensor measurements

NASA Astrophysics Data System (ADS)

Appel, Pontus

2005-01-01

For full 3-axes attitude determination the magnetic field vector and the Sun vector can be used. A Coarse Sun Sensor consisting of six solar cells placed on each of the six outer surfaces of the satellite is used for Sun vector determination. This robust and low cost setup is sensitive to surrounding light sources as it sees the whole sky. To compensate for the largest error source, the Earth, an albedo model is developed. The total albedo light vector has contributions from the Earth surface which is illuminated by the Sun and visible from the satellite. Depending on the reflectivity of the Earth surface, the satellite's position and the Sun's position the albedo light changes. This cannot be calculated analytically and hence a numerical model is developed. For on-board computer use the Earth albedo model consisting of data tables is transferred into polynomial functions in order to save memory space. For an absolute worst case the attitude determination error can be held below 2∘. In a nominal case it is better than 1∘.

Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Carter, Jonathan; Shalf, John; Skinner, David; Ethier, Stephane; Biswas, Rupak; Djomehri, Jahed; VanderWijngaart, Rob

2003-01-01

The growing gap between sustained and peak performance for scientific applications has become a well-known problem in high performance computing. The recent development of parallel vector systems offers the potential to bridge this gap for a significant number of computational science codes and deliver a substantial increase in computing capabilities. This paper examines the intranode performance of the NEC SX6 vector processor and the cache-based IBM Power3/4 superscalar architectures across a number of key scientific computing areas. First, we present the performance of a microbenchmark suite that examines a full spectrum of low-level machine characteristics. Next, we study the behavior of the NAS Parallel Benchmarks using some simple optimizations. Finally, we evaluate the perfor- mance of several numerical codes from key scientific computing domains. Overall results demonstrate that the SX6 achieves high performance on a large fraction of our application suite and in many cases significantly outperforms the RISC-based architectures. However, certain classes of applications are not easily amenable to vectorization and would likely require extensive reengineering of both algorithm and implementation to utilize the SX6 effectively.

General MoM Solutions for Large Arrays

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

Fasenfest, B; Capolino, F; Wilton, D R

2003-07-22

This paper focuses on a numerical procedure that addresses the difficulties of dealing with large, finite arrays while preserving the generality and robustness of full-wave methods. We present a fast method based on approximating interactions between sufficiently separated array elements via a relatively coarse interpolation of the Green's function on a uniform grid commensurate with the array's periodicity. The interaction between the basis and testing functions is reduced to a three-stage process. The first stage is a projection of standard (e.g., RWG) subdomain bases onto a set of interpolation functions that interpolate the Green's function on the array face. Thismore » projection, which is used in a matrix/vector product for each array cell in an iterative solution process, need only be carried out once for a single cell and results in a low-rank matrix. An intermediate stage matrix/vector product computation involving the uniformly sampled Green's function is of convolutional form in the lateral (transverse) directions so that a 2D FFT may be used. The final stage is a third matrix/vector product computation involving a matrix resulting from projecting testing functions onto the Green's function interpolation functions; the low-rank matrix is either identical to (using Galerkin's method) or similar to that for the bases projection. An effective MoM solution scheme is developed for large arrays using a modification of the AIM (Adaptive Integral Method) method. The method permits the analysis of arrays with arbitrary contours and nonplanar elements. Both fill and solve times within the MoM method are improved with respect to more standard MoM solvers.« less

Vector wavefront propagation modeling for the TPF coronagraph

NASA Astrophysics Data System (ADS)

Lieber, Michael D.; Neureuther, Andrew R.; Ceperley, Dan; Kasdin, N. Jeremy; Ter-Gabrielyan, Nikolay

2004-10-01

The TPF mission to search for exo-solar planets is extremely challenging both technically and from a performance modeling perspective. For the visible light coronagraph approach, the requirements for 1e10 rejection of star light to planet signal has not yet been achieved in laboratory testing and full-scale testing on the ground has many more obstacles and may not be possible. Therefore, end-to-end performance modeling will be relied upon to fully predict performance. One of the key technologies developed for achieving the rejection ratios uses shaped pupil masks to selectively cancel starlight in planet search regions by taking advantage of diffraction. Modeling results published to date have been based upon scalar wavefront propagation theory to compute the residual star and planet images. This ignores the 3D structure of the mask and the interaction of light with matter. In this paper we discuss previous work with a system model of the TPF coronagraph and propose an approach for coupling in a vector propagation model using the Finite Difference Time Domain (FDTD) method. This method, implemented in a software package called TEMPEST, allows us to propagate wavefronts through a mask structure to an integrated system model to explore the vector propagation aspects of the problem. We can then do rigorous mask scatter modeling to understand the effects of real physical mask structures on the magnitude, phase, polarization, and wavelength dependence of the transmitted light near edges. Shaped mask technology is reviewed, and computational aspects and interface issues to a TPF integrated system model are also discussed.

Development and comparison of advanced reduced-basis methods for the transient structural analysis of unconstrained structures

NASA Technical Reports Server (NTRS)

Mcgowan, David M.; Bostic, Susan W.; Camarda, Charles J.

1993-01-01

The development of two advanced reduced-basis methods, the force derivative method and the Lanczos method, and two widely used modal methods, the mode displacement method and the mode acceleration method, for transient structural analysis of unconstrained structures is presented. Two example structural problems are studied: an undamped, unconstrained beam subject to a uniformly distributed load which varies as a sinusoidal function of time and an undamped high-speed civil transport aircraft subject to a normal wing tip load which varies as a sinusoidal function of time. These example problems are used to verify the methods and to compare the relative effectiveness of each of the four reduced-basis methods for performing transient structural analyses on unconstrained structures. The methods are verified with a solution obtained by integrating directly the full system of equations of motion, and they are compared using the number of basis vectors required to obtain a desired level of accuracy and the associated computational times as comparison criteria.

Macroscopic theory of dark sector

NASA Astrophysics Data System (ADS)

Meierovich, Boris

A simple Lagrangian with squared covariant divergence of a vector field as a kinetic term turned out an adequate tool for macroscopic description of the dark sector. The zero-mass field acts as the dark energy. Its energy-momentum tensor is a simple additive to the cosmological constant [1]. Space-like and time-like massive vector fields describe two different forms of dark matter. The space-like massive vector field is attractive. It is responsible for the observed plateau in galaxy rotation curves [2]. The time-like massive field displays repulsive elasticity. In balance with dark energy and ordinary matter it provides a four parametric diversity of regular solutions of the Einstein equations describing different possible cosmological and oscillating non-singular scenarios of evolution of the universe [3]. In particular, the singular big bang turns into a regular inflation-like transition from contraction to expansion with the accelerate expansion at late times. The fine-tuned Friedman-Robertson-Walker singular solution corresponds to the particular limiting case at the boundary of existence of regular oscillating solutions in the absence of vector fields. The simplicity of the general covariant expression for the energy-momentum tensor allows to analyse the main properties of the dark sector analytically and avoid unnecessary model assumptions. It opens a possibility to trace how the additional attraction of the space-like dark matter, dominating in the galaxy scale, transforms into the elastic repulsion of the time-like dark matter, dominating in the scale of the Universe. 1. B. E. Meierovich. "Vector fields in multidimensional cosmology". Phys. Rev. D 84, 064037 (2011). 2. B. E. Meierovich. "Galaxy rotation curves driven by massive vector fields: Key to the theory of the dark sector". Phys. Rev. D 87, 103510, (2013). 3. B. E. Meierovich. "Towards the theory of the evolution of the Universe". Phys. Rev. D 85, 123544 (2012).

Field evaluation of picaridin repellents reveals differences in repellent sensitivity between Southeast Asian vectors of malaria and arboviruses.

