Exact analytical modeling of magnetic vector potential in surface inset permanent magnet DC machines considering magnet segmentation

NASA Astrophysics Data System (ADS)

Jabbari, Ali

2018-01-01

Surface inset permanent magnet DC machine can be used as an alternative in automation systems due to their high efficiency and robustness. Magnet segmentation is a common technique in order to mitigate pulsating torque components in permanent magnet machines. An accurate computation of air-gap magnetic field distribution is necessary in order to calculate machine performance. An exact analytical method for magnetic vector potential calculation in surface inset permanent magnet machines considering magnet segmentation has been proposed in this paper. The analytical method is based on the resolution of Laplace and Poisson equations as well as Maxwell equation in polar coordinate by using sub-domain method. One of the main contributions of the paper is to derive an expression for the magnetic vector potential in the segmented PM region by using hyperbolic functions. The developed method is applied on the performance computation of two prototype surface inset magnet segmented motors with open circuit and on load conditions. The results of these models are validated through FEM method.

Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates

USDA-ARS?s Scientific Manuscript database

Methods based on sequence data analysis facilitate the tracking of disease outbreaks, allow relationships between strains to be reconstructed and virulence factors to be identified. However, these methods are used postfactum after an outbreak has happened. Here, we show that support vector machine a...

Numerical simulation using vorticity-vector potential formulation

NASA Technical Reports Server (NTRS)

Tokunaga, Hiroshi

1993-01-01

An accurate and efficient computational method is needed for three-dimensional incompressible viscous flows in engineering applications. On solving the turbulent shear flows directly or using the subgrid scale model, it is indispensable to resolve the small scale fluid motions as well as the large scale motions. From this point of view, the pseudo-spectral method is used so far as the computational method. However, the finite difference or the finite element methods are widely applied for computing the flow with practical importance since these methods are easily applied to the flows with complex geometric configurations. However, there exist several problems in applying the finite difference method to direct and large eddy simulations. Accuracy is one of most important problems. This point was already addressed by the present author on the direct simulations on the instability of the plane Poiseuille flow and also on the transition to turbulence. In order to obtain high efficiency, the multi-grid Poisson solver is combined with the higher-order, accurate finite difference method. The formulation method is also one of the most important problems in applying the finite difference method to the incompressible turbulent flows. The three-dimensional Navier-Stokes equations have been solved so far in the primitive variables formulation. One of the major difficulties of this method is the rigorous satisfaction of the equation of continuity. In general, the staggered grid is used for the satisfaction of the solenoidal condition for the velocity field at the wall boundary. However, the velocity field satisfies the equation of continuity automatically in the vorticity-vector potential formulation. From this point of view, the vorticity-vector potential method was extended to the generalized coordinate system. In the present article, we adopt the vorticity-vector potential formulation, the generalized coordinate system, and the 4th-order accurate difference method as the computational method. We present the computational method and apply the present method to computations of flows in a square cavity at large Reynolds number in order to investigate its effectiveness.

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.

Measuring magnetic field vector by stimulated Raman transitions

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

Wang, Wenli; Wei, Rong, E-mail: weirong@siom.ac.cn; Lin, Jinda

2016-03-21

We present a method for measuring the magnetic field vector in an atomic fountain by probing the line strength of stimulated Raman transitions. The relative line strength for a Λ-type level system with an existing magnetic field is theoretically analyzed. The magnetic field vector measured by our proposed method is consistent well with that by the traditional bias magnetic field method with an axial resolution of 6.1 mrad and a radial resolution of 0.16 rad. Dependences of the Raman transitions on laser polarization schemes are also analyzed. Our method offers the potential advantages for magnetic field measurement without requiring additional bias fields,more » beyond the limitation of magnetic field intensity, and extending the spatial measurement range. The proposed method can be widely used for measuring magnetic field vector in other precision measurement fields.« less

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.

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.

[Adeno-associated viral vectors: methods for production and purification for gene therapy applications].

PubMed

Mena-Enriquez, Mayra; Flores-Contreras, Lucia; Armendáriz-Borunda, Juan

2012-01-01

Viral vectors based on adeno-associated virus (AAV) are widely used in gene therapy protocols, because they have characteristics that make them valuable for the treatment of genetic and chronic degenerative diseases. AAV2 serotype had been the best characterized to date. However, the AAV vectors developed from other serotypes is of special interest, since they have organ-specific tropism which increases their potential for transgene delivery to target cells for performing their therapeutic effects. This article summarizes AAV generalities, methods for their production and purification. It also discusses the use of these vectors in vitro, in vivo and their application in gene therapy clinical trials.

A dimension-wise analysis method for the structural-acoustic system with interval parameters

NASA Astrophysics Data System (ADS)

Xu, Menghui; Du, Jianke; Wang, Chong; Li, Yunlong

2017-04-01

The interval structural-acoustic analysis is mainly accomplished by interval and subinterval perturbation methods. Potential limitations for these intrusive methods include overestimation or interval translation effect for the former and prohibitive computational cost for the latter. In this paper, a dimension-wise analysis method is thus proposed to overcome these potential limitations. In this method, a sectional curve of the system response surface along each input dimensionality is firstly extracted, the minimal and maximal points of which are identified based on its Legendre polynomial approximation. And two input vectors, i.e. the minimal and maximal input vectors, are dimension-wisely assembled by the minimal and maximal points of all sectional curves. Finally, the lower and upper bounds of system response are computed by deterministic finite element analysis at the two input vectors. Two numerical examples are studied to demonstrate the effectiveness of the proposed method and show that, compared to the interval and subinterval perturbation method, a better accuracy is achieved without much compromise on efficiency by the proposed method, especially for nonlinear problems with large interval parameters.

Nonviral vectors for cancer gene therapy: prospects for integrating vectors and combination therapies.

PubMed

Ohlfest, John R; Freese, Andrew B; Largaespada, David A

2005-12-01

Gene therapy has the potential to improve the clinical outcome of many cancers by transferring therapeutic genes into tumor cells or normal host tissue. Gene transfer into tumor cells or tumor-associated stroma is being employed to induce tumor cell death, stimulate anti-tumor immune response, inhibit angiogenesis, and control tumor cell growth. Viral vectors have been used to achieve this proof of principle in animal models and, in select cases, in human clinical trials. Nevertheless, there has been considerable interest in developing nonviral vectors for cancer gene therapy. Nonviral vectors are simpler, more amenable to large-scale manufacture, and potentially safer for clinical use. Nonviral vectors were once limited by low gene transfer efficiency and transient or steadily declining gene expression. However, recent improvements in plasmid-based vectors and delivery methods are showing promise in circumventing these obstacles. This article reviews the current status of nonviral cancer gene therapy, with an emphasis on combination strategies, long-term gene transfer using transposons and bacteriophage integrases, and future directions.

Off disk-center potential field calculations using vector magnetograms

NASA Technical Reports Server (NTRS)

Venkatakrishnan, P.; Gary, G. Allen

1989-01-01

A potential field calculation for off disk-center vector magnetograms that uses all the three components of the measured field is investigated. There is neither any need for interpolation of grid points between the image plane and the heliographic plane nor for an extension or a truncation to a heliographic rectangle. Hence, the method provides the maximum information content from the photospheric field as well as the most consistent potential field independent of the viewing angle. The introduction of polarimetric noise produces a less tolerant extrapolation procedure than using the line-of-sight extrapolation, but the resultant standard deviation is still small enough for the practical utility of this method.

Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control.

PubMed

Kaur, Navneet; Hasegawa, Daniel K; Ling, Kai-Shu; Wintermantel, William M

2016-10-01

The relationships between plant viruses and their vectors have evolved over the millennia, and yet, studies on viruses began <150 years ago and investigations into the virus and vector interactions even more recently. The advent of next generation sequencing, including rapid genome and transcriptome analysis, methods for evaluation of small RNAs, and the related disciplines of proteomics and metabolomics offer a significant shift in the ability to elucidate molecular mechanisms involved in virus infection and transmission by insect vectors. Genomic technologies offer an unprecedented opportunity to examine the response of insect vectors to the presence of ingested viruses through gene expression changes and altered biochemical pathways. This review focuses on the interactions between viruses and their whitefly or thrips vectors and on potential applications of genomics-driven control of the insect vectors. Recent studies have evaluated gene expression in vectors during feeding on plants infected with begomoviruses, criniviruses, and tospoviruses, which exhibit very different types of virus-vector interactions. These studies demonstrate the advantages of genomics and the potential complementary studies that rapidly advance our understanding of the biology of virus transmission by insect vectors and offer additional opportunities to design novel genetic strategies to manage insect vectors and the viruses they transmit.

Studies of Solar Helicity Using Vector Magnetograms

NASA Technical Reports Server (NTRS)

Hagyard, Mona J.; Pevstov, Alexei A.

1999-01-01

observations of photospheric magnetic fields made with vector magnetographs have been used recently to study solar helicity. In this paper we indicate what can and cannot be derived from vector magnetograms, and point out some potential problems in these data that could affect the calculations of 'helicity'. Among these problems are magnetic saturation, Faraday rotation, low spectral resolution, and the method of resolving the ambiguity in the azimuth.

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.

Calculation of induced voltages on overhead lines caused by inclined lightning strokes

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

Sakakibara, A.

1989-01-01

Equations to calculate the inducing scalar and vector potentials produced by inclined return strokes are shown. Equations are also shown for calculating the induced voltages on overhead lines where horizontal components of inducing vector potential exist. The adequacy of the calculation method is demonstrated by field experiments. Using these equations, induced voltages on overhead lines are calculated for a variety of directions of return strokes.

Direct discretization of planar div-curl problems

NASA Technical Reports Server (NTRS)

Nicolaides, R. A.

1989-01-01

A control volume method is proposed for planar div-curl systems. The method is independent of potential and least squares formulations, and works directly with the div-curl system. The novelty of the technique lies in its use of a single local vector field component and two control volumes rather than the other way around. A discrete vector field theory comes quite naturally from this idea and is developed. Error estimates are proved for the method, and other ramifications investigated.

Eigenenergies of a Relativistic Particle in an Infinite Range Linear Potential Using WKB Method

ERIC Educational Resources Information Center

Shivalingaswamy, T.; Kagali, B. A.

2011-01-01

Energy eigenvalues for a non-relativistic particle in a linear potential well are available. In this paper we obtain the eigenenergies for a relativistic spin less particle in a similar potential using an extension of the well-known WKB method treating the potential as the time component of a four-vector potential. Since genuine bound states do…

An application of the Braunbeck method to the Maggi-Rubinowicz field representation

NASA Technical Reports Server (NTRS)

Meneghini, R.

1982-01-01

The Braunbek method is applied to the generalized vector potential associated with the Maggi-rubinowicz representation. Under certain approximations, an asymptotic evaluation of the vector potential is obtained. For observation points away from caustics or shadow boundaries, the field derived from this quantity is the same as that determined from the geometrical theory of diffraction on a singly diffracted edge ray. An evaluation of the field for the simple case of a plane wave normally incident on a circular aperture is presented showing that the field predicted by the Maggi-Rubinowicz theory is continuous across the shadow boundary.

An application of the Braunbeck method to the Maggi-Rubinowicz field representation

NASA Astrophysics Data System (ADS)

Meneghini, R.

1982-06-01

The Braunbek method is applied to the generalized vector potential associated with the Maggi-rubinowicz representation. Under certain approximations, an asymptotic evaluation of the vector potential is obtained. For observation points away from caustics or shadow boundaries, the field derived from this quantity is the same as that determined from the geometrical theory of diffraction on a singly diffracted edge ray. An evaluation of the field for the simple case of a plane wave normally incident on a circular aperture is presented showing that the field predicted by the Maggi-Rubinowicz theory is continuous across the shadow boundary.

Internal and external potential-field estimation from regional vector data at varying satellite altitude

NASA Astrophysics Data System (ADS)

Plattner, Alain; Simons, Frederik J.

2017-10-01

When modelling satellite data to recover a global planetary magnetic or gravitational potential field, the method of choice remains their analysis in terms of spherical harmonics. When only regional data are available, or when data quality varies strongly with geographic location, the inversion problem becomes severely ill-posed. In those cases, adopting explicitly local methods is to be preferred over adapting global ones (e.g. by regularization). Here, we develop the theory behind a procedure to invert for planetary potential fields from vector observations collected within a spatially bounded region at varying satellite altitude. Our method relies on the construction of spatiospectrally localized bases of functions that mitigate the noise amplification caused by downward continuation (from the satellite altitude to the source) while balancing the conflicting demands for spatial concentration and spectral limitation. The `altitude-cognizant' gradient vector Slepian functions (AC-GVSF) enjoy a noise tolerance under downward continuation that is much improved relative to the `classical' gradient vector Slepian functions (CL-GVSF), which do not factor satellite altitude into their construction. Furthermore, venturing beyond the realm of their first application, published in a preceding paper, in the present article we extend the theory to being able to handle both internal and external potential-field estimation. Solving simultaneously for internal and external fields under the limitation of regional data availability reduces internal-field artefacts introduced by downward-continuing unmodelled external fields, as we show with numerical examples. We explain our solution strategies on the basis of analytic expressions for the behaviour of the estimation bias and variance of models for which signal and noise are uncorrelated, (essentially) space- and band-limited, and spectrally (almost) white. The AC-GVSF are optimal linear combinations of vector spherical harmonics. Their construction is not altogether very computationally demanding when the concentration domains (the regions of spatial concentration) have circular symmetry, for example, on spherical caps or rings—even when the spherical-harmonic bandwidth is large. Data inversion proceeds by solving for the expansion coefficients of truncated function sequences, by least-squares analysis in a reduced-dimensional space. Hence, our method brings high-resolution regional potential-field modelling from incomplete and noisy vector-valued satellite data within reach of contemporary desktop machines.

A vectorization of the Hess McDonnell Douglas potential flow program NUED for the STAR-100 computer

NASA Technical Reports Server (NTRS)

Boney, L. R.; Smith, R. E., Jr.

1979-01-01

The computer program NUED for analyzing potential flow about arbitrary three dimensional lifting bodies using the panel method was modified to use vector operations and run on the STAR-100 computer. A high speed of computation and ability to approximate the body surface with a large number of panels are characteristics of NUEDV. The new program shows that vector operations can be readily implemented in programs of this type to increase the computational speed on the STAR-100 computer. The virtual memory architecture of the STAR-100 facilitates the use of large numbers of panels to approximate the body surface.

Forward and Inverse Modeling of Self-potential. A Tomography of Groundwater Flow and Comparison Between Deterministic and Stochastic Inversion Methods

NASA Astrophysics Data System (ADS)

Quintero-Chavarria, E.; Ochoa Gutierrez, L. H.

2016-12-01

Applications of the Self-potential Method in the fields of Hydrogeology and Environmental Sciences have had significant developments during the last two decades with a strong use on groundwater flows identification. Although only few authors deal with the forward problem's solution -especially in geophysics literature- different inversion procedures are currently being developed but in most cases they are compared with unconventional groundwater velocity fields and restricted to structured meshes. This research solves the forward problem based on the finite element method using the St. Venant's Principle to transform a point dipole, which is the field generated by a single vector, into a distribution of electrical monopoles. Then, two simple aquifer models were generated with specific boundary conditions and head potentials, velocity fields and electric potentials in the medium were computed. With the model's surface electric potential, the inverse problem is solved to retrieve the source of electric potential (vector field associated to groundwater flow) using deterministic and stochastic approaches. The first approach was carried out by implementing a Tikhonov regularization with a stabilized operator adapted to the finite element mesh while for the second a hierarchical Bayesian model based on Markov chain Monte Carlo (McMC) and Markov Random Fields (MRF) was constructed. For all implemented methods, the result between the direct and inverse models was contrasted in two ways: 1) shape and distribution of the vector field, and 2) magnitude's histogram. Finally, it was concluded that inversion procedures are improved when the velocity field's behavior is considered, thus, the deterministic method is more suitable for unconfined aquifers than confined ones. McMC has restricted applications and requires a lot of information (particularly in potentials fields) while MRF has a remarkable response especially when dealing with confined aquifers.

Using Hydrologic Modeling to Screen Potential Environmental Management Methods for Malaria Vector Control in Niger

NASA Astrophysics Data System (ADS)

Gianotti, R. L.; Bomblies, A.; Eltahir, E. A.

2008-12-01

This study describes the use of HYDREMATS, a physically-based distributed hydrology model, to investigate environmental management methods for malaria vector control in the Sahelian village of Banizoumbou, Niger. The model operates at fine spatial and temporal scales to enable explicit simulation of individual pool dynamics and isolation of mosquito breeding habitats. The results showed that leveling of topographic depressions where temporary breeding habitats form during the rainy season could reduce the persistence time of a pool to less than the time needed for establishment of mosquito breeding, approximately 7 days. Increasing the surface soil permeability by ploughing could also reduce the persistence time of a pool but this technique was not as effective as leveling. Therefore it is considered that leveling should be the preferred of the two options where possible. This investigation demonstrates that management methods that modify the hydrologic environment have significant potential to contribute to malaria vector control and human health improvement in Sahelian Africa.

New Method for Solving Inductive Electric Fields in the Ionosphere

NASA Astrophysics Data System (ADS)

Vanhamäki, H.

2005-12-01

We present a new method for calculating inductive electric fields in the ionosphere. It is well established that on large scales the ionospheric electric field is a potential field. This is understandable, since the temporal variations of large scale current systems are generally quite slow, in the timescales of several minutes, so inductive effects should be small. However, studies of Alfven wave reflection have indicated that in some situations inductive phenomena could well play a significant role in the reflection process, and thus modify the nature of ionosphere-magnetosphere coupling. The input to our calculation method are the time series of the potential part of the ionospheric electric field together with the Hall and Pedersen conductances. 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 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 Alfven wave reflection from uniformly conducting ionosphere.

Long-distance Lienard-Wiechert potentials and qq-bar spin dependence

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

Childers, R.W.

1987-12-15

The long-range spin dependence of the qq interaction is considered in a model in which the confining potential is required to be the static limit of retarded scalar and vector potentials analogous to the Lienard-Wiechert potentials of classical electrodynamics. A generalization of Darwin's method is used to obtain the corresponding Hamiltonian. The long-distance spin-dependent interaction is found to be determined completely by only two potentials: namely, the static scalar and vector potentials. This is to be compared with the four potentials required in Eichten and Feinberg's general formulation. Two different solutions are allowed by Gromes's theorem. In one, the scalarmore » potential can be linear; in the other, it must be logarithmic.« less

Numerical assessment of low-frequency dosimetry from sampled magnetic fields

NASA Astrophysics Data System (ADS)

Freschi, Fabio; Giaccone, Luca; Cirimele, Vincenzo; Canova, Aldo

2018-01-01

Low-frequency dosimetry is commonly assessed by evaluating the electric field in the human body using the scalar potential finite difference method. This method is effective only when the sources of the magnetic field are completely known and the magnetic vector potential can be analytically computed. The aim of the paper is to present a rigorous method to characterize the source term when only the magnetic flux density is available at discrete points, e.g. in case of field measurements. The method is based on the solution of the discrete magnetic curl equation. The system is restricted to the independent set of magnetic fluxes and circulations of magnetic vector potential using the topological information of the computational mesh. The solenoidality of the magnetic flux density is preserved using a divergence-free interpolator based on vector radial basis functions. The analysis of a benchmark problem shows that the complexity of the proposed algorithm is linearly dependent on the number of elements with a controllable accuracy. The method proposed in this paper also proves to be useful and effective when applied to a real world scenario, where the magnetic flux density is measured in proximity of a power transformer. A 8 million voxel body model is then used for the numerical dosimetric analysis. The complete assessment is completed in less than 5 min, that is more than acceptable for these problems.

Numerical assessment of low-frequency dosimetry from sampled magnetic fields.

PubMed

Freschi, Fabio; Giaccone, Luca; Cirimele, Vincenzo; Canova, Aldo

2017-12-29

Low-frequency dosimetry is commonly assessed by evaluating the electric field in the human body using the scalar potential finite difference method. This method is effective only when the sources of the magnetic field are completely known and the magnetic vector potential can be analytically computed. The aim of the paper is to present a rigorous method to characterize the source term when only the magnetic flux density is available at discrete points, e.g. in case of field measurements. The method is based on the solution of the discrete magnetic curl equation. The system is restricted to the independent set of magnetic fluxes and circulations of magnetic vector potential using the topological information of the computational mesh. The solenoidality of the magnetic flux density is preserved using a divergence-free interpolator based on vector radial basis functions. The analysis of a benchmark problem shows that the complexity of the proposed algorithm is linearly dependent on the number of elements with a controllable accuracy. The method proposed in this paper also proves to be useful and effective when applied to a real world scenario, where the magnetic flux density is measured in proximity of a power transformer. A 8 million voxel body model is then used for the numerical dosimetric analysis. The complete assessment is completed in less than 5 min, that is more than acceptable for these problems.

Assessing the potential for AAV vector genotoxicity in a murine model

PubMed Central

Li, Hojun; Malani, Nirav; Hamilton, Shari R.; Schlachterman, Alexander; Bussadori, Giulio; Edmonson, Shyrie E.; Shah, Rachel; Arruda, Valder R.; Mingozzi, Federico; Fraser Wright, J.; Bushman, Frederic D.

2011-01-01

Gene transfer using adeno-associated virus (AAV) vectors has great potential for treating human disease. Recently, questions have arisen about the safety of AAV vectors, specifically, whether integration of vector DNA in transduced cell genomes promotes tumor formation. This study addresses these questions with high-dose liver-directed AAV-mediated gene transfer in the adult mouse as a model (80 AAV-injected mice and 52 controls). After 18 months of follow-up, AAV-injected mice did not show a significantly higher rate of hepatocellular carcinoma compared with controls. Tumors in mice treated with AAV vectors did not have significantly different amounts of vector DNA compared with adjacent normal tissue. A novel high-throughput method for identifying AAV vector integration sites was developed and used to clone 1029 integrants. Integration patterns in tumor tissue and adjacent normal tissue were similar to each other, showing preferences for active genes, cytosine-phosphate-guanosine islands, and guanosine/cysteine-rich regions. Gene expression data showed that genes near integration sites did not show significant changes in expression patterns compared with genes more distal to integration sites. No integration events were identified as causing increased oncogene expression. Thus, we did not find evidence that AAV vectors cause insertional activation of oncogenes and subsequent tumor formation. PMID:21106988

Application of the scalar and vector potentials to the aerodynamics of jets

NASA Technical Reports Server (NTRS)

Russell, H. L.; Skifstad, J. G.

1973-01-01

The applicability of a method based on the Stokes potentials (vector and scalar potentials) to computations associated with the aerodynamics of jets was examined. The aerodynamic field near the nozzle could be represented and that the influence of a nonuniform velocity profile at the nozzle exit plane could be determined. Also computations were made for an axisymmetric jet exhausting into a quiescient atmosphere. The velocity at the axis of the jet, and the location of the half-velocity points along the jet yield accurate aerodynamic field computations. Inconsistencies among the different theoretical characterizations of jet flowfields are shown.

Storage and computationally efficient permutations of factorized covariance and square-root information arrays

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector stored Upper triangular Diagonal factorized covariance and vector stored upper triangular Square Root Information arrays is presented. The method involves cyclic permutation of the rows and columns of the arrays and retriangularization with fast (slow) Givens rotations (reflections). Minimal computation is performed, and a one dimensional scratch array is required. To make the method efficient for large arrays on a virtual memory machine, computations are arranged so as to avoid expensive paging faults. This method is potentially important for processing large volumes of radio metric data in the Deep Space Network.

Theoretical and numerical difficulties in 3-D vector potential methods in finite element magnetostatic computations

NASA Technical Reports Server (NTRS)

Demerdash, N. A.; Wang, R.

1990-01-01

This paper describes the results of application of three well known 3D magnetic vector potential (MVP) based finite element formulations for computation of magnetostatic fields in electrical devices. The three methods were identically applied to three practical examples, the first of which contains only one medium (free space), while the second and third examples contained a mix of free space and iron. The first of these methods is based on the unconstrained curl-curl of the MVP, while the second and third methods are predicated upon constraining the divergence of the MVP 10 zero (Coulomb's Gauge). It was found that the two latter methods cease to give useful and meaningful results when the global solution region contains a mix of media of high and low permeabilities. Furthermore, it was found that their results do not achieve the intended zero constraint on the divergence of the MVP.

Vector matter waves in two-component Bose-Einstein condensates with spatially modulated nonlinearities

NASA Astrophysics Data System (ADS)

Xu, Si-Liu; He, Jun-Rong; Xue, Li; Belić, Milivoj R.

2018-02-01

We demonstrate three-dimensional (3D) vector solitary waves in the coupled (3 + 1)-D nonlinear Gross-Pitaevskii equations with variable nonlinearity coefficients. The analysis is carried out in spherical coordinates, providing novel localized solutions that depend on three modal numbers, l, m, and n. Using the similarity transformation (ST) method in 3D, vector solitary waves are built with the help of a combination of harmonic and trapping potentials, including multipole solutions and necklace rings. In general, the solutions found are stable for low values of the modal numbers; for values larger than 2, the solutions are found to be unstable. Variable nonlinearity allows the utilization of soliton management methods.

Comparison Study of Three Different Image Reconstruction Algorithms for MAT-MI

PubMed Central

Xia, Rongmin; Li, Xu

2010-01-01

We report a theoretical study on magnetoacoustic tomography with magnetic induction (MAT-MI). According to the description of signal generation mechanism using Green’s function, the acoustic dipole model was proposed to describe acoustic source excited by the Lorentz force. Using Green’s function, three kinds of reconstruction algorithms based on different models of acoustic source (potential energy, vectored acoustic pressure, and divergence of Lorenz force) are deduced and compared, and corresponding numerical simulations were conducted to compare these three kinds of reconstruction algorithms. The computer simulation results indicate that the potential energy method and vectored pressure method can directly reconstruct the Lorentz force distribution and give a more accurate reconstruction of electrical conductivity. PMID:19846363

Analysis of Discontinuities in a Rectangular Waveguide Using Dyadic Green's Function Approach in Conjunction with Method of Moments

NASA Technical Reports Server (NTRS)

Deshpande, M. D.

1997-01-01

The dyadic Green's function for an electric current source placed in a rectangular waveguide is derived using a magnetic vector potential approach. A complete solution for the electric and magnetic fields including the source location is obtained by simple differentiation of the vector potential around the source location. The simple differentiation approach which gives electric and magnetic fields identical to an earlier derivation is overlooked by the earlier workers in the derivation of the dyadic Green's function particularly around the source location. Numerical results obtained using the Green's function approach are compared with the results obtained using the Finite Element Method (FEM).

Scalar/Vector potential formulation for compressible viscous unsteady flows

NASA Technical Reports Server (NTRS)

Morino, L.

1985-01-01

A scalar/vector potential formulation for unsteady viscous compressible flows is presented. The scalar/vector potential formulation is based on the classical Helmholtz decomposition of any vector field into the sum of an irrotational and a solenoidal field. The formulation is derived from fundamental principles of mechanics and thermodynamics. The governing equations for the scalar potential and vector potential are obtained, without restrictive assumptions on either the equation of state or the constitutive relations or the stress tensor and the heat flux vector.

Vector mode conversion based on tilted fiber Bragg grating in ring-core fibers

NASA Astrophysics Data System (ADS)

Mi, Yuean; Ren, Guobin; Gao, Yixiao; Li, Haisu; Zhu, Bofeng; Liu, Yu

2018-03-01

We propose a vector mode conversion approach based on tilted fiber Bragg grating (TFBG) written in ring-core fiber with effective separation of eigenmodes. The mode coupling properties of TFBG are numerically investigated. It is shown that under the constraint of phase matching, the conversion of high-order vector modes could be achieved at specific wavelengths. Moreover, the polarization of incident light and tilt angle of TFBG play critical roles in mode coupling process. The proposed TFBG provides an efficient method to realize high-order vector mode conversion, and it shows great potential for fibers based OAM beam generation and fiber lasers with vortex beams output.

Electromagnetic potential vectors and the Lagrangian of a charged particle

NASA Technical Reports Server (NTRS)

Shebalin, John V.

1992-01-01

Maxwell's equations can be shown to imply the existence of two independent three-dimensional potential vectors. A comparison between the potential vectors and the electric and magnetic field vectors, using a spatial Fourier transformation, reveals six independent potential components but only four independent electromagnetic field components for each mode. Although the electromagnetic fields determined by Maxwell's equations give a complete description of all possible classical electromagnetic phenomena, potential vectors contains more information and allow for a description of such quantum mechanical phenomena as the Aharonov-Bohm effect. A new result is that a charged particle Lagrangian written in terms of potential vectors automatically contains a 'spontaneous symmetry breaking' potential.

New Evaluation Vector through the Stanford Mobile Inquiry-Based Learning Environment (SMILE) for Participatory Action Research

PubMed Central

An, Ji-Young

2016-01-01

Objectives This article reviews an evaluation vector model driven from a participatory action research leveraging a collective inquiry system named SMILE (Stanford Mobile Inquiry-based Learning Environment). Methods SMILE has been implemented in a diverse set of collective inquiry generation and analysis scenarios including community health care-specific professional development sessions and community-based participatory action research projects. In each scenario, participants are given opportunities to construct inquiries around physical and emotional health-related phenomena in their own community. Results Participants formulated inquiries as well as potential clinical treatments and hypothetical scenarios to address health concerns or clarify misunderstandings or misdiagnoses often found in their community practices. From medical universities to rural village health promotion organizations, all participatory inquiries and potential solutions can be collected and analyzed. The inquiry and solution sets represent an evaluation vector which helps educators better understand community health issues at a much deeper level. Conclusions SMILE helps collect problems that are most important and central to their community health concerns. The evaluation vector, consisting participatory and collective inquiries and potential solutions, helps the researchers assess the participants' level of understanding on issues around health concerns and practices while helping the community adequately formulate follow-up action plans. The method used in SMILE requires much further enhancement with machine learning and advanced data visualization. PMID:27525157

Genetically engineering adenoviral vectors for gene therapy.

PubMed

Coughlan, Lynda

2014-01-01

Adenoviral (Ad) vectors are commonly used for various gene therapy applications. Significant advances in the genetic engineering of Ad vectors in recent years has highlighted their potential for the treatment of metastatic disease. There are several methods to genetically modify the Ad genome to incorporate retargeting peptides which will redirect the natural tropism of the viruses, including homologous recombination in bacteria or yeast. However, homologous recombination in yeast is highly efficient and can be achieved without the need for extensive cloning strategies. In addition, the method does not rely on the presence of unique restriction sites within the Ad genome and the reagents required for this method are widely available and inexpensive. Large plasmids containing the entire adenoviral genome (~36 kbp) can be modified within Saccharomyces cerevisiae yeast and genomes easily rescued in Escherichia coli hosts for analysis or amplification. A method for two-step homologous recombination in yeast is described in this chapter.

Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

PubMed Central

Bii, Victor M.; Trobridge, Grant D.

2016-01-01

Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types. PMID:27792127

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.

Zoom in at African country level: potential climate induced changes in areas of suitability for survival of malaria vectors

PubMed Central

2014-01-01

Background Predicting anopheles vectors’ population densities and boundary shifts is crucial in preparing for malaria risks and unanticipated outbreaks. Although shifts in the distribution and boundaries of the major malaria vectors (Anopheles gambiae s.s. and An. arabiensis) across Africa have been predicted, quantified areas of absolute change in zone of suitability for their survival have not been defined. In this study, we have quantified areas of absolute change conducive for the establishment and survival of these vectors, per African country, under two climate change scenarios and based on our findings, highlight practical measures for effective malaria control in the face of changing climatic patterns. Methods We developed a model using CLIMEX simulation platform to estimate the potential geographical distribution and seasonal abundance of these malaria vectors in relation to climatic factors (temperature, rainfall and relative humidity). The model yielded an eco-climatic index (EI) describing the total favourable geographical locations for the species. The EI values were classified and exported to a GIS package. Using ArcGIS, the EI shape points were clipped to the extent of Africa and then converted to a raster layer using Inverse Distance Weighted (IDW) interpolation method. Generated maps were then transformed into polygon-based geo-referenced data set and their areas computed and expressed in square kilometers (km2). Results Five classes of EI were derived indicating the level of survivorship of these malaria vectors. The proportion of areas increasing or decreasing in level of survival of these malaria vectors will be more pronounced in eastern and southern African countries than those in western Africa. Angola, Ethiopia, Kenya, Mozambique, Tanzania, South Africa and Zambia appear most likely to be affected in terms of absolute change of malaria vectors suitability zones under the selected climate change scenarios. Conclusion The potential shifts of these malaria vectors have implications for human exposure to malaria, as recrudescence of the disease is likely to be recorded in several new areas and regions. Therefore, the need to develop, compile and share malaria preventive measures, which can be adapted to different climatic scenarios, remains crucial. PMID:24885061

Potential theory of radiation

NASA Technical Reports Server (NTRS)

Chiu, Huei-Huang

1989-01-01

A theoretical method is being developed by which the structure of a radiation field can be predicted by a radiation potential theory, similar to a classical potential theory. The introduction of a scalar potential is justified on the grounds that the spectral intensity vector is irrotational. The vector is also solenoidal in the limits of a radiation field in complete radiative equilibrium or in a vacuum. This method provides an exact, elliptic type equation that will upgrade the accuracy and the efficiency of the current CFD programs required for the prediction of radiation and flow fields. A number of interesting results emerge from the present study. First, a steady state radiation field exhibits an optically modulated inverse square law distribution character. Secondly, the unsteady radiation field is structured with two conjugate scalar potentials. Each is governed by a Klein-Gordon equation with a frictional force and a restoring force. This steady potential field structure and the propagation of radiation potentials are consistent with the well known results of classical electromagnetic theory. The extension of the radiation potential theory for spray combustion and hypersonic flow is also recommended.

Numerical computation of gravitational field for general axisymmetric objects

NASA Astrophysics Data System (ADS)

Fukushima, Toshio

2016-10-01

We developed a numerical method to compute the gravitational field of a general axisymmetric object. The method (I) numerically evaluates a double integral of the ring potential by the split quadrature method using the double exponential rules, and (II) derives the acceleration vector by numerically differentiating the numerically integrated potential by Ridder's algorithm. Numerical comparison with the analytical solutions for a finite uniform spheroid and an infinitely extended object of the Miyamoto-Nagai density distribution confirmed the 13- and 11-digit accuracy of the potential and the acceleration vector computed by the method, respectively. By using the method, we present the gravitational potential contour map and/or the rotation curve of various axisymmetric objects: (I) finite uniform objects covering rhombic spindles and circular toroids, (II) infinitely extended spheroids including Sérsic and Navarro-Frenk-White spheroids, and (III) other axisymmetric objects such as an X/peanut-shaped object like NGC 128, a power-law disc with a central hole like the protoplanetary disc of TW Hya, and a tear-drop-shaped toroid like an axisymmetric equilibrium solution of plasma charge distribution in an International Thermonuclear Experimental Reactor-like tokamak. The method is directly applicable to the electrostatic field and will be easily extended for the magnetostatic field. The FORTRAN 90 programs of the new method and some test results are electronically available.

The q-G method : A q-version of the Steepest Descent method for global optimization.

PubMed

Soterroni, Aline C; Galski, Roberto L; Scarabello, Marluce C; Ramos, Fernando M

2015-01-01

In this work, the q-Gradient (q-G) method, a q-version of the Steepest Descent method, is presented. The main idea behind the q-G method is the use of the negative of the q-gradient vector of the objective function as the search direction. The q-gradient vector, or simply the q-gradient, is a generalization of the classical gradient vector based on the concept of Jackson's derivative from the q-calculus. Its use provides the algorithm an effective mechanism for escaping from local minima. The q-G method reduces to the Steepest Descent method when the parameter q tends to 1. The algorithm has three free parameters and it is implemented so that the search process gradually shifts from global exploration in the beginning to local exploitation in the end. We evaluated the q-G method on 34 test functions, and compared its performance with 34 optimization algorithms, including derivative-free algorithms and the Steepest Descent method. Our results show that the q-G method is competitive and has a great potential for solving multimodal optimization problems.

Grid-based lattice summation of electrostatic potentials by assembled rank-structured tensor approximation

NASA Astrophysics Data System (ADS)

Khoromskaia, Venera; Khoromskij, Boris N.

2014-12-01

Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N × N × N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L × L × L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N) , while the numerical cost is estimated by O(NL) . For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n = N / L, while the numerical cost reduces to O(N) , that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3 log N) . The complexity in the grid parameter N can be reduced even to the logarithmic scale O(log N) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.

A conservative scheme for electromagnetic simulation of magnetized plasmas with kinetic electrons

NASA Astrophysics Data System (ADS)

Bao, J.; Lin, Z.; Lu, Z. X.

2018-02-01

A conservative scheme has been formulated and verified for gyrokinetic particle simulations of electromagnetic waves and instabilities in magnetized plasmas. An electron continuity equation derived from the drift kinetic equation is used to time advance the electron density perturbation by using the perturbed mechanical flow calculated from the parallel vector potential, and the parallel vector potential is solved by using the perturbed canonical flow from the perturbed distribution function. In gyrokinetic particle simulations using this new scheme, the shear Alfvén wave dispersion relation in the shearless slab and continuum damping in the sheared cylinder have been recovered. The new scheme overcomes the stringent requirement in the conventional perturbative simulation method that perpendicular grid size needs to be as small as electron collisionless skin depth even for the long wavelength Alfvén waves. The new scheme also avoids the problem in the conventional method that an unphysically large parallel electric field arises due to the inconsistency between electrostatic potential calculated from the perturbed density and vector potential calculated from the perturbed canonical flow. Finally, the gyrokinetic particle simulations of the Alfvén waves in sheared cylinder have superior numerical properties compared with the fluid simulations, which suffer from numerical difficulties associated with singular mode structures.

A review of plague persistence with special emphasis on fleas

USGS Publications Warehouse

Wimsatt, Jeffrey; Biggins, Dean E.

2009-01-01

Here, we note a potentially pivotal role for fleas. These epizootic plague vectors should be closely studied with newer more exacting methods to determine their potential to serve as participants in or accomplices to a plague persistence reservoir.

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

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

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

DOE PAGES

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; ...

2016-10-26

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

Three dimensional magnetic fields in extra high speed modified Lundell alternators computed by a combined vector-scalar magnetic potential finite element method

NASA Technical Reports Server (NTRS)

Demerdash, N. A.; Wang, R.; Secunde, R.

1992-01-01

A 3D finite element (FE) approach was developed and implemented for computation of global magnetic fields in a 14.3 kVA modified Lundell alternator. The essence of the new method is the combined use of magnetic vector and scalar potential formulations in 3D FEs. This approach makes it practical, using state of the art supercomputer resources, to globally analyze magnetic fields and operating performances of rotating machines which have truly 3D magnetic flux patterns. The 3D FE-computed fields and machine inductances as well as various machine performance simulations of the 14.3 kVA machine are presented in this paper and its two companion papers.

A Principal Component Analysis/Fuzzy Comprehensive Evaluation for Rockburst Potential in Kimberlite

NASA Astrophysics Data System (ADS)

Pu, Yuanyuan; Apel, Derek; Xu, Huawei

2018-02-01

Kimberlite is an igneous rock which sometimes bears diamonds. Most of the diamonds mined in the world today are found in kimberlite ores. Burst potential in kimberlite has not been investigated, because kimberlite is mostly mined using open-pit mining, which poses very little threat of rock bursting. However, as the mining depth keeps increasing, the mines convert to underground mining methods, which can pose a threat of rock bursting in kimberlite. This paper focuses on the burst potential of kimberlite at a diamond mine in northern Canada. A combined model with the methods of principal component analysis (PCA) and fuzzy comprehensive evaluation (FCE) is developed to process data from 12 different locations in kimberlite pipes. Based on calculated 12 fuzzy evaluation vectors, 8 locations show a moderate burst potential, 2 locations show no burst potential, and 2 locations show strong and violent burst potential, respectively. Using statistical principles, a Mahalanobis distance is adopted to build a comprehensive fuzzy evaluation vector for the whole mine and the final evaluation for burst potential is moderate, which is verified by a practical rockbursting situation at mine site.

Integrated vector management: a critical strategy for combating vector-borne diseases in South Sudan.

PubMed

Chanda, Emmanuel; Govere, John M; Macdonald, Michael B; Lako, Richard L; Haque, Ubydul; Baba, Samson P; Mnzava, Abraham

2013-10-25

Integrated vector management (IVM) based vector control is encouraged by the World Health Organization (WHO). However, operational experience with the IVM strategy has mostly come from countries with relatively well-established health systems and with malaria control focused programmes. Little is known about deployment of IVM for combating multiple vector-borne diseases in post-emergency settings, where delivery structures are less developed or absent. This manuscript reports on the feasibility of operational IVM for combating vector-borne diseases in South Sudan. A methodical review of published and unpublished documents on vector-borne diseases for South Sudan was conducted via systematic literature search of online electronic databases, Google Scholar, PubMed and WHO, using a combination of search terms. Additional, non-peer reviewed literature was examined for information related to the subject. South Sudan is among the heartlands of vector-borne diseases in the world, characterized by enormous infrastructure, human and financial resource constraints and a weak health system against an increasing number of refugees, returnees and internally displaced people. The presence of a multiplicity of vector-borne diseases in this post-conflict situation presents a unique opportunity to explore the potential of a rational IVM strategy for multiple disease control and optimize limited resource utilization, while maximizing the benefits and providing a model for countries in a similar situation. The potential of integrating vector-borne disease control is enormous in South Sudan. However, strengthened coordination, intersectoral collaboration and institutional and technical capacity for entomological monitoring and evaluation, including enforcement of appropriate legislation are crucial.

Integrated vector management: a critical strategy for combating vector-borne diseases in South Sudan

PubMed Central

2013-01-01

Background Integrated vector management (IVM) based vector control is encouraged by the World Health Organization (WHO). However, operational experience with the IVM strategy has mostly come from countries with relatively well-established health systems and with malaria control focused programmes. Little is known about deployment of IVM for combating multiple vector-borne diseases in post-emergency settings, where delivery structures are less developed or absent. This manuscript reports on the feasibility of operational IVM for combating vector-borne diseases in South Sudan. Case description A methodical review of published and unpublished documents on vector-borne diseases for South Sudan was conducted via systematic literature search of online electronic databases, Google Scholar, PubMed and WHO, using a combination of search terms. Additional, non-peer reviewed literature was examined for information related to the subject. Discussion South Sudan is among the heartlands of vector-borne diseases in the world, characterized by enormous infrastructure, human and financial resource constraints and a weak health system against an increasing number of refugees, returnees and internally displaced people. The presence of a multiplicity of vector-borne diseases in this post-conflict situation presents a unique opportunity to explore the potential of a rational IVM strategy for multiple disease control and optimize limited resource utilization, while maximizing the benefits and providing a model for countries in a similar situation. Conclusion The potential of integrating vector-borne disease control is enormous in South Sudan. However, strengthened coordination, intersectoral collaboration and institutional and technical capacity for entomological monitoring and evaluation, including enforcement of appropriate legislation are crucial. PMID:24156749

Testing of the Support Vector Machine for Binary-Class Classification

NASA Technical Reports Server (NTRS)

Scholten, Matthew

2011-01-01

The Support Vector Machine is a powerful algorithm, useful in classifying data in to species. The Support Vector Machines implemented in this research were used as classifiers for the final stage in a Multistage Autonomous Target Recognition system. A single kernel SVM known as SVMlight, and a modified version known as a Support Vector Machine with K-Means Clustering were used. These SVM algorithms were tested as classifiers under varying conditions. Image noise levels varied, and the orientation of the targets changed. The classifiers were then optimized to demonstrate their maximum potential as classifiers. Results demonstrate the reliability of SMV as a method for classification. From trial to trial, SVM produces consistent results

Development of nonhuman adenoviruses as vaccine vectors

PubMed Central

Bangari, Dinesh S.; Mittal, Suresh K.

2006-01-01

Human adenoviral (HAd) vectors have demonstrated great potential as vaccine vectors. Preclinical and clinical studies have demonstrated the feasibility of vector design, robust antigen expression and protective immunity using this system. However, clinical use of adenoviral vectors for vaccine purposes is anticipated to be limited by vector immunity that is either preexisting or develops rapidly following the first inoculation with adenoviral vectors. Vector immunity inactivates the vector particles and rapidly removes the transduced cells, thereby limiting the duration of transgene expression. Due to strong vector immunity, subsequent use of the same vector is usually less efficient. In order to circumvent this limitation, nonhuman adenoviral vectors have been proposed as alternative vectors. In addition to eluding HAd immunity, these vectors possess most of the attractive features of HAd vectors. Several replication-competent or replication-defective nonhuman adenoviral vectors have been developed and investigated for their potential as vaccine delivery vectors. Here, we review recent advances in the design and characterization of various nonhuman adenoviral vectors, and discuss their potential applications for human and animal vaccination. PMID:16297508

Meta-analyses of the proportion of Japanese encephalitis virus infection in vectors and vertebrate hosts.

PubMed

Oliveira, Ana R S; Cohnstaedt, Lee W; Strathe, Erin; Hernández, Luciana Etcheverry; McVey, D Scott; Piaggio, José; Cernicchiaro, Natalia

2017-09-07

Japanese encephalitis (JE) is a zoonosis in Southeast Asia vectored by mosquitoes infected with the Japanese encephalitis virus (JEV). Japanese encephalitis is considered an emerging exotic infectious disease with potential for introduction in currently JEV-free countries. Pigs and ardeid birds are reservoir hosts and play a major role on the transmission dynamics of the disease. The objective of the study was to quantitatively summarize the proportion of JEV infection in vectors and vertebrate hosts from data pertaining to observational studies obtained in a systematic review of the literature on vector and host competence for JEV, using meta-analyses. Data gathered in this study pertained to three outcomes: proportion of JEV infection in vectors, proportion of JEV infection in vertebrate hosts, and minimum infection rate (MIR) in vectors. Random-effects subgroup meta-analysis models were fitted by species (mosquito or vertebrate host species) to estimate pooled summary measures, as well as to compute the variance between studies. Meta-regression models were fitted to assess the association between different predictors and the outcomes of interest and to identify sources of heterogeneity among studies. Predictors included in all models were mosquito/vertebrate host species, diagnostic methods, mosquito capture methods, season, country/region, age category, and number of mosquitos per pool. Mosquito species, diagnostic method, country, and capture method represented important sources of heterogeneity associated with the proportion of JEV infection; host species and region were considered sources of heterogeneity associated with the proportion of JEV infection in hosts; and diagnostic and mosquito capture methods were deemed important contributors of heterogeneity for the MIR outcome. Our findings provide reference pooled summary estimates of vector competence for JEV for some mosquito species, as well as of sources of variability for these outcomes. Moreover, this work provides useful guidelines when interpreting vector and host infection proportions or prevalence from observational studies, and contributes to further our understanding of vector and vertebrate host competence for JEV, elucidating information on the relative importance of vectors and hosts on JEV introduction and transmission.

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

Helper-Free Foamy Virus Vectors

PubMed Central

TROBRIDGE, GRANT D.; RUSSELL, DAVID W.

2010-01-01

Retroviral vectors based on human foamy virus (HFV) have been developed and show promise as gene therapy vehicles. Here we describe a method for the production of HFV vector stocks free of detectable helper virus. The helper and vector plasmid constructs used both lack the HFV bel genes, so recombination between these constructs cannot create a wild-type virus. A fusion promoter that combines portions of the cytomegalovirus (CMV) immediate-early and HFV long terminal repeat (LTR) promoters was used to drive expression of both the helper and vector constructs. The CMV–LTR fusion promoter allows for HFV vector production in the absence of the Bel-1 trans-activator protein, which would otherwise be necessary for efficient transcription from the HFV LTR. Vector stocks containing either neomycin phosphotransferase or alkaline phosphatase reporter genes were produced by transient transfection at titers greater than 105 transducing units/ml. G418-resistant BHK-21 cells obtained by transduction with neo vectors contained randomly integrated HFV vector proviruses without detectable deletions or rearrangements. The vector stocks generated were free of replication-competent retrovirus (RCR), as determined by assays for LTR trans-activation and a marker rescue assay developed here for the detection of Bel-independent RCR. OVERVIEW SUMMARY Vectors based on human foamy virus have been developed but low titers and the presence of replication-competent retrovirus (RCR) in vector stocks have prevented their use in preclinical animal experiments. We have developed a transient transfection method that can be used to produce replication-incompetent HFV vector stocks at titers greater than 105/ml, and that does not produce contaminating RCR. The use of CMV-HFV LTR fusion promoters in the helper and vector constructs has circumvented the requirement for the HFV Bel-1 trans-activator protein. Consequently, the potential for generating wild-type HFV by recombination between helper and vector constructs during vector production has been eliminated. Here we describe HFV vector production using this Bel-independent system. PMID:9853518

Spherical Harmonic Inductive Detection Coils and their use In Dynamic Pre-emphasis for Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Edler, Karl T.

The issue of eddy currents induced by the rapid switching of magnetic field gradients is a long-standing problem in magnetic resonance imaging. A new method for dealing with this problem is presented whereby spatial harmonic components of the magnetic field are continuously sensed, through their temporal rates of change, and corrected. In this way, the effects of the eddy currents on multiple spatial harmonic components of the magnetic field can be detected and corrections applied during the rise time of the gradients. Sensing the temporal changes in each spatial harmonic is made possible with specially designed detection coils. However to make the design of these coils possible, general relationships between the spatial harmonics of the field, scalar potential, and vector potential are found within the quasi-static approximation. These relationships allow the vector potential to be found from the field -- an inverse curl operation -- and may be of use beyond the specific problem of detection coil design. Using the detection coils as sensors, methods are developed for designing a negative feedback system to control the eddy current effects and optimizing that system with respect to image noise and distortion. The design methods are successfully tested in a series of proof-of-principle experiments which lead to a discussion of how to incorporate similar designs into an operational MRI. Keywords: magnetic resonance imaging, eddy currents, dynamic shimming, negative feedback, quasi-static fields, vector potential, inverse curl

CD25 Preselective Anti-HIV Vectors for Improved HIV Gene Therapy

PubMed Central

Kalomoiris, Stefanos; Lawson, Je'Tai; Chen, Rachel X.; Bauer, Gerhard; Nolta, Jan A.

2012-01-01

Abstract As HIV continues to be a global public health problem with no effective vaccine available, new and innovative therapies, including HIV gene therapies, need to be developed. Due to low transduction efficiencies that lead to low in vivo gene marking, therapeutically relevant efficacy of HIV gene therapy has been difficult to achieve in a clinical setting. Methods to improve the transplantation of enriched populations of anti-HIV vector-transduced cells may greatly increase the in vivo efficacy of HIV gene therapies. Here we describe the development of preselective anti-HIV lentiviral vectors that allow for the purification of vector-transduced cells to achieve an enriched population of HIV-resistant cells. A selectable protein, human CD25, not normally found on CD34+ hematopoietic progenitor cells (HPCs), was incorporated into a triple combination anti-HIV lentiviral vector. Upon purification of cells transduced with the preselective anti-HIV vector, safety was demonstrated in CD34+ HPCs and in HPC-derived macrophages in vitro. Upon challenge with HIV-1, improved efficacy was observed in purified preselective anti-HIV vector-transduced macrophages compared to unpurified cells. These proof-of-concept results highlight the potential use of this method to improve HIV stem cell gene therapy for future clinical applications. PMID:23216020

Lentiviral vectors encoding shRNAs efficiently transduce and knockdown LINGO-1 but induce an interferon response and cytotoxicity in CNS neurons

PubMed Central

Hutson, Thomas H.; Foster, Edmund; Dawes, John M.; Hindges, Robert; Yáñez-Muñoz, Rafael J.; Moon, Lawrence D.F.

2017-01-01

Background Knocking down neuronal LINGO-1 using short hairpin RNAs (shRNAs) might enhance axon regeneration in the CNS. Integration-deficient lentiviral vectors have great potential as a therapeutic delivery system for CNS injuries. However, recent studies have revealed that shRNAs can induce an interferon response resulting in off-target effects and cytotoxicity. Methods CNS neurons were transduced with integration-deficient lentiviral vectors in vitro. The transcriptional effect of shRNA expression was analysed using qRT-PCR and northern blots were used to assess shRNA production. Results Integration-deficient lentiviral vectors efficiently transduced CNS neurons and knocked down LINGO-1 mRNA in vitro. However, an increase in cell death was observed when lentiviral vectors encoding an shRNA were applied or when high vector concentrations were used. We demonstrate that high doses of vector or the use of vectors encoding shRNAs can induce an up-regulation of interferon stimulated genes (OAS1 and PKR) and a down-regulation of off- target genes (including p75NTR and NgR1). Furthermore, the northern blot demonstrated that these negative consequences occur even when lentiviral vectors express low levels of shRNAs. Together, these results may explain why neurite outgrowth was not enhanced on an inhibitory substrate after transduction with lentiviral vectors encoding an shRNA targeting LINGO-1. Conclusions These findings highlight the importance of including appropriate controls to verify silencing specificity and the requirement to check for an interferon response when conducting RNA interference experiments. However, the potential benefits that RNA interference and viral vectors offer to gene-based therapies to CNS injuries cannot be overlooked and demand further investigation. PMID:22499506

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 ...

Relativistic extension of the Kay-Moses method for constructing transparent potentials in quantum mechanics

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

Toyama, F.M.; Nogami, Y.; Zhao, Z.

1993-02-01

For the Dirac equation in one space dimension with a potential of the Lorentz scalar type, we present a complete solution for the problem of constructing a transparent potential. This is a relativistic extension of the Kay-Moses method which was developed for the nonrelativistic Schroedinger equation. There is an infinite family of transparent potentials. The potentials are all related to solutions of a class of coupled, nonlinear Dirac equations. In addition, it is argued that an admixture of a Lorentz vector component in the potential impairs perfect transparency.

Integrating vector control across diseases.

PubMed

Golding, Nick; Wilson, Anne L; Moyes, Catherine L; Cano, Jorge; Pigott, David M; Velayudhan, Raman; Brooker, Simon J; Smith, David L; Hay, Simon I; Lindsay, Steve W

2015-10-01

Vector-borne diseases cause a significant proportion of the overall burden of disease across the globe, accounting for over 10 % of the burden of infectious diseases. Despite the availability of effective interventions for many of these diseases, a lack of resources prevents their effective control. Many existing vector control interventions are known to be effective against multiple diseases, so combining vector control programmes to simultaneously tackle several diseases could offer more cost-effective and therefore sustainable disease reductions. The highly successful cross-disease integration of vaccine and mass drug administration programmes in low-resource settings acts a precedent for cross-disease vector control. Whilst deliberate implementation of vector control programmes across multiple diseases has yet to be trialled on a large scale, a number of examples of 'accidental' cross-disease vector control suggest the potential of such an approach. Combining contemporary high-resolution global maps of the major vector-borne pathogens enables us to quantify overlap in their distributions and to estimate the populations jointly at risk of multiple diseases. Such an analysis shows that over 80 % of the global population live in regions of the world at risk from one vector-borne disease, and more than half the world's population live in areas where at least two different vector-borne diseases pose a threat to health. Combining information on co-endemicity with an assessment of the overlap of vector control methods effective against these diseases allows us to highlight opportunities for such integration. Malaria, leishmaniasis, lymphatic filariasis, and dengue are prime candidates for combined vector control. All four of these diseases overlap considerably in their distributions and there is a growing body of evidence for the effectiveness of insecticide-treated nets, screens, and curtains for controlling all of their vectors. The real-world effectiveness of cross-disease vector control programmes can only be evaluated by large-scale trials, but there is clear evidence of the potential of such an approach to enable greater overall health benefit using the limited funds available.

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.

PCA-LBG-based algorithms for VQ codebook generation

NASA Astrophysics Data System (ADS)

Tsai, Jinn-Tsong; Yang, Po-Yuan

2015-04-01

Vector quantisation (VQ) codebooks are generated by combining principal component analysis (PCA) algorithms with Linde-Buzo-Gray (LBG) algorithms. All training vectors are grouped according to the projected values of the principal components. The PCA-LBG-based algorithms include (1) PCA-LBG-Median, which selects the median vector of each group, (2) PCA-LBG-Centroid, which adopts the centroid vector of each group, and (3) PCA-LBG-Random, which randomly selects a vector of each group. The LBG algorithm finds a codebook based on the better vectors sent to an initial codebook by the PCA. The PCA performs an orthogonal transformation to convert a set of potentially correlated variables into a set of variables that are not linearly correlated. Because the orthogonal transformation efficiently distinguishes test image vectors, the proposed PCA-LBG-based algorithm is expected to outperform conventional algorithms in designing VQ codebooks. The experimental results confirm that the proposed PCA-LBG-based algorithms indeed obtain better results compared to existing methods reported in the literature.

Influence of sequence and size of DNA on packaging efficiency of parvovirus MVM-based vectors.

PubMed

Brandenburger, A; Coessens, E; El Bakkouri, K; Velu, T

1999-05-01

We have derived a vector from the autonomous parvovirus MVM(p), which expresses human IL-2 specifically in transformed cells (Russell et al., J. Virol 1992;66:2821-2828). Testing the therapeutic potential of these vectors in vivo requires high-titer stocks. Stocks with a titer of 10(9) can be obtained after concentration and purification (Avalosse et al., J. Virol. Methods 1996;62:179-183), but this method requires large culture volumes and cannot easily be scaled up. We wanted to increase the production of recombinant virus at the initial transfection step. Poor vector titers could be due to inadequate genome amplification or to inefficient packaging. Here we show that intracellular amplification of MVM vector genomes is not the limiting factor for vector production. Several vector genomes of different size and/or structure were amplified to an equal extent. Their amplification was also equivalent to that of a cotransfected wild-type genome. We did not observe any interference between vector and wild-type genomes at the level of DNA amplification. Despite equivalent genome amplification, vector titers varied greatly between the different genomes, presumably owing to differences in packaging efficiency. Genomes with a size close to 100% that of wild type were packaged most efficiently with loss of efficiency at lower and higher sizes. However, certain genomes of identical size showed different packaging efficiencies, illustrating the importance of the DNA sequence, and probably its structure.

Practical Integration-Free Episomal Methods for Generating Human Induced Pluripotent Stem Cells.

PubMed

Kime, Cody; Rand, Tim A; Ivey, Kathryn N; Srivastava, Deepak; Yamanaka, Shinya; Tomoda, Kiichiro

2015-10-06

The advent of induced pluripotent stem (iPS) cell technology has revolutionized biomedicine and basic research by yielding cells with embryonic stem (ES) cell-like properties. The use of iPS-derived cells for cell-based therapies and modeling of human disease holds great potential. While the initial description of iPS cells involved overexpression of four transcription factors via viral vectors that integrated within genomic DNA, advances in recent years by our group and others have led to safer and higher quality iPS cells with greater efficiency. Here, we describe commonly practiced methods for non-integrating induced pluripotent stem cell generation using nucleofection of episomal reprogramming plasmids. These methods are adapted from recent studies that demonstrate increased hiPS cell reprogramming efficacy with the application of three powerful episomal hiPS cell reprogramming factor vectors and the inclusion of an accessory vector expressing EBNA1. Copyright © 2015 John Wiley & Sons, Inc.

Krylov subspace methods on supercomputers

NASA Technical Reports Server (NTRS)

Saad, Youcef

1988-01-01

A short survey of recent research on Krylov subspace methods with emphasis on implementation on vector and parallel computers is presented. Conjugate gradient methods have proven very useful on traditional scalar computers, and their popularity is likely to increase as three-dimensional models gain importance. A conservative approach to derive effective iterative techniques for supercomputers has been to find efficient parallel/vector implementations of the standard algorithms. The main source of difficulty in the incomplete factorization preconditionings is in the solution of the triangular systems at each step. A few approaches consisting of implementing efficient forward and backward triangular solutions are described in detail. Polynomial preconditioning as an alternative to standard incomplete factorization techniques is also discussed. Another efficient approach is to reorder the equations so as to improve the structure of the matrix to achieve better parallelism or vectorization. An overview of these and other ideas and their effectiveness or potential for different types of architectures is given.

Vectorization of Nucleic Acids for Therapeutic Approach: Tutorial Review.

PubMed

Geinguenaud, Frederic; Guenin, Erwann; Lalatonne, Yoann; Motte, Laurence

2016-05-20

Oligonucleotides present a high therapeutic potential for a wide variety of diseases. However, their clinical development is limited by their degradation by nucleases and their poor blood circulation time. Depending on the administration mode and the cellular target, these macromolecules will have to cross the vascular endothelium, to diffuse through the extracellular matrix, to be transported through the cell membrane, and finally to reach the cytoplasm. To overcome these physiological barriers, many strategies have been developed. Here, we review different methods of DNA vectorization, discuss limitations and advantages of the various vectors, and provide new perspectives for future development.

