Implicity restarted Arnoldi/Lanczos methods for large scale eigenvalue calculations

NASA Technical Reports Server (NTRS)

Sorensen, Danny C.

1996-01-01

Eigenvalues and eigenfunctions of linear operators are important to many areas of applied mathematics. The ability to approximate these quantities numerically is becoming increasingly important in a wide variety of applications. This increasing demand has fueled interest in the development of new methods and software for the numerical solution of large-scale algebraic eigenvalue problems. In turn, the existence of these new methods and software, along with the dramatically increased computational capabilities now available, has enabled the solution of problems that would not even have been posed five or ten years ago. Until very recently, software for large-scale nonsymmetric problems was virtually non-existent. Fortunately, the situation is improving rapidly. The purpose of this article is to provide an overview of the numerical solution of large-scale algebraic eigenvalue problems. The focus will be on a class of methods called Krylov subspace projection methods. The well-known Lanczos method is the premier member of this class. The Arnoldi method generalizes the Lanczos method to the nonsymmetric case. A recently developed variant of the Arnoldi/Lanczos scheme called the Implicitly Restarted Arnoldi Method is presented here in some depth. This method is highlighted because of its suitability as a basis for software development.

The Riemann-Lanczos equations in general relativity and their integrability

NASA Astrophysics Data System (ADS)

Dolan, P.; Gerber, A.

2008-06-01

The aim of this paper is to examine the Riemann-Lanczos equations and how they can be made integrable. They consist of a system of linear first-order partial differential equations that arise in general relativity, whereby the Riemann curvature tensor is generated by an unknown third-order tensor potential field called the Lanczos tensor. Our approach is based on the theory of jet bundles, where all field variables and all their partial derivatives of all relevant orders are treated as independent variables alongside the local manifold coordinates (xa) on the given space-time manifold M. This approach is adopted in (a) Cartan's method of exterior differential systems, (b) Vessiot's dual method using vector field systems, and (c) the Janet-Riquier theory of systems of partial differential equations. All three methods allow for the most general situations under which integrability conditions can be found. They give equivalent results, namely, that involutivity is always achieved at all generic points of the jet manifold M after a finite number of prolongations. Two alternative methods that appear in the general relativity literature to find integrability conditions for the Riemann-Lanczos equations generate new partial differential equations for the Lanczos potential that introduce a source term, which is nonlinear in the components of the Riemann tensor. We show that such sources do not occur when either of method (a), (b), or (c) are used.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures.

PubMed

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)PRBMDO0163-182910.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)PRLTAO0031-900710.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S=1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

NASA Astrophysics Data System (ADS)

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003), 10.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013), 10.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S =1 /2 , we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Two aspects of black hole entropy in Lanczos-Lovelock models of gravity

NASA Astrophysics Data System (ADS)

Kolekar, Sanved; Kothawala, Dawood; Padmanabhan, T.

2012-03-01

We consider two specific approaches to evaluate the black hole entropy which are known to produce correct results in the case of Einstein’s theory and generalize them to Lanczos-Lovelock models. In the first approach (which could be called extrinsic), we use a procedure motivated by earlier work by Pretorius, Vollick, and Israel, and by Oppenheim, and evaluate the entropy of a configuration of densely packed gravitating shells on the verge of forming a black hole in Lanczos-Lovelock theories of gravity. We find that this matter entropy is not equal to (it is less than) Wald entropy, except in the case of Einstein theory, where they are equal. The matter entropy is proportional to the Wald entropy if we consider a specific mth-order Lanczos-Lovelock model, with the proportionality constant depending on the spacetime dimensions D and the order m of the Lanczos-Lovelock theory as (D-2m)/(D-2). Since the proportionality constant depends on m, the proportionality between matter entropy and Wald entropy breaks down when we consider a sum of Lanczos-Lovelock actions involving different m. In the second approach (which could be called intrinsic), we generalize a procedure, previously introduced by Padmanabhan in the context of general relativity, to study off-shell entropy of a class of metrics with horizon using a path integral method. We consider the Euclidean action of Lanczos-Lovelock models for a class of metrics off shell and interpret it as a partition function. We show that in the case of spherically symmetric metrics, one can interpret the Euclidean action as the free energy and read off both the entropy and energy of a black hole spacetime. Surprisingly enough, this leads to exactly the Wald entropy and the energy of the spacetime in Lanczos-Lovelock models obtained by other methods. We comment on possible implications of the result.

Accurate numerical solution of the Helmholtz equation by iterative Lanczos reduction.

PubMed

Ratowsky, R P; Fleck, J A

1991-06-01

The Lanczos recursion algorithm is used to determine forward-propagating solutions for both the paraxial and Helmholtz wave equations for longitudinally invariant refractive indices. By eigenvalue analysis it is demonstrated that the method gives extremely accurate solutions to both equations.

A complex guided spectral transform Lanczos method for studying quantum resonance states

DOE PAGES

Yu, Hua-Gen

2014-12-28

A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos (cFOL) polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the originalmore » Hamiltonian in the spectral range of interest. Therefore the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO₂, and compared to previous calculations.« less

An implementation of the look-ahead Lanczos algorithm for non-Hermitian matrices, part 2

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noel M.

1990-01-01

It is shown how the look-ahead Lanczos process (combined with a quasi-minimal residual QMR) approach) can be used to develop a robust black box solver for large sparse non-Hermitian linear systems. Details of an implementation of the resulting QMR algorithm are presented. It is demonstrated that the QMR method is closely related to the biconjugate gradient (BCG) algorithm; however, unlike BCG, the QMR algorithm has smooth convergence curves and good numerical properties. We report numerical experiments with our implementation of the look-ahead Lanczos algorithm, both for eigenvalue problem and linear systems. Also, program listings of FORTRAN implementations of the look-ahead algorithm and the QMR method are included.

Cucheb: A GPU implementation of the filtered Lanczos procedure

NASA Astrophysics Data System (ADS)

Aurentz, Jared L.; Kalantzis, Vassilis; Saad, Yousef

2017-11-01

This paper describes the software package Cucheb, a GPU implementation of the filtered Lanczos procedure for the solution of large sparse symmetric eigenvalue problems. The filtered Lanczos procedure uses a carefully chosen polynomial spectral transformation to accelerate convergence of the Lanczos method when computing eigenvalues within a desired interval. This method has proven particularly effective for eigenvalue problems that arise in electronic structure calculations and density functional theory. We compare our implementation against an equivalent CPU implementation and show that using the GPU can reduce the computation time by more than a factor of 10. Program Summary Program title: Cucheb Program Files doi:http://dx.doi.org/10.17632/rjr9tzchmh.1 Licensing provisions: MIT Programming language: CUDA C/C++ Nature of problem: Electronic structure calculations require the computation of all eigenvalue-eigenvector pairs of a symmetric matrix that lie inside a user-defined real interval. Solution method: To compute all the eigenvalues within a given interval a polynomial spectral transformation is constructed that maps the desired eigenvalues of the original matrix to the exterior of the spectrum of the transformed matrix. The Lanczos method is then used to compute the desired eigenvectors of the transformed matrix, which are then used to recover the desired eigenvalues of the original matrix. The bulk of the operations are executed in parallel using a graphics processing unit (GPU). Runtime: Variable, depending on the number of eigenvalues sought and the size and sparsity of the matrix. Additional comments: Cucheb is compatible with CUDA Toolkit v7.0 or greater.

New Parallel Algorithms for Structural Analysis and Design of Aerospace Structures

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.

1998-01-01

Subspace and Lanczos iterations have been developed, well documented, and widely accepted as efficient methods for obtaining p-lowest eigen-pair solutions of large-scale, practical engineering problems. The focus of this paper is to incorporate recent developments in vectorized sparse technologies in conjunction with Subspace and Lanczos iterative algorithms for computational enhancements. Numerical performance, in terms of accuracy and efficiency of the proposed sparse strategies for Subspace and Lanczos algorithm, is demonstrated by solving for the lowest frequencies and mode shapes of structural problems on the IBM-R6000/590 and SunSparc 20 workstations.

Quantum and electromagnetic propagation with the conjugate symmetric Lanczos method.

PubMed

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

2008-02-14

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

A structure preserving Lanczos algorithm for computing the optical absorption spectrum

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

Shao, Meiyue; Jornada, Felipe H. da; Lin, Lin

2016-11-16

We present a new structure preserving Lanczos algorithm for approximating the optical absorption spectrum in the context of solving full Bethe-Salpeter equation without Tamm-Dancoff approximation. The new algorithm is based on a structure preserving Lanczos procedure, which exploits the special block structure of Bethe-Salpeter Hamiltonian matrices. A recently developed technique of generalized averaged Gauss quadrature is incorporated to accelerate the convergence. We also establish the connection between our structure preserving Lanczos procedure with several existing Lanczos procedures developed in different contexts. Numerical examples are presented to demonstrate the effectiveness of our Lanczos algorithm.

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

NASA Astrophysics Data System (ADS)

Shao, Meiyue; Aktulga, H. Metin; Yang, Chao; Ng, Esmond G.; Maris, Pieter; Vary, James P.

2018-01-01

We describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. The use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. We also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.

Implementation details of the coupled QMR algorithm

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noel M.

1992-01-01

The original quasi-minimal residual method (QMR) relies on the three-term look-ahead Lanczos process, to generate basis vectors for the underlying Krylov subspaces. However, empirical observations indicate that, in finite precision arithmetic, three-term vector recurrences are less robust than mathematically equivalent coupled two-term recurrences. Therefore, we recently proposed a new implementation of the QMR method based on a coupled two-term look-ahead Lanczos procedure. In this paper, we describe implementation details of this coupled QMR algorithm, and we present results of numerical experiments.

Stiffness-generated rigid-body mode shapes for Lanczos eigensolution with SUPORT DOF by way of a MSC/NASTRAN DMAP alter

NASA Technical Reports Server (NTRS)

Abdallah, Ayman A.; Barnett, Alan R.; Widrick, Timothy W.; Manella, Richard T.; Miller, Robert P.

1994-01-01

When using all MSC/NASTRAN eigensolution methods except Lanczos, the analyst can replace the coupled system rigid-body modes calculated within DMAP module READ with mass orthogonalized and normalized rigid-body modes generated from the system stiffness. This option is invoked by defining MSC/NASTRAN r-set degrees of freedom via the SUPORT bulk data card. The newly calculated modes are required if the rigid-body modes calculated by the eigensolver are not 'clean' due to numerical roundoffs in the solution. When performing transient structural dynamic load analysis, the numerical roundoffs can result in inaccurate rigid-body accelerations which affect steady-state responses. Unfortunately, when using the Lanczos method and defining r-set degrees of freedom, the rigid-body modes calculated within DMAP module REIGL are retained. To overcome this limitation and to allow MSC/NASTRAN to handle SUPORT degrees of freedom identically for all eigensolvers, a DMAP Alter has been written which replaces Lanczos-calculated rigid-body modes with stiffness-generated rigid-body modes. The newly generated rigid-body modes are normalized with respect to the system mass and orthogonalized using the Gram-Schmidt technique. This algorithm has been implemented as an enhancement to an existing coupled loads methodology.

An implementation of the QMR method based on coupled two-term recurrences

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noeel M.

1992-01-01

The authors have proposed a new Krylov subspace iteration, the quasi-minimal residual algorithm (QMR), for solving non-Hermitian linear systems. In the original implementation of the QMR method, the Lanczos process with look-ahead is used to generate basis vectors for the underlying Krylov subspaces. In the Lanczos algorithm, these basis vectors are computed by means of three-term recurrences. It has been observed that, in finite precision arithmetic, vector iterations based on three-term recursions are usually less robust than mathematically equivalent coupled two-term vector recurrences. This paper presents a look-ahead algorithm that constructs the Lanczos basis vectors by means of coupled two-term recursions. Implementation details are given, and the look-ahead strategy is described. A new implementation of the QMR method, based on this coupled two-term algorithm, is described. A simplified version of the QMR algorithm without look-ahead is also presented, and the special case of QMR for complex symmetric linear systems is considered. Results of numerical experiments comparing the original and the new implementations of the QMR method are reported.

Properties of highly frustrated magnetic molecules studied by the finite-temperature Lanczos method

NASA Astrophysics Data System (ADS)

Schnack, J.; Wendland, O.

2010-12-01

The very interesting magnetic properties of frustrated magnetic molecules are often hardly accessible due to the prohibitive size of the related Hilbert spaces. The finite-temperature Lanczos method is able to treat spin systems for Hilbert space sizes up to 109. Here we first demonstrate for exactly solvable systems that the method is indeed accurate. Then we discuss the thermal properties of one of the biggest magnetic molecules synthesized to date, the icosidodecahedron with antiferromagnetically coupled spins of s = 1/2. We show how genuine quantum features such as the magnetization plateau behave as a function of temperature.

The Weyl-Lanczos equations and the Lanczos wave equation in four dimensions as systems in involution

NASA Astrophysics Data System (ADS)

Dolan, P.; Gerber, A.

2003-07-01

The Weyl-Lanczos equations in four dimensions form a system in involution. We compute its Cartan characters explicitly and use Janet-Riquier theory to confirm the results in the case of all space-times with a diagonal metric tensor and for the plane wave limit of space-times. We write the Lanczos wave equation as an exterior differential system and, with assistance from Janet-Riquier theory, we compute its Cartan characters and find that it forms a system in involution. We compare these Cartan characters with those of the Weyl-Lanczos equations. All results hold for the real analytic case.

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

DOE PAGES

Shao, Meiyue; Aktulga, H.  Metin; Yang, Chao; ...

2017-09-14

In this paper, we describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. Themore » use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. Finally, we also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.« less

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

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

Shao, Meiyue; Aktulga, H.  Metin; Yang, Chao

In this paper, we describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. Themore » use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. Finally, we also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.« less

Eigenvalue routines in NASTRAN: A comparison with the Block Lanczos method

NASA Technical Reports Server (NTRS)

Tischler, V. A.; Venkayya, Vipperla B.

1993-01-01

The NASA STRuctural ANalysis (NASTRAN) program is one of the most extensively used engineering applications software in the world. It contains a wealth of matrix operations and numerical solution techniques, and they were used to construct efficient eigenvalue routines. The purpose of this paper is to examine the current eigenvalue routines in NASTRAN and to make efficiency comparisons with a more recent implementation of the Block Lanczos algorithm by Boeing Computer Services (BCS). This eigenvalue routine is now available in the BCS mathematics library as well as in several commercial versions of NASTRAN. In addition, CRAY maintains a modified version of this routine on their network. Several example problems, with a varying number of degrees of freedom, were selected primarily for efficiency bench-marking. Accuracy is not an issue, because they all gave comparable results. The Block Lanczos algorithm was found to be extremely efficient, in particular, for very large size problems.

Unsymmetric Lanczos model reduction and linear state function observer for flexible structures

NASA Technical Reports Server (NTRS)

Su, Tzu-Jeng; Craig, Roy R., Jr.

1991-01-01

This report summarizes part of the research work accomplished during the second year of a two-year grant. The research, entitled 'Application of Lanczos Vectors to Control Design of Flexible Structures' concerns various ways to use Lanczos vectors and Krylov vectors to obtain reduced-order mathematical models for use in the dynamic response analyses and in control design studies. This report presents a one-sided, unsymmetric block Lanczos algorithm for model reduction of structural dynamics systems with unsymmetric damping matrix, and a control design procedure based on the theory of linear state function observers to design low-order controllers for flexible structures.

A Thick-Restart Lanczos Algorithm with Polynomial Filtering for Hermitian Eigenvalue Problems

DOE PAGES

Li, Ruipeng; Xi, Yuanzhe; Vecharynski, Eugene; ...

2016-08-16

Polynomial filtering can provide a highly effective means of computing all eigenvalues of a real symmetric (or complex Hermitian) matrix that are located in a given interval, anywhere in the spectrum. This paper describes a technique for tackling this problem by combining a thick-restart version of the Lanczos algorithm with deflation ("locking'') and a new type of polynomial filter obtained from a least-squares technique. Furthermore, the resulting algorithm can be utilized in a “spectrum-slicing” approach whereby a very large number of eigenvalues and associated eigenvectors of the matrix are computed by extracting eigenpairs located in different subintervals independently from onemore » another.« less

An application of the discrete-time Toda lattice to the progressive algorithm by Lanczos and related problems

NASA Astrophysics Data System (ADS)

Nakamura, Yoshimasa; Sekido, Hiroto

2018-04-01

The finite or the semi-infinite discrete-time Toda lattice has many applications to various areas in applied mathematics. The purpose of this paper is to review how the Toda lattice appears in the Lanczos algorithm through the quotient-difference algorithm and its progressive form (pqd). Then a multistep progressive algorithm (MPA) for solving linear systems is presented. The extended Lanczos parameters can be given not by computing inner products of the extended Lanczos vectors but by using the pqd algorithm with highly relative accuracy in a lower cost. The asymptotic behavior of the pqd algorithm brings us some applications of MPA related to eigenvectors.

Conjugate gradient type methods for linear systems with complex symmetric coefficient matrices

NASA Technical Reports Server (NTRS)

Freund, Roland

1989-01-01

We consider conjugate gradient type methods for the solution of large sparse linear system Ax equals b with complex symmetric coefficient matrices A equals A(T). Such linear systems arise in important applications, such as the numerical solution of the complex Helmholtz equation. Furthermore, most complex non-Hermitian linear systems which occur in practice are actually complex symmetric. We investigate conjugate gradient type iterations which are based on a variant of the nonsymmetric Lanczos algorithm for complex symmetric matrices. We propose a new approach with iterates defined by a quasi-minimal residual property. The resulting algorithm presents several advantages over the standard biconjugate gradient method. We also include some remarks on the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

A novel derivation of the boundary term for the action in Lanczos-Lovelock gravity

NASA Astrophysics Data System (ADS)

Chakraborty, Sumanta; Parattu, Krishnamohan; Padmanabhan, T.

2017-09-01

We present a novel derivation of the boundary term for the action in Lanczos-Lovelock gravity, starting from the boundary contribution in the variation of the Lanczos-Lovelock action. The derivation presented here is straightforward, i.e., one starts from the Lanczos-Lovelock action principle and the action itself dictates the boundary structure and hence the boundary term one needs to add to the action to make it well-posed. It also gives the full structure of the contribution at the boundary of the complete action, enabling us to read off the degrees of freedom to be fixed at the boundary, their corresponding conjugate momenta and the total derivative contribution on the boundary. We also provide a separate derivation of the Gauss-Bonnet case.

Application of Lanczos vectors to control design of flexible structures

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.; Su, Tzu-Jeng

1990-01-01

This report covers research conducted during the first year of the two-year grant. The research, entitled 'Application of Lanczos Vectors to Control Design of Flexible Structures' concerns various ways to obtain reduced-order mathematical models for use in dynamic response analyses and in control design studies. This report summarizes research described in several reports and papers that were written under this contract. Extended abstracts are presented for technical papers covering the following topics: controller reduction by preserving impulse response energy; substructuring decomposition and controller synthesis; model reduction methods for structural control design; and recent literature on structural modeling, identification, and analysis.

Resolving the issue of branched Hamiltonian in modified Lanczos-Lovelock gravity

NASA Astrophysics Data System (ADS)

Ruz, Soumendranath; Mandal, Ranajit; Debnath, Subhra; Sanyal, Abhik Kumar

2016-07-01

The Hamiltonian constraint H_c = N{H} = 0, defines a diffeomorphic structure on spatial manifolds by the lapse function N in general theory of relativity. However, it is not manifest in Lanczos-Lovelock gravity, since the expression for velocity in terms of the momentum is multivalued. Thus the Hamiltonian is a branch function of momentum. Here we propose an extended theory of Lanczos-Lovelock gravity to construct a unique Hamiltonian in its minisuperspace version, which results in manifest diffeomorphic invariance and canonical quantization.

A LSQR-type method provides a computationally efficient automated optimal choice of regularization parameter in diffuse optical tomography.

PubMed

Prakash, Jaya; Yalavarthy, Phaneendra K

2013-03-01

Developing a computationally efficient automated method for the optimal choice of regularization parameter in diffuse optical tomography. The least-squares QR (LSQR)-type method that uses Lanczos bidiagonalization is known to be computationally efficient in performing the reconstruction procedure in diffuse optical tomography. The same is effectively deployed via an optimization procedure that uses the simplex method to find the optimal regularization parameter. The proposed LSQR-type method is compared with the traditional methods such as L-curve, generalized cross-validation (GCV), and recently proposed minimal residual method (MRM)-based choice of regularization parameter using numerical and experimental phantom data. The results indicate that the proposed LSQR-type and MRM-based methods performance in terms of reconstructed image quality is similar and superior compared to L-curve and GCV-based methods. The proposed method computational complexity is at least five times lower compared to MRM-based method, making it an optimal technique. The LSQR-type method was able to overcome the inherent limitation of computationally expensive nature of MRM-based automated way finding the optimal regularization parameter in diffuse optical tomographic imaging, making this method more suitable to be deployed in real-time.

Realization of preconditioned Lanczos and conjugate gradient algorithms on optical linear algebra processors.

PubMed

Ghosh, A

1988-08-01

Lanczos and conjugate gradient algorithms are important in computational linear algebra. In this paper, a parallel pipelined realization of these algorithms on a ring of optical linear algebra processors is described. The flow of data is designed to minimize the idle times of the optical multiprocessor and the redundancy of computations. The effects of optical round-off errors on the solutions obtained by the optical Lanczos and conjugate gradient algorithms are analyzed, and it is shown that optical preconditioning can improve the accuracy of these algorithms substantially. Algorithms for optical preconditioning and results of numerical experiments on solving linear systems of equations arising from partial differential equations are discussed. Since the Lanczos algorithm is used mostly with sparse matrices, a folded storage scheme to represent sparse matrices on spatial light modulators is also described.

Quasi-Newton parallel geometry optimization methods

NASA Astrophysics Data System (ADS)

Burger, Steven K.; Ayers, Paul W.

2010-07-01

Algorithms for parallel unconstrained minimization of molecular systems are examined. The overall framework of minimization is the same except for the choice of directions for updating the quasi-Newton Hessian. Ideally these directions are chosen so the updated Hessian gives steps that are same as using the Newton method. Three approaches to determine the directions for updating are presented: the straightforward approach of simply cycling through the Cartesian unit vectors (finite difference), a concurrent set of minimizations, and the Lanczos method. We show the importance of using preconditioning and a multiple secant update in these approaches. For the Lanczos algorithm, an initial set of directions is required to start the method, and a number of possibilities are explored. To test the methods we used the standard 50-dimensional analytic Rosenbrock function. Results are also reported for the histidine dipeptide, the isoleucine tripeptide, and cyclic adenosine monophosphate. All of these systems show a significant speed-up with the number of processors up to about eight processors.

Reducing Memory Cost of Exact Diagonalization using Singular Value Decomposition

NASA Astrophysics Data System (ADS)

Weinstein, Marvin; Chandra, Ravi; Auerbach, Assa

2012-02-01

We present a modified Lanczos algorithm to diagonalize lattice Hamiltonians with dramatically reduced memory requirements. In contrast to variational approaches and most implementations of DMRG, Lanczos rotations towards the ground state do not involve incremental minimizations, (e.g. sweeping procedures) which may get stuck in false local minima. The lattice of size N is partitioned into two subclusters. At each iteration the rotating Lanczos vector is compressed into two sets of nsvd small subcluster vectors using singular value decomposition. For low entanglement entropy See, (satisfied by short range Hamiltonians), the truncation error is bounded by (-nsvd^1/See). Convergence is tested for the Heisenberg model on Kagom'e clusters of 24, 30 and 36 sites, with no lattice symmetries exploited, using less than 15GB of dynamical memory. Generalization of the Lanczos-SVD algorithm to multiple partitioning is discussed, and comparisons to other techniques are given. Reference: arXiv:1105.0007

A Shifted Block Lanczos Algorithm 1: The Block Recurrence

NASA Technical Reports Server (NTRS)

Grimes, Roger G.; Lewis, John G.; Simon, Horst D.

1990-01-01

In this paper we describe a block Lanczos algorithm that is used as the key building block of a software package for the extraction of eigenvalues and eigenvectors of large sparse symmetric generalized eigenproblems. The software package comprises: a version of the block Lanczos algorithm specialized for spectrally transformed eigenproblems; an adaptive strategy for choosing shifts, and efficient codes for factoring large sparse symmetric indefinite matrices. This paper describes the algorithmic details of our block Lanczos recurrence. This uses a novel combination of block generalizations of several features that have only been investigated independently in the past. In particular new forms of partial reorthogonalization, selective reorthogonalization and local reorthogonalization are used, as is a new algorithm for obtaining the M-orthogonal factorization of a matrix. The heuristic shifting strategy, the integration with sparse linear equation solvers and numerical experience with the code are described in a companion paper.

Accurate solution of the Helmholtz equation by Lanczos orthogonalization for media with loss or gain.

PubMed

Ratowsky, R P; Fleck, J A; Feit, M D

1992-01-01

The numerical scheme for solving the Helmholtz equation, based on the Lanczos orthogonalization scheme, is generalized so that it can be applied to media with space-dependent absorption or gain profiles.

An extended basis inexact shift-invert Lanczos for the efficient solution of large-scale generalized eigenproblems

NASA Astrophysics Data System (ADS)

Rewieński, M.; Lamecki, A.; Mrozowski, M.

2013-09-01

This paper proposes a technique, based on the Inexact Shift-Invert Lanczos (ISIL) method with Inexact Jacobi Orthogonal Component Correction (IJOCC) refinement, and a preconditioned conjugate-gradient (PCG) linear solver with multilevel preconditioner, for finding several eigenvalues for generalized symmetric eigenproblems. Several eigenvalues are found by constructing (with the ISIL process) an extended projection basis. Presented results of numerical experiments confirm the technique can be effectively applied to challenging, large-scale problems characterized by very dense spectra, such as resonant cavities with spatial dimensions which are large with respect to wavelengths of the resonating electromagnetic fields. It is also shown that the proposed scheme based on inexact linear solves delivers superior performance, as compared to methods which rely on exact linear solves, indicating tremendous potential of the 'inexact solve' concept. Finally, the scheme which generates an extended projection basis is found to provide a cost-efficient alternative to classical deflation schemes when several eigenvalues are computed.

LANZ: Software solving the large sparse symmetric generalized eigenproblem

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1990-01-01

A package, LANZ, for solving the large symmetric generalized eigenproblem is described. The package was tested on four different architectures: Convex 200, CRAY Y-MP, Sun-3, and Sun-4. The package uses a Lanczos' method and is based on recent research into solving the generalized eigenproblem.

Avoiding Communication in the Lanczos Bidiagonalization Routine and Associated Least Squares QR Solver

DTIC Science & Technology

2015-04-12

Avoiding communication in the Lanczos bidiagonalization routine and associated Least Squares QR solver Erin Carson Electrical Engineering and...Bidiagonalization Routine and Associated Least Squares QR Solver 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...throughout scienti c codes , are often the bottlenecks in application perfor- mance due to a low computation/communication ratio. In this paper we develop

Dynamic Restarting Schemes for Eigenvalue Problems

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

Wu, Kesheng; Simon, Horst D.

1999-03-10

In studies of restarted Davidson method, a dynamic thick-restart scheme was found to be excellent in improving the overall effectiveness of the eigen value method. This paper extends the study of the dynamic thick-restart scheme to the Lanczos method for symmetric eigen value problems and systematically explore a range of heuristics and strategies. We conduct a series of numerical tests to determine their relative strength and weakness on a class of electronic structure calculation problems.

Numerically Exact Calculation of Rovibrational Levels of Cl^-H_2O

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2014-06-01

Large amplitude vibrations of Van der Waals clusters are important because they reveal large regions of a potential energy surface (PES). To calculate spectra of Van der Waals clusters it is common to use an adiabatic approximation. When coupling between intra- and inter-molecular coordinates is important non-adiabatic coupling cannot be neglected and it is therefore critical to develop and test theoretical methods that couple both types of coordinates. We have developed new product basis and contracted basis Lanczos methods for Van der Waals complexes and tested them by computing rovibrational energy levels of Cl^-H_2O. The new product basis is made of functions of the inter-monomer distance, Wigner functions that depend on Euler angles specifying the orientation of H_2O with respect to a frame attached to the inter-monomer Jacobi vector, basis functions for H_2O vibration, and Wigner functions that depend on Euler angles specifying the orientation of the inter-monomer Jacobi vector with respect to a space-fixed frame. An advantage of this product basis is that it can be used to make an efficient contracted basis by replacing the vibrational basis functions for the monomer with monomer vibrational wavefunctions. Due to weak coupling between intra- and inter-molecular coordinates, only a few tens of monomer vibrational wavefunctions are necessary. The validity of the two new methods is established by comparing energy levels with benchmark rovibrational levels obtained with polyspherical coordinates and spherical harmonic type basis functions. For all bases, product structure is exploited to calculate eigenvalues with the Lanczos algorithm. For Cl^-H_2O, we are able, for the first time, to compute accurate splittings due to tunnelling between the two equivalent C_s minima. We use the PES of Rheinecker and Bowman (RB). Our results are in good agreement with experiment for the five fundamental bands observed. J. Rheinecker and J. M. Bowman, J. Chem. Phys. 124 131102 (2006) J. Rheinecker and J. M. Bowman, J. Chem. Phys. 125 133206 (2006)} S. Horvath, A. B. McCoy, B. M. Elliott, G. H. Weddle, J. R. Roscioli, and M. A. Johnson J. Phys. Chem. A 114 1556 (2010)

Application of Lanczos vectors to control design of flexible structures, part 2

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.; Su, Tzu-Jeng

1992-01-01

This report covers the period of the grant from January 1991 until its expiration in June 1992. Together with an Interim Report (Ref. 9), it summarizes the research conducted under NASA Grant NAG9-357 on the topic 'Application of Lanczos Vectors to Control Design of Flexible Structures.' The research concerns various ways to obtain reduced-order mathematical models of complex structures for use in dynamics analysis and in the design of control systems for these structures. This report summarizes the research.

Implementation of a block Lanczos algorithm for Eigenproblem solution of gyroscopic systems

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.; Lawson, Charles L.

1987-01-01

The details of implementation of a general numerical procedure developed for the accurate and economical computation of natural frequencies and associated modes of any elastic structure rotating along an arbitrary axis are described. A block version of the Lanczos algorithm is derived for the solution that fully exploits associated matrix sparsity and employs only real numbers in all relevant computations. It is also capable of determining multiple roots and proves to be most efficient when compared to other, similar, exisiting techniques.

Lanczos eigensolution method for high-performance computers

NASA Technical Reports Server (NTRS)

Bostic, Susan W.

1991-01-01

The theory, computational analysis, and applications are presented of a Lanczos algorithm on high performance computers. The computationally intensive steps of the algorithm are identified as: the matrix factorization, the forward/backward equation solution, and the matrix vector multiples. These computational steps are optimized to exploit the vector and parallel capabilities of high performance computers. The savings in computational time from applying optimization techniques such as: variable band and sparse data storage and access, loop unrolling, use of local memory, and compiler directives are presented. Two large scale structural analysis applications are described: the buckling of a composite blade stiffened panel with a cutout, and the vibration analysis of a high speed civil transport. The sequential computational time for the panel problem executed on a CONVEX computer of 181.6 seconds was decreased to 14.1 seconds with the optimized vector algorithm. The best computational time of 23 seconds for the transport problem with 17,000 degs of freedom was on the the Cray-YMP using an average of 3.63 processors.

A Posteriori Error Analysis and Uncertainty Quantification for Adaptive Multiscale Operator Decomposition Methods for Multiphysics Problems

DTIC Science & Technology

2013-06-24

Barrier methods for critical exponent problems in geometric analysis and mathematical physics, J. Erway and M. Hoist, Submitted for publication . • Finite...1996. [20] C. LANCZOS, Linear Differential Operators, Dover Publications , Mineola, NY, 1997. [21] G.I. MARCHUK, Adjoint Equations and Analysis of...NUMBER(S) 16. SECURITY CLASSIFICATION OF: 19b. TELEPHONE NUMBER (Include area code) The public reporting burden for this collection of information is

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

Jing Yanfei, E-mail: yanfeijing@uestc.edu.c; Huang Tingzhu, E-mail: tzhuang@uestc.edu.c; Duan Yong, E-mail: duanyong@yahoo.c

This study is mainly focused on iterative solutions with simple diagonal preconditioning to two complex-valued nonsymmetric systems of linear equations arising from a computational chemistry model problem proposed by Sherry Li of NERSC. Numerical experiments show the feasibility of iterative methods to some extent when applied to the problems and reveal the competitiveness of our recently proposed Lanczos biconjugate A-orthonormalization methods to other classic and popular iterative methods. By the way, experiment results also indicate that application specific preconditioners may be mandatory and required for accelerating convergence.

The wide-angle equation and its solution through the short-time iterative Lanczos method.

PubMed

Campos-Martínez, José; Coalson, Rob D

2003-03-20

Properties of the wide-angle equation (WAEQ), a nonparaxial scalar wave equation used to propagate light through media characterized by inhomogeneous refractive-index profiles, are studied. In particular, it is shown that the WAEQ is not equivalent to the more complicated but more fundamental Helmholtz equation (HEQ) when the index of refraction profile depends on the position along the propagation axis. This includes all nonstraight waveguides. To study the quality of the WAEQ approximation, we present a novel method for computing solutions to the WAEQ. This method, based on a short-time iterative Lanczos (SIL) algorithm, can be applied directly to the full three-dimensional case, i.e., systems consisting of the propagation axis coordinate and two transverse coordinates. Furthermore, the SIL method avoids series-expansion procedures (e.g., Padé approximants) and thus convergence problems associated with such procedures. Detailed comparisons of solutions to the HEQ, WAEQ, and the paraxial equation (PEQ) are presented for two cases in which numerically exact solutions to the HEQ can be obtained by independent analysis, namely, (i) propagation in a uniform dielectric medium and (ii) propagation along a straight waveguide that has been tilted at an angle to the propagation axis. The quality of WAEQ and PEQ, compared with exact HEQ results, is investigated. Cases are found for which the WAEQ actually performs worse than the PEQ.

Vision function testing for a suprachoroidal retinal prosthesis: effects of image filtering

NASA Astrophysics Data System (ADS)

Barnes, Nick; Scott, Adele F.; Lieby, Paulette; Petoe, Matthew A.; McCarthy, Chris; Stacey, Ashley; Ayton, Lauren N.; Sinclair, Nicholas C.; Shivdasani, Mohit N.; Lovell, Nigel H.; McDermott, Hugh J.; Walker, Janine G.; BVA Consortium,the

2016-06-01

Objective. One strategy to improve the effectiveness of prosthetic vision devices is to process incoming images to ensure that key information can be perceived by the user. This paper presents the first comprehensive results of vision function testing for a suprachoroidal retinal prosthetic device utilizing of 20 stimulating electrodes. Further, we investigate whether using image filtering can improve results on a light localization task for implanted participants compared to minimal vision processing. No controlled implanted participant studies have yet investigated whether vision processing methods that are not task-specific can lead to improved results. Approach. Three participants with profound vision loss from retinitis pigmentosa were implanted with a suprachoroidal retinal prosthesis. All three completed multiple trials of a light localization test, and one participant completed multiple trials of acuity tests. The visual representations used were: Lanczos2 (a high quality Nyquist bandlimited downsampling filter); minimal vision processing (MVP); wide view regional averaging filtering (WV); scrambled; and, system off. Main results. Using Lanczos2, all three participants successfully completed a light localization task and obtained a significantly higher percentage of correct responses than using MVP (p≤slant 0.025) or with system off (p\\lt 0.0001). Further, in a preliminary result using Lanczos2, one participant successfully completed grating acuity and Landolt C tasks, and showed significantly better performance (p=0.004) compared to WV, scrambled and system off on the grating acuity task. Significance. Participants successfully completed vision tasks using a 20 electrode suprachoroidal retinal prosthesis. Vision processing with a Nyquist bandlimited image filter has shown an advantage for a light localization task. This result suggests that this and targeted, more advanced vision processing schemes may become important components of retinal prostheses to enhance performance. ClinicalTrials.gov Identifier: NCT01603576.