PubMed

Van Roey, Karel; Sokny, Mao; Denis, Leen; Van den Broeck, Nick; Heng, Somony; Siv, Sovannaroth; Sluydts, Vincent; Sochantha, Tho; Coosemans, Marc; Durnez, Lies

2014-12-01

Scaling up of insecticide treated nets has contributed to a substantial malaria decline. However, some malaria vectors, and most arbovirus vectors, bite outdoors and in the early evening. Therefore, topically applied insect repellents may provide crucial additional protection against mosquito-borne pathogens. Among topical repellents, DEET is the most commonly used, followed by others such as picaridin. The protective efficacy of two formulated picaridin repellents against mosquito bites, including arbovirus and malaria vectors, was evaluated in a field study in Cambodia. Over a period of two years, human landing collections were performed on repellent treated persons, with rotation to account for the effect of collection place, time and individual collector. Based on a total of 4996 mosquitoes collected on negative control persons, the overall five hour protection rate was 97.4% [95%CI: 97.1-97.8%], not decreasing over time. Picaridin 20% performed equally well as DEET 20% and better than picaridin 10%. Repellents performed better against Mansonia and Culex spp. as compared to aedines and anophelines. A lower performance was observed against Aedes albopictus as compared to Aedes aegypti, and against Anopheles barbirostris as compared to several vector species. Parity rates were higher in vectors collected on repellent treated person as compared to control persons. As such, field evaluation shows that repellents can provide additional personal protection against early and outdoor biting malaria and arbovirus vectors, with excellent protection up to five hours after application. The heterogeneity in repellent sensitivity between mosquito genera and vector species could however impact the efficacy of repellents in public health programs. Considering its excellent performance and potential to protect against early and outdoor biting vectors, as well as its higher acceptability as compared to DEET, picaridin is an appropriate product to evaluate the epidemiological impact of large scale use of topical repellents on arthropod borne diseases.

Field Evaluation of Picaridin Repellents Reveals Differences in Repellent Sensitivity between Southeast Asian Vectors of Malaria and Arboviruses

PubMed Central

Denis, Leen; Van den Broeck, Nick; Heng, Somony; Siv, Sovannaroth; Sluydts, Vincent; Sochantha, Tho; Coosemans, Marc; Durnez, Lies

2014-01-01

Scaling up of insecticide treated nets has contributed to a substantial malaria decline. However, some malaria vectors, and most arbovirus vectors, bite outdoors and in the early evening. Therefore, topically applied insect repellents may provide crucial additional protection against mosquito-borne pathogens. Among topical repellents, DEET is the most commonly used, followed by others such as picaridin. The protective efficacy of two formulated picaridin repellents against mosquito bites, including arbovirus and malaria vectors, was evaluated in a field study in Cambodia. Over a period of two years, human landing collections were performed on repellent treated persons, with rotation to account for the effect of collection place, time and individual collector. Based on a total of 4996 mosquitoes collected on negative control persons, the overall five hour protection rate was 97.4% [95%CI: 97.1–97.8%], not decreasing over time. Picaridin 20% performed equally well as DEET 20% and better than picaridin 10%. Repellents performed better against Mansonia and Culex spp. as compared to aedines and anophelines. A lower performance was observed against Aedes albopictus as compared to Aedes aegypti, and against Anopheles barbirostris as compared to several vector species. Parity rates were higher in vectors collected on repellent treated person as compared to control persons. As such, field evaluation shows that repellents can provide additional personal protection against early and outdoor biting malaria and arbovirus vectors, with excellent protection up to five hours after application. The heterogeneity in repellent sensitivity between mosquito genera and vector species could however impact the efficacy of repellents in public health programs. Considering its excellent performance and potential to protect against early and outdoor biting vectors, as well as its higher acceptability as compared to DEET, picaridin is an appropriate product to evaluate the epidemiological impact of large scale use of topical repellents on arthropod borne diseases. PMID:25522134

Classification of subsurface objects using singular values derived from signal frames

DOEpatents

Chambers, David H; Paglieroni, David W

2014-05-06

The classification system represents a detected object with a feature vector derived from the return signals acquired by an array of N transceivers operating in multistatic mode. The classification system generates the feature vector by transforming the real-valued return signals into complex-valued spectra, using, for example, a Fast Fourier Transform. The classification system then generates a feature vector of singular values for each user-designated spectral sub-band by applying a singular value decomposition (SVD) to the N.times.N square complex-valued matrix formed from sub-band samples associated with all possible transmitter-receiver pairs. The resulting feature vector of singular values may be transformed into a feature vector of singular value likelihoods and then subjected to a multi-category linear or neural network classifier for object classification.

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.

Spin Manipulating Vector and Tensor Polarized Deuterons Stored in COSY

NASA Astrophysics Data System (ADS)

Morozov, Vassili; Krisch, Alan; Leonova, Maria; Raymond, Richard; Sivers, Dennis; Wong, Victor; Yonehara, Katsuya; Bechstedt, Ulf; Gebel, Ralf; Lehrach, Andreas; Lorentz, Bernd; Maier, Rudolf; Schnase, Alexander; Stockhorst, Hans; Eversheim, Dieter; Hinterberger, Frank; Rohdjess, Heiko; Ulbrich, Kay

2004-05-01

We recently studied spin flipping and spin manipulation of a simultaneously vector and tensor polarized deuteron beam stored in the COSY Cooler Synchrotron at 1.85 GeV/c. Using the EDDA detector we calibrated vector and tensor analyzing powers, which were earlier unknown at this energy; thus, we were able to obtain the absolute values for both the vector and tensor polarizations. We manipulated the deuteron's polarization using a new water-cooled ferrite rf dipole, by adiabatically sweeping its frequency through an rf-induced spin resonance. We first experimentally determined the resonance's frequency and then varied the dipole's frequency range and frequency ramp time. This allowed us to maximize the vector polarization spin-flip efficiency to about 97 ± 1%. We also studied the interesting tensor polarization manipulation in considerable detail.

A combined direct/inverse three-dimensional transonic wing design method for vector computers

NASA Technical Reports Server (NTRS)

Weed, R. A.; Carlson, L. A.; Anderson, W. K.

1984-01-01

A three-dimensional transonic-wing design algorithm for vector computers is developed, and the results of sample computations are presented graphically. The method incorporates the direct/inverse scheme of Carlson (1975), a Cartesian grid system with boundary conditions applied at a mean plane, and a potential-flow solver based on the conservative form of the full potential equation and using the ZEBRA II vectorizable solution algorithm of South et al. (1980). The accuracy and consistency of the method with regard to direct and inverse analysis and trailing-edge closure are verified in the test computations.

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

Probability, arrow of time and decoherence

NASA Astrophysics Data System (ADS)

Bacciagaluppi, Guido

This paper relates both to the metaphysics of probability and to the physics of time asymmetry. Using the formalism of decoherent histories, it investigates whether intuitions about intrinsic time directedness that are often associated with probability can be justified in the context of no-collapse approaches to quantum mechanics. The standard (two-vector) approach to time symmetry in the decoherent histories literature is criticised, and an alternative approach is proposed, based on two decoherence conditions ('forwards' and 'backwards') within the one-vector formalism. In turn, considerations of forwards and backwards decoherence and of decoherence and recoherence suggest that a time-directed interpretation of probabilities, if adopted, should be both contingent and perspectival.

Does health promote economic growth? Portuguese case study: from dictatorship to full democracy.

PubMed

Morgado, Sónia Maria Aniceto

2014-07-01

This paper revisits the debate on health and economic growth (Deaton in J Econ Lit 51:113-158, 2003) focusing on the Portuguese case by testing the relationship between growth and health. We test Portuguese insights, using time series data from 1960 to 2005, taking into account different variables (life expectancy, labour, capital, infant mortality) and considering the years that included major events on the political scene, such as the dictatorship and a closed economy (1960-1974), a revolution (1974) and full democracy and an open economy (1975-2005), factors that influence major economic, cultural, social and politic indicators. Therefore the analysis is carried out adopting Lucas' (J Monet Econ 22(1):3-42, 1988) endogenous growth model that considers human capital as one factor of production, it adopts a VAR (vector autoregressive) model to test the causality between growth and health. Estimates based on the VAR seem to confirm that economic growth influences the health process, but health does not promote growth, during the period under study.