Electron-phonon mediated heat flow in disordered graphene

NASA Astrophysics Data System (ADS)

Chen, Wei; Clerk, Aashish A.

2012-09-01

We calculate the heat flux and electron-phonon thermal conductance in a disordered graphene sheet, going beyond a Fermi’s golden rule approach to fully account for the modification of the electron-phonon interaction by disorder. Using the Keldysh technique combined with standard impurity averaging methods in the regime kFl≫1 (where kF is the Fermi wave vector and l is the mean free path), we consider both scalar potential (i.e., deformation potential) and vector-potential couplings between electrons and phonons. We also consider the effects of electronic screening at the Thomas-Fermi level. We find that the temperature dependence of the heat flux and thermal conductance is sensitive to the presence of disorder and screening, and reflects the underlying chiral nature of electrons in graphene and the corresponding modification of their diffusive behavior. In the case of weak screening, disorder enhances the low-temperature heat flux over the clean system (changing the associated power law from T4 to T3), and the deformation potential dominates. For strong screening, both the deformation potential and vector-potential couplings make comparable contributions, and the low-temperature heat flux obeys a T5 power law.

Establishment of conditional vectors for hairpin siRNA knockdowns

PubMed Central

Matsukura, Shiro; Jones, Peter A.; Takai, Daiya

2003-01-01

Small interference RNA (siRNA) is an emerging methodology in reverse genetics. Here we report the development of a new tetracycline-inducible vector-based siRNA system, which uses a tetracycline-responsive derivative of the U6 promoter and the tetracycline repressor for conditional in vivo transcription of short hairpin RNA. This method prevents potential lethality immediately after transfection of a vector when the targeted gene is indispensable, or the phenotype of the knockdown is lethal or results in a growth abnormality. We show that the controlled knockdown of DNA methyltransferase 1 (DNMT1) in human cancer resulted in growth arrest. Removal of the inducer, doxycycline, from treated cells led to re-expression of the targeted gene. Thus the method allows for a highly controlled approach to gene knockdown. PMID:12888529

A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra

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

Avila, Gustavo, E-mail: Gustavo-Avila@telefonica.net; Carrington, Tucker, E-mail: Tucker.Carrington@queensu.ca

In this paper, we improve the collocation method for computing vibrational spectra that was presented in Avila and Carrington, Jr. [J. Chem. Phys. 139, 134114 (2013)]. Using an iterative eigensolver, energy levels and wavefunctions are determined from values of the potential on a Smolyak grid. The kinetic energy matrix-vector product is evaluated by transforming a vector labelled with (nondirect product) grid indices to a vector labelled by (nondirect product) basis indices. Both the transformation and application of the kinetic energy operator (KEO) scale favorably. Collocation facilitates dealing with complicated KEOs because it obviates the need to calculate integrals of coordinatemore » dependent coefficients of differential operators. The ideas are tested by computing energy levels of HONO using a KEO in bond coordinates.« less

A note on the uniqueness of 2D elastostatic problems formulated by different types of potential functions

NASA Astrophysics Data System (ADS)

Guerrero, José Luis Morales; Vidal, Manuel Cánovas; Nicolás, José Andrés Moreno; López, Francisco Alhama

2018-05-01

New additional conditions required for the uniqueness of the 2D elastostatic problems formulated in terms of potential functions for the derived Papkovich-Neuber representations, are studied. Two cases are considered, each of them formulated by the scalar potential function plus one of the rectangular non-zero components of the vector potential function. For these formulations, in addition to the original (physical) boundary conditions, two new additional conditions are required. In addition, for the complete Papkovich-Neuber formulation, expressed by the scalar potential plus two components of the vector potential, the additional conditions established previously for the three-dimensional case in z-convex domain can be applied. To show the usefulness of these new conditions in a numerical scheme two applications are numerically solved by the network method for the three cases of potential formulations.

The contactless detection of local normal transitions in superconducting coils by using Poynting’s vector method

NASA Astrophysics Data System (ADS)

Habu, K.; Kaminohara, S.; Kimoto, T.; Kawagoe, A.; Sumiyoshi, F.; Okamoto, H.

2010-11-01

We have developed a new monitoring system to detect an unusual event in the superconducting coils without direct contact on the coils, using Poynting's vector method. In this system, the potential leads and pickup coils are set around the superconducting coils to measure local electric and magnetic fields, respectively. By measuring the sets of magnetic and electric fields, the Poynting's vectors around the coil can be obtained. An unusual event in the coil can be detected as the result of the change of the Poynting's vector. This system has no risk of the voltage breakdown which may happen with the balance voltage method, because there is no need of direct contacts on the coil windings. In a previous paper, we have demonstrated that our system can detect the normal transitions in the Bi-2223 coil without direct contact on the coil windings by using a small test system. For our system to be applied to practical devices, it is necessary for the early detection of an unusual event in the coils to be able to detect local normal transitions in the coils. The signal voltages of the small sensors to measure local magnetic and electric fields are small. Although the increase in signals of the pickup coils is attained easily by an increase in the number of turns of the pickup coils, an increase in the signals of the potential lead is not easily attained. In this paper, a new method to amplify the signal of local electric fields around the coil is proposed. The validity of the method has been confirmed by measuring local electric fields around the Bi-2223 coil.

Correlated Topic Vector for Scene Classification.

PubMed

Wei, Pengxu; Qin, Fei; Wan, Fang; Zhu, Yi; Jiao, Jianbin; Ye, Qixiang

2017-07-01

Scene images usually involve semantic correlations, particularly when considering large-scale image data sets. This paper proposes a novel generative image representation, correlated topic vector, to model such semantic correlations. Oriented from the correlated topic model, correlated topic vector intends to naturally utilize the correlations among topics, which are seldom considered in the conventional feature encoding, e.g., Fisher vector, but do exist in scene images. It is expected that the involvement of correlations can increase the discriminative capability of the learned generative model and consequently improve the recognition accuracy. Incorporated with the Fisher kernel method, correlated topic vector inherits the advantages of Fisher vector. The contributions to the topics of visual words have been further employed by incorporating the Fisher kernel framework to indicate the differences among scenes. Combined with the deep convolutional neural network (CNN) features and Gibbs sampling solution, correlated topic vector shows great potential when processing large-scale and complex scene image data sets. Experiments on two scene image data sets demonstrate that correlated topic vector improves significantly the deep CNN features, and outperforms existing Fisher kernel-based features.

Factoring nonviral gene therapy into a cure for hemophilia A.

PubMed

Gabrovsky, Vanessa; Calos, Michele P

2008-10-01

Gene therapy for hemophilia A has fallen short of success despite several clinical trials conducted over the past decade. Challenges to its success include vector immunogenicity, insufficient transgene expression levels of Factor VIII, and inhibitor antibody formation. Gene therapy has been dominated by the use of viral vectors, as well as the immunogenic and oncogenic concerns that accompany these strategies. Because of the complexity of viral vectors, the development of nonviral DNA delivery methods may provide an efficient and safe alternative for the treatment of hemophilia A. New types of nonviral strategies, such as DNA integrating vectors, and the success of several nonviral animal studies, suggest that nonviral gene therapy has curative potential and justifies its clinical development.

Ground states of larger nuclei

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

Pieper, S.C.; Wiringa, R.B.; Pandharipande, V.R.

1995-08-01

The methods used for the few-body nuclei require operations on the complete spin-isospin vector; the size of this vector makes such methods impractical for nuclei with A > 8. During the last few years we developed cluster expansion methods that do not require operations on the complete vector. We use the same Hamiltonians as for the few-body nuclei and variational wave functions of form similar to the few-body wave functions. The cluster expansions are made for the noncentral parts of the wave functions and for the operators whose expectation values are being evaluated. The central pair correlations in the wavemore » functions are treated exactly and this requires the evaluation of 3A-dimensional integrals which are done with Monte Carlo techniques. Most of our effort was on {sup 16}O, other p-shell nuclei, and {sup 40}Ca. In 1993 the Mathematics and Computer Science Division acquired a 128-processor IBM SP which has a theoretical peak speed of 16 Gigaflops (GFLOPS). We converted our program to run on this machine. Because of the large memory on each node of the SP, it was easy to convert the program to parallel form with very low communication overhead. Considerably more effort was needed to restructure the program from one oriented towards long vectors for the Cray computers at NERSC to one that makes efficient use of the cache of the RS6000 architecture. The SP made possible complete five-body cluster calculations of {sup 16}O for the first time; previously we could only do four-body cluster calculations. These calculations show that the expectation value of the two-body potential is converging less rapidly than we had thought, while that of the three-body potential is more rapidly convergent; the net result is no significant change to our predicted binding energy for {sup 16}O using the new Argonne v{sub 18} potential and the Urbana IX three-nucleon potential. This result is in good agreement with experiment.« less

Magnetohydrodynamic cellular automata

NASA Technical Reports Server (NTRS)

Montgomery, David; Doolen, Gary D.

1987-01-01

A generalization of the hexagonal lattice gas model of Frisch, Hasslacher and Pomeau is shown to lead to two-dimensional magnetohydrodynamics. The method relies on the ideal point-wise conservation law for vector potential.

Unique Safety Issues Associated with Virus Vectored Vaccines: Potential for and Theoretical Consequences of Recombination with Wild Type Virus Strains

PubMed Central

Condit, Richard C.; Williamson, Anna-Lise; Sheets, Rebecca; Seligman, Stephen J.; Monath, Thomas P.; Excler, Jean-Louis; Gurwith, Marc; Bok, Karin; Robertson, James S.; Kim, Denny; Hendry, Michael; Singh, Vidisha; Mac, Lisa M.; Chen, Robert T.

2016-01-01

In 2003 and 2013, the World Health Organization convened informal consultations on characterization and quality aspects of vaccines based on live virus vectors. In the resulting reports, one of several issues raised for future study was the potential for recombination of virus-vectored vaccines with wild type pathogenic virus strains. This paper presents an assessment of this issue formulated by the Brighton Collaboration. To provide an appropriate context for understanding the potential for recombination of virus-vectored vaccines, we review briefly the current status of virus vectored vaccines, mechanisms of recombination between viruses, experience with recombination involving live attenuated vaccines in the field, and concerns raised previously in the literature regarding recombination of virus-vectored vaccines with wild type virus strains. We then present a discussion of the major variables that could influence recombination between a virus-vectored vaccine and circulating wild type virus and the consequences of such recombination, including intrinsic recombination properties of the parent virus used as a vector; sequence relatedness of vector and wild virus; virus host range, pathogenesis and transmission; replication competency of vector in target host; mechanism of vector attenuation; additional factors potentially affecting virulence; and circulation of multiple recombinant vectors in the same target population. Finally, we present some guiding principles for vector design and testing intended to anticipate and mitigate the potential for and consequences of recombination of virus-vectored vaccines with wild type pathogenic virus strains. PMID:27346303

Standard Free Droplet Digital Polymerase Chain Reaction as a New Tool for the Quality Control of High-Capacity Adenoviral Vectors in Small-Scale Preparations

PubMed Central

Boehme, Philip; Stellberger, Thorsten; Solanki, Manish; Zhang, Wenli; Schulz, Eric; Bergmann, Thorsten; Liu, Jing; Doerner, Johannes; Baiker, Armin E.

2015-01-01

Abstract High-capacity adenoviral vectors (HCAdVs) are promising tools for gene therapy as well as for genetic engineering. However, one limitation of the HCAdV vector system is the complex, time-consuming, and labor-intensive production process and the following quality control procedure. Since HCAdVs are deleted for all viral coding sequences, a helper virus (HV) is needed in the production process to provide the sequences for all viral proteins in trans. For the purification procedure of HCAdV, cesium chloride density gradient centrifugation is usually performed followed by buffer exchange using dialysis or comparable methods. However, performing these steps is technically difficult, potentially error-prone, and not scalable. Here, we establish a new protocol for small-scale production of HCAdV based on commercially available adenovirus purification systems and a standard method for the quality control of final HCAdV preparations. For titration of final vector preparations, we established a droplet digital polymerase chain reaction (ddPCR) that uses a standard free-end-point PCR in small droplets of defined volume. By using different probes, this method is capable of detecting and quantifying HCAdV and HV in one reaction independent of reference material, rendering this method attractive for accurately comparing viral titers between different laboratories. In summary, we demonstrate that it is possible to produce HCAdV in a small scale of sufficient quality and quantity to perform experiments in cell culture, and we established a reliable protocol for vector titration based on ddPCR. Our method significantly reduces time and required equipment to perform HCAdV production. In the future the ddPCR technology could be advantageous for titration of other viral vectors commonly used in gene therapy. PMID:25640117

All That Glisters Is Not Gold: Sampling-Process Uncertainty in Disease-Vector Surveys with False-Negative and False-Positive Detections

PubMed Central

Abad-Franch, Fernando; Valença-Barbosa, Carolina; Sarquis, Otília; Lima, Marli M.

2014-01-01

Background Vector-borne diseases are major public health concerns worldwide. For many of them, vector control is still key to primary prevention, with control actions planned and evaluated using vector occurrence records. Yet vectors can be difficult to detect, and vector occurrence indices will be biased whenever spurious detection/non-detection records arise during surveys. Here, we investigate the process of Chagas disease vector detection, assessing the performance of the surveillance method used in most control programs – active triatomine-bug searches by trained health agents. Methodology/Principal Findings Control agents conducted triplicate vector searches in 414 man-made ecotopes of two rural localities. Ecotope-specific ‘detection histories’ (vectors or their traces detected or not in each individual search) were analyzed using ordinary methods that disregard detection failures and multiple detection-state site-occupancy models that accommodate false-negative and false-positive detections. Mean (±SE) vector-search sensitivity was ∼0.283±0.057. Vector-detection odds increased as bug colonies grew denser, and were lower in houses than in most peridomestic structures, particularly woodpiles. False-positive detections (non-vector fecal streaks misidentified as signs of vector presence) occurred with probability ∼0.011±0.008. The model-averaged estimate of infestation (44.5±6.4%) was ∼2.4–3.9 times higher than naïve indices computed assuming perfect detection after single vector searches (11.4–18.8%); about 106–137 infestation foci went undetected during such standard searches. Conclusions/Significance We illustrate a relatively straightforward approach to addressing vector detection uncertainty under realistic field survey conditions. Standard vector searches had low sensitivity except in certain singular circumstances. Our findings suggest that many infestation foci may go undetected during routine surveys, especially when vector density is low. Undetected foci can cause control failures and induce bias in entomological indices; this may confound disease risk assessment and mislead program managers into flawed decision making. By helping correct bias in naïve indices, the approach we illustrate has potential to critically strengthen vector-borne disease control-surveillance systems. PMID:25233352

Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem.

PubMed

Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

2018-02-21

Quantum mechanical calculations of ro-vibrational energies of CH 4 , CHD 3 , CH 3 D, and CH 3 F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH 3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH 3 . Euler angles specifying the orientation of a frame attached to CH 3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH 4 , CHD 3 , and CH 3 D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH 3 F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem

NASA Astrophysics Data System (ADS)

Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H.; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

2018-02-01

Quantum mechanical calculations of ro-vibrational energies of CH4, CHD3, CH3D, and CH3F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH3. Euler angles specifying the orientation of a frame attached to CH3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH4, CHD3, and CH3D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH3F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

A Semi-Vectorization Algorithm to Synthesis of Gravitational Anomaly Quantities on the Earth

NASA Astrophysics Data System (ADS)

Abdollahzadeh, M.; Eshagh, M.; Najafi Alamdari, M.

2009-04-01

The Earth's gravitational potential can be expressed by the well-known spherical harmonic expansion. The computational time of summing up this expansion is an important practical issue which can be reduced by an efficient numerical algorithm. This paper proposes such a method for block-wise synthesizing the anomaly quantities on the Earth surface using vectorization. Fully-vectorization means transformation of the summations to the simple matrix and vector products. It is not a practical for the matrices with large dimensions. Here a semi-vectorization algorithm is proposed to avoid working with large vectors and matrices. It speeds up the computations by using one loop for the summation either on degrees or on orders. The former is a good option to synthesize the anomaly quantities on the Earth surface considering a digital elevation model (DEM). This approach is more efficient than the two-step method which computes the quantities on the reference ellipsoid and continues them upward to the Earth surface. The algorithm has been coded in MATLAB which synthesizes a global grid of 5′Ã- 5′ (corresponding 9 million points) of gravity anomaly or geoid height using a geopotential model to degree 360 in 10000 seconds by an ordinary computer with 2G RAM.

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

Applications of lentiviral vectors in molecular imaging.

PubMed

Chatterjee, Sushmita; De, Abhijit

2014-06-01

Molecular imaging provides the ability of simultaneous visual and quantitative estimation of long term gene expression directly from living organisms. To reveal the kinetics of gene expression by imaging method, often sustained expression of the transgene is required. Lentiviral vectors have been extensively used over last fifteen years for delivery of a transgene in a wide variety of cell types. Lentiviral vectors have the well known advantages such as sustained transgene delivery through stable integration into the host genome, the capability of infecting non-dividing and dividing cells, broad tissue tropism, a reasonably large carrying capacity for delivering therapeutic and reporter gene combinations. Additionally, they do not express viral proteins during transduction, have a potentially safe integration site profile, and a relatively easy system for vector manipulation and infective viral particle production. As a result, lentiviral vector mediated therapeutic and imaging reporter gene delivery to various target organs holds promise for the future treatment. In this review, we have conducted a brief survey of important lentiviral vector developments in diverse biomedical fields including reproductive biology.

Evolutionary decay and the prospects for long-term disease intervention using engineered insect vectors

PubMed Central

2015-01-01

After a long history of applying the sterile insect technique to suppress populations of disease vectors and agricultural pests, there is growing interest in using genetic engineering both to improve old methods and to enable new methods. The two goals of interventions are to suppress populations, possibly eradicating a species altogether, or to abolish the vector’s competence to transmit a parasite. New methods enabled by genetic engineering include the use of selfish genes toward either goal as well as a variety of killer-rescue systems that could be used for vector competence reduction. This article reviews old and new methods with an emphasis on the potential for evolution of resistance to these strategies. Established methods of population suppression did not obviously face a problem from resistance evolution, but newer technologies might. Resistance to these newer interventions will often be mechanism-specific, and while it is too early to know where resistance evolution will become a problem, it is at least possible to propose properties of interventions that will be more or less effective in blocking resistance evolution. PMID:26160736

Transport in a magnetic field modulated graphene superlattice.

PubMed

Li, Yu-Xian

2010-01-13

Using the transfer matrix method, we study the transport properties through a magnetic field modulated graphene superlattice. It is found that the electrostatic barrier, the magnetic vector potential, and the number of wells in a superlattice modify the transmission remarkably. The angular dependent transmission is blocked by the magnetic vector potential because of the appearance of the evanescent states at certain incident angles, and the region of Klein tunneling shifts to the left. The angularly averaged conductivities exhibit oscillatory behavior. The magnitude and period of oscillation depend sensitively on the height of the electrostatic barrier, the number of wells, and the strength of the modulated magnetic field.

Image Coding Based on Address Vector Quantization.

NASA Astrophysics Data System (ADS)

Feng, Yushu

Image coding is finding increased application in teleconferencing, archiving, and remote sensing. This thesis investigates the potential of Vector Quantization (VQ), a relatively new source coding technique, for compression of monochromatic and color images. Extensions of the Vector Quantization technique to the Address Vector Quantization method have been investigated. In Vector Quantization, the image data to be encoded are first processed to yield a set of vectors. A codeword from the codebook which best matches the input image vector is then selected. Compression is achieved by replacing the image vector with the index of the code-word which produced the best match, the index is sent to the channel. Reconstruction of the image is done by using a table lookup technique, where the label is simply used as an address for a table containing the representative vectors. A code-book of representative vectors (codewords) is generated using an iterative clustering algorithm such as K-means, or the generalized Lloyd algorithm. A review of different Vector Quantization techniques are given in chapter 1. Chapter 2 gives an overview of codebook design methods including the Kohonen neural network to design codebook. During the encoding process, the correlation of the address is considered and Address Vector Quantization is developed for color image and monochrome image coding. Address VQ which includes static and dynamic processes is introduced in chapter 3. In order to overcome the problems in Hierarchical VQ, Multi-layer Address Vector Quantization is proposed in chapter 4. This approach gives the same performance as that of the normal VQ scheme but the bit rate is about 1/2 to 1/3 as that of the normal VQ method. In chapter 5, a Dynamic Finite State VQ based on a probability transition matrix to select the best subcodebook to encode the image is developed. In chapter 6, a new adaptive vector quantization scheme, suitable for color video coding, called "A Self -Organizing Adaptive VQ Technique" is presented. In addition to chapters 2 through 6 which report on new work, this dissertation includes one chapter (chapter 1) and part of chapter 2 which review previous work on VQ and image coding, respectively. Finally, a short discussion of directions for further research is presented in conclusion.

SVPWM Technique with Varying DC-Link Voltage for Common Mode Voltage Reduction in a Matrix Converter and Analytical Estimation of its Output Voltage Distortion

NASA Astrophysics Data System (ADS)

Padhee, Varsha

Common Mode Voltage (CMV) in any power converter has been the major contributor to premature motor failures, bearing deterioration, shaft voltage build up and electromagnetic interference. Intelligent control methods like Space Vector Pulse Width Modulation (SVPWM) techniques provide immense potential and flexibility to reduce CMV, thereby targeting all the afore mentioned problems. Other solutions like passive filters, shielded cables and EMI filters add to the volume and cost metrics of the entire system. Smart SVPWM techniques therefore, come with a very important advantage of being an economical solution. This thesis discusses a modified space vector technique applied to an Indirect Matrix Converter (IMC) which results in the reduction of common mode voltages and other advanced features. The conventional indirect space vector pulse-width modulation (SVPWM) method of controlling matrix converters involves the usage of two adjacent active vectors and one zero vector for both rectifying and inverting stages of the converter. By suitable selection of space vectors, the rectifying stage of the matrix converter can generate different levels of virtual DC-link voltage. This capability can be exploited for operation of the converter in different ranges of modulation indices for varying machine speeds. This results in lower common mode voltage and improves the harmonic spectrum of the output voltage, without increasing the number of switching transitions as compared to conventional modulation. To summarize it can be said that the responsibility of formulating output voltages with a particular magnitude and frequency has been transferred solely to the rectifying stage of the IMC. Estimation of degree of distortion in the three phase output voltage is another facet discussed in this thesis. An understanding of the SVPWM technique and the switching sequence of the space vectors in detail gives the potential to estimate the RMS value of the switched output voltage of any converter. This conceivably aids the sizing and design of output passive filters. An analytical estimation method has been presented to achieve this purpose for am IMC. Knowledge of the fundamental component in output voltage can be utilized to calculate its Total Harmonic Distortion (THD). The effectiveness of the proposed SVPWM algorithms and the analytical estimation technique is substantiated by simulations in MATLAB / Simulink and experiments on a laboratory prototype of the IMC. Proper comparison plots have been provided to contrast the performance of the proposed methods with the conventional SVPWM method. The behavior of output voltage distortion and CMV with variation in operating parameters like modulation index and output frequency has also been analyzed.

The poultry red mite (Dermanyssus gallinae): a potential vector of pathogenic agents.

PubMed

Valiente Moro, Claire; De Luna, Carlos J; Tod, Alexander; Guy, Jonathan H; Sparagano, Olivier A E; Zenner, Lionel

2009-06-01

The poultry red mite, D. gallinae has been involved in the transmission of many pathogenic agents, responsible for serious diseases both in animals and humans. Nowadays, few effective methods are available to control the ectoparasite in poultry farms. Consequently, this is an emerging problem which must be taken into account to maintain good health in commercial egg production. This paper addresses the vector capacity of the ectoparasite with special emphasis on salmonellae, pathogenic agents responsible for many of the most important outbreaks of food-borne diseases worlwide. It has been experimentally shown that D. gallinae could act as a biological vector of S. enteritidis and natural carriage of these bacteria by the mite on poultry premises has also been reported. It was also found that D. gallinae carried other pathogens such as E. coli, Shigella sp., and Staphylococcus, thus increasing the list of pathogenic agents potentially transmitted by the mite.

Serendipity in dark photon searches

NASA Astrophysics Data System (ADS)

Ilten, Philip; Soreq, Yotam; Williams, Mike; Xue, Wei

2018-06-01

Searches for dark photons provide serendipitous discovery potential for other types of vector particles. We develop a framework for recasting dark photon searches to obtain constraints on more general theories, which includes a data-driven method for determining hadronic decay rates. We demonstrate our approach by deriving constraints on a vector that couples to the B-L current, a leptophobic B boson that couples directly to baryon number and to leptons via B- γ kinetic mixing, and on a vector that mediates a protophobic force. Our approach can easily be generalized to any massive gauge boson with vector couplings to the Standard Model fermions, and software to perform any such recasting is provided at https://gitlab.com/philten/darkcast .

The magnetic universe through vector potential SPMHD simulations

NASA Astrophysics Data System (ADS)

Stasyszyn, F. A.

2017-10-01

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

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.

UAV formation control design with obstacle avoidance in dynamic three-dimensional environment.

PubMed

Chang, Kai; Xia, Yuanqing; Huang, Kaoli

2016-01-01

This paper considers the artificial potential field method combined with rotational vectors for a general problem of multi-unmanned aerial vehicle (UAV) systems tracking a moving target in dynamic three-dimensional environment. An attractive potential field is generated between the leader and the target. It drives the leader to track the target based on the relative position of them. The other UAVs in the formation are controlled to follow the leader by the attractive control force. The repulsive force affects among the UAVs to avoid collisions and distribute the UAVs evenly on the spherical surface whose center is the leader-UAV. Specific orders or positions of the UAVs are not required. The trajectories of avoidance obstacle can be obtained through two kinds of potential field with rotation vectors. Every UAV can choose the optimal trajectory to avoid the obstacle and reconfigure the formation after passing the obstacle. Simulations study on UAV are presented to demonstrate the effectiveness of proposed method.

Field investigation on the repellent activity of some aromatic plants by traditional means against Anopheles arabiensis and An. pharoensis (Diptera: Culicidae) around Koka, central Ethiopia.

PubMed

Dugassa, Sisay; Medhin, Girmay; Balkew, Meshesha; Seyoum, Aklilu; Gebre-Michael, Teshome

2009-10-01

A study was undertaken to evaluate the impact of traditional application methods of mosquito repellent plants in the reduction of the human-vector contact of malaria vectors in central Ethiopia. The plants (Corymbia citriodora, Eucalyptus camaldulensis, Ocimum suave and Ocimum basilicum) were tested by thermal expulsion and direct burning on traditional stoves in the field against two important malaria vectors in Ethiopia (Anopheles arabiensis and An. pharoensis). A Latin-square design was applied for randomly assigning the treatment plants and control to experimental houses over different nights. The percentage repellency of each candidate plant by both application methods was estimated from the catches of mosquitoes in the treatment and control houses. On direct burning of the plants, O. basilicum showed the highest percentage repellency (73.11%, P<0.001) and E. camaldulensis the least repellency (65.29%, P<0.001) against An. arabiensis. By the same method of application, C. citriodora on the other hand gave the highest repellency (72.87%, P<0.001) while E. camaldulensis was still the least repellent plant (66.60%, P<0.001) against An. pharoensis. On thermal expulsion, C. citriodora exhibited the highest repellency (78.69%, P<0.001) while E. camaldulensis was the lowest repellent plant (71.91%, P<0.001) against An. arabiensis. Against An. pharoensis, C. citriodora gave the highest repellency (72.9%, P<0.001) while E. camaldulensis still gave the least repellency (72.2%, P<0.001) on the same method of application. All the tested plants by both methods of application gave partial but significant protection (>65%) against the house-entry and biting of two important malaria vectors in Ethiopia, and thus have a potential to be used at least as supplements to other control methods. However, feasibility and actual impact on disease transmission need to be known on these and other potentially useful plants.

Lentiviral vector-mediated genetic modification of human neural progenitor cells for ex vivo gene therapy.

PubMed

Capowski, Elizabeth E; Schneider, Bernard L; Ebert, Allison D; Seehus, Corey R; Szulc, Jolanta; Zufferey, Romain; Aebischer, Patrick; Svendsen, Clive N

2007-07-30

Human neural progenitor cells (hNPC) hold great potential as an ex vivo system for delivery of therapeutic proteins to the central nervous system. When cultured as aggregates, termed neurospheres, hNPC are capable of significant in vitro expansion. In the current study, we present a robust method for lentiviral vector-mediated gene delivery into hNPC that maintains the differentiation and proliferative properties of neurosphere cultures while minimizing the amount of viral vector used and controlling the number of insertion sites per population. This method results in long-term, stable expression even after differentiation of the hNPC to neurons and astrocytes and allows for generation of equivalent transgenic populations of hNPC. In addition, the in vitro analysis presented predicts the behavior of transgenic lines in vivo when transplanted into a rodent model of Parkinson's disease. The methods presented provide a powerful tool for assessing the impact of factors such as promoter systems or different transgenes on the therapeutic utility of these cells.

Solving magnetostatic field problems with NASTRAN

NASA Technical Reports Server (NTRS)

Hurwitz, M. M.; Schroeder, E. A.

1978-01-01

Determining the three-dimensional magnetostatic field in current-induced situations has usually involved vector potentials, which can lead to excessive computational times. How such magnetic fields may be determined using scalar potentials is reviewed. It is shown how the heat transfer capability of NASTRAN level 17 was modified to take advantage of the new method.

Efficient solution of 3D electromagnetic eddy-current problems within the finite volume framework of OpenFOAM

NASA Astrophysics Data System (ADS)

Beckstein, Pascal; Galindo, Vladimir; Vukčević, Vuko

2017-09-01

Eddy-current problems occur in a wide range of industrial and metallurgical applications where conducting material is processed inductively. Motivated by realising coupled multi-physics simulations, we present a new method for the solution of such problems in the finite volume framework of foam-extend, an extended version of the very popular OpenFOAM software. The numerical procedure involves a semi-coupled multi-mesh approach to solve Maxwell's equations for non-magnetic materials by means of the Coulomb gauged magnetic vector potential A and the electric scalar potential ϕ. The concept is further extended on the basis of the impressed and reduced magnetic vector potential and its usage in accordance with Biot-Savart's law to achieve a very efficient overall modelling even for complex three-dimensional geometries. Moreover, we present a special discretisation scheme to account for possible discontinuities in the electrical conductivity. To complement our numerical method, an extensive validation is completing the paper, which provides insight into the behaviour and the potential of our approach.

Zoom in at African country level: potential climate induced changes in areas of suitability for survival of malaria vectors.

PubMed

Tonnang, Henri E Z; Tchouassi, David P; Juarez, Henry S; Igweta, Lilian K; Djouaka, Rousseau F

2014-05-07

Predicting anopheles vectors' population densities and boundary shifts is crucial in preparing for malaria risks and unanticipated outbreaks. Although shifts in the distribution and boundaries of the major malaria vectors (Anopheles gambiae s.s. and An. arabiensis) across Africa have been predicted, quantified areas of absolute change in zone of suitability for their survival have not been defined. In this study, we have quantified areas of absolute change conducive for the establishment and survival of these vectors, per African country, under two climate change scenarios and based on our findings, highlight practical measures for effective malaria control in the face of changing climatic patterns. We developed a model using CLIMEX simulation platform to estimate the potential geographical distribution and seasonal abundance of these malaria vectors in relation to climatic factors (temperature, rainfall and relative humidity). The model yielded an eco-climatic index (EI) describing the total favourable geographical locations for the species. The EI values were classified and exported to a GIS package. Using ArcGIS, the EI shape points were clipped to the extent of Africa and then converted to a raster layer using Inverse Distance Weighted (IDW) interpolation method. Generated maps were then transformed into polygon-based geo-referenced data set and their areas computed and expressed in square kilometers (km(2)). Five classes of EI were derived indicating the level of survivorship of these malaria vectors. The proportion of areas increasing or decreasing in level of survival of these malaria vectors will be more pronounced in eastern and southern African countries than those in western Africa. Angola, Ethiopia, Kenya, Mozambique, Tanzania, South Africa and Zambia appear most likely to be affected in terms of absolute change of malaria vectors suitability zones under the selected climate change scenarios. The potential shifts of these malaria vectors have implications for human exposure to malaria, as recrudescence of the disease is likely to be recorded in several new areas and regions. Therefore, the need to develop, compile and share malaria preventive measures, which can be adapted to different climatic scenarios, remains crucial.

RNA Interference in Infectious Tropical Diseases

PubMed Central

Hong, Young S.

2008-01-01

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi. PMID:18344671

In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering

PubMed Central

Wu, Yuyong; You, Lili; Li, Shengchun; Ma, Meiqi; Wu, Mengting; Ma, Lixin; Bock, Ralph; Chang, Ling; Zhang, Jiang

2017-01-01

Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC) technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP) expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5′ untranslated region (UTR) from gene10 of bacteriophage T7 and the transcript-stabilizing 3′UTR from the E. coli ribosomal RNA operon rrnB. Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids. PMID:28871270

In vivo Assembly in Escherichia coli of Transformation Vectors for Plastid Genome Engineering.

PubMed

Wu, Yuyong; You, Lili; Li, Shengchun; Ma, Meiqi; Wu, Mengting; Ma, Lixin; Bock, Ralph; Chang, Ling; Zhang, Jiang

2017-01-01

Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps. In this study, we describe the adoption of an in vivo Escherichia coli cloning (iVEC) technology to quickly assemble a plastid transformation vector. The method enables simple and seamless build-up of a complete plastid transformation vector from five DNA fragments in a single step. The vector assembled for demonstration purposes contains an enhanced green fluorescent protein (GFP) expression cassette, in which the gfp transgene is driven by the tobacco plastid ribosomal RNA operon promoter fused to the 5' untranslated region (UTR) from gene10 of bacteriophage T7 and the transcript-stabilizing 3'UTR from the E. coli ribosomal RNA operon rrnB . Successful transformation of the tobacco plastid genome was verified by Southern blot analysis and seed assays. High-level expression of the GFP reporter in the transplastomic plants was visualized by confocal microscopy and Coomassie staining, and GFP accumulation was ~9% of the total soluble protein. The iVEC method represents a simple and efficient approach for construction of plastid transformation vector, and offers great potential for the assembly of increasingly complex vectors for synthetic biology applications in plastids.

Opportunities for Improved Chagas Disease Vector Control Based on Knowledge, Attitudes and Practices of Communities in the Yucatan Peninsula, Mexico

PubMed Central

Rosecrans, Kathryn; Cruz-Martin, Gabriela; King, Ashley; Dumonteil, Eric

2014-01-01

Background Chagas disease is a vector-borne parasitic disease of major public health importance. Current prevention efforts are based on triatomine vector control to reduce transmission to humans. Success of vector control interventions depends on their acceptability and value to affected communities. We aimed to identify opportunities for and barriers to improved vector control strategies in the Yucatan peninsula, Mexico. Methodology/principal findings We employed a sequence of qualitative and quantitative research methods to investigate knowledge, attitudes and practices surrounding Chagas disease, triatomines and vector control in three rural communities. Our combined data show that community members are well aware of triatomines and are knowledgeable about their habits. However, most have a limited understanding of the transmission dynamics and clinical manifestations of Chagas disease. While triatomine control is not a priority for community members, they frequently use domestic insecticide products including insecticide spray, mosquito coils and plug-in repellents. Families spend about $32 US per year on these products. Alternative methods such as yard cleaning and window screens are perceived as desirable and potentially more effective. Screens are nonetheless described as unaffordable, in spite of a cost comparable to the average annual spending on insecticide products. Conclusion/Significance Further education campaigns and possibly financing schemes may lead families to redirect their current vector control spending from insecticide products to window screens. Also, synergism with mosquito control efforts should be further explored to motivate community involvement and ensure sustainability of Chagas disease vector control. PMID:24676038

Modification and identification of a vector for making a large phage antibody library.

PubMed

Zhang, Guo-min; Chen, Yü-ping; Guan, Yuan-zhi; Wang, Yan; An, Yun-qing

2007-11-20

The large phage antibody library is used to obtain high-affinity human antibody, and the Loxp/cre site-specific recombination system is a potential method for constructing a large phage antibody library. In the present study, a phage antibody library vector pDF was reconstructed to construct diabody more quickly and conveniently without injury to homologous recombination and the expression function of the vector and thus to integrate construction of the large phage antibody library with the preparation of diabodies. scFv was obtained by overlap polymerase chain reaction (PCR) amplification with the newly designed VL and VH extension primers. loxp511 was flanked by VL and VH and the endonuclease ACC III encoding sequences were introduced on both sides of loxp511. scFv was cloned into the vector pDF to obtain the vector pDscFv. The vector expression function was identified and the feasibility of diabody preparation was evaluated. A large phage antibody library was constructed in pDscFv. Several antigens were used to screen the antibody library and the quality of the antibody library was evaluated. The phage antibody library expression vector pDscFv was successfully constructed and confirmed to express functional scFv. The large phage antibody library constructed using this vector was of high diversity. Screening of the library on 6 antigens confirmed the generation of specific antibodies to these antigens. Two antibodies were subjected to enzymatic digestion and were prepared into diabody with functional expression. The reconstructed vector pDscFv retains its recombination capability and expression function and can be used to construct large phage antibody libraries. It can be used as a convenient and quick method for preparing diabodies after simple enzymatic digestion, which facilitates clinical trials and application of antibody therapy.

Thrust vector control algorithm design for the Cassini spacecraft

NASA Technical Reports Server (NTRS)

Enright, Paul J.

1993-01-01

This paper describes a preliminary design of the thrust vector control algorithm for the interplanetary spacecraft, Cassini. Topics of discussion include flight software architecture, modeling of sensors, actuators, and vehicle dynamics, and controller design and analysis via classical methods. Special attention is paid to potential interactions with structural flexibilities and propellant dynamics. Controller performance is evaluated in a simulation environment built around a multi-body dynamics model, which contains nonlinear models of the relevant hardware and preliminary versions of supporting attitude determination and control functions.

Application of support vector machines for copper potential mapping in Kerman region, Iran

NASA Astrophysics Data System (ADS)

Shabankareh, Mahdi; Hezarkhani, Ardeshir

2017-04-01

The first step in systematic exploration studies is mineral potential mapping, which involves classification of the study area to favorable and unfavorable parts. Support vector machines (SVM) are designed for supervised classification based on statistical learning theory. This method named support vector classification (SVC). This paper describes SVC model, which combine exploration data in the regional-scale for copper potential mapping in Kerman copper bearing belt in south of Iran. Data layers or evidential maps were in six datasets namely lithology, tectonic, airborne geophysics, ferric alteration, hydroxide alteration and geochemistry. The SVC modeling result selected 2220 pixels as favorable zones, approximately 25 percent of the study area. Besides, 66 out of 86 copper indices, approximately 78.6% of all, were located in favorable zones. Other main goal of this study was to determine how each input affects favorable output. For this purpose, the histogram of each normalized input data to its favorable output was drawn. The histograms of each input dataset for favorable output showed that each information layer had a certain pattern. These patterns of SVC results could be considered as regional copper exploration characteristics.

Accurate computation of gravitational field of a tesseroid

NASA Astrophysics Data System (ADS)

Fukushima, Toshio

2018-02-01

We developed an accurate method to compute the gravitational field of a tesseroid. The method numerically integrates a surface integral representation of the gravitational potential of the tesseroid by conditionally splitting its line integration intervals and by using the double exponential quadrature rule. Then, it evaluates the gravitational acceleration vector and the gravity gradient tensor by numerically differentiating the numerically integrated potential. The numerical differentiation is conducted by appropriately switching the central and the single-sided second-order difference formulas with a suitable choice of the test argument displacement. If necessary, the new method is extended to the case of a general tesseroid with the variable density profile, the variable surface height functions, and/or the variable intervals in longitude or in latitude. The new method is capable of computing the gravitational field of the tesseroid independently on the location of the evaluation point, namely whether outside, near the surface of, on the surface of, or inside the tesseroid. The achievable precision is 14-15 digits for the potential, 9-11 digits for the acceleration vector, and 6-8 digits for the gradient tensor in the double precision environment. The correct digits are roughly doubled if employing the quadruple precision computation. The new method provides a reliable procedure to compute the topographic gravitational field, especially that near, on, and below the surface. Also, it could potentially serve as a sure reference to complement and elaborate the existing approaches using the Gauss-Legendre quadrature or other standard methods of numerical integration.

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning.

PubMed

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝ d , and the dictionary is learned from the training data using the vector space structure of ℝ d and its Euclidean L 2 -metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis.

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning

PubMed Central

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝd, and the dictionary is learned from the training data using the vector space structure of ℝd and its Euclidean L2-metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis. PMID:24129583

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.

Simple algorithm for improved security in the FDDI protocol

NASA Astrophysics Data System (ADS)

Lundy, G. M.; Jones, Benjamin

1993-02-01

We propose a modification to the Fiber Distributed Data Interface (FDDI) protocol based on a simple algorithm which will improve confidential communication capability. This proposed modification provides a simple and reliable system which exploits some of the inherent security properties in a fiber optic ring network. This method differs from conventional methods in that end to end encryption can be facilitated at the media access control sublayer of the data link layer in the OSI network model. Our method is based on a variation of the bit stream cipher method. The transmitting station takes the intended confidential message and uses a simple modulo two addition operation against an initialization vector. The encrypted message is virtually unbreakable without the initialization vector. None of the stations on the ring will have access to both the encrypted message and the initialization vector except the transmitting and receiving stations. The generation of the initialization vector is unique for each confidential transmission and thus provides a unique approach to the key distribution problem. The FDDI protocol is of particular interest to the military in terms of LAN/MAN implementations. Both the Army and the Navy are considering the standard as the basis for future network systems. A simple and reliable security mechanism with the potential to support realtime communications is a necessary consideration in the implementation of these systems. The proposed method offers several advantages over traditional methods in terms of speed, reliability, and standardization.

Light bullets in coupled nonlinear Schrödinger equations with variable coefficients and a trapping potential.

PubMed

Xu, Si-Liu; Zhao, Guo-Peng; Belić, Milivoj R; He, Jun-Rong; Xue, Li

2017-04-17

We analyze three-dimensional (3D) vector solitary waves in a system of coupled nonlinear Schrödinger equations with spatially modulated diffraction and nonlinearity, under action of a composite self-consistent trapping potential. Exact vector solitary waves, or light bullets (LBs), are found using the self-similarity method. The stability of vortex 3D LB pairs is examined by direct numerical simulations; the results show that only low-order vortex soliton pairs with the mode parameter values n ≤ 1, l ≤ 1 and m = 0 can be supported by the spatially modulated interaction in the composite trap. Higher-order LBs are found unstable over prolonged distances.

The ecological foundations of transmission potential and vector-borne disease in urban landscapes.

PubMed

LaDeau, Shannon L; Allan, Brian F; Leisnham, Paul T; Levy, Michael Z

2015-07-01

Urban transmission of arthropod-vectored disease has increased in recent decades. Understanding and managing transmission potential in urban landscapes requires integration of sociological and ecological processes that regulate vector population dynamics, feeding behavior, and vector-pathogen interactions in these unique ecosystems. Vectorial capacity is a key metric for generating predictive understanding about transmission potential in systems with obligate vector transmission. This review evaluates how urban conditions, specifically habitat suitability and local temperature regimes, and the heterogeneity of urban landscapes can influence the biologically-relevant parameters that define vectorial capacity: vector density, survivorship, biting rate, extrinsic incubation period, and vector competence.Urban landscapes represent unique mosaics of habitat. Incidence of vector-borne disease in urban host populations is rarely, if ever, evenly distributed across an urban area. The persistence and quality of vector habitat can vary significantly across socio-economic boundaries to influence vector species composition and abundance, often generating socio-economically distinct gradients of transmission potential across neighborhoods.Urban regions often experience unique temperature regimes, broadly termed urban heat islands (UHI). Arthropod vectors are ectothermic organisms and their growth, survival, and behavior are highly sensitive to environmental temperatures. Vector response to UHI conditions is dependent on regional temperature profiles relative to the vector's thermal performance range. In temperate climates UHI can facilitate increased vector development rates while having countervailing influence on survival and feeding behavior. Understanding how urban heat island (UHI) conditions alter thermal and moisture constraints across the vector life cycle to influence transmission processes is an important direction for both empirical and modeling research.There remain persistent gaps in understanding of vital rates and drivers in mosquito-vectored disease systems, and vast holes in understanding for other arthropod vectored diseases. Empirical studies are needed to better understand the physiological constraints and socio-ecological processes that generate heterogeneity in critical transmission parameters, including vector survival and fitness. Likewise, laboratory experiments and transmission models must evaluate vector response to realistic field conditions, including variability in sociological and environmental conditions.

Electron Beam Propagation Through a Magnetic Wiggler with Random Field Errors

DTIC Science & Technology

1989-08-21

Another quantity of interest is the vector potential 6.A,.(:) associated with the field error 6B,,,(:). Defining the normalized vector potentials ba = ebA...then follows that the correlation of the normalized vector potential errors is given by 1 . 12 (-a.(zj)a.,(z2)) = a,k,, dz’ , dz" (bBE(z’)bB , (z")) a2...Throughout the following, terms of order O(z:/z) will be neglected. Similarly, for the y-component of the normalized vector potential errors, one

Loa loa vectors Chrysops spp.: perspectives on research, distribution, bionomics, and implications for elimination of lymphatic filariasis and onchocerciasis.

PubMed

Kelly-Hope, Louise; Paulo, Rossely; Thomas, Brent; Brito, Miguel; Unnasch, Thomas R; Molyneux, David

2017-04-05

Loiasis is a filarial disease caused Loa loa. The main vectors are Chrysops silacea and C. dimidiata which are confined to the tropical rainforests of Central and West Africa. Loiasis is a mild disease, but individuals with high microfilaria loads may suffer from severe adverse events if treated with ivermectin during mass drug administration campaigns for the elimination of lymphatic filariasis and onchocerciasis. This poses significant challenges for elimination programmes and alternative interventions are required in L. loa co-endemic areas. The control of Chrysops has not been considered as a viable cost-effective intervention; we reviewed the current knowledge of Chrysops vectors to assess the potential for control as well as identified areas for future research. We identified 89 primary published documents on the two main L. loa vectors C. silacea and C dimidiata. These were collated into a database summarising the publication, field and laboratory procedures, species distributions, ecology, habitats and methods of vector control. The majority of articles were from the 1950-1960s. Field studies conducted in Cameroon, Democratic Republic of Congo, Equatorial Guinea, Nigeria and Sudan highlighted that C. silacea is the most important and widespread vector. This species breeds in muddy streams or swampy areas of forests or plantations, descends from forest canopies to feed on humans during the day, is more readily adapted to human dwellings and attracted to wood fires. Main vector targeted measures proposed to impact on L. loa transmission included personal repellents, household screening, indoor residual spraying, community-based environmental management, adulticiding and larviciding. This is the first comprehensive review of the major L. loa vectors for several decades. It highlights key vector transmission characteristics that may be targeted for vector control providing insights into the potential for integrated vector management, with multiple diseases being targeted simultaneously, with shared human and financial resources and multiple impact. Integrated vector management programmes for filarial infections, especially in low transmission areas of onchocerciasis, require innovative approaches and alternative strategies if the elimination targets established by the World Health Organization are to be achieved.

The stethoscope in the Emergency Department: a vector of infection?

PubMed Central

Núñez, S.; Moreno, A.; Green, K.; Villar, J.

2000-01-01

The purposes of this study were to determine whether microorganisms can be isolated from the membranes of stethoscopes used by clinicians and nurses, and to analyse whether or not the degree of bacterial colonization could be reduced with different cleaning methods. We designed a transversal before-after study in which 122 stethoscopes were examined. Coagulase negative staphylococci (which are also potentially pathogenic microorganisms) were isolated together with 13 other potentially pathogenic microorganisms, including S. aureus, Acinetobacter sp. and Enterobacter agglomerans. The most effective antiseptic was propyl alcohol. Analysis of the cleaning habits of the Emergency Department (ED) staff, showed that 45% cleaned the stethoscope annually or never. The isolation of potentially pathogenic microorganisms suggests that the stethoscope must be considered as a potential vector of infection not only in the ED but also in other hospital wards and out-patient clinics. PMID:10813148

Combined magnetic vector-scalar potential finite element computation of 3D magnetic field and performance of modified Lundell alternators in Space Station applications. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Wang, Ren H.

1991-01-01

A method of combined use of magnetic vector potential (MVP) based finite element (FE) formulations and magnetic scalar potential (MSP) based FE formulations for computation of three-dimensional (3D) magnetostatic fields is developed. This combined MVP-MSP 3D-FE method leads to considerable reduction by nearly a factor of 3 in the number of unknowns in comparison to the number of unknowns which must be computed in global MVP based FE solutions. This method allows one to incorporate portions of iron cores sandwiched in between coils (conductors) in current-carrying regions. Thus, it greatly simplifies the geometries of current carrying regions (in comparison with the exclusive MSP based methods) in electric machinery applications. A unique feature of this approach is that the global MSP solution is single valued in nature, that is, no branch cut is needed. This is again a superiority over the exclusive MSP based methods. A Newton-Raphson procedure with a concept of an adaptive relaxation factor was developed and successfully used in solving the 3D-FE problem with magnetic material anisotropy and nonlinearity. Accordingly, this combined MVP-MSP 3D-FE method is most suited for solution of large scale global type magnetic field computations in rotating electric machinery with very complex magnetic circuit geometries, as well as nonlinear and anisotropic material properties.

3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides.

PubMed

Reißer, Sabine; Strandberg, Erik; Steinbrecher, Thomas; Ulrich, Anne S

2014-06-03

The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Interframe vector wavelet coding technique

NASA Astrophysics Data System (ADS)

Wus, John P.; Li, Weiping

1997-01-01

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

A regularization method for extrapolation of solar potential magnetic fields

NASA Technical Reports Server (NTRS)

Gary, G. A.; Musielak, Z. E.

1992-01-01

The mathematical basis of a Tikhonov regularization method for extrapolating the chromospheric-coronal magnetic field using photospheric vector magnetograms is discussed. The basic techniques show that the Cauchy initial value problem can be formulated for potential magnetic fields. The potential field analysis considers a set of linear, elliptic partial differential equations. It is found that, by introducing an appropriate smoothing of the initial data of the Cauchy potential problem, an approximate Fourier integral solution is found, and an upper bound to the error in the solution is derived. This specific regularization technique, which is a function of magnetograph measurement sensitivities, provides a method to extrapolate the potential magnetic field above an active region into the chromosphere and low corona.

Path planning for assembly of strut-based structures. Thesis

NASA Technical Reports Server (NTRS)

Muenger, Rolf

1991-01-01

A path planning method with collision avoidance for a general single chain nonredundant or redundant robot is proposed. Joint range boundary overruns are also avoided. The result is a sequence of joint vectors which are passed to a trajectory planner. A potential field algorithm in joint space computes incremental joint vectors delta-q = delta-q(sub a) + delta-q(sub c) + delta-q(sub r). Adding delta-q to the robot's current joint vector leads to the next step in the path. Delta-q(sub a) is obtained by computing the minimum norm solution of the underdetermined linear system J delta-q(sub a) = x(sub a) where x(sub a) is a translational and rotational force vector that attracts the robot to its goal position and orientation. J is the manipulator Jacobian. Delta-q(sub c) is a collision avoidance term encompassing collisions between the robot (links and payload) and obstacles in the environment as well as collisions among links and payload of the robot themselves. It is obtained in joint space directly. Delta-q(sub r) is a function of the current joint vector and avoids joint range overruns. A higher level discrete search over candidate safe positions is used to provide alternatives in case the potential field algorithm encounters a local minimum and thus fails to reach the goal. The best first search algorithm A* is used for graph search. Symmetry properties of the payload and equivalent rotations are exploited to further enlarge the number of alternatives passed to the potential field algorithm.

Improving vector-borne pathogen surveillance: A laboratory-based study exploring the potential to detect dengue virus and malaria parasites in mosquito saliva.

PubMed

Melanson, Vanessa R; Jochim, Ryan; Yarnell, Michael; Ferlez, Karen Bingham; Shashikumar, Soumya; Richardson, Jason H

2017-01-01

Vector-borne pathogen surveillance programmes typically rely on the collection of large numbers of potential vectors followed by screening protocols focused on detecting pathogens in the arthropods. These processes are laborious, time consuming, expensive, and require screening of large numbers of samples. To streamline the surveillance process, increase sample throughput, and improve cost-effectiveness, a method to detect dengue virus and malaria parasites (Plasmodium falciparum) by leveraging the sugar-feeding behaviour of mosquitoes and their habit of expectorating infectious agents in their saliva during feeding was investigated in this study. Dengue virus 2 (DENV-2) infected female Aedes aegypti mosquitoes and P. falciparum infected female Anopheles stephensi mosquitoes were allowed to feed on honey coated Flinders Technical Associates -FTA® cards dyed with blue food colouring. The feeding resulted in deposition of saliva containing either DENV-2 particles or P. falciparum sporozoites onto the FTA card. Nucleic acid was extracted from each card and the appropriate real-time PCR (qPCR) assay was run to detect the pathogen of interest. As little as one plaque forming unit (PFU) of DENV-2 and as few as 60 P. falciparum parasites deposited on FTA cards from infected mosquitoes were detected via qPCR. Hence, their use to collect mosquito saliva for pathogen detection is a relevant technique for vector surveillance. This study provides laboratory confirmation that FTA cards can be used to capture and stabilize expectorated DENV-2 particles and P. falciparum sporozoites from infectious, sugar-feeding mosquitoes in very low numbers. Thus, the FTA card-based mosquito saliva capture method offers promise to overcome current limitations and revolutionize traditional mosquito-based pathogen surveillance programmes. Field testing and further method development are required to optimize this strategy.

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.

Optimal Cloning of PCR Fragments by Homologous Recombination in Escherichia coli

PubMed Central

Jacobus, Ana Paula; Gross, Jeferson

2015-01-01

PCR fragments and linear vectors containing overlapping ends are easily assembled into a propagative plasmid by homologous recombination in Escherichia coli. Although this gap-repair cloning approach is straightforward, its existence is virtually unknown to most molecular biologists. To popularize this method, we tested critical parameters influencing the efficiency of PCR fragments cloning into PCR-amplified vectors by homologous recombination in the widely used E. coli strain DH5α. We found that the number of positive colonies after transformation increases with the length of overlap between the PCR fragment and linear vector. For most practical purposes, a 20 bp identity already ensures high-cloning yields. With an insert to vector ratio of 2:1, higher colony forming numbers are obtained when the amount of vector is in the range of 100 to 250 ng. An undesirable cloning background of empty vectors can be minimized during vector PCR amplification by applying a reduced amount of plasmid template or by using primers in which the 5′ termini are separated by a large gap. DpnI digestion of the plasmid template after PCR is also effective to decrease the background of negative colonies. We tested these optimized cloning parameters during the assembly of five independent DNA constructs and obtained 94% positive clones out of 100 colonies probed. We further demonstrated the efficient and simultaneous cloning of two PCR fragments into a vector. These results support the idea that homologous recombination in E. coli might be one of the most effective methods for cloning one or two PCR fragments. For its simplicity and high efficiency, we believe that recombinational cloning in E. coli has a great potential to become a routine procedure in most molecular biology-oriented laboratories. PMID:25774528

Vector potential of houseflies for the bacterium Aeromonas caviae.

PubMed

Nayduch, D; Noblet, G Pittman; Stutzenberger, F J

2002-06-01

Houseflies, Musca domestica Linnaeus (Diptera: Muscidae), have been implicated as vectors or transporters of numerous gastrointestinal pathogens encountered during feeding and ovipositing on faeces. The putative enteropathogen Aeromonas caviae (Proteobacteria: Aeromonadaceae) may be present in faeces of humans and livestock. Recently A. caviae was detected in houseflies by PCR and isolated by culture methods. In this study, we assessed the vector potential of houseflies for A. caviae relative to multiplication and persistence of the bacterium in the fly and to contamination of other flies and food materials. In experimentally fed houseflies, the number of bacteria increased up to 2 days post-ingestion (d PI) and then decreased significantly 3 d PI. A large number of bacteria was detected in the vomitus and faeces of infected flies at 2-3 d PI. The bacteria persisted in flies for up to 8 d PI, but numbers were low. Experimentally infected flies transmitted A. caviae to chicken meat, and transmissibility was directly correlated with exposure time. Flies contaminated the meat for up to 7 d PI; however, a significant decrease in contamination was observed 2-3 d PI. In the fly-to-fly transmission experiments, the transmission of A. caviae was observed and was apparently mediated by flies sharing food. These results support houseflies as potential vectors for A. caviae because the bacterium multiplied, persisted in flies for up to 8 d PI, and could be transmitted to human food items.

Potential mosquito (Diptera:Culicidae) vector of Dirofilaria repens and Dirofilaria immitis in urban areas of Eastern Slovakia.

PubMed

Bocková, Eva; Iglódyová, Adriana; Kočišová, Alica

2015-12-01

This paper follows the study from 2013 focused on the molecular screening of mosquitoes as vectors of Dirofilaria spp. which provided the information on Aedes vexans as a potential vector of Dirofilaria repens in Slovakia. Current entomological and molecular research indicates that Ae. vexans can participate also in the transmission of Dirofilaria immitis within the region. Using the standard PCR method, we examined 10,500 mosquitoes (Ae. vexans, Ae. rossicus, Anopheles maculipennis s.l., Ochlerotatus sticticus, Ochlerotatus cantans, Ochlerotatus caspius, Culex pipiens/Culex torrentium, Coquillettidia richiardii), collected using CO2-baited traps at six locations in the Eastern Slovakia. Out of 105 pools, 6 pools of mosquitoes Ae. vexans were positive for D. repens DNA (minimum infective rate in Ae. vexas was 6:6.900, i.e. 0.8 per 1.000 mosquitoes), within which 4 were concurrently positive for D. immitis (minimum infective rate in Ae. vexans was 4:6.900 i.e. 0.5 per 1.000 mosquitoes).

Reversible Vector Ratchet Effect in Skyrmion Systems

NASA Astrophysics Data System (ADS)

Ma, Xiaoyu; Reichhardt, Charles; Reichhardt, Cynthia

Magnetic skyrmions are topological non-trivial spin textures found in several magnetic materials. Since their motion can be controlled using ultralow current densities, skyrmions are appealing for potential applications in spintronics as information carriers and processing devices. In this work, we studied the collective transport properties of driven skyrmions based on a particle-like model with molecular dynamics (MD) simulation. Our results show that ac driven skyrmions interacting with an asymmetric substrate provide a realization of a new 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 up to 360 degrees relative to the substrate asymmetry direction. This could represent a new method for controlling skyrmion motion for spintronic applications.

Representation of magnetic fields in space. [special attention to Geomagnetic fields and Magnetospheric models

NASA Technical Reports Server (NTRS)

Stern, D. P.

1976-01-01

Several mathematical methods which are available for the description of magnetic fields in space are reviewed. Examples of the application of such methods are given, with particular emphasis on work related to the geomagnetic field, and their individual properties and associated problems are described. The methods are grouped in five main classes: (1) methods based on the current density, (2) methods using the scalar magnetic potential, (3) toroidal and poloidal components of the field and spherical vector harmonics, (4) Euler potentials, and (5) local expansions of the field near a given reference point. Special attention is devoted to models of the magnetosphere, to the uniqueness of the scalar potential as derived from observed data, and to the L parameter.