Quantum lattice model solver HΦ

NASA Astrophysics Data System (ADS)

Kawamura, Mitsuaki; Yoshimi, Kazuyoshi; Misawa, Takahiro; Yamaji, Youhei; Todo, Synge; Kawashima, Naoki

2017-08-01

HΦ [aitch-phi ] is a program package based on the Lanczos-type eigenvalue solution applicable to a broad range of quantum lattice models, i.e., arbitrary quantum lattice models with two-body interactions, including the Heisenberg model, the Kitaev model, the Hubbard model and the Kondo-lattice model. While it works well on PCs and PC-clusters, HΦ also runs efficiently on massively parallel computers, which considerably extends the tractable range of the system size. In addition, unlike most existing packages, HΦ supports finite-temperature calculations through the method of thermal pure quantum (TPQ) states. In this paper, we explain theoretical background and user-interface of HΦ. We also show the benchmark results of HΦ on supercomputers such as the K computer at RIKEN Advanced Institute for Computational Science (AICS) and SGI ICE XA (Sekirei) at the Institute for the Solid State Physics (ISSP).

Optical spectrum of proflavine and its ions

NASA Astrophysics Data System (ADS)

Bonaca, A.; Bilalbegović, G.

2010-06-01

Motivated by possible astrophysical and biological applications we calculate visible and near UV spectral lines of proflavine (C13H11N3, 3,6-diaminoacridine) in vacuum, as well as its anion, cation, and dication. The pseudopotential density functional and time-dependent density functional methods are used. We find a good agreement in spectral line positions calculated by two real-time propagation methods and the Lanczos chain method. Spectra of proflavine and its ions show characteristic UV lines which are good candidates for a detection of these molecules in interstellar space and various biological processes.

Extending the eigCG algorithm to nonsymmetric Lanczos for linear systems with multiple right-hand sides

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

Abdel-Rehim, A M; Stathopoulos, Andreas; Orginos, Kostas

2014-08-01

The technique that was used to build the EigCG algorithm for sparse symmetric linear systems is extended to the nonsymmetric case using the BiCG algorithm. We show that, similarly to the symmetric case, we can build an algorithm that is capable of computing a few smallest magnitude eigenvalues and their corresponding left and right eigenvectors of a nonsymmetric matrix using only a small window of the BiCG residuals while simultaneously solving a linear system with that matrix. For a system with multiple right-hand sides, we give an algorithm that computes incrementally more eigenvalues while solving the first few systems andmore » then uses the computed eigenvectors to deflate BiCGStab for the remaining systems. Our experiments on various test problems, including Lattice QCD, show the remarkable ability of EigBiCG to compute spectral approximations with accuracy comparable to that of the unrestarted, nonsymmetric Lanczos. Furthermore, our incremental EigBiCG followed by appropriately restarted and deflated BiCGStab provides a competitive method for systems with multiple right-hand sides.« less

Fast Eigensolver for Computing 3D Earth's Normal Modes

NASA Astrophysics Data System (ADS)

Shi, J.; De Hoop, M. V.; Li, R.; Xi, Y.; Saad, Y.

2017-12-01

We present a novel parallel computational approach to compute Earth's normal modes. We discretize Earth via an unstructured tetrahedral mesh and apply the continuous Galerkin finite element method to the elasto-gravitational system. To resolve the eigenvalue pollution issue, following the analysis separating the seismic point spectrum, we utilize explicitly a representation of the displacement for describing the oscillations of the non-seismic modes in the fluid outer core. Effectively, we separate out the essential spectrum which is naturally related to the Brunt-Väisälä frequency. We introduce two Lanczos approaches with polynomial and rational filtering for solving this generalized eigenvalue problem in prescribed intervals. The polynomial filtering technique only accesses the matrix pair through matrix-vector products and is an ideal candidate for solving three-dimensional large-scale eigenvalue problems. The matrix-free scheme allows us to deal with fluid separation and self-gravitation in an efficient way, while the standard shift-and-invert method typically needs an explicit shifted matrix and its factorization. The rational filtering method converges much faster than the standard shift-and-invert procedure when computing all the eigenvalues inside an interval. Both two Lanczos approaches solve for the internal eigenvalues extremely accurately, comparing with the standard eigensolver. In our computational experiments, we compare our results with the radial earth model benchmark, and visualize the normal modes using vector plots to illustrate the properties of the displacements in different modes.

Can model Hamiltonians describe the electron-electron interaction in π-conjugated systems?: PAH and graphene

NASA Astrophysics Data System (ADS)

Chiappe, G.; Louis, E.; San-Fabián, E.; Vergés, J. A.

2015-11-01

Model Hamiltonians have been, and still are, a valuable tool for investigating the electronic structure of systems for which mean field theories work poorly. This review will concentrate on the application of Pariser-Parr-Pople (PPP) and Hubbard Hamiltonians to investigate some relevant properties of polycyclic aromatic hydrocarbons (PAH) and graphene. When presenting these two Hamiltonians we will resort to second quantisation which, although not the way chosen in its original proposal of the former, is much clearer. We will not attempt to be comprehensive, but rather our objective will be to try to provide the reader with information on what kinds of problems they will encounter and what tools they will need to solve them. One of the key issues concerning model Hamiltonians that will be treated in detail is the choice of model parameters. Although model Hamiltonians reduce the complexity of the original Hamiltonian, they cannot be solved in most cases exactly. So, we shall first consider the Hartree-Fock approximation, still the only tool for handling large systems, besides density functional theory (DFT) approaches. We proceed by discussing to what extent one may exactly solve model Hamiltonians and the Lanczos approach. We shall describe the configuration interaction (CI) method, a common technology in quantum chemistry but one rarely used to solve model Hamiltonians. In particular, we propose a variant of the Lanczos method, inspired by CI, that has the novelty of using as the seed of the Lanczos process a mean field (Hartree-Fock) determinant (the method will be named LCI). Two questions of interest related to model Hamiltonians will be discussed: (i) when including long-range interactions, how crucial is including in the Hamiltonian the electronic charge that compensates ion charges? (ii) Is it possible to reduce a Hamiltonian incorporating Coulomb interactions (PPP) to an ‘effective’ Hamiltonian including only on-site interactions (Hubbard)? The performance of CI will be checked on small molecules. The electronic structure of azulene and fused azulene will be used to illustrate several aspects of the method. As regards graphene, several questions will be considered: (i) paramagnetic versus antiferromagnetic solutions, (ii) forbidden gap versus dot size, (iii) graphene nano-ribbons, and (iv) optical properties.

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

NASA Astrophysics Data System (ADS)

Yu, Hua-Gen

2016-08-01

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH4 and H2CO are given, together with a comparison with previous results.

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

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

Yu, Hua-Gen, E-mail: hgy@bnl.gov

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using amore » multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH{sub 4} and H{sub 2}CO are given, together with a comparison with previous results.« less

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Variational study on the vibrational level structure and IVR behavior of highly vibrationally excited S0 formaldehyde.

PubMed

Rashev, Svetoslav; Moule, David C

2012-02-15

We perform large scale converged variational vibrational calculations on S(0) formaldehyde up to very high excess vibrational energies (E(v)), E(v)∼17,000cm(-1), using our vibrational method, consisting of a specific search/selection/Lanczos iteration procedure. Using the same method we investigate the vibrational level structure and intramolecular vibrational redistribution (IVR) characteristics for various vibrational levels in this energy range in order to assess the onset of IVR. Copyright © 2011 Elsevier B.V. All rights reserved.

Harnessing molecular excited states with Lanczos chains.

PubMed

Baroni, Stefano; Gebauer, Ralph; Bariş Malcioğlu, O; Saad, Yousef; Umari, Paolo; Xian, Jiawei

2010-02-24

The recursion method of Haydock, Heine and Kelly is a powerful tool for calculating diagonal matrix elements of the resolvent of quantum-mechanical Hamiltonian operators by elegantly expressing them in terms of continued fractions. In this paper we extend the recursion method to off-diagonal matrix elements of general (possibly non-Hermitian) operators and apply it to the simulation of molecular optical absorption and photoemission spectra within time-dependent density-functional and many-body perturbation theories, respectively. This method is demonstrated with a couple of applications to the optical absorption and photoemission spectra of the caffeine molecule.

Harnessing molecular excited states with Lanczos chains

NASA Astrophysics Data System (ADS)

Baroni, Stefano; Gebauer, Ralph; Bariş Malcioğlu, O.; Saad, Yousef; Umari, Paolo; Xian, Jiawei

2010-02-01

The recursion method of Haydock, Heine and Kelly is a powerful tool for calculating diagonal matrix elements of the resolvent of quantum-mechanical Hamiltonian operators by elegantly expressing them in terms of continued fractions. In this paper we extend the recursion method to off-diagonal matrix elements of general (possibly non-Hermitian) operators and apply it to the simulation of molecular optical absorption and photoemission spectra within time-dependent density-functional and many-body perturbation theories, respectively. This method is demonstrated with a couple of applications to the optical absorption and photoemission spectra of the caffeine molecule.

A Fresh Math Perspective Opens New Possibilities for Computational Chemistry

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

Vu, Linda; Govind, Niranjan; Yang, Chao

2017-05-26

By reformulating the TDDFT problem as a matrix function approximation, making use of a special transformation and taking advantage of the underlying symmetry with respect to a non-Euclidean metric, Yang and his colleagues were able to apply the Lanczos algorithm and a Kernal Polynomial Method (KPM) to approximate the absorption spectrum of several molecules. Both of these algorithms require relatively low-memory compared to non-symmetrical alternatives, which is the key to the computational savings.

Removing tidal-period variations from time-series data using low-pass digital filters

USGS Publications Warehouse

Walters, Roy A.; Heston, Cynthia

1982-01-01

Several low-pass, digital filters are examined for their ability to remove tidal Period Variations from a time-series of water surface elevation for San Francisco Bay. The most efficient filter is the one which is applied to the Fourier coefficients of the transformed data, and the filtered data recovered through an inverse transform. The ability of the filters to remove the tidal components increased in the following order: 1) cosine-Lanczos filter, 2) cosine-Lanczos squared filter; 3) Godin filter; and 4) a transform fitter. The Godin fitter is not sufficiently sharp to prevent severe attenuation of 2–3 day variations in surface elevation resulting from weather events.

Total photoionization cross-sections of excited electronic states by the algebraic diagrammatic construction-Stieltjes-Lanczos method.

PubMed

Ruberti, M; Yun, R; Gokhberg, K; Kopelke, S; Cederbaum, L S; Tarantelli, F; Averbukh, V

2014-05-14

Here, we extend the L2 ab initio method for molecular photoionization cross-sections introduced in Gokhberg et al. [J. Chem. Phys. 130, 064104 (2009)] and benchmarked in Ruberti et al. [J. Chem. Phys. 139, 144107 (2013)] to the calculation of total photoionization cross-sections of molecules in electronically excited states. The method is based on the ab initio description of molecular electronic states within the many-electron Green's function approach, known as algebraic diagrammatic construction (ADC), and on the application of Stieltjes-Chebyshev moment theory to Lanczos pseudospectra of the ADC electronic Hamiltonian. The intermediate state representation of the dipole operator in the ADC basis is used to compute the transition moments between the excited states of the molecule. We compare the results obtained using different levels of the many-body theory, i.e., ADC(1), ADC(2), and ADC(2)x for the first two excited states of CO, N2, and H2O both at the ground state and the excited state equilibrium or saddle point geometries. We find that the single excitation ADC(1) method is not adequate even at the qualitative level and that the inclusion of double electronic excitations for description of excited state photoionization is essential. Moreover, we show that the use of the extended ADC(2)x method leads to a substantial systematic difference from the strictly second-order ADC(2). Our calculations demonstrate that a theoretical modelling of photoionization of excited states requires an intrinsically double excitation theory with respect to the ground state and cannot be achieved by the standard single excitation methods with the ground state as a reference.

Total photoionization cross-sections of excited electronic states by the algebraic diagrammatic construction-Stieltjes-Lanczos method

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

Ruberti, M.; Yun, R.; Averbukh, V.

2014-05-14

Here, we extend the L{sup 2} ab initio method for molecular photoionization cross-sections introduced in Gokhberg et al. [J. Chem. Phys. 130, 064104 (2009)] and benchmarked in Ruberti et al. [J. Chem. Phys. 139, 144107 (2013)] to the calculation of total photoionization cross-sections of molecules in electronically excited states. The method is based on the ab initio description of molecular electronic states within the many-electron Green's function approach, known as algebraic diagrammatic construction (ADC), and on the application of Stieltjes-Chebyshev moment theory to Lanczos pseudospectra of the ADC electronic Hamiltonian. The intermediate state representation of the dipole operator in themore » ADC basis is used to compute the transition moments between the excited states of the molecule. We compare the results obtained using different levels of the many-body theory, i.e., ADC(1), ADC(2), and ADC(2)x for the first two excited states of CO, N{sub 2}, and H{sub 2}O both at the ground state and the excited state equilibrium or saddle point geometries. We find that the single excitation ADC(1) method is not adequate even at the qualitative level and that the inclusion of double electronic excitations for description of excited state photoionization is essential. Moreover, we show that the use of the extended ADC(2)x method leads to a substantial systematic difference from the strictly second-order ADC(2). Our calculations demonstrate that a theoretical modelling of photoionization of excited states requires an intrinsically double excitation theory with respect to the ground state and cannot be achieved by the standard single excitation methods with the ground state as a reference.« less

Low-lying Photoexcited States of a One-Dimensional Ionic Extended Hubbard Model

NASA Astrophysics Data System (ADS)

Yokoi, Kota; Maeshima, Nobuya; Hino, Ken-ichi

2017-10-01

We investigate the properties of low-lying photoexcited states of a one-dimensional (1D) ionic extended Hubbard model at half-filling. Numerical analysis by using the full and Lanczos diagonalization methods shows that, in the ionic phase, there exist low-lying photoexcited states below the charge transfer gap. As a result of comparison with numerical data for the 1D antiferromagnetic (AF) Heisenberg model, it was found that, for a small alternating potential Δ, these low-lying photoexcited states are spin excitations, which is consistent with a previous analytical study [Katsura et al., Phys. Rev. Lett. 103, 177402 (2009)]. As Δ increases, the spectral intensity of the 1D ionic extended Hubbard model rapidly deviates from that of the 1D AF Heisenberg model and it is clarified that this deviation is due to the neutral-ionic domain wall, an elementary excitation near the neutral-ionic transition point.

Computing interior eigenvalues of nonsymmetric matrices: application to three-dimensional metamaterial composites.

PubMed

Terao, Takamichi

2010-08-01

We propose a numerical method to calculate interior eigenvalues and corresponding eigenvectors for nonsymmetric matrices. Based on the subspace projection technique onto expanded Ritz subspace, it becomes possible to obtain eigenvalues and eigenvectors with sufficiently high precision. This method overcomes the difficulties of the traditional nonsymmetric Lanczos algorithm, and improves the accuracy of the obtained interior eigenvalues and eigenvectors. Using this algorithm, we investigate three-dimensional metamaterial composites consisting of positive and negative refractive index materials, and it is demonstrated that the finite-difference frequency-domain algorithm is applicable to analyze these metamaterial composites.

NEUTRON ENERGY LEVELS IN A DIFFUSE POTENTIAL

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

Ghosh, A.; Sil, N.C.

1960-06-01

The energy eigenvalues of neutrons within the nucleus for a spherically symmetrical potential V(r) = --V/sub 0/STAl + exp{(r-- R)/a}!/sup -1/ are investigated by following a new method of Lanczos for solving the differential equation. The s- and p-state energy levels are calculated for atomic mass 200 with the values of parameters adopted by Feshbach et al. in their calculation of the neutron strength function with a similar potential. The results of the calculation agree closely with those of Malenka. (auth)

Bunch-Kaufman factorization for real symmetric indefinite banded matrices

NASA Technical Reports Server (NTRS)

Jones, Mark T.; Patrick, Merrell L.

1989-01-01

The Bunch-Kaufman algorithm for factoring symmetric indefinite matrices was rejected for banded matrices because it destroys the banded structure of the matrix. Herein, it is shown that for a subclass of real symmetric matrices which arise in solving the generalized eigenvalue problem using Lanczos's method, the Bunch-Kaufman algorithm does not result in major destruction of the bandwidth. Space time complexities of the algorithm are given and used to show that the Bunch-Kaufman algorithm is a significant improvement over LU factorization.

Exact diagonalization of quantum lattice models on coprocessors

NASA Astrophysics Data System (ADS)

Siro, T.; Harju, A.

2016-10-01

We implement the Lanczos algorithm on an Intel Xeon Phi coprocessor and compare its performance to a multi-core Intel Xeon CPU and an NVIDIA graphics processor. The Xeon and the Xeon Phi are parallelized with OpenMP and the graphics processor is programmed with CUDA. The performance is evaluated by measuring the execution time of a single step in the Lanczos algorithm. We study two quantum lattice models with different particle numbers, and conclude that for small systems, the multi-core CPU is the fastest platform, while for large systems, the graphics processor is the clear winner, reaching speedups of up to 7.6 compared to the CPU. The Xeon Phi outperforms the CPU with sufficiently large particle number, reaching a speedup of 2.5.

Rigid Body Modes Influence On Microvibration Analysis-Application To Swarm

NASA Astrophysics Data System (ADS)

Laduree, G.; Fransen, S.; Baldesi, G.; Pflieger, I.

2012-07-01

Microvibrations are defined as low level mechanical disturbances affecting payload performance, generated by mobile parts or mechanism operating on-board the spacecraft, like momentum or reaction wheels, pointing mechanism, cryo-coolers or thrusters. The disturbances caused by these sources are transmitted through the spacecraft structure and excite modes of that structure or elements of the payload impacting its performance (e.g. Line of sight rotations inducing some image quality degradation). The dynamic interaction between these three elements (noise source, spacecraft structure and sensitive receiver) makes the microvibration prediction a delicate problem. Microvibration sources are generally of concern in the frequency range from a few Hz to 1000 Hz. However, in some specific cases, high stability at lower frequencies might be requested. This is the case of the SWARM mission, whose objectives are to provide the best ever survey of the geomagnetic field and its temporal evolution as well as supplementary information for studying the interaction of the magnetic field with other physical quantities describing the Earth system (e.g. ocean circulation). Among its instruments, SWARM is embarking a very sensitive 6-axis accelerometer in the low frequency range (10-8 m/s2 or rad/s2 between 10-4 and 0.1 Hz) located at its Centre of Gravity and an Absolute Scalar Magnetometer located at the tip of a boom far from the spacecraft body. The ASM performs its measurements by rotating an alternative magnetic field around its main axis thanks to a piezo-electric motor. This repeated disturbance might generate some pollution of the accelerometer science data. The objective of this work is to focus on the interaction of the rigid body mode calculation method with the elastic contribution of the normal modes excited by the noise source frequency content. It has indeed been reported in the past that NASTRAN Lanczos rigid body modes may lead to inaccurate rigid-body accelerations affecting steady state responses due to numerical roundoffs coming from the coupled mode shape extraction method and from the associated non numerical zeros frequencies. Geometric rigid body modes are usually the preferred solution for dynamic transient analysis but are not retained by NASTRAN when the chosen eigensolver is Lanczos, even using a SUPORT card. The SWARM microvibration problem described above has been considered as a benchmark case for various codes (NASTRAN, PERMAS, DCAP - multi-body software) and methods (direct or modal transients). A specific DMAP in NASTRAN has been written to overcome the limitation imposed by the Lanczos method and considerations on the conditioning of the FEM are discussed. An assessment on the accuracy of the different rigid body modes calculation methods is finally proposed.

Projection methods for the numerical solution of Markov chain models

NASA Technical Reports Server (NTRS)

Saad, Youcef

1989-01-01

Projection methods for computing stationary probability distributions for Markov chain models are presented. A general projection method is a method which seeks an approximation from a subspace of small dimension to the original problem. Thus, the original matrix problem of size N is approximated by one of dimension m, typically much smaller than N. A particularly successful class of methods based on this principle is that of Krylov subspace methods which utilize subspaces of the form span(v,av,...,A(exp m-1)v). These methods are effective in solving linear systems and eigenvalue problems (Lanczos, Arnoldi,...) as well as nonlinear equations. They can be combined with more traditional iterative methods such as successive overrelaxation, symmetric successive overrelaxation, or with incomplete factorization methods to enhance convergence.

QMR: A Quasi-Minimal Residual method for non-Hermitian linear systems

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noel M.

1990-01-01

The biconjugate gradient (BCG) method is the natural generalization of the classical conjugate gradient algorithm for Hermitian positive definite matrices to general non-Hermitian linear systems. Unfortunately, the original BCG algorithm is susceptible to possible breakdowns and numerical instabilities. A novel BCG like approach is presented called the quasi-minimal residual (QMR) method, which overcomes the problems of BCG. An implementation of QMR based on a look-ahead version of the nonsymmetric Lanczos algorithm is proposed. It is shown how BCG iterates can be recovered stably from the QMR process. Some further properties of the QMR approach are given and an error bound is presented. Finally, numerical experiments are reported.

Near-Edge X-ray Absorption Fine Structure within Multilevel Coupled Cluster Theory.

PubMed

Myhre, Rolf H; Coriani, Sonia; Koch, Henrik

2016-06-14

Core excited states are challenging to calculate, mainly because they are embedded in a manifold of high-energy valence-excited states. However, their locality makes their determination ideal for local correlation methods. In this paper, we demonstrate the performance of multilevel coupled cluster theory in computing core spectra both within the core-valence separated and the asymmetric Lanczos implementations of coupled cluster linear response theory. We also propose a visualization tool to analyze the excitations using the difference between the ground-state and excited-state electron densities.

Solving large sparse eigenvalue problems on supercomputers

NASA Technical Reports Server (NTRS)

Philippe, Bernard; Saad, Youcef

1988-01-01

An important problem in scientific computing consists in finding a few eigenvalues and corresponding eigenvectors of a very large and sparse matrix. The most popular methods to solve these problems are based on projection techniques on appropriate subspaces. The main attraction of these methods is that they only require the use of the matrix in the form of matrix by vector multiplications. The implementations on supercomputers of two such methods for symmetric matrices, namely Lanczos' method and Davidson's method are compared. Since one of the most important operations in these two methods is the multiplication of vectors by the sparse matrix, methods of performing this operation efficiently are discussed. The advantages and the disadvantages of each method are compared and implementation aspects are discussed. Numerical experiments on a one processor CRAY 2 and CRAY X-MP are reported. Possible parallel implementations are also discussed.

Efficient generalized cross-validation with applications to parametric image restoration and resolution enhancement.

PubMed

Nguyen, N; Milanfar, P; Golub, G

2001-01-01

In many image restoration/resolution enhancement applications, the blurring process, i.e., point spread function (PSF) of the imaging system, is not known or is known only to within a set of parameters. We estimate these PSF parameters for this ill-posed class of inverse problem from raw data, along with the regularization parameters required to stabilize the solution, using the generalized cross-validation method (GCV). We propose efficient approximation techniques based on the Lanczos algorithm and Gauss quadrature theory, reducing the computational complexity of the GCV. Data-driven PSF and regularization parameter estimation experiments with synthetic and real image sequences are presented to demonstrate the effectiveness and robustness of our method.

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

DOE PAGES

Li, Ruipeng; Saad, Yousef

2017-08-01

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

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

Li, Ruipeng; Saad, Yousef

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

Nonperturbative light-front Hamiltonian methods

NASA Astrophysics Data System (ADS)

Hiller, J. R.

2016-09-01

We examine the current state-of-the-art in nonperturbative calculations done with Hamiltonians constructed in light-front quantization of various field theories. The language of light-front quantization is introduced, and important (numerical) techniques, such as Pauli-Villars regularization, discrete light-cone quantization, basis light-front quantization, the light-front coupled-cluster method, the renormalization group procedure for effective particles, sector-dependent renormalization, and the Lanczos diagonalization method, are surveyed. Specific applications are discussed for quenched scalar Yukawa theory, ϕ4 theory, ordinary Yukawa theory, supersymmetric Yang-Mills theory, quantum electrodynamics, and quantum chromodynamics. The content should serve as an introduction to these methods for anyone interested in doing such calculations and as a rallying point for those who wish to solve quantum chromodynamics in terms of wave functions rather than random samplings of Euclidean field configurations.

Brown-York quasilocal energy in Lanczos-Lovelock gravity and black hole horizons

NASA Astrophysics Data System (ADS)

Chakraborty, Sumanta; Dadhich, Naresh

2015-12-01

A standard candidate for quasilocal energy in general relativity is the Brown-York energy, which is essentially a two dimensional surface integral of the extrinsic curvature on the two-boundary of a spacelike hypersurface referenced to flat spacetime. Several years back one of us had conjectured that the black hole horizon is defined by equipartition of gravitational and non-gravitational energy. By employing the above definition of quasilocal Brown-York energy, we have verified the equipartition conjecture for static charged and charged axi-symmetric black holes in general relativity. We have further generalized the Brown-York formalism to all orders in Lanczos-Lovelock theories of gravity and have verified the conjecture for pure Lovelock charged black hole in all even d = 2 m + 2 dimensions, where m is the degree of Lovelock action. It turns out that the equipartition conjecture works only for pure Lovelock, and not for Einstein-Lovelock black holes.

Algorithm 971: An Implementation of a Randomized Algorithm for Principal Component Analysis

PubMed Central

LI, HUAMIN; LINDERMAN, GEORGE C.; SZLAM, ARTHUR; STANTON, KELLY P.; KLUGER, YUVAL; TYGERT, MARK

2017-01-01

Recent years have witnessed intense development of randomized methods for low-rank approximation. These methods target principal component analysis and the calculation of truncated singular value decompositions. The present article presents an essentially black-box, foolproof implementation for Mathworks’ MATLAB, a popular software platform for numerical computation. As illustrated via several tests, the randomized algorithms for low-rank approximation outperform or at least match the classical deterministic techniques (such as Lanczos iterations run to convergence) in basically all respects: accuracy, computational efficiency (both speed and memory usage), ease-of-use, parallelizability, and reliability. However, the classical procedures remain the methods of choice for estimating spectral norms and are far superior for calculating the least singular values and corresponding singular vectors (or singular subspaces). PMID:28983138

Inflationary dynamics for matrix eigenvalue problems

PubMed Central

Heller, Eric J.; Kaplan, Lev; Pollmann, Frank

2008-01-01

Many fields of science and engineering require finding eigenvalues and eigenvectors of large matrices. The solutions can represent oscillatory modes of a bridge, a violin, the disposition of electrons around an atom or molecule, the acoustic modes of a concert hall, or hundreds of other physical quantities. Often only the few eigenpairs with the lowest or highest frequency (extremal solutions) are needed. Methods that have been developed over the past 60 years to solve such problems include the Lanczos algorithm, Jacobi–Davidson techniques, and the conjugate gradient method. Here, we present a way to solve the extremal eigenvalue/eigenvector problem, turning it into a nonlinear classical mechanical system with a modified Lagrangian constraint. The constraint induces exponential inflationary growth of the desired extremal solutions. PMID:18511564

Development and comparison of advanced reduced-basis methods for the transient structural analysis of unconstrained structures

NASA Technical Reports Server (NTRS)

Mcgowan, David M.; Bostic, Susan W.; Camarda, Charles J.

1993-01-01

The development of two advanced reduced-basis methods, the force derivative method and the Lanczos method, and two widely used modal methods, the mode displacement method and the mode acceleration method, for transient structural analysis of unconstrained structures is presented. Two example structural problems are studied: an undamped, unconstrained beam subject to a uniformly distributed load which varies as a sinusoidal function of time and an undamped high-speed civil transport aircraft subject to a normal wing tip load which varies as a sinusoidal function of time. These example problems are used to verify the methods and to compare the relative effectiveness of each of the four reduced-basis methods for performing transient structural analyses on unconstrained structures. The methods are verified with a solution obtained by integrating directly the full system of equations of motion, and they are compared using the number of basis vectors required to obtain a desired level of accuracy and the associated computational times as comparison criteria.

Variational study on the vibrational level structure and vibrational level mixing of highly vibrationally excited S₀ D₂CO.

PubMed

Rashev, Svetoslav; Moule, David C; Rashev, Vladimir

2012-11-01

We perform converged high precision variational calculations to determine the frequencies of a large number of vibrational levels in S(0) D(2)CO, extending from low to very high excess vibrational energies. For the calculations we use our specific vibrational method (recently employed for studies on H(2)CO), consisting of a combination of a search/selection algorithm and a Lanczos iteration procedure. Using the same method we perform large scale converged calculations on the vibrational level spectral structure and fragmentation at selected highly excited overtone states, up to excess vibrational energies of ∼17,000 cm(-1), in order to study the characteristics of intramolecular vibrational redistribution (IVR), vibrational level density and mode selectivity. Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient numerical method for investigating diatomic molecules with single active electron subjected to intense and ultrashort laser fields

NASA Astrophysics Data System (ADS)

Kiss, Gellért Zsolt; Borbély, Sándor; Nagy, Ladislau

2017-12-01

We have presented here an efficient numerical approach for the ab initio numerical solution of the time-dependent Schrödinger Equation describing diatomic molecules, which interact with ultrafast laser pulses. During the construction of the model we have assumed a frozen nuclear configuration and a single active electron. In order to increase efficiency our system was described using prolate spheroidal coordinates, where the wave function was discretized using the finite-element discrete variable representation (FE-DVR) method. The discretized wave functions were efficiently propagated in time using the short-iterative Lanczos algorithm. As a first test we have studied here how the laser induced bound state dynamics in H2+ is influenced by the strength of the driving laser field.

Review of inversion techniques using analysis of different tests

NASA Astrophysics Data System (ADS)

Smaglichenko, T. A.

2012-04-01

Tomographic techniques are tools, which estimate the Earth's deep interior by inverting seismic data. Reliability of visualization provides adequate understanding of geodynamic processes for prediction of natural hazard and protection of environment. This presentation focuses on two interrelated factors, which affect on the reliability namely: particularities of geophysical medium and strategy for choice of inversion method. Three main techniques are under review. First, the standard LSQR algorithm is derived directly by the Lanczos algebraic application. The Double Difference tomography widely incorporates this algorithm and its expansion. Next, the CSSA technique, or method of subtraction has been introduced into seismology by Nikolaev et al. in 1985. This method got farther development in 2003 (Smaglichenko et al.) as the coordinate method of possible directions, which has been already known in the theory of numerical methods. And finally, the new Differentiated Approach (DA) tomography that has been recently developed by the author for seismology and introduced into applied mathematics as the modification of Gaussian elimination. Different test models are presented by detecting various properties of the medium and having a value for the mining sector as well for prediction of seismic activity. They are: 1) checker-board resolution test; 2) the single anomalous block surrounded by an uniform zone; 3) the large-size structure; 4) the most complicated case, when the model consist of contrast layers and the observation response is equal zero value. The geometry of experiment for all models is given in the note of Leveque et al., 1993. It was assumed that errors in experimental data are in limits of pre-assigned accuracy. The testing showed that LSQR is effective, when the small-size structure (1) is retrieved, while CSSA works faster under reconstruction of the separated anomaly (2). The large-size structure (3) can be reconstructed applying DA, which uses both Lanczos's method and CSSA as composed parts of the inversion process. Difficulty of the model of contrast layers (4) can be overcome with a priori information that could allow the DA implementation. The testing leads us to the following conclusion. Careful analyze and weighted assumptions about characteristics of the being investigated medium should be done before start of data inversion. The choice of suitable technique will provide reliability of solution. Nevertheless, DA is preferred in the case of noisy and large data.

Using a Nondirect Product Basis to Compute J > 0 Rovibrational States of H3+

NASA Astrophysics Data System (ADS)

Jaquet, Ralph; Carrington, Tucker

2013-10-01

We have used a Lanczos algorithm with a nondirect product basis to compute energy levels of H3+ with J values as large as 46. Energy levels computed on the potential surface of M. Pavanello, et al. (J. Chem. Phys. 2012, 136, 184303) agree well with previous calculations for low J values.

The hydrogen tunneling splitting in malonaldehyde: A full-dimensional time-independent quantum mechanical method

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

Wu, Feng; Ren, Yinghui; Bian, Wensheng, E-mail: bian@iccas.ac.cn

The accurate time-independent quantum dynamics calculations on the ground-state tunneling splitting of malonaldehyde in full dimensionality are reported for the first time. This is achieved with an efficient method developed by us. In our method, the basis functions are customized for the hydrogen transfer process which has the effect of greatly reducing the size of the final Hamiltonian matrix, and the Lanczos method and parallel strategy are used to further overcome the memory and central processing unit time bottlenecks. The obtained ground-state tunneling splitting of 24.5 cm{sup −1} is in excellent agreement with the benchmark value of 23.8 cm{sup −1}more » computed with the full-dimensional, multi-configurational time-dependent Hartree approach on the same potential energy surface, and we estimate that our reported value has an uncertainty of less than 0.5 cm{sup −1}. Moreover, the role of various vibrational modes strongly coupled to the hydrogen transfer process is revealed.« less

Application of vector-valued rational approximations to the matrix eigenvalue problem and connections with Krylov subspace methods

NASA Technical Reports Server (NTRS)

Sidi, Avram

1992-01-01

Let F(z) be a vectored-valued function F: C approaches C sup N, which is analytic at z=0 and meromorphic in a neighborhood of z=0, and let its Maclaurin series be given. We use vector-valued rational approximation procedures for F(z) that are based on its Maclaurin series in conjunction with power iterations to develop bona fide generalizations of the power method for an arbitrary N X N matrix that may be diagonalizable or not. These generalizations can be used to obtain simultaneously several of the largest distinct eigenvalues and the corresponding invariant subspaces, and present a detailed convergence theory for them. In addition, it is shown that the generalized power methods of this work are equivalent to some Krylov subspace methods, among them the methods of Arnoldi and Lanczos. Thus, the theory provides a set of completely new results and constructions for these Krylov subspace methods. This theory suggests at the same time a new mode of usage for these Krylov subspace methods that were observed to possess computational advantages over their common mode of usage.

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

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

Timrov, Iurii; Biancardi, Alessandro; Andreussi, Oliviero

2015-01-21

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem andmore » a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.« less

Exponential propagators for the Schrödinger equation with a time-dependent potential.

PubMed

Bader, Philipp; Blanes, Sergio; Kopylov, Nikita

2018-06-28

We consider the numerical integration of the Schrödinger equation with a time-dependent Hamiltonian given as the sum of the kinetic energy and a time-dependent potential. Commutator-free (CF) propagators are exponential propagators that have shown to be highly efficient for general time-dependent Hamiltonians. We propose new CF propagators that are tailored for Hamiltonians of the said structure, showing a considerably improved performance. We obtain new fourth- and sixth-order CF propagators as well as a novel sixth-order propagator that incorporates a double commutator that only depends on coordinates, so this term can be considered as cost-free. The algorithms require the computation of the action of exponentials on a vector similar to the well-known exponential midpoint propagator, and this is carried out using the Lanczos method. We illustrate the performance of the new methods on several numerical examples.