Development of advanced Navier-Stokes solver

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan

1994-01-01

The objective of research was to develop and validate new computational algorithms for solving the steady and unsteady Euler and Navier-Stokes equations. The end-products are new three-dimensional Euler and Navier-Stokes codes that are faster, more reliable, more accurate, and easier to use. The three-dimensional Euler and full/thin-layer Reynolds-averaged Navier-Stokes equations for compressible/incompressible flows are solved on structured hexahedral grids. The Baldwin-Lomax algebraic turbulence model is used for closure. The space discretization is based on a cell-centered finite-volume method augmented by a variety of numerical dissipation models with optional total variation diminishing limiters. The governing equations are integrated in time by an implicit method based on lower-upper factorization and symmetric Gauss-Seidel relaxation. The algorithm is vectorized on diagonal planes of sweep using two-dimensional indices in three dimensions. Convergence rates and the robustness of the codes are enhanced by the use of an implicit full approximation storage multigrid method.

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

Song, Hongwei, E-mail: hwsong@wipm.ac.cn; Yang, Minghui; Lu, Yunpeng

An initial state selected time-dependent wave packet method is applied to study the dynamics of the OH + CHD{sub 3} reaction with a six-dimensional model on a newly developed full-dimensional ab initio potential energy surface (PES). This quantum dynamical (QD) study is complemented by full-dimensional quasi-classical trajectory (QCT) calculations on the same PES. The QD results indicate that both translational energy and the excitation of the CH stretching mode significantly promote the reaction while the excitation of the umbrella mode has a negligible effect on the reactivity. For this early barrier reaction, interestingly, the CH stretching mode is more effectivemore » than translational energy in promoting the reaction except at very low collision energies. These QD observations are supported by QCT results. The higher efficacy of the CH stretching model in promoting this early barrier reaction is inconsistent with the prediction of the naively extended Polanyi’s rules, but can be rationalized by the recently proposed sudden vector projection model.« less

PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.

PubMed

Gao, Yubang; Wang, Huiyuan; Zhang, Hangxiao; Wang, Yongsheng; Chen, Jinfeng; Gu, Lianfeng

2018-05-01

The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results. The Dockerfile of PRAPI is available at http://www.bioinfor.org/tool/PRAPI. lfgu@fafu.edu.cn.

Defining the Role of Alpha-Synuclein in Enteric Dysfunction in Parkinsons Disease

DTIC Science & Technology

2017-10-01

direction. o What were the major goals of the project?  Animal use approvals – accomplished pre-funding  Vector production - 1st round of vector...August 2017. 100% Complete  Vector injections. We injected all animals for the long-term survival group as well as additional subjects for shorter...time points. However, as noted below, the transgene expression seen in these animals was below that which was expected/intended. Thus, we are currently

Thrust vectoring of broad ion beams for spacecraft attitude control

NASA Technical Reports Server (NTRS)

Collett, C. R.; King, H. J.

1973-01-01

Thrust vectoring is shown to increase the attractiveness of ion thrusters for satellite control applications. Incorporating beam deflection into ion thrusters makes it possible to achieve attitude control without adding any thrusters. Two beam vectoring systems are described that can provide up to 10-deg beam deflection in any azimuth. Both systems have been subjected to extended life tests on a 5-cm thruster which resulted in projected life times of from 7500 to 20,000 hours.

Mapping of courses on vector biology and vector-borne diseases systems: time for a worldwide effort.

PubMed

Casas, Jérôme; Lazzari, Claudio; Insausti, Teresita; Launois, Pascal; Fouque, Florence

2016-11-01

Major emergency efforts are being mounted for each vector-borne disease epidemiological crisis anew, while knowledge about the biology of arthropods vectors is dwindling slowly but continuously, as is the number of field entomologists. The discrepancy between the rates of production of knowledge and its use and need for solving crises is widening, in particular due to the highly differing time spans of the two concurrent processes. A worldwide web based search using multiple key words and search engines of onsite and online courses in English, Spanish, Portuguese, French, Italian and German concerned with the biology of vectors identified over 140 courses. They are geographically and thematically scattered, the vast majority of them are on-site, with very few courses using the latest massive open online course (MOOC) powerfulness. Over two third of them is given in English and Western Africa is particularity poorly represented. The taxonomic groups covered are highly unbalanced towards mosquitoes. A worldwide unique portal to guide students of all grades and levels of expertise, in particular those in remote locations, is badly needed. This is the objective a new activity supported by the Special Programme for Research and Training in Tropical Diseases (TDR).

CFD evaluation of an advanced thrust vector control concept

NASA Technical Reports Server (NTRS)

Tiarn, Weihnurng; Cavalleri, Robert

1990-01-01

A potential concept that can offer an alternate method for thrust vector control of the Space Shuttle Solid Rocket Booster is the use of a cylindrical probe that is inserted (on demand) through the wall of the rocket nozzle. This Probe Thrust Vector Control (PTVC) concept is an alternate to that of a gimbaled nozzle or a Liquid Injection Thrust Vector (LITVC) system. The viability of the PTVC concept can be assessed either experimentally and/or with the use of CFD. A purely experimental assessment can be time consuming and expensive, whereas a CFD assessment can be very time- and cost-effective. Two key requirements of the proposed concept are PTVC vectoring performance and the active cooling requirements for the probe to maintain its thermal and structural integrity. An active thermal cooling method is the injection of coolant around the pheriphery of the probe. How much coolant is required and how this coolant distributes itself in the flow field is of major concern. The objective of the work reported here is the use of CFD to answer these question and in the design of test hardware to substantiate the results of the CFD predictions.

Mapping of courses on vector biology and vector-borne diseases systems: time for a worldwide effort

PubMed Central

Casas, Jérôme; Lazzari, Claudio; Insausti, Teresita; Launois, Pascal; Fouque, Florence

2016-01-01

Major emergency efforts are being mounted for each vector-borne disease epidemiological crisis anew, while knowledge about the biology of arthropods vectors is dwindling slowly but continuously, as is the number of field entomologists. The discrepancy between the rates of production of knowledge and its use and need for solving crises is widening, in particular due to the highly differing time spans of the two concurrent processes. A worldwide web based search using multiple key words and search engines of onsite and online courses in English, Spanish, Portuguese, French, Italian and German concerned with the biology of vectors identified over 140 courses. They are geographically and thematically scattered, the vast majority of them are on-site, with very few courses using the latest massive open online course (MOOC) powerfulness. Over two third of them is given in English and Western Africa is particularity poorly represented. The taxonomic groups covered are highly unbalanced towards mosquitoes. A worldwide unique portal to guide students of all grades and levels of expertise, in particular those in remote locations, is badly needed. This is the objective a new activity supported by the Special Programme for Research and Training in Tropical Diseases (TDR). PMID:27759770

Automatic event detection in low SNR microseismic signals based on multi-scale permutation entropy and a support vector machine

NASA Astrophysics Data System (ADS)

Jia, Rui-Sheng; Sun, Hong-Mei; Peng, Yan-Jun; Liang, Yong-Quan; Lu, Xin-Ming

2017-07-01

Microseismic monitoring is an effective means for providing early warning of rock or coal dynamical disasters, and its first step is microseismic event detection, although low SNR microseismic signals often cannot effectively be detected by routine methods. To solve this problem, this paper presents permutation entropy and a support vector machine to detect low SNR microseismic events. First, an extraction method of signal features based on multi-scale permutation entropy is proposed by studying the influence of the scale factor on the signal permutation entropy. Second, the detection model of low SNR microseismic events based on the least squares support vector machine is built by performing a multi-scale permutation entropy calculation for the collected vibration signals, constructing a feature vector set of signals. Finally, a comparative analysis of the microseismic events and noise signals in the experiment proves that the different characteristics of the two can be fully expressed by using multi-scale permutation entropy. The detection model of microseismic events combined with the support vector machine, which has the features of high classification accuracy and fast real-time algorithms, can meet the requirements of online, real-time extractions of microseismic events.