A reporter system for replication-competent gammaretroviruses: the inGluc-MLV-DERSE assay

PubMed Central

Aloia, Amanda L.; Duffy, Lisa; Pak, Vladimir; Lee, KyeongEun; Sanchez-Martinez, Silvia; Derse, David; Heidecker, Gisela; Cornetta, Kenneth; Rein, Alan

2012-01-01

While novel retroviral vectors for use in gene-therapy products are reducing the potential for formation of replication-competent retrovirus (RCR), it remains crucial to screen products for RCR for both research and clinical purposes. For clinical grade gammaretrovirus-based vectors, RCR screening is achieved by an extended S+L− or marker rescue assay, while standard methods for replication-competent lentivirus detection are still in development. In this report, we describe a rapid and sensitive method for replication-competent gammaretrovirus detection. We used this assay to detect three members of the gammaretrovirus family and compared the sensitivity of our assay with well-established methods for retrovirus detection, including the extended S+L− assay. Results presented here demonstrate that this assay should be useful for gene-therapy product testing. PMID:22402321

An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS1[OPEN

PubMed Central

2018-01-01

Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is the instability of the foreign gene fragment (insert) in the vector during VIGS. Here, we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence. Modification of the BMV RNA3 sequence yielded a vector, BMVCP5, that better maintained phytoene desaturase and heat shock protein70-1 (HSP70-1) inserts in Nicotiana benthamiana and maize (Zea mays). Longer maintenance of inserts was correlated with greater target gene silencing and more extensive visible silencing phenotypes displaying greater tissue penetration and involving more leaves. The modified vector accumulated similarly to the original vector in N. benthamiana after agroinfiltration, thus maintaining a high titer of virus in this intermediate host used to produce virus inoculum for grass hosts. For HSP70, silencing one family member led to a large increase in the expression of another family member, an increase likely related to the target gene knockdown and not a general effect of virus infection. The cause of the increased insert stability in the modified vector is discussed in relationship to its recombination and accumulation potential. The modified vector will improve functional genomic studies in grasses, and the conceptual methods used to improve the vector may be applied to other VIGS vectors. PMID:29127260

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

Adenovirus-based genetic vaccines for biodefense.

PubMed

Boyer, Julie L; Kobinger, Gary; Wilson, James M; Crystal, Ronald G

2005-02-01

The robust host responses elicited against transgenes encoded by (E1-)(E3-) adenovirus (Ad) gene transfer vectors can be used to develop Ad-based vectors as platform technologies for vaccines against potential bioterror pathogens. This review focuses on pathogens of major concern as bioterror agents and why Ad vectors are ideal as anti-bioterror vaccine platforms, providing examples from our laboratories of using Ad vectors as vaccines against potential bioterror pathogens and how Ad vectors can be developed to enhance vaccine efficacy in the bioterror war.

Climate change influences on the potential geographic distribution of the disease vector tick Ixodes ricinus

PubMed Central

Peterson, A. Townsend; Samy, Abdallah M.

2017-01-01

Background Ixodes ricinus is a species of hard tick that transmits several important diseases in Europe and North Africa, including Lyme borreliosis and tick-borne encephalitis. Climate change is affecting the geographic distributions and abundances of arthropod vectors, which in turn influence the geographic distribution and epidemiology of associated vector-borne diseases. To date, few studies have investigated effects of climate change on the spatial distribution of I. ricinus at continental extents. Here, we assessed the potential distribution of I. ricinus under current and future climate conditions to understand how climate change will influence the geographic distribution of this important tick vector in coming decades. Method We used ecological niche modeling to estimate the geographic distribution of I. ricinus with respect to current climate, and then assessed its future potential distribution under different climate change scenarios. This approach integrates occurrence records of I. ricinus with six relevant environmental variables over a continental extent that includes Europe, North Africa, and the Middle East. Future projections were based on climate data from 17 general circulation models (GCMs) under 2 representative concentration pathway emissions scenarios (RCPs), for the years 2050 and 2070. Result The present and future potential distributions of I. ricinus showed broad overlap across most of western and central Europe, and in more narrow zones in eastern and northern Europe, and North Africa. Potential expansions were observed in northern and eastern Europe. These results indicate that I. ricinus populations could emerge in areas in which they are currently lacking, posing increased risks to human health in those areas. However, the future of I. ricinus ticks in some important regions such the Mediterranean was unclear owing to high uncertainty in model predictions. PMID:29206879

Calculating vibrational spectra with sum of product basis functions without storing full-dimensional vectors or matrices.

PubMed

Leclerc, Arnaud; Carrington, Tucker

2014-05-07

We propose an iterative method for computing vibrational spectra that significantly reduces the memory cost of calculations. It uses a direct product primitive basis, but does not require storing vectors with as many components as there are product basis functions. Wavefunctions are represented in a basis each of whose functions is a sum of products (SOP) and the factorizable structure of the Hamiltonian is exploited. If the factors of the SOP basis functions are properly chosen, wavefunctions are linear combinations of a small number of SOP basis functions. The SOP basis functions are generated using a shifted block power method. The factors are refined with a rank reduction algorithm to cap the number of terms in a SOP basis function. The ideas are tested on a 20-D model Hamiltonian and a realistic CH3CN (12 dimensional) potential. For the 20-D problem, to use a standard direct product iterative approach one would need to store vectors with about 10(20) components and would hence require about 8 × 10(11) GB. With the approach of this paper only 1 GB of memory is necessary. Results for CH3CN agree well with those of a previous calculation on the same potential.

Evaluation of linear induction motor characteristics : the Yamamura model

DOT National Transportation Integrated Search

1975-04-30

The Yamamura theory of the double-sided linear induction motor (LIM) excited by a constant current source is discussed in some detail. The report begins with a derivation of thrust and airgap power using the method of vector potentials and theorem of...

Numerical computation of gravitational field of general extended body and its application to rotation curve study of galaxies

NASA Astrophysics Data System (ADS)

Fukushima, Toshio

2017-06-01

Reviewed are recently developed methods of the numerical integration of the gravitational field of general two- or three-dimensional bodies with arbitrary shape and mass density distribution: (i) an axisymmetric infinitely-thin disc (Fukushima 2016a, MNRAS, 456, 3702), (ii) a general infinitely-thin plate (Fukushima 2016b, MNRAS, 459, 3825), (iii) a plane-symmetric and axisymmetric ring-like object (Fukushima 2016c, AJ, 152, 35), (iv) an axisymmetric thick disc (Fukushima 2016d, MNRAS, 462, 2138), and (v) a general three-dimensional body (Fukushima 2016e, MNRAS, 463, 1500). The key techniques employed are (a) the split quadrature method using the double exponential rule (Takahashi and Mori, 1973, Numer. Math., 21, 206), (b) the precise and fast computation of complete elliptic integrals (Fukushima 2015, J. Comp. Appl. Math., 282, 71), (c) Ridder's algorithm of numerical differentiaion (Ridder 1982, Adv. Eng. Softw., 4, 75), (d) the recursive computation of the zonal toroidal harmonics, and (e) the integration variable transformation to the local spherical polar coordinates. These devices succesfully regularize the Newton kernel in the integrands so as to provide accurate integral values. For example, the general 3D potential is regularly integrated as Φ (\\vec{x}) = - G \\int_0^∞ ( \\int_{-1}^1 ( \\int_0^{2π} ρ (\\vec{x}+\\vec{q}) dψ ) dγ ) q dq, where \\vec{q} = q (√{1-γ^2} cos ψ, √{1-γ^2} sin ψ, γ), is the relative position vector referred to \\vec{x}, the position vector at which the potential is evaluated. As a result, the new methods can compute the potential and acceleration vector very accurately. In fact, the axisymmetric integration reproduces the Miyamoto-Nagai potential with 14 correct digits. The developed methods are applied to the gravitational field study of galaxies and protoplanetary discs. Among them, the investigation on the rotation curve of M33 supports a disc-like structure of the dark matter with a double-power-law surface mass density distribution. Fortran 90 subroutines to execute these methods and their test programs and sample outputs are available from the author's WEB site: https://www.researchgate.net/profile/Toshio_Fukushima/

Vector spherical quasi-Gaussian vortex beams

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2014-02-01

Model equations for describing and efficiently computing the radiation profiles of tightly spherically focused higher-order electromagnetic beams of vortex nature are derived stemming from a vectorial analysis with the complex-source-point method. This solution, termed as a high-order quasi-Gaussian (qG) vortex beam, exactly satisfies the vector Helmholtz and Maxwell's equations. It is characterized by a nonzero integer degree and order (n,m), respectively, an arbitrary waist w0, a diffraction convergence length known as the Rayleigh range zR, and an azimuthal phase dependency in the form of a complex exponential corresponding to a vortex beam. An attractive feature of the high-order solution is the rigorous description of strongly focused (or strongly divergent) vortex wave fields without the need of either the higher-order corrections or the numerically intensive methods. Closed-form expressions and computational results illustrate the analysis and some properties of the high-order qG vortex beams based on the axial and transverse polarization schemes of the vector potentials with emphasis on the beam waist.

PCR-based detection of gene transfer vectors: application to gene doping surveillance.

PubMed

Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

2013-12-01

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.

Fat grafting as a vehicle for the delivery of recombinant adenoassociated viral vectors to achieve gene modification of muscle flaps.

PubMed

Carruthers, Katherine H; During, Matthew J; Muravlev, Alexander; Wang, Chuansong; Kocak, Ergun

2013-06-01

The combination of gene therapy and plastic surgery may have the potential to improve the specificity that is needed to achieve clinically applicable treatment regimens. Our goal was to develop a method for gene modification that would yield sustainable production of gene products but would be less time consuming than existing protocols. An adenoassociated virus was used to deliver gene products to pectoralis muscle flaps. Gene modification was accomplished via either direct injection or novel fat grafting techniques. The production of gene product was observable by both in vivo imaging and immunohistochemical staining. Gene products were not detected in tissues that were not in contact with the fat grafts that were incubated with the viral vector, indicating that the transduction stayed local to the flap. Using novel recombinant adenoassociated virus vectors, we have developed a method for gene delivery that is highly efficient and applicable to muscle flaps.

Shuttle of lentiviral vectors via transplanted cells in vivo.

PubMed

Blömer, U; Gruh, I; Witschel, H; Haverich, A; Martin, U

2005-01-01

Lentiviral vectors have turned out to be an efficient method for stable gene transfer in vitro and in vivo. Not only do fields of application include cell marking and tracing following transplantation in vivo, but also the stable delivery of biological active proteins for gene therapy. A variety of cells, however, need immediate transplantation after preparation, for example, to prevent cell death, differentiation or de-differentiation. Although these cells are usually washed several times following lentiviral transduction, there may be the risk of viral vector shuttle via transplanted cells resulting in undesired in vivo transduction of recipient cells. We investigated whether infectious lentiviral particles are transmitted via ex vivo lentivirally transduced cells. To this end, we explored potential viral shuttle via ex vivo lentivirally transduced cardiomyocytes in vitro and following transplantation into the brain and peripheral muscle. We demonstrate that, even after extensive washing, infectious viral vector particles can be detected in cell suspensions. Those lentiviral vector particles were able to transduce target cells in transwell experiments. Moreover, transmitted vector particles stably transduced resident cells of the recipient central nervous system and muscle in vivo. Our results of lentiviral vector shuttle via transduced cardiomyocytes are significant for both ex vivo gene therapy and for lentiviral cell tracing, in particular for investigation of stem cell differentiation in transplantation models and co-cultivation systems.

Vector-control personnel’s knowledge, perceptions and practices towards insecticides used for indoor residual spraying in Limpopo Province, South Africa

PubMed Central

2013-01-01

Background Contradictory arguments regarding the benefits and harm of insecticides, especially DDT, have caused concerns in different societal circles, threatening to undermine the achievements of the indoor residual spraying (IRS) programme in South Africa. These concerns were exacerbated by the screening of a documentary on South African Broadcasting Corporation (SABC) Television with anti-DDT sentiments. Consequently, Limpopo Malaria Control Programme (LMCP) Management advocated for an investigation to determine the potential effect of such campaigns on vector-control personnel’s knowledge and perceived effects of insecticides on human health, with a view to improving the educational materials designed for use in training vector-control personnel. Methods The study was a cross-sectional descriptive survey using a structured field-piloted questionnaire, administered to 233 randomly selected vector-control personnel. Ethical clearance was granted by the University of KwaZulu-Natal. Approval for the study was granted by the Department of Health, Limpopo. Participation in the study was voluntary and all respondents signed informed consent. Descriptive statistics were used to analyse the collected data. Results Most respondents (96.6%) had a positive perception of IRS as a method to control malaria. Despite their positive perception, 93.6% viewed IRS insecticides to be potentially harmful to the users. DDT was perceived to cause long-term reproductive and respiratory effects, whereas alpha-cypermethrin and deltamethrin were largely associated with skin irritation/itchiness and skin burn. Study participants were more worried about DDT’s potential effects on their reproductive system, including poor sexual performance, decline in libido, miscarriage and bearing children with genetic defects. However, none reported personal experience of bearing a child with genetic defects or miscarriage. Most anti-insecticide messages, especially relating to DDT, emanated from sources external to the LMCP, mainly through radio (62%) and television (33.9%) and about 70% believed such messages. While most respondents preferred to work with a moderately itchy deltamethrin, DDT was admittedly the most effective insecticide. Conclusion Vector-control personnel faced health and ethical dilemmas, in that, while they perceived insecticides used for IRS in Limpopo to be potentially harmful to the health of users, as purported through media, they also viewed IRS using insecticides to be effective in controlling malaria. PMID:23618516

Magnetic potential, vector and gradient tensor fields of a tesseroid in a geocentric spherical coordinate system

NASA Astrophysics Data System (ADS)

Du, Jinsong; Chen, Chao; Lesur, Vincent; Lane, Richard; Wang, Huilin

2015-06-01

We examined the mathematical and computational aspects of the magnetic potential, vector and gradient tensor fields of a tesseroid in a geocentric spherical coordinate system (SCS). This work is relevant for 3-D modelling that is performed with lithospheric vertical scales and global, continent or large regional horizontal scales. The curvature of the Earth is significant at these scales and hence, a SCS is more appropriate than the usual Cartesian coordinate system (CCS). The 3-D arrays of spherical prisms (SP; `tesseroids') can be used to model the response of volumes with variable magnetic properties. Analytical solutions do not exist for these model elements and numerical or mixed numerical and analytical solutions must be employed. We compared various methods for calculating the response in terms of accuracy and computational efficiency. The methods were (1) the spherical coordinate magnetic dipole method (MD), (2) variants of the 3-D Gauss-Legendre quadrature integration method (3-D GLQI) with (i) different numbers of nodes in each of the three directions, and (ii) models where we subdivided each SP into a number of smaller tesseroid volume elements, (3) a procedure that we term revised Gauss-Legendre quadrature integration (3-D RGLQI) where the magnetization direction which is constant in a SCS is assumed to be constant in a CCS and equal to the direction at the geometric centre of each tesseroid, (4) the Taylor's series expansion method (TSE) and (5) the rectangular prism method (RP). In any realistic application, both the accuracy and the computational efficiency factors must be considered to determine the optimum approach to employ. In all instances, accuracy improves with increasing distance from the source. It is higher in the percentage terms for potential than the vector or tensor response. The tensor errors are the largest, but they decrease more quickly with distance from the source. In our comparisons of relative computational efficiency, we found that the magnetic potential takes less time to compute than the vector response, which in turn takes less time to compute than the tensor gradient response. The MD method takes less time to compute than either the TSE or RP methods. The efficiency of the (GLQI and) RGLQI methods depends on the polynomial order, but the response typically takes longer to compute than it does for the other methods. The optimum method is a complex function of the desired accuracy, the size of the volume elements, the element latitude and the distance between the source and the observation. For a model of global extent with typical model element size (e.g. 1 degree horizontally and 10 km radially) and observations at altitudes of 10s to 100s of km, a mixture of methods based on the horizontal separation of the source and observation separation would be the optimum approach. To demonstrate the RGLQI method described within this paper, we applied it to the computation of the response for a global magnetization model for observations at 300 and 30 km altitude.

Spatial distribution of sand fly species (Psychodidae: Phlebtominae), ecological niche, and climatic regionalization in zoonotic foci of cutaneous leishmaniasis, southwest of Iran.

PubMed

Ebrahimi, Sahar; Bordbar, Ali; Rastaghi, Ahmad R Esmaeili; Parvizi, Parviz

2016-06-01

Cutaneous leishmaniasis (CL) is a complex vector-borne disease caused by Leishmania parasites that are transmitted by the bite of several species of infected female phlebotomine sand flies. Monthly factor analysis of climatic variables indicated fundamental variables. Principal component-based regionalization was used for recognition of climatic zones using a clustering integrated method that identified five climatic zones based on factor analysis. To investigate spatial distribution of the sand fly species, the kriging method was used as an advanced geostatistical procedure in the ArcGIS modeling system that is beneficial to design measurement plans and to predict the transmission cycle in various regions of Khuzestan province, southwest of Iran. However, more than an 80% probability of P. papatasi was observed in rainy and temperate bio-climatic zones with a high potential of CL transmission. Finding P. sergenti revealed the probability of transmission and distribution patterns of a non-native vector of CL in related zones. These findings could be used as models indicating climatic zones and environmental variables connected to sand fly presence and vector distribution. Furthermore, this information is appropriate for future research efforts into the ecology of Phlebotomine sand flies and for the prevention of CL vector transmission as a public health priority. © 2016 The Society for Vector Ecology.

Summary of Fluidic Thrust Vectoring Research Conducted at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Deere, Karen A.

2003-01-01

Interest in low-observable aircraft and in lowering an aircraft's exhaust system weight sparked decades of research for fixed geometry exhaust nozzles. The desire for such integrated exhaust nozzles was the catalyst for new fluidic control techniques; including throat area control, expansion control, and thrust-vector angle control. This paper summarizes a variety of fluidic thrust vectoring concepts that have been tested both experimentally and computationally at NASA Langley Research Center. The nozzle concepts are divided into three categories according to the method used for fluidic thrust vectoring: the shock vector control method, the throat shifting method, and the counterflow method. This paper explains the thrust vectoring mechanism for each fluidic method, provides examples of configurations tested for each method, and discusses the advantages and disadvantages of each method.

An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS.

PubMed

Ding, Xin Shun; Mannas, Stephen W; Bishop, Bethany A; Rao, Xiaolan; Lecoultre, Mitchell; Kwon, Soonil; Nelson, Richard S

2018-01-01

Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is the instability of the foreign gene fragment (insert) in the vector during VIGS. Here, we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence. Modification of the BMV RNA3 sequence yielded a vector, BMVCP5, that better maintained phytoene desaturase and heat shock protein70-1 ( HSP70-1 ) inserts in Nicotiana benthamiana and maize ( Zea mays ). Longer maintenance of inserts was correlated with greater target gene silencing and more extensive visible silencing phenotypes displaying greater tissue penetration and involving more leaves. The modified vector accumulated similarly to the original vector in N. benthamiana after agroinfiltration, thus maintaining a high titer of virus in this intermediate host used to produce virus inoculum for grass hosts. For HSP70 , silencing one family member led to a large increase in the expression of another family member, an increase likely related to the target gene knockdown and not a general effect of virus infection. The cause of the increased insert stability in the modified vector is discussed in relationship to its recombination and accumulation potential. The modified vector will improve functional genomic studies in grasses, and the conceptual methods used to improve the vector may be applied to other VIGS vectors. © 2018 American Society of Plant Biologists. All Rights Reserved.

Status of pesticide management in the practice of vector control: a global survey in countries at risk of malaria or other major vector-borne diseases

PubMed Central

2011-01-01

Background It is critical that vector control pesticides are used for their acceptable purpose without causing adverse effects on health and the environment. This paper provides a global overview of the current status of pesticides management in the practice of vector control. Methods A questionnaire was distributed to WHO member states and completed either by the director of the vector-borne disease control programme or by the national manager for vector control. In all, 113 countries responded to the questionnaire (80% response rate), representing 94% of the total population of the countries targeted. Results Major gaps were evident in countries in pesticide procurement practices, training on vector control decision making, certification and quality control of pesticide application, monitoring of worker safety, public awareness programmes, and safe disposal of pesticide-related waste. Nevertheless, basic conditions of policy and coordination have been established in many countries through which the management of vector control pesticides could potentially be improved. Most countries responded that they have adopted relevant recommendations by the WHO. Conclusions Given the deficiencies identified in this first global survey on public health pesticide management and the recent rise in pesticide use for malaria control, the effectiveness and safety of pesticide use are being compromised. This highlights the urgent need for countries to strengthen their capacity on pesticide management and evidence-based decision making within the context of an integrated vector management approach. PMID:21569601

Classification of ECG signal with Support Vector Machine Method for Arrhythmia Detection

NASA Astrophysics Data System (ADS)

Turnip, Arjon; Ilham Rizqywan, M.; Kusumandari, Dwi E.; Turnip, Mardi; Sihombing, Poltak

2018-03-01

An electrocardiogram is a potential bioelectric record that occurs as a result of cardiac activity. QRS Detection with zero crossing calculation is one method that can precisely determine peak R of QRS wave as part of arrhythmia detection. In this paper, two experimental scheme (2 minutes duration with different activities: relaxed and, typing) were conducted. From the two experiments it were obtained: accuracy, sensitivity, and positive predictivity about 100% each for the first experiment and about 79%, 93%, 83% for the second experiment, respectively. Furthermore, the feature set of MIT-BIH arrhythmia using the support vector machine (SVM) method on the WEKA software is evaluated. By combining the available attributes on the WEKA algorithm, the result is constant since all classes of SVM goes to the normal class with average 88.49% accuracy.

Potential for entomopathogenic fungi to control Triatoma dimidiata (Hemiptera: Reduviidae), a vector of Chagas disease in Mexico.

PubMed

Vázquez-Martínez, María Guadalupe; Cirerol-Cruz, Blanca Elva; Torres-Estrada, José Luis; López, Mario Henry Rodríguez

2014-01-01

The use of entomopathogenic fungi to control disease vectors has become relevant because traditional chemical control methods have caused damage to the environment and led to the development of resistance among vectors. Thus, this study assessed the pathogenicity of entomopathogenic fungi in Triatoma dimidiata. Preparations of 108 conidia/ml of Gliocladium virens, Talaromyces flavus, Beauveria bassiana and Metarhizium anisopliae were applied topically on T. dimidiata nymphs and adults. Controls were treated with the 0.0001% Tween-80 vehicle. Mortality was evaluated and recorded daily for 30 days. The concentration required to kill 50% of T. dimidiata (LC50) was then calculated for the most pathogenic isolate. Pathogenicity in adults was similar among B. bassiana, G. virens and T. flavus (p>0.05) and differed from that in triatomine nymphs (p=0.009). The most entomopathogenic strains in adult triatomines were B. bassiana and G. virens, which both caused 100% mortality. In nymphs, the most entomopathogenic strain was B. bassiana, followed by G. virens. The native strain with the highest pathogenicity was G. virens, for which the LC50 for T. dimidiata nymphs was 1.98 x108 conidia/ml at 13 days after inoculation. Beauveria bassiana and G. virens showed entomopathogenic potential in T. dimidiata nymphs and adults. However, the native G. virens strain presents a higher probability of success in the field, and G. virens should thus be considered a potential candidate for the biological control of triatomine Chagas disease vectors.

Chemosterilants for Control of Insects and Insect Vectors of Disease.

PubMed

Baxter, Richard H G

2016-10-01

Both historically and at present, vector control is the most generally effective means of controlling malaria transmission. Insecticides are the predominant method of vector control, but the sterile insect technique (SIT) is a complementary strategy with a successful track record in both agricultural and public health sectors. Strategies of genetic and radiation-induced sterilization of Anopheles have to date been limited by logistical and/or regulatory hurdles. A safe and effective mosquito chemosterilant would therefore be of major utility to future deployment of SIT for malaria control. Here we review the prior and current use of chemosterilants in SIT, and assess the potential for future research. Recent genomic and proteomic studies reveal opportunities for specific targeting of seminal fluid proteins, and the capacity to interfere with sperm motility and storage in the female.

Trypanosoma cruzi reservoir—triatomine vector co-occurrence networks reveal meta-community effects by synanthropic mammals on geographic dispersal

PubMed Central

Valiente-Banuet, Leopoldo; Sánchez-Cordero, Víctor; Stephens, Christopher R.

2017-01-01

Contemporary patterns of land use and global climate change are modifying regional pools of parasite host species. The impact of host community changes on human disease risk, however, is difficult to assess due to a lack of information about zoonotic parasite host assemblages. We have used a recently developed method to infer parasite-host interactions for Chagas Disease (CD) from vector-host co-occurrence networks. Vector-host networks were constructed to analyze topological characteristics of the network and ecological traits of species’ nodes, which could provide information regarding parasite regional dispersal in Mexico. Twenty-eight triatomine species (vectors) and 396 mammal species (potential hosts) were included using a data-mining approach to develop models to infer most-likely interactions. The final network contained 1,576 links which were analyzed to calculate centrality, connectivity, and modularity. The model predicted links of independently registered Trypanosoma cruzi hosts, which correlated with the degree of parasite-vector co-occurrence. Wiring patterns differed according to node location, while edge density was greater in Neotropical as compared to Nearctic regions. Vectors with greatest public health importance (i.e., Triatoma dimidiata, T. barberi, T. pallidipennis, T. longipennis, etc), did not have stronger links with particular host species, although they had a greater frequency of significant links. In contrast, hosts classified as important based on network properties were synanthropic mammals. The latter were the most common parasite hosts and are likely bridge species between these communities, thereby integrating meta-community scenarios beneficial for long-range parasite dispersal. This was particularly true for rodents, >50% of species are synanthropic and more than 20% have been identified as T. cruzi hosts. In addition to predicting potential host species using the co-occurrence networks, they reveal regions with greater expected parasite mobility. The Neotropical region, which includes the Mexican south and southeast, and the Transvolcanic belt, had greatest potential active T. cruzi dispersal, as well as greatest edge density. This information could be directly applied for stratification of transmission risk and to design and analyze human-infected vector contact intervention efficacy. PMID:28413725

A Potential Food-Grade Cloning Vector for Streptococcus thermophilus That Uses Cadmium Resistance as the Selectable Marker

PubMed Central

Wong, Wing Yee; Su, Ping; Allison, Gwen E.; Liu, Chun-Qiang; Dunn, Noel W.

2003-01-01

A potential food-grade cloning vector, pND919, was constructed and transformed into S. thermophilus ST3-1, a plasmid-free strain. The vector contains DNAs from two different food-approved organisms, Streptococcus thermophilus and Lactococcus lactis. The 5.0-kb pND919 is a derivative of the cloning vector pND918 (9.3 kb) and was constructed by deletion of the 4.3-kb region of pND918 which contained DNA from non-food-approved organisms. pND919 carries a heterologous native cadmium resistance selectable marker from L. lactis M71 and expresses the Cdr phenotype in S. thermophilus transformants. With the S. thermophilus replicon derived from the shuttle vector pND913, pND919 is able to replicate in the two S. thermophilus industrial strains tested, ST3-1 and ST4-1. Its relatively high retention rate in S. thermophilus further indicates its usefulness as a potential food-grade cloning vector. To our knowledge, this is the first report of a replicative potential food-grade vector for the industrially important organism S. thermophilus. PMID:14532023

A potential food-grade cloning vector for Streptococcus thermophilus that uses cadmium resistance as the selectable marker.

PubMed

Wong, Wing Yee; Su, Ping; Allison, Gwen E; Liu, Chun-Qiang; Dunn, Noel W

2003-10-01

A potential food-grade cloning vector, pND919, was constructed and transformed into S. thermophilus ST3-1, a plasmid-free strain. The vector contains DNAs from two different food-approved organisms, Streptococcus thermophilus and Lactococcus lactis. The 5.0-kb pND919 is a derivative of the cloning vector pND918 (9.3 kb) and was constructed by deletion of the 4.3-kb region of pND918 which contained DNA from non-food-approved organisms. pND919 carries a heterologous native cadmium resistance selectable marker from L. lactis M71 and expresses the Cd(r) phenotype in S. thermophilus transformants. With the S. thermophilus replicon derived from the shuttle vector pND913, pND919 is able to replicate in the two S. thermophilus industrial strains tested, ST3-1 and ST4-1. Its relatively high retention rate in S. thermophilus further indicates its usefulness as a potential food-grade cloning vector. To our knowledge, this is the first report of a replicative potential food-grade vector for the industrially important organism S. thermophilus.

The LAM-PCR Method to Sequence LV Integration Sites.

PubMed

Wang, Wei; Bartholomae, Cynthia C; Gabriel, Richard; Deichmann, Annette; Schmidt, Manfred

2016-01-01

Integrating viral gene transfer vectors are commonly used gene delivery tools in clinical gene therapy trials providing stable integration and continuous gene expression of the transgene in the treated host cell. However, integration of the reverse-transcribed vector DNA into the host genome is a potentially mutagenic event that may directly contribute to unwanted side effects. A comprehensive and accurate analysis of the integration site (IS) repertoire is indispensable to study clonality in transduced cells obtained from patients undergoing gene therapy and to identify potential in vivo selection of affected cell clones. To date, next-generation sequencing (NGS) of vector-genome junctions allows sophisticated studies on the integration repertoire in vitro and in vivo. We have explored the use of the Illumina MiSeq Personal Sequencer platform to sequence vector ISs amplified by non-restrictive linear amplification-mediated PCR (nrLAM-PCR) and LAM-PCR. MiSeq-based high-quality IS sequence retrieval is accomplished by the introduction of a double-barcode strategy that substantially minimizes the frequency of IS sequence collisions compared to the conventionally used single-barcode protocol. Here, we present an updated protocol of (nr)LAM-PCR for the analysis of lentiviral IS using a double-barcode system and followed by deep sequencing using the MiSeq device.

Integrated pest management and allocation of control efforts for vector-borne diseases

USGS Publications Warehouse

Ginsberg, H.S.

2001-01-01

Applications of various control methods were evaluated to determine how to integrate methods so as to minimize the number of human cases of vector-borne diseases. These diseases can be controlled by lowering the number of vector-human contacts (e.g., by pesticide applications or use of repellents), or by lowering the proportion of vectors infected with pathogens (e.g., by lowering or vaccinating reservoir host populations). Control methods should be combined in such a way as to most efficiently lower the probability of human encounter with an infected vector. Simulations using a simple probabilistic model of pathogen transmission suggest that the most efficient way to integrate different control methods is to combine methods that have the same effect (e.g., combine treatments that lower the vector population; or combine treatments that lower pathogen prevalence in vectors). Combining techniques that have different effects (e.g., a technique that lowers vector populations with a technique that lowers pathogen prevalence in vectors) will be less efficient than combining two techniques that both lower vector populations or combining two techniques that both lower pathogen prevalence, costs being the same. Costs of alternative control methods generally differ, so the efficiency of various combinations at lowering human contact with infected vectors should be estimated at available funding levels. Data should be collected from initial trials to improve the effects of subsequent interventions on the number of human cases.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

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

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

Electric fields and vector potentials of thin cylindrical antennas

NASA Astrophysics Data System (ADS)

King, Ronold W. P.

1990-09-01

The vector potential and electric field generated by the current in a center-driven or parasitic dipole antenna that extends from z = -h to z = h are investigated for each of the several components of the current. These include sin k(h - absolute value of z), sin k (absolute value of z) - sin kh, cos kz - cos kh, and cos kz/2 - cos kh/2. Of special interest are the interactions among the variously spaced elements in parallel nonstaggered arrays. These depend on the mutual vector potentials. It is shown that at a radial distance rho approximately = h and in the range z = -h to h, the vector potentials due to all four components become alike and have an approximately plane-wave form. Simple approximate formulas for the electric fields and vector potentials generated by each of the four distributions are derived and compared with the exact results. The application of the new formulas to large arrays is discussed.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction.

PubMed

Prabhat, K C; Aditya Mohan, K; Phatak, Charudatta; Bouman, Charles; De Graef, Marc

2017-11-01

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach. Copyright © 2017 Elsevier B.V. All rights reserved.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE PAGES

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta; ...

2017-07-03

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

Versatile generation of optical vector fields and vector beams using a non-interferometric approach.

PubMed

Tripathi, Santosh; Toussaint, Kimani C

2012-05-07

We present a versatile, non-interferometric method for generating vector fields and vector beams which can produce all the states of polarization represented on a higher-order Poincaré sphere. The versatility and non-interferometric nature of this method is expected to enable exploration of various exotic properties of vector fields and vector beams. To illustrate this, we study the propagation properties of some vector fields and find that, in general, propagation alters both their intensity and polarization distribution, and more interestingly, converts some vector fields into vector beams. In the article, we also suggest a modified Jones vector formalism to represent vector fields and vector beams.

Quantum detectors of vector potential and their modeling

NASA Astrophysics Data System (ADS)

Gulian, Armen; Melkonyan, Gurgen; Gulian, Ellen

Proportionality of current to vector potential is a feature not allowed in classical physics, but is one of the pillars in quantum theory. For superconductors, in particular, it allows us to describe the Meissner effect. Since the phase of the quantum wave function couples with the vector-potential, the related expressions are gauge-invariant. Is it possible to measure this gauge-invariant quantity locally? The answer is definitely ``yes'', as soon as the current is involved. Indeed, the electric current generates a magnetic field which can be measured straightforwardly. However, one can consider situations like the Aharonov-Bohm effect where the classical magnetic field is locally absent in the area occupied by the quantum object (i.e., superconductor in our case). Despite the local absence of the magnetic field, current is, nevertheless, building up. From what source is it acquiring its energy? Locally, only a vector potential is present. Is the current formation a result of a truly non-local quantum action, or does the local action of the vector potential have experimental consequences on the quantum system, which then can be considered as a detector of the vector potential? We discuss possible experimental schemes on the level of COMSOL modeling. This research is supported in part by the ONR Grant N000141612269.

Cloning strategy for producing brush-forming protein-based polymers.

PubMed

Henderson, Douglas B; Davis, Richey M; Ducker, William A; Van Cott, Kevin E

2005-01-01

Brush-forming polymers are being used in a variety of applications, and by using recombinant DNA technology, there exists the potential to produce protein-based polymers that incorporate unique structures and functions in these brush layers. Despite this potential, production of protein-based brush-forming polymers is not routinely performed. For the design and production of new protein-based polymers with optimal brush-forming properties, it would be desirable to have a cloning strategy that allows an iterative approach wherein the protein based-polymer product can be produced and evaluated, and then if necessary, it can be sequentially modified in a controlled manner to obtain optimal surface density and brush extension. In this work, we report on the development of a cloning strategy intended for the production of protein-based brush-forming polymers. This strategy is based on the assembly of modules of DNA that encode for blocks of protein-based polymers into a commercially available expression vector; there is no need for custom-modified vectors and no need for intermediate cloning vectors. Additionally, because the design of new protein-based biopolymers can be an iterative process, our method enables sequential modification of a protein-based polymer product. With at least 21 bacterial expression vectors and 11 yeast expression vectors compatible with this strategy, there are a number of options available for production of protein-based polymers. It is our intent that this strategy will aid in advancing the production of protein-based brush-forming polymers.

Climate Change and Risk of Leishmaniasis in North America: Predictions from Ecological Niche Models of Vector and Reservoir Species

PubMed Central

González, Camila; Wang, Ophelia; Strutz, Stavana E.; González-Salazar, Constantino; Sánchez-Cordero, Víctor; Sarkar, Sahotra

2010-01-01

Background Climate change is increasingly being implicated in species' range shifts throughout the world, including those of important vector and reservoir species for infectious diseases. In North America (México, United States, and Canada), leishmaniasis is a vector-borne disease that is autochthonous in México and Texas and has begun to expand its range northward. Further expansion to the north may be facilitated by climate change as more habitat becomes suitable for vector and reservoir species for leishmaniasis. Methods and Findings The analysis began with the construction of ecological niche models using a maximum entropy algorithm for the distribution of two sand fly vector species (Lutzomyia anthophora and L. diabolica), three confirmed rodent reservoir species (Neotoma albigula, N. floridana, and N. micropus), and one potential rodent reservoir species (N. mexicana) for leishmaniasis in northern México and the United States. As input, these models used species' occurrence records with topographic and climatic parameters as explanatory variables. Models were tested for their ability to predict correctly both a specified fraction of occurrence points set aside for this purpose and occurrence points from an independently derived data set. These models were refined to obtain predicted species' geographical distributions under increasingly strict assumptions about the ability of a species to disperse to suitable habitat and to persist in it, as modulated by its ecological suitability. Models successful at predictions were fitted to the extreme A2 and relatively conservative B2 projected climate scenarios for 2020, 2050, and 2080 using publicly available interpolated climate data from the Third Intergovernmental Panel on Climate Change Assessment Report. Further analyses included estimation of the projected human population that could potentially be exposed to leishmaniasis in 2020, 2050, and 2080 under the A2 and B2 scenarios. All confirmed vector and reservoir species will see an expansion of their potential range towards the north. Thus, leishmaniasis has the potential to expand northwards from México and the southern United States. In the eastern United States its spread is predicted to be limited by the range of L. diabolica; further west, L. anthophora may play the same role. In the east it may even reach the southern boundary of Canada. The risk of spread is greater for the A2 scenario than for the B2 scenario. Even in the latter case, with restrictive (contiguous) models for dispersal of vector and reservoir species, and limiting vector and reservoir species occupancy to only the top 10% of their potential suitable habitat, the expected number of human individuals exposed to leishmaniasis by 2080 will at least double its present value. Conclusions These models predict that climate change will exacerbate the ecological risk of human exposure to leishmaniasis in areas outside its present range in the United States and, possibly, in parts of southern Canada. This prediction suggests the adoption of measures such as surveillance for leishmaniasis north of Texas as disease cases spread northwards. Potential vector and reservoir control strategies—besides direct intervention in disease cases—should also be further investigated. PMID:20098495

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization.

PubMed

Moss, Caitlin E; Robson, Andrew; Fikrig, Erol; Narasimhan, Sukanya

2018-06-01

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these diseases, do not exist in isolation when they colonize the vector; rather, they likely engage in interactions with resident microorganisms in the gut lumen. The vector microbiota has been demonstrated to play an important role in pathogen transmission for several vector-borne diseases. Whether resident bacteria in the gut of the Ixodes scapularis tick, the vector of several human pathogens including Borrelia burgdorferi, influence tick transmission of pathogens is not determined. We require methods for characterizing the composition of the bacteria associated with the tick gut to facilitate a better understanding of potential interspecies interactions in the tick gut. Using whole-mount in situ hybridization to visualize RNA transcripts associated with particular bacterial species allows for the collection of qualitative data regarding the abundance and distribution of the microbiota in intact tissue. This technique can be used to examine changes in the gut microbiota milieu over the course of tick feeding and can also be applied to analyze expression of tick genes. Staining of whole tick guts yield information about the gross spatial distribution of target RNA in the tissue without the need for three-dimensional reconstruction and is less affected by environmental contamination, which often confounds the sequencing-based methods frequently used to study complex microbial communities. Overall, this technique is a valuable tool that can be used to better understand vector-pathogen-microbiota interactions and their role in disease transmission.

A Guided Tour of Mathematical Methods

NASA Astrophysics Data System (ADS)

Snieder, Roel

2009-04-01

1. Introduction; 2. Dimensional analysis; 3. Power series; 4. Spherical and cylindrical co-ordinates; 5. The gradient; 6. The divergence of a vector field; 7. The curl of a vector field; 8. The theorem of Gauss; 9. The theorem of Stokes; 10. The Laplacian; 11. Conservation laws; 12. Scale analysis; 13. Linear algebra; 14. The Dirac delta function; 15. Fourier analysis; 16. Analytic functions; 17. Complex integration; 18. Green's functions: principles; 19. Green's functions: examples; 20. Normal modes; 21. Potential theory; 22. Cartesian tensors; 23. Perturbation theory; 24. Asymptotic evaluation of integrals; 25. Variational calculus; 26. Epilogue, on power and knowledge; References.

Attenuated Shigella as a DNA Delivery Vehicle for DNA-Mediated Immunization

NASA Astrophysics Data System (ADS)

Sizemore, Donata R.; Branstrom, Arthur A.; Sadoff, Jerald C.

1995-10-01

Direct inoculation of DNA, in the form of purified bacterial plasmids that are unable to replicate in mammalian cells but are able to direct cell synthesis of foreign proteins, is being explored as an approach to vaccine development. Here, a highly attenuated Shigella vector invaded mammalian cells and delivered such plasmids into the cytoplasm of cells, and subsequent production of functional foreign protein was measured. Because this Shigella vector was designed to deliver DNA to colonic mucosa, the method is a potential basis for oral and other mucosal DNA immunization and gene therapy strategies.

Mosquito Avoidance Practices and Knowledge of Arboviral Diseases in Cities with Differing Recent History of Disease

PubMed Central

Haenchen, Steven D.; Hayden, Mary H.; Dickinson, Katherine L.; Walker, Kathleen; Jacobs, Elizabeth E.; Brown, Heidi E.; Gunn, Jayleen K. L.; Kohler, Lindsay N.; Ernst, Kacey C.

2016-01-01

As the range of dengue virus (DENV) transmission expands, an understanding of community uptake of prevention and control strategies is needed both in geographic areas where the virus has recently been circulating and in areas with the potential for DENV introduction. Personal protective behaviors such as the use of mosquito repellent to limit human–vector contact and the reduction of vector density through elimination of oviposition sites are the primary control methods for Aedes aegypti, the main vector of DENV. Here, we examined personal mosquito control measures taken by individuals in Key West, FL, in 2012, which had experienced a recent outbreak of DENV, and Tucson, AZ, which has a high potential for introduction but has not yet experienced autochthonous transmission. In both cities, there was a positive association between the numbers of mosquitoes noticed outdoors and the overall number of avoidance behaviors, use of repellent, and removal of standing water. Increased awareness and perceived risk of DENV were associated with increases in one of the most effective household prevention behaviors, removal of standing water, but only in Key West. PMID:27527634

A Discriminant Distance Based Composite Vector Selection Method for Odor Classification

PubMed Central

Choi, Sang-Il; Jeong, Gu-Min

2014-01-01

We present a composite vector selection method for an effective electronic nose system that performs well even in noisy environments. Each composite vector generated from a electronic nose data sample is evaluated by computing the discriminant distance. By quantitatively measuring the amount of discriminative information in each composite vector, composite vectors containing informative variables can be distinguished and the final composite features for odor classification are extracted using the selected composite vectors. Using the only informative composite vectors can be also helpful to extract better composite features instead of using all the generated composite vectors. Experimental results with different volatile organic compound data show that the proposed system has good classification performance even in a noisy environment compared to other methods. PMID:24747735

Killing-Yano tensors in spaces admitting a hypersurface orthogonal Killing vector

NASA Astrophysics Data System (ADS)

Garfinkle, David; Glass, E. N.

2013-03-01

Methods are presented for finding Killing-Yano tensors, conformal Killing-Yano tensors, and conformal Killing vectors in spacetimes with a hypersurface orthogonal Killing vector. These methods are similar to a method developed by the authors for finding Killing tensors. In all cases one decomposes both the tensor and the equation it satisfies into pieces along the Killing vector and pieces orthogonal to the Killing vector. Solving the separate equations that result from this decomposition requires less computing than integrating the original equation. In each case, examples are given to illustrate the method.

Computing general-relativistic effects from Newtonian N-body simulations: Frame dragging in the post-Friedmann approach

NASA Astrophysics Data System (ADS)

Bruni, Marco; Thomas, Daniel B.; Wands, David

2014-02-01

We present the first calculation of an intrinsically relativistic quantity, the leading-order correction to Newtonian theory, in fully nonlinear cosmological large-scale structure studies. Traditionally, nonlinear structure formation in standard ΛCDM cosmology is studied using N-body simulations, based on Newtonian gravitational dynamics on an expanding background. When one derives the Newtonian regime in a way that is a consistent approximation to the Einstein equations, the first relativistic correction to the usual Newtonian scalar potential is a gravitomagnetic vector potential, giving rise to frame dragging. At leading order, this vector potential does not affect the matter dynamics, thus it can be computed from Newtonian N-body simulations. We explain how we compute the vector potential from simulations in ΛCDM and examine its magnitude relative to the scalar potential, finding that the power spectrum of the vector potential is of the order 10-5 times the scalar power spectrum over the range of nonlinear scales we consider. On these scales the vector potential is up to two orders of magnitudes larger than the value predicted by second-order perturbation theory extrapolated to the same scales. We also discuss some possible observable effects and future developments.

Relative Abundance and Plasmodium Infection Rates of Malaria Vectors in and around Jabalpur, a Malaria Endemic Region in Madhya Pradesh State, Central India.

PubMed

Singh, Neeru; Mishra, Ashok K; Chand, Sunil K; Bharti, Praveen K; Singh, Mrigendra P; Nanda, Nutan; Singh, Om P; Sodagiri, Kranti; Udhyakumar, Venkatachalam

2015-01-01

This study was undertaken in two Primary Health Centers (PHCs) of malaria endemic district Jabalpur in Madhya Pradesh (Central India). In this study we had investigated the relative frequencies of the different anopheline species collected within the study areas by using indoor resting catches, CDC light trap and human landing methods. Sibling species of malaria vectors were identified by cytogenetic and molecular techniques. The role of each vector and its sibling species in the transmission of the different Plasmodium species was ascertained by using sporozoite ELISA. A total of 52,857 specimens comprising of 17 anopheline species were collected by three different methods (39,964 by indoor resting collections, 1059 by human landing and 11,834 by CDC light trap). Anopheles culicifacies was most predominant species in all collections (55, 71 and 32% in indoor resting, human landing and light trap collections respectively) followed by An. subpictus and An. annularis. All five sibling species of An. culicifacies viz. species A, B, C, D and E were found while only species T and S of An. fluviatilis were collected. The overall sporozoite rate in An. culicifacies and An. fluviatilis were 0.42% (0.25% for P. falciparum and 0.17% for P. vivax) and 0.90% (0.45% for P. falciparum and 0.45% for P. vivax) respectively. An. culicifacies and An. fluviatilis were found harbouring both P. vivax variants VK-210 and VK-247, and P. falciparum. An. culicifacies sibling species C and D were incriminated as vectors during most part of the year while sibling species T of An. fluviatilis was identified as potential vector in monsoon and post monsoon season. An. culicifacies species C (59%) was the most abundant species followed by An. culicifacies D (24%), B (8.7%), E (6.7%) and A (1.5%). Among An. fluviatilis sibling species, species T was common (99%) and only few specimens of S were found. Our study provides crucial information on the prevalence of An. culicifacies and An. fluviatilis sibling species and their potential in malaria transmission which will assist in developing strategic control measures against these vectors.

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.

Optical computation using residue arithmetic.

PubMed

Huang, A; Tsunoda, Y; Goodman, J W; Ishihara, S

1979-01-15

Using residue arithmetic it is possible to perform additions, subtractions, multiplications, and polynomial evaluation without the necessity for carry operations. Calculations can, therefore, be performed in a fully parallel manner. Several different optical methods for performing residue arithmetic operations are described. A possible combination of such methods to form a matrix vector multiplier is considered. The potential advantages of optics in performing these kinds of operations are discussed.

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.

3D magnetization vector inversion based on fuzzy clustering: inversion algorithm, uncertainty analysis, and application to geology differentiation

NASA Astrophysics Data System (ADS)

Sun, J.; Li, Y.

2017-12-01

Magnetic data contain important information about the subsurface rocks that were magnetized in the geological history, which provides an important avenue to the study of the crustal heterogeneities associated with magmatic and hydrothermal activities. Interpretation of magnetic data has been widely used in mineral exploration, basement characterization and large scale crustal studies for several decades. However, interpreting magnetic data has been often complicated by the presence of remanent magnetizations with unknown magnetization directions. Researchers have developed different methods to deal with the challenges posed by remanence. We have developed a new and effective approach to inverting magnetic data for magnetization vector distributions characterized by region-wise consistency in the magnetization directions. This approach combines the classical Tikhonov inversion scheme with fuzzy C-means clustering algorithm, and constrains the estimated magnetization vectors to a specified small number of possible directions while fitting the observed magnetic data to within noise level. Our magnetization vector inversion recovers both the magnitudes and the directions of the magnetizations in the subsurface. Magnetization directions reflect the unique geological or hydrothermal processes applied to each geological unit, and therefore, can potentially be used for the purpose of differentiating various geological units. We have developed a practically convenient and effective way of assessing the uncertainty associated with the inverted magnetization directions (Figure 1), and investigated how geological differentiation results might be affected (Figure 2). The algorithm and procedures we have developed for magnetization vector inversion and uncertainty analysis open up new possibilities of extracting useful information from magnetic data affected by remanence. We will use a field data example from exploration of an iron-oxide-copper-gold (IOCG) deposit in Brazil to illustrate how to solve the inverse problem, assess uncertainty, and perform geology differentiation in practice. We will also discuss the potential applications of this new method to large scale crustal studies.

Experimental Evaluation of the High-Speed Motion Vector Measurement by Combining Synthetic Aperture Array Processing with Constrained Least Square Method

NASA Astrophysics Data System (ADS)

Yokoyama, Ryouta; Yagi, Shin-ichi; Tamura, Kiyoshi; Sato, Masakazu

2009-07-01

Ultrahigh speed dynamic elastography has promising potential capabilities in applying clinical diagnosis and therapy of living soft tissues. In order to realize the ultrahigh speed motion tracking at speeds of over thousand frames per second, synthetic aperture (SA) array signal processing technology must be introduced. Furthermore, the overall system performance should overcome the fine quantitative evaluation in accuracy and variance of echo phase changes distributed across a tissue medium. On spatial evaluation of local phase changes caused by pulsed excitation on a tissue phantom, investigation was made with the proposed SA signal system utilizing different virtual point sources that were generated by an array transducer to probe each component of local tissue displacement vectors. The final results derived from the cross-correlation method (CCM) brought about almost the same performance as obtained by the constrained least square method (LSM) extended to successive echo frames. These frames were reconstructed by SA processing after the real-time acquisition triggered by the pulsed irradiation from a point source. The continuous behavior of spatial motion vectors demonstrated the dynamic generation and traveling of the pulsed shear wave at a speed of one thousand frames per second.

Citrus tristeza virus-based RNAi in citrus plants induces gene silencing in Diaphorina citri, a phloem-sap sucking insect vector of citrus greening disease (Huanglongbing).

PubMed

Hajeri, Subhas; Killiny, Nabil; El-Mohtar, Choaa; Dawson, William O; Gowda, Siddarame

2014-04-20

A transient expression vector based on Citrus tristeza virus (CTV) is unusually stable. Because of its stability it is being considered for use in the field to control Huanglongbing (HLB), which is caused by Candidatus Liberibacter asiaticus (CLas) and vectored by Asian citrus psyllid, Diaphorina citri. In the absence of effective control strategies for CLas, emphasis has been on control of D. citri. Coincident cohabitation in phloem tissue by CLas, D. citri and CTV was exploited to develop a novel method to mitigate HLB through RNA interference (RNAi). Since CTV has three RNA silencing suppressors, it was not known if CTV-based vector could induce RNAi in citrus. Yet, expression of sequences targeting citrus phytoene desaturase gene by CTV-RNAi resulted in photo-bleaching phenotype. CTV-RNAi vector, engineered with truncated abnormal wing disc (Awd) gene of D. citri, induced altered Awd expression when silencing triggers ingested by feeding D. citri nymphs. Decreased Awd in nymphs resulted in malformed-wing phenotype in adults and increased adult mortality. This impaired ability of D. citri to fly would potentially limit the successful vectoring of CLas bacteria between citrus trees in the grove. CTV-RNAi vector would be relevant for fast-track screening of candidate sequences for RNAi-mediated pest control. Copyright © 2014. Published by Elsevier B.V.

Ex Vivo Adenoviral Vector Gene Delivery Results in Decreased Vector-associated Inflammation Pre- and Post–lung Transplantation in the Pig

PubMed Central

Yeung, Jonathan C; Wagnetz, Dirk; Cypel, Marcelo; Rubacha, Matthew; Koike, Terumoto; Chun, Yi-Min; Hu, Jim; Waddell, Thomas K; Hwang, David M; Liu, Mingyao; Keshavjee, Shaf

2012-01-01

Acellular normothermic ex vivo lung perfusion (EVLP) is a novel method of donor lung preservation for transplantation. As cellular metabolism is preserved during perfusion, it represents a potential platform for effective gene transduction in donor lungs. We hypothesized that vector-associated inflammation would be reduced during ex vivo delivery due to isolation from the host immune system response. We compared ex vivo with in vivo intratracheal delivery of an E1-, E3-deleted adenoviral vector encoding either green fluorescent protein (GFP) or interleukin-10 (IL-10) to porcine lungs. Twelve hours after delivery, the lung was transplanted and the post-transplant function assessed. We identified significant transgene expression by 12 hours in both in vivo and ex vivo delivered groups. Lung function remained excellent in all ex vivo groups after viral vector delivery; however, as expected, lung function decreased in the in vivo delivered adenovirus vector encoding GFP (AdGFP) group with corresponding increases in IL-1β levels. Transplanted lung function was excellent in the ex vivo transduced lungs and inferior lung function was seen in the in vivo group after transplantation. In summary, ex vivo delivery of adenoviral gene therapy to the donor lung is superior to in vivo delivery in that it leads to less vector-associated inflammation and provides superior post-transplant lung function. PMID:22453765

Functional and morphological analysis of putative chemoreception-related proteins in the lone star tick, Amblyomma americanum

USDA-ARS?s Scientific Manuscript database

Ehrlichiosis, a potentially fatal infection, is caused by rickettsial bacteria transmitted by the lone star tick, Amblyomma americanum. We previously analyzed the chemosensory appendage proteome of A. americanum as part of a project to develop new chemosensory-based vector control methods. Among the...

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

Current Knowledge of Leishmania Vectors in Mexico: How Geographic Distributions of Species Relate to Transmission Areas

PubMed Central

González, Camila; Rebollar-Téllez, Eduardo A.; Ibáñez-Bernal, Sergio; Becker-Fauser, Ingeborg; Martínez-Meyer, Enrique; Peterson, A. Townsend; Sánchez-Cordero, Víctor

2011-01-01

Leishmaniases are a group of vector-borne diseases with different clinical manifestations caused by parasites transmitted by sand fly vectors. In Mexico, the sand fly Lutzomyia olmeca olmeca is the only vector proven to transmit the parasite Leishmania mexicana to humans, which causes leishmaniasis. Other vector species with potential medical importance have been obtained, but their geographic distributions and relation to transmission areas have never been assessed. We modeled the ecological niches of nine sand fly species and projected niches to estimate potential distributions by using known occurrences, environmental coverages, and the algorithms GARP and Maxent. All vector species were distributed in areas with known recurrent transmission, except for Lu. diabolica, which appeared to be related only to areas of occasional transmission in northern Mexico. The distribution of Lu. o. olmeca does not overlap with all reported cutaneous leishmaniasis cases, suggesting that Lu. cruciata and Lu. shannoni are likely also involved as primary vectors in those areas. Our study provides useful information of potential risk areas of leishmaniasis transmission in Mexico. PMID:22049037

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.

Detection of potential mosquito breeding sites based on community sourced geotagged images

NASA Astrophysics Data System (ADS)

Agarwal, Ankit; Chaudhuri, Usashi; Chaudhuri, Subhasis; Seetharaman, Guna

2014-06-01

Various initiatives have been taken all over the world to involve the citizens in the collection and reporting of data to make better and informed data-driven decisions. Our work shows how the geotagged images collected through the general population can be used to combat Malaria and Dengue by identifying and visualizing localities that contain potential mosquito breeding sites. Our method first employs image quality assessment on the client side to reject the images with distortions like blur and artifacts. Each geotagged image received on the server is converted into a feature vector using the bag of visual words model. We train an SVM classifier on a histogram-based feature vector obtained after the vector quantization of SIFT features to discriminate images containing either a small stagnant water body like puddle, or open containers and tires, bushes etc. from those that contain flowing water, manicured lawns, tires attached to a vehicle etc. A geographical heat map is generated by assigning a specific location a probability value of it being a potential mosquito breeding ground of mosquito using feature level fusion or the max approach presented in the paper. The heat map thus generated can be used by concerned health authorities to take appropriate action and to promote civic awareness.

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.

PubMed

Song, Jiangning; Yuan, Zheng; Tan, Hao; Huber, Thomas; Burrage, Kevin

2007-12-01

Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications. We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects. The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfide

TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species

PubMed Central

Márcia de Oliveira, Luciana; Nogueira de Brito, Raissa; Anderson Souza Guimarães, Paul; Vitor Mastrângelo Amaro dos Santos, Rômulo; Gonçalves Diotaiuti, Liléia; de Cássia Moreira de Souza, Rita

2017-01-01

Abstract Triatomines are blood-sucking insects that transmit the causative agent of Chagas disease, Trypanosoma cruzi. Despite being recognized as a difficult task, the correct taxonomic identification of triatomine species is crucial for vector control in Latin America, where the disease is endemic. In this context, we have developed a web and mobile tool based on PostgreSQL database to help healthcare technicians to overcome the difficulties to identify triatomine vectors when the technical expertise is missing. The web and mobile version makes use of real triatomine species pictures and dichotomous key method to support the identification of potential vectors that occur in Brazil. It provides a user example-driven interface with simple language. TriatoKey can also be useful for educational purposes. Database URL: http://triatokey.cpqrr.fiocruz.br PMID:28605769

Polynomial chaos representation of databases on manifolds

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

Soize, C., E-mail: christian.soize@univ-paris-est.fr; Ghanem, R., E-mail: ghanem@usc.edu

2017-04-15

Characterizing the polynomial chaos expansion (PCE) of a vector-valued random variable with probability distribution concentrated on a manifold is a relevant problem in data-driven settings. The probability distribution of such random vectors is multimodal in general, leading to potentially very slow convergence of the PCE. In this paper, we build on a recent development for estimating and sampling from probabilities concentrated on a diffusion manifold. The proposed methodology constructs a PCE of the random vector together with an associated generator that samples from the target probability distribution which is estimated from data concentrated in the neighborhood of the manifold. Themore » method is robust and remains efficient for high dimension and large datasets. The resulting polynomial chaos construction on manifolds permits the adaptation of many uncertainty quantification and statistical tools to emerging questions motivated by data-driven queries.« less

Personal protection against biting insects and ticks

PubMed Central

2011-01-01

Recent events with the first cases of local transmission of chikungunya and dengue fever virus in southern France by Aedes albopictus, adding to the nuisance and potential vectors that can be encountered when traveling in tropical or sub-tropical countries, has shown the value of a reflection on the Personal protection against vectors (PPAV). It is seen during an outbreak of vector-borne disease, or simply because of nuisance arthropods, that our fellow citizens try to protect themselves individually by using an arsenal of resources available on the market. Yet most of these means have been neither checked for effectiveness or safety tests, however, essential. Travellers, staff on mission or assignment, are looking for specific information on how to protect themselves or their families. Health workers had at their disposal so far indications that vary widely from one source to another. Therefore it seemed important to the Society of Travel Medicine (SMV) and the French Society of Parasitology (SFP) to initiate a reflection on this theme. This reflection took the form of recommendations for good practice, following the outline established by the French High Health Authority (HAS). The aim was to gather all relevant information, verified and validated and the format to be used not only by health personnel (doctors, pharmacists, nurses), but also by travel agents and individuals. This document highlights the need to take into account the risk of vector-borne diseases, some deadly, and the benefit of various methods of personal protection. The choice of methods is clearly oriented towards those whose effectiveness has been proven and potential risks assessed. The paper finally proposes two decision trees based on the transmission type (day or night) and kind of stay (short or roaming, long and steady). It concerns travellers, but also expatriates, residents and nomads. PMID:21395212

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.

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue

PubMed Central

Kjeldsen, Henrik D.; Kaiser, Marcus; Whittington, Miles A.

2015-01-01

Background Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. New method Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. Results The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. Comparison with existing methods The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Conclusions Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions without bias from any prior assumptions on anatomical connectivity. PMID:26026581

Disentangling Vector-Borne Transmission Networks: A Universal DNA Barcoding Method to Identify Vertebrate Hosts from Arthropod Bloodmeals

PubMed Central

Alcaide, Miguel; Rico, Ciro; Ruiz, Santiago; Soriguer, Ramón; Muñoz, Joaquín; Figuerola, Jordi

2009-01-01

Emerging infectious diseases represent a challenge for global economies and public health. About one fourth of the last pandemics have been originated by the spread of vector-borne pathogens. In this sense, the advent of modern molecular techniques has enhanced our capabilities to understand vector-host interactions and disease ecology. However, host identification protocols have poorly profited of international DNA barcoding initiatives and/or have focused exclusively on a limited array of vector species. Therefore, ascertaining the potential afforded by DNA barcoding tools in other vector-host systems of human and veterinary importance would represent a major advance in tracking pathogen life cycles and hosts. Here, we show the applicability of a novel and efficient molecular method for the identification of the vertebrate host's DNA contained in the midgut of blood-feeding arthropods. To this end, we designed a eukaryote-universal forward primer and a vertebrate-specific reverse primer to selectively amplify 758 base pairs (bp) of the vertebrate mitochondrial Cytochrome c Oxidase Subunit I (COI) gene. Our method was validated using both extensive sequence surveys from the public domain and Polymerase Chain Reaction (PCR) experiments carried out over specimens from different Classes of vertebrates (Mammalia, Aves, Reptilia and Amphibia) and invertebrate ectoparasites (Arachnida and Insecta). The analysis of mosquito, culicoid, phlebotomie, sucking bugs, and tick bloodmeals revealed up to 40 vertebrate hosts, including 23 avian, 16 mammalian and one reptilian species. Importantly, the inspection and analysis of direct sequencing electropherograms also assisted the resolving of mixed bloodmeals. We therefore provide a universal and high-throughput diagnostic tool for the study of the ecology of haematophagous invertebrates in relation to their vertebrate hosts. Such information is crucial to support the efficient management of initiatives aimed at reducing epidemiologic risks of arthropod vector-borne pathogens, a priority for public health. PMID:19768113

Evaluation of the concentration and bioactivity of adenovirus vectors for gene therapy.