Communication: A novel implementation to compute MP2 correlation energies without basis set superposition errors and complete basis set extrapolation.

PubMed

Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario

2017-06-07

By using a formulation based on the dynamical polarizability, we propose a novel implementation of second-order Møller-Plesset perturbation (MP2) theory within a plane wave (PW) basis set. Because of the intrinsic properties of PWs, this method is not affected by basis set superposition errors. Additionally, results are converged without relying on complete basis set extrapolation techniques; this is achieved by using the eigenvectors of the static polarizability as an auxiliary basis set to compactly and accurately represent the response functions involved in the MP2 equations. Summations over the large number of virtual states are avoided by using a formalism inspired by density functional perturbation theory, and the Lanczos algorithm is used to include dynamical effects. To demonstrate this method, applications to three weakly interacting dimers are presented.

Flexible configuration-interaction shell-model many-body solver

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

Johnson, Calvin W.; Ormand, W. Erich; McElvain, Kenneth S.

BIGSTICK Is a flexible configuration-Interaction open-source shell-model code for the many-fermion problem In a shell model (occupation representation) framework. BIGSTICK can generate energy spectra, static and transition one-body densities, and expectation values of scalar operators. Using the built-in Lanczos algorithm one can compute transition probabflity distributions and decompose wave functions into components defined by group theory.

Numerical study of the Kitaev-Heisenberg chain

NASA Astrophysics Data System (ADS)

Agrapidis, Cliò Efthimia; van den Brink, Jeroen; Nishimoto, Satoshi

2018-05-01

We study the one-dimensional Kitaev-Heisenberg model as a possible realization of magnetic degrees of freedom of the K-intercalated honeycomb-lattice ruthenium trichloride α-RuCl3, denoted as K0.5RuClm. First, we discuss the possible charge ordering pattern in K0.5RuClm, where half of the j =1/2 spins are replaced by nonmagnetic ions in the honeycomb layer. Next, we investigate the low-energy excitations of the 1D Kitaev-Heisenberg model by calculating the dynamical spin structure factor using the Lanczos exact-diagonalization method. In the vicinity of Kitaev limit, there exist two well-separated dispersions. The bandwidth of each dispersion depends on the Heisenberg and Kitaev terms. This result may be relevant to the low-lying magnetic excitations of K0.5RuClm.

An exact variational method to calculate vibrational energies of five atom molecules beyond the normal mode approach

DOE PAGES

Yu, Hua-Gen

2002-01-01

We present a full dimensional variational algorithm to calculate vibrational energies of penta-atomic molecules. The quantum mechanical Hamiltonian of the system for J=0 is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame without any dynamical approximation. Moreover, the vibrational Hamiltonian has been obtained in an explicitly Hermitian form. Variational calculations are performed in a direct product discrete variable representation basis set. The sine functions are used for the radial coordinates, whereas the Legendre polynomials are employed for the polar angles. For the azimuthal angles, the symmetrically adapted Fourier–Chebyshev basis functions are utilized. The eigenvalue problem ismore » solved by a Lanczos iterative diagonalization algorithm. The preliminary application to methane is given. Ultimately, we made a comparison with previous results.« less

Metallic Interface at the Boundary Between Band and Mott Insulators

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

Kancharla, Srivenkateswara S; Dagotto, Elbio R

2006-01-01

Motivated by experiments on atomically smooth layers of LaTiO3, a Mott insulator, sandwiched between layers of SrTiO3, a band insulator, a simple model for such heterostructures is studied using quasi one-dimensional lattices and the Lanczos method. Taking both the local and long-range Coulomb interactions into account, and computing the layer dependent local density of states, a metallic state was found at the interface whose extent strongly depends on the dielectric constant of the material. We also observed that the antiferromagnetic correlations in the bulk Mott phase persist into the metallic region. Our conclusions are in excellent agreement with recently reportedmore » results for this model in the opposite limit of infinite dimensions6,7, thus providing an alternative tool to study electronic reconstruction effects in heterostructures.« less

On adaptive weighted polynomial preconditioning for Hermitian positive definite matrices

NASA Technical Reports Server (NTRS)

Fischer, Bernd; Freund, Roland W.

1992-01-01

The conjugate gradient algorithm for solving Hermitian positive definite linear systems is usually combined with preconditioning in order to speed up convergence. In recent years, there has been a revival of polynomial preconditioning, motivated by the attractive features of the method on modern architectures. Standard techniques for choosing the preconditioning polynomial are based only on bounds for the extreme eigenvalues. Here a different approach is proposed, which aims at adapting the preconditioner to the eigenvalue distribution of the coefficient matrix. The technique is based on the observation that good estimates for the eigenvalue distribution can be derived after only a few steps of the Lanczos process. This information is then used to construct a weight function for a suitable Chebyshev approximation problem. The solution of this problem yields the polynomial preconditioner. In particular, we investigate the use of Bernstein-Szego weights.

Mixed models and reduction method for dynamic analysis of anisotropic shells

NASA Technical Reports Server (NTRS)

Noor, A. K.; Peters, J. M.

1985-01-01

A time-domain computational procedure is presented for predicting the dynamic response of laminated anisotropic shells. The two key elements of the procedure are: (1) use of mixed finite element models having independent interpolation (shape) functions for stress resultants and generalized displacements for the spatial discretization of the shell, with the stress resultants allowed to be discontinuous at interelement boundaries; and (2) use of a dynamic reduction method, with the global approximation vectors consisting of the static solution and an orthogonal set of Lanczos vectors. The dynamic reduction is accomplished by means of successive application of the finite element method and the classical Rayleigh-Ritz technique. The finite element method is first used to generate the global approximation vectors. Then the Rayleigh-Ritz technique is used to generate a reduced system of ordinary differential equations in the amplitudes of these modes. The temporal integration of the reduced differential equations is performed by using an explicit half-station central difference scheme (Leap-frog method). The effectiveness of the proposed procedure is demonstrated by means of a numerical example and its advantages over reduction methods used with the displacement formulation are discussed.

HO2 rovibrational eigenvalue studies for nonzero angular momentum

NASA Astrophysics Data System (ADS)

Wu, Xudong T.; Hayes, Edward F.

1997-08-01

An efficient parallel algorithm is reported for determining all bound rovibrational energy levels for the HO2 molecule for nonzero angular momentum values, J=1, 2, and 3. Performance tests on the CRAY T3D indicate that the algorithm scales almost linearly when up to 128 processors are used. Sustained performance levels of up to 3.8 Gflops have been achieved using 128 processors for J=3. The algorithm uses a direct product discrete variable representation (DVR) basis and the implicitly restarted Lanczos method (IRLM) of Sorensen to compute the eigenvalues of the polyatomic Hamiltonian. Since the IRLM is an iterative method, it does not require storage of the full Hamiltonian matrix—it only requires the multiplication of the Hamiltonian matrix by a vector. When the IRLM is combined with a formulation such as DVR, which produces a very sparse matrix, both memory and computation times can be reduced dramatically. This algorithm has the potential to achieve even higher performance levels for larger values of the total angular momentum.

Progress report on Nuclear Density project with Lawrence Livermore National Lab Year 2010

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

Johnson, C W; Krastev, P; Ormand, W E

2011-03-11

The main goal for year 2010 was to improve parallelization of the configuration interaction code BIGSTICK, co-written by W. Erich Ormand (LLNL) and Calvin W. Johnson (SDSU), with the parallelization carried out primarily by Plamen Krastev, a postdoc at SDSU and funded in part by this grant. The central computational algorithm is the Lanczos algorithm, which consists of a matrix-vector multiplication (matvec), followed by a Gram-Schmidt reorthogonalization.

Many Masses on One Stroke:. Economic Computation of Quark Propagators

NASA Astrophysics Data System (ADS)

Frommer, Andreas; Nöckel, Bertold; Güsken, Stephan; Lippert, Thomas; Schilling, Klaus

The computational effort in the calculation of Wilson fermion quark propagators in Lattice Quantum Chromodynamics can be considerably reduced by exploiting the Wilson fermion matrix structure in inversion algorithms based on the non-symmetric Lanczos process. We consider two such methods: QMR (quasi minimal residual) and BCG (biconjugate gradients). Based on the decomposition M/κ = 1/κ-D of the Wilson mass matrix, using QMR, one can carry out inversions on a whole trajectory of masses simultaneously, merely at the computational expense of a single propagator computation. In other words, one has to compute the propagator corresponding to the lightest mass only, while all the heavier masses are given for free, at the price of extra storage. Moreover, the symmetry γ5M = M†γ5 can be used to cut the computational effort in QMR and BCG by a factor of two. We show that both methods then become — in the critical regime of small quark masses — competitive to BiCGStab and significantly better than the standard MR method, with optimal relaxation factor, and CG as applied to the normal equations.

Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2016-10-01

We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

A new method for computation of eigenvector derivatives with distinct and repeated eigenvalues in structural dynamic analysis

NASA Astrophysics Data System (ADS)

Li, Zhengguang; Lai, Siu-Kai; Wu, Baisheng

2018-07-01

Determining eigenvector derivatives is a challenging task due to the singularity of the coefficient matrices of the governing equations, especially for those structural dynamic systems with repeated eigenvalues. An effective strategy is proposed to construct a non-singular coefficient matrix, which can be directly used to obtain the eigenvector derivatives with distinct and repeated eigenvalues. This approach also has an advantage that only requires eigenvalues and eigenvectors of interest, without solving the particular solutions of eigenvector derivatives. The Symmetric Quasi-Minimal Residual (SQMR) method is then adopted to solve the governing equations, only the existing factored (shifted) stiffness matrix from an iterative eigensolution such as the subspace iteration method or the Lanczos algorithm is utilized. The present method can deal with both cases of simple and repeated eigenvalues in a unified manner. Three numerical examples are given to illustrate the accuracy and validity of the proposed algorithm. Highly accurate approximations to the eigenvector derivatives are obtained within a few iteration steps, making a significant reduction of the computational effort. This method can be incorporated into a coupled eigensolver/derivative software module. In particular, it is applicable for finite element models with large sparse matrices.

Large scale shell model study of nuclear spectroscopy in nuclei around 132Sn

NASA Astrophysics Data System (ADS)

Lo Iudice, N.; Bianco, D.; Andreozzi, F.; Porrino, A.; Knapp, F.

2012-10-01

The properties of low-lying 2+ states in chains of nuclei in the proximity of the magic number N=82 are investigated within a new shell model approach exploiting an iterative algorithm alternative to Lanczos. The calculation yields levels and transition strengths in overall good agreement with experiments. The comparative analysis of the E2 and M1 transitions supports, in many cases, the scheme provided by the interacting boson model.

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

PubMed

Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

2018-05-09

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

Finite element stress, vibration, and buckling analysis of laminated beams with the use of refined elements

NASA Astrophysics Data System (ADS)

Borovkov, Alexei I.; Avdeev, Ilya V.; Artemyev, A.

1999-05-01

In present work, the stress, vibration and buckling finite element analysis of laminated beams is performed. Review of the equivalent single-layer (ESL) laminate theories is done. Finite element algorithms and procedures integrated into the original FEA program system and based on the classical laminated plate theory (CLPT), first-order shear deformation theory (FSDT), third-order theory of Reddy (TSDT-R) and third- order theory of Kant (TSDT-K) with the use of the Lanczos method for solving of the eigenproblem are developed. Several numerical tests and examples of bending, free vibration and buckling of multilayered and sandwich beams with various material, geometry properties and boundary conditions are solved. New effective higher-order hierarchical element for the accurate calculation of transverse shear stress is proposed. The comparative analysis of results obtained by the considered models and solutions of 2D problems of the heterogeneous anisotropic elasticity is fulfilled.

Local Complex Potential Based Time Dependent Wave Packet Approach to Calculation of Vibrational Excitation Cross-sections in e-N2, e-H2 and e-CO Scattering

NASA Astrophysics Data System (ADS)

Sarma, Manabendra; Singh, Raman K.; Mishra, Manoj K.

2007-12-01

Vibrational excitation cross-sections σn←m(E) in resonant e-N2, e-CO and e-H2 scattering are calculated from transition matrix elements Tn←m(E) obtained using Fourier transform of the cross correlation function <φn(R)|ψm(R,t)> where ψm(R,t); e-iHA-(R)t/ℏφm(R). Time evolution under the influence of the resonance anionic Hamiltonian HA-(A- = N2-/CO/H2-) is effected using Lanczos and fast Fourier transforms and the target (A) vibrational eigenfunctions φm(R) and φn(R) are calculated using Fourier grid Hamiltonian method applied to PE curve of the neutral target. The resulting vibrational excitation cross-section profiles provide reasonable agreement with experimental results and the cross correlation functions offer an unequivocal differentiation between the boomerang and impulse models.

Systematic Dimensionality Reduction for Quantum Walks: Optimal Spatial Search and Transport on Non-Regular Graphs

PubMed Central

Novo, Leonardo; Chakraborty, Shantanav; Mohseni, Masoud; Neven, Hartmut; Omar, Yasser

2015-01-01

Continuous time quantum walks provide an important framework for designing new algorithms and modelling quantum transport and state transfer problems. Often, the graph representing the structure of a problem contains certain symmetries that confine the dynamics to a smaller subspace of the full Hilbert space. In this work, we use invariant subspace methods, that can be computed systematically using the Lanczos algorithm, to obtain the reduced set of states that encompass the dynamics of the problem at hand without the specific knowledge of underlying symmetries. First, we apply this method to obtain new instances of graphs where the spatial quantum search algorithm is optimal: complete graphs with broken links and complete bipartite graphs, in particular, the star graph. These examples show that regularity and high-connectivity are not needed to achieve optimal spatial search. We also show that this method considerably simplifies the calculation of quantum transport efficiencies. Furthermore, we observe improved efficiencies by removing a few links from highly symmetric graphs. Finally, we show that this reduction method also allows us to obtain an upper bound for the fidelity of a single qubit transfer on an XY spin network. PMID:26330082

Inverse scattering theory: Inverse scattering series method for one dimensional non-compact support potential

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

Yao, Jie, E-mail: yjie2@uh.edu; Lesage, Anne-Cécile; Hussain, Fazle

2014-12-15

The reversion of the Born-Neumann series of the Lippmann-Schwinger equation is one of the standard ways to solve the inverse acoustic scattering problem. One limitation of the current inversion methods based on the reversion of the Born-Neumann series is that the velocity potential should have compact support. However, this assumption cannot be satisfied in certain cases, especially in seismic inversion. Based on the idea of distorted wave scattering, we explore an inverse scattering method for velocity potentials without compact support. The strategy is to decompose the actual medium as a known single interface reference medium, which has the same asymptoticmore » form as the actual medium and a perturbative scattering potential with compact support. After introducing the method to calculate the Green’s function for the known reference potential, the inverse scattering series and Volterra inverse scattering series are derived for the perturbative potential. Analytical and numerical examples demonstrate the feasibility and effectiveness of this method. Besides, to ensure stability of the numerical computation, the Lanczos averaging method is employed as a filter to reduce the Gibbs oscillations for the truncated discrete inverse Fourier transform of each order. Our method provides a rigorous mathematical framework for inverse acoustic scattering with a non-compact support velocity potential.« less

Nuclear shell model code CRUNCHER

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

Resler, D.A.; Grimes, S.M.

1988-05-01

A new nuclear shell model code CRUNCHER, patterned after the code VLADIMIR, has been developed. While CRUNCHER and VLADIMIR employ the techniques of an uncoupled basis and the Lanczos process, improvements in the new code allow it to handle much larger problems than the previous code and to perform them more efficiently. Tests involving a moderately sized calculation indicate that CRUNCHER running on a SUN 3/260 workstation requires approximately one-half the central processing unit (CPU) time required by VLADIMIR running on a CRAY-1 supercomputer.

A coupled-cluster study of photodetachment cross sections of closed-shell anions

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Decleva, Piero; Coriani, Sonia

2014-11-01

We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H-, Li-, Na-, F-, Cl-, and OH-. The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

A coupled-cluster study of photodetachment cross sections of closed-shell anions.

PubMed

Cukras, Janusz; Decleva, Piero; Coriani, Sonia

2014-11-07

We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H(-), Li(-), Na(-), F(-), Cl(-), and OH(-). The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

Advanced UXO Detection and Discrimination Using Magnetic Data Based on Extended Euler Deconvolution and Shape Identification Through Multipole Moments

DTIC Science & Technology

2011-04-01

detection. We also thank Len Pasion and Todd Meglich for helpful discussions on the Camp Sibert data set. Finally, we thank Kris Davis from Colorado...depth of potential UXO using a continuous wavelet transform: Conference proceedings, 1012– 1022, SPIE. Billings, S. D., L. R. Pasion , and D. W...1638 2009 Annual Report. Lanczos, C., 1988, Applied analysis: Courier Dover Publications. Li, Y., Krahenbuhl, R., Meglich, T., Pasion , L

Density-matrix-based algorithm for solving eigenvalue problems

NASA Astrophysics Data System (ADS)

Polizzi, Eric

2009-03-01

A fast and stable numerical algorithm for solving the symmetric eigenvalue problem is presented. The technique deviates fundamentally from the traditional Krylov subspace iteration based techniques (Arnoldi and Lanczos algorithms) or other Davidson-Jacobi techniques and takes its inspiration from the contour integration and density-matrix representation in quantum mechanics. It will be shown that this algorithm—named FEAST—exhibits high efficiency, robustness, accuracy, and scalability on parallel architectures. Examples from electronic structure calculations of carbon nanotubes are presented, and numerical performances and capabilities are discussed.

Reducing errors in the GRACE gravity solutions using regularization

NASA Astrophysics Data System (ADS)

Save, Himanshu; Bettadpur, Srinivas; Tapley, Byron D.

2012-09-01

The nature of the gravity field inverse problem amplifies the noise in the GRACE data, which creeps into the mid and high degree and order harmonic coefficients of the Earth's monthly gravity fields provided by GRACE. Due to the use of imperfect background models and data noise, these errors are manifested as north-south striping in the monthly global maps of equivalent water heights. In order to reduce these errors, this study investigates the use of the L-curve method with Tikhonov regularization. L-curve is a popular aid for determining a suitable value of the regularization parameter when solving linear discrete ill-posed problems using Tikhonov regularization. However, the computational effort required to determine the L-curve is prohibitively high for a large-scale problem like GRACE. This study implements a parameter-choice method, using Lanczos bidiagonalization which is a computationally inexpensive approximation to L-curve. Lanczos bidiagonalization is implemented with orthogonal transformation in a parallel computing environment and projects a large estimation problem on a problem of the size of about 2 orders of magnitude smaller for computing the regularization parameter. Errors in the GRACE solution time series have certain characteristics that vary depending on the ground track coverage of the solutions. These errors increase with increasing degree and order. In addition, certain resonant and near-resonant harmonic coefficients have higher errors as compared with the other coefficients. Using the knowledge of these characteristics, this study designs a regularization matrix that provides a constraint on the geopotential coefficients as a function of its degree and order. This regularization matrix is then used to compute the appropriate regularization parameter for each monthly solution. A 7-year time-series of the candidate regularized solutions (Mar 2003-Feb 2010) show markedly reduced error stripes compared with the unconstrained GRACE release 4 solutions (RL04) from the Center for Space Research (CSR). Post-fit residual analysis shows that the regularized solutions fit the data to within the noise level of GRACE. A time series of filtered hydrological model is used to confirm that signal attenuation for basins in the Total Runoff Integrating Pathways (TRIP) database over 320 km radii is less than 1 cm equivalent water height RMS, which is within the noise level of GRACE.

Minimally doubled fermions and spontaneous chiral symmetry breaking

NASA Astrophysics Data System (ADS)

Osmanaj (Zeqirllari), Rudina; Hyka (Xhako), Dafina

2018-03-01

Chiral symmetry breaking in massless QCD is a very important feature in the current understanding of low energy physics. Low - lying Dirac modes are suitable to help us understand the spontaneous chiral symmetry breaking, since the formation of a non zero chiral condensate is an effect of their accumulation near zero. The Banks - Casher relation links the spectral density of the Dirac operator to the condensate with an identity that can be read in both directions. In this work we propose a spectral method to achieve a reliable determination of the density of eigenvalues of Dirac operator near zero using the Gauss - Lanczos quadrature. In order to understand better the dynamical chiral symmetry breaking and use the method we propose, we have chosen to work with minimally doubled fermions. These kind of fermions have been proposed as a strictly local discretization of the QCD fermions action, which preserves chiral symmetry at finite cut-off. Being chiral fermions, is easier to work with them and their low - lying Dirac modes and to understand the dynamical spontaneous chiral symmetry breaking.

New directions in photonics simulation: Lanczos recursion and finite-difference time-domain

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

Hawkins, R.J.; McLeod, R.R.; Kallman, J.S.

1992-06-01

Computational Integrated Photonics (CIP) is the area of computational physics that treats the propagation of light in optical fibers and in integrated optical circuits. The purpose of integrated photonics simulation is to develop the computational tools that will support the design of photonic and optoelectronic integrated devices. CIP has, in general, two thrusts: (1) predictive models of photonic device behavior that can be used reliably to enhance significantly the speed with which designs axe optimized for development applications, and (2) to further our ability to describe the linear and nonlinear processes that occur - and can be exploited - inmore » real photonic devices. Experimental integrated optics has been around for over a decade with much of the work during this period. centered on proof-of-principle devices that could be described using simple analytic and numerical models. Recent advances in material growths, photolithography, and device complexity have conspired to reduce significantly the number of devices that can be designed with simple models and to increase dramatically the interest in CIP. In the area of device design, CIP is viewed as critical to understanding device behavior and to optimization. In the area of propagation physics, CIP is an important tool in the study of nonlinear processes in integrated optical devices and fibers. In this talk I will discuss two of the new directions we have been investigating in CIP: Lanczos recursion and finite-difference time-domain.« less

A novel CFS-PML boundary condition for transient electromagnetic simulation using a fictitious wave domain method

NASA Astrophysics Data System (ADS)

Hu, Yanpu; Egbert, Gary; Ji, Yanju; Fang, Guangyou

2017-01-01

In this study, we apply fictitious wave domain (FWD) methods, based on the correspondence principle for the wave and diffusion fields, to finite difference (FD) modeling of transient electromagnetic (TEM) diffusion problems for geophysical applications. A novel complex frequency shifted perfectly matched layer (PML) boundary condition is adapted to the FWD to truncate the computational domain, with the maximum electromagnetic wave propagation velocity in the FWD used to set the absorbing parameters for the boundary layers. Using domains of varying spatial extent we demonstrate that these boundary conditions offer significant improvements over simpler PML approaches, which can result in spurious reflections and large errors in the FWD solutions, especially for low frequencies and late times. In our development, resistive air layers are directly included in the FWD, allowing simulation of TEM responses in the presence of topography, as is commonly encountered in geophysical applications. We compare responses obtained by our new FD-FWD approach and with the spectral Lanczos decomposition method on 3-D resistivity models of varying complexity. The comparisons demonstrate that our absorbing boundary condition in FWD for the TEM diffusion problems works well even in complex high-contrast conductivity models.

A full-dimensional ab initio potential energy surface and rovibrational energies of the Ar–HF complex

NASA Astrophysics Data System (ADS)

Huang, Jing; Zhou, Yanzi; Xie, Daiqian

2018-04-01

We report a new full-dimensional ab initio potential energy surface for the Ar-HF van der Waals complex at the level of coupled-cluster singles and doubles with noniterative inclusion of connected triples levels [CCSD(T)] using augmented correlation-consistent quintuple-zeta basis set (aV5Z) plus bond functions. Full counterpoise correction was employed to correct the basis-set superposition error. The hypersurface was fitted using artificial neural network method with a root mean square error of 0.1085 cm-1 for more than 8000 ab initio points. The complex was found to prefer a linear Ar-H-F equilibrium structure. The three-dimensional discrete variable representation method and the Lanczos propagation algorithm were then employed to calculate the rovibrational states without separating inter- and intra- molecular nuclear motions. The calculated vibrational energies of Ar-HF differ from the experiment values within about 1 cm-1 on the first four HF vibrational states, and the predicted pure rotational energies on (0000) and (1000) vibrational states are deviated from the observed value by about 1%, which shows the accuracy of our new PES.

Investigation of the highest bound ro-vibrational states of H+ 3, DH+ 2, HD+ 2, D+ 3, and T+ 3: use of a non-direct product basis to compute the highest allowed J > 0 states

NASA Astrophysics Data System (ADS)

Jaquet, Ralph

2013-09-01

A Lanczos algorithm with a non-direct product basis was used to compute energy levels of H+ 3, H2D+, D2H+, D+ 3, and T+ 3 with J values as large as 46, 53, 66, 66, and 81. The energy levels are based on a modified potential surface of M. Pavanello et al. that is better adapted to the ab initio energies near the dissociation limit.

New 2D dilaton gravity for nonsingular black holes

NASA Astrophysics Data System (ADS)

Kunstatter, Gabor; Maeda, Hideki; Taves, Tim

2016-05-01

We construct a two-dimensional action that is an extension of spherically symmetric Einstein-Lanczos-Lovelock (ELL) gravity. The action contains arbitrary functions of the areal radius and the norm squared of its gradient, but the field equations are second order and obey Birkhoff’s theorem. In complete analogy with spherically symmetric ELL gravity, the field equations admit the generalized Misner-Sharp mass as the first integral that determines the form of the vacuum solution. The arbitrary functions in the action allow for vacuum solutions that describe a larger class of interesting nonsingular black hole spacetimes than previously available.

Rare-Region-Induced Avoided Quantum Criticality in Disordered Three-Dimensional Dirac and Weyl Semimetals

NASA Astrophysics Data System (ADS)

Pixley, J. H.; Huse, David A.; Das Sarma, S.

2016-04-01

We numerically study the effect of short-ranged potential disorder on massless noninteracting three-dimensional Dirac and Weyl fermions, with a focus on the question of the proposed (and extensively theoretically studied) quantum critical point separating semimetal and diffusive-metal phases. We determine the properties of the eigenstates of the disordered Dirac Hamiltonian (H ) and exactly calculate the density of states (DOS) near zero energy, using a combination of Lanczos on H2 and the kernel polynomial method on H . We establish the existence of two distinct types of low-energy eigenstates contributing to the disordered density of states in the weak-disorder semimetal regime. These are (i) typical eigenstates that are well described by linearly dispersing perturbatively dressed Dirac states and (ii) nonperturbative rare eigenstates that are weakly dispersive and quasilocalized in the real-space regions with the largest (and rarest) local random potential. Using twisted boundary conditions, we are able to systematically find and study these two (essentially independent) types of eigenstates. We find that the Dirac states contribute low-energy peaks in the finite-size DOS that arise from the clean eigenstates which shift and broaden in the presence of disorder. On the other hand, we establish that the rare quasilocalized eigenstates contribute a nonzero background DOS which is only weakly energy dependent near zero energy and is exponentially small at weak disorder. We also find that the expected semimetal to diffusive-metal quantum critical point is converted to an avoided quantum criticality that is "rounded out" by nonperturbative effects, with no signs of any singular behavior in the DOS at the energy of the clean Dirac point. However, the crossover effects of the avoided (or hidden) criticality manifest themselves in a so-called quantum critical fan region away from the Dirac energy. We discuss the implications of our results for disordered Dirac and Weyl semimetals, and reconcile the large body of existing numerical work showing quantum criticality with the existence of these nonperturbative effects.

Lorentz violation in the gravity sector: The t puzzle

NASA Astrophysics Data System (ADS)

Bonder, Yuri

2015-06-01

Lorentz violation is a candidate quantum-gravity signal, and the Standard-Model Extension (SME) is a widely used parametrization of such a violation. In the gravitational SME sector, there is an elusive coefficient for which no effects have been found. This is known as the t puzzle and, to date, it has no compelling explanation. This paper analyzes whether there is a fundamental explanation for the t puzzle. To tackle this question, several approaches are followed. Mainly, redefinitions of the dynamical fields are studied, showing that other SME coefficients can be moved to nongravitational sectors. It is also found that the gravity SME sector can be consistently treated à la Palatini, and that, in the presence of spacetime boundaries, it is possible to correct its action to get the desired equations of motion. Moreover, through a reformulation as a Lanczos-type tensor, some problematic features of the t term, which should arise at the phenomenological level, are revealed. The most important conclusion of the paper is that there is no evidence of a fundamental explanation for the t puzzle, suggesting that it may be linked to the approximations taken at the phenomenological level.

Numerical modelling of thin-walled Z-columns made of general laminates subjected to uniform shortening

NASA Astrophysics Data System (ADS)

Teter, Andrzej; Kolakowski, Zbigniew

2018-01-01

The numerical modelling of a plate structure was performed with the finite element method and a one-mode approach based on Koiter's method. The first order approximation of Koiter's method enables one to solve the eigenvalue problem. The second order approximation describes post-buckling equilibrium paths. In the finite element analysis, the Lanczos method was used to solve the linear problem of buckling. Simulations of the non-linear problem were performed with the Newton-Raphson method. Detailed calculations were carried out for a short Z-column made of general laminates. Configurations of laminated layers were non-symmetric. Due to possibilities of its application, the general laminate is very interesting. The length of the samples was chosen to obtain the lowest value of local buckling load. The amplitude of initial imperfections was 10% of the wall thickness. Thin-walled structures were simply supported on both ends. The numerical results were verified in experimental tests. A strain-gauge technique was applied. A static compression test was performed on a universal testing machine and a special grip, which consisted of two rigid steel plates and clamping sleeves, was used. Specimens were obtained with an autoclave technique. Tests were performed at a constant velocity of the cross-bar equal to 2 mm/min. The compressive load was less than 150% of the bifurcation load. Additionally, soft and thin pads were used to reduce inaccuracy of the sample ends.

Fast calculation of the `ILC norm' in iterative learning control

NASA Astrophysics Data System (ADS)

Rice, Justin K.; van Wingerden, Jan-Willem

2013-06-01

In this paper, we discuss and demonstrate a method for the exploitation of matrix structure in computations for iterative learning control (ILC). In Barton, Bristow, and Alleyne [International Journal of Control, 83(2), 1-8 (2010)], a special insight into the structure of the lifted convolution matrices involved in ILC is used along with a modified Lanczos method to achieve very fast computational bounds on the learning convergence, by calculating the 'ILC norm' in ? computational complexity. In this paper, we show how their method is equivalent to a special instance of the sequentially semi-separable (SSS) matrix arithmetic, and thus can be extended to many other computations in ILC, and specialised in some cases to even faster methods. Our SSS-based methodology will be demonstrated on two examples: a linear time-varying example resulting in the same ? complexity as in Barton et al., and a linear time-invariant example where our approach reduces the computational complexity to ?, thus decreasing the computation time, for an example, from the literature by a factor of almost 100. This improvement is achieved by transforming the norm computation via a linear matrix inequality into a check of positive definiteness - which allows us to further exploit the almost-Toeplitz properties of the matrix, and additionally provides explicit upper and lower bounds on the norm of the matrix, instead of the indirect Ritz estimate. These methods are now implemented in a MATLAB toolbox, freely available on the Internet.

Dynamical structure factor of the J1-J2 Heisenberg model in one dimension: The variational Monte Carlo approach

NASA Astrophysics Data System (ADS)

Ferrari, Francesco; Parola, Alberto; Sorella, Sandro; Becca, Federico

2018-06-01

The dynamical spin structure factor is computed within a variational framework to study the one-dimensional J1-J2 Heisenberg model. Starting from Gutzwiller-projected fermionic wave functions, the low-energy spectrum is constructed from two-spinon excitations. The direct comparison with Lanczos calculations on small clusters demonstrates the excellent description of both gapless and gapped (dimerized) phases, including incommensurate structures for J2/J1>0.5 . Calculations on large clusters show how the intensity evolves when increasing the frustrating ratio and give an unprecedented accurate characterization of the dynamical properties of (nonintegrable) frustrated spin models.

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

Fu, Bo; Zhu, Wei; Shi, Qinwei

Exploiting the enabling power of the Lanczos method in momentum space, we determine accurately the quasiparticle and scaling properties of disordered three-dimensional Dirac semimetals surrounding the quantum critical point separating the semimetal and diffusive metal regimes. We unveil that the imaginary part of the quasiparticle self-energy obeys a common power law before, at, and after the quantum phase transition, but the power law is nonuniversal, whose exponent is dependent on the disorder strength. More intriguingly, whereas a common power law is also found for the real part of the self-energy before and after the phase transition, a distinctly different behaviormore » is identified at the critical point, characterized by the existence of a nonanalytic logarithmic singularity. This nonanalytical correction serves as the very basis for the unusual power-law behaviors of the quasiparticles and many other physical properties surrounding the quantum critical point. Our approach also allows the ready and reliable determination of the scaling properties of the correlation length and dynamical exponents. Furthermore, we show that the central findings are valid for both uncorrelated and correlated disorder distributions and should be directly comparable with future experimental observations.« less

Ordering Unstructured Meshes for Sparse Matrix Computations on Leading Parallel Systems

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Li, Xiaoye; Heber, Gerd; Biswas, Rupak

2000-01-01

The ability of computers to solve hitherto intractable problems and simulate complex processes using mathematical models makes them an indispensable part of modern science and engineering. Computer simulations of large-scale realistic applications usually require solving a set of non-linear partial differential equations (PDES) over a finite region. For example, one thrust area in the DOE Grand Challenge projects is to design future accelerators such as the SpaHation Neutron Source (SNS). Our colleagues at SLAC need to model complex RFQ cavities with large aspect ratios. Unstructured grids are currently used to resolve the small features in a large computational domain; dynamic mesh adaptation will be added in the future for additional efficiency. The PDEs for electromagnetics are discretized by the FEM method, which leads to a generalized eigenvalue problem Kx = AMx, where K and M are the stiffness and mass matrices, and are very sparse. In a typical cavity model, the number of degrees of freedom is about one million. For such large eigenproblems, direct solution techniques quickly reach the memory limits. Instead, the most widely-used methods are Krylov subspace methods, such as Lanczos or Jacobi-Davidson. In all the Krylov-based algorithms, sparse matrix-vector multiplication (SPMV) must be performed repeatedly. Therefore, the efficiency of SPMV usually determines the eigensolver speed. SPMV is also one of the most heavily used kernels in large-scale numerical simulations.

Eigensolver for a Sparse, Large Hermitian Matrix

NASA Technical Reports Server (NTRS)

Tisdale, E. Robert; Oyafuso, Fabiano; Klimeck, Gerhard; Brown, R. Chris

2003-01-01

A parallel-processing computer program finds a few eigenvalues in a sparse Hermitian matrix that contains as many as 100 million diagonal elements. This program finds the eigenvalues faster, using less memory, than do other, comparable eigensolver programs. This program implements a Lanczos algorithm in the American National Standards Institute/ International Organization for Standardization (ANSI/ISO) C computing language, using the Message Passing Interface (MPI) standard to complement an eigensolver in PARPACK. [PARPACK (Parallel Arnoldi Package) is an extension, to parallel-processing computer architectures, of ARPACK (Arnoldi Package), which is a collection of Fortran 77 subroutines that solve large-scale eigenvalue problems.] The eigensolver runs on Beowulf clusters of computers at the Jet Propulsion Laboratory (JPL).