Personal Computer Transport Analysis Program

NASA Technical Reports Server (NTRS)

DiStefano, Frank, III; Wobick, Craig; Chapman, Kirt; McCloud, Peter

2012-01-01

The Personal Computer Transport Analysis Program (PCTAP) is C++ software used for analysis of thermal fluid systems. The program predicts thermal fluid system and component transients. The output consists of temperatures, flow rates, pressures, delta pressures, tank quantities, and gas quantities in the air, along with air scrubbing component performance. PCTAP s solution process assumes that the tubes in the system are well insulated so that only the heat transfer between fluid and tube wall and between adjacent tubes is modeled. The system described in the model file is broken down into its individual components; i.e., tubes, cold plates, heat exchangers, etc. A solution vector is built from the components and a flow is then simulated with fluid being transferred from one component to the next. The solution vector of components in the model file is built at the initiation of the run. This solution vector is simply a list of components in the order of their inlet dependency on other components. The component parameters are updated in the order in which they appear in the list at every time step. Once the solution vectors have been determined, PCTAP cycles through the components in the solution vector, executing their outlet function for each time-step increment.

Transmission of Xylella fastidiosa to Grapevine by the Meadow Spittlebug.

PubMed

Cornara, D; Sicard, A; Zeilinger, A R; Porcelli, F; Purcell, A H; Almeida, R P P

2016-11-01

There is little information available on Xylella fastidiosa transmission by spittlebugs (Hemiptera, Cercopoidea). This group of insect vectors may be of epidemiological relevance in certain diseases, so it is important to better understand the basic parameters of X. fastidiosa transmission by spittlebugs. We used grapevines as a host plant and the aphrophorid Philaenus spumarius as a vector to estimate the effect of plant access time on X. fastidiosa transmission to plants; in addition, bacterial population estimates in the heads of vectors were determined and correlated with plant infection status. Results show that transmission efficiency of X. fastidiosa by P. spumarius increased with plant access time, similarly to insect vectors in another family (Hemiptera, Cicadellidae). Furthermore, a positive correlation between pathogen populations in P. spumarius and transmission to plants was observed. Bacterial populations in insects were one to two orders of magnitude lower than those observed in leafhopper vectors, and population size peaked within 3 days of plant access period. These results suggest that P. spumarius has either a limited number of sites in the foregut that may be colonized, or that fluid dynamics in the mouthparts of these insects is different from that in leafhoppers. Altogether our results indicate that X. fastidiosa transmission by spittlebugs is similar to that by leafhoppers. In addition, the relationship between cell numbers in vectors and plant infection may have under-appreciated consequences to pathogen spread.

Are Bred Vectors The Same As Lyapunov Vectors?

NASA Astrophysics Data System (ADS)

Kalnay, E.; Corazza, M.; Cai, M.