PubMed Central

Mittereder, N; March, K L; Trapnell, B C

1996-01-01

Development of adenovirus vectors as potential therapeutic agents for multiple applications of in vivo human gene therapy has resulted in numerous preclinical and clinical studies. However, lack of standardization of the methods for quantifying the physical concentration and functionally active fraction of virions in these studies has often made comparison between various studies difficult or impossible. This study was therefore carried out to define the variables for quantification of the concentration of adenovirus vectors. The methods for evaluation of total virion concentration included electron microscopy and optical absorbance. The methods for evaluation of the concentration of functional virions included detection of gene transfer (transgene transfer and expression) and the plaque assay on 293 cells. Enumeration of total virion concentration by optical absorbance was found to be a precise procedure, but accuracy was dependent on physical disruption of the virion to eliminate artifacts from light scattering and also on a correct value for the extinction coefficient. Both biological assays for enumerating functional virions were highly dependent on the assay conditions and in particular the time of virion adsorption and adsorption volume. Under optimal conditions, the bioactivity of the vector, defined as the fraction of total virions which leads to detected target cell infection, was determined to be 0.10 in the plaque assay and 0.29 in the gene transfer assay. This difference is most likely due to the fact that detection by gene transfer requires only measurement of levels of transgene expression in the infected cell whereas plaque formation is dependent on a series of biological events of much greater complexity. These results show that the exact conditions for determination of infectious virion concentration and bioactivity of recombinant adenovirus vectors are critical and must be standardized for comparability. These observations may be very useful in comparison of data from different preclinical and clinical studies and may also have important implications for how adenovirus vectors can optimally be used in human gene therapy. PMID:8892868

Entomological investigations into an epidemic of Japanese encephalitis (JE) in northern districts of West Bengal, India (2011-2012)

PubMed Central

Mariappan, T.; Samuel, P. Philip; Thenmozhi, V.; Paramasivan, R.; Sharma, Puran Kumar; Biswas, Asit Kumar; Tyagi, B.K.

2014-01-01

Background & objectives: Japanese encephalitis (JE) is one of the most important arboviral diseases of human beings with outbreaks in many parts of Southeast Asia including India. We present the entomological findings of an outbreak occurred in northern part of West Bengal during 2011-2012 with special emphasis on the role of JE vectors in different seasons. Methods: Adult mosquito collections were made with the help of mouth aspirators, aided by flash lights during day time resting inside human and animal habitations as indoor, and resting outside field grasses, bushes, underneath of culverts and bridges as outdoor, and in and around the pig enclosures and cattle sheds during dusk period in JE affected villages from Cooch Behar, Dakshin Dinajpur, Darjeeling and Jalpaiguri districts in North West Bengal. In all study villages, a long handled with enamel bowl dipper was used to obtain immature stages of mosquitoes from various breeding habitats. Results: A total of 19 different types of mosquito breeding habitats were examined for vectors of JE. From these habitats, 23.7 per cent were positive for breeding during the study period. Overall, nine different species were recorded through emergence, but none was positive for JE virus when subjected for detection of virus. Adult mosquitoes of more than 50 per cent of the potential JE vector species obtained through dusk and the rest through indoor and outdoor collections in all seasons. Altogether, 27 different species were recorded. Most of these were JE vectors. Interpretation & conclusions: Our results showed that in addition to Cx. vishnui subgroup, detection of JE virus antigen in Cx. quinquefasciatus indicated the possible maintenance of JE virus in nature through poor vector mosquitoes throughout the year. Since, all potential vector species reported elsewhere in India were also found in this region and fluctuated in density in different seasons, a proper integrated vector control programme needs to be implemented to control JE transmission. PMID:25027086

Visualization of flow by vector analysis of multidirectional cine MR velocity mapping.

PubMed

Mohiaddin, R H; Yang, G Z; Kilner, P J

1994-01-01

We describe a noninvasive method for visualization of flow and demonstrate its application in a flow phantom and in the great vessels of healthy volunteers and patients with aortic and pulmonary arterial disease. The technique uses multidirectional MR velocity mapping acquired in selected planes. Maps of orthogonal velocity components were then processed into a graphic form immediately recognizable as flow. Cine MR velocity maps of orthogonal velocity components in selected planes were acquired in a flow phantom, 10 healthy volunteers, and 13 patients with dilated great vessels. Velocities were presented by multiple computer-generated streaks whose orientation, length, and movement corresponded to velocity vectors in the chosen plane. The velocity vector maps allowed visualization of complex patterns of primary and secondary flow in the thoracic aorta and pulmonary arteries. The technique revealed coherent, helical forward blood movements in the normal thoracic aorta during midsystole and a reverse flow during early diastole. Abnormal flow patterns with secondary vortices were seen in patients with dilated arteries. The potential of MR velocity vector mapping for in vitro and in vivo visualization of flow patterns is demonstrated. Although this study was limited to two-directional flow in a single anatomical plane, the method provides information that might advance our understanding of the human vascular system in health and disease. Further developments to reduce the acquisition time and the handling and presenting of three-directional velocity data are required to enhance the capability of this method.

Virus immobilization on biomaterial scaffolds through biotin-avidin interaction for improving bone regeneration.

PubMed

Hu, Wei-Wen; Wang, Zhuo; Krebsbach, Paul H

2016-02-01

To spatially control therapeutic gene delivery for potential tissue engineering applications, a biotin-avidin interaction strategy was applied to immobilize viral vectors on biomaterial scaffolds. Both adenoviral vectors and gelatin sponges were biotinylated and avidin was applied to link them in a virus-biotin-avidin-biotin-material (VBABM) arrangement. The tethered viral particles were stably maintained within scaffolds and SEM images illustrated that viral particles were evenly distributed in three-dimensional (3D) gelatin sponges. An in vivo study demonstrated that transgene expression was restricted to the implant sites only and transduction efficiency was improved using this conjugation method. For an orthotopic bone regeneration model, adenovirus encoding BMP-2 (AdBMP2) was immobilized to gelatin sponges before implanting into critical-sized bone defects in rat calvaria. Compared to gelatin sponges with AdBMP2 loaded in a freely suspended form, the VBABM method enhanced gene transfer and bone regeneration was significantly improved. These results suggest that biotin-avidin immobilization of viral vectors to biomaterial scaffolds may be an effective strategy to facilitate tissue regeneration. Copyright © 2013 John Wiley & Sons, Ltd.

The Effects of Climate Change and Globalization on Mosquito Vectors: Evidence from Jeju Island, South Korea on the Potential for Asian Tiger Mosquito (Aedes albopictus) Influxes and Survival from Vietnam Rather Than Japan

PubMed Central

Jeong, Ji Yeon; Yoo, Seung Jin; Koh, Young-Sang; Lee, Seogjae; Heo, Sang Taek; Seong, Seung-Yong; Lee, Keun Hwa

2013-01-01

Background Climate change affects the survival and transmission of arthropod vectors as well as the development rates of vector-borne pathogens. Increased international travel is also an important factor in the spread of vector-borne diseases (VBDs) such as dengue, West Nile, yellow fever, chikungunya, and malaria. Dengue is the most important vector-borne viral disease. An estimated 2.5 billion people are at risk of infection in the world and there are approximately 50 million dengue infections and an estimated 500,000 individuals are hospitalized with dengue haemorrhagic fever annually. The Asian tiger mosquito (Aedes albopictus) is one of the vectors of dengue virus, and populations already exist on Jeju Island, South Korea. Currently, colder winter temperatures kill off Asian tiger mosquito populations and there is no evidence of the mosquitos being vectors for the dengue virus in this location. However, dengue virus-bearing mosquito vectors can inflow to Jeju Island from endemic area such as Vietnam by increased international travel, and this mosquito vector's survival during colder winter months will likely occur due to the effects of climate change. Methods and Results In this section, we show the geographical distribution of medically important mosquito vectors such as Ae. albopictus, a vector of both dengue and chikungunya viruses; Culex pipiens, a vector of West Nile virus; and Anopheles sinensis, a vector of Plasmodium vivax, within Jeju Island, South Korea. We found a significant association between the mean temperature, amount of precipitation, and density of mosquitoes. The phylogenetic analyses show that an Ae. albopictus, collected in southern area of Jeju Island, was identical to specimens found in Ho Chi Minh, Vietnam, and not Nagasaki, Japan. Conclusion Our results suggest that mosquito vectors or virus-bearing vectors can transmit from epidemic regions of Southeast Asia to Jeju Island and can survive during colder winter months. Therefore, Jeju Island is no longer safe from vector borne diseases (VBDs) due to the effects of globalization and climate change, and we should immediately monitor regional climate change to identify newly emerging VBDs. PMID:23894312

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.

Exploring the Use of Alfven Waves in Magnetometer Calibration at Geosynchronous Orbit

NASA Technical Reports Server (NTRS)

Bentley, John; Sheppard, David; RIch, Frederick; Redmon, Robert; Loto'aniu, Paul; Chu, Donald

2016-01-01

An Alfven wave is a type magnetohydrodynamicwave that travels through a conducting fluid under the influence of a magnetic field. Researchers have successfully calculated offset vectors of magnetometers in interplanetary space by optimizing the offset to maximize certain Alfvenic properties of observed waves (Leinweber, Belcher). If suitable Alfven waves can be found in the magnetosphere at geosynchronous altitude then these techniques could be used to augment the overall calibration plan for magnetometers in this region such as on the GOES spacecraft, possibly increasing the time between regular maneuvers. Calibration maneuvers may be undesirable because they disrupt the activities of other instruments. Various algorithms to calculate an offset using Alfven waves were considered. A new variation of the Davis-Smith method was derived because it can be mathematically shown that the Davis-Smith method tolerates filtered data, which expands potential applications. The variant developed was designed to find only the offset in the plane normal to the main field because the overall direction of Earth's magnetic field rarely changes, and theory suggests the Alfvenic disturbances occur transverse to the main field. Other variations of the Davis-Smith method encounter problems with data containing waves that propagate in mostly the same direction. A searching algorithm was then designed to look for periods of time with potential Alfven waves in GOES 15 data based on parameters requiring that disturbances be normal to the main field and not change field magnitude. Final waves for calculation were hand-selected. These waves produced credible two-dimensional offset vectors when input to the Davis-Smith method. Multiple two-dimensional solutions in different planes can be combined to get a measurement of the complete offset. The resulting three dimensional offset did not show sufficient precision over several years to be used as a primary calibration method, but reflected changes in the offset fairly well, suggesting that the method could be helpful in monitoring trends of the offset vector when maneuvers cannot be used.

A new EEG measure using the 1D cluster variation method

NASA Astrophysics Data System (ADS)

Maren, Alianna J.; Szu, Harold H.

2015-05-01

A new information measure, drawing on the 1-D Cluster Variation Method (CVM), describes local pattern distributions (nearest-neighbor and next-nearest neighbor) in a binary 1-D vector in terms of a single interaction enthalpy parameter h for the specific case where the fractions of elements in each of two states are the same (x1=x2=0.5). An example application of this method would be for EEG interpretation in Brain-Computer Interfaces (BCIs), especially in the frontier of invariant biometrics based on distinctive and invariant individual responses to stimuli containing an image of a person with whom there is a strong affiliative response (e.g., to a person's grandmother). This measure is obtained by mapping EEG observed configuration variables (z1, z2, z3 for next-nearest neighbor triplets) to h using the analytic function giving h in terms of these variables at equilibrium. This mapping results in a small phase space region of resulting h values, which characterizes local pattern distributions in the source data. The 1-D vector with equal fractions of units in each of the two states can be obtained using the method for transforming natural images into a binarized equi-probability ensemble (Saremi & Sejnowski, 2014; Stephens et al., 2013). An intrinsically 2-D data configuration can be mapped to 1-D using the 1-D Peano-Hilbert space-filling curve, which has demonstrated a 20 dB lower baseline using the method compared with other approaches (cf. SPIE ICA etc. by Hsu & Szu, 2014). This CVM-based method has multiple potential applications; one near-term one is optimizing classification of the EEG signals from a COTS 1-D BCI baseball hat. This can result in a convenient 3-D lab-tethered EEG, configured in a 1-D CVM equiprobable binary vector, and potentially useful for Smartphone wireless display. Longer-range applications include interpreting neural assembly activations via high-density implanted soft, cellular-scale electrodes.

Dual and mixed nonsymmetric stress-based variational formulations for coupled thermoelastodynamics with second sound effect

NASA Astrophysics Data System (ADS)

Tóth, Balázs

2018-03-01

Some new dual and mixed variational formulations based on a priori nonsymmetric stresses will be developed for linearly coupled irreversible thermoelastodynamic problems associated with second sound effect according to the Lord-Shulman theory. Having introduced the entropy flux vector instead of the entropy field and defining the dissipation and the relaxation potential as the function of the entropy flux, a seven-field dual and mixed variational formulation will be derived from the complementary Biot-Hamilton-type variational principle, using the Lagrange multiplier method. The momentum-, the displacement- and the infinitesimal rotation vector, and the a priori nonsymmetric stress tensor, the temperature change, the entropy field and its flux vector are considered as the independent field variables of this formulation. In order to handle appropriately the six different groups of temporal prescriptions in the relaxed- and/or the strong form, two variational integrals will be incorporated into the seven-field functional. Then, eliminating the entropy from this formulation through the strong fulfillment of the constitutive relation for the temperature change with the use of the Legendre transformation between the enthalpy and Gibbs potential, a six-field dual and mixed action functional is obtained. As a further development, the elimination of the momentum- and the velocity vector from the six-field principle through the a priori satisfaction of the kinematic equation and the constitutive relation for the momentum vector leads to a five-field variational formulation. These principles are suitable for the transient analyses of the structures exposed to a thermal shock of short temporal domain or a large heat flux.

Efficient generation of integration-free human induced pluripotent stem cells from keratinocytes by simple transfection of episomal vectors.

PubMed

Piao, Yulan; Hung, Sandy Shen-Chi; Lim, Shiang Y; Wong, Raymond Ching-Bong; Ko, Minoru S H

2014-07-01

Keratinocytes represent an easily accessible cell source for derivation of human induced pluripotent stem (hiPS) cells, reportedly achieving higher reprogramming efficiency than fibroblasts. However, most studies utilized a retroviral or lentiviral method for reprogramming of keratinocytes, which introduces undesirable transgene integrations into the host genome. Moreover, current protocols of generating integration-free hiPS cells from keratinocytes are mostly inefficient. In this paper, we describe a more efficient, simple-to-use, and cost-effective method for generating integration-free hiPS cells from keratinocytes. Our improved method using lipid-mediated transfection achieved a reprogramming efficiency of ∼0.14% on average. Keratinocyte-derived hiPS cells showed no integration of episomal vectors, expressed stem cell-specific markers and possessed potentials to differentiate into all three germ layers by in vitro embryoid body formation as well as in vivo teratoma formation. To our knowledge, this represents the most efficient method to generate integration-free hiPS cells from keratinocytes. ©AlphaMed Press.

Using remote sensing, ecological niche modeling, and Geographic Information Systems for Rift Valley fever risk assessment in the United States

NASA Astrophysics Data System (ADS)

Tedrow, Christine Atkins

The primary goal in this study was to explore remote sensing, ecological niche modeling, and Geographic Information Systems (GIS) as aids in predicting candidate Rift Valley fever (RVF) competent vector abundance and distribution in Virginia, and as means of estimating where risk of establishment in mosquitoes and risk of transmission to human populations would be greatest in Virginia. A second goal in this study was to determine whether the remotely-sensed Normalized Difference Vegetation Index (NDVI) can be used as a proxy variable of local conditions for the development of mosquitoes to predict mosquito species distribution and abundance in Virginia. As part of this study, a mosquito surveillance database was compiled to archive the historical patterns of mosquito species abundance in Virginia. In addition, linkages between mosquito density and local environmental and climatic patterns were spatially and temporally examined. The present study affirms the potential role of remote sensing imagery for species distribution prediction, and it demonstrates that ecological niche modeling is a valuable predictive tool to analyze the distributions of populations. The MaxEnt ecological niche modeling program was used to model predicted ranges for potential RVF competent vectors in Virginia. The MaxEnt model was shown to be robust, and the candidate RVF competent vector predicted distribution map is presented. The Normalized Difference Vegetation Index (NDVI) was found to be the most useful environmental-climatic variable to predict mosquito species distribution and abundance in Virginia. However, these results indicate that a more robust prediction is obtained by including other environmental-climatic factors correlated to mosquito densities (e.g., temperature, precipitation, elevation) with NDVI. The present study demonstrates that remote sensing and GIS can be used with ecological niche and risk modeling methods to estimate risk of virus establishment in mosquitoes and transmission to humans. Maps delineating the geographic areas in Virginia with highest risk for RVF establishment in mosquito populations and RVF disease transmission to human populations were generated in a GIS using human, domestic animal, and white-tailed deer population estimates and the MaxEnt potential RVF competent vector species distribution prediction. The candidate RVF competent vector predicted distribution and RVF risk maps presented in this study can help vector control agencies and public health officials focus Rift Valley fever surveillance efforts in geographic areas with large co-located populations of potential RVF competent vectors and human, domestic animal, and wildlife hosts. Keywords. Rift Valley fever, risk assessment, Ecological Niche Modeling, MaxEnt, Geographic Information System, remote sensing, Pearson's Product-Moment Correlation Coefficient, vectors, mosquito distribution, mosquito density, mosquito surveillance, United States, Virginia, domestic animals, white-tailed deer, ArcGIS

HSV as a vector in vaccine development and gene therapy.

PubMed

Marconi, Peggy; Argnani, Rafaela; Epstein, Alberto L; Manservigi, Roberto

2009-01-01

The very deep knowledge acquired on the genetics and molecular biology of herpes simplex virus (HSV), major human pathogen whose lifestyle is based on a long-term dual interaction with the infected host characterized by the existence of lytic and latent infections, has allowed the development of potential vectors for several applications in human healthcare. These include delivery and expression of human genes to cells of the nervous system, selective destruction of cancer cells, prophylaxis against infection with HSV or other infectious diseases and targeted infection of specific tissues or organs. Three different classes of vectors can be derived from HSV-1: replication-competent attenuated vectors, replication-incompetent recombinant vectors and defective helper-dependent vectors known as amplicons. This chapter highlights the current knowledge concerning design, construction and recent applications, as well as the potential and current limitations of the three different classes of HSV-1-based vectors.

Pre-existing immunity against vaccine vectors – friend or foe?

PubMed Central

Saxena, Manvendra; Van, Thi Thu Hao; Baird, Fiona J.; Coloe, Peter J.

2013-01-01

Over the last century, the successful attenuation of multiple bacterial and viral pathogens has led to an effective, robust and safe form of vaccination. Recently, these vaccines have been evaluated as delivery vectors for heterologous antigens, as a means of simultaneous vaccination against two pathogens. The general consensus from published studies is that these vaccine vectors have the potential to be both safe and efficacious. However, some of the commonly employed vectors, for example Salmonella and adenovirus, often have pre-existing immune responses in the host and this has the potential to modify the subsequent immune response to a vectored antigen. This review examines the literature on this topic, and concludes that for bacterial vectors there can in fact, in some cases, be an enhancement in immunogenicity, typically humoral, while for viral vectors pre-existing immunity is a hindrance for subsequent induction of cell-mediated responses. PMID:23175507

Risk Transmission Indicator of Schistosomiasis Japonicum Considering Human Activities 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

This paper present the method used to determine the areas where schistosomiasis transmission is the higher. A primary work was necessary to this study: identification of potential presence of schistosomiasis japonicum’s vector in Poyang lakeshore area (Jiangxi Province, P.R. China). Results obtained from its first work were crossing with the most risky human activities and with villages to elaborate a level of transmission risk. The first parameter determined concern fishing, which was identified like the most risky activity for schistosomiasis transmission, and fish traps were digitalized using a very high resolution ALOS data. The second parameter is about the risky areas for buffalo grazing, and vector potential presence areas were crossed with village proximity to determine the most risky areas for human transmission. The third parameter built is a level of risk for each village digitalized around Poyang Lake, taking into account the proximity and level of potential presence of vector’s areas.

Competence of Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus Mosquitoes as Zika Virus Vectors, China.

PubMed

Liu, Zhuanzhuan; Zhou, Tengfei; Lai, Zetian; Zhang, Zhenhong; Jia, Zhirong; Zhou, Guofa; Williams, Tricia; Xu, Jiabao; Gu, Jinbao; Zhou, Xiaohong; Lin, Lifeng; Yan, Guiyun; Chen, Xiao-Guang

2017-07-01

In China, the prevention and control of Zika virus disease has been a public health threat since the first imported case was reported in February 2016. To determine the vector competence of potential vector mosquito species, we experimentally infected Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus mosquitoes and determined infection rates, dissemination rates, and transmission rates. We found the highest vector competence for the imported Zika virus in Ae. aegypti mosquitoes, some susceptibility of Ae. albopictus mosquitoes, but no transmission ability for Cx. quinquefasciatus mosquitoes. Considering that, in China, Ae. albopictus mosquitoes are widely distributed but Ae. aegypti mosquito distribution is limited, Ae. albopictus mosquitoes are a potential primary vector for Zika virus and should be targeted in vector control strategies.

Competence of Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus Mosquitoes as Zika Virus Vectors, China

PubMed Central

Liu, Zhuanzhuan; Zhou, Tengfei; Lai, Zetian; Zhang, Zhenhong; Jia, Zhirong; Zhou, Guofa; Williams, Tricia; Xu, Jiabao; Gu, Jinbao; Zhou, Xiaohong; Lin, Lifeng; Yan, Guiyun

2017-01-01

In China, the prevention and control of Zika virus disease has been a public health threat since the first imported case was reported in February 2016. To determine the vector competence of potential vector mosquito species, we experimentally infected Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus mosquitoes and determined infection rates, dissemination rates, and transmission rates. We found the highest vector competence for the imported Zika virus in Ae. aegypti mosquitoes, some susceptibility of Ae. albopictus mosquitoes, but no transmission ability for Cx. quinquefasciatus mosquitoes. Considering that, in China, Ae. albopictus mosquitoes are widely distributed but Ae. aegypti mosquito distribution is limited, Ae. albopictus mosquitoes are a potential primary vector for Zika virus and should be targeted in vector control strategies. PMID:28430562

A Guided Tour of Mathematical Methods for the Physical Sciences

NASA Astrophysics Data System (ADS)

Snieder, Roel; van Wijk, Kasper

2015-05-01

1. Introduction; 2. Dimensional analysis; 3. Power series; 4. Spherical and cylindrical coordinates; 5. Gradient; 6. Divergence of a vector field; 7. Curl of a vector field; 8. Theorem of Gauss; 9. Theorem of Stokes; 10. The Laplacian; 11. Scale analysis; 12. Linear algebra; 13. Dirac delta function; 14. Fourier analysis; 15. Analytic functions; 16. Complex integration; 17. Green's functions: principles; 18. Green's functions: examples; 19. Normal modes; 20. Potential-field theory; 21. Probability and statistics; 22. Inverse problems; 23. Perturbation theory; 24. Asymptotic evaluation of integrals; 25. Conservation laws; 26. Cartesian tensors; 27. Variational calculus; 28. Epilogue on power and knowledge.

Optimization of Support Vector Machine (SVM) for Object Classification

NASA Technical Reports Server (NTRS)

Scholten, Matthew; Dhingra, Neil; Lu, Thomas T.; Chao, Tien-Hsin

2012-01-01

The Support Vector Machine (SVM) is a powerful algorithm, useful in classifying data into species. The SVMs implemented in this research were used as classifiers for the final stage in a Multistage Automatic Target Recognition (ATR) system. A single kernel SVM known as SVMlight, and a modified version known as a SVM with K-Means Clustering were used. These SVM algorithms were tested as classifiers under varying conditions. Image noise levels varied, and the orientation of the targets changed. The classifiers were then optimized to demonstrate their maximum potential as classifiers. Results demonstrate the reliability of SVM as a method for classification. From trial to trial, SVM produces consistent results.

Direct model-based predictive control scheme without cost function for voltage source inverters with reduced common-mode voltage

NASA Astrophysics Data System (ADS)

Kim, Jae-Chang; Moon, Sung-Ki; Kwak, Sangshin

2018-04-01

This paper presents a direct model-based predictive control scheme for voltage source inverters (VSIs) with reduced common-mode voltages (CMVs). The developed method directly finds optimal vectors without using repetitive calculation of a cost function. To adjust output currents with the CMVs in the range of -Vdc/6 to +Vdc/6, the developed method uses voltage vectors, as finite control resources, excluding zero voltage vectors which produce the CMVs in the VSI within ±Vdc/2. In a model-based predictive control (MPC), not using zero voltage vectors increases the output current ripples and the current errors. To alleviate these problems, the developed method uses two non-zero voltage vectors in one sampling step. In addition, the voltage vectors scheduled to be used are directly selected at every sampling step once the developed method calculates the future reference voltage vector, saving the efforts of repeatedly calculating the cost function. And the two non-zero voltage vectors are optimally allocated to make the output current approach the reference current as close as possible. Thus, low CMV, rapid current-following capability and sufficient output current ripple performance are attained by the developed method. The results of a simulation and an experiment verify the effectiveness of the developed method.

The Dynamic Force Table

ERIC Educational Resources Information Center

Geddes, John B.; Black, Kelly

2008-01-01

We examine an experimental apparatus that is used to motivate the connections between the basic properties of vectors, potential functions, systems of nonlinear equations, and Newton's method for nonlinear systems of equations. The apparatus is an adaptation of a force table where we remove the center-pin and allow the center-ring to move freely.…

Full potential methods for analysis/design of complex aerospace configurations

NASA Technical Reports Server (NTRS)

Shankar, Vijaya; Szema, Kuo-Yen; Bonner, Ellwood

1986-01-01

The steady form of the full potential equation, in conservative form, is employed to analyze and design a wide variety of complex aerodynamic shapes. The nonlinear method is based on the theory of characteristic signal propagation coupled with novel flux biasing concepts and body-fitted mapping procedures. The resulting codes are vectorized for the CRAY XMP and the VPS-32 supercomputers. Use of the full potential nonlinear theory is demonstrated for a single-point supersonic wing design and a multipoint design for transonic maneuver/supersonic cruise/maneuver conditions. Achievement of high aerodynamic efficiency through numerical design is verified by wind tunnel tests. Other studies reported include analyses of a canard/wing/nacelle fighter geometry.

Spherical earth gravity and magnetic anomaly analysis by equivalent point source inversion

NASA Technical Reports Server (NTRS)

Von Frese, R. R. B.; Hinze, W. J.; Braile, L. W.

1981-01-01

To facilitate geologic interpretation of satellite elevation potential field data, analysis techniques are developed and verified in the spherical domain that are commensurate with conventional flat earth methods of potential field interpretation. A powerful approach to the spherical earth problem relates potential field anomalies to a distribution of equivalent point sources by least squares matrix inversion. Linear transformations of the equivalent source field lead to corresponding geoidal anomalies, pseudo-anomalies, vector anomaly components, spatial derivatives, continuations, and differential magnetic pole reductions. A number of examples using 1 deg-averaged surface free-air gravity anomalies of POGO satellite magnetometer data for the United States, Mexico, and Central America illustrate the capabilities of the method.

A multistage motion vector processing method for motion-compensated frame interpolation.

PubMed

Huang, Ai- Mei; Nguyen, Truong Q

2008-05-01

In this paper, a novel, low-complexity motion vector processing algorithm at the decoder is proposed for motion-compensated frame interpolation or frame rate up-conversion. We address the problems of having broken edges and deformed structures in an interpolated frame by hierarchically refining motion vectors on different block sizes. Our method explicitly considers the reliability of each received motion vector and has the capability of preserving the structure information. This is achieved by analyzing the distribution of residual energies and effectively merging blocks that have unreliable motion vectors. The motion vector reliability information is also used as a prior knowledge in motion vector refinement using a constrained vector median filter to avoid choosing identical unreliable one. We also propose using chrominance information in our method. Experimental results show that the proposed scheme has better visual quality and is also robust, even in video sequences with complex scenes and fast motion.

Recent advances in reduction methods for nonlinear problems. [in structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1981-01-01

Status and some recent developments in the application of reduction methods to nonlinear structural mechanics problems are summarized. The aspects of reduction methods discussed herein include: (1) selection of basis vectors in nonlinear static and dynamic problems, (2) application of reduction methods in nonlinear static analysis of structures subjected to prescribed edge displacements, and (3) use of reduction methods in conjunction with mixed finite element models. Numerical examples are presented to demonstrate the effectiveness of reduction methods in nonlinear problems. Also, a number of research areas which have high potential for application of reduction methods are identified.

Detection of ferromagnetic target based on mobile magnetic gradient tensor system

NASA Astrophysics Data System (ADS)

Gang, Y. I. N.; Yingtang, Zhang; Zhining, Li; Hongbo, Fan; Guoquan, Ren

2016-03-01

Attitude change of mobile magnetic gradient tensor system critically affects the precision of gradient measurements, thereby increasing ambiguity in target detection. This paper presents a rotational invariant-based method for locating and identifying ferromagnetic targets. Firstly, unit magnetic moment vector was derived based on the geometrical invariant, such that the intermediate eigenvector of the magnetic gradient tensor is perpendicular to the magnetic moment vector and the source-sensor displacement vector. Secondly, unit source-sensor displacement vector was derived based on the characteristic that the angle between magnetic moment vector and source-sensor displacement is a rotational invariant. By introducing a displacement vector between two measurement points, the magnetic moment vector and the source-sensor displacement vector were theoretically derived. To resolve the problem of measurement noises existing in the realistic detection applications, linear equations were formulated using invariants corresponding to several distinct measurement points and least square solution of magnetic moment vector and source-sensor displacement vector were obtained. Results of simulation and principal verification experiment showed the correctness of the analytical method, along with the practicability of the least square method.

Screening Mosquito House Entry Points as a Potential Method for Integrated Control of Endophagic Filariasis, Arbovirus and Malaria Vectors

PubMed Central

Ogoma, Sheila B.; Lweitoijera, Dickson W.; Ngonyani, Hassan; Furer, Benjamin; Russell, Tanya L.; Mukabana, Wolfgang R.; Killeen, Gerry F.; Moore, Sarah J.

2010-01-01

Background Partial mosquito-proofing of houses with screens and ceilings has the potential to reduce indoor densities of malaria mosquitoes. We wish to measure whether it will also reduce indoor densities of vectors of neglected tropical diseases. Methodology The main house entry points preferred by anopheline and culicine vectors were determined through controlled experiments using specially designed experimental huts and village houses in Lupiro village, southern Tanzania. The benefit of screening different entry points (eaves, windows and doors) using PVC-coated fibre glass netting material in terms of reduced indoor densities of mosquitoes was evaluated compared to the control. Findings 23,027 mosquitoes were caught with CDC light traps; 77.9% (17,929) were Anopheles gambiae sensu lato, of which 66.2% were An. arabiensis and 33.8% An. gambiae sensu stricto. The remainder comprised 0.2% (50) An. funestus, 10.2% (2359) Culex spp. and 11.6% (2664) Mansonia spp. Screening eaves reduced densities of Anopheles gambiae s. l. (Relative ratio (RR)  = 0.91; 95% CI = 0.84, 0.98; P = 0.01); Mansonia africana (RR = 0.43; 95% CI = 0.26, 0.76; P<0.001) and Mansonia uniformis (RR = 0.37; 95% CI = 0.25, 0.56; P<0.001) but not Culex quinquefasciatus, Cx. univittatus or Cx. theileri. Numbers of these species were reduced by screening windows and doors but this was not significant. Significance This study confirms that across Africa, screening eaves protects households against important mosquito vectors of filariasis, Rift Valley Fever and O'Nyong nyong as well as malaria. While full house screening is required to exclude Culex species mosquitoes, screening of eaves alone or fitting ceilings has considerable potential for integrated control of other vectors of filariasis, arbovirus and malaria. PMID:20689815

The maximum vector-angular margin classifier and its fast training on large datasets using a core vector machine.

PubMed

Hu, Wenjun; Chung, Fu-Lai; Wang, Shitong

2012-03-01

Although pattern classification has been extensively studied in the past decades, how to effectively solve the corresponding training on large datasets is a problem that still requires particular attention. Many kernelized classification methods, such as SVM and SVDD, can be formulated as the corresponding quadratic programming (QP) problems, but computing the associated kernel matrices requires O(n2)(or even up to O(n3)) computational complexity, where n is the size of the training patterns, which heavily limits the applicability of these methods for large datasets. In this paper, a new classification method called the maximum vector-angular margin classifier (MAMC) is first proposed based on the vector-angular margin to find an optimal vector c in the pattern feature space, and all the testing patterns can be classified in terms of the maximum vector-angular margin ρ, between the vector c and all the training data points. Accordingly, it is proved that the kernelized MAMC can be equivalently formulated as the kernelized Minimum Enclosing Ball (MEB), which leads to a distinctive merit of MAMC, i.e., it has the flexibility of controlling the sum of support vectors like v-SVC and may be extended to a maximum vector-angular margin core vector machine (MAMCVM) by connecting the core vector machine (CVM) method with MAMC such that the corresponding fast training on large datasets can be effectively achieved. Experimental results on artificial and real datasets are provided to validate the power of the proposed methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

Identification of cardiac rhythm features by mathematical analysis of vector fields.

PubMed

Fitzgerald, Tamara N; Brooks, Dana H; Triedman, John K

2005-01-01

Automated techniques for locating cardiac arrhythmia features are limited, and cardiologists generally rely on isochronal maps to infer patterns in the cardiac activation sequence during an ablation procedure. Velocity vector mapping has been proposed as an alternative method to study cardiac activation in both clinical and research environments. In addition to the visual cues that vector maps can provide, vector fields can be analyzed using mathematical operators such as the divergence and curl. In the current study, conduction features were extracted from velocity vector fields computed from cardiac mapping data. The divergence was used to locate ectopic foci and wavefront collisions, and the curl to identify central obstacles in reentrant circuits. Both operators were applied to simulated rhythms created from a two-dimensional cellular automaton model, to measured data from an in situ experimental canine model, and to complex three-dimensional human cardiac mapping data sets. Analysis of simulated vector fields indicated that the divergence is useful in identifying ectopic foci, with a relatively small number of vectors and with errors of up to 30 degrees in the angle measurements. The curl was useful for identifying central obstacles in reentrant circuits, and the number of velocity vectors needed increased as the rhythm became more complex. The divergence was able to accurately identify canine in situ pacing sites, areas of breakthrough activation, and wavefront collisions. In data from human arrhythmias, the divergence reliably estimated origins of electrical activity and wavefront collisions, but the curl was less reliable at locating central obstacles in reentrant circuits, possibly due to the retrospective nature of data collection. The results indicate that the curl and divergence operators applied to velocity vector maps have the potential to add valuable information in cardiac mapping and can be used to supplement human pattern recognition.

Genetic engineering of human embryonic stem cells with lentiviral vectors.

PubMed

Xiong, Chen; Tang, Dong-Qi; Xie, Chang-Qing; Zhang, Li; Xu, Ke-Feng; Thompson, Winston E; Chou, Wayne; Gibbons, Gary H; Chang, Lung-Ji; Yang, Li-Jun; Chen, Yuqing E

2005-08-01

Human embryonic stem (hES) cells present a valuable source of cells with a vast therapeutic potential. However, the low efficiency of directed differentiation of hES cells remains a major obstacle in their uses for regenerative medicine. While differentiation may be controlled by the genetic manipulation, effective and efficient gene transfer into hES cells has been an elusive goal. Here, we show stable and efficient genetic manipulations of hES cells using lentiviral vectors. This method resulted in the establishment of stable gene expression without loss of pluripotency in hES cells. In addition, lentiviral vectors were effective in conveying the expression of an U6 promoter-driven small interfering RNA (siRNA), which was effective in silencing its specific target. Taken together, our results suggest that lentiviral gene delivery holds great promise for hES cell research and application.

Feature Vector Construction Method for IRIS Recognition

NASA Astrophysics Data System (ADS)

Odinokikh, G.; Fartukov, A.; Korobkin, M.; Yoo, J.

2017-05-01

One of the basic stages of iris recognition pipeline is iris feature vector construction procedure. The procedure represents the extraction of iris texture information relevant to its subsequent comparison. Thorough investigation of feature vectors obtained from iris showed that not all the vector elements are equally relevant. There are two characteristics which determine the vector element utility: fragility and discriminability. Conventional iris feature extraction methods consider the concept of fragility as the feature vector instability without respect to the nature of such instability appearance. This work separates sources of the instability into natural and encodinginduced which helps deeply investigate each source of instability independently. According to the separation concept, a novel approach of iris feature vector construction is proposed. The approach consists of two steps: iris feature extraction using Gabor filtering with optimal parameters and quantization with separated preliminary optimized fragility thresholds. The proposed method has been tested on two different datasets of iris images captured under changing environmental conditions. The testing results show that the proposed method surpasses all the methods considered as a prior art by recognition accuracy on both datasets.

Human action classification using procrustes shape theory

NASA Astrophysics Data System (ADS)

Cho, Wanhyun; Kim, Sangkyoon; Park, Soonyoung; Lee, Myungeun

2015-02-01

In this paper, we propose new method that can classify a human action using Procrustes shape theory. First, we extract a pre-shape configuration vector of landmarks from each frame of an image sequence representing an arbitrary human action, and then we have derived the Procrustes fit vector for pre-shape configuration vector. Second, we extract a set of pre-shape vectors from tanning sample stored at database, and we compute a Procrustes mean shape vector for these preshape vectors. Third, we extract a sequence of the pre-shape vectors from input video, and we project this sequence of pre-shape vectors on the tangent space with respect to the pole taking as a sequence of mean shape vectors corresponding with a target video. And we calculate the Procrustes distance between two sequences of the projection pre-shape vectors on the tangent space and the mean shape vectors. Finally, we classify the input video into the human action class with minimum Procrustes distance. We assess a performance of the proposed method using one public dataset, namely Weizmann human action dataset. Experimental results reveal that the proposed method performs very good on this dataset.

Vectorized Monte Carlo methods for reactor lattice analysis

NASA Technical Reports Server (NTRS)

Brown, F. B.

1984-01-01

Some of the new computational methods and equivalent mathematical representations of physics models used in the MCV code, a vectorized continuous-enery Monte Carlo code for use on the CYBER-205 computer are discussed. While the principal application of MCV is the neutronics analysis of repeating reactor lattices, the new methods used in MCV should be generally useful for vectorizing Monte Carlo for other applications. For background, a brief overview of the vector processing features of the CYBER-205 is included, followed by a discussion of the fundamentals of Monte Carlo vectorization. The physics models used in the MCV vectorized Monte Carlo code are then summarized. The new methods used in scattering analysis are presented along with details of several key, highly specialized computational routines. Finally, speedups relative to CDC-7600 scalar Monte Carlo are discussed.

Construction and Characterization of an in-vivo Linear Covalently Closed DNA Vector Production System

PubMed Central

2012-01-01

Background While safer than their viral counterparts, conventional non-viral gene delivery DNA vectors offer a limited safety profile. They often result in the delivery of unwanted prokaryotic sequences, antibiotic resistance genes, and the bacterial origins of replication to the target, which may lead to the stimulation of unwanted immunological responses due to their chimeric DNA composition. Such vectors may also impart the potential for chromosomal integration, thus potentiating oncogenesis. We sought to engineer an in vivo system for the quick and simple production of safer DNA vector alternatives that were devoid of non-transgene bacterial sequences and would lethally disrupt the host chromosome in the event of an unwanted vector integration event. Results We constructed a parent eukaryotic expression vector possessing a specialized manufactured multi-target site called “Super Sequence”, and engineered E. coli cells (R-cell) that conditionally produce phage-derived recombinase Tel (PY54), TelN (N15), or Cre (P1). Passage of the parent plasmid vector through R-cells under optimized conditions, resulted in rapid, efficient, and one step in vivo generation of mini lcc—linear covalently closed (Tel/TelN-cell), or mini ccc—circular covalently closed (Cre-cell), DNA constructs, separated from the backbone plasmid DNA. Site-specific integration of lcc plasmids into the host chromosome resulted in chromosomal disruption and 105 fold lower viability than that seen with the ccc counterpart. Conclusion We offer a high efficiency mini DNA vector production system that confers simple, rapid and scalable in vivo production of mini lcc DNA vectors that possess all the benefits of “minicircle” DNA vectors and virtually eliminate the potential for undesirable vector integration events. PMID:23216697

Construction and characterization of an in-vivo linear covalently closed DNA vector production system.

PubMed

Nafissi, Nafiseh; Slavcev, Roderick

2012-12-06

While safer than their viral counterparts, conventional non-viral gene delivery DNA vectors offer a limited safety profile. They often result in the delivery of unwanted prokaryotic sequences, antibiotic resistance genes, and the bacterial origins of replication to the target, which may lead to the stimulation of unwanted immunological responses due to their chimeric DNA composition. Such vectors may also impart the potential for chromosomal integration, thus potentiating oncogenesis. We sought to engineer an in vivo system for the quick and simple production of safer DNA vector alternatives that were devoid of non-transgene bacterial sequences and would lethally disrupt the host chromosome in the event of an unwanted vector integration event. We constructed a parent eukaryotic expression vector possessing a specialized manufactured multi-target site called "Super Sequence", and engineered E. coli cells (R-cell) that conditionally produce phage-derived recombinase Tel (PY54), TelN (N15), or Cre (P1). Passage of the parent plasmid vector through R-cells under optimized conditions, resulted in rapid, efficient, and one step in vivo generation of mini lcc--linear covalently closed (Tel/TelN-cell), or mini ccc--circular covalently closed (Cre-cell), DNA constructs, separated from the backbone plasmid DNA. Site-specific integration of lcc plasmids into the host chromosome resulted in chromosomal disruption and 10(5) fold lower viability than that seen with the ccc counterpart. We offer a high efficiency mini DNA vector production system that confers simple, rapid and scalable in vivo production of mini lcc DNA vectors that possess all the benefits of "minicircle" DNA vectors and virtually eliminate the potential for undesirable vector integration events.

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.

Robust and accurate vectorization of line drawings.

PubMed

Hilaire, Xavier; Tombre, Karl

2006-06-01

This paper presents a method for vectorizing the graphical parts of paper-based line drawings. The method consists of separating the input binary image into layers of homogeneous thickness, skeletonizing each layer, segmenting the skeleton by a method based on random sampling, and simplifying the result. The segmentation method is robust with a best bound of 50 percent noise reached for indefinitely long primitives. Accurate estimation of the recognized vector's parameters is enabled by explicitly computing their feasibility domains. Theoretical performance analysis and expression of the complexity of the segmentation method are derived. Experimental results and comparisons with other vectorization systems are also provided.

Method and system for operating an electric motor

DOEpatents

Gallegos-Lopez, Gabriel; Hiti, Silva; Perisic, Milun

2013-01-22

Methods and systems for operating an electric motor having a plurality of windings with an inverter having a plurality of switches coupled to a voltage source are provided. A first plurality of switching vectors is applied to the plurality of switches. The first plurality of switching vectors includes a first ratio of first magnitude switching vectors to second magnitude switching vectors. A direct current (DC) current associated with the voltage source is monitored during the applying of the first plurality of switching vectors to the plurality of switches. A second ratio of the first magnitude switching vectors to the second magnitude switching vectors is selected based on the monitoring of the DC current associated with the voltage source. A second plurality of switching vectors is applied to the plurality of switches. The second plurality of switching vectors includes the second ratio of the first magnitude switching vectors to the second magnitude switching vectors.

Sine Rotation Vector Method for Attitude Estimation of an Underwater Robot

PubMed Central

Ko, Nak Yong; Jeong, Seokki; Bae, Youngchul

2016-01-01

This paper describes a method for estimating the attitude of an underwater robot. The method employs a new concept of sine rotation vector and uses both an attitude heading and reference system (AHRS) and a Doppler velocity log (DVL) for the purpose of measurement. First, the acceleration and magnetic-field measurements are transformed into sine rotation vectors and combined. The combined sine rotation vector is then transformed into the differences between the Euler angles of the measured attitude and the predicted attitude; the differences are used to correct the predicted attitude. The method was evaluated according to field-test data and simulation data and compared to existing methods that calculate angular differences directly without a preceding sine rotation vector transformation. The comparison verifies that the proposed method improves the attitude estimation performance. PMID:27490549

Monitoring Malaria Vector Control Interventions: Effectiveness of Five Different Adult Mosquito Sampling Methods

PubMed Central

Onyango, Shirley A.; Kitron, Uriel; Mungai, Peter; Muchiri, Eric M.; Kokwaro, Elizabeth; King, Charles H.; Mutuku, Francis M.

2014-01-01

Long-term success of ongoing malaria control efforts based on mosquito bed nets (long-lasting insecticidal net) and indoor residual spraying is dependent on continuous monitoring of mosquito vectors, and thus on effective mosquito sampling tools. The objective of our study was to identify the most efficient mosquito sampling tool(s) for routine vector surveillance for malaria and lymphatic filariasis transmission in coastal Kenya. We evaluated relative efficacy of five collection methods—light traps associated with a person sleeping under a net, pyrethrum spray catches, Prokopack aspirator, clay pots, and urine-baited traps—in four villages representing three ecological settings along the south coast of Kenya. Of the five methods, light traps were the most efficient for collecting female Anopheles gambiae s.l. (Giles) (Diptera: Culicidae) and Anopheles funestus (Giles) (Diptera: Culicidae) mosquitoes, whereas the Prokopack aspirator was most efficient in collecting Culex quinquefasciatus (Say) (Diptera: Culicidae) and other culicines. With the low vector densities here, and across much of sub-Saharan Africa, wherever malaria interventions, long-lasting insecticidal nets, and/or indoor residual spraying are in place, the use of a single mosquito collection method will not be sufficient to achieve a representative sample of mosquito population structure. Light traps will remain a relevant tool for host-seeking mosquitoes, especially in the absence of human landing catches. For a fair representation of the indoor mosquito population, light traps will have to be supplemented with aspirator use, which has potential for routine monitoring of indoor resting mosquitoes, and can substitute the more labor-intensive and intrusive pyrethrum spray catches. There are still no sufficiently efficient mosquito collection methods for sampling outdoor mosquitoes, particularly those that are bloodfed. PMID:24180120

Development and evaluation of mosquito-electrocuting traps as alternatives to the human landing catch technique for sampling host-seeking malaria vectors.

PubMed

Maliti, Deodatus V; Govella, Nicodem J; Killeen, Gerry F; Mirzai, Nosrat; Johnson, Paul C D; Kreppel, Katharina; Ferguson, Heather M

2015-12-15

The human landing catch (HLC) is the gold standard method for sampling host-seeking malaria vectors. However, the HLC is ethically questionable because it requires exposure of humans to potentially infectious mosquito bites. Two exposure-free methods for sampling host-seeking mosquitoes were evaluated using electrocuting surfaces as potential replacements for HLC: (1) a previously evaluated, commercially available electrocuting grid (CA-EG) designed for killing flies, and (2) a custom-made mosquito electrocuting trap (MET) designed to kill African malaria vectors. The MET and the CA-EG were evaluated relative to the HLC in a Latin Square experiment conducted in the Kilombero Valley, Tanzania. The sampling consistency of the traps across the night and at varying mosquito densities was investigated. Estimates of the proportion of mosquitoes caught indoors (P(i)), proportion of human exposure occurring indoors (π(i)), and proportion of mosquitoes caught when most people are likely to be indoors (P(fl)) were compared for all traps. Whereas the CA-EG performed poorly (<10% of catch of HLC), sampling efficiency of the MET for sampling Anopheles funestus s.l. was indistinguishable from HLC indoors and outdoors. For Anopheles gambiae s.l., sampling sensitivity of MET was 20.9% (95% CI 10.3-42.2) indoors and 58.5% (95% CI 32.2-106.2) outdoors relative to HLC. There was no evidence of density-dependent sampling by the MET or CA-EG. Similar estimates of P(i) were obtained for An. gambiae s.l. and An. funestus s.l. from all trapping methods. The proportion of mosquitoes caught when people are usually indoors (P(fl)) was underestimated by the CA-EG and MET for An. gambiae s.l., but similar to the HLC for An. funestus. Estimates of the proportion of human exposure occurring indoors (π(i)) obtained from the CA-EG and MET were similar to the HLC for An. gambiae s.l., but overestimated for An. funestus. The MET showed promise as an outdoor sampling tool for malaria vectors where it achieved >50% sampling sensitivity relative to the HLC. The CA-EG had poor sampling sensitivity outdoors and inside. With further modification, the MET could provide an efficient and safer alternative to the HLC for the surveillance of mosquito vectors outdoors.

A dual potential formulation of the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Gegg, S. G.; Pletcher, R. H.; Steger, J. L.

1989-01-01

A dual potential formulation for numerically solving the Navier-Stokes equations is developed and presented. The velocity field is decomposed using a scalar and vector potential. Vorticity and dilatation are used as the dependent variables in the momentum equations. Test cases in two dimensions verify the capability to solve flows using approximations from potential flow to full Navier-Stokes simulations. A three-dimensional incompressible flow formulation is also described. An interesting feature of this approach to solving the Navier-Stokes equations is the decomposition of the velocity field into a rotational part (vector potential) and an irrotational part (scalar potential). The Helmholtz decomposition theorem allows this splitting of the velocity field. This approach has had only limited use since it increases the number of dependent variables in the solution. However, it has often been used for incompressible flows where the solution scheme is known to be fast and accurate. This research extends the usage of this method to fully compressible Navier-Stokes simulations by using the dilatation variable along with vorticity. A time-accurate, iterative algorithm is used for the uncoupled solution of the governing equations. Several levels of flow approximation are available within the framework of this method. Potential flow, Euler and full Navier-Stokes solutions are possible using the dual potential formulation. Solution efficiency can be enhanced in a straightforward way. For some flows, the vorticity and/or dilatation may be negligible in certain regions (e.g., far from a viscous boundary in an external flow). It is possible to drop the calculation of these variables then and optimize the solution speed. Also, efficient Poisson solvers are available for the potentials. The relative merits of non-primitive variables versus primitive variables for solution of the Navier-Stokes equations are also discussed.

Predation scars may influence host susceptibility to pathogens: evaluating the role of corallivores as vectors of coral disease.

PubMed

Nicolet, K J; Chong-Seng, K M; Pratchett, M S; Willis, B L; Hoogenboom, M O

2018-03-27

Infectious diseases not regulated by host density, such as vector-borne diseases, have the potential to drive population declines and extinctions. Here we test the vector potential of the snail Drupella sp. and butterflyfish Chaetodon plebeius for two coral diseases, black band (BBD) and brown band (BrB) disease. Drupella transmitted BrB to healthy corals in 40% of cases immediately following feeding on infected corals, and even in 12% of cases 12 and 24 hours following feeding. However, Drupella was unable to transmit BBD in either transmission treatment. In a field experiment testing the vector potential of naturally-occurring fish assemblages, equivalent numbers of caged and uncaged coral fragments became infected with either BrB, BBD or skeletal eroding band, indicating that corallivorous fish were unlikely to have caused transmission. In aquaria, C. plebeius did not transmit either BBD or BrB, even following extended feeding on both infected and healthy nubbins. A literature review confirmed only four known coral disease vectors, all invertebrates, corroborating our conclusion that polyp-feeding fishes are unlikely to be vectors of coral diseases. This potentially because polyp-feeding fishes produce shallow lesions, not allowing pathogens to invade coral tissues. In contrast, corallivorous invertebrates that create deeper feeding scars increase pathogens transmission.

A Computational Study of a New Dual Throat Fluidic Thrust Vectoring Nozzle Concept

NASA Technical Reports Server (NTRS)

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

2005-01-01

A computational investigation of a two-dimensional nozzle was completed to assess the use of fluidic injection to manipulate flow separation and cause thrust vectoring of the primary jet thrust. The nozzle was designed with a recessed cavity to enhance the throat shifting method of fluidic thrust vectoring. Several design cycles with the structured-grid, computational fluid dynamics code PAB3D and with experiments in the NASA Langley Research Center Jet Exit Test Facility have been completed to guide the nozzle design and analyze performance. This paper presents computational results on potential design improvements for best experimental configuration tested to date. Nozzle design variables included cavity divergence angle, cavity convergence angle and upstream throat height. Pulsed fluidic injection was also investigated for its ability to decrease mass flow requirements. Internal nozzle performance (wind-off conditions) and thrust vector angles were computed for several configurations over a range of nozzle pressure ratios from 2 to 7, with the fluidic injection flow rate equal to 3 percent of the primary flow rate. Computational results indicate that increasing cavity divergence angle beyond 10 is detrimental to thrust vectoring efficiency, while increasing cavity convergence angle from 20 to 30 improves thrust vectoring efficiency at nozzle pressure ratios greater than 2, albeit at the expense of discharge coefficient. Pulsed injection was no more efficient than steady injection for the Dual Throat Nozzle concept.

Sleeping Beauty Transposon Vectors in Liver-directed Gene Delivery of LDLR and VLDLR for Gene Therapy of Familial Hypercholesterolemia

PubMed Central

Turunen, Tytteli A K; Kurkipuro, Jere; Heikura, Tommi; Vuorio, Taina; Hytönen, Elisa; Izsvák, Zsuzsanna; Ylä-Herttuala, Seppo

2016-01-01

Plasmid-based Sleeping Beauty (SB) transposon vectors were developed and used to deliver genes for low-density lipoprotein and very-low-density lipoprotein receptors (LDLR and VLDLR, respectively) or lacZ reporter into liver of an LDLR-deficient mouse model of familial hypercholesterolemia (FH). SB transposase, SB100x, was used to integrate the therapeutic transposons into mice livers for evaluating the feasibility of the vectors in reducing high blood cholesterol and the progression of atherosclerosis. Hydrodynamic gene delivery of transposon-VLDLR into the livers of the mice resulted in initial 17–19% reductions in plasma cholesterol, and at the later time points, in a significant stabilization of the cholesterol level for the 6.5-month duration of the study compared to the control mice. Transposon-LDLR-treated animals also demonstrated a trend of stabilization in the cholesterol levels in the long term. Vector-treated mice had slightly less lipid accumulation in the liver and reduced aortic atherosclerosis. Clinical chemistry and histological analyses revealed normal liver function and morphology comparable to that of the controls during the follow-up with no safety issues regarding the vector type, transgenes, or the gene transfer method. The study demonstrates the safety and potential benefits of the SB transposon vectors in the treatment of FH. PMID:26670130

Distribution of AAV-TK following intracranial convection-enhanced delivery into rats.

PubMed

Cunningham, J; Oiwa, Y; Nagy, D; Podsakoff, G; Colosi, P; Bankiewicz, K S

2000-01-01

Adeno-associated virus (AAV)-based vectors are being tested in animal models as viable treatments for glioma and neurodegenerative disease and could potentially be employed to target a variety of central nervous system disorders. The relationship between dose of injected vector and its resulting distribution in brain tissue has not been previously reported nor has the most efficient method of delivery been determined. Here we report that convection-enhanced delivery (CED) of 2.5 x 10(8), 2.5 x 10(9), or 2.5 x 10(10) particles of AAV-thymidine kinase (AAV-TK) into rat brain revealed a clear dose response. In the high-dose group, a volume of 300 mm3 of brain tissue was partially transduced. Results showed that infusion pump and subcutaneous osmotic pumps were both capable of delivering vector via CED and that total particle number was the most important determining factor in obtaining efficient expression. Results further showed differences in histopathology between the delivery groups. While administration of vector using infusion pump had relatively benign effects, the use of osmotic pumps resulted in notable toxicity to the surrounding brain tissue. To determine tissue distribution of vector following intracranial delivery, PCR analysis was performed on tissues from rats that received high doses of AAV-TK. Three weeks following CED, vector could be detected in both hemispheres of the brain, spinal cord, spleen, and kidney.

Climate variability and change in the United States: potential impacts on vector- and rodent-borne diseases.

PubMed Central

Gubler, D J; Reiter, P; Ebi, K L; Yap, W; Nasci, R; Patz, J A

2001-01-01

Diseases such as plague, typhus, malaria, yellow fever, and dengue fever, transmitted between humans by blood-feeding arthropods, were once common in the United States. Many of these diseases are no longer present, mainly because of changes in land use, agricultural methods, residential patterns, human behavior, and vector control. However, diseases that may be transmitted to humans from wild birds or mammals (zoonoses) continue to circulate in nature in many parts of the country. Most vector-borne diseases exhibit a distinct seasonal pattern, which clearly suggests that they are weather sensitive. Rainfall, temperature, and other weather variables affect in many ways both the vectors and the pathogens they transmit. For example, high temperatures can increase or reduce survival rate, depending on the vector, its behavior, ecology, and many other factors. Thus, the probability of transmission may or may not be increased by higher temperatures. The tremendous growth in international travel increases the risk of importation of vector-borne diseases, some of which can be transmitted locally under suitable circumstances at the right time of the year. But demographic and sociologic factors also play a critical role in determining disease incidence, and it is unlikely that these diseases will cause major epidemics in the United States if the public health infrastructure is maintained and improved. PMID:11359689

Mutual coupling effects in antenna arrays, volume 1

NASA Technical Reports Server (NTRS)

Collin, R. E.

1986-01-01

Mutual coupling between rectangular apertures in a finite antenna array, in an infinite ground plane, is analyzed using the vector potential approach. The method of moments is used to solve the equations that result from setting the tangential magnetic fields across each aperture equal. The approximation uses a set of vector potential model functions to solve for equivalent magnetic currents. A computer program was written to carry out this analysis and the resulting currents were used to determine the co- and cross-polarized far zone radiation patterns. Numerical results for various arrays using several modes in the approximation are presented. Results for one and two aperture arrays are compared against published data to check on the agreement of this model with previous work. Computer derived results are also compared against experimental results to test the accuracy of the model. These tests of the accuracy of the program showed that it yields valid data.

Gene transfer into the kidney: current status and limitations.

PubMed

Moullier, P; Salvetti, A; Champion-Arnaud, P; Ronco, P M

1997-01-01

Gene therapy is obviously a controversial issue and a wave of suspicion has dampened the initial enthusiasm raised by this new therapeutic approach. It has now become fashionable to downplay the potential for gene therapy in most fields including kidney-related diseases. In our opinion, this is an unfair and unrealistic view of the future. In fact, gene therapy of well-selected kidney diseases will certainly become feasible, but a large data base on vectors and transfer methods both in the normal kidney and in disease models has first to be collected. Any significant progress in the biology of the vectors, in the cellular interactions of the newly introduced DNA, and in the regulation and persistency of the transgene should be rapidly translated to the kidney in relevant experimental models. Herein, we present the use and current limitations of gene transfer to the kidney and the potential therapeutic perspectives.

Improved dengue fever prevention through innovative intervention methods in the city of Salto, Uruguay

PubMed Central

Basso, César; García da Rosa, Elsa; Romero, Sonnia; González, Cristina; Lairihoy, Rosario; Roche, Ingrid; Caffera, Ruben M.; da Rosa, Ricardo; Calfani, Marisel; Alfonso-Sierra, Eduardo; Petzold, Max; Kroeger, Axel; Sommerfeld, Johannes

2015-01-01

Background Uruguay is located at the southern border of Aedes aegypti distribution on the South American sub-continent. The reported dengue cases in the country are all imported from surrounding countries. One of the cities at higher risk of local dengue transmission is Salto, a border city with heavy traffic from dengue endemic areas. Methods We completed an intervention study using a cluster randomized trial design in 20 randomly selected ‘clusters’ in Salto. The clusters were located in neighborhoods of differing geography and economic, cultural and social aspects. Results Entomological surveys were carried out to measure the impact of the intervention on vector densities. Through participatory processes of all stakeholders, an appropriate ecosystem management intervention was defined. Residents collected the abundant small water holding containers and the Ministry of Public Health and the Municipality of Salto were responsible for collecting and eliminating them. Additional vector breeding places were large water tanks; they were either altered so that they could not hold water any more or covered so that oviposition by mosquitoes could not take place. Conclusions The response from the community and national programme managers was encouraging. The intervention evidenced opportunities for cost savings and reducing dengue vector densities (although not to statistically significant levels). The observed low vector density limits the potential reduction due to the intervention. A larger sample size is needed to obtain a statistically significant difference. PMID:25604764

Revival of cloaking effect in a driven bilayer graphene vector barrier

NASA Astrophysics Data System (ADS)

Maiti, S.; Panigrahi, A.; Biswas, R.; Sinha, C.