The two-phase method for finding a great number of eigenpairs of the symmetric or weakly non-symmetric large eigenvalue problems

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

Dul, F.A.; Arczewski, K.

1994-03-01

Although it has been stated that [open quotes]an attempt to solve (very large problems) by subspace iterations seems futile[close quotes], we will show that the statement is not true, especially for extremely large eigenproblems. In this paper a new two-phase subspace iteration/Rayleigh quotient/conjugate gradient method for generalized, large, symmetric eigenproblems Ax = [lambda]Bx is presented. It has the ability of solving extremely large eigenproblems, N = 216,000, for example, and finding a large number of leftmost or rightmost eigenpairs, up to 1000 or more. Multiple eigenpairs, even those with multiplicity 100, can be easily found. The use of the proposedmore » method for solving the big full eigenproblems (N [approximately] 10[sup 3]), as well as for large weakly non-symmetric eigenproblems, have been considered also. The proposed method is fully iterative; thus the factorization of matrices ins avoided. The key idea consists in joining two methods: subspace and Rayleigh quotient iterations. The systems of indefinite and almost singular linear equations (a - [sigma]B)x = By are solved by various iterative conjugate gradient method can be used without danger of breaking down due to its property that may be called [open quotes]self-correction towards the eigenvector,[close quotes] discovered recently by us. The use of various preconditioners (SSOR and IC) has also been considered. The main features of the proposed method have been analyzed in detail. Comparisons with other methods, such as, accelerated subspace iteration, Lanczos, Davidson, TLIME, TRACMN, and SRQMCG, are presented. The results of numerical tests for various physical problems (acoustic, vibrations of structures, quantum chemistry) are presented as well. 40 refs., 12 figs., 2 tabs.« less

Optical potential from first principles

DOE PAGES

Rotureau, J.; Danielewicz, P.; Hagen, G.; ...

2017-02-15

Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16O. For the computation of the ground-state of 16O, we use the coupled-cluster method in the singles-and-doubles approximation, while for themore » A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.« less

An approach to unbiased subsample interpolation for motion tracking.

PubMed

McCormick, Matthew M; Varghese, Tomy

2013-04-01

Accurate subsample displacement estimation is necessary for ultrasound elastography because of the small deformations that occur and the subsequent application of a derivative operation on local displacements. Many of the commonly used subsample estimation techniques introduce significant bias errors. This article addresses a reduced bias approach to subsample displacement estimations that consists of a two-dimensional windowed-sinc interpolation with numerical optimization. It is shown that a Welch or Lanczos window with a Nelder-Mead simplex or regular-step gradient-descent optimization is well suited for this purpose. Little improvement results from a sinc window radius greater than four data samples. The strain signal-to-noise ratio (SNR) obtained in a uniformly elastic phantom is compared with other parabolic and cosine interpolation methods; it is found that the strain SNR ratio is improved over parabolic interpolation from 11.0 to 13.6 in the axial direction and 0.7 to 1.1 in the lateral direction for an applied 1% axial deformation. The improvement was most significant for small strains and displacement tracking in the lateral direction. This approach does not rely on special properties of the image or similarity function, which is demonstrated by its effectiveness with the application of a previously described regularization technique.

Ordered states in the Kitaev-Heisenberg model: From 1D chains to 2D honeycomb.

PubMed

Agrapidis, Cliò Efthimia; van den Brink, Jeroen; Nishimoto, Satoshi

2018-01-29

We study the ground state of the 1D Kitaev-Heisenberg (KH) model using the density-matrix renormalization group and Lanczos exact diagonalization methods. We obtain a rich ground-state phase diagram as a function of the ratio between Heisenberg (J = cosϕ) and Kitaev (K = sinϕ) interactions. Depending on the ratio, the system exhibits four long-range ordered states: ferromagnetic-z, ferromagnetic-xy, staggered-xy, Néel-z, and two liquid states: Tomonaga-Luttinger liquid and spiral-xy. The two Kitaev points [Formula: see text] and [Formula: see text] are singular. The ϕ-dependent phase diagram is similar to that for the 2D honeycomb-lattice KH model. Remarkably, all the ordered states of the honeycomb-lattice KH model can be interpreted in terms of the coupled KH chains. We also discuss the magnetic structure of the K-intercalated RuCl 3 , a potential Kitaev material, in the framework of the 1D KH model. Furthermore, we demonstrate that the low-lying excitations of the 1D KH Hamiltonian can be explained within the combination of the known six-vertex model and spin-wave theory.

Model Based Predictive Control of Multivariable Hammerstein Processes with Fuzzy Logic Hypercube Interpolated Models

PubMed Central

Coelho, Antonio Augusto Rodrigues

2016-01-01

This paper introduces the Fuzzy Logic Hypercube Interpolator (FLHI) and demonstrates applications in control of multiple-input single-output (MISO) and multiple-input multiple-output (MIMO) processes with Hammerstein nonlinearities. FLHI consists of a Takagi-Sugeno fuzzy inference system where membership functions act as kernel functions of an interpolator. Conjunction of membership functions in an unitary hypercube space enables multivariable interpolation of N-dimensions. Membership functions act as interpolation kernels, such that choice of membership functions determines interpolation characteristics, allowing FLHI to behave as a nearest-neighbor, linear, cubic, spline or Lanczos interpolator, to name a few. The proposed interpolator is presented as a solution to the modeling problem of static nonlinearities since it is capable of modeling both a function and its inverse function. Three study cases from literature are presented, a single-input single-output (SISO) system, a MISO and a MIMO system. Good results are obtained regarding performance metrics such as set-point tracking, control variation and robustness. Results demonstrate applicability of the proposed method in modeling Hammerstein nonlinearities and their inverse functions for implementation of an output compensator with Model Based Predictive Control (MBPC), in particular Dynamic Matrix Control (DMC). PMID:27657723

Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

NASA Astrophysics Data System (ADS)

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-01

A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

EvArnoldi: A New Algorithm for Large-Scale Eigenvalue Problems.

PubMed

Tal-Ezer, Hillel

2016-05-19

Eigenvalues and eigenvectors are an essential theme in numerical linear algebra. Their study is mainly motivated by their high importance in a wide range of applications. Knowledge of eigenvalues is essential in quantum molecular science. Solutions of the Schrödinger equation for the electrons composing the molecule are the basis of electronic structure theory. Electronic eigenvalues compose the potential energy surfaces for nuclear motion. The eigenvectors allow calculation of diople transition matrix elements, the core of spectroscopy. The vibrational dynamics molecule also requires knowledge of the eigenvalues of the vibrational Hamiltonian. Typically in these problems, the dimension of Hilbert space is huge. Practically, only a small subset of eigenvalues is required. In this paper, we present a highly efficient algorithm, named EvArnoldi, for solving the large-scale eigenvalues problem. The algorithm, in its basic formulation, is mathematically equivalent to ARPACK ( Sorensen , D. C. Implicitly Restarted Arnoldi/Lanczos Methods for Large Scale Eigenvalue Calculations ; Springer , 1997 ; Lehoucq , R. B. ; Sorensen , D. C. SIAM Journal on Matrix Analysis and Applications 1996 , 17 , 789 ; Calvetti , D. ; Reichel , L. ; Sorensen , D. C. Electronic Transactions on Numerical Analysis 1994 , 2 , 21 ) (or Eigs of Matlab) but significantly simpler.

Accurate Determination of the Quasiparticle and Scaling Properties Surrounding the Quantum Critical Point of Disordered Three-Dimensional Dirac Semimetals.

PubMed

Fu, Bo; Zhu, Wei; Shi, Qinwei; Li, Qunxiang; Yang, Jinlong; Zhang, Zhenyu

2017-04-07

Exploiting the enabling power of the Lanczos method in momentum space, we determine accurately the quasiparticle and scaling properties of disordered three-dimensional Dirac semimetals surrounding the quantum critical point separating the semimetal and diffusive metal regimes. We unveil that the imaginary part of the quasiparticle self-energy obeys a common power law before, at, and after the quantum phase transition, but the power law is nonuniversal, whose exponent is dependent on the disorder strength. More intriguingly, whereas a common power law is also found for the real part of the self-energy before and after the phase transition, a distinctly different behavior is identified at the critical point, characterized by the existence of a nonanalytic logarithmic singularity. This nonanalytical correction serves as the very basis for the unusual power-law behaviors of the quasiparticles and many other physical properties surrounding the quantum critical point. Our approach also allows the ready and reliable determination of the scaling properties of the correlation length and dynamical exponents. We further show that the central findings are valid for both uncorrelated and correlated disorder distributions and should be directly comparable with future experimental observations.

Accurate Determination of the Quasiparticle and Scaling Properties Surrounding the Quantum Critical Point of Disordered Three-dimensional Dirac Semimetals

DOE PAGES

Fu, Bo; Zhu, Wei; Shi, Qinwei; ...

2017-04-03

Exploiting the enabling power of the Lanczos method in momentum space, we determine accurately the quasiparticle and scaling properties of disordered three-dimensional Dirac semimetals surrounding the quantum critical point separating the semimetal and diffusive metal regimes. We unveil that the imaginary part of the quasiparticle self-energy obeys a common power law before, at, and after the quantum phase transition, but the power law is nonuniversal, whose exponent is dependent on the disorder strength. More intriguingly, whereas a common power law is also found for the real part of the self-energy before and after the phase transition, a distinctly different behaviormore » is identified at the critical point, characterized by the existence of a nonanalytic logarithmic singularity. This nonanalytical correction serves as the very basis for the unusual power-law behaviors of the quasiparticles and many other physical properties surrounding the quantum critical point. Our approach also allows the ready and reliable determination of the scaling properties of the correlation length and dynamical exponents. Furthermore, we show that the central findings are valid for both uncorrelated and correlated disorder distributions and should be directly comparable with future experimental observations.« less

Singlet Orbital Ordering in Bilayer Sr_{3}Cr_{2}O_{7}.

PubMed

Jeanneau, Justin; Toulemonde, Pierre; Remenyi, Gyorgy; Sulpice, André; Colin, Claire; Nassif, Vivian; Suard, Emmanuelle; Salas Colera, Eduardo; Castro, Germán R; Gay, Frederic; Urdaniz, Corina; Weht, Ruben; Fevrier, Clement; Ralko, Arnaud; Lacroix, Claudine; Aligia, Armando A; Núñez-Regueiro, Manuel

2017-05-19

We perform an extensive study of Sr_{3}Cr_{2}O_{7}, the n=2 member of the Ruddlesden-Popper Sr_{n+1}Cr_{n}O_{3n+1} system. An antiferromagnetic ordering is clearly visible in the magnetization and the specific heat, which yields a huge transition entropy, Rln(6). By neutron diffraction as a function of temperature we have determined the antiferromagnetic structure that coincides with the one obtained from density functional theory calculations. It is accompanied by anomalous asymmetric distortions of the CrO_{6} octahedra. Strong coupling and Lanczos calculations on a derived Kugel-Khomskii Hamiltonian yield a simultaneous orbital and moment ordering. Our results favor an exotic ordered phase of orbital singlets not originated by frustration.

Gravitational surface Hamiltonian and entropy quantization

NASA Astrophysics Data System (ADS)

Bakshi, Ashish; Majhi, Bibhas Ranjan; Samanta, Saurav

2017-02-01

The surface Hamiltonian corresponding to the surface part of a gravitational action has xp structure where p is conjugate momentum of x. Moreover, it leads to TS on the horizon of a black hole. Here T and S are temperature and entropy of the horizon. Imposing the hermiticity condition we quantize this Hamiltonian. This leads to an equidistant spectrum of its eigenvalues. Using this we show that the entropy of the horizon is quantized. This analysis holds for any order of Lanczos-Lovelock gravity. For general relativity, the area spectrum is consistent with Bekenstein's observation. This provides a more robust confirmation of this earlier result as the calculation is based on the direct quantization of the Hamiltonian in the sense of usual quantum mechanics.

Modal Test/Analysis Correlation of Space Station Structures Using Nonlinear Sensitivity

NASA Technical Reports Server (NTRS)

Gupta, Viney K.; Newell, James F.; Berke, Laszlo; Armand, Sasan

1992-01-01

The modal correlation problem is formulated as a constrained optimization problem for validation of finite element models (FEM's). For large-scale structural applications, a pragmatic procedure for substructuring, model verification, and system integration is described to achieve effective modal correlation. The space station substructure FEM's are reduced using Lanczos vectors and integrated into a system FEM using Craig-Bampton component modal synthesis. The optimization code is interfaced with MSC/NASTRAN to solve the problem of modal test/analysis correlation; that is, the problem of validating FEM's for launch and on-orbit coupled loads analysis against experimentally observed frequencies and mode shapes. An iterative perturbation algorithm is derived and implemented to update nonlinear sensitivity (derivatives of eigenvalues and eigenvectors) during optimizer iterations, which reduced the number of finite element analyses.

Modal test/analysis correlation of Space Station structures using nonlinear sensitivity

NASA Technical Reports Server (NTRS)

Gupta, Viney K.; Newell, James F.; Berke, Laszlo; Armand, Sasan

1992-01-01

The modal correlation problem is formulated as a constrained optimization problem for validation of finite element models (FEM's). For large-scale structural applications, a pragmatic procedure for substructuring, model verification, and system integration is described to achieve effective modal correlations. The space station substructure FEM's are reduced using Lanczos vectors and integrated into a system FEM using Craig-Bampton component modal synthesis. The optimization code is interfaced with MSC/NASTRAN to solve the problem of modal test/analysis correlation; that is, the problem of validating FEM's for launch and on-orbit coupled loads analysis against experimentally observed frequencies and mode shapes. An iterative perturbation algorithm is derived and implemented to update nonlinear sensitivity (derivatives of eigenvalues and eigenvectors) during optimizer iterations, which reduced the number of finite element analyses.

Frequency-selective quantitation of short-echo time 1H magnetic resonance spectra

NASA Astrophysics Data System (ADS)

Poullet, Jean-Baptiste; Sima, Diana M.; Van Huffel, Sabine; Van Hecke, Paul

2007-06-01

Accurate and efficient filtering techniques are required to suppress large nuisance components present in short-echo time magnetic resonance (MR) spectra. This paper discusses two powerful filtering techniques used in long-echo time MR spectral quantitation, the maximum-phase FIR filter (MP-FIR) and the Hankel-Lanczos Singular Value Decomposition with Partial ReOrthogonalization (HLSVD-PRO), and shows that they can be applied to their more complex short-echo time spectral counterparts. Both filters are validated and compared through extensive simulations. Their properties are discussed. In particular, the capability of MP-FIR for dealing with macromolecular components is emphasized. Although this property does not make a large difference for long-echo time MR spectra, it can be important when quantifying short-echo time spectra.

An Approach to Unbiased Subsample Interpolation for Motion Tracking

PubMed Central

McCormick, Matthew M.; Varghese, Tomy

2013-01-01

Accurate subsample displacement estimation is necessary for ultrasound elastography because of the small deformations that occur and the subsequent application of a derivative operation on local displacements. Many of the commonly used subsample estimation techniques introduce significant bias errors. This article addresses a reduced bias approach to subsample displacement estimations that consists of a two-dimensional windowed-sinc interpolation with numerical optimization. It is shown that a Welch or Lanczos window with a Nelder–Mead simplex or regular-step gradient-descent optimization is well suited for this purpose. Little improvement results from a sinc window radius greater than four data samples. The strain signal-to-noise ratio (SNR) obtained in a uniformly elastic phantom is compared with other parabolic and cosine interpolation methods; it is found that the strain SNR ratio is improved over parabolic interpolation from 11.0 to 13.6 in the axial direction and 0.7 to 1.1 in the lateral direction for an applied 1% axial deformation. The improvement was most significant for small strains and displacement tracking in the lateral direction. This approach does not rely on special properties of the image or similarity function, which is demonstrated by its effectiveness with the application of a previously described regularization technique. PMID:23493609

Spatial structure of correlations around a quantum impurity at the edge of a two-dimensional topological insulator

NASA Astrophysics Data System (ADS)

Allerdt, Andrew; Feiguin, A. E.; Martins, G. B.

2017-07-01

We calculate exact zero-temperature real-space properties of a substitutional magnetic impurity coupled to the edge of a zigzag silicenelike nanoribbon. Using a Lanczos transformation [A. Allerdt et al., Phys. Rev. B 91, 085101 (2015), 10.1103/PhysRevB.91.085101] and the density-matrix renormalization-group method, we obtain a realistic description of stanene and germanene that includes the bulk and the edges as boundary one-dimensional helical metallic states. Our results for substitutional impurities indicate that the development of a Kondo state and the structure of the spin correlations between the impurity and the electron spins in the metallic edge state depend considerably on the location of the impurity. More specifically, our real-space resolution allows us to conclude that there is a sharp distinction between the impurity being located at a crest or a trough site at the zigzag edge. We also observe, as expected, that the spin correlations are anisotropic due to an emerging Dzyaloshinskii-Moriya interaction with the conduction electrons and that the edges scatter from the impurity and "snake" or circle around it. Our estimates for the Kondo temperature indicate that there is a very weak enhancement due to the presence of spin-orbit coupling.

Comparative Investigation on Modal analysis of LM25 Aluminium alloy with other Aluminim alloys using Finite element analysis software

NASA Astrophysics Data System (ADS)

Arunkumar, S.; Baskaralal, V. P. M.; Muthuraman, V.

2017-03-01

The rudimentary steps of the modal analysis and simulation are carried out. The modal analysis is carried out on the different Aluminum Alloys cantilever beam. The cantilever beam is designed in the graphical environment of the ANSYS. The cantilever beam was fine-tuned on one end with all degree of liberation on this end were taken, beam cannot move and rotate. Mode shapes and natural frequencies are premeditated in platforms ANSYS with arithmetical formulation of the direct solver including the block Lanczos method. Aluminum alloys are widely utilized in much application due to their estimable weight to vigor property. Many examination works have been distributed out to make developments the mechanical properties of aluminum alloys. The composition of alloying elements plays a consequential role in deciding the properties of an alloy. In this study a numerical analysis implement i.e., finite element analysis (FEA) is utilized. The work obtainable in this paper is aimed at the study of effect of modal analysis of different aluminum alloys. The modeling and analysis is carried out utilizing ANSYS FEA software. A modal analysis is carried out to understand the modes of frequency demeanor of the material considered. The modal analysis play a vital role in the design of components subjected to high vibration.

Simple systematization of vibrational excitation cross-section calculations for resonant electron-molecule scattering in the boomerang and impulse models.

PubMed

Sarma, Manabendra; Adhikari, S; Mishra, Manoj K

2007-01-28

Vibrational excitation (nu(f)<--nu(i)) cross-sections sigma(nu(f)<--nu(i) )(E) in resonant e-N(2) and e-H(2) scattering are calculated from transition matrix elements T(nu(f),nu(i) )(E) obtained using Fourier transform of the cross correlation function , where psi(nu(i))(R,t) approximately =e(-iH(A(2))-(R)t/h phi(nu(i))(R) with time evolution under the influence of the resonance anionic Hamiltonian H(A(2) (-))(A(2) (-)=N(2)(-)/H(2) (-)) implemented using Lanczos and fast Fourier transforms. The target (A(2)) vibrational eigenfunctions phi(nu(i))(R) and phi(nu(f))(R) are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curves of the neutral target. Application of this simple systematization to calculate vibrational structure in e-N(2) and e-H(2) scattering cross-sections provides mechanistic insights into features underlying presence/absence of structure in e-N(2) and e-H(2) scattering cross-sections. The results obtained with approximate PE curves are in reasonable agreement with experimental/calculated cross-section profiles, and cross correlation functions provide a simple demarcation between the boomerang and impulse models.

Ground-State of the Bose-Hubbard Model

NASA Astrophysics Data System (ADS)

Mancini, J. D.; Fessatidis, V.; Bowen, S. P.; Murawski, R. K.; Maly, J.

The Bose-Hubbard Model represents a s simple theoretical model to describe the physics of interacting Boson systems. In particular it has proved to be an effective description of a number of physical systems such as arrays of Josephson arrays as well as dilute alkali gases in optical lattices. Here we wish to study the ground-state of this system using two disparate but related moments calculational schemes: the Lanczos (tridiagonal) method as well as a Generalized moments approach. The Hamiltonian to be studied is given by (in second-quantized notation): H = - t ∑ < i , j > bi†bj +U/2 ∑ inini - 1 - μ ∑ ini . Here i is summed over all lattice sites, and < i , j > denotes summation over all neighbhoring sites i and j, while bi† and bi are bosonic creation and annihilation operators. ni = bi†bi gives the number of particles on site i. Parameter t is the hopping amplitude, describing mobility of bosons in the lattice. Parameter U describes the on-site interaction, repulsive, if U > 0 , and attractive for U < 0 . μ is the chemical potential. Both the ground-state energy and energy gap are evaluated as a function of t, U and μ.

Geodetic imaging: Reservoir monitoring using satellite interferometry

USGS Publications Warehouse

Vasco, D.W.; Wicks, C.; Karasaki, K.; Marques, O.

2002-01-01

Fluid fluxes within subsurface reservoirs give rise to surface displacements, particularly over periods of a year or more. Observations of such deformation provide a powerful tool for mapping fluid migration within the Earth, providing new insights into reservoir dynamics. In this paper we use Interferometric Synthetic Aperture Radar (InSAR) range changes to infer subsurface fluid volume strain at the Coso geothermal field. Furthermore, we conduct a complete model assessment, using an iterative approach to compute model parameter resolution and covariance matrices. The method is a generalization of a Lanczos-based technique which allows us to include fairly general regularization, such as roughness penalties. We find that we can resolve quite detailed lateral variations in volume strain both within the reservoir depth range (0.4-2.5 km) and below the geothermal production zone (2.5-5.0 km). The fractional volume change in all three layers of the model exceeds the estimated model parameter uncertainly by a factor of two or more. In the reservoir depth interval (0.4-2.5 km), the predominant volume change is associated with northerly and westerly oriented faults and their intersections. However, below the geothermal production zone proper [the depth range 2.5-5.0 km], there is the suggestion that both north- and northeast-trending faults may act as conduits for fluid flow.

Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

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

Han, Huixian; School of Physics, Northwest University, Xi’an, Shaanxi 710069; Li, Anyang

2014-12-28

A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies upmore » to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.« less

Quantum mechanical model for the anticarcinogenic effect of extremely-low-frequency electromagnetic fields on early chemical hepatocarcinogenesis

NASA Astrophysics Data System (ADS)

Godina-Nava, Juan José; Torres-Vega, Gabino; López-Riquelme, Germán Octavio; López-Sandoval, Eduardo; Samana, Arturo Rodolfo; García Velasco, Fermín; Hernández-Aguilar, Claudia; Domínguez-Pacheco, Arturo

2017-02-01

Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2017-03-14

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H 2 O-Cl - . When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H 2 O-Cl - , there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2017-03-01

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H2O-Cl-. When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H2O-Cl-, there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Ground state of a Heisenberg chain with next-nearest-neighbor bond alternation

NASA Astrophysics Data System (ADS)

Capriotti, Luca; Becca, Federico; Sorella, Sandro; Parola, Alberto

2003-05-01

We investigate the ground-state properties of the spin-half J1-J2 Heisenberg chain with a next-nearest-neighbor spin-Peierls dimerization using conformal field theory and Lanczos exact diagonalizations. In agreement with the results of a recent bosonization analysis by Sarkar and Sen [Phys. Rev. B 65, 172408 (2002)], we find that for small frustration (J2/J1) the system is in a Luttinger spin-fluid phase, with gapless excitations, and a finite spin-wave velocity. In the regime of strong frustration the ground state is spontaneously dimerized and the bond alternation reduces the triplet gap, leading to a slight enhancement of the critical point separating the Luttinger phase from the gapped one. An accurate determination of the phase boundary is obtained numerically from the study of the excitation spectrum.

Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS-H2

NASA Astrophysics Data System (ADS)

Liu, Jing-Min; Zhai, Yu; Li, Hui

2017-07-01

An effective six-dimensional ab initio potential energy surface (PES) for H2-OCS which explicitly includes the intramolecular stretch normal modes of carbonyl sulfide (OCS) is presented. The electronic structure computations are carried out using the explicitly correlated coupled cluster [CCSD(T)-F12] method with the augmented correlation-consistent aug-cc-pVTZ basis set, and the accuracy is critically tested by performing a series of benchmark calculations. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies to the Morse/long-range potential model. These fits to 13 485 points have a root-mean-square deviation (RMSD) of 0.16 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for five isotopic species of the OCS-hydrogen complexes. The predicted transition frequencies and intensities based on the resulting vibrationally averaged PESs are in good agreement with the available experimental values, whose RMSDs are smaller than 0.004 cm-1 for five different species of OCS-hydrogen complexes. The calculated infrared band origin shifts for all five species of OCS-hydrogen complexes are only 0.03 cm-1 smaller than the corresponding experimental values. These validate the high quality of our PESs which can be used for modeling OCS doped in hydrogen clusters to further study quantum solution and microscopic superfluidity. In addition, the analytic coordinate transformation functions between isotopologues are also derived due to the center of mass shifting of different isotope substitutes.

Accelerating atomistic calculations of quantum energy eigenstates on graphic cards

NASA Astrophysics Data System (ADS)

Rodrigues, Walter; Pecchia, A.; Lopez, M.; Auf der Maur, M.; Di Carlo, A.

2014-10-01

Electronic properties of nanoscale materials require the calculation of eigenvalues and eigenvectors of large matrices. This bottleneck can be overcome by parallel computing techniques or the introduction of faster algorithms. In this paper we report a custom implementation of the Lanczos algorithm with simple restart, optimized for graphical processing units (GPUs). The whole algorithm has been developed using CUDA and runs entirely on the GPU, with a specialized implementation that spares memory and reduces at most machine-to-device data transfers. Furthermore parallel distribution over several GPUs has been attained using the standard message passing interface (MPI). Benchmark calculations performed on a GaN/AlGaN wurtzite quantum dot with up to 600,000 atoms are presented. The empirical tight-binding (ETB) model with an sp3d5s∗+spin-orbit parametrization has been used to build the system Hamiltonian (H).

Aspects of Quantum Theory

NASA Astrophysics Data System (ADS)

Salam, Abdus; Wigner, E. P.

2010-03-01

Preface; List of contributors; Bibliography of P. A. M. Dirac; 1. Dirac in Cambridge R. J. Eden and J. C. Polkinghorne; 2. Travels with Dirac in the Rockies J. H. Van Vleck; 3. 'The golden age of theoretical physics': P. A. M. Dirac's scientific work from 1924 to 1933 Jagdish Mehra; 4. Foundation of quantum field theory Res Jost; 5. The early history of the theory of electron: 1897-1947 A. Pais; 6. The Dirac equation A. S. Wightman; 7. Fermi-Dirac statistics Rudolph Peierls; 8. Indefinite metric in state space W. Heisenberg; 9. On bras and kets J. M. Jauch; 10. The Poisson bracket C. Lanczos; 11. La 'fonction' et les noyaux L. Schwartz; 12. On the Dirac magnetic poles Edoardo Amadli and Nicola Cabibbo; 13. The fundamental constants and their time variation Freeman J. Dyson; 14. On the time-energy uncertainty relation Eugene P. Wigner; 15. The path-integral quantisation of gravity Abdus Salam and J. Strathdee; Index; Plates.

Brane surgery: energy conditions, traversable wormholes, and voids

NASA Astrophysics Data System (ADS)

Barceló1, C.; Visser, M.

2000-09-01

Branes are ubiquitous elements of any low-energy limit of string theory. We point out that negative tension branes violate all the standard energy conditions of the higher-dimensional spacetime they are embedded in; this opens the door to very peculiar solutions of the higher-dimensional Einstein equations. Building upon the (/3+1)-dimensional implementation of fundamental string theory, we illustrate the possibilities by considering a toy model consisting of a (/2+1)-dimensional brane propagating through our observable (/3+1)-dimensional universe. Developing a notion of ``brane surgery'', based on the Israel-Lanczos-Sen ``thin shell'' formalism of general relativity, we analyze the dynamics and find traversable wormholes, closed baby universes, voids (holes in the spacetime manifold), and an evasion (not a violation) of both the singularity theorems and the positive mass theorem. These features appear generic to any brane model that permits negative tension branes: This includes the Randall-Sundrum models and their variants.

Persistence of the gapless spin liquid in the breathing kagome Heisenberg antiferromagnet

NASA Astrophysics Data System (ADS)

Iqbal, Yasir; Poilblanc, Didier; Thomale, Ronny; Becca, Federico

2018-03-01

The nature of the ground state of the spin S =1 /2 Heisenberg antiferromagnet on the kagome lattice with breathing anisotropy (i.e., with different superexchange couplings J▵ and J▿ within elementary up- and down-pointing triangles) is investigated within the framework of Gutzwiller projected fermionic wave functions and Monte Carlo methods. We analyze the stability of the U(1 ) Dirac spin liquid with respect to the presence of fermionic pairing that leads to a gapped Z2 spin liquid. For several values of the ratio J▿/J▵ , the size scaling of the energy gain due to the pairing fields and the variational parameters are reported. Our results show that the energy gain of the gapped spin liquid with respect to the gapless state either vanishes for large enough system size or scales to zero in the thermodynamic limit. Similarly, the optimized pairing amplitudes (responsible for opening the spin gap) are shown to vanish in the thermodynamic limit. Our outcome is corroborated by the application of one and two Lanczos steps to the gapless and gapped wave functions, for which no energy gain of the gapped state is detected when improving the quality of the variational states. Finally, we discuss the competition with the "simplex" Z2 resonating-valence-bond spin liquid, valence-bond crystal, and nematic states in the strongly anisotropic regime, i.e., J▿≪J▵ .

Large scale Brownian dynamics of confined suspensions of rigid particles

NASA Astrophysics Data System (ADS)

Sprinkle, Brennan; Balboa Usabiaga, Florencio; Patankar, Neelesh A.; Donev, Aleksandar

2017-12-01

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.

Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces

NASA Astrophysics Data System (ADS)

Bajaj, Pushp; Wang, Xiao-Gang; Carrington, Tucker; Paesani, Francesco

2018-03-01

Full-dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range. Specifically, while both models describe long-range interactions through the combination of two-body dispersion and many-body classical electrostatics, the relatively simple Born-Mayer functions employed in the TTM-nrg PEFs to represent short-range interactions are replaced in the MB-nrg PEFs by permutationally invariant polynomials to achieve chemical accuracy. For all dimers, the MB-nrg vibrational spectra are in close agreement with the available experimental data, correctly reproducing anharmonic and nuclear quantum effects. In contrast, the vibrational frequencies calculated with the TTM-nrg PEFs exhibit significant deviations from the experimental values. The comparison between the TTM-nrg and MB-nrg results thus reinforces the notion that an accurate representation of both short-range interactions associated with electron density overlap and long-range many-body electrostatic interactions is necessary for a correct description of hydration phenomena at the molecular level.

Computational study of the rovibrational spectrum of CO₂-CS₂.

PubMed

Brown, James; Wang, Xiao-Gang; Carrington, Tucker; Grubbs, G S; Dawes, Richard

2014-03-21

A new intermolecular potential energy surface, rovibrational transition frequencies, and line strengths are computed for CO2-CS2. The potential is made by fitting energies obtained from explicitly correlated coupled-cluster calculations using an interpolating moving least squares method. The rovibrational Schrödinger equation is solved with a symmetry-adapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. In agreement with previous experiments, the global minimum of the potential energy surface (PES) is cross shaped. The PES also has slipped-parallel minima. Rovibrational wavefunctions are localized in the cross minima and the slipped-parallel minima. Vibrational parent analysis was used to assign vibrational labels to rovibrational states. Tunneling occurs between the two cross minima. Because more than one symmetry operation interconverts the two wells, the symmetry (-oo) of the upper component of the tunneling doublet is different from the symmetry (-ee) of the tunneling coordinate. This unusual situation is due to the multidimensional nature of the double well tunneling. For the cross ground vibrational state, calculated rotational constants differ from their experimental counterparts by less than 0.0001 cm(-1). Most rovibrational states were found to be incompatible with the standard effective rotational Hamiltonian often used to fit spectra. This appears to be due to coupling between internal and overall rotation of the dimer. A simple 2D model accounting for internal rotation was used for two cross-shaped fundamentals to obtain good fits.

Influence of the piezoelectric parameters on the dynamics of an active rotor

NASA Astrophysics Data System (ADS)

Gawryluk, Jarosław; Mitura, Andrzej; Teter, Andrzej

2018-01-01

The main aim of this paper is an experimental and numerical analysis of the dynamic behavior of an active rotor with three composite blades. The study focuses on developing an effective FE modeling technique of a macro fiber composite element (denoted as MFC or active element) for the dynamic tests of active structures. The active rotor under consideration consists of a hub with a drive shaft, three grips and three glass-epoxy laminate blades with embedded active elements. A simplified FE model of the macro fiber composite element exhibiting the d33 piezoelectric effect is developed using the Abaqus software package. The discussed transducer is modeled as quasi-homogeneous piezoelectric material, and voltage is applied to the opposite faces of the element. In this case, the effective (equivalent) piezoelectric constant d33* is specified. Both static and dynamic tests are performed to verify the proposed model. First, static deflections of the active blade caused by the voltage signal are determined by numerical and experimental analyses. Next, a numerical modal analysis of the active rotor is performed. The eigenmodes and corresponding eigenfrequencies are determined by the Lanczos method. The influence of the model parameters (i.e., the effective piezoelectric constant d33 *, voltage signal, angular velocity) on the dynamics of the active rotor is examined. Finally, selected numerical results are validated in experimental tests. The experimental findings demonstrate that the structural stiffening effect caused by the active element strongly depends on the value of the effective piezoelectric constant.

Fast Katz and Commuters: Efficient Estimation of Social Relatedness in Large Networks

NASA Astrophysics Data System (ADS)

Esfandiar, Pooya; Bonchi, Francesco; Gleich, David F.; Greif, Chen; Lakshmanan, Laks V. S.; On, Byung-Won

Motivated by social network data mining problems such as link prediction and collaborative filtering, significant research effort has been devoted to computing topological measures including the Katz score and the commute time. Existing approaches typically approximate all pairwise relationships simultaneously. In this paper, we are interested in computing: the score for a single pair of nodes, and the top-k nodes with the best scores from a given source node. For the pairwise problem, we apply an iterative algorithm that computes upper and lower bounds for the measures we seek. This algorithm exploits a relationship between the Lanczos process and a quadrature rule. For the top-k problem, we propose an algorithm that only accesses a small portion of the graph and is related to techniques used in personalized PageRank computing. To test the scalability and accuracy of our algorithms we experiment with three real-world networks and find that these algorithms run in milliseconds to seconds without any preprocessing.

Fast katz and commuters : efficient estimation of social relatedness in large networks.