Regional loss of predictability is an indication of the instability of the underlying flow, where small errors in the initial conditions (or imperfections in the model) grow to large amplitudes in finite times. The stability properties of evolving flows have been studied using Lyapunov vectors (e.g., Alligood et al, 1996, Ott, 1993, Kalnay, 2002), singular vectors (e.g., Lorenz, 1965, Farrell, 1988, Molteni and Palmer, 1993), and, more recently, with bred vectors (e.g., Szunyogh et al, 1997, Cai et al, 2001). Bred vectors (BVs) are, by construction, closely related to Lyapunov vectors (LVs). In fact, after an infinitely long breeding time, and with the use of infinitesimal ampli- tudes, bred vectors are identical to leading Lyapunov vectors. In practical applications, however, bred vectors are different from Lyapunov vectors in two important ways: a) bred vectors are never globally orthogonalized and are intrinsically local in space and time, and b) they are finite-amplitude, finite-time vectors. These two differences are very significant in a dynamical system whose size is very large. For example, the at- mosphere is large enough to have "room" for several synoptic scale instabilities (e.g., storms) to develop independently in different regions (say, North America and Aus- tralia), and it is complex enough to have several different possible types of instabilities (such as barotropic, baroclinic, convective, and even Brownian motion). Bred vectors share some of their properties with leading LVs (Corazza et al, 2001a, 2001b, Toth and Kalnay, 1993, 1997, Cai et al, 2001). For example, 1) Bred vectors are independent of the norm used to define the size of the perturba- tion. Corazza et al. (2001) showed that bred vectors obtained using a potential enstro- phy norm were indistinguishable from bred vectors obtained using a streamfunction squared norm, in contrast with singular vectors. 2) Bred vectors are independent of the length of the rescaling period as long as the perturbations remain approximately linear (for example, for atmospheric models the interval for rescaling could be varied between a single time step and 1 day without affecting qualitatively the characteristics of the bred vectors. However, the finite-amplitude, finite-time, and lack of orthogonalization of the BVs introduces important differences with LVs: 1) In regions that undergo strong instabilities, the bred vectors tend to be locally domi- 1 nated by simple, low-dimensional structures. Patil et al (2001) showed that the BV-dim (appendix) gives a good estimate of the number of dominant directions (shapes) of the local k bred vectors. For example, if half of them are aligned in one direction, and half in a different direction, the BV-dim is about two. If the majority of the bred vectors are aligned predominantly in one direction and only a few are aligned in a second direction, then the BV-dim is between 1 and 2. Patil et al., (2001) showed that the regions with low dimensionality cover about 20% of the atmosphere. They also found that these low-dimensionality regions have a very well defined vertical structure, and a typical lifetime of 3-7 days. The low dimensionality identifies regions where the in- stability of the basic flow has manifested itself in a low number of preferred directions of perturbation growth. 2) Using a Quasi-Geostrophic simulation system of data assimilation developed by Morss (1999), Corazza et al (2001a, b) found that bred vectors have structures that closely resemble the background (short forecasts used as first guess) errors, which in turn dominate the local analysis errors. This is especially true in regions of low dimensionality, which is not surprising if these are unstable regions where errors grow in preferred shapes. 3) The number of bred vectors needed to represent the unstable subspace in the QG system is small (about 6-10). This was shown by computing the local BV-dim as a function of the number of independent bred vectors. Convergence in the local dimen- sion starts to occur at about 6 BVs, and is essentially complete when the number of vectors is about 10-15 (Corazza et al, 2001a). This should be contrasted with the re- sults of Snyder and Joly (1998) and Palmer et al (1998) who showed that hundreds of Lyapunov vectors with positive Lyapunov exponents are needed to represent the attractor of the system in quasi-geostrophic models. 4) Since only a few bred vectors are needed, and background errors project strongly in the subspace of bred vectors, Corazza et al (2001b) were able to develop cost-efficient methods to improve the 3D-Var data assimilation by adding to the background error covariance terms proportional to the outer product of the bred vectors, thus represent- ing the "errors of the day". This approach led to a reduction of analysis error variance of about 40% at very low cost. 5) The fact that BVs have finite amplitude provides a natural way to filter out instabil- ities present in the system that have fast growth, but saturate nonlinearly at such small amplitudes that they are irrelevant for ensemble perturbations. As shown by Lorenz (1996) Lyapunov vectors (and singular vectors) of models including these physical phenomena would be dominated by the fast but small amplitude instabilities, unless they are explicitly excluded from the linearized models. Bred vectors, on the other 2 hand, through the choice of an appropriate size for the perturbation, provide a natural filter based on nonlinear saturation of fast but irrelevant instabilities. 6) Every bred vector is qualitatively similar to the *leading* LV. LVs beyond the leading LV are obtained by orthogonalization after each time step with respect to the previous LVs subspace. The orthogonalization requires the introduction of a norm. With an enstrophy norm, the successive LVs have larger and larger horizontal scales, and a choice of a stream function norm would lead to successively smaller scales in the LVs. Beyond the first few LVs, there is little qualitative similarity between the background errors and the LVs. In summary, in a system like the atmosphere with enough physical space for several independent local instabilities, BVs and LVs share some properties but they also have significant differences. BV are finite-amplitude, finite-time, and because they are not globally orthogonalized, they have local properties in space. Bred vectors are akin to the leading LV, but bred vectors derived from different arbitrary initial perturba- tions remain distinct from each other, instead of collapsing into a single leading vec- tor, presumably because the nonlinear terms and physical parameterizations introduce sufficient stochastic forcing to avoid such convergence. As a result, there is no need for global orthogonalization, and the number of bred vectors required to describe the natural instabilities in an atmospheric system (from a local point of view) is much smaller than the number of Lyapunov vectors with positive Lyapunov exponents. The BVs are independent of the norm, whereas the LVs beyond the first one do depend on the choice of norm: for example, they become larger in scale with a vorticity norm, and smaller with a stream function norm. These properties of BVs result in significant advantages for data assimilation and en- semble forecasting for the atmosphere. Errors in the analysis have structures very similar to bred vectors, and it is found that they project very strongly on the subspace of a few bred vectors. This is not true for either Lyapunov vectors beyond the lead- ing LVs, or for singular vectors unless they are constructed with a norm based on the analysis error covariance matrix (or a bred vector covariance). The similarity between bred vectors and analysis errors leads to the ability to include "errors of the day" in the background error covariance and a significant improvement of the analysis beyond 3D-Var at a very low cost (Corazza, 2001b). References Alligood K. T., T. D. Sauer and J. A. Yorke, 1996: Chaos: an introduction to dynamical systems. Springer-Verlag, New York. Buizza R., J. Tribbia, F. Molteni and T. Palmer, 1993: Computation of optimal unstable 3 structures for numerical weather prediction models. Tellus, 45A, 388-407. Cai, M., E. Kalnay and Z. Toth, 2001: Potential impact of bred vectors on ensemble forecasting and data assimilation in the Zebiak-Cane model. Submitted to J of Climate. Corazza, M., E. Kalnay, D. J. Patil, R. Morss, M. Cai, I. Szunyogh, B. R. Hunt, E. Ott and J. Yorke, 2001: Use of the breeding technique to determine the structure of the "errors of the day". Submitted to Nonlinear Processes in Geophysics. Corazza, M., E. Kalnay, DJ Patil, E. Ott, J. Yorke, I Szunyogh and M. Cai, 2001: Use of the breeding technique in the estimation of the background error covariance matrix for a quasigeostrophic model. AMS Symposium on Observations, Data Assimilation and Predictability, Preprints volume, Orlando, FA, 14-17 January 2002. Farrell, B., 1988: Small error dynamics and the predictability of atmospheric flow, J. Atmos. Sciences, 45, 163-172. Kalnay, E 2002: Atmospheric modeling, data assimilation and predictability. Chapter 6. Cambridge University Press, UK. In press. Kalnay E and Z Toth 1994: Removing growing errors in the analysis. Preprints, Tenth Conference on Numerical Weather Prediction, pp 212-215. Amer. Meteor. Soc., July 18-22, 1994. Lorenz, E.N., 1965: A study of the predictability of a 28-variable atmospheric model. Tellus, 21, 289-307. Lorenz, E.N., 1996: Predictability- A problem partly solved. Proceedings of the ECMWF Seminar on Predictability, Reading, England, Vol. 1 1-18. Molteni F. and TN Palmer, 1993: Predictability and finite-time instability of the north- ern winter circulation. Q. J. Roy. Meteorol. Soc. 119, 269-298. Morss, R.E.: 1999: Adaptive observations: Idealized sampling strategies for improving numerical weather prediction. Ph.D. Thesis, Massachussetts Institute of Technology, 225pp. Ott, E., 1993: Chaos in Dynamical Systems. Cambridge University Press. New York. Palmer, TN, R. Gelaro, J. Barkmeijer and R. Buizza, 1998: Singular vectors, metrics and adaptive observations. J. Atmos Sciences, 55, 633-653. Patil, DJ, BR Hunt, E Kalnay, J. Yorke, and E. Ott, 2001: Local low dimensionality of atmospheric dynamics. Phys. Rev. Lett., 86, 5878. Patil, DJ, I. Szunyogh, BR Hunt, E Kalnay, E Ott, and J. Yorke, 2001: Using large 4 member ensembles to isolate local low dimensionality of atmospheric dynamics. AMS Symposium on Observations, Data Assimilation and Predictability, Preprints volume, Orlando, FA, 14-17 January 2002. Snyder, C. and A. Joly, 1998: Development of perturbations within growing baroclinic waves. Q. J. Roy. Meteor. Soc., 124, pp 1961. Szunyogh, I, E. Kalnay and Z. Toth, 1997: A comparison of Lyapunov and Singular vectors in a low resolution GCM. Tellus, 49A, 200-227. Toth, Z and E Kalnay 1993: Ensemble forecasting at NMC - the generation of pertur- bations. Bull. Amer. Meteorol. Soc., 74, 2317-2330. Toth, Z and E Kalnay 1997: Ensemble forecasting at NCEP and the breeding method. Mon Wea Rev, 125, 3297-3319. * Corresponding author address: Eugenia Kalnay, Meteorology Depart- ment, University of Maryland, College Park, MD 20742-2425, USA; email: ekalnay@atmos.umd.edu Appendix: BV-dimension Patil et al., (2001) defined local bred vectors around a point in the 3-dimensional grid of the model by taking the 24 closest horizontal neighbors. If there are k bred vectors available, and N model variables for each grid point, the k local bred vectors form the columns of a 25Nxk matrix B. The kxk covariance matrix is C=B^T B. Its eigen- values are positive, and its eigenvectors v(i) are the singular vectors of the local bred vector subspace. The Bred Vector dimension (BV-dim) measures the local effective dimension: BV-dim[s,s,...,s(k)]={SUM[s(i)]}^2/SUM[s(i)]^2 where s(i) are the square roots of the eigenvalues of the covariance matrix. 5

Biological Response to the Dynamic Spectral-Polarized Underwater Light Field

DTIC Science & Technology

2013-09-30

Z39-18 2 optical suite including underwater video- polarimetry (full Stokes vector video-imaging camera custom-built Cummings; and “SALSA” (Bossa...operations, we couple polarimetry measurements of live, free-swimming animals in their environments with a full suite of optical measurements...Ahmed). We also restrain live, awake animals to take polarimetry measurements (in the field and laboratory) under a complete set of viewing angles and

Visceral Leishmaniasis on the Indian Subcontinent: Modelling the Dynamic Relationship between Vector Control Schemes and Vector Life Cycles.

PubMed

Poché, David M; Grant, William E; Wang, Hsiao-Hsuan

2016-08-01

Visceral leishmaniasis (VL) is a disease caused by two known vector-borne parasite species (Leishmania donovani, L. infantum), transmitted to man by phlebotomine sand flies (species: Phlebotomus and Lutzomyia), resulting in ≈50,000 human fatalities annually, ≈67% occurring on the Indian subcontinent. Indoor residual spraying is the current method of sand fly control in India, but alternative means of vector control, such as the treatment of livestock with systemic insecticide-based drugs, are being evaluated. We describe an individual-based, stochastic, life-stage-structured model that represents a sand fly vector population within a village in India and simulates the effects of vector control via fipronil-based drugs orally administered to cattle, which target both blood-feeding adults and larvae that feed on host feces. Simulation results indicated efficacy of fipronil-based control schemes in reducing sand fly abundance depended on timing of drug applications relative to seasonality of the sand fly life cycle. Taking into account cost-effectiveness and logistical feasibility, two of the most efficacious treatment schemes reduced population peaks occurring from April through August by ≈90% (applications 3 times per year at 2-month intervals initiated in March) and >95% (applications 6 times per year at 2-month intervals initiated in January) relative to no control, with the cumulative number of sand fly days occurring April-August reduced by ≈83% and ≈97%, respectively, and more specifically during the summer months of peak human exposure (June-August) by ≈85% and ≈97%, respectively. Our model should prove useful in a priori evaluation of the efficacy of fipronil-based drugs in controlling leishmaniasis on the Indian subcontinent and beyond.