2018-05-01

Transmission profiles in bilayer graphene are studied theoretically through a rectangular vector potential (magnetic) barrier with and without the presence of an oscillatory potential. Unlike the electrostatic barrier, the Fano resonances (FR) are noted in the transmission spectra both for normal and glancing incidences due to non-conservation of chirality for a static vector barrier. The results for normal incidence indicate that the cloaking effect is a manifestation of the chirality conservation in charge transport through bilayer graphene scalar barriers. It is also noted that the aforesaid FR for a static vector barrier might disappear (photon induced electronic cloaking effect) due to the predominant photon exchange processes in presence of an external oscillating potential. The study of Fano resonances in transmission spectrum is in high demand in respect of localization of charge carriers in graphene nano structures for its potential applications in digital device fabrications.

Video Vectorization via Tetrahedral Remeshing.

PubMed

Wang, Chuan; Zhu, Jie; Guo, Yanwen; Wang, Wenping

2017-02-09

We present a video vectorization method that generates a video in vector representation from an input video in raster representation. A vector-based video representation offers the benefits of vector graphics, such as compactness and scalability. The vector video we generate is represented by a simplified tetrahedral control mesh over the spatial-temporal video volume, with color attributes defined at the mesh vertices. We present novel techniques for simplification and subdivision of a tetrahedral mesh to achieve high simplification ratio while preserving features and ensuring color fidelity. From an input raster video, our method is capable of generating a compact video in vector representation that allows a faithful reconstruction with low reconstruction errors.

What does not kill them makes them stronger: larval environment and infectious dose alter mosquito potential to transmit filarial worms.

PubMed

Breaux, Jennifer A; Schumacher, Molly K; Juliano, Steven A

2014-07-07

For organisms with complex life cycles, larval environments can modify adult phenotypes. For mosquitoes and other vectors, when physiological impacts of stressors acting on larvae carry over into the adult stage they may interact with infectious dose of a vector-borne pathogen, producing a range of phenotypes for vector potential. Investigation of impacts of a common source of stress, larval crowding and intraspecific competition, on adult vector interactions with pathogens may increase our understanding of the dynamics of pathogen transmission by mosquito vectors. Using Aedes aegypti and the nematode parasite Brugia pahangi, we demonstrate dose dependency of fitness effects of B. pahangi infection on the mosquito, as well as interactions between competitive stress among larvae and infectious dose for resulting adults that affect the physiological and functional ability of mosquitoes to act as vectors. Contrary to results from studies on mosquito-arbovirus interactions, our results suggest that adults from crowded larvae may limit infection better than do adults from uncrowded controls, and that mosquitoes from high-quality larval environments are more physiologically and functionally capable vectors of B. pahangi. Our results provide another example of how the larval environment can have profound effects on vector potential of resulting adults. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Accurate motion parameter estimation for colonoscopy tracking using a regression method

NASA Astrophysics Data System (ADS)

Liu, Jianfei; Subramanian, Kalpathi R.; Yoo, Terry S.

2010-03-01

Co-located optical and virtual colonoscopy images have the potential to provide important clinical information during routine colonoscopy procedures. In our earlier work, we presented an optical flow based algorithm to compute egomotion from live colonoscopy video, permitting navigation and visualization of the corresponding patient anatomy. In the original algorithm, motion parameters were estimated using the traditional Least Sum of squares(LS) procedure which can be unstable in the context of optical flow vectors with large errors. In the improved algorithm, we use the Least Median of Squares (LMS) method, a robust regression method for motion parameter estimation. Using the LMS method, we iteratively analyze and converge toward the main distribution of the flow vectors, while disregarding outliers. We show through three experiments the improvement in tracking results obtained using the LMS method, in comparison to the LS estimator. The first experiment demonstrates better spatial accuracy in positioning the virtual camera in the sigmoid colon. The second and third experiments demonstrate the robustness of this estimator, resulting in longer tracked sequences: from 300 to 1310 in the ascending colon, and 410 to 1316 in the transverse colon.

Electric and magnetic superlattices in trilayer graphene

NASA Astrophysics Data System (ADS)

Uddin, Salah; Chan, K. S.

2016-01-01

The properties of one dimensional Kronig-Penney type of periodic electric and vector potential on ABC-trilayer graphene superlattices are investigated. The energy spectra obtained with periodic vector potentials shows the emergence of extra Dirac points in the energy spectrum with finite energies. For identical barrier and well widths, the original as well as the extra Dirac points are located in the ky = 0 plane. An asymmetry between the barrier and well widths causes a shift in the extra Dirac points away from the ky = 0 plane. Extra Dirac points having same electron hole crossing energy as that of the original Dirac point as well as finite energy Dirac points are generated in the energy spectrum when periodic electric potential is applied to the system. By applying electric and vector potential together, the symmetry of the energy spectrum about the Fermi level is broken. A tunable band gap is induced in the energy spectrum by applying both electric and vector potential simultaneously with different barrier and well widths.

Spacetime algebra as a powerful tool for electromagnetism

NASA Astrophysics Data System (ADS)

Dressel, Justin; Bliokh, Konstantin Y.; Nori, Franco

2015-08-01

We present a comprehensive introduction to spacetime algebra that emphasizes its practicality and power as a tool for the study of electromagnetism. We carefully develop this natural (Clifford) algebra of the Minkowski spacetime geometry, with a particular focus on its intrinsic (and often overlooked) complex structure. Notably, the scalar imaginary that appears throughout the electromagnetic theory properly corresponds to the unit 4-volume of spacetime itself, and thus has physical meaning. The electric and magnetic fields are combined into a single complex and frame-independent bivector field, which generalizes the Riemann-Silberstein complex vector that has recently resurfaced in studies of the single photon wavefunction. The complex structure of spacetime also underpins the emergence of electromagnetic waves, circular polarizations, the normal variables for canonical quantization, the distinction between electric and magnetic charge, complex spinor representations of Lorentz transformations, and the dual (electric-magnetic field exchange) symmetry that produces helicity conservation in vacuum fields. This latter symmetry manifests as an arbitrary global phase of the complex field, motivating the use of a complex vector potential, along with an associated transverse and gauge-invariant bivector potential, as well as complex (bivector and scalar) Hertz potentials. Our detailed treatment aims to encourage the use of spacetime algebra as a readily available and mature extension to existing vector calculus and tensor methods that can greatly simplify the analysis of fundamentally relativistic objects like the electromagnetic field.

Mosquito species composition and phenology (Diptera, Culicidae) in two German zoological gardens imply different risks of mosquito-borne pathogen transmission.

PubMed

Heym, Eva C; Kampen, Helge; Walther, Doreen

2018-06-01

Due to their large diversity of potential blood hosts, breeding habitats, and resting sites, zoological gardens represent highly interesting places to study mosquito ecology. In order to better assess the risk of mosquito-borne disease-agent transmission in zoos, potential vector species must be known, as well as the communities in which they occur. For this reason, species composition and dynamics were examined in 2016 in two zoological gardens in Germany. Using different methods for mosquito sampling, a total of 2,257 specimens belonging to 20 taxa were collected. Species spectra depended on the collection method but generally differed between the two zoos, while species compositions and relative abundances varied seasonally in both of them. As both sampled zoos were located in the same climatic region and potential breeding sites within the zoos were similar, the differences in mosquito compositions are attributed to immigration of specimens from surrounding landscapes, although the different sizes of the zoos and the different blood host populations available probably also have an impact. Based on the differences in species composition and the various biological characteristics of the species, the risk of certain pathogens to be transmitted must also be expected to differ between the zoos. © 2018 The Society for Vector Ecology.

First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

NASA Technical Reports Server (NTRS)

Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

2014-01-01

Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

Comparison of transmission parameters between Anopheles argyritarsis and Anopheles pseudopunctipennis in two ecologically different localities of Bolivia

PubMed Central

2013-01-01

Background Anopheles (Anopheles) pseudopunctipennis is a recognized malaria vector in the slopes of the Andes of Bolivia. There, other species might be involved in malaria transmission and one candidate could be Anopheles argyritarsis. Although it is generally admitted that this species is not a malaria vector in the neotropical region, its potential role in transmission is still controversial and this situation has to be cleared, at least for Bolivia. Comparing the vectorial efficiency of An. pseudopunctipennis with that of An. argyritarsis could solve the question. Methods The two species were sampled throughout Bolivia to estimate their degree of co-existence in their distribution range. Vectorial efficiencies of the two species were compared in two ecologically different localities where the species were sympatric by analysing their vectorial capacities and components (i e, human biting rates, human biting index, survival, durations of the gonotrophic cycle and extrinsic cycle), and the entomological inoculation rates (EIR). Mosquitoes were sampled monthly during more than one year in the two localities. A monthly sample consisted in hourly captures in four houses (inside and outside) in each locality, during four consecutive nights. Climatic variables (temperature, humidity, potential evapo-transpiration and precipitations) were recorded to better understand variability in the entomological parameters. Relationships were analysed using multivariate methods. Results Anopheles pseudopunctipennis and An. argyritarsis are “altitude” species, sharing the same geographical distribution range in the Andes of Bolivia. No Plasmodium parasite was identified in An. argyritarsis and estimates of the vectorial capacity indicated that it is not a malaria vector in the two studied localities, unlike An. pseudopunctipennis which showed positive EIRs. This latter species, although not a very good malaria vector, exhibited better life traits values and better behavioural characteristics in favour of transmission as compared to An. argyritarsis. Conclusions In the Andes of Bolivia, above 1000 m of altitude, An. pseudopunctipennis is likely to be the only malaria vector. There, it is present almost everywhere and priority control effort should be directed toward this species. Below 1000 m of altitude, vector incrimination should also be focused on other sympatric species (likely not An. argyritarsis) that might be locally important. From the present study, candidates would be among Anopheles rangeli, Anopheles triannulatus s.l., Anopheles trinkae, Anopheles nuneztovari s.l., Anopheles oswaldoi s.l. and Anopheles benarrochi s.l. PMID:23941216

Instruction-based clinical eye-tracking study on the visual interpretation of divergence: How do students look at vector field plots?

NASA Astrophysics Data System (ADS)

Klein, P.; Viiri, J.; Mozaffari, S.; Dengel, A.; Kuhn, J.

2018-06-01

Relating mathematical concepts to graphical representations is a challenging task for students. In this paper, we introduce two visual strategies to qualitatively interpret the divergence of graphical vector field representations. One strategy is based on the graphical interpretation of partial derivatives, while the other is based on the flux concept. We test the effectiveness of both strategies in an instruction-based eye-tracking study with N =41 physics majors. We found that students' performance improved when both strategies were introduced (74% correct) instead of only one strategy (64% correct), and students performed best when they were free to choose between the two strategies (88% correct). This finding supports the idea of introducing multiple representations of a physical concept to foster student understanding. Relevant eye-tracking measures demonstrate that both strategies imply different visual processing of the vector field plots, therefore reflecting conceptual differences between the strategies. Advanced analysis methods further reveal significant differences in eye movements between the best and worst performing students. For instance, the best students performed predominantly horizontal and vertical saccades, indicating correct interpretation of partial derivatives. They also focused on smaller regions when they balanced positive and negative flux. This mixed-method research leads to new insights into student visual processing of vector field representations, highlights the advantages and limitations of eye-tracking methodologies in this context, and discusses implications for teaching and for future research. The introduction of saccadic direction analysis expands traditional methods, and shows the potential to discover new insights into student understanding and learning difficulties.

AAV-mediated targeting of gene expression to the peri-infarct region in rat cortical stroke model.

PubMed

Mätlik, Kert; Abo-Ramadan, Usama; Harvey, Brandon K; Arumäe, Urmas; Airavaara, Mikko

2014-10-30

For stroke patients the recovery of cognitive and behavioral functions is often incomplete. Functional recovery is thought to be mediated largely by connectivity rearrangements in the peri-infarct region. A method for manipulating gene expression in this region would be useful for identifying new recovery-enhancing treatments. We have characterized a way of targeting adeno-associated virus (AAV) vectors to the peri-infarct region of cortical ischemic lesion in rats 2days after middle cerebral artery occlusion (MCAo). We used magnetic resonance imaging (MRI) to show that the altered properties of post-ischemic brain tissue facilitate the spreading of intrastriatally injected nanoparticles toward the infarct. We show that subcortical injection of green fluorescent protein-encoding dsAAV7-GFP resulted in transduction of cells in and around the white matter tract underlying the lesion, and in the cortex proximal to the lesion. A similar result was achieved with dsAAV7 vector encoding the cerebral dopamine neurotrophic factor (CDNF), a protein with therapeutic potential. Viral vector-mediated intracerebral gene delivery has been used before in rodent models of ischemic injury. However, the method of targeting gene expression to the peri-infarct region, after the initial phase of ischemic cell death, has not been described before. We demonstrate a straightforward and robust way to target AAV vector-mediated over-expression of genes to the peri-infarct region in a rat stroke model. This method will be useful for studying the action of specific proteins in peri-infarct region during the recovery process. Copyright © 2014 Elsevier B.V. All rights reserved.

More than one rabbit out of the hat: Radiation, transgenic and symbiont-based approaches for sustainable management of mosquito and tsetse fly populations.

PubMed

Bourtzis, Kostas; Lees, Rosemary Susan; Hendrichs, Jorge; Vreysen, Marc J B

2016-05-01

Mosquitoes (Diptera: Culicidae) and tsetse flies (Diptera: Glossinidae) are bloodsucking vectors of human and animal pathogens. Mosquito-borne diseases (malaria, filariasis, dengue, zika, and chikungunya) cause severe mortality and morbidity annually, and tsetse fly-borne diseases (African trypanosomes causing sleeping sickness in humans and nagana in livestock) cost Sub-Saharan Africa an estimated US$ 4750 million annually. Current reliance on insecticides for vector control is unsustainable: due to increasing insecticide resistance and growing concerns about health and environmental impacts of chemical control there is a growing need for novel, effective and safe biologically-based methods that are more sustainable. The integration of the sterile insect technique has proven successful to manage crop pests and disease vectors, particularly tsetse flies, and is likely to prove effective against mosquito vectors, particularly once sex-separation methods are improved. Transgenic and symbiont-based approaches are in development, and more advanced in (particularly Aedes) mosquitoes than in tsetse flies; however, issues around stability, sustainability and biosecurity have to be addressed, especially when considering population replacement approaches. Regulatory issues and those relating to intellectual property and economic cost of application must also be overcome. Standardised methods to assess insect quality are required to compare and predict efficacy of the different approaches. Different combinations of these three approaches could be integrated to maximise their benefits, and all have the potential to be used in tsetse and mosquito area-wide integrated pest management programmes. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Vector and Raster Data Storage Based on Morton Code

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Evolution of relative magnetic helicity. New boundary conditions for the vector potential

NASA Astrophysics Data System (ADS)

Yang, Shangbin; Büchner, Jörg; Skála, Jan; Zhang, Hongqi

2018-05-01

Context. For a better understanding of the dynamics of the solar corona, it is important to analyse the evolution of the helicity of the magnetic field. Since the helicity cannot be directly determined by observations, we have recently proposed a method to calculate the relative magnetic helicity in a finite volume for a given magnetic field, which however required the flux to be balanced separately on all the sides of the considered volume. Aims: We developed a scheme to obtain the vector potential in a volume without the above restriction at the boundary. We studied the dissipation and escape of relative magnetic helicity from an active region. Methods: In order to allow finite magnetic fluxes through the boundaries, a Coulomb gauge was constructed that allows for global magnetic flux balance. The property of sinusoidal function was used to obtain the vector potentials at the 12 edges of the considered rectangular volume extending above an active region. We tested and verified our method in a theoretical fore-free magnetic field model. Results: We applied the new method to the former calculation data and found a difference of less than 1.2%. We also applied our method to the magnetic field above active region NOAA 11429 obtained by a new photospheric-data-driven magnetohydrodynamics (MHD) model code GOEMHD3. We analysed the magnetic helicity evolution in the solar corona using our new method. We find that the normalized magnetic helicity (H/Φ2) is equal to -0.038 when fast magnetic reconnection is triggered. This value is comparable to the previous value (-0.029) in the MHD simulations when magnetic reconnection happened and the observed normalized magnetic helicity (-0.036) from the eruption of newly emerging active regions. We find that only 8% of the accumulated magnetic helicity is dissipated after it is injected through the bottom boundary. This is in accordance with the Woltjer conjecture. Only 2% of the magnetic helicity injected from the bottom boundary escapes through the corona. This is consistent with the observation of magnetic clouds, which could take magnetic helicity into the interplanetary space. In the case considered here, several halo coronal mass ejections (CMEs) and two X-class solar flares originate from this active region.

R0 for vector-borne diseases: impact of the assumption for the duration of the extrinsic incubation period.

PubMed

Hartemink, Nienke; Cianci, Daniela; Reiter, Paul

2015-03-01

Mathematical modeling and notably the basic reproduction number R0 have become popular tools for the description of vector-borne disease dynamics. We compare two widely used methods to calculate the probability of a vector to survive the extrinsic incubation period. The two methods are based on different assumptions for the duration of the extrinsic incubation period; one method assumes a fixed period and the other method assumes a fixed daily rate of becoming infectious. We conclude that the outcomes differ substantially between the methods when the average life span of the vector is short compared to the extrinsic incubation period.

Data-driven identification of potential Zika virus vectors

PubMed Central

Evans, Michelle V; Dallas, Tad A; Han, Barbara A; Murdock, Courtney C; Drake, John M

2017-01-01

Zika is an emerging virus whose rapid spread is of great public health concern. Knowledge about transmission remains incomplete, especially concerning potential transmission in geographic areas in which it has not yet been introduced. To identify unknown vectors of Zika, we developed a data-driven model linking vector species and the Zika virus via vector-virus trait combinations that confer a propensity toward associations in an ecological network connecting flaviviruses and their mosquito vectors. Our model predicts that thirty-five species may be able to transmit the virus, seven of which are found in the continental United States, including Culex quinquefasciatus and Cx. pipiens. We suggest that empirical studies prioritize these species to confirm predictions of vector competence, enabling the correct identification of populations at risk for transmission within the United States. DOI: http://dx.doi.org/10.7554/eLife.22053.001 PMID:28244371

Viral Vectors for Gene Delivery to the Central Nervous System

PubMed Central

Lentz, Thomas B.; Gray, Steven J.; Samulski, R. Jude

2011-01-01

The potential benefits of gene therapy for neurological diseases such as Parkinson’s, Amyotrophic Lateral Sclerosis (ALS), Epilepsy, and Alzheimer’s are enormous. Even a delay in the onset of severe symptoms would be invaluable to patients suffering from these and other diseases. Significant effort has been placed in developing vectors capable of delivering therapeutic genes to the CNS in order to treat neurological disorders. At the forefront of potential vectors, viral systems have evolved to efficiently deliver their genetic material to a cell. The biology of different viruses offers unique solutions to the challenges of gene therapy, such as cell targeting, transgene expression and vector production. It is important to consider the natural biology of a vector when deciding whether it will be the most effective for a specific therapeutic function. In this review, we outline desired features of the ideal vector for gene delivery to the CNS and discuss how well available viral vectors compare to this model. Adeno-associated virus, retrovirus, adenovirus and herpesvirus vectors are covered. Focus is placed on features of the natural biology that have made these viruses effective tools for gene delivery with emphasis on their application in the CNS. Our goal is to provide insight into features of the optimal vector and which viral vectors can provide these features. PMID:22001604

Degradable polyethylenimine derivate coupled to a bifunctional peptide R13 as a new gene-delivery vector

PubMed Central

Liu, Kehai; Wang, Xiaoyu; Fan, Wei; Zhu, Qing; Yang, Jingya; Gao, Jing; Gao, Shen

2012-01-01

Background To solve the efficiency versus cytotoxicity and tumor-targeting problems of polyethylenimine (PEI) used as a nonviral gene delivery vector, a degradable PEI derivate coupled to a bifunctional peptide R13 was developed. Methods First, we synthesized a degradable PEI derivate by crosslinking low-molecular-weight PEI with pluronic P123, then used tumor-targeting peptide arginine-glycine-aspartate-cysteine (RGDC), in conjunction with the cell-penetrating peptide Tat (49–57), to yield a bifunctional peptide RGDC-Tat (49–57) named R13, which can improve cell selection and increase cellular uptake, and, lastly, adopted R13 to modify the PEI derivates so as to prepare a new polymeric gene vector (P123-PEI-R13). The new gene vector was characterized in terms of its chemical structure and biophysical parameters. We also investigated the specificity, cytotoxicity, and gene transfection efficiency of this vector in αvβ3-positive human cervical carcinoma Hela cells and murine melanoma B16 cells in vitro. Results The vector showed controlled degradation, strong targeting specificity to αvβ3 receptor, and noncytotoxicity in Hela cells and B16 cells at higher doses, in contrast to PEI 25 KDa. The particle size of P123-PEI-R13/DNA complexes was around 100–250 nm, with proper zeta potential. The nanoparticles can protect plasmid DNA from being digested by DNase I at a concentration of 6 U DNase I/μg DNA. The nanoparticles were resistant to dissociation induced by 50% fetal bovine serum and 600 μg/mL sodium heparin. P123-PEI-R13 also revealed higher transfection efficiency in two cell lines as compared with PEI 25 KDa. Conclusion P123-PEI-R13 is a potential candidate as a safe and efficient gene-delivery carrier for gene therapy. PMID:22412301

Underpinning Sustainable Vector Control through Informed Insecticide Resistance Management

PubMed Central

Hemmings, Kay; Hughes, Angela J.; Chanda, Emmanuel; Musapa, Mulenga; Kamuliwo, Mulakwa; Phiri, Faustina N.; Muzia, Lucy; Chanda, Javan; Kandyata, Alister; Chirwa, Brian; Poer, Kathleen; Hemingway, Janet; Wondji, Charles S.; Ranson, Hilary; Coleman, Michael

2014-01-01

Background There has been rapid scale-up of malaria vector control in the last ten years. Both of the primary control strategies, long-lasting pyrethroid treated nets and indoor residual spraying, rely on the use of a limited number of insecticides. Insecticide resistance, as measured by bioassay, has rapidly increased in prevalence and has come to the forefront as an issue that needs to be addressed to maintain the sustainability of malaria control and the drive to elimination. Zambia's programme reported high levels of resistance to the insecticides it used in 2010, and, as a result, increased its investment in resistance monitoring to support informed resistance management decisions. Methodology/Principal Findings A country-wide survey on insecticide resistance in Zambian malaria vectors was performed using WHO bioassays to detect resistant phenotypes. Molecular techniques were used to detect target-site mutations and microarray to detect metabolic resistance mechanisms. Anopheles gambiae s.s. was resistant to pyrethroids, DDT and carbamates, with potential organophosphate resistance in one population. The resistant phenotypes were conferred by both target-site and metabolic mechanisms. Anopheles funestus s.s. was largely resistant to pyrethroids and carbamates, with potential resistance to DDT in two locations. The resistant phenotypes were conferred by elevated levels of cytochrome p450s. Conclusions/Significance Currently, the Zambia National Malaria Control Centre is using these results to inform their vector control strategy. The methods employed here can serve as a template to all malaria-endemic countries striving to create a sustainable insecticide resistance management plan. PMID:24932861

A high-accuracy two-position alignment inertial navigation system for lunar rovers aided by a star sensor with a calibration and positioning function

NASA Astrophysics Data System (ADS)

Lu, Jiazhen; Lei, Chaohua; Yang, Yanqiang; Liu, Ming

2016-12-01

An integrated inertial/celestial navigation system (INS/CNS) has wide applicability in lunar rovers as it provides accurate and autonomous navigational information. Initialization is particularly vital for a INS. This paper proposes a two-position initialization method based on a standard Kalman filter. The difference between the computed star vector and the measured star vector is measured. With the aid of a star sensor and the two positions, the attitudinal and positional errors can be greatly reduced, and the biases of three gyros and accelerometers can also be estimated. The semi-physical simulation results show that the positional and attitudinal errors converge within 0.07″ and 0.1 m, respectively, when the given initial positional error is 1 km and the attitudinal error is 10°. These good results show that the proposed method can accomplish alignment, positioning and calibration functions simultaneously. Thus the proposed two-position initialization method has the potential for application in lunar rover navigation.

A comprehensive data processing plan for crop calendar MSS signature development from satellite imagery: Crop identification using vegetation phenology

NASA Technical Reports Server (NTRS)

Hlavka, C. A. (Principal Investigator); Carlyle, S. M.; Haralick, R. M.; Yokoyama, R.

1978-01-01

The author has identified the following significant results. The phenological method of crop identification involves the creation of crop signatures which characterize multispectral observations as phenological growth states. The phenological signature models spectral reflectance explicitly as a function of crop maturity rather than as a function of date. A correspondence of time to growth state is established which minimizes the smallest difference between the given multispectral multitemporal vector and a category mean vector. The application of the method to the identification of winter wheat and corn shows (1) the method is capable of discriminating crop type with about the same degree of accuracy as more traditional classifiers; (2) the use of LANDSAT observations on two or more dates yields better results than the use of a single observation; and (3) some potential is demonstrated for labeling the degree of maturity of the crop, as well as the crop type.

Characteristics of Minimally Oversized Adeno-Associated Virus Vectors Encoding Human Factor VIII Generated Using Producer Cell Lines and Triple Transfection.

PubMed

Nambiar, Bindu; Cornell Sookdeo, Cathleen; Berthelette, Patricia; Jackson, Robert; Piraino, Susan; Burnham, Brenda; Nass, Shelley; Souza, David; O'Riordan, Catherine R; Vincent, Karen A; Cheng, Seng H; Armentano, Donna; Kyostio-Moore, Sirkka

2017-02-01

Several ongoing clinical studies are evaluating recombinant adeno-associated virus (rAAV) vectors as gene delivery vehicles for a variety of diseases. However, the production of vectors with genomes >4.7 kb is challenging, with vector preparations frequently containing truncated genomes. To determine whether the generation of oversized rAAVs can be improved using a producer cell-line (PCL) process, HeLaS3-cell lines harboring either a 5.1 or 5.4 kb rAAV vector genome encoding codon-optimized cDNA for human B-domain deleted Factor VIII (FVIII) were isolated. High-producing "masterwells" (MWs), defined as producing >50,000 vg/cell, were identified for each oversized vector. These MWs provided stable vector production for >20 passages. The quality and potency of the AAVrh8R/FVIII-5.1 and AAVrh8R/FVIII-5.4 vectors generated by the PCL method were then compared to those prepared via transient transfection (TXN). Southern and dot blot analyses demonstrated that both production methods resulted in packaging of heterogeneously sized genomes. However, the PCL-derived rAAV vector preparations contained some genomes >4.7 kb, whereas the majority of genomes generated by the TXN method were ≤4.7 kb. The PCL process reduced packaging of non-vector DNA for both the AAVrh8R/FVIII-5.1 and the AAVrh8R/FVIII-5.4 kb vector preparations. Furthermore, more DNA-containing viral particles were obtained for the AAVrh8R/FVIII-5.1 vector. In a mouse model of hemophilia A, animals administered a PCL-derived rAAV vector exhibited twofold higher plasma FVIII activity and increased levels of vector genomes in the liver than mice treated with vector produced via TXN did. Hence, the quality of oversized vectors prepared using the PCL method is greater than that of vectors generated using the TXN process, and importantly this improvement translates to enhanced performance in vivo.

Complexity of Kronecker Operations on Sparse Matrices with Applications to the Solution of Markov Models

NASA Technical Reports Server (NTRS)

Buchholz, Peter; Ciardo, Gianfranco; Donatelli, Susanna; Kemper, Peter

1997-01-01

We present a systematic discussion of algorithms to multiply a vector by a matrix expressed as the Kronecker product of sparse matrices, extending previous work in a unified notational framework. Then, we use our results to define new algorithms for the solution of large structured Markov models. In addition to a comprehensive overview of existing approaches, we give new results with respect to: (1) managing certain types of state-dependent behavior without incurring extra cost; (2) supporting both Jacobi-style and Gauss-Seidel-style methods by appropriate multiplication algorithms; (3) speeding up algorithms that consider probability vectors of size equal to the "actual" state space instead of the "potential" state space.

A Coarse Alignment Method Based on Digital Filters and Reconstructed Observation Vectors

PubMed Central

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Wang, Zhicheng

2017-01-01

In this paper, a coarse alignment method based on apparent gravitational motion is proposed. Due to the interference of the complex situations, the true observation vectors, which are calculated by the apparent gravity, are contaminated. The sources of the interference are analyzed in detail, and then a low-pass digital filter is designed in this paper for eliminating the high-frequency noise of the measurement observation vectors. To extract the effective observation vectors from the inertial sensors’ outputs, a parameter recognition and vector reconstruction method are designed, where an adaptive Kalman filter is employed to estimate the unknown parameters. Furthermore, a robust filter, which is based on Huber’s M-estimation theory, is developed for addressing the outliers of the measurement observation vectors due to the maneuver of the vehicle. A comprehensive experiment, which contains a simulation test and physical test, is designed to verify the performance of the proposed method, and the results show that the proposed method is equivalent to the popular apparent velocity method in swaying mode, but it is superior to the current methods while in moving mode when the strapdown inertial navigation system (SINS) is under entirely self-contained conditions. PMID:28353682

Strongly nonlinear composite dielectrics: A perturbation method for finding the potential field and bulk effective properties

NASA Astrophysics Data System (ADS)

Blumenfeld, Raphael; Bergman, David J.

1991-10-01

A class of strongly nonlinear composite dielectrics is studied. We develop a general method to reduce the scalar-potential-field problem to the solution of a set of linear Poisson-type equations in rescaled coordinates. The method is applicable for a large variety of nonlinear materials. For a power-law relation between the displacement and the electric fields, it is used to solve explicitly for the value of the bulk effective dielectric constant ɛe to second order in the fluctuations of its local value. A simlar procedure for the vector potential, whose curl is the displacement field, yields a quantity analogous to the inverse dielectric constant in linear dielectrics. The bulk effective dielectric constant is given by a set of linear integral expressions in the rescaled coordinates and exact bounds for it are derived.

Parvovirus-like particles as vaccine vectors.

PubMed

Casal, J I; Rueda, P; Hurtado, A

1999-09-01

A wide array of systems have been developed to improve "classic" vaccines. The use of small polypeptides able to elicit potent antibody and cytotoxic responses seems to have enormous potential in the design of safer vaccines. While peptide coupling to large soluble proteins such as keyhole limpet hemocyanin is the current method of choice for eliciting antibody responses and insertion in live viruses for cytotoxic T-lymphocyte responses, alternative cheaper and/or safer methods will clearly be required in the future. Virus-like particles constitute very immunogenic molecules that allow for covalent coupling of the epitopes of interest in a simple way. In this article, we detail the methodology employed for the preparation of efficient virus vectors as delivery systems. We used parvovirus as the model for the design of new vaccine vectors. Recently parvovirus-like particles have been engineered to express foreign polypeptides in certain positions, resulting in the production of large quantities of highly immunogenic peptides, and to induce strong antibody, helper-T-cell, and cytotoxic T-lymphocyte responses. We discuss the different alternatives and the necessary steps to carry out this process, placing special emphasis on the flow of decisions that need to be made during the project. Copyright 1999 Academic Press.

Blood Cell-Derived Induced Pluripotent Stem Cells Free of Reprogramming Factors Generated by Sendai Viral Vectors

PubMed Central

Muench, Marcus O.; Fusaki, Noemi; Beyer, Ashley I.; Wang, Jiaming; Qi, Zhongxia; Yu, Jingwei

2013-01-01

The discovery of induced pluripotent stem cells (iPSCs) holds great promise for regenerative medicine since it is possible to produce patient-specific pluripotent stem cells from affected individuals for potential autologous treatment. Using nonintegrating cytoplasmic Sendai viral vectors, we generated iPSCs efficiently from adult mobilized CD34+ and peripheral blood mononuclear cells. After 5–8 passages, the Sendai viral genome could not be detected by real-time quantitative reverse transcription-polymerase chain reaction. Using the spin embryoid body method, we showed that these blood cell-derived iPSCs could efficiently be differentiated into hematopoietic stem and progenitor cells without the need of coculture with either mouse or human stromal cells. We obtained up to 40% CD34+ of which ∼25% were CD34+/CD43+ hematopoietic precursors that could readily be differentiated into mature blood cells. Our study demonstrated a reproducible protocol for reprogramming blood cells into transgene-free iPSCs by the Sendai viral vector method. Maintenance of the genomic integrity of iPSCs without integration of exogenous DNA should allow the development of therapeutic-grade stem cells for regenerative medicine. PMID:23847002

Determining conduction patterns on a sparse electrode grid: Implications for the analysis of clinical arrhythmias

NASA Astrophysics Data System (ADS)

Vidmar, David; Narayan, Sanjiv M.; Krummen, David E.; Rappel, Wouter-Jan

2016-11-01

We present a general method of utilizing bioelectric recordings from a spatially sparse electrode grid to compute a dynamic vector field describing the underlying propagation of electrical activity. This vector field, termed the wave-front flow field, permits quantitative analysis of the magnitude of rotational activity (vorticity) and focal activity (divergence) at each spatial point. We apply this method to signals recorded during arrhythmias in human atria and ventricles using a multipolar contact catheter and show that the flow fields correlate with corresponding activation maps. Further, regions of elevated vorticity and divergence correspond to sites identified as clinically significant rotors and focal sources where therapeutic intervention can be effective. These flow fields can provide quantitative insights into the dynamics of normal and abnormal conduction in humans and could potentially be used to enhance therapies for cardiac arrhythmias.

Nucleic acid delivery using magnetic nanoparticles: the Magnetofection technology.

PubMed

Laurentt, Nicolas; Sapet, Cédric; Le Gourrierec, Loic; Bertosio, Elodie; Zelphati, Olivier

2011-04-01

In recent years, gene therapy has received considerable interest as a potential method for the treatment of numerous inherited and acquired diseases. However, successes have so far been hampered by several limitations, including safety issues of viral-based nucleic acid vectors and poor in vivo efficiency of nonviral vectors. Magnetofection has been introduced as a novel and powerful tool to deliver genetic material into cells. This technology is defined as the delivery of nucleic acids, either 'naked' or packaged (as complexes with lipids or polymers, and viruses) using magnetic nanoparticles under the guidance of an external magnetic field. This article first discusses the principles of the Magnetofection technology and its benefits as compared with standard transfection methods. A number of relevant examples of its use, both in vitro and in vivo, will then be highlighted. Future trends in the development of new magnetic nanoparticle formulations will also be outlined.

A support vector machine based control application to the experimental three-tank system.

PubMed

Iplikci, Serdar

2010-07-01

This paper presents a support vector machine (SVM) approach to generalized predictive control (GPC) of multiple-input multiple-output (MIMO) nonlinear systems. The possession of higher generalization potential and at the same time avoidance of getting stuck into the local minima have motivated us to employ SVM algorithms for modeling MIMO systems. Based on the SVM model, detailed and compact formulations for calculating predictions and gradient information, which are used in the computation of the optimal control action, are given in the paper. The proposed MIMO SVM-based GPC method has been verified on an experimental three-tank liquid level control system. Experimental results have shown that the proposed method can handle the control task successfully for different reference trajectories. Moreover, a detailed discussion on data gathering, model selection and effects of the control parameters have been given in this paper. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Onchocerciasis transmission in Ghana: the human blood index of sibling species of the Simulium damnosum complex.

PubMed

Lamberton, Poppy H L; Cheke, Robert A; Walker, Martin; Winskill, Peter; Crainey, J Lee; Boakye, Daniel A; Osei-Atweneboana, Mike Y; Tirados, Iñaki; Wilson, Michael D; Tetteh-Kumah, Anthony; Otoo, Sampson; Post, Rory J; Basañez, María-Gloria

2016-08-05

Vector-biting behaviour is important for vector-borne disease (VBD) epidemiology. The proportion of blood meals taken on humans (the human blood index, HBI), is a component of the biting rate per vector on humans in VBD transmission models. Humans are the definitive host of Onchocerca volvulus, but the simuliid vectors feed on a range of animals and HBI is a key indicator of the potential for human onchocerciasis transmission. Ghana has a diversity of Simulium damnosum complex members, which are likely to vary in their HBIs, an important consideration for parameterization of onchocerciasis control and elimination models. Host-seeking and ovipositing S. damnosum (sensu lato) (s.l.) were collected from seven villages in four Ghanaian regions. Taxa were morphologically and molecularly identified. Blood meals from individually stored blackfly abdomens were used for DNA profiling, to identify previous host choice. Household, domestic animal, wild mammal and bird surveys were performed to estimate the density and diversity of potential blood hosts of blackflies. A total of 11,107 abdomens of simuliid females (which would have obtained blood meal(s) previously) were tested, with blood meals successfully amplified in 3,772 (34 %). A single-host species was identified in 2,857 (75.7 %) of the blood meals, of which 2,162 (75.7 %) were human. Simulium soubrense Beffa form, S. squamosum C and S. sanctipauli Pra form were the most anthropophagic (HBI = 0.92, 0.86 and 0.70, respectively); S. squamosum E, S. yahense and S. damnosum (sensu stricto) (s.s.)/S. sirbanum were the most zoophagic (HBI = 0.44, 0.53 and 0.63, respectively). The degree of anthropophagy decreased (but not statistically significantly) with increasing ratio of non-human/human blood hosts. Vector to human ratios ranged from 139 to 1,198 blackflies/person. DNA profiling can successfully identify blood meals from host-seeking and ovipositing blackflies. Host choice varies according to sibling species, season and capture site/method. There was no evidence that HBI is vector and/or host density dependent. Transmission breakpoints will vary among locations due to differing cytospecies compositions and vector abundances.

Chagas disease vector blood meal sources identified by protein mass spectrometry

PubMed Central

Keller, Judith I.; Ballif, Bryan A.; St. Clair, Riley M.; Vincent, James J.; Monroy, M. Carlota

2017-01-01

Chagas disease is a complex vector borne parasitic disease involving blood feeding Triatominae (Hemiptera: Reduviidae) insects, also known as kissing bugs, and the vertebrates they feed on. This disease has tremendous impacts on millions of people and is a global health problem. The etiological agent of Chagas disease, Trypanosoma cruzi (Kinetoplastea: Trypanosomatida: Trypanosomatidae), is deposited on the mammalian host in the insect’s feces during a blood meal, and enters the host’s blood stream through mucous membranes or a break in the skin. Identifying the blood meal sources of triatomine vectors is critical in understanding Chagas disease transmission dynamics, can lead to identification of other vertebrates important in the transmission cycle, and aids management decisions. The latter is particularly important as there is little in the way of effective therapeutics for Chagas disease. Several techniques, mostly DNA-based, are available for blood meal identification. However, further methods are needed, particularly when sample conditions lead to low-quality DNA or to assess the risk of human cross-contamination. We demonstrate a proteomics-based approach, using liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify host-specific hemoglobin peptides for blood meal identification in mouse blood control samples and apply LC-MS/MS for the first time to Triatoma dimidiata insect vectors, tracing blood sources to species. In contrast to most proteins, hemoglobin, stabilized by iron, is incredibly stable even being preserved through geologic time. We compared blood stored with and without an anticoagulant and examined field-collected insect specimens stored in suboptimal conditions such as at room temperature for long periods of time. To our knowledge, this is the first study using LC-MS/MS on field-collected arthropod disease vectors to identify blood meal composition, and where blood meal identification was confirmed with more traditional DNA-based methods. We also demonstrate the potential of synthetic peptide standards to estimate relative amounts of hemoglobin acquired when insects feed on multiple blood sources. These LC-MS/MS methods can contribute to developing Ecohealth control strategies for Chagas disease transmission and can be applied to other arthropod disease vectors. PMID:29232402

A superhydrophobic cone to facilitate the xenomonitoring of filarial parasites, malaria, and trypanosomes using mosquito excreta/feces.

PubMed

Cook, Darren A N; Pilotte, Nils; Minetti, Corrado; Williams, Steven A; Reimer, Lisa J

2017-11-06

Background: Molecular xenomonitoring (MX), the testing of insect vectors for the presence of human pathogens, has the potential to provide a non-invasive and cost-effective method for monitoring the prevalence of disease within a community. Current MX methods require the capture and processing of large numbers of mosquitoes, particularly in areas of low endemicity, increasing the time, cost and labour required. Screening the excreta/feces (E/F) released from mosquitoes, rather than whole carcasses, improves the throughput by removing the need to discriminate vector species since non-vectors release ingested pathogens in E/F. It also enables larger numbers of mosquitoes to be processed per pool. However, this new screening approach requires a method of efficiently collecting E/F. Methods: We developed a cone with a superhydrophobic surface to allow for the efficient collection of E/F. Using mosquitoes exposed to either Plasmodium falciparum , Brugia malayi or Trypanosoma brucei brucei, we tested the performance of the superhydrophobic cone alongside two other collection methods. Results: All collection methods enabled the detection of DNA from the three parasites. Using the superhydrophobic cone to deposit E/F into a small tube provided the highest number of positive samples (16 out of 18) and facilitated detection of parasite DNA in E/F from individual mosquitoes. Further tests showed that following a simple washing step, the cone can be reused multiple times, further improving its cost-effectiveness. Conclusions: Incorporating the superhydrophobic cone into mosquito traps or holding containers could provide a simple and efficient method for collecting E/F. Where this is not possible, swabbing the container or using the washing method facilitates the detection of the three parasites used in this study.

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.

PubMed

Liu, Bin; Wang, Xiaolong; Lin, Lei; Dong, Qiwen; Wang, Xuan

2008-12-01

Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.

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

A New Unified Analysis of Estimate Errors by Model-Matching Phase-Estimation Methods for Sensorless Drive of Permanent-Magnet Synchronous Motors and New Trajectory-Oriented Vector Control, Part II

NASA Astrophysics Data System (ADS)

Shinnaka, Shinji

This paper presents a new unified analysis of estimate errors by model-matching extended-back-EMF estimation methods for sensorless drive of permanent-magnet synchronous motors. Analytical solutions about estimate errors, whose validity is confirmed by numerical experiments, are rich in universality and applicability. As an example of universality and applicability, a new trajectory-oriented vector control method is proposed, which can realize directly quasi-optimal strategy minimizing total losses with no additional computational loads by simply orienting one of vector-control coordinates to the associated quasi-optimal trajectory. The coordinate orientation rule, which is analytically derived, is surprisingly simple. Consequently the trajectory-oriented vector control method can be applied to a number of conventional vector control systems using model-matching extended-back-EMF estimation methods.

A new method for the prediction of chatter stability lobes based on dynamic cutting force simulation model and support vector machine

NASA Astrophysics Data System (ADS)

Peng, Chong; Wang, Lun; Liao, T. Warren

2015-10-01

Currently, chatter has become the critical factor in hindering machining quality and productivity in machining processes. To avoid cutting chatter, a new method based on dynamic cutting force simulation model and support vector machine (SVM) is presented for the prediction of chatter stability lobes. The cutting force is selected as the monitoring signal, and the wavelet energy entropy theory is used to extract the feature vectors. A support vector machine is constructed using the MATLAB LIBSVM toolbox for pattern classification based on the feature vectors derived from the experimental cutting data. Then combining with the dynamic cutting force simulation model, the stability lobes diagram (SLD) can be estimated. Finally, the predicted results are compared with existing methods such as zero-order analytical (ZOA) and semi-discretization (SD) method as well as actual cutting experimental results to confirm the validity of this new method.

A projection method for low speed flows

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

Colella, P.; Pao, K.

The authors propose a decomposition applicable to low speed, inviscid flows of all Mach numbers less than 1. By using the Hodge decomposition, they may write the velocity field as the sum of a divergence-free vector field and a gradient of a scalar function. Evolution equations for these parts are presented. A numerical procedure based on this decomposition is designed, using projection methods for solving the incompressible variables and a backward-Euler method for solving the potential variables. Numerical experiments are included to illustrate various aspects of the algorithm.

Method for introducing unidirectional nested deletions

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

2001-01-01

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

A method to determine fault vectors in 4H-SiC from stacking sequences observed on high resolution transmission electron microscopy images

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

Wu, Fangzhen; Wang, Huanhuan; Raghothamachar, Balaji

A new method has been developed to determine the fault vectors associated with stacking faults in 4H-SiC from their stacking sequences observed on high resolution TEM images. This method, analogous to the Burgers circuit technique for determination of dislocation Burgers vector, involves determination of the vectors required in the projection of the perfect lattice to correct the deviated path constructed in the faulted material. Results for several different stacking faults were compared with fault vectors determined from X-ray topographic contrast analysis and were found to be consistent. This technique is expected to applicable to all structures comprising corner shared tetrahedra.

A Two-Layer Least Squares Support Vector Machine Approach to Credit Risk Assessment

NASA Astrophysics Data System (ADS)

Liu, Jingli; Li, Jianping; Xu, Weixuan; Shi, Yong

Least squares support vector machine (LS-SVM) is a revised version of support vector machine (SVM) and has been proved to be a useful tool for pattern recognition. LS-SVM had excellent generalization performance and low computational cost. In this paper, we propose a new method called two-layer least squares support vector machine which combines kernel principle component analysis (KPCA) and linear programming form of least square support vector machine. With this method sparseness and robustness is obtained while solving large dimensional and large scale database. A U.S. commercial credit card database is used to test the efficiency of our method and the result proved to be a satisfactory one.

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

NASA Astrophysics Data System (ADS)

Byard, Kevin; Shutler, Paul M. E.

2017-06-01

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

Puromycin-resistant lentiviral control shRNA vector, pLKO.1 induces unexpected cellular differentiation of P19 embryonic stem cells

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

Kanungo, Jyotshna

RNA silencing is used as a common method for investigating loss-of-function effects of genes of interest. In mammalian cells, RNA interference (RNAi) or RNA silencing can be achieved by transient siRNA (small or short interfering RNA) transfection or by stable shRNA (short hairpin RNA) systems. Various vectors are used for efficient delivery of shRNA. Lentiviral vectors offer an efficient delivery system for stable and long-term expression of the shRNA in mammalian cells. The widely used lentiviral pLKO.1 plasmid vector is very popular in RNAi studies. A large RNAi database, a TRC (the RNAi Consortium) library, was established based on themore » pLKO.1-TRC plasmid vector. This plasmid (also called pLKO.1-puro) has a puromycin-resistant gene for selection in mammalian cells along with designs for generating lentiviral particles as well for RNA silencing. While using the pLKO.1-puro TRC control shRNA plasmid for transfection in murine P19 embryonic stem (ES) cells, it was unexpectedly discovered that this plasmid vector induced robust endodermal differentiation. Since P19 ES cells are pluripotent and respond to external stimuli that have the potential to alter the phenotype and thus its stemness, other cell types used in RNA silencing studies do not display the obvious effect and therefore, may affect experiments in subtle ways that would go undetected. This study for the first time provides evidence that raises concern and warrants extreme caution while using the pLKO.1-puro control shRNA vector because of its unexpected non-specific effects on cellular integrity. - Highlights: • In P19 ES cells the pLKO.1-puro lentiviral control shRNA vector induced endodermal differentiation. • P19 ES cells harboring the pCDNA3 plasmid vector retained their stem-ness as opposed to those harboring the pLKO.1-puro vector. • P19 ES cells can serve as a sensor to determine vector safety. • Extreme caution is warranted while using the widely used pLKO.1-puro lentiviral vector for experimental and therapeutic designs.« less

RFDT: A Rotation Forest-based Predictor for Predicting Drug-Target Interactions Using Drug Structure and Protein Sequence Information.

PubMed

Wang, Lei; You, Zhu-Hong; Chen, Xing; Yan, Xin; Liu, Gang; Zhang, Wei

2018-01-01

Identification of interaction between drugs and target proteins plays an important role in discovering new drug candidates. However, through the experimental method to identify the drug-target interactions remain to be extremely time-consuming, expensive and challenging even nowadays. Therefore, it is urgent to develop new computational methods to predict potential drugtarget interactions (DTI). In this article, a novel computational model is developed for predicting potential drug-target interactions under the theory that each drug-target interaction pair can be represented by the structural properties from drugs and evolutionary information derived from proteins. Specifically, the protein sequences are encoded as Position-Specific Scoring Matrix (PSSM) descriptor which contains information of biological evolutionary and the drug molecules are encoded as fingerprint feature vector which represents the existence of certain functional groups or fragments. Four benchmark datasets involving enzymes, ion channels, GPCRs and nuclear receptors, are independently used for establishing predictive models with Rotation Forest (RF) model. The proposed method achieved the prediction accuracy of 91.3%, 89.1%, 84.1% and 71.1% for four datasets respectively. In order to make our method more persuasive, we compared our classifier with the state-of-theart Support Vector Machine (SVM) classifier. We also compared the proposed method with other excellent methods. Experimental results demonstrate that the proposed method is effective in the prediction of DTI, and can provide assistance for new drug research and development. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A Predictive Model for Medical Events Based on Contextual Embedding of Temporal Sequences

PubMed Central

Wang, Zhimu; Huang, Yingxiang; Wang, Shuang; Wang, Fei; Jiang, Xiaoqian

2016-01-01

Background Medical concepts are inherently ambiguous and error-prone due to human fallibility, which makes it hard for them to be fully used by classical machine learning methods (eg, for tasks like early stage disease prediction). Objective Our work was to create a new machine-friendly representation that resembles the semantics of medical concepts. We then developed a sequential predictive model for medical events based on this new representation. Methods We developed novel contextual embedding techniques to combine different medical events (eg, diagnoses, prescriptions, and labs tests). Each medical event is converted into a numerical vector that resembles its “semantics,” via which the similarity between medical events can be easily measured. We developed simple and effective predictive models based on these vectors to predict novel diagnoses. Results We evaluated our sequential prediction model (and standard learning methods) in estimating the risk of potential diseases based on our contextual embedding representation. Our model achieved an area under the receiver operating characteristic (ROC) curve (AUC) of 0.79 on chronic systolic heart failure and an average AUC of 0.67 (over the 80 most common diagnoses) using the Medical Information Mart for Intensive Care III (MIMIC-III) dataset. Conclusions We propose a general early prognosis predictor for 80 different diagnoses. Our method computes numeric representation for each medical event to uncover the potential meaning of those events. Our results demonstrate the efficiency of the proposed method, which will benefit patients and physicians by offering more accurate diagnosis. PMID:27888170

MO-F-CAMPUS-J-02: Automatic Recognition of Patient Treatment Site in Portal Images Using Machine Learning

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

Chang, X; Yang, D

Purpose: To investigate the method to automatically recognize the treatment site in the X-Ray portal images. It could be useful to detect potential treatment errors, and to provide guidance to sequential tasks, e.g. automatically verify the patient daily setup. Methods: The portal images were exported from MOSAIQ as DICOM files, and were 1) processed with a threshold based intensity transformation algorithm to enhance contrast, and 2) where then down-sampled (from 1024×768 to 128×96) by using bi-cubic interpolation algorithm. An appearance-based vector space model (VSM) was used to rearrange the images into vectors. A principal component analysis (PCA) method was usedmore » to reduce the vector dimensions. A multi-class support vector machine (SVM), with radial basis function kernel, was used to build the treatment site recognition models. These models were then used to recognize the treatment sites in the portal image. Portal images of 120 patients were included in the study. The images were selected to cover six treatment sites: brain, head and neck, breast, lung, abdomen and pelvis. Each site had images of the twenty patients. Cross-validation experiments were performed to evaluate the performance. Results: MATLAB image processing Toolbox and scikit-learn (a machine learning library in python) were used to implement the proposed method. The average accuracies using the AP and RT images separately were 95% and 94% respectively. The average accuracy using AP and RT images together was 98%. Computation time was ∼0.16 seconds per patient with AP or RT image, ∼0.33 seconds per patient with both of AP and RT images. Conclusion: The proposed method of treatment site recognition is efficient and accurate. It is not sensitive to the differences of image intensity, size and positions of patients in the portal images. It could be useful for the patient safety assurance. The work was partially supported by a research grant from Varian Medical System.« less

Segmentation of discrete vector fields.

PubMed

Li, Hongyu; Chen, Wenbin; Shen, I-Fan

2006-01-01

In this paper, we propose an approach for 2D discrete vector field segmentation based on the Green function and normalized cut. The method is inspired by discrete Hodge Decomposition such that a discrete vector field can be broken down into three simpler components, namely, curl-free, divergence-free, and harmonic components. We show that the Green Function Method (GFM) can be used to approximate the curl-free and the divergence-free components to achieve our goal of the vector field segmentation. The final segmentation curves that represent the boundaries of the influence region of singularities are obtained from the optimal vector field segmentations. These curves are composed of piecewise smooth contours or streamlines. Our method is applicable to both linear and nonlinear discrete vector fields. Experiments show that the segmentations obtained using our approach essentially agree with human perceptual judgement.

Fast Quaternion Attitude Estimation from Two Vector Measurements

NASA Technical Reports Server (NTRS)

Markley, F. Landis; Bauer, Frank H. (Technical Monitor)

2001-01-01

Many spacecraft attitude determination methods use exactly two vector measurements. The two vectors are typically the unit vector to the Sun and the Earth's magnetic field vector for coarse "sun-mag" attitude determination or unit vectors to two stars tracked by two star trackers for fine attitude determination. Existing closed-form attitude estimates based on Wahba's optimality criterion for two arbitrarily weighted observations are somewhat slow to evaluate. This paper presents two new fast quaternion attitude estimation algorithms using two vector observations, one optimal and one suboptimal. The suboptimal method gives the same estimate as the TRIAD algorithm, at reduced computational cost. Simulations show that the TRIAD estimate is almost as accurate as the optimal estimate in representative test scenarios.

Correlation-based motion vector processing with adaptive interpolation scheme for motion-compensated frame interpolation.

PubMed

Huang, Ai-Mei; Nguyen, Truong

2009-04-01

In this paper, we address the problems of unreliable motion vectors that cause visual artifacts but cannot be detected by high residual energy or bidirectional prediction difference in motion-compensated frame interpolation. A correlation-based motion vector processing method is proposed to detect and correct those unreliable motion vectors by explicitly considering motion vector correlation in the motion vector reliability classification, motion vector correction, and frame interpolation stages. Since our method gradually corrects unreliable motion vectors based on their reliability, we can effectively discover the areas where no motion is reliable to be used, such as occlusions and deformed structures. We also propose an adaptive frame interpolation scheme for the occlusion areas based on the analysis of their surrounding motion distribution. As a result, the interpolated frames using the proposed scheme have clearer structure edges and ghost artifacts are also greatly reduced. Experimental results show that our interpolated results have better visual quality than other methods. In addition, the proposed scheme is robust even for those video sequences that contain multiple and fast motions.

Backward and forward Monte Carlo method for vector radiative transfer in a two-dimensional graded index medium

NASA Astrophysics Data System (ADS)

Qian, Lin-Feng; Shi, Guo-Dong; Huang, Yong; Xing, Yu-Ming

2017-10-01

In vector radiative transfer, backward ray tracing is seldom used. We present a backward and forward Monte Carlo method to simulate vector radiative transfer in a two-dimensional graded index medium, which is new and different from the conventional Monte Carlo method. The backward and forward Monte Carlo method involves dividing the ray tracing into two processes backward tracing and forward tracing. In multidimensional graded index media, the trajectory of a ray is usually a three-dimensional curve. During the transport of a polarization ellipse, the curved ray trajectory will induce geometrical effects and cause Stokes parameters to continuously change. The solution processes for a non-scattering medium and an anisotropic scattering medium are analysed. We also analyse some parameters that influence the Stokes vector in two-dimensional graded index media. The research shows that the Q component of the Stokes vector cannot be ignored. However, the U and V components of the Stokes vector are very small.

Numerical solution of 2D-vector tomography problem using the method of approximate inverse

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

Svetov, Ivan; Maltseva, Svetlana; Polyakova, Anna

2016-08-10

We propose a numerical solution of reconstruction problem of a two-dimensional vector field in a unit disk from the known values of the longitudinal and transverse ray transforms. The algorithm is based on the method of approximate inverse. Numerical simulations confirm that the proposed method yields good results of reconstruction of vector fields.

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.

An Update on Canine Adenovirus Type 2 and Its Vectors

PubMed Central

Bru, Thierry; Salinas, Sara; Kremer, Eric J.

2010-01-01

Adenovirus vectors have significant potential for long- or short-term gene transfer. Preclinical and clinical studies using human derived adenoviruses (HAd) have demonstrated the feasibility of flexible hybrid vector designs, robust expression and induction of protective immunity. However, clinical use of HAd vectors can, under some conditions, be limited by pre-existing vector immunity. Pre-existing humoral and cellular anti-capsid immunity limits the efficacy and duration of transgene expression and is poorly circumvented by injections of larger doses and immuno-suppressing drugs. This review updates canine adenovirus serotype 2 (CAV-2, also known as CAdV-2) biology and gives an overview of the generation of early region 1 (E1)-deleted to helper-dependent (HD) CAV-2 vectors. We also summarize the essential characteristics concerning their interaction with the anti-HAd memory immune responses in humans, the preferential transduction of neurons, and its high level of retrograde axonal transport in the central and peripheral nervous system. CAV-2 vectors are particularly interesting tools to study the pathophysiology and potential treatment of neurodegenerative diseases, as anti-tumoral and anti-viral vaccines, tracer of synaptic junctions, oncolytic virus and as a platform to generate chimeric vectors. PMID:21994722

Epidemiological surveillance methods for vector-borne diseases.

PubMed

Thompson, P N; Etter, E

2015-04-01

Compared with many other diseases, the ever-increasing threat of vector-borne diseases (VBDs) represents a great challenge to public and animal health managers. Complex life cycles, changing distribution ranges, a variety of potential vectors and hosts, and the possible role of reservoirs make surveillance for VBDs a grave concern in a changing environment with increasing economic constraints. Surveillance activities may have various specific objectives and may focus on clinical disease, pathogens, vectors, hosts and/or reservoirs, but ultimately such activities should improve our ability to predict, prevent and/or control the diseases concerned. This paper briefly reviews existing and newly developed tools for the surveillance of VBDs. A range of examples, by no means exhaustive, illustrates that VBD surveillance usually involves a combination of methods to achieve its aims, and is best accomplished when these techniques are adapted to the specific environment and constraints of the region. More so than any other diseases, VBDs respect no administrative boundaries; in addition, animal, human and commodity movements are increasing dramatically, with illegal or unknown movements difficult to quantify. Vector-borne disease surveillance therefore becomes a serious issue for local and national organisations and is being conducted more and more at the regional and international level through multidisciplinary networks. With economic and logistical constraints, tools for optimising and evaluating the performance of surveillance systems are essential and examples of recent developments in this area are included. The continuous development of mapping, analytical and modelling tools provides us with an enhanced ability to interpret, visualise and communicate surveillance results. This review also demonstrates the importance of the link between surveillance and research, with interactions and benefits in both directions.

Towards a resource-based habitat approach for spatial modelling of vector-borne disease risks.