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

On, Byung-Won; Lakshmanan, Laks V. S.; Greif, Chen

Motivated by social network data mining problems such as link prediction and collaborative filtering, significant research effort has been devoted to computing topological measures including the Katz score and the commute time. Existing approaches typically approximate all pairwise relationships simultaneously. In this paper, we are interested in computing: the score for a single pair of nodes, and the top-k nodes with the best scores from a given source node. For the pairwise problem, we apply an iterative algorithm that computes upper and lower bounds for the measures we seek. This algorithm exploits a relationship between the Lanczos process and amore » quadrature rule. For the top-k problem, we propose an algorithm that only accesses a small portion of the graph and is related to techniques used in personalized PageRank computing. To test the scalability and accuracy of our algorithms we experiment with three real-world networks and find that these algorithms run in milliseconds to seconds without any preprocessing.« less

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 rigorous full-dimensional quantum dynamics study of tunneling splitting of rovibrational states of vinyl radical C 2 H 3

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

Yu, Hua-Gen; Song, Hongwei; Yang, Minghui

Here, we report a rigorous quantum mechanical study of the rovibrational energy levels of vinyl radical C 2H 3. The calculations are carried out using a real two-component multi-layer Lanczos algorithm in a set of orthogonal polyspherical coordinates based on a recently developed accurate ab initio potential energy surface of C 2H 3. All well converged 158 vibrational bands up to 3200 cm -1 are determined, together with a comparison to previous calculations and experimental results. Our results show a remarkable multi-dimensional tunneling effect on the vibrational spectra of the radical. The vibrational tunneling splitting is substantially different from thatmore » of previous reduced dimensional calculations. The rotational constants of the fundamental vibrational bands of C 2H 3 are also given. It was found that the rovibrational states are strongly coupled, especially among those bending vibrational modes. Additionally, the perturbative iteration approach of Gruebele has been extended to assign the rovibrational energy levels of C 2H 3 without the requirement of explicit wavefunctions.« less

A rigorous full-dimensional quantum dynamics study of tunneling splitting of rovibrational states of vinyl radical C2H3.

PubMed

Yu, Hua-Gen; Song, Hongwei; Yang, Minghui

2017-06-14

We report a rigorous quantum mechanical study of the rovibrational energy levels of vinyl radical C 2 H 3 . The calculations are carried out using a real two-component multi-layer Lanczos algorithm in a set of orthogonal polyspherical coordinates based on a recently developed accurate ab initio potential energy surface of C 2 H 3 . All well converged 158 vibrational bands up to 3200 cm -1 are determined, together with a comparison to previous calculations and experimental results. Results show a remarkable multi-dimensional tunneling effect on the vibrational spectra of the radical. The vibrational tunneling splitting is substantially different from that of previous reduced dimensional calculations. The rotational constants of the fundamental vibrational bands of C 2 H 3 are also given. It was found that the rovibrational states are strongly coupled, especially among those bending vibrational modes. In addition, the perturbative iteration approach of Gruebele has been extended to assign the rovibrational energy levels of C 2 H 3 without the requirement of explicit wavefunctions.

A rigorous full-dimensional quantum dynamics study of tunneling splitting of rovibrational states of vinyl radical C 2 H 3

DOE PAGES

Yu, Hua-Gen; Song, Hongwei; Yang, Minghui

2017-06-12

Here, we report a rigorous quantum mechanical study of the rovibrational energy levels of vinyl radical C 2H 3. The calculations are carried out using a real two-component multi-layer Lanczos algorithm in a set of orthogonal polyspherical coordinates based on a recently developed accurate ab initio potential energy surface of C 2H 3. All well converged 158 vibrational bands up to 3200 cm -1 are determined, together with a comparison to previous calculations and experimental results. Our results show a remarkable multi-dimensional tunneling effect on the vibrational spectra of the radical. The vibrational tunneling splitting is substantially different from thatmore » of previous reduced dimensional calculations. The rotational constants of the fundamental vibrational bands of C 2H 3 are also given. It was found that the rovibrational states are strongly coupled, especially among those bending vibrational modes. Additionally, the perturbative iteration approach of Gruebele has been extended to assign the rovibrational energy levels of C 2H 3 without the requirement of explicit wavefunctions.« less

The evolution of Brown-York quasilocal energy as due to evolution of Lovelock gravity in a system of M0-branes

NASA Astrophysics Data System (ADS)

Sepehri, Alireza; Rahaman, Farook; Capozziello, Salvatore; Ali, Ahmed Farag; Pradhan, Anirudh

Recently, it has been suggested in [S. Chakraborty and N. Dadhich, Brown-York quasilocal energy in Lanczos-Lovelock gravity and black hole horizons, J. High Energ. Phys. 12 (2015) 003.] that the Brown-York mechanism can be used to measure the quasilocal energy in Lovelock gravity. We have used this method in a system of M0-branes and show that the Brown-York energy evolves in the process of birth and growth of Lovelock gravity. This can help us to predict phenomenological events which are emerged as due to dynamical structure of Lovelock gravity in our universe. In this model, first, M0-branes join each other and form an M3-brane and an anti-M3-branes connected by an M2-brane. This system is named BIon. Universes and anti-universes live on M3-branes and M2 plays the role of wormhole between them. By passing time, M2 dissolves in M3’s and nonlinear massive gravities like Lovelock massive gravity emerges and grows. By closing M3-branes, BIon evolves and wormhole between branes makes a transition to black hole. During this stage, Brown-York energy increases and shrinks to large values at the colliding points of branes. By approaching M3-branes towards each other, the square energy of their system becomes negative and some tachyonic states are produced. To remove these states, M3-branes compact, the sign of compacted gravity changes, anti-gravity is created which leads to getting away of branes from each other. Also, the Lovelock gravity disappears and its energy forms a new M2 between M3-branes. By getting away of branes from each other, Brown-York energy decreases and shrinks to zero.

Large computer simulations on elastic networks: Small eigenvalues and eigenvalue spectra of the Kirchhoff matrix

NASA Astrophysics Data System (ADS)

Shy, L. Y.; Eichinger, B. E.

1989-05-01

Computer simulations of the formation of trifunctional and tetrafunctional polydimethyl-siloxane networks that are crosslinked by condensation of telechelic chains with multifunctional crosslinking agents have been carried out on systems containing up to 1.05×106 chains. Eigenvalue spectra of Kirchhoff matrices for these networks have been evaluated at two levels of approximation: (1) inclusion of all midchain modes, and (2) suppression of midchain modes. By use of the recursion method of Haydock and Nex, we have been able to effectively diagonalize matrices with 730 498 rows and columns without actually constructing matrices of this size. The small eigenvalues have been computed by use of the Lanczos algorithm. We demonstrate the following results: (1) The smallest eigenvalues (with chain modes suppressed) vary as μ-2/3 for sufficiently large μ, where μ is the number of junctions in the network; (2) the eigenvalue spectra of the Kirchhoff matrices are well described by McKay's theory for random regular graphs in the range of the larger eigenvalues, but there are significant departures in the region of small eigenvalues where computed spectra have many more small eigenvalues than random regular graphs; (3) the smallest eigenvalues vary as n-1.78 where n is the number of Rouse beads in the chains that comprise the network. Computations are done for both monodisperse and polydisperse chain length distributions. Large eigenvalues associated with localized motion of the junctions are found as predicted by theory. The relationship between the small eigenvalues and the equilibrium modulus of elasticity is discussed, as is the relationship between viscoelasticity and the band edge of the spectrum.

Break point on the auto-correlation function of Elsässer variable z- in the super-Alfvénic solar wind fluctuations

NASA Astrophysics Data System (ADS)

Wang, X.; Tu, C. Y.; He, J.; Wang, L.

2017-12-01

It has been a longstanding debate on what the nature of Elsässer variables z- observed in the Alfvénic solar wind is. It is widely believed that z- represents inward propagating Alfvén waves and undergoes non-linear interaction with z+ to produce energy cascade. However, z- variations sometimes show nature of convective structures. Here we present a new data analysis on z- autocorrelation functions to get some definite information on its nature. We find that there is usually a break point on the z- auto-correlation function when the fluctuations show nearly pure Alfvénicity. The break point observed by Helios-2 spacecraft near 0.3 AU is at the first time lag ( 81 s), where the autocorrelation coefficient has the value less than that at zero-time lag by a factor of more than 0.4. The autocorrelation function breaks also appear in the WIND observations near 1 AU. The z- autocorrelation function is separated by the break into two parts: fast decreasing part and slowly decreasing part, which cannot be described in a whole by an exponential formula. The breaks in the z- autocorrelation function may represent that the z- time series are composed of high-frequency white noise and low-frequency apparent structures, which correspond to the flat and steep parts of the function, respectively. This explanation is supported by a simple test with a superposition of an artificial random data series and a smoothed random data series. Since in many cases z- autocorrelation functions do not decrease very quickly at large time lag and cannot be considered as the Lanczos type, no reliable value for correlation-time can be derived. Our results showed that in these cases with high Alfvénicity, z- should not be considered as inward-propagating wave. The power-law spectrum of z+ should be made by fluid turbulence cascade process presented by Kolmogorov.

A new approach to spherically symmetric junction surfaces and the matching of FLRW regions

NASA Astrophysics Data System (ADS)

Kirchner, U.

2004-08-01

We investigate timelike junctions (with surface layer) between spherically symmetric solutions of the Einstein-field equation. In contrast to previous investigations, this is done in a coordinate system in which the junction surface motion is absorbed in the metric, while all coordinates are continuous at the junction surface. The evolution equations for all relevant quantities are derived. We discuss the no-surface layer case (boundary surface) and study the behaviour for small surface energies. It is shown that one should expect cases in which the speed of light is reached within a finite proper time. We carefully discuss necessary and sufficient conditions for a possible matching of spherically symmetric sections. For timelike junctions between spherically symmetric spacetime sections we show explicitly that the time component of the Lanczos equation always reduces to an identity (independent of the surface equation of state). The results are applied to the matching of Friedmann Lemaître Robertson Walker (FLRW) models. We discuss 'vacuum bubbles' and closed open junctions in detail. As illustrations several numerical integration results are presented, some of them indicate that (observers comoving with) the junction surface can reach the speed of light within a finite time.

Open-Source Software for Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Oyafuso, Fabiano; Hua, Hook; Tisdale, Edwin; Hart, Don

2004-01-01

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

Numerical Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Oyafuso, Fabiano; Bowen, R. Chris; Boykin, Timothy

2003-01-01

Nanoelectronic Modeling 3-D (NEMO 3-D) is a computer program for numerical modeling of the electronic structure properties of a semiconductor device that is embodied in a crystal containing as many as 16 million atoms in an arbitrary configuration and that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantummechanical behavior of the device resolved to the atomistic level of granularity. The system of electrons in the device is represented by a sparse Hamiltonian matrix that contains hundreds of millions of terms. NEMO 3-D solves the matrix equation on a Beowulf-class cluster computer, by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. In a recent update of NEMO 3-D, a new strain treatment, parameterized for bulk material properties of GaAs and InAs, was developed for two tight-binding submodels. The utility of the NEMO 3-D was demonstrated in an atomistic analysis of the effects of disorder in alloys and, in particular, in bulk In(x)Ga(l-x)As and in In0.6Ga0.4As quantum dots.

Improved L-BFGS diagonal preconditioners for a large-scale 4D-Var inversion system: application to CO2 flux constraints and analysis error calculation

NASA Astrophysics Data System (ADS)

Bousserez, Nicolas; Henze, Daven; Bowman, Kevin; Liu, Junjie; Jones, Dylan; Keller, Martin; Deng, Feng

2013-04-01

This work presents improved analysis error estimates for 4D-Var systems. From operational NWP models to top-down constraints on trace gas emissions, many of today's data assimilation and inversion systems in atmospheric science rely on variational approaches. This success is due to both the mathematical clarity of these formulations and the availability of computationally efficient minimization algorithms. However, unlike Kalman Filter-based algorithms, these methods do not provide an estimate of the analysis or forecast error covariance matrices, these error statistics being propagated only implicitly by the system. From both a practical (cycling assimilation) and scientific perspective, assessing uncertainties in the solution of the variational problem is critical. For large-scale linear systems, deterministic or randomization approaches can be considered based on the equivalence between the inverse Hessian of the cost function and the covariance matrix of analysis error. For perfectly quadratic systems, like incremental 4D-Var, Lanczos/Conjugate-Gradient algorithms have proven to be most efficient in generating low-rank approximations of the Hessian matrix during the minimization. For weakly non-linear systems though, the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS), a quasi-Newton descent algorithm, is usually considered the best method for the minimization. Suitable for large-scale optimization, this method allows one to generate an approximation to the inverse Hessian using the latest m vector/gradient pairs generated during the minimization, m depending upon the available core memory. At each iteration, an initial low-rank approximation to the inverse Hessian has to be provided, which is called preconditioning. The ability of the preconditioner to retain useful information from previous iterations largely determines the efficiency of the algorithm. Here we assess the performance of different preconditioners to estimate the inverse Hessian of a large-scale 4D-Var system. The impact of using the diagonal preconditioners proposed by Gilbert and Le Maréchal (1989) instead of the usual Oren-Spedicato scalar will be first presented. We will also introduce new hybrid methods that combine randomization estimates of the analysis error variance with L-BFGS diagonal updates to improve the inverse Hessian approximation. Results from these new algorithms will be evaluated against standard large ensemble Monte-Carlo simulations. The methods explored here are applied to the problem of inferring global atmospheric CO2 fluxes using remote sensing observations, and are intended to be integrated with the future NASA Carbon Monitoring System.

Applied Mathematics in EM Studies with Special Emphasis on an Uncertainty Quantification and 3-D Integral Equation Modelling

NASA Astrophysics Data System (ADS)

Pankratov, Oleg; Kuvshinov, Alexey

2016-01-01

Despite impressive progress in the development and application of electromagnetic (EM) deterministic inverse schemes to map the 3-D distribution of electrical conductivity within the Earth, there is one question which remains poorly addressed—uncertainty quantification of the recovered conductivity models. Apparently, only an inversion based on a statistical approach provides a systematic framework to quantify such uncertainties. The Metropolis-Hastings (M-H) algorithm is the most popular technique for sampling the posterior probability distribution that describes the solution of the statistical inverse problem. However, all statistical inverse schemes require an enormous amount of forward simulations and thus appear to be extremely demanding computationally, if not prohibitive, if a 3-D set up is invoked. This urges development of fast and scalable 3-D modelling codes which can run large-scale 3-D models of practical interest for fractions of a second on high-performance multi-core platforms. But, even with these codes, the challenge for M-H methods is to construct proposal functions that simultaneously provide a good approximation of the target density function while being inexpensive to be sampled. In this paper we address both of these issues. First we introduce a variant of the M-H method which uses information about the local gradient and Hessian of the penalty function. This, in particular, allows us to exploit adjoint-based machinery that has been instrumental for the fast solution of deterministic inverse problems. We explain why this modification of M-H significantly accelerates sampling of the posterior probability distribution. In addition we show how Hessian handling (inverse, square root) can be made practicable by a low-rank approximation using the Lanczos algorithm. Ultimately we discuss uncertainty analysis based on stochastic inversion results. In addition, we demonstrate how this analysis can be performed within a deterministic approach. In the second part, we summarize modern trends in the development of efficient 3-D EM forward modelling schemes with special emphasis on recent advances in the integral equation approach.

Quantum entanglement and criticality of the antiferromagnetic Heisenberg model in an external field.

PubMed

Liu, Guang-Hua; Li, Ruo-Yan; Tian, Guang-Shan

2012-06-27

By Lanczos exact diagonalization and the infinite time-evolving block decimation (iTEBD) technique, the two-site entanglement as well as the bipartite entanglement, the ground state energy, the nearest-neighbor correlations, and the magnetization in the antiferromagnetic Heisenberg (AFH) model under an external field are investigated. With increasing external field, the small size system shows some distinct upward magnetization stairsteps, accompanied synchronously with some downward two-site entanglement stairsteps. In the thermodynamic limit, the two-site entanglement, as well as the bipartite entanglement, the ground state energy, the nearest-neighbor correlations, and the magnetization are calculated, and the critical magnetic field h(c) = 2.0 is determined exactly. Our numerical results show that the quantum entanglement is sensitive to the subtle changing of the ground state, and can be used to describe the magnetization and quantum phase transition. Based on the discontinuous behavior of the first-order derivative of the entanglement entropy and fidelity per site, we think that the quantum phase transition in this model should belong to the second-order category. Furthermore, in the magnon existence region (h < 2.0), a logarithmically divergent behavior of block entanglement which can be described by a free bosonic field theory is observed, and the central charge c is determined to be 1.

Multidisciplinary aeroelastic analysis of a generic hypersonic vehicle

NASA Technical Reports Server (NTRS)

Gupta, K. K.; Petersen, K. L.

1993-01-01

This paper presents details of a flutter and stability analysis of aerospace structures such as hypersonic vehicles. Both structural and aerodynamic domains are discretized by the common finite element technique. A vibration analysis is first performed by the STARS code employing a block Lanczos solution scheme. This is followed by the generation of a linear aerodynamic grid for subsequent linear flutter analysis within subsonic and supersonic regimes of the flight envelope; the doublet lattice and constant pressure techniques are employed to generate the unsteady aerodynamic forces. Flutter analysis is then performed for several representative flight points. The nonlinear flutter solution is effected by first implementing a CFD solution of the entire vehicle. Thus, a 3-D unstructured grid for the entire flow domain is generated by a moving front technique. A finite element Euler solution is then implemented employing a quasi-implicit as well as an explicit solution scheme. A novel multidisciplinary analysis is next effected that employs modal and aerodynamic data to yield aerodynamic damping characteristics. Such analyses are performed for a number of flight points to yield a large set of pertinent data that define flight flutter characteristics of the vehicle. This paper outlines the finite-element-based integrated analysis procedures in detail, which is followed by the results of numerical analyses of flight flutter simulation.

SHEDDING NEW LIGHT ON EXPLODING STARS: TERASCALE SIMULATIONS OF NEUTRINO-DRIVEN SUPERNOVAE AND THEIR NUCLEOSYNTHESIS

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

Haxton, Wick

2012-03-07

This project was focused on simulations of core-collapse supernovae on parallel platforms. The intent was to address a number of linked issues: the treatment of hydrodynamics and neutrino diffusion in two and three dimensions; the treatment of the underlying nuclear microphysics that governs neutrino transport and neutrino energy deposition; the understanding of the associated nucleosynthesis, including the r-process and neutrino process; the investigation of the consequences of new neutrino phenomena, such as oscillations; and the characterization of the neutrino signal that might be recorded in terrestrial detectors. This was a collaborative effort with Oak Ridge National Laboratory, State University ofmore » New York at Stony Brook, University of Illinois at Urbana-Champaign, University of California at San Diego, University of Tennessee at Knoxville, Florida Atlantic University, North Carolina State University, and Clemson. The collaborations tie together experts in hydrodynamics, nuclear physics, computer science, and neutrino physics. The University of Washington contributions to this effort include the further development of techniques to solve the Bloch-Horowitz equation for effective interactions and operators; collaborative efforts on developing a parallel Lanczos code; investigating the nuclear and neutrino physics governing the r-process and neutrino physics; and exploring the effects of new neutrino physics on the explosion mechanism, nucleosynthesis, and terrestrial supernova neutrino detection.« less

Finite element modeling of acousto-mechanical coupling in the cat middle ear

PubMed Central

Tuck-Lee, James P.; Pinsky, Peter M.; Steele, Charles R.; Puria, Sunil

2008-01-01

The function of the middle ear is to transfer acoustic energy from the ear canal to the cochlea. An essential component of this system is the tympanic membrane. In this paper, a new finite element model of the middle ear of the domestic cat is presented, generated in part from cadaver anatomy via microcomputed tomographic imaging. This model includes a layered composite model of the eardrum, fully coupled with the acoustics in the ear canal and middle-ear cavities. Obtaining the frequency response from 100 Hz to 20 kHz is a computationally challenging task, which has been accomplished by using a new adaptive implementation of the reduced-order matrix Padé-via-Lanczos algorithm. The results are compared to established physiological data. The fully coupled model is applied to study the role of the collagen fiber sublayers of the eardrum and to investigate the relationship between the structure of the middle-ear cavities and its function. Three applications of this model are presented, demonstrating the shift in the middle-ear resonance due to the presence of the septum that divides the middle-ear cavity space, the significance of the radial fiber layer on high frequency transmission, and the importance of the transverse shear modulus in the eardrum microstructure. PMID:18646982

Discrete quantum spectrum of black holes

NASA Astrophysics Data System (ADS)

Lochan, Kinjalk; Chakraborty, Sumanta

2016-04-01

The quantum genesis of Hawking radiation is a long-standing puzzle in black hole physics. Semi-classically one can argue that the spectrum of radiation emitted by a black hole look very much sparse unlike what is expected from a thermal object. It was demonstrated through a simple quantum model that a quantum black hole will retain a discrete profile, at least in the weak energy regime. However, it was suggested that this discreteness might be an artifact of the simplicity of eigen-spectrum of the model considered. Different quantum theories can, in principle, give rise to different complicated spectra and make the radiation from black hole dense enough in transition lines, to make them look continuous in profile. We show that such a hope from a geometry-quantized black hole is not realized as long as large enough black holes are dubbed with a classical mass area relation in any gravity theory ranging from GR, Lanczos-Lovelock to f(R) gravity. We show that the smallest frequency of emission from black hole in any quantum description, is bounded from below, to be of the order of its inverse mass. That leaves the emission with only two possibilities. It can either be non-thermal, or it can be thermal only with the temperature being much larger than 1/M.

The vibration-rotation-tunneling levels of N2-H2O and N2-D2O.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2015-07-14

In this paper, we report vibration-rotation-tunneling levels of the van der Waals clusters N2-H2O and N2-D2O computed from an ab initio potential energy surface. The only dynamical approximation is that the monomers are rigid. We use a symmetry adapted Lanczos algorithm and an uncoupled product basis set. The pattern of the cluster's levels is complicated by splittings caused by H-H exchange tunneling (larger splitting) and N-N exchange tunneling (smaller splitting). An interesting result that emerges from our calculation is that whereas in N2-H2O, the symmetric H-H tunnelling state is below the anti-symmetric H-H tunnelling state for both K = 0 and K = 1, the order is reversed in N2-D2O for K = 1. The only experimental splitting measurements are the D-D exchange tunneling splittings reported by Zhu et al. [J. Chem. Phys. 139, 214309 (2013)] for N2-D2O in the v2 = 1 region of D2O. Due to the inverted order of the split levels, they measure the sum of the K = 0 and K = 1 tunneling splittings, which is in excellent agreement with our calculated result. Other splittings we predict, in particular those of N2-H2O, may guide future experiments.

The vibration-rotation-tunneling levels of N2-H2O and N2-D2O

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2015-07-01

In this paper, we report vibration-rotation-tunneling levels of the van der Waals clusters N2-H2O and N2-D2O computed from an ab initio potential energy surface. The only dynamical approximation is that the monomers are rigid. We use a symmetry adapted Lanczos algorithm and an uncoupled product basis set. The pattern of the cluster's levels is complicated by splittings caused by H-H exchange tunneling (larger splitting) and N-N exchange tunneling (smaller splitting). An interesting result that emerges from our calculation is that whereas in N2-H2O, the symmetric H-H tunnelling state is below the anti-symmetric H-H tunnelling state for both K = 0 and K = 1, the order is reversed in N2-D2O for K = 1. The only experimental splitting measurements are the D-D exchange tunneling splittings reported by Zhu et al. [J. Chem. Phys. 139, 214309 (2013)] for N2-D2O in the v2 = 1 region of D2O. Due to the inverted order of the split levels, they measure the sum of the K = 0 and K = 1 tunneling splittings, which is in excellent agreement with our calculated result. Other splittings we predict, in particular those of N2-H2O, may guide future experiments.

Using high sampling rate (10/20 Hz) altimeter data for the observation of coastal surface currents: A case study over the northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

Birol, Florence; Delebecque, Caroline

2014-01-01

Satellite altimetry, measuring sea surface heights (SSHs), has unique capabilities to provide information about the ocean dynamics. In this paper, the skill of the original full rate (10/20 Hz) measurements, relative to conventional 1-Hz data, is evaluated in the context of coastal studies in the Northwestern Mediterranean Sea. The performance and the question of the measurement noise are quantified through a comparison with different tide gauge sea level time series. By applying a specific processing, closer than 30 km to the land, the number of valid data is higher for the 10/20-Hz than for the 1-Hz observations: + 4.5% for T/P, + 10.3 for Jason-1 and + 13% for Jason-2. By filtering higher sampling rate measurements (using a 30-km cut-off low-pass Lanczos filter), we can obtain the same level of sea level accuracy as we would using the classical 1-Hz altimeter data. The gain in near-shore data results in a better observation of the Liguro-Provençal-Catalan Current. The seasonal evolution of the currents derived from 20-Hz data is globally consistent with patterns derived from the corresponding 1-Hz observations. But the use of higher frequency altimeter measurements allows us to observe the variability of the regional flow closer to the coast (~ 10-15 km from land).

The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

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

Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long

2016-01-07

The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averagedmore » interaction energies for the (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.« less

A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations

DOE PAGES

Aktulga, Hasan Metin; Afibuzzaman, Md.; Williams, Samuel; ...

2017-06-01

As on-node parallelism increases and the performance gap between the processor and the memory system widens, achieving high performance in large-scale scientific applications requires an architecture-aware design of algorithms and solvers. We focus on the eigenvalue problem arising in nuclear Configuration Interaction (CI) calculations, where a few extreme eigenpairs of a sparse symmetric matrix are needed. Here, we consider a block iterative eigensolver whose main computational kernels are the multiplication of a sparse matrix with multiple vectors (SpMM), and tall-skinny matrix operations. We then present techniques to significantly improve the SpMM and the transpose operation SpMM T by using themore » compressed sparse blocks (CSB) format. We achieve 3-4× speedup on the requisite operations over good implementations with the commonly used compressed sparse row (CSR) format. We develop a performance model that allows us to correctly estimate the performance of our SpMM kernel implementations, and we identify cache bandwidth as a potential performance bottleneck beyond DRAM. We also analyze and optimize the performance of LOBPCG kernels (inner product and linear combinations on multiple vectors) and show up to 15× speedup over using high performance BLAS libraries for these operations. The resulting high performance LOBPCG solver achieves 1.4× to 1.8× speedup over the existing Lanczos solver on a series of CI computations on high-end multicore architectures (Intel Xeons). We also analyze the performance of our techniques on an Intel Xeon Phi Knights Corner (KNC) processor.« less

A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations

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

Aktulga, Hasan Metin; Afibuzzaman, Md.; Williams, Samuel

As on-node parallelism increases and the performance gap between the processor and the memory system widens, achieving high performance in large-scale scientific applications requires an architecture-aware design of algorithms and solvers. We focus on the eigenvalue problem arising in nuclear Configuration Interaction (CI) calculations, where a few extreme eigenpairs of a sparse symmetric matrix are needed. Here, we consider a block iterative eigensolver whose main computational kernels are the multiplication of a sparse matrix with multiple vectors (SpMM), and tall-skinny matrix operations. We then present techniques to significantly improve the SpMM and the transpose operation SpMM T by using themore » compressed sparse blocks (CSB) format. We achieve 3-4× speedup on the requisite operations over good implementations with the commonly used compressed sparse row (CSR) format. We develop a performance model that allows us to correctly estimate the performance of our SpMM kernel implementations, and we identify cache bandwidth as a potential performance bottleneck beyond DRAM. We also analyze and optimize the performance of LOBPCG kernels (inner product and linear combinations on multiple vectors) and show up to 15× speedup over using high performance BLAS libraries for these operations. The resulting high performance LOBPCG solver achieves 1.4× to 1.8× speedup over the existing Lanczos solver on a series of CI computations on high-end multicore architectures (Intel Xeons). We also analyze the performance of our techniques on an Intel Xeon Phi Knights Corner (KNC) processor.« less

Three-dimensional visualization and analysis of a dual-disk resonator with dielectric misalignment and surface anomaly using edge finite elements

NASA Astrophysics Data System (ADS)

Villalva, Gustavo Jose

The search for life in other planets and solar systems by scientists and engineers brings about an effort to design and develop equipment of high standards which extend the capability to listen for signals which have been traveling in space many light years. In this study the purpose was to provide a more realistic and illustrative scientific understanding of one such piece of precision equipment, the dielectric resonator, which designers seek to extend its frequency stability below 10-15. At such tolerances special cryogenic cooling procedures are required. Due to its accuracy it can be used to set short term time and frequency standards to correct the atomic clock. A theoretical means of studying this type of resonant device is necessary. One contribution made in extending the current understanding of such a device is the scientific tool developed specifically for this dissertation. It applies the Minimum Theorem from variational calculus using edge finite elements for numerical modeling. The use of quasi-linear vector basis functions allowed an implementation of Helmholtz's three-dimensional equation without a penalty term. Furthermore, the intermixing of spurious solutions with the true ones due to a nodal basis was eliminated. Calculation of the average edge electric fields was made possible by applying the Rayleigh-Ritz criterion. Model enclosure was provided by a cylindrical metal shield situated in a rectangular coordinate system. Linear, homogeneous, nonmagnetic, lossless, uniaxial, and anisotropic media were considered. Integration of NASA's Unix Lanczos eigensolver permitted the accurate estimation of the smaller eigenvalues and associated vectors for large matrices on workstations and personal computers in relatively short computational times. Calculation of the lower frequency modes demonstrated the ability to address device imperfections for two selected cases. Both were influenced by problems encountered in the use of crystals constrained by cost, or because of imperfections in the manufacturing process. The first, considered dielectric properties not aligned with the model axis. And, the second inserted a surface variation on the crystal. Numerically, the general decrease in mode frequencies due to misalignment and overall increase due to a surface anomaly were graphed. Visually, the resulting deformation of electromagnetic mode structures with a high energy concentration in the altered material were shown. Those not visibly affected were modes with less energy in the modified material. An expected effect on their quality factors was given. The research presented provides illustrative scientific understanding using models that are more realistic. Moreover, it aids in resonator design by predicting electromagnetic behavior due to media imperfections.

Development of the WRF-CO2 4D-Var assimilation system v1.0

NASA Astrophysics Data System (ADS)

Zheng, Tao; French, Nancy H. F.; Baxter, Martin

2018-05-01

Regional atmospheric CO2 inversions commonly use Lagrangian particle trajectory model simulations to calculate the required influence function, which quantifies the sensitivity of a receptor to flux sources. In this paper, an adjoint-based four-dimensional variational (4D-Var) assimilation system, WRF-CO2 4D-Var, is developed to provide an alternative approach. This system is developed based on the Weather Research and Forecasting (WRF) modeling system, including the system coupled to chemistry (WRF-Chem), with tangent linear and adjoint codes (WRFPLUS), and with data assimilation (WRFDA), all in version 3.6. In WRF-CO2 4D-Var, CO2 is modeled as a tracer and its feedback to meteorology is ignored. This configuration allows most WRF physical parameterizations to be used in the assimilation system without incurring a large amount of code development. WRF-CO2 4D-Var solves for the optimized CO2 flux scaling factors in a Bayesian framework. Two variational optimization schemes are implemented for the system: the first uses the limited memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) minimization algorithm (L-BFGS-B) and the second uses the Lanczos conjugate gradient (CG) in an incremental approach. WRFPLUS forward, tangent linear, and adjoint models are modified to include the physical and dynamical processes involved in the atmospheric transport of CO2. The system is tested by simulations over a domain covering the continental United States at 48 km × 48 km grid spacing. The accuracy of the tangent linear and adjoint models is assessed by comparing against finite difference sensitivity. The system's effectiveness for CO2 inverse modeling is tested using pseudo-observation data. The results of the sensitivity and inverse modeling tests demonstrate the potential usefulness of WRF-CO2 4D-Var for regional CO2 inversions.

Impact of submesoscales on surface material distribution in a gulf of Mexico mesoscale eddy

NASA Astrophysics Data System (ADS)

Haza, A. C.; Özgökmen, T. M.; Hogan, P.

2016-11-01

Understanding material distribution at the ocean's surface is important for a number of applications, in particular for buoyant pollutants such as oil spills. The main tools to estimate surface flows are satellite altimeters, as well as data-assimilative ocean general circulation models (OGCMs). Current-generation altimeter products rely on the geostrophic approximation to derive surface currents. Recent modeling and experimental work revealed existence of ageostrophic submesoscale motions within the upper ocean boundary layer. The next frontier is how submesoscales influence transport pathways in the upper ocean, which is a multi-scale problem involving the interaction of submesoscale and mesoscale coherent structures. Here we focus on a mesoscale eddy that exhibits submesoscale fluctuations along its rim. The high-resolution OCGM fields are then treated with two filters. A Lanczos filter is applied to velocity fields to remove the kinetic energy over the submesoscales. Then a Gaussian filter is used for the modeled sea surface height to simulate a geostrophic velocity field that would be available from gridded satellite altimeter data. Lagrangian Coherent Structures (LCS) are then generated from full-resolution and filtered fields to compare Lagrangian characteristics corresponding to different realizations of the surface velocity fields. It is found that while mesoscale currents exert a general control over the pathways of the tracer initially launched in the mesoscale eddy, there is a leak across the mesoscale transport barriers, induced by submesoscale motions. This leak is quantified as 20% of the tracer when using the submesoscale filter over one month of advection, while it increases to 50% using the geostrophic velocity field. We conclude that LCS computed from mesoscale surface velocity fields can be considered as a good first-order proxy, but the leakage of material across them in the presence of submesoscales can be significant.

Estimates of Stellar Weak Interaction Rates for Nuclei in the Mass Range A=65-80

NASA Astrophysics Data System (ADS)

Pruet, Jason; Fuller, George M.

2003-11-01

We estimate lepton capture and emission rates, as well as neutrino energy loss rates, for nuclei in the mass range A=65-80. These rates are calculated on a temperature/density grid appropriate for a wide range of astrophysical applications including simulations of late time stellar evolution and X-ray bursts. The basic inputs in our single-particle and empirically inspired model are (i) experimentally measured level information, weak transition matrix elements, and lifetimes, (ii) estimates of matrix elements for allowed experimentally unmeasured transitions based on the systematics of experimentally observed allowed transitions, and (iii) estimates of the centroids of the GT resonances motivated by shell model calculations in the fp shell as well as by (n, p) and (p, n) experiments. Fermi resonances (isobaric analog states) are also included, and it is shown that Fermi transitions dominate the rates for most interesting proton-rich nuclei for which an experimentally determined ground state lifetime is unavailable. For the purposes of comparing our results with more detailed shell model based calculations we also calculate weak rates for nuclei in the mass range A=60-65 for which Langanke & Martinez-Pinedo have provided rates. The typical deviation in the electron capture and β-decay rates for these ~30 nuclei is less than a factor of 2 or 3 for a wide range of temperature and density appropriate for presupernova stellar evolution. We also discuss some subtleties associated with the partition functions used in calculations of stellar weak rates and show that the proper treatment of the partition functions is essential for estimating high-temperature β-decay rates. In particular, we show that partition functions based on unconverged Lanczos calculations can result in errors in estimates of high-temperature β-decay rates.

Vibration Characteristics Determined for Stainless Steel Sandwich Panels With a Metal Foam Core for Lightweight Fan Blade Design

NASA Technical Reports Server (NTRS)

Ghosn, Louis J.; Min, James B.; Raj, Sai V.; Lerch, Bradley A.; Holland, Frederic A., Jr.