A feature selection approach towards progressive vector transmission over the Internet

NASA Astrophysics Data System (ADS)

Miao, Ru; Song, Jia; Feng, Min

2017-09-01

WebGIS has been applied for visualizing and sharing geospatial information popularly over the Internet. In order to improve the efficiency of the client applications, the web-based progressive vector transmission approach is proposed. Important features should be selected and transferred firstly, and the methods for measuring the importance of features should be further considered in the progressive transmission. However, studies on progressive transmission for large-volume vector data have mostly focused on map generalization in the field of cartography, but rarely discussed on the selection of geographic features quantitatively. This paper applies information theory for measuring the feature importance of vector maps. A measurement model for the amount of information of vector features is defined based upon the amount of information for dealing with feature selection issues. The measurement model involves geometry factor, spatial distribution factor and thematic attribute factor. Moreover, a real-time transport protocol (RTP)-based progressive transmission method is then presented to improve the transmission of vector data. To clearly demonstrate the essential methodology and key techniques, a prototype for web-based progressive vector transmission is presented, and an experiment of progressive selection and transmission for vector features is conducted. The experimental results indicate that our approach clearly improves the performance and end-user experience of delivering and manipulating large vector data over the Internet.

Development of versatile non-homologous end joining-based knock-in module for genome editing.

PubMed

Sawatsubashi, Shun; Joko, Yudai; Fukumoto, Seiji; Matsumoto, Toshio; Sugano, Shigeo S

2018-01-12

CRISPR/Cas9-based genome editing has dramatically accelerated genome engineering. An important aspect of genome engineering is efficient knock-in technology. For improved knock-in efficiency, the non-homologous end joining (NHEJ) repair pathway has been used over the homology-dependent repair pathway, but there remains a need to reduce the complexity of the preparation of donor vectors. We developed the versatile NHEJ-based knock-in module for genome editing (VIKING). Using the consensus sequence of the time-honored pUC vector to cut donor vectors, any vector with a pUC backbone could be used as the donor vector without customization. Conditions required to minimize random integration rates of the donor vector were also investigated. We attempted to isolate null lines of the VDR gene in human HaCaT keratinocytes using knock-in/knock-out with a selection marker cassette, and found 75% of clones isolated were successfully knocked-in. Although HaCaT cells have hypotetraploid genome composition, the results suggest multiple clones have VDR null phenotypes. VIKING modules enabled highly efficient knock-in of any vectors harboring pUC vectors. Users now can insert various existing vectors into an arbitrary locus in the genome. VIKING will contribute to low-cost genome engineering.

AAV Vectorization of DSB-mediated Gene Editing Technologies.

PubMed

Moser, Rachel J; Hirsch, Matthew L

2016-01-01

Recent work both at the bench and the bedside demonstrate zinc-finger nucleases (ZFNs), CRISPR/Cas9, and other programmable site-specific endonuclease technologies are being successfully utilized within and alongside AAV vectors to induce therapeutically relevant levels of directed gene editing within the human chromosome. Studies from past decades acknowledge that AAV vector genomes are enhanced substrates for homology-directed repair in the presence or absence of targeted DNA damage within the host genome. Additionally, AAV vectors are currently the most efficient format for in vivo gene delivery with no vector related complications in >100 clinical trials for diverse diseases. At the same time, advancements in the design of custom-engineered site-specific endonucleases and the utilization of elucidated endonuclease formats have resulted in efficient and facile genetic engineering for basic science and for clinical therapies. AAV vectors and gene editing technologies are an obvious marriage, using AAV for the delivery of repair substrate and/or a gene encoding a designer endonuclease; however, while efficient delivery and enhanced gene targeting by vector genomes are advantageous, other attributes of AAV vectors are less desirable for gene editing technologies. This review summarizes the various roles that AAV vectors play in gene editing technologies and provides insight into its trending applications for the treatment of genetic diseases.

A time-frequency classifier for human gait recognition

NASA Astrophysics Data System (ADS)

Mobasseri, Bijan G.; Amin, Moeness G.

2009-05-01

Radar has established itself as an effective all-weather, day or night sensor. Radar signals can penetrate walls and provide information on moving targets. Recently, radar has been used as an effective biometric sensor for classification of gait. The return from a coherent radar system contains a frequency offset in the carrier frequency, known as the Doppler Effect. The movements of arms and legs give rise to micro Doppler which can be clearly detailed in the time-frequency domain using traditional or modern time-frequency signal representation. In this paper we propose a gait classifier based on subspace learning using principal components analysis(PCA). The training set consists of feature vectors defined as either time or frequency snapshots taken from the spectrogram of radar backscatter. We show that gait signature is captured effectively in feature vectors. Feature vectors are then used in training a minimum distance classifier based on Mahalanobis distance metric. Results show that gait classification with high accuracy and short observation window is achievable using the proposed classifier.

Hydrologic modeling to screen potential environmental management methods for malaria vector control in Niger

NASA Astrophysics Data System (ADS)

Gianotti, Rebecca L.; Bomblies, Arne; Eltahir, Elfatih A. B.

2009-08-01

This paper describes the first use of Hydrology-Entomology and Malaria Transmission Simulator (HYDREMATS), a physically based distributed hydrology model, to investigate environmental management methods for malaria vector control in the Sahelian village of Banizoumbou, Niger. The investigation showed that leveling of topographic depressions where temporary breeding habitats form during the rainy season, by altering pool basin microtopography, could reduce the pool persistence time to less than the time needed for establishment of mosquito breeding, approximately 7 days. Undertaking soil surface plowing can also reduce pool persistence time by increasing the infiltration rate through an existing pool basin. Reduction of the pool persistence time to less than the rainfall interstorm period increases the frequency of pool drying events, removing habitat for subadult mosquitoes. Both management approaches could potentially be considered within a given context. This investigation demonstrates that management methods that modify the hydrologic environment have significant potential to contribute to malaria vector control in water-limited, Sahelian Africa.

Autofocus algorithm using one-dimensional Fourier transform and Pearson correlation

NASA Astrophysics Data System (ADS)

Bueno Mario, A.; Alvarez-Borrego, Josue; Acho, L.

2004-10-01

A new autofocus algorithm based on one-dimensional Fourier transform and Pearson correlation for Z automatized microscope is proposed. Our goal is to determine in fast response time and accuracy, the best focused plane through an algorithm. We capture in bright and dark field several images set at different Z distances from biological organism sample. The algorithm uses the one-dimensional Fourier transform to obtain the image frequency content of a vectors pattern previously defined comparing the Pearson correlation of these frequency vectors versus the reference image frequency vector, the most out of focus image, we find the best focusing. Experimental results showed the algorithm has fast response time and accuracy in getting the best focus plane from captured images. In conclusions, the algorithm can be implemented in real time systems due fast response time, accuracy and robustness. The algorithm can be used to get focused images in bright and dark field and it can be extended to include fusion techniques to construct multifocus final images beyond of this paper.

New method for solving inductive electric fields in the non-uniformly conducting ionosphere

NASA Astrophysics Data System (ADS)

Vanhamäki, H.; Amm, O.; Viljanen, A.