PubMed

Hartemink, Nienke; Vanwambeke, Sophie O; Purse, Bethan V; Gilbert, Marius; Van Dyck, Hans

2015-11-01

Given the veterinary and public health impact of vector-borne diseases, there is a clear need to assess the suitability of landscapes for the emergence and spread of these diseases. Current approaches for predicting disease risks neglect key features of the landscape as components of the functional habitat of vectors or hosts, and hence of the pathogen. Empirical-statistical methods do not explicitly incorporate biological mechanisms, whereas current mechanistic models are rarely spatially explicit; both methods ignore the way animals use the landscape (i.e. movement ecology). We argue that applying a functional concept for habitat, i.e. the resource-based habitat concept (RBHC), can solve these issues. The RBHC offers a framework to identify systematically the different ecological resources that are necessary for the completion of the transmission cycle and to relate these resources to (combinations of) landscape features and other environmental factors. The potential of the RBHC as a framework for identifying suitable habitats for vector-borne pathogens is explored and illustrated with the case of bluetongue virus, a midge-transmitted virus affecting ruminants. The concept facilitates the study of functional habitats of the interacting species (vectors as well as hosts) and provides new insight into spatial and temporal variation in transmission opportunities and exposure that ultimately determine disease risks. It may help to identify knowledge gaps and control options arising from changes in the spatial configuration of key resources across the landscape. The RBHC framework may act as a bridge between existing mechanistic and statistical modelling approaches. © 2014 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Global Status of DDT and Its Alternatives for Use in Vector Control to Prevent Disease

PubMed Central

van den Berg, Henk

2009-01-01

Objective I review the status of dichlorodiphenyltrichloroethane (DDT), used for disease vector control, along with current evidence on its benefits and risks in relation to the available alternatives. Data sources and extraction Contemporary data on DDT use were largely obtained from questionnaires and reports. I also conducted a Scopus search to retrieve published articles. Data synthesis DDT has been recommended as part of the arsenal of insecticides available for indoor residual spraying until suitable alternatives are available. Approximately 14 countries use DDT for disease control, and several countries are preparing to reintroduce DDT. The effectiveness of DDT depends on local settings and merits close consideration in relation to the alternatives. Concerns about the continued use of DDT are fueled by recent reports of high levels of human exposure associated with indoor spraying amid accumulating evidence on chronic health effects. There are signs that more malaria vectors are becoming resistant to the toxic action of DDT, and that resistance is spreading to new countries. A comprehensive cost assessment of DDT versus its alternatives that takes side effects into account is missing. Effective chemical methods are available as immediate alternatives to DDT, but the choice of insecticide class is limited, and in certain areas the development of resistance is undermining the efficacy of insecticidal tools. New insecticides are not expected in the short term. Nonchemical methods are potentially important, but their effectiveness at program level needs urgent study. Conclusions To reduce reliance on DDT, support is needed for integrated and multipartner strategies of vector control and for the continued development of new technologies. Integrated vector management provides a framework for developing and implementing effective technologies and strategies as sustainable alternatives to reliance on DDT. PMID:20049114

Adaptive vector validation in image velocimetry to minimise the influence of outlier clusters

NASA Astrophysics Data System (ADS)

Masullo, Alessandro; Theunissen, Raf

2016-03-01

The universal outlier detection scheme (Westerweel and Scarano in Exp Fluids 39:1096-1100, 2005) and the distance-weighted universal outlier detection scheme for unstructured data (Duncan et al. in Meas Sci Technol 21:057002, 2010) are the most common PIV data validation routines. However, such techniques rely on a spatial comparison of each vector with those in a fixed-size neighbourhood and their performance subsequently suffers in the presence of clusters of outliers. This paper proposes an advancement to render outlier detection more robust while reducing the probability of mistakenly invalidating correct vectors. Velocity fields undergo a preliminary evaluation in terms of local coherency, which parametrises the extent of the neighbourhood with which each vector will be compared subsequently. Such adaptivity is shown to reduce the number of undetected outliers, even when implemented in the afore validation schemes. In addition, the authors present an alternative residual definition considering vector magnitude and angle adopting a modified Gaussian-weighted distance-based averaging median. This procedure is able to adapt the degree of acceptable background fluctuations in velocity to the local displacement magnitude. The traditional, extended and recommended validation methods are numerically assessed on the basis of flow fields from an isolated vortex, a turbulent channel flow and a DNS simulation of forced isotropic turbulence. The resulting validation method is adaptive, requires no user-defined parameters and is demonstrated to yield the best performances in terms of outlier under- and over-detection. Finally, the novel validation routine is applied to the PIV analysis of experimental studies focused on the near wake behind a porous disc and on a supersonic jet, illustrating the potential gains in spatial resolution and accuracy.

Estimating nitrogen loading and far-field dispersal potential from background sources and coastal finfish aquaculture: A simple framework and case study in Atlantic Canada

NASA Astrophysics Data System (ADS)

McIver, R.; Milewski, I.; Loucks, R.; Smith, R.

2018-05-01

Far-field nutrient impacts associated with finfish aquaculture have been identified as a topic of concern for regulators, managers, scientists, and the public for over two decades but disentangling aquaculture impacts from those caused by other natural and anthropogenic sources has impeded the development of monitoring metrics and management plans. We apply a bulk, steady-state nitrogen loading model (NLM) framework to estimate the annual input of Total Dissolved Nitrogen (TDN) from point and non-point sources to the watershed surrounding Port Mouton Bay, Nova Scotia (Canada). We then use the results of the NLM together with estimates of dissolved inorganic nitrogen (DIN) loading from a sea-cage trout farm in the Bay and progressive vector diagrams to illustrate potential patterns of DIN dispersal from the trout farm. Our estimated anthropogenic nitrogen contribution to Port Mouton Bay from all terrestrial and atmospheric sources is ∼211,703 kg TDN/year with atmospheric deposition accounting for almost all (98.6%). At a stocking level of ∼400,000 rainbow trout, the Port Mouton Bay sea-cage farm increases the annual anthropogenic TDN loading to the bay by 14.4% or 30,400 kg. Depending on current flow rates, nitrogen flux from the trout farm can be more than double the background concentrations of TDN near the farm site. Although it is unlikely that nitrogen loading from this single fish farm is saturating the DIN requirements of the entire bay, progressive vector diagrams suggest that the dispersal potential may be insufficient to mitigate potential symptoms of eutrophication associated with nitrogen fluxes. We present an accessible and user-friendly tool for managers to estimate baseline nutrient loading in relation to aquaculture and our use of progressive vector diagrams illustrate a practical and simple method for characterizing potential nutrient dispersal based on local conditions and spatial scales. Our study joins numerous studies which have highlighted the need for more effective monitoring and assessment methods to improve the detection of aquaculture effects at far-field scales and to assess those effects in relation to other natural and anthropogenic factors impacting coastal habitats.

Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

PubMed Central

Schmeisser, Falko; Weir, Jerry P

2007-01-01

Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Results Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Conclusion Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors. PMID:17501993

Atmospheric cold plasma inactivation of Escherichia coli 0157:H7 and aerobic microorganisms in cold-stored romaine lettuce packaged in a commerical polyethylene terephthalate container

USDA-ARS?s Scientific Manuscript database

Leafy greens continue to be a significant vector for foodborne pathogens, including Escherichia coli O157:H7. Dielectric barrier discharge atmospheric cold plasma (ACP) treatment is a promising method for microbial decontamination of produce. An important aspect of this technology is the potential f...

Helper-Dependent Adenoviral Vectors.

PubMed

Rosewell, Amanda; Vetrini, Francesco; Ng, Philip

2011-10-29

Helper-dependent adenoviral vectors are devoid of all viral coding sequences, possess a large cloning capacity, and can efficiently transduce a wide variety of cell types from various species independent of the cell cycle to mediate long-term transgene expression without chronic toxicity. These non-integrating vectors hold tremendous potential for a variety of gene transfer and gene therapy applications. Here, we review the production technologies, applications, obstacles to clinical translation and their potential resolutions, and the future challenges and unanswered questions regarding this promising gene transfer technology.

Helper-Dependent Adenoviral Vectors

PubMed Central

Rosewell, Amanda; Vetrini, Francesco; Ng, Philip

2012-01-01

Helper-dependent adenoviral vectors are devoid of all viral coding sequences, possess a large cloning capacity, and can efficiently transduce a wide variety of cell types from various species independent of the cell cycle to mediate long-term transgene expression without chronic toxicity. These non-integrating vectors hold tremendous potential for a variety of gene transfer and gene therapy applications. Here, we review the production technologies, applications, obstacles to clinical translation and their potential resolutions, and the future challenges and unanswered questions regarding this promising gene transfer technology. PMID:24533227

Multiclass Reduced-Set Support Vector Machines

NASA Technical Reports Server (NTRS)

Tang, Benyang; Mazzoni, Dominic

2006-01-01

There are well-established methods for reducing the number of support vectors in a trained binary support vector machine, often with minimal impact on accuracy. We show how reduced-set methods can be applied to multiclass SVMs made up of several binary SVMs, with significantly better results than reducing each binary SVM independently. Our approach is based on Burges' approach that constructs each reduced-set vector as the pre-image of a vector in kernel space, but we extend this by recomputing the SVM weights and bias optimally using the original SVM objective function. This leads to greater accuracy for a binary reduced-set SVM, and also allows vectors to be 'shared' between multiple binary SVMs for greater multiclass accuracy with fewer reduced-set vectors. We also propose computing pre-images using differential evolution, which we have found to be more robust than gradient descent alone. We show experimental results on a variety of problems and find that this new approach is consistently better than previous multiclass reduced-set methods, sometimes with a dramatic difference.

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

Quantum dynamics of relativistic bosons through nonminimal vector square potentials

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

Oliveira, Luiz P. de, E-mail: oliveira.phys@gmail.com

The dynamics of relativistic bosons (scalar and vectorial) through nonminimal vector square (well and barrier) potentials is studied in the Duffin–Kemmer–Petiau (DKP) formalism. We show that the problem can be mapped in effective Schrödinger equations for a component of the DKP spinor. An oscillatory transmission coefficient is found and there is total reflection. Additionally, the energy spectrum of bound states is obtained and reveals the Schiff–Snyder–Weinberg effect, for specific conditions the potential lodges bound states of particles and antiparticles. - Highlights: • DKP bosons in a nonminimal vector square potential are studied. • Spin zero and spin one bosons havemore » the same results. • The Schiff–Snyder–Weinberg effect is observed.« less

Optoelectronic Inner-Product Neural Associative Memory

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang

1993-01-01

Optoelectronic apparatus acts as artificial neural network performing associative recall of binary images. Recall process is iterative one involving optical computation of inner products between binary input vector and one or more reference binary vectors in memory. Inner-product method requires far less memory space than matrix-vector method.

Optimized AAV rh.10 Vectors That Partially Evade Neutralizing Antibodies during Hepatic Gene Transfer

PubMed Central

Selot, Ruchita; Arumugam, Sathyathithan; Mary, Bertin; Cheemadan, Sabna; Jayandharan, Giridhara R.

2017-01-01

Of the 12 common serotypes used for gene delivery applications, Adeno-associated virus (AAV)rh.10 serotype has shown sustained hepatic transduction and has the lowest seropositivity in humans. We have evaluated if further modifications to AAVrh.10 at its phosphodegron like regions or predicted immunogenic epitopes could improve its hepatic gene transfer and immune evasion potential. Mutant AAVrh.10 vectors were generated by site directed mutagenesis of the predicted targets. These mutant vectors were first tested for their transduction efficiency in HeLa and HEK293T cells. The optimal vector was further evaluated for their cellular uptake, entry, and intracellular trafficking by quantitative PCR and time-lapse confocal microscopy. To evaluate their potential during hepatic gene therapy, C57BL/6 mice were administered with wild-type or optimal mutant AAVrh.10 and the luciferase transgene expression was documented by serial bioluminescence imaging at 14, 30, 45, and 72 days post-gene transfer. Their hepatic transduction was further verified by a quantitative PCR analysis of AAV copy number in the liver tissue. The optimal AAVrh.10 vector was further evaluated for their immune escape potential, in animals pre-immunized with human intravenous immunoglobulin. Our results demonstrate that a modified AAVrh.10 S671A vector had enhanced cellular entry (3.6 fold), migrate rapidly to the perinuclear region (1 vs. >2 h for wild type vectors) in vitro, which further translates to modest increase in hepatic gene transfer efficiency in vivo. More importantly, the mutant AAVrh.10 vector was able to partially evade neutralizing antibodies (~27–64 fold) in pre-immunized animals. The development of an AAV vector system that can escape the circulating neutralizing antibodies in the host will substantially widen the scope of gene therapy applications in humans. PMID:28769791

Sparse Method for Direction of Arrival Estimation Using Denoised Fourth-Order Cumulants Vector.

PubMed

Fan, Yangyu; Wang, Jianshu; Du, Rui; Lv, Guoyun

2018-06-04

Fourth-order cumulants (FOCs) vector-based direction of arrival (DOA) estimation methods of non-Gaussian sources may suffer from poor performance for limited snapshots or difficulty in setting parameters. In this paper, a novel FOCs vector-based sparse DOA estimation method is proposed. Firstly, by utilizing the concept of a fourth-order difference co-array (FODCA), an advanced FOCs vector denoising or dimension reduction procedure is presented for arbitrary array geometries. Then, a novel single measurement vector (SMV) model is established by the denoised FOCs vector, and efficiently solved by an off-grid sparse Bayesian inference (OGSBI) method. The estimation errors of FOCs are integrated in the SMV model, and are approximately estimated in a simple way. A necessary condition regarding the number of identifiable sources of our method is presented that, in order to uniquely identify all sources, the number of sources K must fulfill K ≤ ( M 4 - 2 M 3 + 7 M 2 - 6 M ) / 8 . The proposed method suits any geometry, does not need prior knowledge of the number of sources, is insensitive to associated parameters, and has maximum identifiability O ( M 4 ) , where M is the number of sensors in the array. Numerical simulations illustrate the superior performance of the proposed method.

Conference Proceedings on Applied Computational Electromagnetics (3rd) Held in Monterey, California on 24-26 March 1987

DTIC Science & Technology

1987-03-01

the VLSI Implementation of the Electromagnetic Field of an Arbitrary Current Source" B.A. Hoyt, A.J. Terzuoli, A.V. Lair ., Air Force Institute of...method is that cavities of arbitrary three dimensional shapes and nonuniform lossy materials can be analyzed. THEORY OF VECTOR POTENTIAL FINITE...elements used to model the cavity. The method includes the effects of nonuniform lossy materials and can analyze cavities of a wide variety of two- and

Using remote sensing to map larval and adult populations of Anopheles hyrcanus (Diptera: Culicidae) a potential malaria vector in Southern France

PubMed Central

Tran, Annelise; Ponçon, Nicolas; Toty, Céline; Linard, Catherine; Guis, Hélène; Ferré, Jean-Baptiste; Lo Seen, Danny; Roger, François; de la Rocque, Stéphane; Fontenille, Didier; Baldet, Thierry

2008-01-01

Background Although malaria disappeared from southern France more than 60 years ago, suspicions of recent autochthonous transmission in the French Mediterranean coast support the idea that the area could still be subject to malaria transmission. The main potential vector of malaria in the Camargue area, the largest river delta in southern France, is the mosquito Anopheles hyrcanus (Diptera: Culicidae). In the context of recent climatic and landscape changes, the evaluation of the risk of emergence or re-emergence of such a major disease is of great importance in Europe. When assessing the risk of emergence of vector-borne diseases, it is crucial to be able to characterize the arthropod vector's spatial distribution. Given that remote sensing techniques can describe some of the environmental parameters which drive this distribution, satellite imagery or aerial photographs could be used for vector mapping. Results In this study, we propose a method to map larval and adult populations of An. hyrcanus based on environmental indices derived from high spatial resolution imagery. The analysis of the link between entomological field data on An. hyrcanus larvae and environmental indices (biotopes, distance to the nearest main productive breeding sites of this species i.e., rice fields) led to the definition of a larval index, defined as the probability of observing An. hyrcanus larvae in a given site at least once over a year. Independent accuracy assessments showed a good agreement between observed and predicted values (sensitivity and specificity of the logistic regression model being 0.76 and 0.78, respectively). An adult index was derived from the larval index by averaging the larval index within a buffer around the trap location. This index was highly correlated with observed adult abundance values (Pearson r = 0.97, p < 0.05). This allowed us to generate predictive maps of An. hyrcanus larval and adult populations from the landscape indices. Conclusion This work shows that it is possible to use high resolution satellite imagery to map malaria vector spatial distribution. It also confirms the potential of remote sensing to help target risk areas, and constitutes a first essential step in assessing the risk of re-emergence of malaria in southern France. PMID:18302749

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.

Evaluation of signal transduction pathways after transient cutaneous adenoviral gene delivery

PubMed Central

2011-01-01

Background Adenoviral vectors have provided effective methods for in vivo gene delivery in therapeutic applications. However, these vectors can induce immune responses that may severely affect the ability of vector re-application. There is limited information about the mechanisms and signal transduction pathways involved in adenoviral recognition. For optimization of cutaneous gene therapy it is necessary to investigate molecular mechanisms of virus recognition in epidermal cells. The aim of this study was to investigate the signal transduction of the innate immunity after adenoviral DNA internalization in keratinocytes. Methods In vitro, keratinocytes were transfected with DNA, in the presence and absence of inhibitors for signalling molecules. In vivo, immunocompetent and athymic mice (n = 3 per group) were twice transduced with an Ad-vector. Results The results show an acute induction of type-I-interferon after in vitro transfection. Inhibition of PI3K, p38 MAPK, JNK and NFkappaB resulted in a decreased expression of type-I-interferon. In contrast to immunocompetent mice, athymic mice demonstrated a constant transgene expression and reduced inflammatory response in vivo. Conclusion The results suggest an induction of the innate immunity triggered by cytoplasm localised DNA which is mediated by PI3K-, p38 MAPK-, JNK-, NFkappaB-, JAK/STAT- and ERK1/2-dependent pathways. A stable transgene expression and a reduced inflammatory response in immunodeficient mice have been observed. These results provide potential for an effective adenoviral gene delivery into immunosupressed skin. PMID:21255430

Proved and potential vectors of yellow fever in South Africa

PubMed Central

De Meillon, Botha

1954-01-01

This paper, based on records obtained from the Entomology Department of the South African Institute for Medical Research, Johannesburg, gives a summary of the distribution, adult habits, and breeding-places of the proved and potential vectors of yellow fever in South Africa. PMID:13209304

Climate Change and Aedes Vectors: 21st Century Projections for Dengue Transmission in Europe.

PubMed

Liu-Helmersson, Jing; Quam, Mikkel; Wilder-Smith, Annelies; Stenlund, Hans; Ebi, Kristie; Massad, Eduardo; Rocklöv, Joacim

2016-05-01

Warming temperatures may increase the geographic spread of vector-borne diseases into temperate areas. Although a tropical mosquito-borne viral disease, a dengue outbreak occurred in Madeira, Portugal, in 2012; the first in Europe since 1920s. This outbreak emphasizes the potential for dengue re-emergence in Europe given changing climates. We present estimates of dengue epidemic potential using vectorial capacity (VC) based on historic and projected temperature (1901-2099). VC indicates the vectors' ability to spread disease among humans. We calculated temperature-dependent VC for Europe, highlighting 10 European cities and three non-European reference cities. Compared with the tropics, Europe shows pronounced seasonality and geographical heterogeneity. Although low, VC during summer is currently sufficient for dengue outbreaks in Southern Europe to commence-if sufficient vector populations (either Ae. aegypti and Ae. albopictus) were active and virus were introduced. Under various climate change scenarios, the seasonal peak and time window for dengue epidemic potential increases during the 21st century. Our study maps dengue epidemic potential in Europe and identifies seasonal time windows when major cities are most conducive for dengue transmission from 1901 to 2099. Our findings illustrate, that besides vector control, mitigating greenhouse gas emissions crucially reduces the future epidemic potential of dengue in Europe. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Acoustic vector tomography and its application to magnetoacoustic tomography with magnetic induction (MAT-MI).

PubMed

Li, Xu; Xia, Rongmin; He, Bin

2008-01-01

A new tomographic algorithm for reconstructing a curl-free vector field, whose divergence serves as acoustic source is proposed. It is shown that under certain conditions, the scalar acoustic measurements obtained from a surface enclosing the source area can be vectorized according to the known measurement geometry and then be used to reconstruct the vector field. The proposed method is validated by numerical experiments. This method can be easily applied to magnetoacoustic tomography with magnetic induction (MAT-MI). A simulation study of applying this method to MAT-MI shows that compared to existing methods, the proposed method can give an accurate estimation of the induced current distribution and a better reconstruction of electrical conductivity within an object.

Bioengineering a non-genotoxic vector for genetic modification of mesenchymal stem cells.

PubMed

Chen, Xuguang; Nomani, Alireza; Patel, Niket; Nouri, Faranak S; Hatefi, Arash

2018-01-01

Vectors used for stem cell transfection must be non-genotoxic, in addition to possessing high efficiency, because they could potentially transform normal stem cells into cancer-initiating cells. The objective of this research was to bioengineer an efficient vector that can be used for genetic modification of stem cells without any negative somatic or genetic impact. Two types of multifunctional vectors, namely targeted and non-targeted were genetically engineered and purified from E. coli. The targeted vectors were designed to enter stem cells via overexpressed receptors. The non-targeted vectors were equipped with MPG and Pep1 cell penetrating peptides. A series of commercial synthetic non-viral vectors and an adenoviral vector were used as controls. All vectors were evaluated for their efficiency and impact on metabolic activity, cell membrane integrity, chromosomal aberrations (micronuclei formation), gene dysregulation, and differentiation ability of stem cells. The results of this study showed that the bioengineered vector utilizing VEGFR-1 receptors for cellular entry could transfect mesenchymal stem cells with high efficiency without inducing genotoxicity, negative impact on gene function, or ability to differentiate. Overall, the vectors that utilized receptors as ports for cellular entry (viral and non-viral) showed considerably better somato- and genosafety profiles in comparison to those that entered through electrostatic interaction with cellular membrane. The genetically engineered vector in this study demonstrated that it can be safely and efficiently used to genetically modify stem cells with potential applications in tissue engineering and cancer therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

The feasibility of using magnetic nanoparticles modified as gene vector.

PubMed

Chen, D; Tang, Q; Xue, W; Wang, X

2010-06-01

To evaluate the feasibility of using magnetic nanoparticles (MNPs) as gene vector and the effect of magnetic field on efficiency of transfection. Magnetic nanoparticles were prepared by controlling some chemical reaction parameters through a partially reduction precipitation method with ferric chloride aqueous solution as precursor material. The surface of particles was modified by polyethyleneimine (PEI) agents. The appearance, the size distribution, structure and phase constitute of MNPs were characterized by Transmission electron microscope (TEM), X-ray diffraction (XRD); the potential of absorbing DNA of MNPs was analysed by electrophoresis. Transfection was determined by delivering reporter gene, PGL2-control encoding luciferase, to different cell lines using MNPs-PLL as vector. The effect of magnetic field on the efficiency of transfection was determined using Nd-Fe-B permanent magnet. Foreign gene could be delivered to various cell lines by MNPs-PLL and expressed with high efficiency but the transfection efficiency and time course varied in the different cell lines studied. Magnetic field could enhance the efficiency of transfection by 5-10 fold. MNPs- PLL can be used as a novel non-viral gene vector in vitro, which offers a basis for gene delivery in vivo.

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue.

PubMed

Kjeldsen, Henrik D; Kaiser, Marcus; Whittington, Miles A

2015-09-30

Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions without bias from any prior assumptions on anatomical connectivity. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor.

PubMed

Saravanan, Vijayakumar; Gautham, Namasivayam

2015-10-01

Proteins embody epitopes that serve as their antigenic determinants. Epitopes occupy a central place in integrative biology, not to mention as targets for novel vaccine, pharmaceutical, and systems diagnostics development. The presence of T-cell and B-cell epitopes has been extensively studied due to their potential in synthetic vaccine design. However, reliable prediction of linear B-cell epitope remains a formidable challenge. Earlier studies have reported discrepancy in amino acid composition between the epitopes and non-epitopes. Hence, this study proposed and developed a novel amino acid composition-based feature descriptor, Dipeptide Deviation from Expected Mean (DDE), to distinguish the linear B-cell epitopes from non-epitopes effectively. In this study, for the first time, only exact linear B-cell epitopes and non-epitopes have been utilized for developing the prediction method, unlike the use of epitope-containing regions in earlier reports. To evaluate the performance of the DDE feature vector, models have been developed with two widely used machine-learning techniques Support Vector Machine and AdaBoost-Random Forest. Five-fold cross-validation performance of the proposed method with error-free dataset and dataset from other studies achieved an overall accuracy between nearly 61% and 73%, with balance between sensitivity and specificity metrics. Performance of the DDE feature vector was better (with accuracy difference of about 2% to 12%), in comparison to other amino acid-derived features on different datasets. This study reflects the efficiency of the DDE feature vector in enhancing the linear B-cell epitope prediction performance, compared to other feature representations. The proposed method is made as a stand-alone tool available freely for researchers, particularly for those interested in vaccine design and novel molecular target development for systems therapeutics and diagnostics: https://github.com/brsaran/LBEEP.

Progress in developing cationic vectors for non-viral systemic gene therapy against cancer.

PubMed

Morille, Marie; Passirani, Catherine; Vonarbourg, Arnaud; Clavreul, Anne; Benoit, Jean-Pierre

2008-01-01

Initially, gene therapy was viewed as an approach for treating hereditary diseases, but its potential role in the treatment of acquired diseases such as cancer is now widely recognized. The understanding of the molecular mechanisms involved in cancer and the development of nucleic acid delivery systems are two concepts that have led to this development. Systemic gene delivery systems are needed for therapeutic application to cells inaccessible by percutaneous injection and for multi-located tumor sites, i.e. metastases. Non-viral vectors based on the use of cationic lipids or polymers appear to have promising potential, given the problems of safety encountered with viral vectors. Using these non-viral vectors, the current challenge is to obtain a similarly effective transfection to viral ones. Based on the advantages and disadvantages of existing vectors and on the hurdles encountered with these carriers, the aim of this review is to describe the "perfect vector" for systemic gene therapy against cancer.

Two-dimensional PCA-based human gait identification

NASA Astrophysics Data System (ADS)

Chen, Jinyan; Wu, Rongteng

2012-11-01

It is very necessary to recognize person through visual surveillance automatically for public security reason. Human gait based identification focus on recognizing human by his walking video automatically using computer vision and image processing approaches. As a potential biometric measure, human gait identification has attracted more and more researchers. Current human gait identification methods can be divided into two categories: model-based methods and motion-based methods. In this paper a two-Dimensional Principal Component Analysis and temporal-space analysis based human gait identification method is proposed. Using background estimation and image subtraction we can get a binary images sequence from the surveillance video. By comparing the difference of two adjacent images in the gait images sequence, we can get a difference binary images sequence. Every binary difference image indicates the body moving mode during a person walking. We use the following steps to extract the temporal-space features from the difference binary images sequence: Projecting one difference image to Y axis or X axis we can get two vectors. Project every difference image in the difference binary images sequence to Y axis or X axis difference binary images sequence we can get two matrixes. These two matrixes indicate the styles of one walking. Then Two-Dimensional Principal Component Analysis(2DPCA) is used to transform these two matrixes to two vectors while at the same time keep the maximum separability. Finally the similarity of two human gait images is calculated by the Euclidean distance of the two vectors. The performance of our methods is illustrated using the CASIA Gait Database.

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.

System and method for extracting dominant orientations from a scene

DOEpatents

Straub, Julian; Rosman, Guy; Freifeld, Oren; Leonard, John J.; Fisher, III; , John W.

2017-05-30

In one embodiment, a method of identifying the dominant orientations of a scene comprises representing a scene as a plurality of directional vectors. The scene may comprise a three-dimensional representation of a scene, and the plurality of directional vectors may comprise a plurality of surface normals. The method further comprises determining, based on the plurality of directional vectors, a plurality of orientations describing the scene. The determined plurality of orientations explains the directionality of the plurality of directional vectors. In certain embodiments, the plurality of orientations may have independent axes of rotation. The plurality of orientations may be determined by representing the plurality of directional vectors as lying on a mathematical representation of a sphere, and inferring the parameters of a statistical model to adapt the plurality of orientations to explain the positioning of the plurality of directional vectors lying on the mathematical representation of the sphere.

A COMPARISON OF VECTOR AND RASTER GIS METHODS FOR CALCULATING LANDSCAPE METRICS USED IN ENVIRONMENTAL ASSESSMENTS

EPA Science Inventory

GIS-based measurements that combine native raster and native vector data are commonly used to assess environmental quality. Most of these measurements can be calculated using either raster or vector data formats and processing methods. Raster processes are more commonly used beca...

Text analysis devices, articles of manufacture, and text analysis methods

DOEpatents

Turner, Alan E; Hetzler, Elizabeth G; Nakamura, Grant C

2015-03-31

Text analysis devices, articles of manufacture, and text analysis methods are described according to some aspects. In one aspect, a text analysis device includes a display configured to depict visible images, and processing circuitry coupled with the display and wherein the processing circuitry is configured to access a first vector of a text item and which comprises a plurality of components, to access a second vector of the text item and which comprises a plurality of components, to weight the components of the first vector providing a plurality of weighted values, to weight the components of the second vector providing a plurality of weighted values, and to combine the weighted values of the first vector with the weighted values of the second vector to provide a third vector.

Modeling the Dark Matter of Galaxy Clusters Using the Tensor-Vector-Scalar Theory of Alternate Gravity

NASA Astrophysics Data System (ADS)

Ragozzine, Brett

The invocation of dark matter in the universe is predicated upon gravitational observations that cannot be explained by the amount of luminous matter that we detect. There is an ongoing debate over which gravitational model is correct. The work herein tests a prescription of gravity theory known as Tensor-Vector-Scalar and is based upon the work of Angus et al. (2007). We add upon this work by extending the sample of galaxy clusters to five and testing the accepted Navarro, Frenk & White (NFW) dark matter potential (Navarro et al., 1996). Our independent implementation of this method includes weak gravitational lensing analysis to determine the amount of dark matter in these galaxy clusters by calculating the gas fraction ƒgas = Mgas=Mtot. The ability of the Tensor-Vector-Scalar theory to predict a consistent ƒgas across all galaxy clusters is a measure of its liklihood of being the correct gravity model.

Water-soluble polymers bearing phosphorylcholine group and other zwitterionic groups for carrying DNA derivatives.

PubMed

Lin, Xiaojie; Ishihara, Kazuhiko

2014-01-01

Water-soluble polymers with equal positive and negative charges in the same monomer unit, such as the phosphorylcholine group and other zwitterionic groups, exhibit promising potential in gene delivery with appreciable transfection efficiency, compared with the traditional poly(ethylene glycol)-based polycation-gene complexes. These zwitterionic polymers with various architectural structures and properties have been synthesized by various polymerization methods, such as conventional radical polymerization, atom-transfer radical-polymerization, reversible addition-fragmentation chain-transfer polymerization, and nitroxide-mediated radical polymerization. These techniques have been used to efficiently facilitate gene therapy by fabrication of non-viral vectors with high cytocompatibility, large gene-carrying capacity, effective cell-membrane permeability, and in vivo gene-loading/releasing functionality. Zwitterionic polymer-based gene delivery vectors systems can be categorized into soluble-polymer/gene mixing, molecular self-assembly, and polymer-gene conjugation systems. This review describes the preparation and characterization of various zwitterionic polymer-based gene delivery vectors, specifically water-soluble phospholipid polymers for carrying gene derivatives.

The potential of latent semantic analysis for machine grading of clinical case summaries.

PubMed

Kintsch, Walter

2002-02-01

This paper introduces latent semantic analysis (LSA), a machine learning method for representing the meaning of words, sentences, and texts. LSA induces a high-dimensional semantic space from reading a very large amount of texts. The meaning of words and texts can be represented as vectors in this space and hence can be compared automatically and objectively. A generative theory of the mental lexicon based on LSA is described. The word vectors LSA constructs are context free, and each word, irrespective of how many meanings or senses it has, is represented by a single vector. However, when a word is used in different contexts, context appropriate word senses emerge. Several applications of LSA to educational software are described, involving the ability of LSA to quickly compare the content of texts, such as an essay written by a student and a target essay. An LSA-based software tool is sketched for machine grading of clinical case summaries written by medical students.

Anopheline Reproductive Biology: Impacts on Vectorial Capacity and Potential Avenues for Malaria Control.

PubMed

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

Vectorial capacity is a mathematical approximation of the efficiency of vector-borne disease transmission, measured as the number of new infections disseminated per case per day by an insect vector. Multiple elements of mosquito biology govern their vectorial capacity, including survival, population densities, feeding preferences, and vector competence. Intriguingly, biological pathways essential to mosquito reproductive fitness directly or indirectly influence a number of these elements. Here, we explore this complex interaction, focusing on how the interplay between mating and blood feeding in female Anopheles not only shapes their reproductive success but also influences their ability to sustain Plasmodium parasite development. Central to malaria transmission, mosquito reproductive biology has recently become the focus of research strategies aimed at malaria control, and we discuss promising new methods based on the manipulation of key reproductive steps. In light of widespread resistance to all public health-approved insecticides targeting mosquito reproduction may prove crucial to the success of malaria-eradication campaigns. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

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.

Preclinical Demonstration of Lentiviral Vector-mediated Correction of Immunological and Metabolic Abnormalities in Models of Adenosine Deaminase Deficiency

PubMed Central

Carbonaro, Denise A; Zhang, Lin; Jin, Xiangyang; Montiel-Equihua, Claudia; Geiger, Sabine; Carmo, Marlene; Cooper, Aaron; Fairbanks, Lynette; Kaufman, Michael L; Sebire, Neil J; Hollis, Roger P; Blundell, Michael P; Senadheera, Shantha; Fu, Pei-Yu; Sahaghian, Arineh; Chan, Rebecca Y; Wang, Xiaoyan; Cornetta, Kenneth; Thrasher, Adrian J; Kohn, Donald B; Gaspar, H Bobby

2014-01-01

Gene transfer into autologous hematopoietic stem cells by γ-retroviral vectors (gRV) is an effective treatment for adenosine deaminase (ADA)–deficient severe combined immunodeficiency (SCID). However, current gRV have significant potential for insertional mutagenesis as reported in clinical trials for other primary immunodeficiencies. To improve the efficacy and safety of ADA-SCID gene therapy (GT), we generated a self-inactivating lentiviral vector (LV) with a codon-optimized human cADA gene under the control of the short form elongation factor-1α promoter (LV EFS ADA). In ADA−/− mice, LV EFS ADA displayed high-efficiency gene transfer and sufficient ADA expression to rescue ADA−/− mice from their lethal phenotype with good thymic and peripheral T- and B-cell reconstitution. Human ADA-deficient CD34+ cells transduced with 1–5 × 107 TU/ml had 1–3 vector copies/cell and expressed 1–2x of normal endogenous levels of ADA, as assayed in vitro and by transplantation into immune-deficient mice. Importantly, in vitro immortalization assays demonstrated that LV EFS ADA had significantly less transformation potential compared to gRV vectors, and vector integration-site analysis by nrLAM-PCR of transduced human cells grown in immune-deficient mice showed no evidence of clonal skewing. These data demonstrated that the LV EFS ADA vector can effectively transfer the human ADA cDNA and promote immune and metabolic recovery, while reducing the potential for vector-mediated insertional mutagenesis. PMID:24256635

A Kalman Filter for SINS Self-Alignment Based on Vector Observation.

PubMed

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-29

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.

A Kalman Filter for SINS Self-Alignment Based on Vector Observation

PubMed Central

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-01

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q-method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate. PMID:28146059

Strengthening tactical planning and operational frameworks for vector control: the roadmap for malaria elimination in Namibia.

PubMed

Chanda, Emmanuel; Ameneshewa, Birkinesh; Angula, Hans A; Iitula, Iitula; Uusiku, Pentrina; Trune, Desta; Islam, Quazi M; Govere, John M

2015-08-05

Namibia has made tremendous gains in malaria control and the epidemiological trend of the disease has changed significantly over the past years. In 2010, the country reoriented from the objective of reducing disease morbidity and mortality to the goal of achieving malaria elimination by 2020. This manuscript outlines the processes undertaken in strengthening tactical planning and operational frameworks for vector control to facilitate expeditious malaria elimination in Namibia. The information sources for this study included all available data and accessible archived documentary records on malaria vector control in Namibia. A methodical assessment of published and unpublished documents was conducted via a literature search of online electronic databases, Google Scholar, PubMed and WHO, using a combination of search terms. To attain the goal of elimination in Namibia, systems are being strengthened to identify and clear all infections, and significantly reduce human-mosquito contact. Particularly, consolidating vector control for reducing transmission at the identified malaria foci will be critical for accelerated malaria elimination. Thus, guarding against potential challenges and the need for evidence-based and sustainable vector control instigated the strengthening of strategic frameworks by: adopting the integrated vector management (IVM) strategy; initiating implementation of the global plan for insecticide resistance management (GPIRM); intensifying malaria vector surveillance; improving data collection and reporting systems on DDT; updating the indoor residual spraying (IRS) data collection and reporting tool; and, improving geographical reconnaissance using geographical information system-based satellite imagery. Universal coverage with IRS and long-lasting insecticidal nets, supplemented by larval source management in the context of IVM and guided by vector surveillance coupled with rational operationalization of the GPIRM, will enable expeditious attainment of elimination in Namibia. However, national capacity to plan, implement, monitor and evaluate interventions will require adequate and sustained support for technical, physical infrastructure, and human and financial resources for entomology and vector control operations.

Realistic Subsurface Anomaly Discrimination Using Electromagnetic Induction and an SVM Classifier

NASA Astrophysics Data System (ADS)

Pablo Fernández, Juan; Shubitidze, Fridon; Shamatava, Irma; Barrowes, Benjamin E.; O'Neill, Kevin

2010-12-01

The environmental research program of the United States military has set up blind tests for detection and discrimination of unexploded ordnance. One such test consists of measurements taken with the EM-63 sensor at Camp Sibert, AL. We review the performance on the test of a procedure that combines a field-potential (HAP) method to locate targets, the normalized surface magnetic source (NSMS) model to characterize them, and a support vector machine (SVM) to classify them. The HAP method infers location from the scattered magnetic field and its associated scalar potential, the latter reconstructed using equivalent sources. NSMS replaces the target with an enclosing spheroid of equivalent radial magnetization whose integral it uses as a discriminator. SVM generalizes from empirical evidence and can be adapted for multiclass discrimination using a voting system. Our method identifies all potentially dangerous targets correctly and has a false-alarm rate of about 5%.

Implication of vector characteristics of Phlebotomus argentipes in the kala-azar elimination programme in the Indian sub-continent

PubMed Central

Chowdhury, Rajib; Kumar, Vijay; Mondal, Dinesh; Das, Murari Lal; Das, Pradeep; Dash, Aditya Prasad

2016-01-01

Background Visceral leishmaniasis (VL), also known as kala-azar in the Indian sub-continent (ISC), is a major public health concern in Bangladesh, India, and Nepal, where it is caused by Leishmania donovani transmitted by the sand fly Phlebotomus argentipes. Various ecological parameters including air temperature, rainfall, wind speed, relative humidity, soil moisture, pH, and organic carbon are known to influence the oviposition of female sand flies, as well as the survival and development of larvae. However, more detailed knowledge on vector behavior, such as biting times, breeding places, and preferred hosts are needed to design optimal evidence-based vector control interventions. Methods In order to facilitate rational decisions regarding VL vector control, a systematic review was conducted to identify the prevailing practice and knowledge gaps in relation to vector bionomics and behavior. Search terms included ‘sand fly bionomics’, ‘habitat’, and ‘visceral leishmaniasis/kala-azar vector control’ using the Boolean operator AND to identify the country of interest, namely: Bangladesh, India, and Nepal. Both PubMed and Google search engines were used. Additional unpublished documents in the three countries were also analyzed. Results Information on the life cycle of VL vectors, their breeding behavior, infection rate with L. donovani, feeding behavior, and seasonal variation are useful for designing vector control operations. Unfortunately, none of the studies on the life cycle of P. argentipes was conducted in field settings of the ISC, so the publications from other locations had to be used for determining the duration of life cycle and development from egg to adult. However, information about breeding places, seasonal variation of vector densities, and 47 out of the selected 51 papers are available from the ISC and can be used for intelligent design of control operations. Conclusion Vector control services should undertake routine insecticide resistance monitoring and adapt indoor residual spraying rounds to the seasonality of vector densities. Further research is needed on potential animal reservoirs for L. donovani, on the breeding habitat, and life cycle of sand flies in the ISC. PMID:27376500

Introduction to Electrodynamics

NASA Astrophysics Data System (ADS)

Griffiths, David J.

2017-06-01

1. Vector analysis; 2. Electrostatics; 3. Potentials; 4. Electric fields in matter; 5. Magnetostatics; 6. Magnetic fields in matter; 7. Electrodynamics; 8. Conservation laws; 9. Electromagnetic waves; 10. Potentials and fields; 11. Radiation; 12. Electrodynamics and relativity; Appendix A. Vector calculus in curvilinear coordinates; Appendix B. The Helmholtz theorem; Appendix C. Units; Index.

Demodex as a Delivery Vector for Topical Targeted Medications in the Skin for Early Melanoma and Non-Melanoma Skin Cancer.

PubMed

Strobel, Stephen L

2017-09-01

The potential utilization of Demodex mites as delivery vectors for cytotoxic medications directed to early skin cancer is proposed. Potential benefits, proof of concept, and limitations are discussed. © 2017 by the Association of Clinical Scientists, Inc.

Current Advances and Future Challenges in Adenoviral Vector Biology and Targeting

PubMed Central

Campos, Samuel K.; Barry, Michael A.

2008-01-01

Gene delivery vectors based on Adenoviral (Ad) vectors have enormous potential for the treatment of both hereditary and acquired disease. Detailed structural analysis of the Ad virion, combined with functional studies has broadened our knowledge of the structure/function relationships between Ad vectors and host cells/tissues and substantial achievement has been made towards a thorough understanding of the biology of Ad vectors. The widespread use of Ad vectors for clinical gene therapy is compromised by their inherent immunogenicity. The generation of safer and more effective Ad vectors, targeted to the site of disease, has therefore become a great ambition in the field of Ad vector development. This review provides a synopsis of the structure/function relationships between Ad vectors and host systems and summarizes the many innovative approaches towards achieving Ad vector targeting. PMID:17584037

Lexicon generation methods, lexicon generation devices, and lexicon generation articles of manufacture

DOEpatents

Carter, Richard J [Richland, WA; McCall, Jonathon D [West Richland, WA; Whitney, Paul D [Richland, WA; Gregory, Michelle L [Richland, WA; Turner, Alan E [Kennewick, WA; Hetzler, Elizabeth G [Kennewick, WA; White, Amanda M [Kennewick, WA; Posse, Christian [Seattle, WA; Nakamura, Grant C [Kennewick, WA

2010-10-26

Lexicon generation methods, computer implemented lexicon editing methods, lexicon generation devices, lexicon editors, and articles of manufacture are described according to some aspects. In one aspect, a lexicon generation method includes providing a seed vector indicative of occurrences of a plurality of seed terms within a plurality of text items, providing a plurality of content vectors indicative of occurrences of respective ones of a plurality of content terms within the text items, comparing individual ones of the content vectors with respect to the seed vector, and responsive to the comparing, selecting at least one of the content terms as a term of a lexicon usable in sentiment analysis of text.

Searching for transcription factor binding sites in vector spaces

PubMed Central

2012-01-01

Background Computational approaches to transcription factor binding site identification have been actively researched in the past decade. Learning from known binding sites, new binding sites of a transcription factor in unannotated sequences can be identified. A number of search methods have been introduced over the years. However, one can rarely find one single method that performs the best on all the transcription factors. Instead, to identify the best method for a particular transcription factor, one usually has to compare a handful of methods. Hence, it is highly desirable for a method to perform automatic optimization for individual transcription factors. Results We proposed to search for transcription factor binding sites in vector spaces. This framework allows us to identify the best method for each individual transcription factor. We further introduced two novel methods, the negative-to-positive vector (NPV) and optimal discriminating vector (ODV) methods, to construct query vectors to search for binding sites in vector spaces. Extensive cross-validation experiments showed that the proposed methods significantly outperformed the ungapped likelihood under positional background method, a state-of-the-art method, and the widely-used position-specific scoring matrix method. We further demonstrated that motif subtypes of a TF can be readily identified in this framework and two variants called the k NPV and k ODV methods benefited significantly from motif subtype identification. Finally, independent validation on ChIP-seq data showed that the ODV and NPV methods significantly outperformed the other compared methods. Conclusions We conclude that the proposed framework is highly flexible. It enables the two novel methods to automatically identify a TF-specific subspace to search for binding sites. Implementations are available as source code at: http://biogrid.engr.uconn.edu/tfbs_search/. PMID:23244338

Analysis of degree of nonlinearity and stochastic nature of HRV signal during meditation using delay vector variance method.

PubMed

Reddy, L Ram Gopal; Kuntamalla, Srinivas

2011-01-01

Heart rate variability analysis is fast gaining acceptance as a potential non-invasive means of autonomic nervous system assessment in research as well as clinical domains. In this study, a new nonlinear analysis method is used to detect the degree of nonlinearity and stochastic nature of heart rate variability signals during two forms of meditation (Chi and Kundalini). The data obtained from an online and widely used public database (i.e., MIT/BIH physionet database), is used in this study. The method used is the delay vector variance (DVV) method, which is a unified method for detecting the presence of determinism and nonlinearity in a time series and is based upon the examination of local predictability of a signal. From the results it is clear that there is a significant change in the nonlinearity and stochastic nature of the signal before and during the meditation (p value > 0.01). During Chi meditation there is a increase in stochastic nature and decrease in nonlinear nature of the signal. There is a significant decrease in the degree of nonlinearity and stochastic nature during Kundalini meditation.

Method for indexing and retrieving manufacturing-specific digital imagery based on image content

DOEpatents

Ferrell, Regina K.; Karnowski, Thomas P.; Tobin, Jr., Kenneth W.

2004-06-15

A method for indexing and retrieving manufacturing-specific digital images based on image content comprises three steps. First, at least one feature vector can be extracted from a manufacturing-specific digital image stored in an image database. In particular, each extracted feature vector corresponds to a particular characteristic of the manufacturing-specific digital image, for instance, a digital image modality and overall characteristic, a substrate/background characteristic, and an anomaly/defect characteristic. Notably, the extracting step includes generating a defect mask using a detection process. Second, using an unsupervised clustering method, each extracted feature vector can be indexed in a hierarchical search tree. Third, a manufacturing-specific digital image associated with a feature vector stored in the hierarchicial search tree can be retrieved, wherein the manufacturing-specific digital image has image content comparably related to the image content of the query image. More particularly, can include two data reductions, the first performed based upon a query vector extracted from a query image. Subsequently, a user can select relevant images resulting from the first data reduction. From the selection, a prototype vector can be calculated, from which a second-level data reduction can be performed. The second-level data reduction can result in a subset of feature vectors comparable to the prototype vector, and further comparable to the query vector. An additional fourth step can include managing the hierarchical search tree by substituting a vector average for several redundant feature vectors encapsulated by nodes in the hierarchical search tree.

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

PubMed

Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

2017-07-21

Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

Syngeneic AAV pseudo-particles potentiate gene transduction of AAV vectors

USDA-ARS?s Scientific Manuscript database

Gene delivery vectors based on adeno-associated virus (AAV) have emerged as safe and efficient therapeutic platform for numerous diseases. Excessive empty particles were generated as impurities during AAV vector production, but their effects on clinical outcome of AAV gene therapy are unclear. Here,...

Vector boson production in pPb and PbPb collisions at the LHC and its impact on nCTEQ15 PDFs

NASA Astrophysics Data System (ADS)

Kusina, A.; Lyonnet, F.; Clark, D. B.; Godat, E.; Ježo, T.; Kovařík, K.; Olness, F. I.; Schienbein, I.; Yu, J. Y.

2017-07-01

We provide a comprehensive comparison of W^± / Z vector boson production data in pPb and PbPb collisions at the LHC with predictions obtained using the nCTEQ15 PDFs. We identify the measurements which have the largest potential impact on the PDFs, and estimate the effect of including these data using a Bayesian reweighting method. We find this data set can provide information as regards both the nuclear corrections and the heavy flavor (strange quark) PDF components. As for the proton, the parton flavor determination/separation is dependent on nuclear corrections (from heavy target DIS, for example), this information can also help improve the proton PDFs.

A New Unified Analysis of Estimate Errors by Model-Matching Phase-Estimation Methods for Sensorless Drive of Permanent-Magnet Synchronous Motors and New Trajectory-Oriented Vector Control, Part I

NASA Astrophysics Data System (ADS)

Shinnaka, Shinji; Sano, Kousuke

This paper presents a new unified analysis of estimate errors by model-matching phase-estimation methods such as rotor-flux state-observers, back EMF state-observers, and back EMF disturbance-observers, for sensorless drive of permanent-magnet synchronous motors. Analytical solutions about estimate errors, whose validity is confirmed by numerical experiments, are rich in universality and applicability. As an example of universality and applicability, a new trajectory-oriented vector control method is proposed, which can realize directly quasi-optimal strategy minimizing total losses with no additional computational loads by simply orienting one of vector-control coordinates to the associated quasi-optimal trajectory. The coordinate orientation rule, which is analytically derived, is surprisingly simple. Consequently the trajectory-oriented vector control method can be applied to a number of conventional vector control systems using one of the model-matching phase-estimation methods.

Finite-element solutions for geothermal systems

NASA Technical Reports Server (NTRS)

Chen, J. C.; Conel, J. E.

1977-01-01

Vector potential and scalar potential are used to formulate the governing equations for a single-component and single-phase geothermal system. By assuming an initial temperature field, the fluid velocity can be determined which, in turn, is used to calculate the convective heat transfer. The energy equation is then solved by considering convected heat as a distributed source. Using the resulting temperature to compute new source terms, the final results are obtained by iterations of the procedure. Finite-element methods are proposed for modeling of realistic geothermal systems; the advantages of such methods are discussed. The developed methodology is then applied to a sample problem. Favorable agreement is obtained by comparisons with a previous study.

Safe engineering of CAR T cells for adoptive cell therapy of cancer using long-term episomal gene transfer.

PubMed

Jin, Chuan; Fotaki, Grammatiki; Ramachandran, Mohanraj; Nilsson, Berith; Essand, Magnus; Yu, Di

2016-07-01

Chimeric antigen receptor (CAR) T-cell therapy is a new successful treatment for refractory B-cell leukemia. Successful therapeutic outcome depends on long-term expression of CAR transgene in T cells, which is achieved by delivering transgene using integrating gamma retrovirus (RV) or lentivirus (LV). However, uncontrolled RV/LV integration in host cell genomes has the potential risk of causing insertional mutagenesis. Herein, we describe a novel episomal long-term cell engineering method using non-integrating lentiviral (NILV) vector containing a scaffold/matrix attachment region (S/MAR) element, for either expression of transgenes or silencing of target genes. The insertional events of this vector into the genome of host cells are below detection level. CD19 CAR T cells engineered with a NILV-S/MAR vector have similar levels of CAR expression as T cells engineered with an integrating LV vector, even after numerous rounds of cell division. NILV-S/MAR-engineered CD19 CAR T cells exhibited similar cytotoxic capacity upon CD19(+) target cell recognition as LV-engineered T cells and are as effective in controlling tumor growth in vivo We propose that NILV-S/MAR vectors are superior to current options as they enable long-term transgene expression without the risk of insertional mutagenesis and genotoxicity. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Community effectiveness of copepods for dengue vector control: systematic review.

PubMed

Lazaro, A; Han, W W; Manrique-Saide, P; George, L; Velayudhan, R; Toledo, J; Runge Ranzinger, S; Horstick, O

2015-06-01

Vector control remains the only available method for primary prevention of dengue. Several interventions exist for dengue vector control, with limited evidence of their efficacy and community effectiveness. This systematic review compiles and analyses the existing global evidence for community effectiveness of copepods for dengue vector control. The systematic review follows the PRISMA statement, searching six relevant databases. Applying all inclusion and exclusion criteria, 11 articles were included. There is evidence that cyclopoid copepods (Mesocyclops spp.) could potentially be an effective vector control option, as shown in five community effectiveness studies in Vietnam. This includes long-term effectiveness for larval and adult control of Ae. aegypti, as well as dengue incidence. However, this success has so far not been replicated elsewhere (six studies, three community effectiveness studies--Costa Rica, Mexico and USA, and three studies analysing both efficacy and community effectiveness--Honduras, Laos and USA), probably due to community participation, environmental and/or biological factors. Judging by the quality of existing studies, there is a lack of good study design, data quality and appropriate statistics. There is limited evidence for the use of cyclopoid copepods as a single intervention. There are very few studies, and more are needed in other communities and environments. Clear best practice guidelines for the methodology of entomological studies should be developed. © 2015 John Wiley & Sons Ltd.

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

Sugar epitopes as potential universal disease transmission blocking targets.

PubMed

Dinglasan, Rhoel R; Valenzuela, Jesús G; Azad, Abdu F

2005-01-01

One promising method to prevent vector-borne diseases is through the use of transmission blocking vaccines (TBVs). However, developing several anti-pathogen TBVs may be impractical. In this study, we have identified a conserved candidate carbohydrate target in the midguts of several Arthropod vectors. A screen of the novel GlycoChip glycan array found that the anti-carbohydrate malaria transmission blocking monoclonal antibody (MG96) preferentially recognized D-mannose (alpha) and the type II lactosamine disaccharide. The specificity for D-mannose was confirmed by competition ELISA using alpha-methyl mannoside as inhibitor. Con A, which identifies terminal mannose residues, did not inhibit MG96 reactivity with mosquito midgut lysates, suggesting that Con A has differential recognition of this monosaccharide. However, the jack bean lectin, Jacalin, which recognizes D-mannose (alpha), d-galactose (alpha/beta) and the T antigen, not only displays a similar banding profile to that recognized by MG96 on immunoblot but was also shown to effectively inhibit MG96. Wheat-germ agglutinin, which recognizes N-acetyllactosamine units, only partially inhibited MG96 reactivity. This highlights the contribution of both glycan moieties to the MG96 epitope or glycotope. Enzyme deglycosylation results suggest that MG96 recognizes a mannose alpha1-6 substitution on an O-linked oligosaccharide. Taken together, the data suggest that MG96 recognizes a discontinuous glycotope composed of Manalpha1-6 proximal to Galbeta1-4GlcNAc-alpha-O-R glycans on arthropod vector midguts. As such, these glycotopes may represent potential transmission blocking vaccine targets for a wide range of vector-borne pathogens.

Insecticide resistance in the dengue vector Aedes aegypti from Martinique: distribution, mechanisms and relations with environmental factors.

PubMed

Marcombe, Sébastien; Mathieu, Romain Blanc; Pocquet, Nicolas; Riaz, Muhammad-Asam; Poupardin, Rodolphe; Sélior, Serge; Darriet, Frédéric; Reynaud, Stéphane; Yébakima, André; Corbel, Vincent; David, Jean-Philippe; Chandre, Fabrice

2012-01-01

Dengue is an important mosquito borne viral disease in Martinique Island (French West Indies). The viruses responsible for dengue are transmitted by Aedes aegypti, an indoor day-biting mosquito. The most effective proven method for disease prevention has been by vector control by various chemical or biological means. Unfortunately insecticide resistance has already been observed on the Island and recently showed to significantly reduce the efficacy of vector control interventions. In this study, we investigated the distribution of resistance and the underlying mechanisms in nine Ae. aegypti populations. Statistical multifactorial approach was used to investigate the correlations between insecticide resistance levels, associated mechanisms and environmental factors characterizing the mosquito populations. Bioassays revealed high levels of resistance to temephos and deltamethrin and susceptibility to Bti in the 9 populations tested. Biochemical assays showed elevated detoxification enzyme activities of monooxygenases, carboxylesterases and glutathione S-tranferases in most of the populations. Molecular screening for common insecticide target-site mutations, revealed the presence of the "knock-down resistance" V1016I Kdr mutation at high frequency (>87%). Real time quantitative RT-PCR showed the potential involvement of several candidate detoxification genes in insecticide resistance. Principal Component Analysis (PCA) performed with variables characterizing Ae. aegypti from Martinique permitted to underline potential links existing between resistance distribution and other variables such as agriculture practices, vector control interventions and urbanization. Insecticide resistance is widespread but not homogeneously distributed across Martinique. The influence of environmental and operational factors on the evolution of the resistance and mechanisms are discussed.

Insecticide Resistance in the Dengue Vector Aedes aegypti from Martinique: Distribution, Mechanisms and Relations with Environmental Factors

PubMed Central

Marcombe, Sébastien; Mathieu, Romain Blanc; Pocquet, Nicolas; Riaz, Muhammad-Asam; Poupardin, Rodolphe; Sélior, Serge; Darriet, Frédéric; Reynaud, Stéphane; Yébakima, André; Corbel, Vincent; David, Jean-Philippe; Chandre, Fabrice

2012-01-01

Dengue is an important mosquito borne viral disease in Martinique Island (French West Indies). The viruses responsible for dengue are transmitted by Aedes aegypti, an indoor day-biting mosquito. The most effective proven method for disease prevention has been by vector control by various chemical or biological means. Unfortunately insecticide resistance has already been observed on the Island and recently showed to significantly reduce the efficacy of vector control interventions. In this study, we investigated the distribution of resistance and the underlying mechanisms in nine Ae. aegypti populations. Statistical multifactorial approach was used to investigate the correlations between insecticide resistance levels, associated mechanisms and environmental factors characterizing the mosquito populations. Bioassays revealed high levels of resistance to temephos and deltamethrin and susceptibility to Bti in the 9 populations tested. Biochemical assays showed elevated detoxification enzyme activities of monooxygenases, carboxylesterases and glutathione S-tranferases in most of the populations. Molecular screening for common insecticide target-site mutations, revealed the presence of the “knock-down resistance” V1016I Kdr mutation at high frequency (>87%). Real time quantitative RT-PCR showed the potential involvement of several candidate detoxification genes in insecticide resistance. Principal Component Analysis (PCA) performed with variables characterizing Ae. aegypti from Martinique permitted to underline potential links existing between resistance distribution and other variables such as agriculture practices, vector control interventions and urbanization. Insecticide resistance is widespread but not homogeneously distributed across Martinique. The influence of environmental and operational factors on the evolution of the resistance and mechanisms are discussed. PMID:22363529

Zoonotic Malaria – Global Overview and Research and Policy Needs

PubMed Central

Ramasamy, Ranjan

2014-01-01

The four main Plasmodium species that cause human malaria, Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, and Plasmodium ovale, are transmitted between humans by mosquito vectors belonging to the genus Anopheles. It has recently become evident that Plasmodium knowlesi, a parasite that typically infects forest macaque monkeys, can be transmitted by anophelines to cause malaria in humans in Southeast Asia. Plasmodium knowlesi infections are frequently misdiagnosed microscopically as P. malariae. Direct human to human transmission of P. knowlesi by anophelines has not yet been established to occur in nature. Knowlesi malaria must therefore be presently considered a zoonotic disease. Polymerase chain reaction is now the definitive method for differentiating P. knowlesi from P. malariae and other human malaria parasites. The origin of P. falciparum and P. vivax in African apes are examples of ancient zoonoses that may be continuing at the present time with at least P. vivax, and possibly P. malariae and P. ovale. Other non-human primate malaria species, e.g., Plasmodium cynomolgi in Southeast Asia and Plasmodium brasilianum and Plasmodium simium in South America, can be transmitted to humans by mosquito vectors further emphasizing the potential for continuing zoonoses. The potential for zoonosis is influenced by human habitation and behavior as well as the adaptive capabilities of parasites and vectors. There is insufficient knowledge of the bionomics of Anopheles vector populations relevant to the cross-species transfer of malaria parasites and the real extent of malaria zoonoses. Appropriate strategies, based on more research, need to be developed for the prevention, diagnosis, and treatment of zoonotic malaria. PMID:25184118

Updating the Salivary Gland Transcriptome of Phlebotomus papatasi (Tunisian Strain): The Search for Sand Fly-Secreted Immunogenic Proteins for Humans

PubMed Central

Ben Ahmed, Melika; Zhioua, Elyes; Chelbi, Ifhem; Cherni, Saifedine; Louzir, Hechmi; Ribeiro, José M. C.; Valenzuela, Jesus G.

2012-01-01

Introduction Sand fly saliva plays an important role in both blood feeding and outcome of Leishmania infection. A cellular immune response against a Phlebotomus papatasi salivary protein was shown to protect rodents against Leishmania major infection. In humans, P. papatasi salivary proteins induce a systemic cellular immune response as well as a specific antisaliva humoral immune response, making these salivary proteins attractive targets as markers of exposure for this Leishmania vector. Surprisingly, the repertoire of salivary proteins reported for P. papatasi–a model sand fly for Leishmania-vector-host molecular interactions–is very limited compared with other sand fly species. We hypothesize that a more comprehensive study of the transcripts present in the salivary glands of P. papatasi will provide better knowledge of the repertoire of proteins of this important vector and will aid in selection of potential immunogenic proteins for humans and of those proteins that are highly conserved between different sand fly strains. Methods and Findings A cDNA library from P. papatasi (Tunisian strain) salivary glands was constructed, and randomly selected transcripts were sequenced and analyzed. The most abundant transcripts encoding secreted proteins were identified and compared with previously reported sequences. Importantly, we identified salivary proteins not described before in this sand fly species. Conclusions Comparative analysis between the salivary proteins of P. papatasi from Tunisia and Israel strains shows a high level of identity, suggesting these proteins as potential common targets for markers of vector exposure or inducers of cellular immune responses in humans for different geographic areas. PMID:23139741

"RCL-Pooling Assay": A Simplified Method for the Detection of Replication-Competent Lentiviruses in Vector Batches Using Sequential Pooling.