2004-01-01

The goal of this project at the NASA Glenn Research Center is to provide fan materials that are safer, weigh less, and cost less than the currently used titanium alloy or polymer matrix composite fans. The proposed material system is a sandwich fan construction made up of thin solid face sheets and a lightweight metal foam core. The stiffness of the sandwich structure is increased by separating the two face sheets by the foam layer. The resulting structure has a high stiffness and lighter weight in comparison to the solid facesheet material alone. The face sheets carry the applied in-plane and bending loads (ref. 1). The metal foam core must resist the transverse shear and transverse normal loads, as well as keep the facings supported and working as a single unit. Metal foams have ranges of mechanical properties, such as light weight, impact resistance, and vibration suppression (ref. 2), which makes them more suitable for use in lightweight fan structures. Metal foams have been available for decades (refs. 3 and 4), but the difficulties in the original processes and high costs have prevented their widespread use. However, advances in production techniques and cost reduction have created a new interest in this class of materials (ref. 5). The material chosen for the face sheet and the metal foam for this study was the aerospace-grade stainless steel 17-4PH. This steel was chosen because of its attractive mechanical properties and the ease with which it can be made through the powder metallurgy process (ref. 6). The advantages of a metal foam core, in comparison to a typical honeycomb core, are material isotropy and the ease of forming complex geometries, such as fan blades. A section of a 17-4PH sandwich structure is shown in the following photograph. Part of process of designing any blade is to determine the natural frequencies of the particular blade shape. A designer needs to predict the resonance frequencies of a new blade design to properly identify a useful operating range. Operating a blade at or near the resonance frequencies leads to high-cycle fatigue, which ultimately limits the blade's durability and life. So the aim of this study is to determine the variation of the resonance frequencies for an idealized sandwich blade as a function of its face-sheet thickness, core thickness, and foam density. The finite element method is used to determine the natural frequencies for an idealized rectangular sandwich blade. The proven Lanczos method (ref. 7) is used in the study to extract the natural frequency.

The spa typing of methicillin-resistant Staphylococcus aureus isolates by High Resolution Melting (HRM) analysis.

PubMed

Fasihi, Yasser; Fooladi, Saba; Mohammadi, Mohammad Ali; Emaneini, Mohammad; Kalantar-Neyestanaki, Davood

2017-09-06

Molecular typing is an important tool for control and prevention of infection. A suitable molecular typing method for epidemiological investigation must be easy to perform, highly reproducible, inexpensive, rapid and easy to interpret. In this study, two molecular typing methods including the conventional PCR-sequencing method and high resolution melting (HRM) analysis were used for staphylococcal protein A (spa) typing of 30 Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from clinical samples. Based on PCR-sequencing method results, 16 different spa types were identified among the 30 MRSA isolates. Among the 16 different spa types, 14 spa types separated by HRM method. Two spa types including t4718 and t2894 were not separated from each other. According to our results, spa typing based on HRM analysis method is very rapid, easy to perform and cost-effective, but this method must be standardized for different regions, spa types, and real-time machinery.

[Molecular typing methods for Pasteurella multocida-A review].

PubMed

Peng, Zhong; Liang, Wan; Wu, Bin

2016-10-04

Pasteurella multocida is an important gram-negative pathogenic bacterium that could infect wide ranges of animals. Humans could also be infected by P. multocida via animal bite or scratching. Current typing methods for P. multocida include serological typing methods and molecular typing methods. Of them, serological typing methods are based on immunological assays, which are too complicated for clinical bacteriological studies. However, the molecular methods including multiple PCRs and multilocus sequence typing (MLST) methods are more suitable for bacteriological studies of P. multocida in clinic, with their simple operation, high efficiency and accurate detection compared to the traditional serological typing methods, they are therefore widely used. In the current review, we briefly describe the molecular typing methods for P. multocida. Our aim is to provide a knowledge-foundation for clinical bacteriological investigation especially the molecular investigation for P. multocida.

Streptococcus group B typing: comparison of counter-immunoelectrophoresis with the precipitin method.

PubMed

Kubín, V; Jelínková, J; Franêk, J

1977-07-01

The method of counter-immunoelectrophoresis (CIE) was tested for its applicability to group B streptococcus typing. The results obtained were compared with the typing by the ring precipitin test. Identical antigens and identical hyperimmune typing serum batches had been used in both methods. A large majority of 75 freshly isolated strains were typed identically by both methods. Five strains with a weak antigenic outfit were untypable by the ring precipitin test but were typed by CIE owing to a higher sensitivity of CIE method. Two strains were typable by the precipitin test but not by CIE; an explanation for this phenomenon is lacking. The CIE method in group B typing is specific, rapid, highly sensitive and relatively simple. It requires strict maintenance of standard conditions. The method is economical with respect to manipulation and material, requires small amounts of diagnostic antisera. Potent antisera may be used diluted. Moreover, sera for CIE typing need not be absorbed to remove group B antibodies. CIE method is practicable for group B streptococcus typing, especially in laboratories carrying out routine large scale type identification.

Discriminatory Power and Reproducibility of Novel DNA Typing Methods for Mycobacterium tuberculosis Complex Strains

PubMed Central

Kremer, Kristin; Arnold, Catherine; Cataldi, Angel; Gutiérrez, M. Cristina; Haas, Walter H.; Panaiotov, Stefan; Skuce, Robin A.; Supply, Philip; van der Zanden, Adri G. M.; van Soolingen, Dick

2005-01-01

In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. (J. Clin. Microbiol. 37:2607-2618, 1999). This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future. PMID:16272496

The diversity and unit of reactor noise theory

NASA Astrophysics Data System (ADS)

Kuang, Zhifeng

The study of reactor noise theory concerns questions about cause and effect relationships, and utilisation of random noise in nuclear reactor systems. The diversity of reactor noise theory arises from the variety of noise sources, the various mathematical treatments applied and various practical purposes. The neutron noise in zero- energy systems arises from the fluctuations in the number of neutrons per fission, the time between nuclear events, and the type of reactions. It can be used to evaluate system parameters. The mathematical treatment is based on the master equation of stochastic branching processes. The noise in power reactor systems is given rise by random processes of technological origin such as vibration of mechanical parts, boiling of the coolant, fluctuations of temperature and pressure. It can be used to monitor reactor behaviour with the possibility of detecting malfunctions at an early stage. The mathematical treatment is based on the Langevin equation. The unity of reactor noise theory arises from the fact that useful information from noise is embedded in the second moments of random variables, which lends the possibility of building up a unified mathematical description and analysis of the various reactor noise sources. Exploring such possibilities is the main subject among the three major topics reported in this thesis. The first subject is within the zero power noise in steady media, and we reported on the extension of the existing theory to more general cases. In Paper I, by use of the master equation approach, we have derived the most general Feynman- and Rossi-alpha formulae so far by taking the full joint statistics of the prompt and all the six groups of delayed neutron precursors, and a multiple emission source into account. The involved problems are solved with a combination of effective analytical techniques and symbolic algebra codes (Mathematica). Paper II gives a numerical evaluation of these formulae. An assessment of the contribution of the terms that are novel as compared to the traditional formulae has been made. The second subject treats a problem in power reactor noise with the Langevin formalism. With a very few exceptions, in all previous work the diffusion approximation was used. In order to extend the treatment to transport theory, in Paper III, we introduced a novel method, i.e. Padé approximation via Lanczos algorithm to calculate the transfer function of a finite slab reactor described by one-group transport equation. It was found that the local-global decomposition of the neutron noise, formerly only reproduced in at least 2- group theory, can be reconstructed. We have also showed the existence of a boundary layer of the neutron noise close to the boundary. Finally, we have explored the possibility of building up a unified theory to account for the coexistence of zero power and power reactor noise in a system. In Paper IV, a unified description of the neutron noise is given by the use of backward master equations in a model where the cross section fluctuations are given as a simple binary pseudorandom process. The general solution contains both the zero power and power reactor noise concurrently, and they can be extracted individually as limiting cases of the general solution. It justified the separate treatments of zero power and power reactor noise. The result was extended to the case including one group of delayed neutron precursors in Paper V.

Improved Filon-type asymptotic methods for highly oscillatory differential equations with multiple time scales

NASA Astrophysics Data System (ADS)

Wang, Bin; Wu, Xinyuan

2014-11-01

In this paper we consider multi-frequency highly oscillatory second-order differential equations x″ (t) + Mx (t) = f (t , x (t) ,x‧ (t)) where high-frequency oscillations are generated by the linear part Mx (t), and M is positive semi-definite (not necessarily nonsingular). It is known that Filon-type methods are effective approach to numerically solving highly oscillatory problems. Unfortunately, however, existing Filon-type asymptotic methods fail to apply to the highly oscillatory second-order differential equations when M is singular. We study and propose an efficient improvement on the existing Filon-type asymptotic methods, so that the improved Filon-type asymptotic methods can be able to numerically solving this class of multi-frequency highly oscillatory systems with a singular matrix M. The improved Filon-type asymptotic methods are designed by combining Filon-type methods with the asymptotic methods based on the variation-of-constants formula. We also present one efficient and practical improved Filon-type asymptotic method which can be performed at lower cost. Accompanying numerical results show the remarkable efficiency.

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile.

PubMed

Li, Zhirong; Liu, Xiaolei; Zhao, Jianhong; Xu, Kaiyue; Tian, Tiantian; Yang, Jing; Qiang, Cuixin; Shi, Dongyan; Wei, Honglian; Sun, Suju; Cui, Qingqing; Li, Ruxin; Niu, Yanan; Huang, Bixing

2018-04-01

Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs), 26 ribotypes (RTs), and 33 MLST sequence types (STs), respectively. The typing ability of the binary method was better than that of either ribotyping or MLST expressed in Simpson Index (SI) at 0.937, 0.892 and 0.859, respectively. The ease of testing, portability and cost-effectiveness of the new binary typing would make it a useful typing alternative for outbreak investigations within healthcare facilities and epidemiological research. Copyright © 2018 Elsevier B.V. All rights reserved.

Codoping method for the fabrication of low-resistivity wide band-gap semiconductors in p-type GaN, p-type AlN and n-type diamond: prediction versus experiment

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, H.; Nishimatsu, T.; Yamamoto, T.; Orita, N.

2001-10-01

We review our new valence control method of a co-doping for the fabrication of low-resistivity p-type GaN, p-type AlN and n-type diamond. The co-doping method is proposed based upon ab initio electronic structure calculation in order to solve the uni-polarity and the compensation problems in the wide band-gap semiconductors. In the co-doping method, we dope both the acceptors and donors at the same time by forming the meta-stable acceptor-donor-acceptor complexes for the p-type or donor-acceptor-donor complexes for the n-type under thermal non-equilibrium crystal growth conditions. We propose the following co-doping method to fabricate the low-resistivity wide band-gap semiconductors; p-type GaN: [Si + 2 Mg (or Be)], [H + 2 Mg (or Be)], [O + 2 Mg (or Be)], p-type AlN: [O + 2 C] and n-type diamond: [B + 2 N], [H + S], [H + 2 P]. We compare our prediction of the co-doping method with the recent successful experiments to fabricate the low-resistivity p-type GaN, p-type AlN and n-type diamond. We show that the co-doping method is the efficient and universal doping method by which to avoid carrier compensation with an increase of the solubility of the dopant, to increase the activation rate by decreasing the ionization energy of acceptors and donors, and to increase the mobility of the carrier.

Molecular typing of Legionella pneumophila from air-conditioning cooling waters using mip gene, SBT, and FAFLP methods.

PubMed

Gong, Xiangli; Li, Juntao; Zhang, Ying; Hou, Shuiping; Qu, Pinghua; Yang, Zhicong; Chen, Shouyi

2017-08-01

Legionella spp. are important waterborne pathogens. Molecular typing has become an important method for outbreaks investigations and source tracking of Legionnaires. In a survey program conducted by the Guangzhou Center for Disease Control and Prevention, multiple serotypes Legionella pneumophila (L. pneumophila) were isolated from waters in air-conditioning cooling towers in urban Guangzhou region, China between 2008 and 2011. Three genotyping methods, mip (macrophage infectivity potentiator) genotyping, SBT (sequence-based typing), and FAFLP (fluorescent amplified fragment length polymorphism analysis) were used to type these waterborne L. pneumophila isolates. The three methods were capable of typing all the 134 isolates and a reference strain of L. pneumophila (ATCC33153), with discriminatory indices of 0.7034, 0.9218, and 0.9376, for the mip, SBT, and FAFLP methods respectively. Among the 9 serotypes of the 134 isolates, 10, 50, and 34 molecular types were detected by the mip, SBT, and FAFLP methods respectively. The mip genotyping and SBT typing are more feasible for inter-laboratory results sharing and comparison of different types of L. pneumophila. The SBT and FAFLP typing methods were rapid with higher discriminatory abilities. Combinations of two or more of the typing methods enables more accurate typing of Legionella isolates for outbreak investigations and source tracking of Legionnaires. Copyright © 2017 Elsevier B.V. All rights reserved.

nu-TRLan User Guide Version 1.0: A High-Performance Software Package for Large-Scale Harmitian Eigenvalue Problems

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

Yamazaki, Ichitaro; Wu, Kesheng; Simon, Horst

2008-10-27

The original software package TRLan, [TRLan User Guide], page 24, implements the thick restart Lanczos method, [Wu and Simon 2001], page 24, for computing eigenvalues {lambda} and their corresponding eigenvectors v of a symmetric matrix A: Av = {lambda}v. Its effectiveness in computing the exterior eigenvalues of a large matrix has been demonstrated, [LBNL-42982], page 24. However, its performance strongly depends on the user-specified dimension of a projection subspace. If the dimension is too small, TRLan suffers from slow convergence. If it is too large, the computational and memory costs become expensive. Therefore, to balance the solution convergence and costs,more » users must select an appropriate subspace dimension for each eigenvalue problem at hand. To free users from this difficult task, nu-TRLan, [LNBL-1059E], page 23, adjusts the subspace dimension at every restart such that optimal performance in solving the eigenvalue problem is automatically obtained. This document provides a user guide to the nu-TRLan software package. The original TRLan software package was implemented in Fortran 90 to solve symmetric eigenvalue problems using static projection subspace dimensions. nu-TRLan was developed in C and extended to solve Hermitian eigenvalue problems. It can be invoked using either a static or an adaptive subspace dimension. In order to simplify its use for TRLan users, nu-TRLan has interfaces and features similar to those of TRLan: (1) Solver parameters are stored in a single data structure called trl-info, Chapter 4 [trl-info structure], page 7. (2) Most of the numerical computations are performed by BLAS, [BLAS], page 23, and LAPACK, [LAPACK], page 23, subroutines, which allow nu-TRLan to achieve optimized performance across a wide range of platforms. (3) To solve eigenvalue problems on distributed memory systems, the message passing interface (MPI), [MPI forum], page 23, is used. The rest of this document is organized as follows. In Chapter 2 [Installation], page 2, we provide an installation guide of the nu-TRLan software package. In Chapter 3 [Example], page 3, we present a simple nu-TRLan example program. In Chapter 4 [trl-info structure], page 7, and Chapter 5 [trlan subroutine], page 14, we describe the solver parameters and interfaces in detail. In Chapter 6 [Solver parameters], page 21, we discuss the selection of the user-specified parameters. In Chapter 7 [Contact information], page 22, we give the acknowledgements and contact information of the authors. In Chapter 8 [References], page 23, we list reference to related works.« less

Advances in Blood Typing.

PubMed

Quraishy, N; Sapatnekar, S

The clinical importance of blood group antigens relates to their ability to evoke immune antibodies that are capable of causing hemolysis. The most important antigens for safe transfusion are ABO and D (Rh), and typing for these antigens is routinely performed for patients awaiting transfusion, prenatal patients, and blood donors. Typing for other blood group antigens, typically of the Kell, Duffy, Kidd, and MNS blood groups, is sometimes necessary, for patients who have, or are likely to develop antibodies to these antigens. The most commonly used typing method is serological typing, based on hemagglutination reactions against specific antisera. This method is generally reliable and practical for routine use, but it has certain drawbacks. In recent years, molecular typing has emerged as an alternative or supplemental typing method. It is based on detecting the polymorphisms and mutations that control the expression of blood group antigens, and using this information to predict the probable antigen type. Molecular typing methods are useful when traditional serological typing methods cannot be used, as when a patient has been transfused and the sample is contaminated with red blood cells from the transfused blood component. Moreover, molecular typing methods can precisely identify clinically significant variant antigens that cannot be distinguished by serological typing; this capability has been exploited for the resolution of typing discrepancies and shows promise for the improved transfusion management of patients with sickle cell anemia. Despite its advantages, molecular typing has certain limitations, and it should be used in conjunction with serological methods. © 2016 Elsevier Inc. All rights reserved.

Correlation and agreement between eplet mismatches calculated using serological, low-intermediate and high resolution molecular human leukocyte antigen typing methods.

PubMed

Fidler, Samantha; D'Orsogna, Lloyd; Irish, Ashley B; Lewis, Joshua R; Wong, Germaine; Lim, Wai H

2018-03-02

Structural human leukocyte antigen (HLA) matching at the eplet level can be identified by HLAMatchmaker, which requires the entry of four-digit alleles. The aim of this study was to evaluate the agreement between eplet mismatches calculated by serological and two-digit typing methods compared to high-resolution four-digit typing. In a cohort of 264 donor/recipient pairs, the evaluation of measurement error was assessed using intra-class correlation to confirm the absolute agreement between the number of eplet mismatches at class I (HLA-A, -B, C) and II loci (HLA-DQ and -DR) calculated using serological or two-digit molecular typing compared to four-digit molecular typing methods. The proportion of donor/recipient pairs with a difference of >5 eplet mismatches between the HLA typing methods was also determined. Intra-class correlation coefficients between serological and four-digit molecular typing methods were 0.969 (95% confidence intervals [95% CI] 0.960-0.975) and 0.926 (95% CI 0.899-0.944), respectively; and 0.995 (95% CI 0.994-0.996) and 0.993 (95% CI 0.991-0.995), respectively between two-digit and four-digit molecular typing methods. The proportion of donor/recipient pairs with a difference of >5 eplet mismatches at class I and II loci was 4% and 16% for serological versus four-digit molecular typing methods, and 0% and 2% for two-digit versus four-digit molecular typing methods, respectively. In this small predominantly Caucasian population, compared with serology, there is a high level of agreement in the number of eplet mismatches calculated using two-compared to four-digit molecular HLA-typing methods, suggesting that two-digit typing may be sufficient in determining eplet mismatch load in kidney transplantation.

Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.

PubMed

Cholley, Pascal; Stojanov, Milos; Hocquet, Didier; Thouverez, Michelle; Bertrand, Xavier; Blanc, Dominique S

2015-08-01

Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence typing (DLST) method for Pseudomonas aeruginosa to MLST and PFGE on a collection of 281 isolates. DLST was as discriminatory as MLST and was able to recognize "high-risk" epidemic clones. Both methods were highly congruent. Not surprisingly, a higher discriminatory power was observed with PFGE. In conclusion, being a simple method (single-strand sequencing of only 2 loci), DLST is valuable as a first-line typing tool for epidemiological investigations of P. aeruginosa. Coupled to a more discriminant method like PFGE or whole genome sequencing, it might represent an efficient typing strategy to investigate or prevent outbreaks. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of Typing Methods for Epidemiological Surveillance of both Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains▿ †

PubMed Central

Faria, Nuno A.; Carrico, João A.; Oliveira, Duarte C.; Ramirez, Mário; de Lencastre, Hermínia

2008-01-01

Sequence-based methods for typing Staphylococcus aureus, such as multilocus sequence typing (MLST) and spa typing, have increased interlaboratory reproducibility, portability, and speed in obtaining results, but pulsed-field gel electrophoresis (PFGE), remains the method of choice in many laboratories due to the extensive experience with this methodology and the large body of data accumulated using the technique. Comparisons between typing methods have been overwhelmingly based on a qualitative assessment of the overall agreement of results and the relative discriminatory indexes. In this study, we quantitatively assess the congruence of the major typing methods for S. aureus, using a diverse collection of 198 S. aureus strains previously characterized by PFGE, spa typing, MLST, and, in the case of methicillin-resistant S. aureus (MRSA), SCCmec typing in order to establish the quantitative congruence between the typing methods. The results of most typing methods agree in that MRSA and methicillin-susceptible S. aureus (MSSA) differ in terms of diversity of genetic backgrounds, with MSSA being more diverse. Our results show that spa typing has a very good predictive power over the clonal relationships defined by eBURST, while PFGE is less accurate for that purpose but nevertheless provides better typeability and discriminatory power. The combination of PFGE and spa typing provided even better results. Based on these observations, we suggest the use of the conjugation of spa typing and PFGE typing for epidemiological surveillance studies, since this combination provides the ability to infer long-term relationships while maintaining the discriminatory power and typeability needed in short-term studies. PMID:17989188

Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods.

PubMed

Ho, Cheng-Mao; Ho, Mao-Wang; Li, Chi-Yuan; Lu, Jang-Jih

2015-08-01

Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling. There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates. Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates. Copyright © 2013. Published by Elsevier B.V.

Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains.

PubMed

Rodriguez, Marcela; Hogan, Patrick G; Satola, Sarah W; Crispell, Emily; Wylie, Todd; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Burnham, Carey-Ann D; Fritz, Stephanie A

2015-09-01

Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We identified 45 MRSA isolates which were classified as identical by PFGE, MLST, spa typing, and SCCmec typing (USA300, ST8, t008, SCCmec IV, respectively); within this collection, there were 5 distinct strain types identified by repPCR. The typing methods yielded comparable discriminatory power for S. aureus characterization overall; when discriminating among USA300 isolates, repPCR retained the highest discriminatory power. This property is advantageous for investigations conducted in the era of contemporary S. aureus infections.

Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains

PubMed Central

Rodriguez, Marcela; Hogan, Patrick G.; Satola, Sarah W.; Crispell, Emily; Wylie, Todd; Gao, Hongyu; Sodergren, Erica; Weinstock, George M.; Burnham, Carey-Ann D.; Fritz, Stephanie A.

2015-01-01

Abstract Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We identified 45 MRSA isolates which were classified as identical by PFGE, MLST, spa typing, and SCCmec typing (USA300, ST8, t008, SCCmec IV, respectively); within this collection, there were 5 distinct strain types identified by repPCR. The typing methods yielded comparable discriminatory power for S. aureus characterization overall; when discriminating among USA300 isolates, repPCR retained the highest discriminatory power. This property is advantageous for investigations conducted in the era of contemporary S. aureus infections. PMID:26376402

A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays

PubMed Central

Zuckerman, Neta S.; Noam, Yair; Goldsmith, Andrea J.; Lee, Peter P.

2013-01-01

Gene expression analysis is generally performed on heterogeneous tissue samples consisting of multiple cell types. Current methods developed to separate heterogeneous gene expression rely on prior knowledge of the cell-type composition and/or signatures - these are not available in most public datasets. We present a novel method to identify the cell-type composition, signatures and proportions per sample without need for a-priori information. The method was successfully tested on controlled and semi-controlled datasets and performed as accurately as current methods that do require additional information. As such, this method enables the analysis of cell-type specific gene expression using existing large pools of publically available microarray datasets. PMID:23990767

Evaluation of 99mTc-MIBI in thyroid gland imaging for the diagnosis of amiodarone-induced thyrotoxicosis

PubMed Central

Zhang, Ruiguo

2017-01-01

Objective: Amiodarone-induced thyrotoxicosis (AIT) is caused by amiodarone as a side effect of cardiovascular disease treatment. Based on the differences in their pathological and physiological mechanisms, many methods have been developed so far to differentiate AIT subtypes such as colour flow Doppler sonography (CFDS) and 24-h radioiodine uptake (RAIU). However, these methods suffer from inadequate accuracy in distinguishing different types of AITs and sometimes lead to misdiagnosis and delayed treatments. Therefore, there is an unmet demand for an efficient method for accurate classification of AIT. Methods: Technetium-99 methoxyisobutylisonitrile (99mTc-MIBI) thyroid imaging was performed on 15 patients for AIT classification, and the results were compared with other conventional methods such as CFDS, RAIU and 99mTcO4 imaging. Results: High uptake and retention of MIBI in thyroid tissue is characteristic in Type I AIT, while in sharp contrast, low uptake of MIBI in the thyroid tissue was observed in Type II AIT. Mixed-type AIT shows uptake value between Types I and II. MIBI imaging outperforms other methods with a lower misdiagnosis rate. Conclusion: Among the methods evaluated, MIBI imaging enables an accurate identification of Type I, II and mixed-type AITs by showing distinct images for different types of AITs. The results obtained from our selected subjects revealed that MIBI imaging is a reliable method for diagnosis and classification of AITs and MIBI imaging has potential in the treatment of thyroid diseases. Advances in knowledge: 99mTc-MIBI imaging is a useful method for the diagnosis of AIT. It can distinguish different types of AITs especially for mixed-type AIT, which is usually difficult to treat. 99mTc-MIBI has potential advantages over conventional methods in the efficient treatment of AIT. PMID:28106465

Comparison of two methods of MMPI-2 profile classification.

PubMed

Munley, P H; Germain, J M

2000-10-01

The present study investigated the extent of agreement of the highest scale method and the best-fit method in matching MMPI-2 profiles to database code-type profiles and considered profile characteristics that may relate to agreement or disagreement of code-type matches by these two methods. A sample of 519 MMPI-2 profiles that had been classified into database profile code types by these two methods was studied. Resulting code-type matches were classified into three groups: identical (30%), similar (39%), and different (31%), and the profile characteristics of profile elevation, dispersion, and profile code-type definition were studied. Profile code-type definition was significantly different across the three groups with identical and similar match profile groups showing greater profile code-type definition and the different group consisting of profiles that were less well-defined.

Method of fabricating a back-contact solar cell and device thereof

DOEpatents

Li, Bo; Smith, David; Cousins, Peter

2014-07-29

Methods of fabricating back-contact solar cells and devices thereof are described. A method of fabricating a back-contact solar cell includes forming an N-type dopant source layer and a P-type dopant source layer above a material layer disposed above a substrate. The N-type dopant source layer is spaced apart from the P-type dopant source layer. The N-type dopant source layer and the P-type dopant source layer are heated. Subsequently, a trench is formed in the material layer, between the N-type and P-type dopant source layers.

Method of fabricating a back-contact solar cell and device thereof

DOEpatents

Li, Bo; Smith, David; Cousins, Peter

2016-08-02

Methods of fabricating back-contact solar cells and devices thereof are described. A method of fabricating a back-contact solar cell includes forming an N-type dopant source layer and a P-type dopant source layer above a material layer disposed above a substrate. The N-type dopant source layer is spaced apart from the P-type dopant source layer. The N-type dopant source layer and the P-type dopant source layer are heated. Subsequently, a trench is formed in the material layer, between the N-type and P-type dopant source layers.

Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance

PubMed Central

Taboada, Eduardo; Grant, Christopher C. R.; Blakeston, Connie; Pollari, Frank; Marshall, Barbara; Rahn, Kris; MacKinnon, Joanne; Daignault, Danielle; Pillai, Dylan; Ng, Lai-King

2012-01-01

Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population. PMID:22162562

Comparison results on preconditioned SOR-type iterative method for Z-matrices linear systems

NASA Astrophysics Data System (ADS)

Wang, Xue-Zhong; Huang, Ting-Zhu; Fu, Ying-Ding

2007-09-01

In this paper, we present some comparison theorems on preconditioned iterative method for solving Z-matrices linear systems, Comparison results show that the rate of convergence of the Gauss-Seidel-type method is faster than the rate of convergence of the SOR-type iterative method.

Correlation and agreement between eplet mismatches calculated using serological, low-intermediate and high resolution molecular human leukocyte antigen typing methods

PubMed Central

Fidler, Samantha; D’Orsogna, Lloyd; Irish, Ashley B.; Lewis, Joshua R.; Wong, Germaine; Lim, Wai H.

2018-01-01

Structural human leukocyte antigen (HLA) matching at the eplet level can be identified by HLAMatchmaker, which requires the entry of four-digit alleles. The aim of this study was to evaluate the agreement between eplet mismatches calculated by serological and two-digit typing methods compared to high-resolution four-digit typing. In a cohort of 264 donor/recipient pairs, the evaluation of measurement error was assessed using intra-class correlation to confirm the absolute agreement between the number of eplet mismatches at class I (HLA-A, -B, C) and II loci (HLA-DQ and -DR) calculated using serological or two-digit molecular typing compared to four-digit molecular typing methods. The proportion of donor/recipient pairs with a difference of >5 eplet mismatches between the HLA typing methods was also determined. Intra-class correlation coefficients between serological and four-digit molecular typing methods were 0.969 (95% confidence intervals [95% CI] 0.960–0.975) and 0.926 (95% CI 0.899–0.944), respectively; and 0.995 (95% CI 0.994–0.996) and 0.993 (95% CI 0.991–0.995), respectively between two-digit and four-digit molecular typing methods. The proportion of donor/recipient pairs with a difference of >5 eplet mismatches at class I and II loci was 4% and 16% for serological versus four-digit molecular typing methods, and 0% and 2% for two-digit versus four-digit molecular typing methods, respectively. In this small predominantly Caucasian population, compared with serology, there is a high level of agreement in the number of eplet mismatches calculated using two-compared to four-digit molecular HLA-typing methods, suggesting that two-digit typing may be sufficient in determining eplet mismatch load in kidney transplantation. PMID:29568344

A new method for correcting type I and type II constricted (cup and lop) ears.

PubMed

Xiaogeng, Hu; Hongxing, Zhuang; Qinghua, Yang; Haiyue, Jiang; Yanyong, Zhao

2006-01-01

Tanzer suggested the term "constricted ear," denoting a spectrum of deformities limited to the superior third of the ear. Tanzer classified the constricted ear into three types. Type I ears have involvement of the helix, which usually is flattened. Type II ears show involvement of both the helix and the scapha. With type III ears, the auricle is rolled into a nearly tubular form that some authors regard as a form of microtia. The authors' new method for correcting the constricted ear varies in accordance with the diverse degree of deformity. The new method was used to correct constricted ears through a one-stage operation in eight type I cases. For the remaining six type 2 cases, the methods were combined with composite grafting. Most of the patients were satisfied with the final results. Therefore, the authors conclude that their approach is suitable for the treatment of type I and type II constricted ears.

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

PubMed Central

Unemo, Magnus; Dillon, Jo-Anne R.

2011-01-01

Summary: Gonorrhea, which may become untreatable due to multiple resistance to available antibiotics, remains a public health problem worldwide. Precise methods for typing Neisseria gonorrhoeae, together with epidemiological information, are crucial for an enhanced understanding regarding issues involving epidemiology, test of cure and contact tracing, identifying core groups and risk behaviors, and recommending effective antimicrobial treatment, control, and preventive measures. This review evaluates methods for typing N. gonorrhoeae isolates and recommends various methods for different situations. Phenotypic typing methods, as well as some now-outdated DNA-based methods, have limited usefulness in differentiating between strains of N. gonorrhoeae. Genotypic methods based on DNA sequencing are preferred, and the selection of the appropriate genotypic method should be guided by its performance characteristics and whether short-term epidemiology (microepidemiology) or long-term and/or global epidemiology (macroepidemiology) matters are being investigated. Currently, for microepidemiological questions, the best methods for fast, objective, portable, highly discriminatory, reproducible, typeable, and high-throughput characterization are N. gonorrhoeae multiantigen sequence typing (NG-MAST) or full- or extended-length porB gene sequencing. However, pulsed-field gel electrophoresis (PFGE) and Opa typing can be valuable in specific situations, i.e., extreme microepidemiology, despite their limitations. For macroepidemiological studies and phylogenetic studies, DNA sequencing of chromosomal housekeeping genes, such as multilocus sequence typing (MLST), provides a more nuanced understanding. PMID:21734242

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

Buttler, D J

The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) Theymore » cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).« less

Methods for selective functionalization and separation of carbon nanotubes

NASA Technical Reports Server (NTRS)

Strano, Michael S. (Inventor); Usrey, Monica (Inventor); Barone, Paul (Inventor); Dyke, Christopher A. (Inventor); Tour, James M. (Inventor); Kittrell, W. Carter (Inventor); Hauge, Robert H (Inventor); Smalley, Richard E. (Inventor); Marek, legal representative, Irene Marie (Inventor)

2011-01-01

The present invention is directed toward methods of selectively functionalizing carbon nanotubes of a specific type or range of types, based on their electronic properties, using diazonium chemistry. The present invention is also directed toward methods of separating carbon nanotubes into populations of specific types or range(s) of types via selective functionalization and electrophoresis, and also to the novel compositions generated by such separations.

Pyocin-sensitivity testing as a method of typing Pseudomonas aeruginosa: use of "phage-free" preparations of pyocin.

PubMed

Rampling, A; Whitby, J L; Wildy, P

1975-11-01

A method for pyocin-sensitivity typing by means of "phage-free" preparations of pyocin is described. The method was tested on 227 isolates of P. aeruginosa, collected from 34 different foci of infection in hospitals in the British Isles and the results were compared with those for combined serological and phage typing of all strains and pyocin production of 105 of the isolates. It is concluded that pyocin-sensitivity typing is a simple and reliable method giving a high degree of discrimination, comparable to that of combined serological and phage typing, and it is suitable for use in routine hospital laboratories.

Phase formation and UV luminescence of Gd{sup 3+} doped perovskite-type YScO{sub 3}

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

Shimizu, Yuhei; Ueda, Kazushige, E-mail: kueda@che.kyutech.ac.jp

Synthesis of pure and Gd{sup 3+}doped perovskite-type YScO{sub 3} was attempted by a polymerized complex (PC) method and solid state reaction (SSR) method. Crystalline phases and UV luminescence of samples were examined with varying heating temperatures. The perovskite-type single phase was not simply formed in the SSR method, as reported in some literatures, and two cubic C-type phases of starting oxide materials remained forming slightly mixed solid solutions. UV luminescence of Gd{sup 3+} doped samples increased with an increase in heating temperatures and volume of the perovskite-type phase. In contrast, a non-crystalline precursor was crystallized to a single C-type phasemore » at 800 °C in the PC method forming a completely mixed solid solution. Then, the phase of perovskite-type YScO{sub 3} formed at 1200 °C and its single phase was obtained at 1400 °C. It was revealed that high homogeneousness of cations was essential to generate the single perovskite-phase of YScO{sub 3}. Because Gd{sup 3+} ions were also dissolved into the single C-type phase in Gd{sup 3+} doped samples, intense UV luminescence was observed above 800 °C in both C-type phase and perovskite-type phase. - Graphical abstract: A pure perovskite-type YScO{sub 3} phase was successfully synthesized by a polymerized complex (PC) method. The perovskite-type YScO{sub 3} was generated through a solid solution of C-type (Y{sub 0.5}Sc{sub 0.5}){sub 2}O{sub 3} with drastic change of morphology. The PC method enabled a preparation of the single phase of the perovskite-type YScO{sub 3} at lower temperature and in shorter heating time. Gd{sup 3+} doped perovskite-type YScO{sub 3} was found to show a strong sharp UV emission at 314 nm. - Highlights: • Pure YScO{sub 3} phase was successfully synthesized by polymerized complex (PC) method. • Pure perovskite-type YScO{sub 3} phase was generated from pure C-type (Y{sub 0.5}Sc{sub 0.5}){sub 2}O{sub 3} one. • YScO{sub 3} was obtained at lower temperature and in shorter heating time by PC method. • Perovskite-type YScO{sub 3}:Gd{sup 3+} was found to show strong sharp UV emission at 314 nm.« less

Solving the interval type-2 fuzzy polynomial equation using the ranking method

NASA Astrophysics Data System (ADS)

Rahman, Nurhakimah Ab.; Abdullah, Lazim

2014-07-01

Polynomial equations with trapezoidal and triangular fuzzy numbers have attracted some interest among researchers in mathematics, engineering and social sciences. There are some methods that have been developed in order to solve these equations. In this study we are interested in introducing the interval type-2 fuzzy polynomial equation and solving it using the ranking method of fuzzy numbers. The ranking method concept was firstly proposed to find real roots of fuzzy polynomial equation. Therefore, the ranking method is applied to find real roots of the interval type-2 fuzzy polynomial equation. We transform the interval type-2 fuzzy polynomial equation to a system of crisp interval type-2 fuzzy polynomial equation. This transformation is performed using the ranking method of fuzzy numbers based on three parameters, namely value, ambiguity and fuzziness. Finally, we illustrate our approach by numerical example.