2006-10-01

We present a new calculation method for solving inductive electric fields in the ionosphere. The time series of the potential part of the ionospheric electric field, together with the Hall and Pedersen conductances serves as the input to this method. The output is the time series of the induced rotational part of the ionospheric electric field. The calculation method works in the time-domain and can be used with non-uniform, time-dependent conductances. In addition, no particular symmetry requirements are imposed on the input potential electric field. The presented method makes use of special non-local vector basis functions called the Cartesian Elementary Current Systems (CECS). This vector basis offers a convenient way of representing curl-free and divergence-free parts of 2-dimensional vector fields and makes it possible to solve the induction problem using simple linear algebra. The new calculation method is validated by comparing it with previously published results for Alfvén wave reflection from a uniformly conducting ionosphere.

Ribosomal DNA Integrating rAAV-rDNA Vectors Allow for Stable Transgene Expression

PubMed Central

Lisowski, Leszek; Lau, Ashley; Wang, Zhongya; Zhang, Yue; Zhang, Feijie; Grompe, Markus; Kay, Mark A

2012-01-01

Although recombinant adeno-associated virus (rAAV) vectors are proving to be efficacious in clinical trials, the episomal character of the delivered transgene restricts their effectiveness to use in quiescent tissues, and may not provide lifelong expression. In contrast, integrating vectors enhance the risk of insertional mutagenesis. In an attempt to overcome both of these limitations, we created new rAAV-rDNA vectors, with an expression cassette flanked by ribosomal DNA (rDNA) sequences capable of homologous recombination into genomic rDNA. We show that after in vivo delivery the rAAV-rDNA vectors integrated into the genomic rDNA locus 8–13 times more frequently than control vectors, providing an estimate that 23–39% of the integrations were specific to the rDNA locus. Moreover, a rAAV-rDNA vector containing a human factor IX (hFIX) expression cassette resulted in sustained therapeutic levels of serum hFIX even after repeated manipulations to induce liver regeneration. Because of the relative safety of integration in the rDNA locus, these vectors expand the usage of rAAV for therapeutics requiring long-term gene transfer into dividing cells. PMID:22990671

Air travel and vector-borne disease movement.

PubMed

Tatem, A J; Huang, Z; Das, A; Qi, Q; Roth, J; Qiu, Y

2012-12-01

Recent decades have seen substantial expansions in the global air travel network and rapid increases in traffic volumes. The effects of this are well studied in terms of the spread of directly transmitted infections, but the role of air travel in the movement of vector-borne diseases is less well understood. Increasingly however, wider reaching surveillance for vector-borne diseases and our improving abilities to map the distributions of vectors and the diseases they carry, are providing opportunities to better our understanding of the impact of increasing air travel. Here we examine global trends in the continued expansion of air transport and its impact upon epidemiology. Novel malaria and chikungunya examples are presented, detailing how geospatial data in combination with information on air traffic can be used to predict the risks of vector-borne disease importation and establishment. Finally, we describe the development of an online tool, the Vector-Borne Disease Airline Importation Risk (VBD-Air) tool, which brings together spatial data on air traffic and vector-borne disease distributions to quantify the seasonally changing risks for importation to non-endemic regions. Such a framework provides the first steps towards an ultimate goal of adaptive management based on near real time flight data and vector-borne disease surveillance.

Reconstruction of Vectorial Acoustic Sources in Time-Domain Tomography

PubMed Central

Xia, Rongmin; Li, Xu; He, Bin

2009-01-01

A new theory is proposed for the reconstruction of curl-free vector field, whose divergence serves as acoustic source. The theory is applied to reconstruct vector acoustic sources from the scalar acoustic signals measured on a surface enclosing the source area. It is shown that, under certain conditions, the scalar acoustic measurements can be vectorized according to the known measurement geometry and subsequently be used to reconstruct the original vector field. Theoretically, this method extends the application domain of the existing acoustic reciprocity principle from a scalar field to a vector field, indicating that the stimulating vectorial source and the transmitted acoustic pressure vector (acoustic pressure vectorized according to certain measurement geometry) are interchangeable. Computer simulation studies were conducted to evaluate the proposed theory, and the numerical results suggest that reconstruction of a vector field using the proposed theory is not sensitive to variation in the detecting distance. The present theory may be applied to magnetoacoustic tomography with magnetic induction (MAT-MI) for reconstructing current distribution from acoustic measurements. A simulation on MAT-MI shows that, compared to existing methods, the present method can give an accurate estimation on the source current distribution and a better conductivity reconstruction. PMID:19211344

Development of two bacterial artificial chromosome shuttle vectors for a recombination-based cloning and regulated expression of large genes in mammalian cells.

PubMed

Hong, Y K; Kim, D H; Beletskii, A; Lee, C; Memili, E; Strauss, W M

2001-04-01

Most conditional expression vectors designed for mammalian cells have been valuable systems for studying genes of interest by regulating their expressions. The available vectors, however, are reliable for the short-length cDNA clones and not optimal for relatively long fragments of genomic DNA or long cDNAs. Here, we report the construction of two bacterial artificial chromosome (BAC) vectors, capable of harboring large inserts and shuttling among Escherichia coli, yeast, and mammalian cells. These two vectors, pEYMT and pEYMI, contain conditional expression systems which are designed to be regulated by tetracycline and mouse interferons, respectively. To test the properties of the vectors, we cloned in both vectors the green fluorescence protein (GFP) through an in vitro ligation reaction and the 17.8-kb-long X-inactive-specific transcript (Xist) cDNA through homologous recombination in yeast. Subsequently, we characterized their regulated expression properties using real-time quantitative RT-PCR (TaqMan) and RNA-fluorescent in situ hybridization (FISH). We demonstrate that these two BAC vectors are good systems for recombination-based cloning and regulated expression of large genes in mammalian cells. Copyright 2001 Academic Press.

Methods and apparatus for non-acoustic speech characterization and recognition

DOEpatents

Holzrichter, John F.

1999-01-01

By simultaneously recording EM wave reflections and acoustic speech information, the positions and velocities of the speech organs as speech is articulated can be defined for each acoustic speech unit. Well defined time frames and feature vectors describing the speech, to the degree required, can be formed. Such feature vectors can uniquely characterize the speech unit being articulated each time frame. The onset of speech, rejection of external noise, vocalized pitch periods, articulator conditions, accurate timing, the identification of the speaker, acoustic speech unit recognition, and organ mechanical parameters can be determined.

Methods and apparatus for non-acoustic speech characterization and recognition

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

Holzrichter, J.F.

By simultaneously recording EM wave reflections and acoustic speech information, the positions and velocities of the speech organs as speech is articulated can be defined for each acoustic speech unit. Well defined time frames and feature vectors describing the speech, to the degree required, can be formed. Such feature vectors can uniquely characterize the speech unit being articulated each time frame. The onset of speech, rejection of external noise, vocalized pitch periods, articulator conditions, accurate timing, the identification of the speaker, acoustic speech unit recognition, and organ mechanical parameters can be determined.

Permutation entropy with vector embedding delays

NASA Astrophysics Data System (ADS)

Little, Douglas J.; Kane, Deb M.

2017-12-01

Permutation entropy (PE) is a statistic used widely for the detection of structure within a time series. Embedding delay times at which the PE is reduced are characteristic timescales for which such structure exists. Here, a generalized scheme is investigated where embedding delays are represented by vectors rather than scalars, permitting PE to be calculated over a (D -1 ) -dimensional space, where D is the embedding dimension. This scheme is applied to numerically generated noise, sine wave and logistic map series, and experimental data sets taken from a vertical-cavity surface emitting laser exhibiting temporally localized pulse structures within the round-trip time of the laser cavity. Results are visualized as PE maps as a function of embedding delay, with low PE values indicating combinations of embedding delays where correlation structure is present. It is demonstrated that vector embedding delays enable identification of structure that is ambiguous or masked, when the embedding delay is constrained to scalar form.