PubMed

Corre, Guillaume; Dessainte, Michel; Marteau, Jean-Brice; Dalle, Bruno; Fenard, David; Galy, Anne

2016-02-01

Nonreplicative recombinant HIV-1-derived lentiviral vectors (LV) are increasingly used in gene therapy of various genetic diseases, infectious diseases, and cancer. Before they are used in humans, preparations of LV must undergo extensive quality control testing. In particular, testing of LV must demonstrate the absence of replication-competent lentiviruses (RCL) with suitable methods, on representative fractions of vector batches. Current methods based on cell culture are challenging because high titers of vector batches translate into high volumes of cell culture to be tested in RCL assays. As vector batch size and titers are continuously increasing because of the improvement of production and purification methods, it became necessary for us to modify the current RCL assay based on the detection of p24 in cultures of indicator cells. Here, we propose a practical optimization of this method using a pairwise pooling strategy enabling easier testing of higher vector inoculum volumes. These modifications significantly decrease material handling and operator time, leading to a cost-effective method, while maintaining optimal sensibility of the RCL testing. This optimized "RCL-pooling assay" ameliorates the feasibility of the quality control of large-scale batches of clinical-grade LV while maintaining the same sensitivity.

A new implementation of the CMRH method for solving dense linear systems

NASA Astrophysics Data System (ADS)

Heyouni, M.; Sadok, H.

2008-04-01

The CMRH method [H. Sadok, Methodes de projections pour les systemes lineaires et non lineaires, Habilitation thesis, University of Lille1, Lille, France, 1994; H. Sadok, CMRH: A new method for solving nonsymmetric linear systems based on the Hessenberg reduction algorithm, Numer. Algorithms 20 (1999) 303-321] is an algorithm for solving nonsymmetric linear systems in which the Arnoldi component of GMRES is replaced by the Hessenberg process, which generates Krylov basis vectors which are orthogonal to standard unit basis vectors rather than mutually orthogonal. The iterate is formed from these vectors by solving a small least squares problem involving a Hessenberg matrix. Like GMRES, this method requires one matrix-vector product per iteration. However, it can be implemented to require half as much arithmetic work and less storage. Moreover, numerical experiments show that this method performs accurately and reduces the residual about as fast as GMRES. With this new implementation, we show that the CMRH method is the only method with long-term recurrence which requires not storing at the same time the entire Krylov vectors basis and the original matrix as in the GMRES algorithmE A comparison with Gaussian elimination is provided.

Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier.

PubMed

Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Li, Li-Ping; Huang, De-Shuang; Yan, Gui-Ying; Nie, Ru; Huang, Yu-An

2017-04-04

Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era. In this article, we report a novel computational model combining our newly developed discriminative vector machine classifier (DVM) and an improved Weber local descriptor (IWLD) for the prediction of PPIs. Two components, differential excitation and orientation, are exploited to build evolutionary features for each protein sequence. The main characteristics of the proposed method lies in introducing an effective feature descriptor IWLD which can capture highly discriminative evolutionary information from position-specific scoring matrixes (PSSM) of protein data, and employing the powerful and robust DVM classifier. When applying the proposed method to Yeast and H. pylori data sets, we obtained excellent prediction accuracies as high as 96.52% and 91.80%, respectively, which are significantly better than the previous methods. Extensive experiments were then performed for predicting cross-species PPIs and the predictive results were also pretty promising. To further validate the performance of the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier on Human data set. The experimental results obtained indicate that our method is highly effective for PPIs prediction and can be taken as a supplementary tool for future proteomics research.

Predicting asthma exacerbations using artificial intelligence.

PubMed

Finkelstein, Joseph; Wood, Jeffrey

2013-01-01

Modern telemonitoring systems identify a serious patient deterioration when it already occurred. It would be much more beneficial if the upcoming clinical deterioration were identified ahead of time even before a patient actually experiences it. The goal of this study was to assess artificial intelligence approaches which potentially can be used in telemonitoring systems for advance prediction of changes in disease severity before they actually occur. The study dataset was based on daily self-reports submitted by 26 adult asthma patients during home telemonitoring consisting of 7001 records. Two classification algorithms were employed for building predictive models: naïve Bayesian classifier and support vector machines. Using a 7-day window, a support vector machine was able to predict asthma exacerbation to occur on the day 8 with the accuracy of 0.80, sensitivity of 0.84 and specificity of 0.80. Our study showed that methods of artificial intelligence have significant potential in developing individualized decision support for chronic disease telemonitoring systems.

A fusion of minicircle DNA and nanoparticle delivery technologies facilitates therapeutic genetic engineering of autologous canine olfactory mucosal cells.

PubMed

Delaney, Alexander M; Adams, Christopher F; Fernandes, Alinda R; Al-Shakli, Arwa F; Sen, Jon; Carwardine, Darren R; Granger, Nicolas; Chari, Divya M

2017-06-29

Olfactory ensheathing cells (OECs) promote axonal regeneration and improve locomotor function when transplanted into the injured spinal cord. A recent clinical trial demonstrated improved motor function in domestic dogs with spinal injury following autologous OEC transplantation. Their utility in canines offers promise for human translation, as dogs are comparable to humans in terms of clinical management and genetic/environmental variation. Moreover, the autologous, minimally invasive derivation of OECs makes them viable for human spinal injury investigation. Genetic engineering of transplant populations may augment their therapeutic potential, but relies heavily on viral methods which have several drawbacks for clinical translation. We present here the first proof that magnetic particles deployed with applied magnetic fields and advanced DNA minicircle vectors can safely bioengineer OECs to secrete a key neurotrophic factor, with an efficiency approaching that of viral vectors. We suggest that our alternative approach offers high translational potential for the delivery of augmented clinical cell therapies.

Spread of the Tiger: Global Risk of Invasion by the Mosquito Aedes albopictus

PubMed Central

BENEDICT, MARK Q.; LEVINE, REBECCA S.; HAWLEY, WILLIAM A.; LOUNIBOS, L. PHILIP

2008-01-01

Aedes albopictus, commonly known as the Asian tiger mosquito, is currently the most invasive mosquito in the world. It is of medical importance due to its aggressive daytime human-biting behavior and ability to vector many viruses, including dengue, LaCrosse, and West Nile. Invasions into new areas of its potential range are often initiated through the transportation of eggs via the international trade in used tires. We use a genetic algorithm, Genetic Algorithm for Rule Set Production (GARP), to determine the ecological niche of Ae. albopictus and predict a global ecological risk map for the continued spread of the species. We combine this analysis with risk due to importation of tires from infested countries and their proximity to countries that have already been invaded to develop a list of countries most at risk for future introductions and establishments. Methods used here have potential for predicting risks of future invasions of vectors or pathogens. PMID:17417960

Rational Development of A Polycistronic Plasmid with A CpG-Free Bacterial Backbone as A Potential Tool for Direct Reprogramming.

PubMed

Dormiani, Kianoush; Mir Mohammad Sadeghi, Hamid; Sadeghi-Aliabadi, Hojjat; Forouzanfar, Mahboobeh; Baharvand, Hossein; Ghaedi, Kamran; Nasr-Esfahani, Mohammad Hossein

2017-01-01

Induced pluripotent stem cells are generated from somatic cells by direct reprogramming. These reprogrammed pluripotent cells have different applications in biomedical fields such as regenerative medicine. Although viral vectors are widely used for efficient reprogramming, they have limited applications in the clinic due to the risk for immunogenicity and insertional mutagenesis. Accordingly, we designed and developed a small, non-integrating plasmid named pLENSO/Zeo as a 2A-mediated polycistronic expression vector. In this experimental study, we developed a single plasmid which includes a single expression cassette containing open reading frames of human LIN28, NANOG, SOX2 and OCT4 along with an EGFP reporter gene. Each reprogramming factor is separated by an intervening sequence that encodes a 2A self-processing peptide. The reprogramming cassette is located downstream of a CMV promoter. The vector is easily propagated in the E. coli GT115 strain through a CpG-depleted vector backbone. We evaluated the stability of the constructed vector bioinformatically, and its ability to stoichiometric expression of the reprogramming factors using quantitative molecular methods analysis after transient transfection into HEK293 cells. In the present study, we developed a nonviral episomal vector named pLENSO/ Zeo. Our results demonstrated the general structural stability of the plasmid DNA. This relatively small vector showed concomitant, high-level expression of the four reprogramming factors with similar titers, which are considered as the critical parameters for efficient and consistent reprogramming. According to our experimental results, this stable extrachromosomal plasmid expresses reliable amounts of four reprogramming factors simultaneously. Consequently, these promising results encouraged us to evaluate the capability of pLENSO/Zeo as a simple and feasible tool for generation of induced pluripotent stem cells from primary cells in the future.

Covariant kaon dynamics and kaon flow in heavy ion collisions

NASA Astrophysics Data System (ADS)

Zheng, Yu-Ming; Fuchs, C.; Faessler, Amand; Shekhter, K.; Yan, Yu-Peng; Kobdaj, Chinorat

2004-03-01

The influence of the chiral mean field on the K+ transverse flow in heavy ion collisions at SIS energy is investigated within covariant kaon dynamics. For the kaon mesons inside the nuclear medium a quasiparticle picture including scalar and vector fields is adopted and compared to the standard treatment with a static potential. It is confirmed that a Lorentz force from spatial component of the vector field provides an important contribution to the in-medium kaon dynamics and strongly counterbalances the influence of the vector potential on the K+ in-plane flow. The FOPI data can be reasonably described using in-medium kaon potentials based on effective chiral models. The information on the in-medium K+ potential extracted from kaon flow is consistent with the knowledge from other sources.

A machine learning approach to the potential-field method for implicit modeling of geological structures

NASA Astrophysics Data System (ADS)

Gonçalves, Ítalo Gomes; Kumaira, Sissa; Guadagnin, Felipe

2017-06-01

Implicit modeling has experienced a rise in popularity over the last decade due to its advantages in terms of speed and reproducibility in comparison with manual digitization of geological structures. The potential-field method consists in interpolating a scalar function that indicates to which side of a geological boundary a given point belongs to, based on cokriging of point data and structural orientations. This work proposes a vector potential-field solution from a machine learning perspective, recasting the problem as multi-class classification, which alleviates some of the original method's assumptions. The potentials related to each geological class are interpreted in a compositional data framework. Variogram modeling is avoided through the use of maximum likelihood to train the model, and an uncertainty measure is introduced. The methodology was applied to the modeling of a sample dataset provided with the software Move™. The calculations were implemented in the R language and 3D visualizations were prepared with the rgl package.

Schools as Potential Risk Sites for Vector-Borne Disease Transmission: Mosquito Vectors in Rural Schools in Two Municipalities in Colombia.

PubMed

Olano, Víctor Alberto; Matiz, María Inés; Lenhart, Audrey; Cabezas, Laura; Vargas, Sandra Lucía; Jaramillo, Juan Felipe; Sarmiento, Diana; Alexander, Neal; Stenström, Thor Axel; Overgaard, Hans J

2015-09-01

Dengue and other vector-borne diseases are of great public health importance in Colombia. Vector surveillance and control activities are often focused at the household level. Little is known about the importance of nonhousehold sites, including schools, in maintaining vector-borne disease transmission. The objectives of this paper were to determine the mosquito species composition in rural schools in 2 municipalities in Colombia and to assess the potential risk of vector-borne disease transmission in school settings. Entomological surveys were carried out in rural schools during the dry and rainy seasons of 2011. A total of 12 mosquito species were found: Aedes aegypti, Anopheles pseudopunctipennis, Culex coronator, Cx. quinquefasciatus, and Limatus durhamii in both immature and adult forms; Ae. fluviatilis, Cx. nigripalpus, Cx. corniger, and Psorophora ferox in immature forms only; and Ae. angustivittatus, Haemagogus equinus, and Trichoprosopon lampropus in adult forms only. The most common mosquito species was Cx. quinquefasciatus. Classrooms contained the greatest abundance of adult female Ae. aegypti and Cx. quinquefasciatus. The most common Ae. aegypti breeding sites were containers classified as "others" (e.g., cans), followed by containers used for water storage. A high level of Ae. aegypti infestation was found during the wet season. Our results suggest that rural schools are potentially important foci for the transmission of dengue and other mosquito-borne diseases. We propose that public health programs should be implemented in rural schools to prevent vector-borne diseases.

Storage and computationally efficient permutations of factorized covariance and square-root information matrices

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector-stored upper-triangular diagonal factorized covariance (UD) and vector stored upper-triangular square-root information filter (SRIF) arrays is presented. The method involves cyclical permutation of the rows and columns of the arrays and retriangularization with appropriate square-root-free fast Givens rotations or elementary slow Givens reflections. A minimal amount of computation is performed and only one scratch vector of size N is required, where N is the column dimension of the arrays. To make the method efficient for large SRIF arrays on a virtual memory machine, three additional scratch vectors each of size N are used to avoid expensive paging faults. The method discussed is compared with the methods and routines of Bierman's Estimation Subroutine Library (ESL).

Vector potential of hospital houseflies with special reference to Klebsiella species.

PubMed Central

Fotedar, R.; Banerjee, U.; Samantray, J. C.; Shriniwas

1992-01-01

The vector potential of houseflies (Musca domestica) for Klebsiella spp. was investigated. Klebsiella spp. (mostly Klebsiella pneumoniae) were isolated from 36.7% of hospital flies and 28.1% of infected wounds of patients. Antibiograms of Klebsiella spp. showed that 82.0% of isolates from hospital flies and 96.3% from infected wounds were resistant to four or more commonly used antimicrobials. In contrast, from the control group, only 8.7% klebsiella isolates showed similar antimicrobial resistance pattern (P less than 0.001). Similar strains of Klebsiella spp. were encountered among patients and hospital houseflies. The results indicate that flies in the hospital environs are potential vectors of hospital resistant strains of Klebsiella spp. PMID:1499668

Preliminary Observations on the Changing Roles of Malaria Vectors in Southern Belize

DTIC Science & Technology

1993-01-01

darlingi (Diptera: Cu- licidae) de la Ceiba, Atlantida, Honduras. Thesis. Maestria en Entomologia. Universidad de Panama, Panama City, Panama. 456...Brown and C. Cordon-Rosales. 1992. Potential malaria vectors in northern Guatemala (Vectores potenciales de ma- laria in la region norte de Guatemala...Serra de Aqua in June 1946 (Linthicum 1988). We initiated a malaria vector research pro- gram in Belize in 1990 and conducted extensive larval

Creating analytically divergence-free velocity fields from grid-based data

NASA Astrophysics Data System (ADS)

Ravu, Bharath; Rudman, Murray; Metcalfe, Guy; Lester, Daniel R.; Khakhar, Devang V.

2016-10-01

We present a method, based on B-splines, to calculate a C2 continuous analytic vector potential from discrete 3D velocity data on a regular grid. A continuous analytically divergence-free velocity field can then be obtained from the curl of the potential. This field can be used to robustly and accurately integrate particle trajectories in incompressible flow fields. Based on the method of Finn and Chacon (2005) [10] this new method ensures that the analytic velocity field matches the grid values almost everywhere, with errors that are two to four orders of magnitude lower than those of existing methods. We demonstrate its application to three different problems (each in a different coordinate system) and provide details of the specifics required in each case. We show how the additional accuracy of the method results in qualitatively and quantitatively superior trajectories that results in more accurate identification of Lagrangian coherent structures.

Determination of magnetic helicity in the solar wind and implications for cosmic ray propagation

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.

1981-01-01

The mean value of the correlation between local magnetic field and vector potential, known as the magnetic helicity, is a measure of the lack of mirror reflection symmetry of magnetic covariances in a turbulent medium. A method is presented for extraction of helicity spectra from magnetometer data, and applied to an evaluation of the magnetic helicity of interplanetary magnetic fluctuations.

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

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

Using support vector machines with tract-based spatial statistics for automated classification of Tourette syndrome children

NASA Astrophysics Data System (ADS)

Wen, Hongwei; Liu, Yue; Wang, Jieqiong; Zhang, Jishui; Peng, Yun; He, Huiguang

2016-03-01

Tourette syndrome (TS) is a developmental neuropsychiatric disorder with the cardinal symptoms of motor and vocal tics which emerges in early childhood and fluctuates in severity in later years. To date, the neural basis of TS is not fully understood yet and TS has a long-term prognosis that is difficult to accurately estimate. Few studies have looked at the potential of using diffusion tensor imaging (DTI) in conjunction with machine learning algorithms in order to automate the classification of healthy children and TS children. Here we apply Tract-Based Spatial Statistics (TBSS) method to 44 TS children and 48 age and gender matched healthy children in order to extract the diffusion values from each voxel in the white matter (WM) skeleton, and a feature selection algorithm (ReliefF) was used to select the most salient voxels for subsequent classification with support vector machine (SVM). We use a nested cross validation to yield an unbiased assessment of the classification method and prevent overestimation. The accuracy (88.04%), sensitivity (88.64%) and specificity (87.50%) were achieved in our method as peak performance of the SVM classifier was achieved using the axial diffusion (AD) metric, demonstrating the potential of a joint TBSS and SVM pipeline for fast, objective classification of healthy and TS children. These results support that our methods may be useful for the early identification of subjects with TS, and hold promise for predicting prognosis and treatment outcome for individuals with TS.

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.

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.

Maximum entropy PDF projection: A review

NASA Astrophysics Data System (ADS)

Baggenstoss, Paul M.

2017-06-01

We review maximum entropy (MaxEnt) PDF projection, a method with wide potential applications in statistical inference. The method constructs a sampling distribution for a high-dimensional vector x based on knowing the sampling distribution p(z) of a lower-dimensional feature z = T (x). Under mild conditions, the distribution p(x) having highest possible entropy among all distributions consistent with p(z) may be readily found. Furthermore, the MaxEnt p(x) may be sampled, making the approach useful in Monte Carlo methods. We review the theorem and present a case study in model order selection and classification for handwritten character recognition.

On the parallel solution of parabolic equations

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Youcef

1989-01-01

Parallel algorithms for the solution of linear parabolic problems are proposed. The first of these methods is based on using polynomial approximation to the exponential. It does not require solving any linear systems and is highly parallelizable. The two other methods proposed are based on Pade and Chebyshev approximations to the matrix exponential. The parallelization of these methods is achieved by using partial fraction decomposition techniques to solve the resulting systems and thus offers the potential for increased time parallelism in time dependent problems. Experimental results from the Alliant FX/8 and the Cray Y-MP/832 vector multiprocessors are also presented.

Passive acoustic mapping of cavitation using eigenspace-based robust Capon beamformer in ultrasound therapy.

PubMed

Lu, Shukuan; Hu, Hong; Yu, Xianbo; Long, Jiangying; Jing, Bowen; Zong, Yujin; Wan, Mingxi

2018-03-01

Pulse-echo imaging technique can only play a role when high intensity focused ultrasound (HIFU) is turned off due to the interference between the primary HIFU signal and the transmission pulse. Passive acoustic mapping (PAM) has been proposed as a tool for true real-time monitoring of HIFU therapy. However, the most-used PAM algorithm based on time exposure acoustic (TEA) limits the quality of cavitation image. Recently, robust Capon beamformer (RCB) has been used in PAM to provide improved resolution and reduced artifacts over TEA-based PAM, but the presented results have not been satisfactory. In the present study, we applied an eigenspace-based RCB (EISRCB) method to further improve the PAM image quality. The optimal weighting vector of the proposed method was found by projecting the RCB weighting vector onto the desired vector subspace constructed from the eigenstructure of the covariance matrix. The performance of the proposed PAM was validated by both simulations and in vitro histotripsy experiments. The results suggested that the proposed PAM significantly outperformed the conventionally used TEA and RCB-based PAM. The comparison results between pulse-echo images of the residual bubbles and cavitation images showed the potential of our proposed PAM in accurate localization of cavitation activity during HIFU therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

A simplified model for predicting malaria entomologic inoculation rates based on entomologic and parasitologic parameters relevant to control.

PubMed

Killeen, G F; McKenzie, F E; Foy, B D; Schieffelin, C; Billingsley, P F; Beier, J C

2000-05-01

Malaria transmission intensity is modeled from the starting perspective of individual vector mosquitoes and is expressed directly as the entomologic inoculation rate (EIR). The potential of individual mosquitoes to transmit malaria during their lifetime is presented graphically as a function of their feeding cycle length and survival, human biting preferences, and the parasite sporogonic incubation period. The EIR is then calculated as the product of 1) the potential of individual vectors to transmit malaria during their lifetime, 2) vector emergence rate relative to human population size, and 3) the infectiousness of the human population to vectors. Thus, impacts on more than one of these parameters will amplify each other's effects. The EIRs transmitted by the dominant vector species at four malaria-endemic sites from Papua New Guinea, Tanzania, and Nigeria were predicted using field measurements of these characteristics together with human biting rate and human reservoir infectiousness. This model predicted EIRs (+/- SD) that are 1.13 +/- 0.37 (range = 0.84-1.59) times those measured in the field. For these four sites, mosquito emergence rate and lifetime transmission potential were more important determinants of the EIR than human reservoir infectiousness. This model and the input parameters from the four sites allow the potential impacts of various control measures on malaria transmission intensity to be tested under a range of endemic conditions. The model has potential applications for the development and implementation of transmission control measures and for public health education.

Discovery of markers of exposure specific to bites of Lutzomyia longipalpis, the vector of Leishmania infantum chagasi in Latin America.

PubMed

Teixeira, Clarissa; Gomes, Regis; Collin, Nicolas; Reynoso, David; Jochim, Ryan; Oliveira, Fabiano; Seitz, Amy; Elnaiem, Dia-Eldin; Caldas, Arlene; de Souza, Ana Paula; Brodskyn, Cláudia I; de Oliveira, Camila Indiani; Mendonca, Ivete; Costa, Carlos H N; Volf, Petr; Barral, Aldina; Kamhawi, Shaden; Valenzuela, Jesus G

2010-03-23

Sand flies deliver Leishmania parasites to a host alongside salivary molecules that affect infection outcomes. Though some proteins are immunogenic and have potential as markers of vector exposure, their identity and vector specificity remain elusive. We screened human, dog, and fox sera from endemic areas of visceral leishmaniasis to identify potential markers of specific exposure to saliva of Lutzomyia longipalpis. Human and dog sera were further tested against additional sand fly species. Recombinant proteins of nine transcripts encoding secreted salivary molecules of Lu. longipalpis were produced, purified, and tested for antigenicity and specificity. Use of recombinant proteins corresponding to immunogenic molecules in Lu. longipalpis saliva identified LJM17 and LJM11 as potential markers of exposure. LJM17 was recognized by human, dog, and fox sera; LJM11 by humans and dogs. Notably, LJM17 and LJM11 were specifically recognized by humans exposed to Lu. longipalpis but not by individuals exposed to Lu. intermedia. Salivary recombinant proteins are of value as markers of vector exposure. In humans, LJM17 and LJM11 emerged as potential markers of specific exposure to Lu. longipalpis, the vector of Leishmania infantum chagasi in Latin America. In dogs, LJM17, LJM11, LJL13, LJL23, and LJL143 emerged as potential markers of sand fly exposure. Testing these recombinant proteins in large scale studies will validate their usefulness as specific markers of Lu. longipalpis exposure in humans and of sand fly exposure in dogs.

Method for predicting peptide detection in mass spectrometry

DOEpatents

Kangas, Lars [West Richland, WA; Smith, Richard D [Richland, WA; Petritis, Konstantinos [Richland, WA

2010-07-13

A method of predicting whether a peptide present in a biological sample will be detected by analysis with a mass spectrometer. The method uses at least one mass spectrometer to perform repeated analysis of a sample containing peptides from proteins with known amino acids. The method then generates a data set of peptides identified as contained within the sample by the repeated analysis. The method then calculates the probability that a specific peptide in the data set was detected in the repeated analysis. The method then creates a plurality of vectors, where each vector has a plurality of dimensions, and each dimension represents a property of one or more of the amino acids present in each peptide and adjacent peptides in the data set. Using these vectors, the method then generates an algorithm from the plurality of vectors and the calculated probabilities that specific peptides in the data set were detected in the repeated analysis. The algorithm is thus capable of calculating the probability that a hypothetical peptide represented as a vector will be detected by a mass spectrometry based proteomic platform, given that the peptide is present in a sample introduced into a mass spectrometer.

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.

A Comparison of Vector and Raster GIS Methods for Calculating Landscape Metrics Used in Environmental Assessments

Treesearch

Timothy G. Wade; James D. Wickham; Maliha S. Nash; Anne C. Neale; Kurt H. Riitters; K. Bruce Jones

2003-01-01

AbstractGIS-based measurements that combine native raster and native vector data are commonly used in environmental assessments. Most of these measurements can be calculated using either raster or vector data formats and processing methods. Raster processes are more commonly used because they can be significantly faster computationally...

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

PubMed

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

2015-01-01

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

Noninvasive prostate cancer screening based on serum surface-enhanced Raman spectroscopy and support vector machine

NASA Astrophysics Data System (ADS)

Li, Shaoxin; Zhang, Yanjiao; Xu, Junfa; Li, Linfang; Zeng, Qiuyao; Lin, Lin; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Liu, Songhao

2014-09-01

This study aims to present a noninvasive prostate cancer screening methods using serum surface-enhanced Raman scattering (SERS) and support vector machine (SVM) techniques through peripheral blood sample. SERS measurements are performed using serum samples from 93 prostate cancer patients and 68 healthy volunteers by silver nanoparticles. Three types of kernel functions including linear, polynomial, and Gaussian radial basis function (RBF) are employed to build SVM diagnostic models for classifying measured SERS spectra. For comparably evaluating the performance of SVM classification models, the standard multivariate statistic analysis method of principal component analysis (PCA) is also applied to classify the same datasets. The study results show that for the RBF kernel SVM diagnostic model, the diagnostic accuracy of 98.1% is acquired, which is superior to the results of 91.3% obtained from PCA methods. The receiver operating characteristic curve of diagnostic models further confirm above research results. This study demonstrates that label-free serum SERS analysis technique combined with SVM diagnostic algorithm has great potential for noninvasive prostate cancer screening.

Localization of thermal anomalies in electrical equipment using Infrared Thermography and support vector machine

NASA Astrophysics Data System (ADS)

Laib dit Leksir, Y.; Mansour, M.; Moussaoui, A.

2018-03-01

Analysis and processing of databases obtained from infrared thermal inspections made on electrical installations require the development of new tools to obtain more information to visual inspections. Consequently, methods based on the capture of thermal images show a great potential and are increasingly employed in this field. However, there is a need for the development of effective techniques to analyse these databases in order to extract significant information relating to the state of the infrastructures. This paper presents a technique explaining how this approach can be implemented and proposes a system that can help to detect faults in thermal images of electrical installations. The proposed method classifies and identifies the region of interest (ROI). The identification is conducted using support vector machine (SVM) algorithm. The aim here is to capture the faults that exist in electrical equipments during an inspection of some machines using A40 FLIR camera. After that, binarization techniques are employed to select the region of interest. Later the comparative analysis of the obtained misclassification errors using the proposed method with Fuzzy c means and Ostu, has also be addressed.

Current collection in an anisotropic plasma

NASA Technical Reports Server (NTRS)

Li, Wei-Wei

1990-01-01

A general method is given to derive the current-potential relations in anisotropic plasmas. Orbit limit current is assumed. The collector is a conductive sphere or an infinite cylinder. Any distribution which is an arbitrary function of the velocity vector can be considered as a superposition of many mono-energetic beams whose current-potential relations are known. The results for two typical pitch angle distributions are derived and discussed in detail. The general properties of the current potential relations are very similar to that of a Maxwellian plasma except for an effective temperature which varies with the angle between the magnetic field and the charging surface. The conclusions are meaningful to generalized geometries.

A Simple Method to Increase the Transduction Efficiency of Single-Stranded Adeno-Associated Virus Vectors In Vitro and In Vivo

PubMed Central

Ma, Wenqin; Li, Baozheng; Ling, Chen; Jayandharan, Giridhara R.; Byrne, Barry J.

2011-01-01

Abstract We have recently shown that co-administration of conventional single-stranded adeno-associated virus 2 (ssAAV2) vectors with self-complementary (sc) AAV2-protein phosphatase 5 (PP5) vectors leads to a significant increase in the transduction efficiency of ssAAV2 vectors in human cells in vitro as well as in murine hepatocytes in vivo. In the present study, this strategy has been further optimized by generating a mixed population of ssAAV2-EGFP and scAAV2-PP5 vectors at a 10:1 ratio to achieve enhanced green fluorescent protein (EGFP) transgene expression at approximately 5- to 10-fold higher efficiency, both in vitro and in vivo. This simple coproduction method should be adaptable to any ssAAV serotype vector containing transgene cassettes that are too large to be encapsidated in scAAV vectors. PMID:21219084

Estimation of chaotic coupled map lattices using symbolic vector dynamics

NASA Astrophysics Data System (ADS)

Wang, Kai; Pei, Wenjiang; Cheung, Yiu-ming; Shen, Yi; He, Zhenya

2010-01-01

In [K. Wang, W.J. Pei, Z.Y. He, Y.M. Cheung, Phys. Lett. A 367 (2007) 316], an original symbolic vector dynamics based method has been proposed for initial condition estimation in additive white Gaussian noisy environment. The estimation precision of this estimation method is determined by symbolic errors of the symbolic vector sequence gotten by symbolizing the received signal. This Letter further develops the symbolic vector dynamical estimation method. We correct symbolic errors with backward vector and the estimated values by using different symbols, and thus the estimation precision can be improved. Both theoretical and experimental results show that this algorithm enables us to recover initial condition of coupled map lattice exactly in both noisy and noise free cases. Therefore, we provide novel analytical techniques for understanding turbulences in coupled map lattice.

Comparison of scoliosis measurements based on three-dimensional vertebra vectors and conventional two-dimensional measurements: advantages in evaluation of prognosis and surgical results.

PubMed

Illés, Tamás; Somoskeöy, Szabolcs

2013-06-01

A new concept of vertebra vectors based on spinal three-dimensional (3D) reconstructions of images from the EOS system, a new low-dose X-ray imaging device, was recently proposed to facilitate interpretation of EOS 3D data, especially with regard to horizontal plane images. This retrospective study was aimed at the evaluation of the spinal layout visualized by EOS 3D and vertebra vectors before and after surgical correction, the comparison of scoliotic spine measurement values based on 3D vertebra vectors with measurements using conventional two-dimensional (2D) methods, and an evaluation of horizontal plane vector parameters for their relationship with the magnitude of scoliotic deformity. 95 patients with adolescent idiopathic scoliosis operated according to the Cotrel-Dubousset principle were subjected to EOS X-ray examinations pre- and postoperatively, followed by 3D reconstructions and generation of vertebra vectors in a calibrated coordinate system to calculate vector coordinates and parameters, as published earlier. Differences in values of conventional 2D Cobb methods and methods based on vertebra vectors were evaluated by means comparison T test and relationship of corresponding parameters was analysed by bivariate correlation. Relationship of horizontal plane vector parameters with the magnitude of scoliotic deformities and results of surgical correction were analysed by Pearson correlation and linear regression. In comparison to manual 2D methods, a very close relationship was detectable in vertebra vector-based curvature data for coronal curves (preop r 0.950, postop r 0.935) and thoracic kyphosis (preop r 0.893, postop r 0.896), while the found small difference in L1-L5 lordosis values (preop r 0.763, postop r 0.809) was shown to be strongly related to the magnitude of corresponding L5 wedge. The correlation analysis results revealed strong correlation between the magnitude of scoliosis and the lateral translation of apical vertebra in horizontal plane. The horizontal plane coordinates of the terminal and initial points of apical vertebra vectors represent this (r 0.701; r 0.667). Less strong correlation was detected in the axial rotation of apical vertebras and the magnitudes of the frontal curves (r 0.459). Vertebra vectors provide a key opportunity to visualize spinal deformities in all three planes simultaneously. Measurement methods based on vertebral vectors proved to be just as accurate and reliable as conventional measurement methods for coronal and sagittal plane parameters. In addition, the horizontal plane display of the curves can be studied using the same vertebra vectors. Based on the vertebra vectors data, during the surgical treatment of spinal deformities, the diminution of the lateral translation of the vertebras seems to be more important in the results of the surgical correction than the correction of the axial rotation.

Tensor-based tracking of the aorta in phase-contrast MR images

NASA Astrophysics Data System (ADS)

Azad, Yoo-Jin; Malsam, Anton; Ley, Sebastian; Rengier, Fabian; Dillmann, Rüdiger; Unterhinninghofen, Roland

2014-03-01

The velocity-encoded magnetic resonance imaging (PC-MRI) is a valuable technique to measure the blood flow velocity in terms of time-resolved 3D vector fields. For diagnosis, presurgical planning and therapy control monitoring the patient's hemodynamic situation is crucial. Hence, an accurate and robust segmentation of the diseased vessel is the basis for further methods like the computation of the blood pressure. In the literature, there exist some approaches to transfer the methods of processing DT-MR images to PC-MR data, but the potential of this approach is not fully exploited yet. In this paper, we present a method to extract the centerline of the aorta in PC-MR images by applying methods from the DT-MRI. On account of this, in the first step the velocity vector fields are converted into tensor fields. In the next step tensor-based features are derived and by applying a modified tensorline algorithm the tracking of the vessel course is accomplished. The method only uses features derived from the tensor imaging without the use of additional morphology information. For evaluation purposes we applied our method to 4 volunteer as well as 26 clinical patient datasets with good results. In 29 of 30 cases our algorithm accomplished to extract the vessel centerline.

SNPs selection using support vector regression and genetic algorithms in GWAS

PubMed Central

2014-01-01

Introduction This paper proposes a new methodology to simultaneously select the most relevant SNPs markers for the characterization of any measurable phenotype described by a continuous variable using Support Vector Regression with Pearson Universal kernel as fitness function of a binary genetic algorithm. The proposed methodology is multi-attribute towards considering several markers simultaneously to explain the phenotype and is based jointly on statistical tools, machine learning and computational intelligence. Results The suggested method has shown potential in the simulated database 1, with additive effects only, and real database. In this simulated database, with a total of 1,000 markers, and 7 with major effect on the phenotype and the other 993 SNPs representing the noise, the method identified 21 markers. Of this total, 5 are relevant SNPs between the 7 but 16 are false positives. In real database, initially with 50,752 SNPs, we have reduced to 3,073 markers, increasing the accuracy of the model. In the simulated database 2, with additive effects and interactions (epistasis), the proposed method matched to the methodology most commonly used in GWAS. Conclusions The method suggested in this paper demonstrates the effectiveness in explaining the real phenotype (PTA for milk), because with the application of the wrapper based on genetic algorithm and Support Vector Regression with Pearson Universal, many redundant markers were eliminated, increasing the prediction and accuracy of the model on the real database without quality control filters. The PUK demonstrated that it can replicate the performance of linear and RBF kernels. PMID:25573332

Classification of Alzheimer's disease patients with hippocampal shape wrapper-based feature selection and support vector machine

NASA Astrophysics Data System (ADS)

Young, Jonathan; Ridgway, Gerard; Leung, Kelvin; Ourselin, Sebastien

2012-02-01

It is well known that hippocampal atrophy is a marker of the onset of Alzheimer's disease (AD) and as a result hippocampal volumetry has been used in a number of studies to provide early diagnosis of AD and predict conversion of mild cognitive impairment patients to AD. However, rates of atrophy are not uniform across the hippocampus making shape analysis a potentially more accurate biomarker. This study studies the hippocampi from 226 healthy controls, 148 AD patients and 330 MCI patients obtained from T1 weighted structural MRI images from the ADNI database. The hippocampi are anatomically segmented using the MAPS multi-atlas segmentation method, and the resulting binary images are then processed with SPHARM software to decompose their shapes as a weighted sum of spherical harmonic basis functions. The resulting parameterizations are then used as feature vectors in Support Vector Machine (SVM) classification. A wrapper based feature selection method was used as this considers the utility of features in discriminating classes in combination, fully exploiting the multivariate nature of the data and optimizing the selected set of features for the type of classifier that is used. The leave-one-out cross validated accuracy obtained on training data is 88.6% for classifying AD vs controls and 74% for classifying MCI-converters vs MCI-stable with very compact feature sets, showing that this is a highly promising method. There is currently a considerable fall in accuracy on unseen data indicating that the feature selection is sensitive to the data used, however feature ensemble methods may overcome this.

Analytical Approach to the Fuel Optimal Impulsive Transfer Problem Using Primer Vector Method

NASA Astrophysics Data System (ADS)

Fitrianingsih, E.; Armellin, R.

2018-04-01

One of the objectives of mission design is selecting an optimum orbital transfer which often translated as a transfer which requires minimum propellant consumption. In order to assure the selected trajectory meets the requirement, the optimality of transfer should first be analyzed either by directly calculating the ΔV of the candidate trajectories and select the one that gives a minimum value or by evaluating the trajectory according to certain criteria of optimality. The second method is performed by analyzing the profile of the modulus of the thrust direction vector which is known as primer vector. Both methods come with their own advantages and disadvantages. However, it is possible to use the primer vector method to verify if the result from the direct method is truly optimal or if the ΔV can be reduced further by implementing correction maneuver to the reference trajectory. In addition to its capability to evaluate the transfer optimality without the need to calculate the transfer ΔV, primer vector also enables us to identify the time and position to apply correction maneuver in order to optimize a non-optimum transfer. This paper will present the analytical approach to the fuel optimal impulsive transfer using primer vector method. The validity of the method is confirmed by comparing the result to those from the numerical method. The investigation of the optimality of direct transfer is used to give an example of the application of the method. The case under study is the prograde elliptic transfers from Earth to Mars. The study enables us to identify the optimality of all the possible transfers.

Potential Sympatric Vectors and Mammalian Hosts of Venezuelan Equine Encephalitis Virus in Southern Mexico.

PubMed

Sotomayor-Bonilla, Jesús; Abella-Medrano, Carlos Antonio; Chaves, Andrea; Álvarez-Mendizábal, Paulina; Rico-Chávez, Óscar; Ibáñez-Bernal, Sergio; Rostal, Melinda K; Ojeda-Flores, Rafael; Barbachano-Guerrero, Arturo; Gutiérrez-Espeleta, Gustavo; Aguirre, A Alonso; Daszak, Peter; Suzán, Gerardo

2017-07-01

Arboviruses are important zoonotic agents with complex transmission cycles and are not well understood because they may involve many vectors and hosts. We studied sympatric wild mammals and hematophagous mosquitoes having the potential to act as hosts and vectors in two areas of southern Mexico. Mosquitoes, bats, and rodents were captured in Calakmul (Campeche) and Montes Azules (Chiapas), between November 2010 and August 2011. Spleen samples from 146 bats and 14 rodents were tested for molecular evidence of Venezuelan equine encephalitis virus (VEEV), eastern equine encephalitis virus (EEEV), western equine encephalitis virus (WEEV), and West Nile virus (WNV) using PCR protocols. Bat ( Artibeus lituratus , Carollia sowelli , Glossophaga soricina , and Sturnira parvidens) and rodent ( Sigmodon hispidus and Oryzomys alfaroi ) species were positive for VEEV. No individuals were positive for WNV, EEEV, or WEEV. A total of 1,298 mosquitoes were collected at the same sites, and five of the mosquito species collected were known VEEV vectors (Aedes fulvus, Mansonia indubitans, Psorophora ferox, Psorophora cilipes, and Psorophora confinnis). This survey simultaneously presents the first molecular evidence, to our knowledge, of VEEV in bats and rodents from southern Mexico and the identification of potential sympatric vectors. Studies investigating sympatric nonhuman hosts, vectors, and arboviruses must be expanded to determine arboviral dynamics in complex systems in which outbreaks of emerging and reemerging zoonoses are continuously occurring.

A vector space model approach to identify genetically related diseases.

PubMed

Sarkar, Indra Neil

2012-01-01

The relationship between diseases and their causative genes can be complex, especially in the case of polygenic diseases. Further exacerbating the challenges in their study is that many genes may be causally related to multiple diseases. This study explored the relationship between diseases through the adaptation of an approach pioneered in the context of information retrieval: vector space models. A vector space model approach was developed that bridges gene disease knowledge inferred across three knowledge bases: Online Mendelian Inheritance in Man, GenBank, and Medline. The approach was then used to identify potentially related diseases for two target diseases: Alzheimer disease and Prader-Willi Syndrome. In the case of both Alzheimer Disease and Prader-Willi Syndrome, a set of plausible diseases were identified that may warrant further exploration. This study furthers seminal work by Swanson, et al. that demonstrated the potential for mining literature for putative correlations. Using a vector space modeling approach, information from both biomedical literature and genomic resources (like GenBank) can be combined towards identification of putative correlations of interest. To this end, the relevance of the predicted diseases of interest in this study using the vector space modeling approach were validated based on supporting literature. The results of this study suggest that a vector space model approach may be a useful means to identify potential relationships between complex diseases, and thereby enable the coordination of gene-based findings across multiple complex diseases.

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

Wurfelspiel-based training data methods for ATR

NASA Astrophysics Data System (ADS)

Peterson, James K.

2004-09-01

A data object is constructed from a P by M Wurfelspiel matrix W by choosing an entry from each column to construct a sequence A0A1"AM-1. Each of the PM possibilities are designed to correspond to the same category according to some chosen measure. This matrix could encode many types of data. (1) Musical fragments, all of which evoke sadness; each column entry is a 4 beat sequence with a chosen A0A1A2 thus 16 beats long (W is P by 3). (2) Paintings, all of which evoke happiness; each column entry is a layer and a given A0A1A2 is a painting constructed using these layers (W is P by 3). (3) abstract feature vectors corresponding to action potentials evoked from a biological cell's exposure to a toxin. The action potential is divided into four relevant regions and each column entry represents the feature vector of a region. A given A0A1A2 is then an abstraction of the excitable cell's output (W is P by 4). (4) abstract feature vectors corresponding to an object such as a face or vehicle. The object is divided into four categories each assigned an abstract feature vector with the resulting concatenation an abstract representation of the object (W is P by 4). All of the examples above correspond to one particular measure (sad music, happy paintings, an introduced toxin, an object to recognize)and hence, when a Wurfelspiel matrix is constructed, relevant training information for recognition is encoded that can be used in many algorithms. The focus of this paper is on the application of these ideas to automatic target recognition (ATR). In addition, we discuss a larger biologically based model of temporal cortex polymodal sensor fusion which can use the feature vectors extracted from the ATR Wurfelspiel data.

Walsh-Hadamard transform kernel-based feature vector for shot boundary detection.

PubMed

Lakshmi, Priya G G; Domnic, S

2014-12-01

Video shot boundary detection (SBD) is the first step of video analysis, summarization, indexing, and retrieval. In SBD process, videos are segmented into basic units called shots. In this paper, a new SBD method is proposed using color, edge, texture, and motion strength as vector of features (feature vector). Features are extracted by projecting the frames on selected basis vectors of Walsh-Hadamard transform (WHT) kernel and WHT matrix. After extracting the features, based on the significance of the features, weights are calculated. The weighted features are combined to form a single continuity signal, used as input for Procedure Based shot transition Identification process (PBI). Using the procedure, shot transitions are classified into abrupt and gradual transitions. Experimental results are examined using large-scale test sets provided by the TRECVID 2007, which has evaluated hard cut and gradual transition detection. To evaluate the robustness of the proposed method, the system evaluation is performed. The proposed method yields F1-Score of 97.4% for cut, 78% for gradual, and 96.1% for overall transitions. We have also evaluated the proposed feature vector with support vector machine classifier. The results show that WHT-based features can perform well than the other existing methods. In addition to this, few more video sequences are taken from the Openvideo project and the performance of the proposed method is compared with the recent existing SBD method.

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.

Intelligent Design of Metal Oxide Gas Sensor Arrays Using Reciprocal Kernel Support Vector Regression

NASA Astrophysics Data System (ADS)

Dougherty, Andrew W.

Metal oxides are a staple of the sensor industry. The combination of their sensitivity to a number of gases, and the electrical nature of their sensing mechanism, make the particularly attractive in solid state devices. The high temperature stability of the ceramic material also make them ideal for detecting combustion byproducts where exhaust temperatures can be high. However, problems do exist with metal oxide sensors. They are not very selective as they all tend to be sensitive to a number of reduction and oxidation reactions on the oxide's surface. This makes sensors with large numbers of sensors interesting to study as a method for introducing orthogonality to the system. Also, the sensors tend to suffer from long term drift for a number of reasons. In this thesis I will develop a system for intelligently modeling metal oxide sensors and determining their suitability for use in large arrays designed to analyze exhaust gas streams. It will introduce prior knowledge of the metal oxide sensors' response mechanisms in order to produce a response function for each sensor from sparse training data. The system will use the same technique to model and remove any long term drift from the sensor response. It will also provide an efficient means for determining the orthogonality of the sensor to determine whether they are useful in gas sensing arrays. The system is based on least squares support vector regression using the reciprocal kernel. The reciprocal kernel is introduced along with a method of optimizing the free parameters of the reciprocal kernel support vector machine. The reciprocal kernel is shown to be simpler and to perform better than an earlier kernel, the modified reciprocal kernel. Least squares support vector regression is chosen as it uses all of the training points and an emphasis was placed throughout this research for extracting the maximum information from very sparse data. The reciprocal kernel is shown to be effective in modeling the sensor responses in the time, gas and temperature domains, and the dual representation of the support vector regression solution is shown to provide insight into the sensor's sensitivity and potential orthogonality. Finally, the dual weights of the support vector regression solution to the sensor's response are suggested as a fitness function for a genetic algorithm, or some other method for efficiently searching large parameter spaces.

Relative Roles of Weather Variables and Change in Human Population in Malaria: Comparison over Different States of India

PubMed Central

Goswami, Prashant; Murty, Upadhayula Suryanarayana; Mutheneni, Srinivasa Rao; Krishnan, Swathi Trithala

2014-01-01

Background Pro-active and effective control as well as quantitative assessment of impact of climate change on malaria requires identification of the major drivers of the epidemic. Malaria depends on vector abundance which, in turn, depends on a combination of weather variables. However, there remain several gaps in our understanding and assessment of malaria in a changing climate. Most of the studies have considered weekly or even monthly mean values of weather variables, while the malaria vector is sensitive to daily variations. Secondly, rarely all the relevant meteorological variables have been considered together. An important question is the relative roles of weather variables (vector abundance) and change in host (human) population, in the change in disease load. Method We consider the 28 states of India, characterized by diverse climatic zones and changing population as well as complex variability in malaria, as a natural test bed. An annual vector load for each of the 28 states is defined based on the number of vector genesis days computed using daily values of temperature, rainfall and humidity from NCEP daily Reanalysis; a prediction of potential malaria load is defined by taking into consideration changes in the human population and compared with the reported number of malaria cases. Results For most states, the number of malaria cases is very well correlated with the vector load calculated with the combined conditions of daily values of temperature, rainfall and humidity; no single weather variable has any significant association with the observed disease prevalence. Conclusion The association between vector-load and daily values of weather variables is robust and holds for different climatic regions (states of India). Thus use of all the three weather variables provides a reliable means of pro-active and efficient vector sanitation and control as well as assessment of impact of climate change on malaria. PMID:24971510

A spatially explicit metapopulation model and cattle trade analysis suggests key determinants for the recurrent circulation of rift valley Fever virus in a pilot area of madagascar highlands.

PubMed

Nicolas, Gaëlle; Chevalier, Véronique; Tantely, Luciano Michaël; Fontenille, Didier; Durand, Benoît

2014-12-01

Rift Valley fever (RVF) is a vector-borne zoonotic disease that causes high morbidity and mortality in ruminants. In 2008-2009, a RVF outbreak affected the whole Madagascar island, including the Anjozorobe district located in Madagascar highlands. An entomological survey showed the absence of Aedes among the potential RVF virus (RVFV) vector species identified in this area, and an overall low abundance of mosquitoes due to unfavorable climatic conditions during winter. No serological nor virological sign of infection was observed in wild terrestrial mammals of the area, suggesting an absence of wild RVF virus (RVFV) reservoir. However, a three years serological and virological follow-up in cattle showed a recurrent RVFV circulation. The objective of this study was to understand the key determinants of this unexpected recurrent transmission. To achieve this goal, a spatial deterministic discrete-time metapopulation model combined with cattle trade network was designed and parameterized to reproduce the local conditions using observational data collected in the area. Three scenarios that could explain the RVFV recurrent circulation in the area were analyzed: (i) RVFV overwintering thanks to a direct transmission between cattle when viraemic cows calve, vectors being absent during the winter, (ii) a low level vector-based circulation during winter thanks to a residual vector population, without direct transmission between cattle, (iii) combination of both above mentioned mechanisms. Multi-model inference methods resulted in a model incorporating both a low level RVFV winter vector-borne transmission and a direct transmission between animals when viraemic cows calve. Predictions satisfactorily reproduced field observations, 84% of cattle infections being attributed to vector-borne transmission, and 16% to direct transmission. These results appeared robust according to the sensitivity analysis. Interweaving between agricultural works in rice fields, seasonality of vector proliferation, and cattle exchange practices could be a key element for understanding RVFV circulation in this area of Madagascar highlands.

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

PubMed

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

2016-02-01

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

Detecting glaucomatous change in visual fields: Analysis with an optimization framework.

PubMed

Yousefi, Siamak; Goldbaum, Michael H; Varnousfaderani, Ehsan S; Belghith, Akram; Jung, Tzyy-Ping; Medeiros, Felipe A; Zangwill, Linda M; Weinreb, Robert N; Liebmann, Jeffrey M; Girkin, Christopher A; Bowd, Christopher

2015-12-01

Detecting glaucomatous progression is an important aspect of glaucoma management. The assessment of longitudinal series of visual fields, measured using Standard Automated Perimetry (SAP), is considered the reference standard for this effort. We seek efficient techniques for determining progression from longitudinal visual fields by formulating the problem as an optimization framework, learned from a population of glaucoma data. The longitudinal data from each patient's eye were used in a convex optimization framework to find a vector that is representative of the progression direction of the sample population, as a whole. Post-hoc analysis of longitudinal visual fields across the derived vector led to optimal progression (change) detection. The proposed method was compared to recently described progression detection methods and to linear regression of instrument-defined global indices, and showed slightly higher sensitivities at the highest specificities than other methods (a clinically desirable result). The proposed approach is simpler, faster, and more efficient for detecting glaucomatous changes, compared to our previously proposed machine learning-based methods, although it provides somewhat less information. This approach has potential application in glaucoma clinics for patient monitoring and in research centers for classification of study participants. Copyright © 2015 Elsevier Inc. All rights reserved.

wFlu: Characterization and Evaluation of a Native Wolbachia from the Mosquito Aedes fluviatilis as a Potential Vector Control Agent

PubMed Central

Gonçalves, Daniela da Silva; Moreira, Luciano Andrade

2013-01-01

There is currently considerable interest and practical progress in using the endosymbiotic bacteria Wolbachia as a vector control agent for human vector-borne diseases. Such vector control strategies may require the introduction of multiple, different Wolbachia strains into target vector populations, necessitating the identification and characterization of appropriate endosymbiont variants. Here, we report preliminary characterization of wFlu, a native Wolbachia from the neotropical mosquito Aedes fluviatilis, and evaluate its potential as a vector control agent by confirming its ability to cause cytoplasmic incompatibility, and measuring its effect on three parameters determining host fitness (survival, fecundity and fertility), as well as vector competence (susceptibility) for pathogen infection. Using an aposymbiotic strain of Ae. fluviatilis cured of its native Wolbachia by antibiotic treatment, we show that in its natural host wFlu causes incomplete, but high levels of, unidirectional cytoplasmic incompatibility, has high rates of maternal transmission, and no detectable fitness costs, indicating a high capacity to rapidly spread through host populations. However, wFlu does not inhibit, and even enhances, oocyst infection with the avian malaria parasite Plasmodium gallinaceum. The stage- and sex-specific density of wFlu was relatively low, and with limited tissue distribution, consistent with the lack of virulence and pathogen interference/symbiont-mediated protection observed. Unexpectedly, the density of wFlu was also shown to be specifically-reduced in the ovaries after bloodfeeding Ae. fluviatilis. Overall, our observations indicate that the Wolbachia strain wFlu has the potential to be used as a vector control agent, and suggests that appreciable mutualistic coevolution has occurred between this endosymbiont and its natural host. Future work will be needed to determine whether wFlu has virulent host effects and/or exhibits pathogen interference when artificially-transfected to the novel mosquito hosts that are the vectors of human pathogens. PMID:23555728

Leishmaniasis transmission in an ecotourism area: potential vectors in Ilha Grande, Rio de Janeiro State, Brazil

PubMed Central

2013-01-01

Background The south coast of Rio de Janeiro State, in Brazil, is endemic for cutaneous and visceral leishmaniases and is frequently visited by tourists from different parts of the world. Since the complex epidemiology of leishmaniases demands local studies, the goal of this study was to investigate the phlebotomine sand fly fauna and leishmaniases transmission in Ilha Grande, an ecotourism area of Angra dos Reis municipality. Methods Sand fly fauna was sampled in three monitoring stations using HP light traps in domiciles, peridomiciles and forests. Species abundance was evaluated by the Index of Species Abundance. A Leishmania natural infection survey was done using multiplex PCR and dot blot hybridization. Results During 15 consecutive months of sand fly monitoring, 1093 specimens from 16 species were captured. The potential leishmaniases vectors found were Lutzomyia (Nyssomyia) intermedia, L. migonei, L. (N.) flaviscutellata, L. (Psychodopygus) ayrozai and L. (Lutzomyia) longipalpis. Five species were new records in Ilha Grande: L. (Sciopemyia) microps, L. termitophila, L. firmatoi, L. rupicola and L. (P.) ayrozai. Higher species richness was found inside forest areas, although potential leishmaniases vectors were present in deforested areas, peridomiciles and inside houses. Lutzomyia (N.) intermedia and L. migonei were the most abundant species. Females of L. migonei showed a high rate (10.3%) of natural infection by Leishmania (Viannia) sp., probably Leishmania (V.) braziliensis. Conclusions The detection of leishmaniases transmission and potential vectors in Ilha Grande is of public health concern, especially because tourists are frequently visiting the island. Besides reinforcing the epidemiological importance of L. (N.) intermedia in Rio de Janeiro State, the role of L. migonei in cutaneous leishmaniasis transmission is highlighted with its high rate of Leishmania natural infection. The finding of L. (L.) longipalpis confirmed the human autochthonous case of visceral leishmaniasis from the island. The presence of L. (N.) flaviscutellata in peridomestic areas is also an important finding, since the species is involved in the transmission of diffuse cutaneous leishmaniasis. Health education practices directed to the local community and tourists are important control actions that can be taken in Ilha Grande to reduce the burden of leishmaniases. PMID:24499568

Invasive potential of cattle fever ticks in the southern United States

PubMed Central

2014-01-01

Abstract' Background For >100 years cattle production in the southern United States has been threatened by cattle fever. It is caused by an invasive parasite-vector complex that includes the protozoan hemoparasites Babesia bovis and B. bigemina, which are transmitted among domestic cattle via Rhipicephalus tick vectors of the subgenus Boophilus. In 1906 an eradication effort was started and by 1943 Boophilus ticks had been confined to a narrow tick eradication quarantine area (TEQA) along the Texas-Mexico border. However, a dramatic increase in tick infestations in areas outside the TEQA over the last decade suggests these tick vectors may be poised to re-invade the southern United States. We investigated historical and potential future distributions of climatic habitats of cattle fever ticks to assess the potential for a range expansion. Methods We built robust spatial predictions of habitat suitability for the vector species Rhipicephalus (Boophilus) microplus and R. (B.) annulatus across the southern United States for three time periods: 1906, present day (2012), and 2050. We used analysis of molecular variance (AMOVA) to identify persistent tick occurrences and analysis of bias in the climate proximate to these occurrences to identify key environmental parameters associated with the ecology of both species. We then used ecological niche modeling algorithms GARP and Maxent to construct models that related known occurrences of ticks in the TEQA during 2001–2011 with geospatial data layers that summarized important climate parameters at all three time periods. Results We identified persistent tick infestations and specific climate parameters that appear to be drivers of ecological niches of the two tick species. Spatial models projected onto climate data representative of climate in 1906 reproduced historical pre-eradication tick distributions. Present-day predictions, although constrained to areas near the TEQA, extrapolated well onto climate projections for 2050. Conclusions Our models indicate the potential for range expansion of climate suitable for survival of R. microplus and R. annulatus in the southern United States by mid-century, which increases the risk of reintroduction of these ticks and cattle tick fever into major cattle producing areas. PMID:24742062

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.

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.

Effects of Local Anthropogenic Changes on Potential Malaria Vector Anopheles hyrcanus and West Nile Virus Vector Culex modestus, Camargue, France

PubMed Central

Ponçon, Nicolas; Balenghien, Thomas; Toty, Céline; Ferré, Jean Baptiste; Thomas, Cyrille; Dervieux, Alain; L’Ambert, Grégory; Schaffner, Francis; Bardin, Olivier

2007-01-01

Using historical data, we highlight the consequences of anthropogenic ecosystem modifications on the abundance of mosquitoes implicated as the current most important potential malaria vector, Anopheles hyrcanus, and the most important West Nile virus (WNV) vector, Culex modestus, in the Camargue region, France. From World War II to 1971, populations of these species increased as rice cultivation expanded in the region in a political context that supported agriculture. They then fell, likely because of decreased cultivation and increased pesticide use to control a rice pest. The species increased again after 2000 with the advent of more targeted pest-management strategies, mainly the results of European regulations decisions. An intertwined influence of political context, environmental constraints, technical improvements, and social factors led to changes in mosquito abundance that had potential consequences on malaria and WNV transmission. These findings suggest that anthropogenic changes should not be underestimated in vectorborne disease recrudescence. PMID:18258028

Quantized Vector Potential and the Photon Wave-function

NASA Astrophysics Data System (ADS)

Meis, C.; Dahoo, P. R.

2017-12-01

The vector potential function {\\overrightarrow{α }}kλ (\\overrightarrow{r},t) for a k-mode and λ-polarization photon, with the quantized amplitude α 0k (ω k ) = ξω k , satisfies the classical wave propagation equation as well as the Schrodinger’s equation with the relativistic massless Hamiltonian \\mathop{H}\\limits∼ =-i\\hslash c\\overrightarrow{\

The distribution and biology of potential vectors of Xylella fastidiosa on coffee and citrus in Puerto Rico

USDA-ARS?s Scientific Manuscript database

Plant diseases caused by Xylella fastidiosa (Wells et al.) (Xf) surround the Caribbean Basin. Two major commodities of Puerto Rico, coffee and citrus, are highly susceptible to Xf. We surveyed potential vectors of Xf in coffee and citrus farms in western Puerto Rico over an 18 month period. Cicadel...

Vector Potential, Electromagnetic Induction and "Physical Meaning"

ERIC Educational Resources Information Center

Giuliani, G.

2010-01-01

A forgotten experiment by Andre Blondel (1914) proves, as held on the basis of theoretical arguments in a previous paper, that the time variation of the magnetic flux is not the cause of the induced emf; the physical agent is instead the vector potential through the term [equation omitted] (when the induced circuit is at rest). The "good…

Sleeping Beauty-baculovirus hybrid vectors for long-term gene expression in the eye.

PubMed

Turunen, Tytteli Anni Kaarina; Laakkonen, Johanna Päivikki; Alasaarela, Laura; Airenne, Kari Juhani; Ylä-Herttuala, Seppo

2014-01-01

A baculovirus vector is capable of efficiently transducing many nondiving and diving cell types. However, the potential of baculovirus is restricted for many gene delivery applications as a result of the transient gene expression that it mediates. The plasmid-based Sleeping Beauty (SB) transposon system integrates transgenes into target cell genome efficiently with a genomic integration pattern that is generally considered safer than the integration of many other integrating vectors; yet efficient delivery of therapeutic genes into cells of target tissues in vivo is a major challenge for nonviral gene therapy. In the present study, SB was introduced into baculovirus to obtain novel hybrid vectors that would combine the best features of the two vector systems (i.e. effective gene delivery and efficient integration into the genome), thus circumventing the major limitations of these vectors. We constructed and optimized SB-baculovirus hybrid vectors that bear either SB100x transposase or SB transposon in the forward or reverse orientations with respect to the viral backbone The functionality of the novel hybrid vectors was investigated in cell cultures and in a proof-of-concept study in the mouse eye. The hybrid vectors showed high and sustained transgene expression that remained stable and demonstrated no signs of decline during the 2 months follow-up in vitro. These results were verified in the mouse eye where persistent transgene expression was detected two months after intravitreal injection. Our results confirm that (i) SB-baculovirus hybrid vectors mediate long-term gene expression in vitro and in vivo, and (ii) the hybrid vectors are potential new tools for the treatment of ocular diseases. Copyright © 2014 John Wiley & Sons, Ltd.