High performance p-type thermoelectric materials and methods of preparation

NASA Technical Reports Server (NTRS)

Caillat, Thierry (Inventor); Borshchevsky, Alexander (Inventor); Fleurial, Jean-Pierre (Inventor)

2005-01-01

The present invention is embodied in high performance p-type thermoelectric materials having enhanced thermoelectric properties and the methods of preparing such materials. In one aspect of the invention, p-type semiconductors of formula Zn4-xAxSb3-yBy wherein 0?x?4, A is a transition metal, B is a pnicogen, and 0?y?3 are formed for use in manufacturing thermoelectric devices with substantially enhanced operating characteristics and improved efficiency. Two methods of preparing p-type Zn4Sb3 and related alloys of the present invention include a crystal growth method and a powder metallurgy method.

Method of forming contacts for a back-contact solar cell

DOEpatents

Manning, Jane

2015-10-20

Methods of forming contacts for solar cells are described. In one embodiment, a method includes forming a silicon layer above a substrate, forming and patterning a solid-state p-type dopant source on the silicon layer, forming an n-type dopant source layer over exposed regions of the silicon layer and over a plurality of regions of the solid-state p-type dopant source, and heating the substrate to provide a plurality of n-type doped silicon regions among a plurality of p-type doped silicon regions.

Method of forming contacts for a back-contact solar cell

DOEpatents

Manning, Jane

2014-07-15

Methods of forming contacts for solar cells are described. In one embodiment, a method includes forming a silicon layer above a substrate, forming and patterning a solid-state p-type dopant source on the silicon layer, forming an n-type dopant source layer over exposed regions of the silicon layer and over a plurality of regions of the solid-state p-type dopant source, and heating the substrate to provide a plurality of n-type doped silicon regions among a plurality of p-type doped silicon regions.

Cutibacterium acnes molecular typing: time to standardize the method.

PubMed

Dagnelie, M-A; Khammari, A; Dréno, B; Corvec, S

2018-03-12

The Gram-positive, anaerobic/aerotolerant bacterium Cutibacterium acnes is a commensal of healthy human skin; it is subdivided into six main phylogenetic groups or phylotypes: IA1, IA2, IB, IC, II and III. To decipher how far specific subgroups of C. acnes are involved in disease physiopathology, different molecular typing methods have been developed to identify these subgroups: i.e. phylotypes, clonal complexes, and types defined by single-locus sequence typing (SLST). However, as several molecular typing methods have been developed over the last decade, it has become a difficult task to compare the results from one article to another. Based on the scientific literature, the aim of this narrative review is to propose a standardized method to perform molecular typing of C. acnes, according to the degree of resolution needed (phylotypes, clonal complexes, or SLST types). We discuss the existing different typing methods from a critical point of view, emphasizing their advantages and drawbacks, and we identify the most frequently used methods. We propose a consensus algorithm according to the needed phylogeny resolution level. We first propose to use multiplex PCR for phylotype identification, MLST9 for clonal complex determination, and SLST for phylogeny investigation including numerous isolates. There is an obvious need to create a consensus about molecular typing methods for C. acnes. This standardization will facilitate the comparison of results between one article and another, and also the interpretation of clinical data. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Classifying aerosol type using in situ surface spectral aerosol optical properties

NASA Astrophysics Data System (ADS)

Schmeisser, Lauren; Andrews, Elisabeth; Ogren, John A.; Sheridan, Patrick; Jefferson, Anne; Sharma, Sangeeta; Kim, Jeong Eun; Sherman, James P.; Sorribas, Mar; Kalapov, Ivo; Arsov, Todor; Angelov, Christo; Mayol-Bracero, Olga L.; Labuschagne, Casper; Kim, Sang-Woo; Hoffer, András; Lin, Neng-Huei; Chia, Hao-Ping; Bergin, Michael; Sun, Junying; Liu, Peng; Wu, Hao

2017-10-01

Knowledge of aerosol size and composition is important for determining radiative forcing effects of aerosols, identifying aerosol sources and improving aerosol satellite retrieval algorithms. The ability to extrapolate aerosol size and composition, or type, from intensive aerosol optical properties can help expand the current knowledge of spatiotemporal variability in aerosol type globally, particularly where chemical composition measurements do not exist concurrently with optical property measurements. This study uses medians of the scattering Ångström exponent (SAE), absorption Ångström exponent (AAE) and single scattering albedo (SSA) from 24 stations within the NOAA/ESRL Federated Aerosol Monitoring Network to infer aerosol type using previously published aerosol classification schemes.Three methods are implemented to obtain a best estimate of dominant aerosol type at each station using aerosol optical properties. The first method plots station medians into an AAE vs. SAE plot space, so that a unique combination of intensive properties corresponds with an aerosol type. The second typing method expands on the first by introducing a multivariate cluster analysis, which aims to group stations with similar optical characteristics and thus similar dominant aerosol type. The third and final classification method pairs 3-day backward air mass trajectories with median aerosol optical properties to explore the relationship between trajectory origin (proxy for likely aerosol type) and aerosol intensive parameters, while allowing for multiple dominant aerosol types at each station.The three aerosol classification methods have some common, and thus robust, results. In general, estimating dominant aerosol type using optical properties is best suited for site locations with a stable and homogenous aerosol population, particularly continental polluted (carbonaceous aerosol), marine polluted (carbonaceous aerosol mixed with sea salt) and continental dust/biomass sites (dust and carbonaceous aerosol); however, current classification schemes perform poorly when predicting dominant aerosol type at remote marine and Arctic sites and at stations with more complex locations and topography where variable aerosol populations are not well represented by median optical properties. Although the aerosol classification methods presented here provide new ways to reduce ambiguity in typing schemes, there is more work needed to find aerosol typing methods that are useful for a larger range of geographic locations and aerosol populations.

Methods for biological data integration: perspectives and challenges

PubMed Central

Gligorijević, Vladimir; Pržulj, Nataša

2015-01-01

Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

Twostep-by-twostep PIRK-type PC methods with continuous output formulas

NASA Astrophysics Data System (ADS)

Cong, Nguyen Huu; Xuan, Le Ngoc

2008-11-01

This paper deals with parallel predictor-corrector (PC) iteration methods based on collocation Runge-Kutta (RK) corrector methods with continuous output formulas for solving nonstiff initial-value problems (IVPs) for systems of first-order differential equations. At nth step, the continuous output formulas are used not only for predicting the stage values in the PC iteration methods but also for calculating the step values at (n+2)th step. In this case, the integration processes can be proceeded twostep-by-twostep. The resulting twostep-by-twostep (TBT) parallel-iterated RK-type (PIRK-type) methods with continuous output formulas (twostep-by-twostep PIRKC methods or TBTPIRKC methods) give us a faster integration process. Fixed stepsize applications of these TBTPIRKC methods to a few widely-used test problems reveal that the new PC methods are much more efficient when compared with the well-known parallel-iterated RK methods (PIRK methods), parallel-iterated RK-type PC methods with continuous output formulas (PIRKC methods) and sequential explicit RK codes DOPRI5 and DOP853 available from the literature.

spa Typing and Multilocus Sequence Typing Show Comparable Performance in a Macroepidemiologic Study of Staphylococcus aureus in the United States

PubMed Central

O'Hara, F. Patrick; Suaya, Jose A.; Ray, G. Thomas; Baxter, Roger; Brown, Megan L.; Mera, Robertino M.; Close, Nicole M.; Thomas, Elizabeth

2016-01-01

A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLST) (and its clustering algorithm, Based Upon Related Sequence Type [BURST]) with the staphylococcal protein A (spa) typing (and its clustering algorithm, Based Upon Repeat Pattern [BURP]), to assess the utility of these methods for macroepidemiology and evolutionary studies of S. aureus in the United States. We typed a total of 366 clinical isolates of S. aureus by these methods and evaluated indices of diversity and concordance values. Our results show that, when combined with the BURP clustering algorithm to delineate clonal lineages, spa typing produces results that are highly comparable with those produced by MLST/BURST. Therefore, spa typing is appropriate for use in macroepidemiology and evolutionary studies and, given its lower implementation cost, this method appears to be more efficient. The findings are robust and are consistent across different settings, patient ages, and specimen sources. Our results also support a model in which the methicillin-resistant S. aureus (MRSA) population in the United States comprises two major lineages (USA300 and USA100), which each consist of closely related variants. PMID:26669861

Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State.

PubMed

Ahmed, Sara; Besser, Thomas E; Call, Douglas R; Weissman, Scott J; Jones, Lisa P; Davis, Margaret A

2016-05-01

Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli. Copyright © 2016 Elsevier B.V. All rights reserved.

spa Typing and Multilocus Sequence Typing Show Comparable Performance in a Macroepidemiologic Study of Staphylococcus aureus in the United States.

PubMed

O'Hara, F Patrick; Suaya, Jose A; Ray, G Thomas; Baxter, Roger; Brown, Megan L; Mera, Robertino M; Close, Nicole M; Thomas, Elizabeth; Amrine-Madsen, Heather

2016-01-01

A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLST) (and its clustering algorithm, Based Upon Related Sequence Type [BURST]) with the staphylococcal protein A (spa) typing (and its clustering algorithm, Based Upon Repeat Pattern [BURP]), to assess the utility of these methods for macroepidemiology and evolutionary studies of S. aureus in the United States. We typed a total of 366 clinical isolates of S. aureus by these methods and evaluated indices of diversity and concordance values. Our results show that, when combined with the BURP clustering algorithm to delineate clonal lineages, spa typing produces results that are highly comparable with those produced by MLST/BURST. Therefore, spa typing is appropriate for use in macroepidemiology and evolutionary studies and, given its lower implementation cost, this method appears to be more efficient. The findings are robust and are consistent across different settings, patient ages, and specimen sources. Our results also support a model in which the methicillin-resistant S. aureus (MRSA) population in the United States comprises two major lineages (USA300 and USA100), which each consist of closely related variants.

High performance P-type thermoelectric materials and methods of preparation

NASA Technical Reports Server (NTRS)

Caillat, Thierry (Inventor); Borshchevsky, Alexander (Inventor); Fleurial, Jean-Pierre (Inventor)

2002-01-01

The present invention is embodied in high performance p-type thermoelectric materials having enhanced thermoelectric properties and the methods of preparing such materials. In one aspect of the invention, p-type semiconductors of formula Zn.sub.4-x A.sub.x Sb.sub.3-y B.sub.y wherein 0.ltoreq.x.ltoreq.4, A is a transition metal, B is a pnicogen, and 0.ltoreq.y.ltoreq.3 are formed for use in manufacturing thermoelectric devices with substantially enhanced operating characteristics and improved efficiency. Two methods of preparing p-type Zn.sub.4 Sb.sub.3 and related alloys of the present invention include a crystal growth method and a powder metallurgy method.

Upper Water Structure and Mixed Layer Depth in Sub-Tropical Waters: The Seats Station in the Northern South China Sea

NASA Astrophysics Data System (ADS)

Wong, G. T. F.; Tai, J. H.

2014-12-01

702 CTD profiles were collected in the subtropical northern South China Sea at and in the vicinity of the SouthEast Asian Time-series Study (SEATS) station (18.2oN, 115.8oE) between 17.5 and 18.5oN and 115.3 and 116.3oE in 64 cruises in 1997 to 2013. The hydrographic structure of the upper water above the permanent thermocline may be classified into 4 principal types: (a) classic type (an almost isopycnic upper water); (b) stepwise type (with one or more small but significant step-increases in σθ in the upper water); (c) graded type (an approximately constant depth gradient in a monotonic increase in σθ in the upper water); and (d) mixed type (a combination of the stepwise and graded types). The 4 types of upper water were found in 75, 14, 5, and 6% of the cruises, respectively. Ten schemes were applied to these data to determine the mixed layer depth (MLD): 4 fixed temperature difference (FTD) methods (0.2, 0.5, 0.8 and 1.0oC decrease from 10 m); 1 fixed density difference (FDD) method (0.125 σθ increase from 10 m); 1 fixed temperature gradient (FTG) method (at 0.05oC/m); 3 fixed density gradient (FDG) methods (at 0.01, 0.05 and 0.1 σθ/m); and the maximum density gradient (MDG) method. MLD could not be clearly depicted in the 3 minor types of upper water. In the classical type, while similar MLD-s were found in a large majority of the cruises among all 10 methods, substantial discrepancies among methods could be found. The most consistent results, generally within ±5 m, were found among the FDG method at 0.05, 0.1 σθ/m and FTD method at 0.8 and 1.0oC. The MDG method gave consistently deeper MLD by ~8 m. If that difference was taken into account, the results were generally consistent with those from the other 4 methods. The remaining 5 methods could all yield MLD-s shallower than the first 4 methods by >10 m as they failed to capture the bottom of the mixed layer as indicated by visual inspection.

Comparison of gel column, card, and cartridge techniques for dog erythrocyte antigen 1.1 blood typing

PubMed Central

Seth, Mayank; Jackson, Karen V.; Winzelberg, Sarah; Giger, Urs

2012-01-01

Objective To compare accuracy and ease of use of a card agglutination assay, an immunochromatographic cartridge method, and a gel-based method for canine blood typing. Sample Blood samples from 52 healthy blood donor dogs, 10 dogs with immune-mediated hemolytic anemia (IMHA), and 29 dogs with other diseases. Procedures Blood samples were tested in accordance with manufacturer guidelines. Samples with low PCVs were created by the addition of autologous plasma to separately assess the effects of anemia on test results. Results Compared with a composite reference standard of agreement between 2 methods, the gel-based method was found to be 100% accurate. The card agglutination assay was 89% to 91% accurate, depending on test interpretation, and the immunochromatographic cartridge method was 93% accurate but 100% specific. Errors were observed more frequently in samples from diseased dogs, particularly those with IMHA. In the presence of persistent autoagglutination, dog erythrocyte antigen (DEA) 1.1 typing was not possible, except with the immunochromatographic cartridge method. Conclusions and Clinical Relevance The card agglutination assay and immunochromatographic cartridge method, performed by trained personnel, were suitable for in-clinic emergency DEA 1.1 blood typing. There may be errors, particularly for samples from dogs with IMHA, and the immunochromatographic cartridge method may have an advantage of allowing typing of samples with persistent autoagglutination. The laboratory gel-based method would be preferred for routine DEA 1.1 typing of donors and patients if it is available and time permits. Current DEA 1.1 typing techniques appear to be appropriately standardized and easy to use. PMID:22280380

Local Discontinuous Galerkin Methods for the Cahn-Hilliard Type Equations

DTIC Science & Technology

2007-01-01

Kuramoto-Sivashinsky equations , the Ito-type coupled KdV equa- tions, the Kadomtsev - Petviashvili equation , and the Zakharov-Kuznetsov equation . A common...Local discontinuous Galerkin methods for the Cahn-Hilliard type equations Yinhua Xia∗, Yan Xu† and Chi-Wang Shu ‡ Abstract In this paper we develop...local discontinuous Galerkin (LDG) methods for the fourth-order nonlinear Cahn-Hilliard equation and system. The energy stability of the LDG methods is

Statistical Methods in Integrative Genomics

PubMed Central

Richardson, Sylvia; Tseng, George C.; Sun, Wei

2016-01-01

Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

49 CFR Appendix D to Part 173 - Test Methods for Dynamite (Explosive, Blasting, Type A)

Code of Federal Regulations, 2010 CFR

2010-10-01

..., Type A) D Appendix D to Part 173 Transportation Other Regulations Relating to Transportation PIPELINE... REGULATIONS SHIPPERS-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Pt. 173, App. D Appendix D to Part 173—Test Methods for Dynamite (Explosive, Blasting, Type A) 1. Test method D-1—Leakage Test A wooden stick...

mec-associated dru typing in the epidemiological analysis of ST239 MRSA in Malaysia.

PubMed

Ghaznavi-Rad, E; Goering, R V; Nor Shamsudin, M; Weng, P L; Sekawi, Z; Tavakol, M; van Belkum, A; Neela, V

2011-11-01

The usefulness of mec-associated dru typing in the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Malaysia was investigated and compared with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and spa and SCCmec typing. The isolates studied included all MRSA types in Malaysia. Multilocus sequence type ST188 and ST1 isolates were highly clonal by all typing methods. However, the dru typing of ST239 isolates produced the clearest discrimination between SCCmec IIIa and III isolates, yielding more subtypes than any other method. Evaluation of the discriminatory power for each method identified dru typing and PFGE as the most discriminatory, with Simpson's index of diversity (SID) values over 89%, including an isolate which was non-typeable by spa, but dru-typed as dt13j. The discriminatory ability of dru typing, especially with closely related MRSA ST239 strains (e.g., Brazilian and Hungarian), underscores its utility as a tool for the epidemiological investigation of MRSA.

Guidelines for cost control and analysis of cost-type research and development contracts

NASA Technical Reports Server (NTRS)

Sibbers, C. W.

1981-01-01

The cost information which should be obtained from a contractor(s) on a major, cost type research and development contract(s), and the analyses and effective use of these data are discussed. Specific type(s) of information which should be required, methods for analyzing such information, and methods for effectively using the results of such analyses to enhance NASA contract and project management are included. The material presented is based primarily on the principal methods which have been effectively used in the management of major cost type research and development contracts.

Method of forming contacts for a back-contact solar cell

DOEpatents

Manning, Jane

2013-07-23

Methods of forming contacts for back-contact solar cells are described. In one embodiment, a method includes forming a thin dielectric layer on a substrate, forming a polysilicon layer on the thin dielectric layer, forming and patterning a solid-state p-type dopant source on the polysilicon layer, forming an n-type dopant source layer over exposed regions of the polysilicon layer and over a plurality of regions of the solid-state p-type dopant source, and heating the substrate to provide a plurality of n-type doped polysilicon regions among a plurality of p-type doped polysilicon regions.

[Therapeutic strategy for different types of epicanthus].

PubMed

Gaofeng, Li; Jun, Tan; Zihan, Wu; Wei, Ding; Huawei, Ouyang; Fan, Zhang; Mingcan, Luo

2015-11-01

To explore the reasonable therapeutic strategy for different types of epicanthus. Patients with epicanthus were classificated according to the shape, extent and inner canthal distance and treated with different methods appropriately. Modified asymmetric Z plasty with two curve method was used in lower eyelid type epicanthus, inner canthus type epicanthus and severe upper eyelid type epicanthus. Moderate upper epicanthus underwent '-' shape method. Mild Upper epicanthus in two conditions which underwent nasal augumentation and double eyelid formation with normal inner canthal distance need no correction surgery. The other mild epicanthus underwent '-' shape method. A total of 66 cases underwent the classification and the appropriate treatment. All wounds healed well. During 3 to 12 months follow-up period, all epicanthus were corrected completely with natural contour and unconspicuous scars. All patients were satisfied with the results. Classification of epicanthus hosed on the shape, extent and inner canthal distance and correction with appropriate methods is a reasonable therapeutic strategy.

Method for obtaining chromosome painting probes

DOEpatents

Lucas, Joe N.

2000-01-01

A method is provided for determining a clastogenic signature of a sample of chromosomes by quantifying a frequency of a first type of chromosome aberration present in the sample; quantifying a frequency of a second, different type of chromosome aberration present in the sample; and comparing the frequency of the first type of chromosome aberration to the frequency of the second type of chromosome aberration. A method is also provided for using that clastogenic signature to identify a clastogenic agent or dosage to which the cells were exposed.

Interval type-2 fuzzy PID controller for uncertain nonlinear inverted pendulum system.

PubMed

El-Bardini, Mohammad; El-Nagar, Ahmad M

2014-05-01

In this paper, the interval type-2 fuzzy proportional-integral-derivative controller (IT2F-PID) is proposed for controlling an inverted pendulum on a cart system with an uncertain model. The proposed controller is designed using a new method of type-reduction that we have proposed, which is called the simplified type-reduction method. The proposed IT2F-PID controller is able to handle the effect of structure uncertainties due to the structure of the interval type-2 fuzzy logic system (IT2-FLS). The results of the proposed IT2F-PID controller using a new method of type-reduction are compared with the other proposed IT2F-PID controller using the uncertainty bound method and the type-1 fuzzy PID controller (T1F-PID). The simulation and practical results show that the performance of the proposed controller is significantly improved compared with the T1F-PID controller. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

Evaluation of a Method Using Three Genomic Guided Escherichia coli Markers for Phylogenetic Typing of E. coli Isolates of Various Genetic Backgrounds

PubMed Central

Hamamoto, Kouta; Ueda, Shuhei; Yamamoto, Yoshimasa

2015-01-01

Genotyping and characterization of bacterial isolates are essential steps in the identification and control of antibiotic-resistant bacterial infections. Recently, one novel genotyping method using three genomic guided Escherichia coli markers (GIG-EM), dinG, tonB, and dipeptide permease (DPP), was reported. Because GIG-EM has not been fully evaluated using clinical isolates, we assessed this typing method with 72 E. coli collection of reference (ECOR) environmental E. coli reference strains and 63 E. coli isolates of various genetic backgrounds. In this study, we designated 768 bp of dinG, 745 bp of tonB, and 655 bp of DPP target sequences for use in the typing method. Concatenations of the processed marker sequences were used to draw GIG-EM phylogenetic trees. E. coli isolates with identical sequence types as identified by the conventional multilocus sequence typing (MLST) method were localized to the same branch of the GIG-EM phylogenetic tree. Sixteen clinical E. coli isolates were utilized as test isolates without prior characterization by conventional MLST and phylogenetic grouping before GIG-EM typing. Of these, 14 clinical isolates were assigned to a branch including only isolates of a pandemic clone, E. coli B2-ST131-O25b, and these results were confirmed by conventional typing methods. Our results suggested that the GIG-EM typing method and its application to phylogenetic trees might be useful tools for the molecular characterization and determination of the genetic relationships among E. coli isolates. PMID:25809972

Evaluation of a Method Using Three Genomic Guided Escherichia coli Markers for Phylogenetic Typing of E. coli Isolates of Various Genetic Backgrounds.

PubMed

Hamamoto, Kouta; Ueda, Shuhei; Yamamoto, Yoshimasa; Hirai, Itaru

2015-06-01

Genotyping and characterization of bacterial isolates are essential steps in the identification and control of antibiotic-resistant bacterial infections. Recently, one novel genotyping method using three genomic guided Escherichia coli markers (GIG-EM), dinG, tonB, and dipeptide permease (DPP), was reported. Because GIG-EM has not been fully evaluated using clinical isolates, we assessed this typing method with 72 E. coli collection of reference (ECOR) environmental E. coli reference strains and 63 E. coli isolates of various genetic backgrounds. In this study, we designated 768 bp of dinG, 745 bp of tonB, and 655 bp of DPP target sequences for use in the typing method. Concatenations of the processed marker sequences were used to draw GIG-EM phylogenetic trees. E. coli isolates with identical sequence types as identified by the conventional multilocus sequence typing (MLST) method were localized to the same branch of the GIG-EM phylogenetic tree. Sixteen clinical E. coli isolates were utilized as test isolates without prior characterization by conventional MLST and phylogenetic grouping before GIG-EM typing. Of these, 14 clinical isolates were assigned to a branch including only isolates of a pandemic clone, E. coli B2-ST131-O25b, and these results were confirmed by conventional typing methods. Our results suggested that the GIG-EM typing method and its application to phylogenetic trees might be useful tools for the molecular characterization and determination of the genetic relationships among E. coli isolates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

[Differentiation of Staphylococcus aureus isolates based on phenotypical characters].

PubMed

Miedzobrodzki, Jacek; Małachowa, Natalia; Markiewski, Tomasz; Białecka, Anna; Kasprowicz, Andrzej

2008-06-30

Typing of Staphylococcus aureus isolates is a necessary procedure for monitoring the transmission of S. aureus among carriers and in epidemiology. Evaluation of the range of relationship among isolates rely on epidemiological markers and is possible because of the clonal character of S. aureus species. Effective typing shows the scheme of transmission of infection in a selected area, enables identifying the reservoir of the microorganism, and may enhance effective eradication. A set of typing methods for use in analyses of epidemiological correlations and the identification of S. aureus isolates is presented. The following methods of typing are described: biotyping, serotyping, antibiogram, protein electrophoresis, cell protein profiles (proteom), immunoblotting, multilocus enzyme electrophoresis (MLEE), zymotyping, and standard species identification of S. aureus in the diagnostic laboratory. Phenotyping methods for S. aureus isolates used in the past and today in epidemiological investigations and in analyses of correlations among S. aureus isolates are presented in this review. The presented methods use morphological characteristics, physiological properties, and chemical structures of the bacteria as criteria for typing. The precision of these standard methods is not always satisfactory as S. aureus strains with atypical biochemical characters have evolved recently. Therefore it is essential to introduce additional typing procedures using molecular biology methods without neglecting phenotypic methods.

An Improved MLVF Method and Its Comparison with Traditional MLVF, spa Typing, MLST/SCCmec and PFGE for the Typing of Methicillin-Resistant Staphylococcus aureus

PubMed Central

Du, Xue-Fei; Xiao, Meng; Liang, Hong-Yan; Sun, Zhe; Jiang, Yue-Hong; Chen, Guo-Yu; Meng, Xiao-Yu; Zou, Gui-Ling; Zhang, Li; Liu, Ya-Li; Zhang, Hui; Sun, Hong-Li; Jiang, Xiao-Feng; Xu, Ying-Chun

2014-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an improved approach capillary gel electrophoresis based multilocus variable-number tandem-repeat fingerprinting (CGE/MLVF) for rapid MRSA typing. A total of 42 well-characterized strains and 116 non-repetitive clinical MRSA isolates collected from six hospitals in northeast China between 2009 and 2010 were tested. The results obtained by CGE/MLVF against clinical isolates were compared with traditional MLVF, spa typing, Multilocus sequence typing/staphylococcal cassette chromosome mec (MLST/SCCmec) and pulse field gel electrophoresis (PFGE). The discriminatory power estimated by Simpson’s index of diversity was 0.855 (28 types), 0.855 (28 patterns), 0.623 (11 types), 0.517 (8 types) and 0.854 (28 patterns) for CGE/MLVF, traditional MLVF, spa typing, MLST/SCCmec and PFGE, respectively. All methods tested showed a satisfied concordance in clonal complex level calculated by adjusted Rand’s coefficient. CGE/MLVF showed better reproducibility and accuracy than traditional MLVF and PFGE methods. In addition, the CGE/MLVF has potential to produce portable results. In conclusion, CGE/MLVF is a rapid and easy to use MRSA typing method with lower cost, good reproducibility and high discriminatory power for monitoring the outbreak and clonal spread of MRSA isolates. PMID:24406728

An efficient computational method for the approximate solution of nonlinear Lane-Emden type equations arising in astrophysics

NASA Astrophysics Data System (ADS)

Singh, Harendra

2018-04-01

The key purpose of this article is to introduce an efficient computational method for the approximate solution of the homogeneous as well as non-homogeneous nonlinear Lane-Emden type equations. Using proposed computational method given nonlinear equation is converted into a set of nonlinear algebraic equations whose solution gives the approximate solution to the Lane-Emden type equation. Various nonlinear cases of Lane-Emden type equations like standard Lane-Emden equation, the isothermal gas spheres equation and white-dwarf equation are discussed. Results are compared with some well-known numerical methods and it is observed that our results are more accurate.

Structural damage detection-oriented multi-type sensor placement with multi-objective optimization

NASA Astrophysics Data System (ADS)

Lin, Jian-Fu; Xu, You-Lin; Law, Siu-Seong

2018-05-01

A structural damage detection-oriented multi-type sensor placement method with multi-objective optimization is developed in this study. The multi-type response covariance sensitivity-based damage detection method is first introduced. Two objective functions for optimal sensor placement are then introduced in terms of the response covariance sensitivity and the response independence. The multi-objective optimization problem is formed by using the two objective functions, and the non-dominated sorting genetic algorithm (NSGA)-II is adopted to find the solution for the optimal multi-type sensor placement to achieve the best structural damage detection. The proposed method is finally applied to a nine-bay three-dimensional frame structure. Numerical results show that the optimal multi-type sensor placement determined by the proposed method can avoid redundant sensors and provide satisfactory results for structural damage detection. The restriction on the number of each type of sensors in the optimization can reduce the searching space in the optimization to make the proposed method more effective. Moreover, how to select a most optimal sensor placement from the Pareto solutions via the utility function and the knee point method is demonstrated in the case study.

Detection of high-risk mucosal human papillomavirus DNA in human specimens by a novel and sensitive multiplex PCR method combined with DNA microarray.

PubMed

Gheit, Tarik; Tommasino, Massimo

2011-01-01

Epidemiological and functional studies have clearly demonstrated that certain types of human papillomavirus (HPV) from the genus alpha of the HPV phylogenetic tree, referred to as high-risk (HR) types, are the etiological cause of cervical cancer. Several methods for HPV detection and typing have been developed, and their importance in clinical and epidemiological studies has been well demonstrated. However, comparative studies have shown that several assays have different sensitivities for the detection of specific HPV types, particularly in the case of multiple infections. In this chapter, we describe a novel one-shot method for the detection and typing of 19 mucosal HR HPV types (types 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, and 82). The assay combines the advantages of the multiplex PCR methods, i.e., high sensitivity and the possibility to perform multiple amplifications in a single reaction, with an array primer extension (APEX) assay. The latter method offers the benefits of Sanger dideoxy sequencing with the high-throughput potential of the microarray. Initial studies have revealed that the assay is very sensitive in detecting multiple HPV infections.

Phase formation and UV luminescence of Gd3+ doped perovskite-type YScO3

NASA Astrophysics Data System (ADS)

Shimizu, Yuhei; Ueda, Kazushige

2016-10-01

Synthesis of pure and Gd3+doped perovskite-type YScO3 was attempted by a polymerized complex (PC) method and solid state reaction (SSR) method. Crystalline phases and UV luminescence of samples were examined with varying heating temperatures. The perovskite-type single phase was not simply formed in the SSR method, as reported in some literatures, and two cubic C-type phases of starting oxide materials remained forming slightly mixed solid solutions. UV luminescence of Gd3+ doped samples increased with an increase in heating temperatures and volume of the perovskite-type phase. In contrast, a non-crystalline precursor was crystallized to a single C-type phase at 800 °C in the PC method forming a completely mixed solid solution. Then, the phase of perovskite-type YScO3 formed at 1200 °C and its single phase was obtained at 1400 °C. It was revealed that high homogeneousness of cations was essential to generate the single perovskite-phase of YScO3. Because Gd3+ ions were also dissolved into the single C-type phase in Gd3+ doped samples, intense UV luminescence was observed above 800 °C in both C-type phase and perovskite-type phase.

Carbon monoxide sensor and method of use thereof

DOEpatents

McDaniel; Anthony H. , Medlin; J. Will , Bastasz; Robert J.

2007-09-04

Carbon monoxide sensors suitable for use in hydrogen feed streams and methods of use thereof are disclosed. The sensors are palladium metal/insulator/semiconductor (Pd-MIS) sensors which may possess a gate metal layer having uniform, Type 1, or non-uniform, Type 2, film morphology. Type 1 sensors display an increased sensor response in the presence of carbon monoxide while Type 2 sensors display a decreased response to carbon monoxide. The methods and sensors disclosed herein are particularly suitable for use in proton exchange membrane fuel cells (PEMFCs).

Rapid method for measuring clastogenic fingerprints using fluorescence in situ hybridization

DOEpatents

Lucas, Joe N.

2000-01-01

A method is provided for determining a clastogenic signature of a sample of chromosomes by quantifying a frequency of a first type of chromosome aberration present in the sample; quantifying a frequency of a second, different type of chromosome aberration present in the sample; and comparing the frequency of the first type of chromosome aberration to the frequency of the second type of chromosome aberration. A method is also provided for using that clastogenic signature to identify a clastogenic agent or dosage to which the cells were exposed.

Method for detecting a pericentric inversion in a chromosome

DOEpatents

Lucas, Joe N.

2000-01-01

A method is provided for determining a clastogenic signature of a sample of chromosomes by quantifying a frequency of a first type of chromosome aberration present in the sample; quantifying a frequency of a second, different type of chromosome aberration present in the sample; and comparing the frequency of the first type of chromosome aberration to the frequency of the second type of chromosome aberration. A method is also provided for using that clastogenic signature to identify a clastogenic agent or dosage to which the cells were exposed.

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

PubMed Central

Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R.; Afshar, Baharak; Underwood, Anthony; Harrison, Timothy G.

2016-01-01

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current “gold standard” typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila. However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard “typing panel,” previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila. PMID:27280420

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines.

PubMed

David, Sophia; Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R; Afshar, Baharak; Underwood, Anthony; Fry, Norman K; Parkhill, Julian; Harrison, Timothy G

2016-08-01

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current "gold standard" typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard "typing panel," previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila. Copyright © 2016 David et al.

Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis

PubMed Central

Malorny, Burkhard; Junker, Ernst; Helmuth, Reiner

2008-01-01

Background Salmonella enterica subsp. enterica serotype Enteritidis is known as an important and pathogenic clonal group which continues to cause worldwide sporadic cases and outbreaks in humans. Here a new multiple-locus variable-number tandem repeat analysis (MLVA) method is reported for highly-discriminative subtyping of Salmonella Enteritidis. Emphasis was given on the most predominant phage types PT4 and PT8. The method comprises multiplex PCR specifically amplifying repeated sequences from nine different loci followed by an automatic fragment size analysis using a multicolor capillary electrophoresis instrument. A total of 240 human, animal, food and environmental isolates of S. Enteritidis including 23 definite phage types were used for development and validation. Furthermore, the MLVA types were compared to the phage types of several isolates from two recent outbreaks to determine the concordance between both methods and to estimate their in vivo stability. The in vitro stability of the two MLVA types specifically for PT4 and PT8 strains were determined by multiple freeze-thaw cycles. Results Seventy-nine different MLVA types were identified in 240 S. Enteritidis strains. The Simpson's diversity index for the MLVA method was 0.919 and Nei diversity values for the nine VNTR loci ranged from 0.07 to 0.65. Twenty-four MLVA types could be assigned to 62 PT4 strains and 21 types to 81 PT8 strains. All outbreak isolates had an indistinguishable outbreak specific MLVA type. The in vitro stability experiments showed no changes of the MLVA type compared to the original isolate. Conclusion This MLVA method is useful to discriminate S. Enteritidis strains even within a single phage type. It is easy in use, fast, and cheap compared to other high-resolution molecular methods and therefore an important tool for surveillance and outbreak studies for S. Enteritidis. PMID:18513386

Current Methods in the Molecular Typing of Mycobacterium tuberculosis and Other Mycobacteria

PubMed Central

van Ingen, Jakko; Dziadek, Jarosław; Mazur, Paweł K.; Bielecki, Jacek

2014-01-01

In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed. PMID:24527454

Low acuity and general practice-type presentations to emergency departments: a rural perspective.