Time-specific ecological niche modeling predicts spatial dynamics of vector insects and human dengue cases.

PubMed

Peterson, A Townsend; Martínez-Campos, Carmen; Nakazawa, Yoshinori; Martínez-Meyer, Enrique

2005-09-01

Numerous human diseases-malaria, dengue, yellow fever and leishmaniasis, to name a few-are transmitted by insect vectors with brief life cycles and biting activity that varies in both space and time. Although the general geographic distributions of these epidemiologically important species are known, the spatiotemporal variation in their emergence and activity remains poorly understood. We used ecological niche modeling via a genetic algorithm to produce time-specific predictive models of monthly distributions of Aedes aegypti in Mexico in 1995. Significant predictions of monthly mosquito activity and distributions indicate that predicting spatiotemporal dynamics of disease vector species is feasible; significant coincidence with human cases of dengue indicate that these dynamics probably translate directly into transmission of dengue virus to humans. This approach provides new potential for optimizing use of resources for disease prevention and remediation via automated forecasting of disease transmission risk.

Indicator Development for Potential Presence of Schistosomiasis Japonicum's Vector in Lake and Marshland Regions- A Case Study of Poyang Lake, Jiangxi Province, P.R. China

NASA Astrophysics Data System (ADS)

Marie, Tiphanie; Yesou, Herve; Huber, Claire; De Fraipont, Paul; Uribe, Carlos; Lacaux, Jean-Pierre; Lafaye, Murielle; Lai, Xijun; Desnos, Yves-Louis

2013-01-01

Earth observation data and bibliography on environmental parameters were used for mapping Oncomelania hupensis distribution, the Schistosomiasis japonicum’s intermediate host snail, within Poyang Lake (Jiangxi Province, P.R. China). Areas suitable for the development of O. hupensis, the vector of schistosomiasis, were derived from submersion time parameters and vegetation community indicators. ENVISAT time series data acquired from 2000 to 2009 were used for submersion times mapping, and 5 Beijing-1 data acquired during the dry season between 2006 and 2008 were used to map suitable vegetation for vector development. Yearly maps obtained indicate four principally potential endemic areas: the Gan Delta, the bank of the Fu He River, the Dalianzi Hu sector and the Poyang Lake Nature Reserve. Monthly maps from December 2005 to December 2008 show the dynamic of potential O. hupensis presence areas.

Mach's principle: Exact frame-dragging via gravitomagnetism in perturbed Friedmann-Robertson-Walker universes with K=({+-}1,0)

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

Schmid, Christoph

We show that there is exact dragging of the axis directions of local inertial frames by a weighted average of the cosmological energy currents via gravitomagnetism for all linear perturbations of all Friedmann-Robertson-Walker (FRW) universes and of Einstein's static closed universe, and for all energy-momentum-stress tensors and in the presence of a cosmological constant. This includes FRW universes arbitrarily close to the Milne Universe and the de Sitter universe. Hence the postulate formulated by Ernst Mach about the physical cause for the time-evolution of inertial axes is shown to hold in general relativity for linear perturbations of FRW universes. -more » The time-evolution of local inertial axes (relative to given local fiducial axes) is given experimentally by the precession angular velocity {omega}-vector{sub gyro} of local gyroscopes, which in turn gives the operational definition of the gravitomagnetic field: B-vector{sub g}{identical_to}-2{omega}-vector{sub gyro}. The gravitomagnetic field is caused by energy currents J-vector{sub {epsilon}} via the momentum constraint, Einstein's G{sup 0-}circumflex{sub i-circumflex} equation, (-{delta}+{mu}{sup 2})A-vector{sub g}=-16{pi}G{sub N}J-vector{sub {epsilon}} with B-vector{sub g}=curl A-vector{sub g}. This equation is analogous to Ampere's law, but it holds for all time-dependent situations. {delta} is the de Rham-Hodge Laplacian, and {delta}=-curl curl for the vorticity sector in Riemannian 3-space. - In the solution for an open universe the 1/r{sup 2}-force of Ampere is replaced by a Yukawa force Y{sub {mu}}(r)=(-d/dr)[(1/R)exp(-{mu}r)], form-identical for FRW backgrounds with K=(-1,0). Here r is the measured geodesic distance from the gyroscope to the cosmological source, and 2{pi}R is the measured circumference of the sphere centered at the gyroscope and going through the source point. The scale of the exponential cutoff is the H-dot radius, where H is the Hubble rate, dot is the derivative with respect to cosmic time, and {mu}{sup 2}=-4(dH/dt). Analogous results hold in closed FRW universes and in Einstein's closed static universe.--We list six fundamental tests for the principle formulated by Mach: all of them are explicitly fulfilled by our solutions.--We show that only energy currents in the toroidal vorticity sector with l=1 can affect the precession of gyroscopes. We show that the harmonic decomposition of toroidal vorticity fields in terms of vector spherical harmonics X-vector{sub lm}{sup -} has radial functions which are form-identical for the 3-sphere, the hyperbolic 3-space, and Euclidean 3-space, and are form-identical with the spherical Bessel-, Neumann-, and Hankel functions. - The Appendix gives the de Rham-Hodge Laplacian on vorticity fields in Riemannian 3-spaces by equations connecting the calculus of differential forms with the curl notation. We also give the derivation the Weitzenboeck formula for the difference between the de Rham-Hodge Laplacian {delta} and the ''rough'' Laplacian {nabla}{sup 2} on vector fields.« less

Quasi-local action of curl-less vector potential on vortex dynamics in superconductors

NASA Astrophysics Data System (ADS)

Gulian, Armen M.; Nikoghosyan, Vahan R.; Gulian, Ellen D.; Melkonyan, Gurgen G.

2018-04-01

Studies of the Abrikosov vortex motion in superconductors based on time-dependent Ginzburg-Landau equations reveal an opportunity to detect the values of the Aharonov-Bohm type curl-less vector potentials without closed-loop electron trajectories encompassing the magnetic flux.

Hybrid Adeno-Associated Viral Vectors Utilizing Transposase-Mediated Somatic Integration for Stable Transgene Expression in Human Cells

PubMed Central

Zhang, Wenli; Solanki, Manish; Müther, Nadine; Ebel, Melanie; Wang, Jichang; Sun, Chuanbo; Izsvak, Zsuzsanna; Ehrhardt, Anja

2013-01-01

Recombinant adeno-associated viral (AAV) vectors have been shown to be one of the most promising vectors for therapeutic gene delivery because they can induce efficient and long-term transduction in non-dividing cells with negligible side-effects. However, as AAV vectors mostly remain episomal, vector genomes and transgene expression are lost in dividing cells. Therefore, to stably transduce cells, we developed a novel AAV/transposase hybrid-vector. To facilitate SB-mediated transposition from the rAAV genome, we established a system in which one AAV vector contains the transposon with the gene of interest and the second vector delivers the hyperactive Sleeping Beauty (SB) transposase SB100X. Human cells were infected with the AAV-transposon vector and the transposase was provided in trans either by transient and stable plasmid transfection or by AAV vector transduction. We found that groups which received the hyperactive transposase SB100X showed significantly increased colony forming numbers indicating enhanced integration efficiencies. Furthermore, we found that transgene copy numbers in transduced cells were dose-dependent and that predominantly SB transposase-mediated transposition contributed to stabilization of the transgene. Based on a plasmid rescue strategy and a linear-amplification mediated PCR (LAM-PCR) protocol we analysed the SB100X-mediated integration profile after transposition from the AAV vector. A total of 1840 integration events were identified which revealed a close to random integration profile. In summary, we show for the first time that AAV vectors can serve as template for SB transposase mediated somatic integration. We developed the first prototype of this hybrid-vector system which with further improvements may be explored for treatment of diseases which originate from rapidly dividing cells. PMID:24116154