Market implementation of the MVA platform for pre-pandemic and pandemic influenza vaccines: A quantitative key opinion leader analysis

PubMed Central

Ramezanpour, Bahar; Pronker, Esther S.; Kreijtz, Joost H.C.M.; Osterhaus, Albert D.M.E.; Claassen, E.

2015-01-01

A quantitative method is presented to rank strengths, weaknesses, opportunities, and threats (SWOT) of modified vaccinia virus Ankara (MVA) as a platform for pre-pandemic and pandemic influenza vaccines. Analytic hierarchy process (AHP) was applied to achieve pairwise comparisons among SWOT factors in order to prioritize them. Key opinion leaders (KOLs) in the influenza vaccine field were interviewed to collect a unique dataset to evaluate the market potential of this platform. The purpose of this study, to evaluate commercial potential of the MVA platform for the development of novel generation pandemic influenza vaccines, is accomplished by using a SWOT and AHP combined analytic method. Application of the SWOT–AHP model indicates that its strengths are considered more important by KOLs than its weaknesses, opportunities, and threats. Particularly, the inherent immunogenicity capability of MVA without the requirement of an adjuvant is the most important factor to increase commercial attractiveness of this platform. Concerns regarding vector vaccines and anti-vector immunity are considered its most important weakness, which might lower public health value of this platform. Furthermore, evaluation of the results of this study emphasizes equally important role that threats and opportunities of this platform play. This study further highlights unmet needs in the influenza vaccine market, which could be addressed by the implementation of the MVA platform. Broad use of MVA in clinical trials shows great promise for this vector as vaccine platform for pre-pandemic and pandemic influenza and threats by other respiratory viruses. Moreover, from the results of the clinical trials seem that MVA is particularly attractive for development of vaccines against pathogens for which no, or only insufficiently effective vaccines, are available. PMID:26048779

Market implementation of the MVA platform for pre-pandemic and pandemic influenza vaccines: A quantitative key opinion leader analysis.

PubMed

Ramezanpour, Bahar; Pronker, Esther S; Kreijtz, Joost H C M; Osterhaus, Albert D M E; Claassen, E

2015-08-20

A quantitative method is presented to rank strengths, weaknesses, opportunities, and threats (SWOT) of modified vaccinia virus Ankara (MVA) as a platform for pre-pandemic and pandemic influenza vaccines. Analytic hierarchy process (AHP) was applied to achieve pairwise comparisons among SWOT factors in order to prioritize them. Key opinion leaders (KOLs) in the influenza vaccine field were interviewed to collect a unique dataset to evaluate the market potential of this platform. The purpose of this study, to evaluate commercial potential of the MVA platform for the development of novel generation pandemic influenza vaccines, is accomplished by using a SWOT and AHP combined analytic method. Application of the SWOT-AHP model indicates that its strengths are considered more important by KOLs than its weaknesses, opportunities, and threats. Particularly, the inherent immunogenicity capability of MVA without the requirement of an adjuvant is the most important factor to increase commercial attractiveness of this platform. Concerns regarding vector vaccines and anti-vector immunity are considered its most important weakness, which might lower public health value of this platform. Furthermore, evaluation of the results of this study emphasizes equally important role that threats and opportunities of this platform play. This study further highlights unmet needs in the influenza vaccine market, which could be addressed by the implementation of the MVA platform. Broad use of MVA in clinical trials shows great promise for this vector as vaccine platform for pre-pandemic and pandemic influenza and threats by other respiratory viruses. Moreover, from the results of the clinical trials seem that MVA is particularly attractive for development of vaccines against pathogens for which no, or only insufficiently effective vaccines, are available. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modelling malaria control by introduction of larvivorous fish.

PubMed

Lou, Yijun; Zhao, Xiao-Qiang

2011-10-01

Malaria creates serious health and economic problems which call for integrated management strategies to disrupt interactions among mosquitoes, the parasite and humans. In order to reduce the intensity of malaria transmission, malaria vector control may be implemented to protect individuals against infective mosquito bites. As a sustainable larval control method, the use of larvivorous fish is promoted in some circumstances. To evaluate the potential impacts of this biological control measure on malaria transmission, we propose and investigate a mathematical model describing the linked dynamics between the host-vector interaction and the predator-prey interaction. The model, which consists of five ordinary differential equations, is rigorously analysed via theories and methods of dynamical systems. We derive four biologically plausible and insightful quantities (reproduction numbers) that completely determine the community composition. Our results suggest that the introduction of larvivorous fish can, in principle, have important consequences for malaria dynamics, but also indicate that this would require strong predators on larval mosquitoes. Integrated strategies of malaria control are analysed to demonstrate the biological application of our developed theory.

The Perfect Burrow, but for What? Identifying Local Habitat Conditions Promoting the Presence of the Host and Vector Species in the Kazakh Plague System

PubMed Central

Wilschut, Liesbeth; Addink, Elisabeth; Ageyev, Vladimir; Yeszhanov, Aidyn; Sapozhnikov, Valerij; Belayev, Alexander; Davydova, Tania; Eagle, Sally; Begon, Mike

2015-01-01

Introduction The wildlife plague system in the Pre-Balkhash desert of Kazakhstan has been a subject of study for many years. Much progress has been made in generating a method of predicting outbreaks of the disease (infection by the gram negative bacterium Yersinia pestis) but existing methods are not yet accurate enough to inform public health planning. The present study aimed to identify characteristics of individual mammalian host (Rhombomys opimus) burrows related to and potentially predictive of the presence of R.opimus and the dominant flea vectors (Xenopsylla spp.). Methods Over four seasons, burrow characteristics, their current occupancy status, and flea and tick burden of the occupants were recorded in the field. A second data set was generated of long term occupancy trends by recording the occupancy status of specific burrows over multiple occasions. Generalised linear mixed models were constructed to identify potential burrow properties predictive of either occupancy or flea burden. Results At the burrow level, it was identified that a burrow being occupied by Rhombomys, and remaining occupied, were both related to the characteristics of the sediment in which the burrow was constructed. The flea burden of Rhombomys in a burrow was found to be related to the tick burden. Further larger scale properties were also identified as being related to both Rhombomys and flea presence, including latitudinal position and the season. Conclusions Therefore, in advancing our current predictions of plague in Kazakhstan, we must consider the landscape at this local level to increase our accuracy in predicting the dynamics of gerbil and flea populations. Furthermore this demonstrates that in other zoonotic systems, it may be useful to consider the distribution and location of suitable habitat for both host and vector species at this fine scale to accurately predict future epizootics. PMID:26325073

A convergent 2D finite-difference scheme for the Dirac–Poisson system and the simulation of graphene

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

Brinkman, D., E-mail: Daniel.Brinkman@asu.edu; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287; Heitzinger, C., E-mail: Clemens.Heitzinger@asu.edu

2014-01-15

We present a convergent finite-difference scheme of second order in both space and time for the 2D electromagnetic Dirac equation. We apply this method in the self-consistent Dirac–Poisson system to the simulation of graphene. The model is justified for low energies, where the particles have wave vectors sufficiently close to the Dirac points. In particular, we demonstrate that our method can be used to calculate solutions of the Dirac–Poisson system where potentials act as beam splitters or Veselago lenses.

Investigations of medium wavelength magnetic anomalies in the eastern Pacific using MAGSAT data

NASA Technical Reports Server (NTRS)

Harrison, C. G. A. (Principal Investigator)

1981-01-01

The suitability of using magnetic field measurements obtained by MAGSAT is discussed with regard to resolving the medium wavelength anomaly problem. A procedure for removing the external field component from the measured field is outlined. Various methods of determining crustal magnetizations are examined in light of satellite orbital parameters resulting in the selection of the equivalent source technique for evaluating scalar measurements. A matrix inversion of the vector components is suggested as a method for arriving at a scalar potential representation of the field.

Isolation of infectious chikungunya virus and dengue virus using anionic polymer-coated magnetic beads.

PubMed

Patramool, Sirilaksana; Bernard, Eric; Hamel, Rodolphe; Natthanej, Luplertlop; Chazal, Nathalie; Surasombatpattana, Pornapat; Ekchariyawat, Peeraya; Daoust, Simon; Thongrungkiat, Supatra; Thomas, Frédéric; Briant, Laurence; Missé, Dorothée

2013-10-01

Mosquitoes-borne viruses are a major threat for human populations. Among them, chikungunya virus (CHIKV) and dengue virus (DENV) cause thousands of cases worldwide. The recent propagation of mosquito vectors competent to transmit these viruses to temperate areas increases their potential impact on susceptible human populations. The development of sensitive methods allowing the detection and isolation of infectious viruses is of crucial interest for determination of virus contamination in humans and in competent mosquito vectors. However, simple and rapid method allowing the capture of infectious CHIKV and DENV from samples with low viral titers useful for further genetic and functional characterization of circulating strains is lacking. The present study reports a fast and sensitive isolation technique based on viral particles adsorption on magnetic beads coated with anionic polymer, poly(methyl vinyl ether-maleic anhydrate) and suitable for isolation of infectious CHIKV and DENV from the four serotypes. Starting from quite reduced biological material, this method was accurate to combine with conventional detection techniques, including qRT-PCR and immunoblotting and allowed isolation of infectious particles without resorting to a step of cultivation. The use of polymer-coated magnetic beads is therefore of high interest for rapid detection and isolation of CHIKV and DENV from samples with reduced viral loads and represents an accurate approach for the surveillance of mosquito vector in area at risk for arbovirus outbreaks. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Adaptive compressive learning for prediction of protein-protein interactions from primary sequence.

PubMed

Zhang, Ya-Nan; Pan, Xiao-Yong; Huang, Yan; Shen, Hong-Bin

2011-08-21

Protein-protein interactions (PPIs) play an important role in biological processes. Although much effort has been devoted to the identification of novel PPIs by integrating experimental biological knowledge, there are still many difficulties because of lacking enough protein structural and functional information. It is highly desired to develop methods based only on amino acid sequences for predicting PPIs. However, sequence-based predictors are often struggling with the high-dimensionality causing over-fitting and high computational complexity problems, as well as the redundancy of sequential feature vectors. In this paper, a novel computational approach based on compressed sensing theory is proposed to predict yeast Saccharomyces cerevisiae PPIs from primary sequence and has achieved promising results. The key advantage of the proposed compressed sensing algorithm is that it can compress the original high-dimensional protein sequential feature vector into a much lower but more condensed space taking the sparsity property of the original signal into account. What makes compressed sensing much more attractive in protein sequence analysis is its compressed signal can be reconstructed from far fewer measurements than what is usually considered necessary in traditional Nyquist sampling theory. Experimental results demonstrate that proposed compressed sensing method is powerful for analyzing noisy biological data and reducing redundancy in feature vectors. The proposed method represents a new strategy of dealing with high-dimensional protein discrete model and has great potentiality to be extended to deal with many other complicated biological systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Japanese encephalitis: the vectors, ecology and potential for expansion.

PubMed

Pearce, James C; Learoyd, Tristan P; Langendorf, Benjamin J; Logan, James G

2018-05-01

Japanese encephalitis (JE) is a viral disease predominantly located in South East Asia and commonly associated with transmission between amplifying hosts, such as pigs, and the mosquito Culex tritaeniorhynchus, where human infection represents a dead end in the life cycle of the virus. The expansion of JE beyond an Asiatic confine is dependent on a multitude of complex factors that stem back to genetic subtype variation. A complex interplay of the genetic variation and vector competencies combine with variables such as geography, climate change and urbanization. Our understanding of JE is still at an early stage with long-term longitudinal vector surveillance necessary to better understand the dynamics of JE transmission and to characterize the role of potential secondary vectors such as Cx. pipiens and Cx. bitaeniorhynchus. The authors review the vectors indicated in transmission and the ecological, genetic and anthropological factors that affect the disease's range and epidemiology. Monitoring for the presence of JE virus in mosquitoes in general can be used to estimate levels of potential JE exposure, intensity of viral activity and genetic variation of JEV throughout surveyed areas. Increased surveillance and diagnosis of viral encephalitis caused by genotype 5 JE virus is required in particular, with the expansion in epidemiology and disease prevalence in new geographic areas an issue of great concern. Additional studies that measure the impact of vectors (e.g. bionomics and vector competence) in the transmission of JEV and that incorporate environmental factors (e.g. weekly rainfall) are needed to define the roles of Culex species in the viral pathogenesis during outbreak and non-outbreak years.

Method and system of filtering and recommending documents

DOEpatents

Patton, Robert M.; Potok, Thomas E.

2016-02-09

Disclosed is a method and system for discovering documents using a computer and providing a small set of the most relevant documents to the attention of a human observer. Using the method, the computer obtains a seed document from the user and generates a seed document vector using term frequency-inverse corpus frequency weighting. A keyword index for a plurality of source documents can be compared with the weighted terms of the seed document vector. The comparison is then filtered to reduce the number of documents, which define an initial subset of the source documents. Initial subset vectors are generated and compared to the seed document vector to obtain a similarity value for each comparison. Based on the similarity value, the method then recommends one or more of the source documents.

Extrapolation methods for vector sequences

NASA Technical Reports Server (NTRS)

Smith, David A.; Ford, William F.; Sidi, Avram

1987-01-01

This paper derives, describes, and compares five extrapolation methods for accelerating convergence of vector sequences or transforming divergent vector sequences to convergent ones. These methods are the scalar epsilon algorithm (SEA), vector epsilon algorithm (VEA), topological epsilon algorithm (TEA), minimal polynomial extrapolation (MPE), and reduced rank extrapolation (RRE). MPE and RRE are first derived and proven to give the exact solution for the right 'essential degree' k. Then, Brezinski's (1975) generalization of the Shanks-Schmidt transform is presented; the generalized form leads from systems of equations to TEA. The necessary connections are then made with SEA and VEA. The algorithms are extended to the nonlinear case by cycling, the error analysis for MPE and VEA is sketched, and the theoretical support for quadratic convergence is discussed. Strategies for practical implementation of the methods are considered.

Genetic shifting: a novel approach for controlling vector-borne diseases.

PubMed

Powell, Jeffrey R; Tabachnick, Walter J

2014-06-01

Rendering populations of vectors of diseases incapable of transmitting pathogens through genetic methods has long been a goal of vector geneticists. We outline a method to achieve this goal that does not involve the introduction of any new genetic variants to the target population. Rather we propose that shifting the frequencies of naturally occurring alleles that confer refractoriness to transmission can reduce transmission below a sustainable level. The program employs methods successfully used in plant and animal breeding. Because no artificially constructed genetically modified organisms (GMOs) are introduced into the environment, the method is minimally controversial. We use Aedes aegypti and dengue virus (DENV) for illustrative purposes but point out that the proposed program is generally applicable to vector-borne disease control. Copyright © 2014 Elsevier Ltd. All rights reserved.

A simple method for construction of artificial microRNA vector in plant.

PubMed

Li, Yang; Li, Yang; Zhao, Sunping; Zhong, Sheng; Wang, Zhaohai; Ding, Bo; Li, Yangsheng

2014-10-01

Artificial microRNA (amiRNA) is a powerful tool for silencing genes in many plant species. Here we provide an easy method to construct amiRNA vectors that reinvents the Golden Gate cloning approach and features a novel system called top speed amiRNA construction (TAC). This speedy approach accomplishes one restriction-ligation step in only 5 min, allowing easy and high-throughput vector construction. Three primers were annealed to be a specific adaptor, then digested and ligated on our novel vector pTAC. Importantly, this method allows the recombined amiRNA constructs to maintain the precursor of osa-miR528 with exception of the desired amiRNA/amiRNA* sequences. Using this method, our results showed the expected decrease of targeted genes in Nicotiana benthamiana and Oryza sativa.

Altered environment and risk of malaria outbreak in South Andaman, Andaman & Nicobar Islands, India affected by tsunami disaster

PubMed Central

Krishnamoorthy, Kaliannagoun; Jambulingam, Purushothaman; Natarajan, R; Shriram, AN; Das, Pradeep K; Sehgal, SC

2005-01-01

Background Pools of salt water and puddles created by giant waves from the sea due to the tsunami that occurred on 26th December 2004 would facilitate increased breeding of brackish water malaria vector, Anopheles sundaicus. Land uplifts in North Andaman and subsidence in South Andaman have been reported and subsidence may lead to environmental disturbances and vector proliferation. This warrants a situation analysis and vector surveillance in the tsunami hit areas endemic for malaria transmitted by brackish water mosquito, An. sundaicus to predict the risk of outbreak. Methods An extensive survey was carried out in the tsunami-affected areas in Andaman district of the Andaman and Nicobar Islands, India to assess the extent of breeding of malaria vectors in the habitats created by seawater flooding. Types of habitats in relation to source of seawater inundation and frequency were identified. The salinity of the water samples and the mosquito species present in the larval samples collected from these habitats were recorded. The malaria situation in the area was also analysed. Results South Andaman, covering Port Blair and Ferrargunj sub districts, is still under the recurring phenomenon of seawater intrusion either directly from the sea or through a network of creeks. Both daily cycles of high tides and periodical spring tides continue to cause flooding. Low-lying paddy fields and fallow land, with a salinity ranging from 3,000 to 42,505 ppm, were found to support profuse breeding of An. sundaicus, the local malaria vector, and Anopheles subpictus, a vector implicated elsewhere. This area is endemic for both vivax and falciparum malaria. Malaria slide positivity rate has started increasing during post-tsunami period, which can be considered as an indication of risk of malaria outbreak. Conclusion Paddy fields and fallow land with freshwater, hitherto not considered as potential sites for An. sundaicus, are now major breeding sites due to saline water. Consequently, there is a risk of vector abundance with enhanced malaria transmission potential, due to the vastness of these tsunami-created breeding grounds and likelihood of them becoming permanent due to continued flooding in view of land subsidence. The close proximity of the houses and paucity of cattle may lead to a higher degree of man/vector contact causing a threat of malaria outbreak in this densely populated area. Measures to prevent the possible outbreak of malaria in this tsunami-affected area are discussed. PMID:16029514

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

Efficient production of recombinant adeno-associated viral vector, serotype DJ/8, carrying the GFP gene.

PubMed

Hashimoto, Haruo; Mizushima, Tomoko; Chijiwa, Tsuyoshi; Nakamura, Masato; Suemizu, Hiroshi

2017-06-15

The purpose of this study was to establish an efficient method for the preparation of an adeno-associated viral (AAV), serotype DJ/8, carrying the GFP gene (AAV-DJ/8-GFP). We compared the yields of AAV-DJ/8 vector, which were produced by three different combination methods, consisting of two plasmid DNA transfection methods (lipofectamine and calcium phosphate co-precipitation; CaPi) and two virus DNA purification methods (iodixanol and cesium chloride; CsCl). The results showed that the highest yield of AAV-DJ/8-GFP vector was accomplished with the combination method of lipofectamine transfection and iodixanol purification. The viral protein expression levels and the transduction efficacy in HEK293 and CHO cells were not different among four different combination methods for AAV-DJ/8-GFP vectors. We confirmed that the AAV-DJ/8-GFP vector could transduce to human and murine hepatocyte-derived cell lines. These results show that AAV-DJ/8-GFP, purified by the combination of lipofectamine and iodixanol, produces an efficient yield without altering the characteristics of protein expression and AAV gene transduction. Copyright © 2017 Elsevier B.V. All rights reserved.

[The role of the Aedes aegypti vector in the epidemiology of dengue in Mexico].

PubMed

Fernández-Salas, I; Flores-Leal, A

1995-01-01

The role of Aedes aegypti (Lineo) in the epidemiology of dengue fever in Mexico is herein discussed based on the vectorial capacity model. Comments on the advantages and disadvantages of each model component at the time of field determinations are also presented. Emphasis is made on the impact of sampling and method bias on the results of vectorial capacity studies. The paper also addresses the need to increase vector biology knowledge as an input for epidemiological work to explain and predict dengue fever outbreaks. Comments on potential entomological variables not considered by the quantitative model are included. Finally, we elaborate on the introduction of Aedes albopictus (Skuse) in Mexico as a new risk factor and on its implications for the understanding of dengue fever transmission in Mexico.

Discrete Fourier Transform Analysis in a Complex Vector Space

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2009-01-01

Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.

Vector boson production in pPb and PbPb collisions at the LHC and its impact on nCTEQ15 PDFs

DOE PAGES

Kusina, A.; Lyonnet, F.; Clark, D. B.; ...

2017-07-21

Here, we provide a comprehensive comparison of W ±/Z vector boson production data in pPb and PbPb collisions at the LHC with predictions obtained using the nCTEQ15 PDFs. We also identify the measurements which have the largest potential impact on the PDFs, and estimate the effect of including these data using a Bayesian reweighting method. We find this data set can provide information as regards both the nuclear corrections and the heavy flavor (strange quark) PDF components. As for the proton, the parton flavor determination/separation is dependent on nuclear corrections (from heavy target DIS, for example), this information can alsomore » help improve the proton PDFs.« less

Vector boson production in pPb and PbPb collisions at the LHC and its impact on nCTEQ15 PDFs

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

Kusina, A.; Lyonnet, F.; Clark, D. B.

Here, we provide a comprehensive comparison of W ±/Z vector boson production data in pPb and PbPb collisions at the LHC with predictions obtained using the nCTEQ15 PDFs. We also identify the measurements which have the largest potential impact on the PDFs, and estimate the effect of including these data using a Bayesian reweighting method. We find this data set can provide information as regards both the nuclear corrections and the heavy flavor (strange quark) PDF components. As for the proton, the parton flavor determination/separation is dependent on nuclear corrections (from heavy target DIS, for example), this information can alsomore » help improve the proton PDFs.« less

State-vector formalism and the Legendre polynomial solution for modelling guided waves in anisotropic plates

NASA Astrophysics Data System (ADS)

Zheng, Mingfang; He, Cunfu; Lu, Yan; Wu, Bin

2018-01-01

We presented a numerical method to solve phase dispersion curve in general anisotropic plates. This approach involves an exact solution to the problem in the form of the Legendre polynomial of multiple integrals, which we substituted into the state-vector formalism. In order to improve the efficiency of the proposed method, we made a special effort to demonstrate the analytical methodology. Furthermore, we analyzed the algebraic symmetries of the matrices in the state-vector formalism for anisotropic plates. The basic feature of the proposed method was the expansion of field quantities by Legendre polynomials. The Legendre polynomial method avoid to solve the transcendental dispersion equation, which can only be solved numerically. This state-vector formalism combined with Legendre polynomial expansion distinguished the adjacent dispersion mode clearly, even when the modes were very close. We then illustrated the theoretical solutions of the dispersion curves by this method for isotropic and anisotropic plates. Finally, we compared the proposed method with the global matrix method (GMM), which shows excellent agreement.

A hybrid method for accurate star tracking using star sensor and gyros.

PubMed

Lu, Jiazhen; Yang, Lie; Zhang, Hao

2017-10-01

Star tracking is the primary operating mode of star sensors. To improve tracking accuracy and efficiency, a hybrid method using a star sensor and gyroscopes is proposed in this study. In this method, the dynamic conditions of an aircraft are determined first by the estimated angular acceleration. Under low dynamic conditions, the star sensor is used to measure the star vector and the vector difference method is adopted to estimate the current angular velocity. Under high dynamic conditions, the angular velocity is obtained by the calibrated gyros. The star position is predicted based on the estimated angular velocity and calibrated gyros using the star vector measurements. The results of the semi-physical experiment show that this hybrid method is accurate and feasible. In contrast with the star vector difference and gyro-assisted methods, the star position prediction result of the hybrid method is verified to be more accurate in two different cases under the given random noise of the star centroid.

Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

PubMed

Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

2014-11-01

Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates heterologous expression of large gene clusters for drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Long-lasting insecticide-treated house screens and targeted treatment of productive breeding-sites for dengue vector control in Acapulco, Mexico

PubMed Central

Che-Mendoza, Azael; Guillermo-May, Guillermo; Herrera-Bojórquez, Josué; Barrera-Pérez, Mario; Dzul-Manzanilla, Felipe; Gutierrez-Castro, Cipriano; Arredondo-Jiménez, Juan I.; Sánchez-Tejeda, Gustavo; Vazquez-Prokopec, Gonzalo; Ranson, Hilary; Lenhart, Audrey; Sommerfeld, Johannes; McCall, Philip J.; Kroeger, Axel; Manrique-Saide, Pablo

2015-01-01

Background Long-lasting insecticidal net screens (LLIS) fitted to domestic windows and doors in combination with targeted treatment (TT) of the most productive Aedes aegypti breeding sites were evaluated for their impact on dengue vector indices in a cluster-randomised trial in Mexico between 2011 and 2013. Methods Sequentially over 2 years, LLIS and TT were deployed in 10 treatment clusters (100 houses/cluster) and followed up over 24 months. Cross-sectional surveys quantified infestations of adult mosquitoes, immature stages at baseline (pre-intervention) and in four post-intervention samples at 6-monthly intervals. Identical surveys were carried out in 10 control clusters that received no treatment. Results LLIS clusters had significantly lower infestations compared to control clusters at 5 and 12 months after installation, as measured by adult (male and female) and pupal-based vector indices. After addition of TT to the intervention houses in intervention clusters, indices remained significantly lower in the treated clusters until 18 (immature and adult stage indices) and 24 months (adult indices only) post-intervention. Conclusions These safe, simple affordable vector control tools were well-accepted by study participants and are potentially suitable in many regions at risk from dengue worldwide. PMID:25604761

Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application

NASA Astrophysics Data System (ADS)

Miao, Xijiang; Mukhopadhyay, Rishi; Valafar, Homayoun

2008-10-01

Advances in NMR instrumentation and pulse sequence design have resulted in easier acquisition of Residual Dipolar Coupling (RDC) data. However, computational and theoretical analysis of this type of data has continued to challenge the international community of investigators because of their complexity and rich information content. Contemporary use of RDC data has required a-priori assignment, which significantly increases the overall cost of structural analysis. This article introduces a novel algorithm that utilizes unassigned RDC data acquired from multiple alignment media ( nD-RDC, n ⩾ 3) for simultaneous extraction of the relative order tensor matrices and reconstruction of the interacting vectors in space. Estimation of the relative order tensors and reconstruction of the interacting vectors can be invaluable in a number of endeavors. An example application has been presented where the reconstructed vectors have been used to quantify the fitness of a template protein structure to the unknown protein structure. This work has other important direct applications such as verification of the novelty of an unknown protein and validation of the accuracy of an available protein structure model in drug design. More importantly, the presented work has the potential to bridge the gap between experimental and computational methods of structure determination.

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

PubMed Central

Li, Yushuang; Yang, Jiasheng; Zhang, Yi

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector. PMID:27918587

f(R) gravity on non-linear scales: the post-Friedmann expansion and the vector potential

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

Thomas, D.B.; Bruni, M.; Koyama, K.

2015-07-01

Many modified gravity theories are under consideration in cosmology as the source of the accelerated expansion of the universe and linear perturbation theory, valid on the largest scales, has been examined in many of these models. However, smaller non-linear scales offer a richer phenomenology with which to constrain modified gravity theories. Here, we consider the Hu-Sawicki form of f(R) gravity and apply the post-Friedmann approach to derive the leading order equations for non-linear scales, i.e. the equations valid in the Newtonian-like regime. We reproduce the standard equations for the scalar field, gravitational slip and the modified Poisson equation in amore » coherent framework. In addition, we derive the equation for the leading order correction to the Newtonian regime, the vector potential. We measure this vector potential from f(R) N-body simulations at redshift zero and one, for two values of the f{sub R{sub 0}} parameter. We find that the vector potential at redshift zero in f(R) gravity can be close to 50% larger than in GR on small scales for |f{sub R{sub 0}}|=1.289 × 10{sup −5}, although this is less for larger scales, earlier times and smaller values of the f{sub R{sub 0}} parameter. Similarly to in GR, the small amplitude of this vector potential suggests that the Newtonian approximation is highly accurate for f(R) gravity, and also that the non-linear cosmological behaviour of f(R) gravity can be completely described by just the scalar potentials and the f(R) field.« less

Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination.

PubMed

Kim, Junho; Maeng, Ju Heon; Lim, Jae Seok; Son, Hyeonju; Lee, Junehawk; Lee, Jeong Ho; Kim, Sangwoo

2016-10-15

Advances in sequencing technologies have remarkably lowered the detection limit of somatic variants to a low frequency. However, calling mutations at this range is still confounded by many factors including environmental contamination. Vector contamination is a continuously occurring issue and is especially problematic since vector inserts are hardly distinguishable from the sample sequences. Such inserts, which may harbor polymorphisms and engineered functional mutations, can result in calling false variants at corresponding sites. Numerous vector-screening methods have been developed, but none could handle contamination from inserts because they are focusing on vector backbone sequences alone. We developed a novel method-Vecuum-that identifies vector-originated reads and resultant false variants. Since vector inserts are generally constructed from intron-less cDNAs, Vecuum identifies vector-originated reads by inspecting the clipping patterns at exon junctions. False variant calls are further detected based on the biased distribution of mutant alleles to vector-originated reads. Tests on simulated and spike-in experimental data validated that Vecuum could detect 93% of vector contaminants and could remove up to 87% of variant-like false calls with 100% precision. Application to public sequence datasets demonstrated the utility of Vecuum in detecting false variants resulting from various types of external contamination. Java-based implementation of the method is available at http://vecuum.sourceforge.net/ CONTACT: swkim@yuhs.acSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions.

PubMed

Harris, Frank E

2016-05-28

Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance rij. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validated by showing that they yield correct results for a large number of integrals published by other investigators.

Symbolic computer vector analysis

NASA Technical Reports Server (NTRS)

Stoutemyer, D. R.

1977-01-01

A MACSYMA program is described which performs symbolic vector algebra and vector calculus. The program can combine and simplify symbolic expressions including dot products and cross products, together with the gradient, divergence, curl, and Laplacian operators. The distribution of these operators over sums or products is under user control, as are various other expansions, including expansion into components in any specific orthogonal coordinate system. There is also a capability for deriving the scalar or vector potential of a vector field. Examples include derivation of the partial differential equations describing fluid flow and magnetohydrodynamics, for 12 different classic orthogonal curvilinear coordinate systems.

Harmonic reduction of Direct Torque Control of six-phase induction motor.

PubMed

Taheri, A

2016-07-01

In this paper, a new switching method in Direct Torque Control (DTC) of a six-phase induction machine for reduction of current harmonics is introduced. Selecting a suitable vector in each sampling period is an ordinal method in the ST-DTC drive of a six-phase induction machine. The six-phase induction machine has 64 voltage vectors and divided further into four groups. In the proposed DTC method, the suitable voltage vectors are selected from two vector groups. By a suitable selection of two vectors in each sampling period, the harmonic amplitude is decreased more, in and various comparison to that of the ST-DTC drive. The harmonics loss is greater reduced, while the electromechanical energy is decreased with switching loss showing a little increase. Spectrum analysis of the phase current in the standard and new switching table DTC of the six-phase induction machine and determination for the amplitude of each harmonics is proposed in this paper. The proposed method has a less sampling time in comparison to the ordinary method. The Harmonic analyses of the current in the low and high speed shows the performance of the presented method. The simplicity of the proposed method and its implementation without any extra hardware is other advantages of the proposed method. The simulation and experimental results show the preference of the proposed method. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Alpharetroviral Vector-mediated Gene Therapy for X-CGD: Functional Correction and Lack of Aberrant Splicing

PubMed Central

Kaufmann, Kerstin B.; Brendel, Christian; Suerth, Julia D.; Mueller-Kuller, Uta; Chen-Wichmann, Linping; Schwäble, Joachim; Pahujani, Shweta; Kunkel, Hana; Schambach, Axel; Baum, Christopher; Grez, Manuel

2013-01-01

Comparative integrome analysis has revealed that the most neutral integration pattern among retroviruses is attributed to alpharetroviruses. We chose X-linked chronic granulomatous disease (X-CGD) as model to evaluate the potential of self-inactivating (SIN) alpharetroviral vectors for gene therapy of monogenic diseases. Therefore, we combined the alpharetroviral vector backbone with the elongation factor-1α short promoter, both considered to possess a low genotoxic profile, to drive transgene (gp91phox) expression. Following efficient transduction transgene expression was sustained and provided functional correction of the CGD phenotype in a cell line model at low vector copy number. Further analysis in a murine X-CGD transplantation model revealed gene-marking of bone marrow cells and oxidase positive granulocytes in peripheral blood. Transduction of human X-CGD CD34+ cells provided functional correction up to wild-type levels and long-term expression upon transplantation into a humanized mouse model. In contrast to lentiviral vectors, no aberrantly spliced transcripts containing cellular exons fused to alpharetroviral sequences were found in transduced cells, implying that the safety profile of alpharetroviral vectors may extend beyond their neutral integration profile. Taken together, this highlights the potential of this SIN alpharetroviral system as a platform for new candidate vectors for future gene therapy of hematopoietic disorders. PMID:23207695

Challenges in predicting climate and environmental effects on vector-borne disease episystems in a changing world.

PubMed

Tabachnick, W J

2010-03-15

Vector-borne pathogens cause enormous suffering to humans and animals. Many are expanding their range into new areas. Dengue, West Nile and Chikungunya have recently caused substantial human epidemics. Arthropod-borne animal diseases like Bluetongue, Rift Valley fever and African horse sickness pose substantial threats to livestock economies around the world. Climate change can impact the vector-borne disease epidemiology. Changes in climate will influence arthropod vectors, their life cycles and life histories, resulting in changes in both vector and pathogen distribution and changes in the ability of arthropods to transmit pathogens. Climate can affect the way pathogens interact with both the arthropod vector and the human or animal host. Predicting and mitigating the effects of future changes in the environment like climate change on the complex arthropod-pathogen-host epidemiological cycle requires understanding of a variety of complex mechanisms from the molecular to the population level. Although there has been substantial progress on many fronts the challenges to effectively understand and mitigate the impact of potential changes in the environment on vector-borne pathogens are formidable and at an early stage of development. The challenges will be explored using several arthropod-borne pathogen systems as illustration, and potential avenues to meet the challenges will be presented.

Biosafety challenges for use of lentiviral vectors in gene therapy.

PubMed

Rothe, Michael; Modlich, Ute; Schambach, Axel

2013-12-01

Lentiviral vectors are promising tools for the genetic modification of cells in biomedical research and gene therapy. Their use in recent clinical trials for the treatment of adrenoleukodystrophy, β-thalassemia, Wiskott-Aldrich- Syndrome and metachromatic leukodystrophy underlined their efficacy for therapies especially in case of hereditary diseases. In comparison to gammaretroviral LTR-driven vectors, which were employed in the first clinical trials, lentiviral vectors present with some favorable features like the ability to transduce also non-dividing cells and a potentially safer insertion profile. However, genetic modification with viral vectors in general and stable integration of the therapeutic gene into the host cell genome bear concerns with respect to different levels of personal or environmental safety. Among them, insertional mutagenesis by enhancer mediated dysregulation of neighboring genes or aberrant splicing is still the biggest concern. However, also risks like immunogenicity of vector particles, the phenotoxicity of the transgene and potential vertical or horizontal transmission by replication competent retroviruses need to be taken into account. This review will give an overview on biosafety aspects that are relevant to the use of lentiviral vectors for genetic modification and gene therapy. Furthermore, assay systems aiming at evaluating biosafety in preclinical settings and recent promising clinical trials including efforts of monitoring of patients after gene therapy will be discussed.

Invasive mutualisms between a plant pathogen and insect vectors in the Middle East and Brazil

PubMed Central

Queiroz, Renan Batista; Silva, Fábio Nascimento; Al-Mahmmoli, Issa Hashil; Al-Sadi, Abdullah Mohammed; Carvalho, Claudine Márcia; Elliot, Simon L.

2016-01-01

Complex multi-trophic interactions in vectorborne diseases limit our understanding and ability to predict outbreaks. Arthropod-vectored pathogens are especially problematic, with the potential for novel interspecific interactions during invasions. Variations and novelties in plant–arthropod–pathogen triumvirates present significant threats to global food security. We examined aspects of a phytoplasma pathogen of citrus across two continents. ‘Candidatus Phytoplasma aurantifolia’ causes Witches' Broom Disease of Lime (WBDL) and has devastated citrus production in the Middle East. A variant of this phytoplasma currently displays asymptomatic or ‘silent’ infections in Brazil. We first studied vector capacity and fitness impacts of the pathogen on its vectors. The potential for co-occurring weed species to act as pathogen reservoirs was analysed and key transmission periods in the year were also studied. We demonstrate that two invasive hemipteran insects—Diaphorina citri and Hishimonus phycitis—can vector the phytoplasma. Feeding on phytoplasma-infected hosts greatly increased reproduction of its invasive vector D. citri both in Oman and Brazil; suggesting that increased fitness of invasive insect vectors thereby further increases the pathogen's capacity to spread. Based on our findings, this is a robust system for studying the effects of invasions on vectorborne diseases and highlights concerns about its spread to warmer, drier regions of Brazil. PMID:28083099

Harnessing mosquito-Wolbachia symbiosis for vector and disease control.

PubMed

Bourtzis, Kostas; Dobson, Stephen L; Xi, Zhiyong; Rasgon, Jason L; Calvitti, Maurizio; Moreira, Luciano A; Bossin, Hervé C; Moretti, Riccardo; Baton, Luke Anthony; Hughes, Grant L; Mavingui, Patrick; Gilles, Jeremie R L

2014-04-01

Mosquito species, members of the genera Aedes, Anopheles and Culex, are the major vectors of human pathogens including protozoa (Plasmodium sp.), filariae and of a variety of viruses (causing dengue, chikungunya, yellow fever, West Nile). There is lack of efficient methods and tools to treat many of the diseases caused by these major human pathogens, since no efficient vaccines or drugs are available; even in malaria where insecticide use and drug therapies have reduced incidence, 219 million cases still occurred in 2010. Therefore efforts are currently focused on the control of vector populations. Insecticides alone are insufficient to control mosquito populations since reduced susceptibility and even resistance is being observed more and more frequently. There is also increased concern about the toxic effects of insecticides on non-target (even beneficial) insect populations, on humans and the environment. During recent years, the role of symbionts in the biology, ecology and evolution of insect species has been well-documented and has led to suggestions that they could potentially be used as tools to control pests and therefore diseases. Wolbachia is perhaps the most renowned insect symbiont, mainly due to its ability to manipulate insect reproduction and to interfere with major human pathogens thus providing new avenues for pest control. We herein present recent achievements in the field of mosquito-Wolbachia symbiosis with an emphasis on Aedes albopictus. We also discuss how Wolbachia symbiosis can be harnessed for vector control as well as the potential to combine the sterile insect technique and Wolbachia-based approaches for the enhancement of population suppression programs. Copyright © 2013 International Atomic Energy Agency 2013. Published by Elsevier B.V. All rights reserved.

A tool box for operational mosquito larval control: preliminary results and early lessons from the Urban Malaria Control Programme in Dar es Salaam, Tanzania

PubMed Central

Fillinger, Ulrike; Kannady, Khadija; William, George; Vanek, Michael J; Dongus, Stefan; Nyika, Dickson; Geissbühler, Yvonne; Chaki, Prosper P; Govella, Nico J; Mathenge, Evan M; Singer, Burton H; Mshinda, Hassan; Lindsay, Steven W; Tanner, Marcel; Mtasiwa, Deo; de Castro, Marcia C; Killeen, Gerry F

2008-01-01

Background As the population of Africa rapidly urbanizes, large populations could be protected from malaria by controlling aquatic stages of mosquitoes if cost-effective and scalable implementation systems can be designed. Methods A recently initiated Urban Malaria Control Programme in Dar es Salaam delegates responsibility for routine mosquito control and surveillance to modestly-paid community members, known as Community-Owned Resource Persons (CORPs). New vector surveillance, larviciding and management systems were designed and evaluated in 15 city wards to allow timely collection, interpretation and reaction to entomologic monitoring data using practical procedures that rely on minimal technology. After one year of baseline data collection, operational larviciding with Bacillus thuringiensis var. israelensis commenced in March 2006 in three selected wards. Results The procedures and staff management systems described greatly improved standards of larval surveillance relative to that reported at the outset of this programme. In the first year of the programme, over 65,000 potential Anopheles habitats were surveyed by 90 CORPs on a weekly basis. Reaction times to vector surveillance at observations were one day, week and month at ward, municipal and city levels, respectively. One year of community-based larviciding reduced transmission by the primary malaria vector, Anopheles gambiae s.l., by 31% (95% C.I. = 21.6–37.6%; p = 0.04). Conclusion This novel management, monitoring and evaluation system for implementing routine larviciding of malaria vectors in African cities has shown considerable potential for sustained, rapidly responsive, data-driven and affordable application. Nevertheless, the true programmatic value of larviciding in urban Africa can only be established through longer-term programmes which are stably financed and allow the operational teams and management infrastructures to mature by learning from experience. PMID:18218148

Absence of haemosporidian parasite infections in the long-lived Cory's shearwater: evidence from molecular analyses and review of the literature.

PubMed

Campioni, Letizia; Martínez-de la Puente, Josué; Figuerola, Jordi; Granadeiro, José Pedro; Silva, Mónica C; Catry, Paulo

2018-01-01

The apparent scarcity or absence of blood parasites in some avian groups, such as seabirds, has been related to intrinsic and extrinsic factors including host immunological capacity, host-parasite assemblage, and ecological parameters, but also to reduced sensitivity of some methods to detect low parasite prevalence/intensities of infection. Here, we examined the haemosporidian parasite prevalence in a breeding population of Cory's shearwater Calonectris diomedea borealis, a long-distance migrant seabird, nesting in the Macaronesian region, in the Eastern Atlantic. Previous studies on Calonectris diomedea complex were based on small sample sizes providing weak evidence for a lack of infections by haemoparasites. Here, we investigated the presence of both parasite infections in C. d. borealis and larvae of potential mosquito vectors on the area. By employing a PCR-based assay, we extensively examined the prevalence of blood parasites belonging to the genera Plasmodium, Haemoproteus, and Leucocytozoon in 286 individuals from different life stages (i.e., chicks, immatures, sabbatical, and breeding adults), facing their specific energetic trade-offs (immunological functions vs. life history activities). We sampled immatures and adult shearwaters, of different sexes, ages, and migratory origins, from two sub-colonies. None of the sampled individuals were infected by these parasites, supporting the hypothesis that there was no in situ or ex situ transmission of vector-borne parasites in marine habitats irrespective of host's life stage and in spite of the presence of the potential Plasmodium vector Culiseta longiareolata breeding in the area. These results suggest that the lack of transmission of haemosporidian parasites on Selvagem Grande may be related to the lack of suitable dipteran vectors at the study sites, which may result from the geographic isolation of this area.

Engaging scientists: An online survey exploring the experience of innovative biotechnological approaches to controlling vector-borne diseases.

PubMed

Boëte, Christophe; Beisel, Uli; Reis Castro, Luísa; Césard, Nicolas; Reeves, R Guy

2015-08-10

Pioneering technologies (e.g., nanotechnology, synthetic biology or climate engineering) are often associated with potential new risks and uncertainties that can become sources of controversy. The communication of information during their development and open exchanges between stakeholders is generally considered a key issue in their acceptance. While the attitudes of the public to novel technologies have been widely considered there has been relatively little investigation of the perceptions and awareness of scientists working on human or animal diseases transmitted by arthropods. Consequently, we conducted a global survey on 1889 scientists working on aspects of vector-borne diseases, exploring, under the light of a variety of demographic and professional factors, their knowledge and awareness of an emerging biotechnology that has the potential to revolutionize the control of pest insect populations. Despite extensive media coverage of key developments (including releases of manipulated mosquitoes into human communities) this has in only one instance resulted in scientist awareness exceeding 50% on a national or regional scale. We document that awareness of pioneering releases significantly relied on private communication sources that were not equally accessible to scientists from countries with endemic vector-borne diseases (dengue and malaria). In addition, we provide quantitative analysis of the perceptions and knowledge of specific biotechnological approaches to controlling vector-borne disease, which are likely to impact the way in which scientists around the world engage in the debate about their value. Our results indicate that there is scope to strengthen already effective methods of communication, in addition to a strong demand by scientists (expressed by 79.9% of respondents) to develop new, creative modes of public engagement.

Assessing the importance of four sandfly species (Diptera: Psychodidae) as vectors of Leishmania mexicana in Campeche, Mexico.

PubMed

Pech-May, A; Peraza-Herrera, G; Moo-Llanes, D A; Escobedo-Ortegón, J; Berzunza-Cruz, M; Becker-Fauser, I; Montes DE Oca-Aguilar, A C; Rebollar-Téllez, E A

2016-09-01

Localized cutaneous leishmaniasis represents a public health problem in many areas of Mexico, especially in the Yucatan Peninsula. An understanding of vector ecology and bionomics is of great importance in evaluations of the transmission dynamics of Leishmania parasites. A field study was conducted in the county of Calakmul, state of Campeche, during the period from November 2006 to March 2007. Phlebotomine sandfly vectors were sampled using Centers for Disease Control light traps, baited Disney traps and Shannon traps. A total of 3374 specimens were captured in the two villages of Once de Mayo (93.8%) and Arroyo Negro (6.1%). In Once de Mayo, the most abundant species were Psathyromyia shannoni, Lutzomyia cruciata, Bichromomyia olmeca olmeca and Psychodopygus panamensis (all: Diptera: Psychodidae). The Shannon trap was by far the most efficient method of collection. The infection rate, as determined by Leishmania mexicana-specific polymerase chain reaction, was 0.3% in Once de Mayo and infected sandflies included Psy. panamensis, B. o. olmeca and Psa. shannoni. There were significant differences in human biting rates across sandfly species and month of sampling. Ecological niche modelling analyses showed an overall overlap of 39.1% for the four species in the whole state of Campeche. In addition, the finding of nine vector-reservoir pairs indicates a potential interaction. The roles of the various sandfly vectors in Calakmul are discussed. © 2016 The Royal Entomological Society.

New perspectives in tracing vector-borne interaction networks.

PubMed

Gómez-Díaz, Elena; Figuerola, Jordi

2010-10-01

Disentangling trophic interaction networks in vector-borne systems has important implications in epidemiological and evolutionary studies. Molecular methods based on bloodmeal typing in vectors have been increasingly used to identify hosts. Although most molecular approaches benefit from good specificity and sensitivity, their temporal resolution is limited by the often rapid digestion of blood, and mixed bloodmeals still remain a challenge for bloodmeal identification in multi-host vector systems. Stable isotope analyses represent a novel complementary tool that can overcome some of these problems. The utility of these methods using examples from different vector-borne systems are discussed and the extents to which they are complementary and versatile are highlighted. There are excellent opportunities for progress in the study of vector-borne transmission networks resulting from the integration of both molecular and stable isotope approaches. Copyright © 2010 Elsevier Ltd. All rights reserved.

Reprogramming Methods Do Not Affect Gene Expression Profile of Human Induced Pluripotent Stem Cells.

PubMed

Trevisan, Marta; Desole, Giovanna; Costanzi, Giulia; Lavezzo, Enrico; Palù, Giorgio; Barzon, Luisa

2017-01-20

Induced pluripotent stem cells (iPSCs) are pluripotent cells derived from adult somatic cells. After the pioneering work by Yamanaka, who first generated iPSCs by retroviral transduction of four reprogramming factors, several alternative methods to obtain iPSCs have been developed in order to increase the yield and safety of the process. However, the question remains open on whether the different reprogramming methods can influence the pluripotency features of the derived lines. In this study, three different strategies, based on retroviral vectors, episomal vectors, and Sendai virus vectors, were applied to derive iPSCs from human fibroblasts. The reprogramming efficiency of the methods based on episomal and Sendai virus vectors was higher than that of the retroviral vector-based approach. All human iPSC clones derived with the different methods showed the typical features of pluripotent stem cells, including the expression of alkaline phosphatase and stemness maker genes, and could give rise to the three germ layer derivatives upon embryoid bodies assay. Microarray analysis confirmed the presence of typical stem cell gene expression profiles in all iPSC clones and did not identify any significant difference among reprogramming methods. In conclusion, the use of different reprogramming methods is equivalent and does not affect gene expression profile of the derived human iPSCs.

A SIMPLIFIED MODEL FOR PREDICTING MALARIA ENTOMOLOGIC INOCULATION RATES BASED ON ENTOMOLOGIC AND PARASITOLOGIC PARAMETERS RELEVANT TO CONTROL

PubMed Central

KILLEEN, GERRY F.; McKENZIE, F. ELLIS; FOY, BRIAN D.; SCHIEFFELIN, CATHERINE; BILLINGSLEY, PETER F.; BEIER, JOHN C.

2008-01-01

Malaria transmission intensity is modeled from the starting perspective of individual vector mosquitoes and is expressed directly as the entomologic inoculation rate (EIR). The potential of individual mosquitoes to transmit malaria during their lifetime is presented graphically as a function of their feeding cycle length and survival, human biting preferences, and the parasite sporogonic incubation period. The EIR is then calculated as the product of 1) the potential of individual vectors to transmit malaria during their lifetime, 2) vector emergence rate relative to human population size, and 3) the infectiousness of the human population to vectors. Thus, impacts on more than one of these parameters will amplify each other’s effects. The EIRs transmitted by the dominant vector species at four malaria-endemic sites from Papua New Guinea, Tanzania, and Nigeria were predicted using field measurements of these characteristics together with human biting rate and human reservoir infectiousness. This model predicted EIRs (± SD) that are 1.13 ± 0.37 (range = 0.84–1.59) times those measured in the field. For these four sites, mosquito emergence rate and lifetime transmission potential were more important determinants of the EIR than human reservoir infectiousness. This model and the input parameters from the four sites allow the potential impacts of various control measures on malaria transmission intensity to be tested under a range of endemic conditions. The model has potential applications for the development and implementation of transmission control measures and for public health education. PMID:11289661

Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

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

Li, Jun; Jiang, Bin; Guo, Hua, E-mail: hguo@unm.edu

2013-11-28

A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resultingmore » in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.« less

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Malaria vector control: from past to future.

PubMed

Raghavendra, Kamaraju; Barik, Tapan K; Reddy, B P Niranjan; Sharma, Poonam; Dash, Aditya P

2011-04-01

Malaria is one of the most common vector-borne diseases widespread in the tropical and subtropical regions. Despite considerable success of malaria control programs in the past, malaria still continues as a major public health problem in several countries. Vector control is an essential part for reducing malaria transmission and became less effective in recent years, due to many technical and administrative reasons, including poor or no adoption of alternative tools. Of the different strategies available for vector control, the most successful are indoor residual spraying and insecticide-treated nets (ITNs), including long-lasting ITNs and materials. Earlier DDT spray has shown spectacular success in decimating disease vectors but resulted in development of insecticide resistance, and to control the resistant mosquitoes, organophosphates, carbamates, and synthetic pyrethroids were introduced in indoor residual spraying with needed success but subsequently resulted in the development of widespread multiple insecticide resistance in vectors. Vector control in many countries still use insecticides in the absence of viable alternatives. Few developments for vector control, using ovitraps, space spray, biological control agents, etc., were encouraging when used in limited scale. Likewise, recent introduction of safer vector control agents, such as insect growth regulators, biocontrol agents, and natural plant products have yet to gain the needed scale of utility for vector control. Bacterial pesticides are promising and are effective in many countries. Environmental management has shown sufficient promise for vector control and disease management but still needs advocacy for inter-sectoral coordination and sometimes are very work-intensive. The more recent genetic manipulation and sterile insect techniques are under development and consideration for use in routine vector control and for these, standardized procedures and methods are available but need thorough understanding of biology, ethical considerations, and sufficiently trained manpower for implementation being technically intensive methods. All the methods mentioned in the review that are being implemented or proposed for implementation needs effective inter-sectoral coordination and community participation. The latest strategy is evolution-proof insecticides that include fungal biopesticides, Wolbachia, and Denso virus that essentially manipulate the life cycle of the mosquitoes were found effective but needs more research. However, for effective vector control, integrated vector management methods, involving use of combination of effective tools, is needed and is also suggested by Global Malaria Control Strategy. This review article raises issues associated with the present-day vector control strategies and state opportunities with a focus on ongoing research and recent advances to enable to sustain the gains achieved so far.

Improvements in Block-Krylov Ritz Vectors and the Boundary Flexibility Method of Component Synthesis

NASA Technical Reports Server (NTRS)

Carney, Kelly Scott

1997-01-01

A method of dynamic substructuring is presented which utilizes a set of static Ritz vectors as a replacement for normal eigenvectors in component mode synthesis. This set of Ritz vectors is generated in a recurrence relationship, proposed by Wilson, which has the form of a block-Krylov subspace. The initial seed to the recurrence algorithm is based upon the boundary flexibility vectors of the component. Improvements have been made in the formulation of the initial seed to the Krylov sequence, through the use of block-filtering. A method to shift the Krylov sequence to create Ritz vectors that will represent the dynamic behavior of the component at target frequencies, the target frequency being determined by the applied forcing functions, has been developed. A method to terminate the Krylov sequence has also been developed. Various orthonormalization schemes have been developed and evaluated, including the Cholesky/QR method. Several auxiliary theorems and proofs which illustrate issues in component mode synthesis and loss of orthogonality in the Krylov sequence have also been presented. The resulting methodology is applicable to both fixed and free- interface boundary components, and results in a general component model appropriate for any type of dynamic analysis. The accuracy is found to be comparable to that of component synthesis based upon normal modes, using fewer generalized coordinates. In addition, the block-Krylov recurrence algorithm is a series of static solutions and so requires significantly less computation than solving the normal eigenspace problem. The requirement for less vectors to form the component, coupled with the lower computational expense of calculating these Ritz vectors, combine to create a method more efficient than traditional component mode synthesis.

Stationary states of fermions in a sign potential with a mixed vector–scalar coupling

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

Castilho, W.M., E-mail: castilho.w@gmail.com; Castro, A.S. de, E-mail: castro@pq.cnpq.br

2014-01-15

The scattering of a fermion in the background of a sign potential is considered with a general mixing of vector and scalar Lorentz structures with the scalar coupling stronger than or equal to the vector coupling under the Sturm–Liouville perspective. When the vector coupling and the scalar coupling have different magnitudes, an isolated solution shows that the fermion under a strong potential can be trapped in a highly localized region without manifestation of Klein’s paradox. It is also shown that the lonely bound-state solution disappears asymptotically as one approaches the conditions for the realization of spin and pseudospin symmetries. --more » Highlights: •Scattering of fermions in a sign potential assessed under a Sturm–Liouville perspective. •An isolated bounded solution. •No pair production despite the high localization. •No bounded solution under exact spin and pseudospin symmetries.« less

Role of nonthermal electron on the dynamics of relativistic electromagnetic soliton in the interaction of laser-plasma

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

Rostampooran, Shabnam; Dorranian, Davoud, E-mail: doran@srbiau.ac.ir

A system of nonlinear one-dimensional equations of the electron hydrodynamics with Maxwell's equations was developed to describe electromagnetic (EM) solitons in plasma with nonthermal electrons. Equation of vector potential was derived in relativistic regime by implementing the multiple scales technique, and their solitonic answers were introduced. The allowed regions for bright and dark electromagnetic solitons were discussed in detail. Roles of number density of nonthermal electrons, temperature of electrons, and frequency of fast participate of vector potential on the Sagdeev potential and properties of EM soliton were investigated. Results show that with increasing the number of nonthermal electrons, the amplitudemore » of vector potential of bright solitons increases. By increasing the number of nonthermal electrons, dark EM solitons may be changed to bright solitons. Increasing the energy of nonthermal electrons leads to generation of high amplitude solitons.« less

Pseudacteon decapitating flies (Diptera: Phoridae): Are they potential vectors of the fire ant pathogens Kneallhazia(=Thelohania)solenopsae (Microsporidia: Thelohaniidae)and Vairimorpha invictae (Microsporidia: Burenellidae)?

USDA-ARS?s Scientific Manuscript database

Fire ant decapitating flies in the genus Pseudacteon were tested for their potential as hosts or vectors of two microsporidian pathogens of the red imported fire ant, Solenopsis invicta. Decapitating flies which attacked or were reared from S. invicta workers infected by Kneallhazia (=Thelohania)...

SSM/I and ECMWF Wind Vector Comparison

NASA Technical Reports Server (NTRS)

Wentz, Frank J.; Ashcroft, Peter D.

1996-01-01

Wentz was the first to convincingly show that satellite microwave radiometers have the potential to measure the oceanic wind vector. The most compelling evidence for this conclusion was the monthly wind vector maps derived solely from a statistical analysis of Special Sensor Microwave Imager (SSM/I) observations. In a qualitative sense, these maps clearly showed the general circulation over the world's oceans. In this report we take a closer look at the SSM/I monthly wind vector maps and compare them to European Center for Medium-Range Weather Forecasts (ECMWF) wind fields. This investigation leads both to an empirical comparison of SSM/I calculated wind vectors with ECMWF wind vectors, and to an examination of possible reasons that the SSM/I calculated wind vector direction would be inherently more reliable at some locations than others.

Predicting and mapping malaria under climate change scenarios: the potential redistribution of malaria vectors in Africa.

PubMed

Tonnang, Henri E Z; Kangalawe, Richard Y M; Yanda, Pius Z

2010-04-23

Malaria is rampant in Africa and causes untold mortality and morbidity. Vector-borne diseases are climate sensitive and this has raised considerable concern over the implications of climate change on future disease risk. The problem of malaria vectors (Anopheles mosquitoes) shifting from their traditional locations to invade new zones is an important concern. The vision of this study was to exploit the sets of information previously generated by entomologists, e.g. on geographical range of vectors and malaria distribution, to build models that will enable prediction and mapping the potential redistribution of Anopheles mosquitoes in Africa. The development of the modelling tool was carried out through calibration of CLIMEX parameters. The model helped estimate the potential geographical distribution and seasonal abundance of the species in relation to climatic factors. These included temperature, rainfall and relative humidity, which characterized the living environment for Anopheles mosquitoes. The same parameters were used in determining the ecoclimatic index (EI). The EI values were exported to a GIS package for special analysis and proper mapping of the potential future distribution of Anopheles gambiae and Anophles arabiensis within the African continent under three climate change scenarios. These results have shown that shifts in these species boundaries southward and eastward of Africa may occur rather than jumps into quite different climatic environments. In the absence of adequate control, these predictions are crucial in understanding the possible future geographical range of the vectors and the disease, which could facilitate planning for various adaptation options. Thus, the outputs from this study will be helpful at various levels of decision making, for example, in setting up of an early warning and sustainable strategies for climate change and climate change adaptation for malaria vectors control programmes in Africa.

Tailless Vectored Fighters Theory. Laboratory and Flight Tests, Including Vectorable Inlets/Nozzles and Tailless Flying Models vs. Pilot’s Tolerances Affecting Maximum Post-Stall Vectoring Agility.

DTIC Science & Technology

1991-07-01

nose bodyj Top view of velocity probe PropllerRotating shaft ’V Generator Aerodynamic shape like a small elevator RPV’s attitude Irrespctiveduring...28 Part It: Maximizing Thrust-Vectoring Control Power and Agility Metrics ............ 29 Laboratory & Flight...8217Ideal Standards’ - Ba- ror maximizing PST-TV-aglilty/rIlght-control power , iI - Extracting new TV-potentials to further reduce any righter’s optical

[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.

Novel method of finding extreme edges in a convex set of N-dimension vectors

NASA Astrophysics Data System (ADS)

Hu, Chia-Lun J.

2001-11-01

As we published in the last few years, for a binary neural network pattern recognition system to learn a given mapping {Um mapped to Vm, m=1 to M} where um is an N- dimension analog (pattern) vector, Vm is a P-bit binary (classification) vector, the if-and-only-if (IFF) condition that this network can learn this mapping is that each i-set in {Ymi, m=1 to M} (where Ymithere existsVmiUm and Vmi=+1 or -1, is the i-th bit of VR-m).)(i=1 to P and there are P sets included here.) Is POSITIVELY, LINEARLY, INDEPENDENT or PLI. We have shown that this PLI condition is MORE GENERAL than the convexity condition applied to a set of N-vectors. In the design of old learning machines, we know that if a set of N-dimension analog vectors form a convex set, and if the machine can learn the boundary vectors (or extreme edges) of this set, then it can definitely learn the inside vectors contained in this POLYHEDRON CONE. This paper reports a new method and new algorithm to find the boundary vectors of a convex set of ND analog vectors.