PubMed

Allen, Penny; Cheek, Colleen; Foster, Simon; Ruigrok, Marielle; Wilson, Deborah; Shires, Lizzi

2015-04-01

To estimate the number of general practice (GP)-type patients attending a rural ED and provide a comparative rural estimate to a metropolitan study. Analysis of presentations to the two EDs in Northwest Tasmania from 1 January 2009 to 31 December 2013 using the Diagnosis, Sprivulis, Australian College of Emergency Medicine (ACEM) and the Australian Institute of Health and Welfare (AIHW) methods to estimate the number of GP-type presentations. There were 255,365 ED presentations in Northwest Tasmania during the study period. There were 86,973 GP-type presentations using the ACEM method, 142,006 using the AIHW method, 174,748 using the Diagnosis method and 28,922 low acuity patients identified using the Sprivulis method. The proportion of GP-type presentations identified using the four methods ranged from 15% to 69%. The results suggest that triage status and self-referral are not reliable indicators of low acuity in this rural area. In rural areas with a shortage of GPs, it is likely that many people appropriately self-refer to ED because they cannot access a GP. The results indicate that the ACEM method might be most useful for identifying GP-type patients in rural ED. However, this requires validation in other regions of Australia. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

Selective functionalization of carbon nanotubes

NASA Technical Reports Server (NTRS)

Strano, Michael S. (Inventor); Usrey, Monica (Inventor); Barone, Paul (Inventor); Dyke, Christopher A. (Inventor); Tour, James M. (Inventor); Kittrell, W. Carter (Inventor); Hauge, Robert H. (Inventor); Smalley, Richard E. (Inventor)

2009-01-01

The present invention is directed toward methods of selectively functionalizing carbon nanotubes of a specific type or range of types, based on their electronic properties, using diazonium chemistry. The present invention is also directed toward methods of separating carbon nanotubes into populations of specific types or range(s) of types via selective functionalization and electrophoresis, and also to the novel compositions generated by such separations.

Estimation of vegetation-type areas by linear measurement

Treesearch

A.A. Hasel

1941-01-01

Maps are very useful in providing a picture of the location of vegetation types, but mapping as a method for determining type areas may be inadequate or costly. The measurement of vegetation type areas by means of line surveys is discussed in the following article, and the method is tested in connection with detailed studies on plots. The results indicate that the...

[An object-based information extraction technology for dominant tree species group types].

PubMed

Tian, Tian; Fan, Wen-yi; Lu, Wei; Xiao, Xiang

2015-06-01

Information extraction for dominant tree group types is difficult in remote sensing image classification, howevers, the object-oriented classification method using high spatial resolution remote sensing data is a new method to realize the accurate type information extraction. In this paper, taking the Jiangle Forest Farm in Fujian Province as the research area, based on the Quickbird image data in 2013, the object-oriented method was adopted to identify the farmland, shrub-herbaceous plant, young afforested land, Pinus massoniana, Cunninghamia lanceolata and broad-leave tree types. Three types of classification factors including spectral, texture, and different vegetation indices were used to establish a class hierarchy. According to the different levels, membership functions and the decision tree classification rules were adopted. The results showed that the method based on the object-oriented method by using texture, spectrum and the vegetation indices achieved the classification accuracy of 91.3%, which was increased by 5.7% compared with that by only using the texture and spectrum.

Convolutional neural network with transfer learning for rice type classification

NASA Astrophysics Data System (ADS)

Patel, Vaibhav Amit; Joshi, Manjunath V.

2018-04-01

Presently, rice type is identified manually by humans, which is time consuming and error prone. Therefore, there is a need to do this by machine which makes it faster with greater accuracy. This paper proposes a deep learning based method for classification of rice types. We propose two methods to classify the rice types. In the first method, we train a deep convolutional neural network (CNN) using the given segmented rice images. In the second method, we train a combination of a pretrained VGG16 network and the proposed method, while using transfer learning in which the weights of a pretrained network are used to achieve better accuracy. Our approach can also be used for classification of rice grain as broken or fine. We train a 5-class model for classifying rice types using 4000 training images and another 2- class model for the classification of broken and normal rice using 1600 training images. We observe that despite having distinct rice images, our architecture, pretrained on ImageNet data boosts classification accuracy significantly.

Comparison and Evaluation of the Molecular Typing Methods for Toxigenic Vibrio cholerae in Southwest China.

PubMed

Liao, Feng; Mo, Zhishuo; Chen, Meiling; Pang, Bo; Fu, Xiaoqing; Xu, Wen; Jing, Huaiqi; Kan, Biao; Gu, Wenpeng

2018-01-01

Vibrio cholerae O1 strains taken from the repository of Yunnan province, southwest China, were abundant and special. We selected 70 typical toxigenic V. cholerae (69 O1 and one O139 serogroup strains) isolated from Yunnan province, performed the pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and MLST of virulence gene (V-MLST) methods, and evaluated the resolution abilities for typing methods. The ctxB subunit sequence analysis for all strains have shown that cholera between 1986 and 1995 was associated with mixed infections with El Tor and El Tor variants, while infections after 1996 were all caused by El Tor variant strains. Seventy V. cholerae obtained 50 PFGE patterns, with a high resolution. The strains could be divided into three groups with predominance of strains isolated during 1980s, 1990s, and 2000s, respectively, showing a good consistency with the epidemiological investigation. We also evaluated two MLST method for V. cholerae , one was used seven housekeeping genes ( adk , gyrB , metE , pntA , mdh , purM , and pyrC ), and all the isolates belonged to ST69; another was used nine housekeeping genes ( cat , chi , dnaE , gyrB , lap , pgm , recA , rstA , and gmd ). A total of seven sequence types (STs) were found by using this method for all the strains; among them, rstA gene had five alleles, recA and gmd have two alleles, and others had only one allele. The virulence gene sequence typing method ( ctxAB , tcpA , and toxR ) showed that 70 strains were divided into nine STs; among them, tcpA gene had six alleles, toxR had five alleles, while ctxAB was identical for all the strains. The latter two sequences based typing methods also had consistency with epidemiology of the strains. PFGE had a higher resolution ability compared with the sequence based typing method, and MLST used seven housekeeping genes showed the lower resolution power than nine housekeeping genes and virulence genes methods. These two sequence typing methods could distinguish some epidemiological special strains in local area.

Prototype Procedures to Describe Army Jobs

DTIC Science & Technology

2010-07-01

ratings for the same MOS. Consistent with a multi-trait multi- method framework, high profile similarities (or low mean differences ) among different ...rater types for the same MOS would indicate convergent validity. That is, different methods (i.e., rater types) yield converging results for the same... different methods of data collection depends upon the type of data collected. For example, it could be that data on work-oriented descriptors are most

Proteomics in the study of the molecular taxonomy and epidemiology of bacterial pathogens.

PubMed

Cash, Phillip

2009-06-01

The ability to discriminate bacterial isolates is important for a number of areas of research in Medical Microbiology, particularly in defining bacterial taxonomy and monitoring transmission in epidemiological investigations. Molecular techniques capable of typing bacteria at the level of the genome and proteome are now widely used for these investigations. This review considers two electrophoretic methods for typing bacteria on the basis of their proteomes, namely 1-D SDS-PAGE and 2-DE. The application of these two techniques for bacterial typing is described with reference to two publications that appeared in Electrophoresis [Costa, Electrophoresis 1990, 11, 382-391 and Cash et al., Electrophoresis 1997, 18, 1472-1482]. Even though these methods have been used for nearly 20 years to differentiate bacterial isolates they remain key technologies in proteome-based typing methods. The developments that have arisen from the two key papers are described in order to highlight the advantages and disadvantages in typing bacteria at the level of their proteomes. Some of the difficulties associated with electrophoretic typing methods can be overcome by using non-gel proteomic methods based on MS to provide improved sensitivity and specificity. The application of proteomic methods to investigate bacterial taxonomy, epidemiology and pathogenesis in general has significant potential in furthering our understanding of infectious diseases.

Chosen interval methods for solving linear interval systems with special type of matrix

NASA Astrophysics Data System (ADS)

Szyszka, Barbara

2013-10-01

The paper is devoted to chosen direct interval methods for solving linear interval systems with special type of matrix. This kind of matrix: band matrix with a parameter, from finite difference problem is obtained. Such linear systems occur while solving one dimensional wave equation (Partial Differential Equations of hyperbolic type) by using the central difference interval method of the second order. Interval methods are constructed so as the errors of method are enclosed in obtained results, therefore presented linear interval systems contain elements that determining the errors of difference method. The chosen direct algorithms have been applied for solving linear systems because they have no errors of method. All calculations were performed in floating-point interval arithmetic.

New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.

PubMed

Li, Hao; Li, Peng; Xie, Jing; Yi, Shengjie; Yang, Chaojie; Wang, Jian; Sun, Jichao; Liu, Nan; Wang, Xu; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Wang, Yong; Jia, Leili; Li, Kaiqin; Qiu, Shaofu; Song, Hongbin

2014-08-01

A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Characterization of non-typable strains of Staphylococcus aureus from cases of hospital infection.

PubMed Central

Vindel, A.; Martín-Bourgon, C.; Saez-Nieto, J. A.

1987-01-01

A high percentage of non-typable (NT) Staphylococcus aureus strains was isolated in Spanish hospitals during 1984 and 1985. Several alternative methods of typing were employed to study these isolates. These were: phage-typing at 1000 X RTD, phage-typing after heat-treatment (48 degrees C), thermal shock (56 degrees C), reverse-typing and induction of additional phages. Using these methods the number of NT isolates was reduced by 60%. Best results were obtained with heat-treatment. Additional phages and reverse-typing were also useful. A scheme for the study of outbreaks and sporadic cases caused by NT strains is proposed using the methods described. PMID:3609172

Classification of Children Intelligence with Fuzzy Logic Method

NASA Astrophysics Data System (ADS)

Syahminan; ika Hidayati, Permata

2018-04-01

Intelligence of children s An Important Thing To Know The Parents Early on. Typing Can be done With a Child’s intelligence Grouping Dominant Characteristics Of each Type of Intelligence. To Make it easier for Parents in Determining The type of Children’s intelligence And How to Overcome them, for It Created A Classification System Intelligence Grouping Children By Using Fuzzy logic method For determination Of a Child’s degree of intelligence type. From the analysis We concluded that The presence of Intelligence Classification systems Pendulum Children With Fuzzy Logic Method Of determining The type of The Child’s intelligence Can be Done in a way That is easier And The results More accurate Conclusions Than Manual tests.

An evaluation of authentication methods for smartphone based on users’ preferences

NASA Astrophysics Data System (ADS)

Sari, P. K.; Ratnasari, G. S.; Prasetio, A.

2016-04-01

This study discusses about smartphone screen lock preferences using some types of authentication methods. The purpose is to determine the user behaviours based on the perceived security and convenience, as well as the preferences for different types of authentication methods. Variables used are the considerations for locking the screens and the types of authentication methods. The population consists of the smartphone users with the total samples of 400 respondents within a nonprobability sampling method. Data analysis method used is the descriptive analysis. The results showed that the convenience factor is still the major consideration for locking the smartphone screens. Majority of the users chose the pattern unlock as the most convenient method to use. Meanwhile, fingerprint unlock becomes the most secure method in the users’ perceptions and as the method chosen to be used in the future.

[New assessment scale based on the type of person desired by an employer].

PubMed

Sasaki, Kenichi; Toyoda, Hideki

2011-10-01

In many cases, aptitude tests used in the hiring process fail to connect the measurement scale with the emotional type of the person desired by an employer. This experimental study introduced a new measuring method, in which the measurement scale could be adjusted according to the type of person an employer is seeking. Then the effectiveness of this method was verified by comparing the results of an aptitude test utilizing the method and the results of the typical hiring process carried out by the new method in hiring.

Solutions of interval type-2 fuzzy polynomials using a new ranking method

NASA Astrophysics Data System (ADS)

Rahman, Nurhakimah Ab.; Abdullah, Lazim; Ghani, Ahmad Termimi Ab.; Ahmad, Noor'Ani

2015-10-01

A few years ago, a ranking method have been introduced in the fuzzy polynomial equations. Concept of the ranking method is proposed to find actual roots of fuzzy polynomials (if exists). Fuzzy polynomials are transformed to system of crisp polynomials, performed by using ranking method based on three parameters namely, Value, Ambiguity and Fuzziness. However, it was found that solutions based on these three parameters are quite inefficient to produce answers. Therefore in this study a new ranking method have been developed with the aim to overcome the inherent weakness. The new ranking method which have four parameters are then applied in the interval type-2 fuzzy polynomials, covering the interval type-2 of fuzzy polynomial equation, dual fuzzy polynomial equations and system of fuzzy polynomials. The efficiency of the new ranking method then numerically considered in the triangular fuzzy numbers and the trapezoidal fuzzy numbers. Finally, the approximate solutions produced from the numerical examples indicate that the new ranking method successfully produced actual roots for the interval type-2 fuzzy polynomials.

Method for the determination of natural ester-type gum bases used as food additives via direct analysis of their constituent wax esters using high-temperature GC/MS.

PubMed

Tada, Atsuko; Ishizuki, Kyoko; Yamazaki, Takeshi; Sugimoto, Naoki; Akiyama, Hiroshi

2014-07-01

Natural ester-type gum bases, which are used worldwide as food additives, mainly consist of wax esters composed of long-chain fatty acids and long-chain fatty alcohols. There are many varieties of ester-type gum bases, and thus a useful method for their discrimination is needed in order to establish official specifications and manage their quality control. Herein is reported a rapid and simple method for the analysis of different ester-type gum bases used as food additives by high-temperature gas chromatography/mass spectrometry (GC/MS). With this method, the constituent wax esters in ester-type gum bases can be detected without hydrolysis and derivatization. The method was applied to the determination of 10 types of gum bases, including beeswax, carnauba wax, lanolin, and jojoba wax, and it was demonstrated that the gum bases derived from identical origins have specific and characteristic total ion chromatogram (TIC) patterns and ester compositions. Food additive gum bases were thus distinguished from one another based on their TIC patterns and then more clearly discriminated using simultaneous monitoring of the fragment ions corresponding to the fatty acid moieties of the individual molecular species of the wax esters. This direct high-temperature GC/MS method was shown to be very useful for the rapid and simple discrimination of varieties of ester-type gum bases used as food additives.

Method for the determination of natural ester-type gum bases used as food additives via direct analysis of their constituent wax esters using high-temperature GC/MS

PubMed Central

Tada, Atsuko; Ishizuki, Kyoko; Yamazaki, Takeshi; Sugimoto, Naoki; Akiyama, Hiroshi

2014-01-01

Natural ester-type gum bases, which are used worldwide as food additives, mainly consist of wax esters composed of long-chain fatty acids and long-chain fatty alcohols. There are many varieties of ester-type gum bases, and thus a useful method for their discrimination is needed in order to establish official specifications and manage their quality control. Herein is reported a rapid and simple method for the analysis of different ester-type gum bases used as food additives by high-temperature gas chromatography/mass spectrometry (GC/MS). With this method, the constituent wax esters in ester-type gum bases can be detected without hydrolysis and derivatization. The method was applied to the determination of 10 types of gum bases, including beeswax, carnauba wax, lanolin, and jojoba wax, and it was demonstrated that the gum bases derived from identical origins have specific and characteristic total ion chromatogram (TIC) patterns and ester compositions. Food additive gum bases were thus distinguished from one another based on their TIC patterns and then more clearly discriminated using simultaneous monitoring of the fragment ions corresponding to the fatty acid moieties of the individual molecular species of the wax esters. This direct high-temperature GC/MS method was shown to be very useful for the rapid and simple discrimination of varieties of ester-type gum bases used as food additives. PMID:25473499

Analysis of hard coal quality for narrow size fraction under 20 mm

NASA Astrophysics Data System (ADS)

Niedoba, Tomasz; Pięta, Paulina

2018-01-01

The paper presents the results of an analysis of hard coal quality diversion in narrow size fraction by using taxonomic methods. Raw material samples were collected in selected mines of Upper Silesian Industrial Region and they were classified according to the Polish classification as types 31, 34.2 and 35. Then, each size fraction was characterized in terms of the following properties: density, ash content, calorific content, volatile content, total sulfur content and analytical moisture. As a result of the analysis it can be stated that the best quality in the entire range of the tested size fractions was the 34.2 coking coal type. At the same time, in terms of price parameters, high quality of raw material characterised the following size fractions: 0-6.3 mm of 31 energetic coal type and 0-3.15 mm of 35 coking coal type. The methods of grouping (Ward's method) and agglomeration (k-means method) have shown that the size fraction below 10 mm was characterized by higher quality in all the analyzed hard coal types. However, the selected taxonomic methods do not make it possible to identify individual size fraction or hard coal types based on chosen parameters.

Clustering self-organizing maps (SOM) method for human papillomavirus (HPV) DNA as the main cause of cervical cancer disease

NASA Astrophysics Data System (ADS)

Bustamam, A.; Aldila, D.; Fatimah, Arimbi, M. D.

2017-07-01

One of the most widely used clustering method, since it has advantage on its robustness, is Self-Organizing Maps (SOM) method. This paper discusses the application of SOM method on Human Papillomavirus (HPV) DNA which is the main cause of cervical cancer disease, the most dangerous cancer in developing countries. We use 18 types of HPV DNA-based on the newest complete genome. By using open-source-based program R, clustering process can separate 18 types of HPV into two different clusters. There are two types of HPV in the first cluster while 16 others in the second cluster. The analyzing result of 18 types HPV based on the malignancy of the virus (the difficultness to cure). Two of HPV types the first cluster can be classified as tame HPV, while 16 others in the second cluster are classified as vicious HPV.

29 CFR 1910.1026 - Chromium (VI).

Code of Federal Regulations, 2012 CFR

2012-07-01

... resembling the processes, types of material, control methods, work practices, and environmental conditions in... resembling the processes, types of material, control methods, work practices, and environmental conditions in..., work practices, or control methods that may result in new or additional exposures to chromium (VI), or...

29 CFR 1910.1026 - Chromium (VI).

Code of Federal Regulations, 2014 CFR

2014-07-01

... resembling the processes, types of material, control methods, work practices, and environmental conditions in... resembling the processes, types of material, control methods, work practices, and environmental conditions in..., work practices, or control methods that may result in new or additional exposures to chromium (VI), or...

A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach.

PubMed

Wang, Hsin-Yao; Lee, Tzong-Yi; Tseng, Yi-Ju; Liu, Tsui-Ping; Huang, Kai-Yao; Chang, Yung-Ta; Chen, Chun-Hsien; Lu, Jang-Jih

2018-01-01

Methicillin-resistant Staphylococcus aureus (MRSA), one of the most important clinical pathogens, conducts an increasing number of morbidity and mortality in the world. Rapid and accurate strain typing of bacteria would facilitate epidemiological investigation and infection control in near real time. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid and cost-effective tool for presumptive strain typing. To develop robust method for strain typing based on MALDI-TOF spectrum, machine learning (ML) is a promising algorithm for the construction of predictive model. In this study, a strategy of building templates of specific types was used to facilitate generating predictive models of methicillin-resistant Staphylococcus aureus (MRSA) strain typing through various ML methods. The strain types of the isolates were determined through multilocus sequence typing (MLST). The area under the receiver operating characteristic curve (AUC) and the predictive accuracy of the models were compared. ST5, ST59, and ST239 were the major MLST types, and ST45 was the minor type. For binary classification, the AUC values of various ML methods ranged from 0.76 to 0.99 for ST5, ST59, and ST239 types. In multiclass classification, the predictive accuracy of all generated models was more than 0.83. This study has demonstrated that ML methods can serve as a cost-effective and promising tool that provides preliminary strain typing information about major MRSA lineages on the basis of MALDI-TOF spectra.

Dai-Kou type conjugate gradient methods with a line search only using gradient.

PubMed

Huang, Yuanyuan; Liu, Changhe

2017-01-01

In this paper, the Dai-Kou type conjugate gradient methods are developed to solve the optimality condition of an unconstrained optimization, they only utilize gradient information and have broader application scope. Under suitable conditions, the developed methods are globally convergent. Numerical tests and comparisons with the PRP+ conjugate gradient method only using gradient show that the methods are efficient.

Quantifying the proportion of general practice and low-acuity patients in the emergency department.

PubMed

Nagree, Yusuf; Camarda, Vanessa J; Fatovich, Daniel M; Cameron, Peter A; Dey, Ian; Gosbell, Andrew D; McCarthy, Sally M; Mountain, David

2013-06-17

To accurately estimate the proportion of patients presenting to the emergency department (ED) who may have been suitable to be seen in general practice. Using data sourced from the Emergency Department Information Systems for the calendar 2013s 2009 to 2011 at three major tertiary hospitals in Perth, Western Australia, we compared four methods for calculating general practice-type patients. These were the validated Sprivulis method, the widely used Australasian College for Emergency Medicine method, a discharge diagnosis method developed by the Tasmanian Department of Human and Health Services, and the Australian Institute of Health and Welfare (AIHW) method. General practice-type patient attendances to EDs, estimated using the four methods. All methods except the AIHW method showed that 10%-12% of patients attending tertiary EDs in Perth may have been suitable for general practice. These attendances comprised 3%-5% of total ED length of stay. The AIHW method produced different results (general practice-type patients accounted for about 25% of attendances, comprising 10%-11% of total ED length of stay). General practice-type patient attendances were not evenly distributed across the week, with proportionally more patients presenting during weekday daytime (08:00-17:00) and proportionally fewer overnight (00:00-08:00). This suggests that it is not a lack of general practitioners that drives patients to the ED, as weekday working hours are the time of greatest GP availability. The estimated proportion of general practice-type patients attending the EDs of Perth's major hospitals is 10%-12%, and this accounts for < 5% of the total ED length of stay. The AIHW methodology overestimates the actual proportion of general practice-type patient attendances.

Measuring Ambiguity in HLA Typing Methods

PubMed Central

Madbouly, Abeer; Freeman, John; Maiers, Martin

2012-01-01

In hematopoietic stem cell transplantation, donor selection is based primarily on matching donor and patient HLA genes. These genes are highly polymorphic and their typing can result in exact allele assignment at each gene (the resolution at which patients and donors are matched), but it can also result in a set of ambiguous assignments, depending on the typing methodology used. To facilitate rapid identification of matched donors, registries employ statistical algorithms to infer HLA alleles from ambiguous genotypes. Linkage disequilibrium information encapsulated in haplotype frequencies is used to facilitate prediction of the most likely haplotype assignment. An HLA typing with less ambiguity produces fewer high-probability haplotypes and a more reliable prediction. We estimated ambiguity for several HLA typing methods across four continental populations using an information theory-based measure, Shannon's entropy. We used allele and haplotype frequencies to calculate entropy for different sets of 1,000 subjects with simulated HLA typing. Using allele frequencies we calculated an average entropy in Caucasians of 1.65 for serology, 1.06 for allele family level, 0.49 for a 2002-era SSO kit, and 0.076 for single-pass SBT. When using haplotype frequencies in entropy calculations, we found average entropies of 0.72 for serology, 0.73 for allele family level, 0.05 for SSO, and 0.002 for single-pass SBT. Application of haplotype frequencies further reduces HLA typing ambiguity. We also estimated expected confirmatory typing mismatch rates for simulated subjects. In a hypothetical registry with all donors typed using the same method, the entropy values based on haplotype frequencies correspond to confirmatory typing mismatch rates of 1.31% for SSO versus only 0.08% for SBT. Intermediate-resolution single-pass SBT contains the least ambiguity of the methods we evaluated and therefore the most certainty in allele prediction. The presented measure objectively evaluates HLA typing methods and can help define acceptable HLA typing for donor recruitment. PMID:22952712

Multilocus sequence typing of total-genome-sequenced bacteria.

PubMed

Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

2012-04-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-07-21

A method is disclosed for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe. 11 figs.

n-Type diamond and method for producing same

DOEpatents

Anderson, Richard J.

2002-01-01

A new n-type semiconducting diamond is disclosed, which is doped with n-type dopant atoms. Such diamond is advantageously formed by chemical vapor deposition from a source gas mixture comprising a carbon source compound for the diamond, and a volatile hot wire filament for the n-type impurity species, so that the n-type impurity atoms are doped in the diamond during its formation. A corresponding chemical vapor deposition method of forming the n-type semiconducting diamond is disclosed. The n-type semiconducting diamond of the invention may be usefully employed in the formation of diamond-based transistor devices comprising pn diamond junctions, and in other microelectronic device applications.

RAPD- and ERIC-Based Typing of Clinical and Environmental Pseudomonas aeruginosa Isolates.

PubMed

Auda, Ibtesam Ghadban; Al-Kadmy, Israa M S; Kareem, Sawsan Mohammed; Lafta, Aliaa Khyuon; A'Affus, Mustafa Hussein Obeid; Khit, Ibrahim Abd Aloahd; Al Kheraif, Abdulaziz Abdullah; Divakar, Darshan Devang; Ramakrishnaiah, Ravikumar

2017-03-01

Pseudomonas aeruginosa is a major cause of nosocomial infection in children and adults, resulting in significant morbidity and mortality due to its ability to acquire drug resistance. The ability of P. aeruginosa in the environment to cause infection in individuals has been reported previously; henceforth, surveillance of the emergence and transmission of P. aeruginosa strains among patients is important for infection control in a clinical setup. Various gene-typing methods have been used for epidemiological typing of P. aeruginosa isolates for the purpose of surveillance. In this work, the suitability and comparability of two typing methods, enterobacterial repetitive intergenic consensus (ERIC)-PCR and random amplification of polymorphic DNA (RAPD)-PCR fingerprinting, were studied to characterize P. aeruginosa strains isolated from clinical and environmental sources. Forty-four clinical and environmental bacterial isolates of P. aeruginosa were collected between October 2015 and January 2016. DNA extraction, ERIC-PCR and RAPD-PCR, agarose gel electrophoresis, and phylogenetic analyses were carried using the unweighted pair-group method with mean. RAPD typing revealed less clonality among clinical isolates, whereas the ERIC method showed greater similarity in comparison with RAPD. Environmental isolates, however, showed greater similarity using RAPD compared with ERIC typing. With only a few exceptions, most clinical isolates were distinct from environmental isolates, irrespective of the typing method. In conclusion, both the RAPD and ERIC typing methods proved to be good tools in understanding clonal diversity. The results also suggest that there is no relationship between clinical and environmental isolates. The absence of clonality among the clinical isolates may indicate that most P. aeruginosa infection cases could be endemic and not epidemic and that endemic infections may be due to nonclonal strains of P. aeruginosa.

Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.

PubMed

Said, Halima M; Krishnamani, Keshav; Omar, Shaheed V; Dreyer, Andries W; Sansom, Bianca; Fallows, Dorothy; Ismail, Nazir A

2016-10-01

The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A (2+1)-dimensional Korteweg-de Vries type equation in water waves: Lie symmetry analysis; multiple exp-function method; conservation laws

NASA Astrophysics Data System (ADS)

Adem, Abdullahi Rashid

2016-05-01

We consider a (2+1)-dimensional Korteweg-de Vries type equation which models the shallow-water waves, surface and internal waves. In the analysis, we use the Lie symmetry method and the multiple exp-function method. Furthermore, conservation laws are computed using the multiplier method.

Assessing and evaluating multidisciplinary translational teams: a mixed methods approach.

PubMed

Wooten, Kevin C; Rose, Robert M; Ostir, Glenn V; Calhoun, William J; Ameredes, Bill T; Brasier, Allan R

2014-03-01

A case report illustrates how multidisciplinary translational teams can be assessed using outcome, process, and developmental types of evaluation using a mixed-methods approach. Types of evaluation appropriate for teams are considered in relation to relevant research questions and assessment methods. Logic models are applied to scientific projects and team development to inform choices between methods within a mixed-methods design. Use of an expert panel is reviewed, culminating in consensus ratings of 11 multidisciplinary teams and a final evaluation within a team-type taxonomy. Based on team maturation and scientific progress, teams were designated as (a) early in development, (b) traditional, (c) process focused, or (d) exemplary. Lessons learned from data reduction, use of mixed methods, and use of expert panels are explored.

A new serotyping method for Klebsiella species: development of the technique.

PubMed Central

Riser, E; Noone, P; Poulton, T A

1976-01-01

A new serotyping method for Klebsiella species using indirect immunofluorescence is described. Nonspecific fluorescence has been minimized by carrying out the capsular antigen-antibody reaction at pH 9.0. Commercial antisera have been tested with the 72 antigenic types of Klebsiella, and appropriate dilutions of each pool and specific antisera have been proposed for use in routine typing. Dilutions were chosen to allow strong fluorescence with each type and its specific antiserum and minimal fluorescence with cross reacting antisera. Where the pool antisera gave a weak reaction for one or more of the component types, it is recommended that the specific antisera for these types be added to the pool dilution. The few remaining cross reactions, with the pool and specific antisera in test dilution, are listed in a table. The unique cross reacting patterns of particular types have been found to be useful in identification. Typing Klebsiella by the fluorescent antibody technique is easy to perform and interpret; the results are reproducible, and it is less expensive than the existing capsular swelling method as it is more sensitive and requires less concentrated antisera. This new method of typing should facilitate detailed epidemiological studies of the mode of transmission of Klebsiella species in hospitals and thus allow more effective infection control measures to be instituted. Images PMID:777042

Calcite phase determination of CaCO3 nanoparticles synthesized by one step drying method

NASA Astrophysics Data System (ADS)

Sulimai, N. H.; Rani, Rozina Abdul; Khusaimi, Z.; Abdullah, S.; Salifairus, M. J.; Alrokayan, Salman; Khan, Haseeb; Rusop, M.

2018-05-01

Calcium Carbonate (CaCO3) is a type of carbonic salt. It exist naturally as white odourless solid and may also be synthesized by chemical reactions. This work studies one-step precipitation of CaCO3 that was prepared by novel method of one-step precipitation method. The method was then proceeded by different types of drying. The first type is by normal drying in oven whereas the second type is with the presence of hydrothermal influence. From the results, precipitated CaCO3 dried by normal drying method produces CaCO3 with two polymorphs present; calcite and vaterite. Normal drying at 500°C has no vaterite phase left. Drying by hydrothermal precipitated CaCO3 has Nitrogen (N) left on the surfaces of the precipitated CaCO3. This work successfully identified calcite phase in the precipitated CaCO3.

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

PubMed

Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

2005-11-01

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Homotopy perturbation method with Laplace Transform (LT-HPM) for solving Lane-Emden type differential equations (LETDEs).

PubMed

Tripathi, Rajnee; Mishra, Hradyesh Kumar

2016-01-01

In this communication, we describe the Homotopy Perturbation Method with Laplace Transform (LT-HPM), which is used to solve the Lane-Emden type differential equations. It's very difficult to solve numerically the Lane-Emden types of the differential equation. Here we implemented this method for two linear homogeneous, two linear nonhomogeneous, and four nonlinear homogeneous Lane-Emden type differential equations and use their appropriate comparisons with exact solutions. In the current study, some examples are better than other existing methods with their nearer results in the form of power series. The Laplace transform used to accelerate the convergence of power series and the results are shown in the tables and graphs which have good agreement with the other existing method in the literature. The results show that LT-HPM is very effective and easy to implement.

Study on a magnetic spiral-type wireless capsule endoscope controlled by rotational external permanent magnet

NASA Astrophysics Data System (ADS)

Ye, Bo; Zhang, Wei; Sun, Zhen-jun; Guo, Lin; Deng, Chao; Chen, Ya-qi; Zhang, Hong-hai; Liu, Sheng

2015-12-01

In this paper, the authors propose rotating an external permanent magnet (EPM) to manipulate the synchronous rotation of a magnetic spiral-type wireless capsule endoscope (WCE), and the synchronous rotation of the WCE is converted to its translational motion in intestinal tract. In order to preliminarily verify the feasibility of this method, a handheld actuator (HA) controlled by micro controller unit, a magnetic spiral-type WCE and a bracket were fabricated, theoretical analysis and simulations about the control distance of this method were performed, and in ex-vivo tests were examined in porcine small intestine to verify the control distance and control performances of this method. It was demonstrated that this method showed good performances in controlling the translational motion of the magnetic spiral-type WCE, and this method has great potential to be used in clinical application.

Maintenance Budgeting.

ERIC Educational Resources Information Center

Smith, J. McCree

Three methods for the preparation of maintenance budgets are discussed--(1) a traditional method, inconclusive and obsolete, based on gross square footage, (2) the formula approach method based on building classification (wood-frame, masonry-wood, masonry-concrete) with maintenance cost factors for each type plus custodial service rates by type of…

Evaluation of LABType® SSO HLA Typing using the Luminex Platform: Cord Blood Registry Typing for the Korean Population.

PubMed

Roh, Eun-Youn; Song, Eun-Young; Chang, Jee-Young; Yoon, Jong-Hyun; Shin, Sue

2016-08-01

The performance of a new intermediate-resolution method using a PCR-Luminex platform and LABType® SSO A, B DRB1 kits as an HLA typing method for the cord blood (CB) registry of the Korean population was investigated. A total of 1,413 cord blood units (CBUs) were enrolled - 1,382 from Koreans and 31 from non-Koreans or mixed-ancestry individuals. HLA-A, -B, and -DRB1 typing was performed using the LABType® SSO typing kits. HLA typing with the DNA method and 2-digit results are mandatory for the public CB bank in Korea according to the "CB Act." The proportions of ambiguous results in the 2-digit assignment were 14.6% (206/1,413) and 14.8% (205/ 1,382) among the total subjects and the Korean donors, respectively. In the 2-digit resolution, 3 different HLA-A types (69 CBUs), 31 HLA-B types (124 CBUs), and 3 HLA-DRB1 types (13 CBUs) showed ambiguous results. The 'most probable type' to the ambiguous results based on the reported Korean HLA allele frequencies were able to be assigned. The most probable results were 100% consistent with the confirmed types as determined by the HD kits (DRB1) and additional PCR-SBT or PCR-SSP tests (A and B). Luminex technology is more automated and less labor intensive than the conventional SSO typing method, and the results are less affected by differences between inspectors. Although it is not satisfactory as a sole confirmation test and cannot be used as a replacement for the PCR-SBT test, the combination of Luminex technology with LABType® SSO kits and population frequency data provides a proper typing platform that can be used as a qualifying test for CB registries.

[A wavelet-transform-based method for the automatic detection of late-type stars].

PubMed

Liu, Zhong-tian; Zhao, Rrui-zhen; Zhao, Yong-heng; Wu, Fu-chao

2005-07-01

The LAMOST project, the world largest sky survey project, urgently needs an automatic late-type stars detection system. However, to our knowledge, no effective methods for automatic late-type stars detection have been reported in the literature up to now. The present study work is intended to explore possible ways to deal with this issue. Here, by "late-type stars" we mean those stars with strong molecule absorption bands, including oxygen-rich M, L and T type stars and carbon-rich C stars. Based on experimental results, the authors find that after a wavelet transform with 5 scales on the late-type stars spectra, their frequency spectrum of the transformed coefficient on the 5th scale consistently manifests a unimodal distribution, and the energy of frequency spectrum is largely concentrated on a small neighborhood centered around the unique peak. However, for the spectra of other celestial bodies, the corresponding frequency spectrum is of multimodal and the energy of frequency spectrum is dispersible. Based on such a finding, the authors presented a wavelet-transform-based automatic late-type stars detection method. The proposed method is shown by extensive experiments to be practical and of good robustness.

Beluga whale, Delphinapterus leucas, vocalizations from the Churchill River, Manitoba, Canada.

PubMed

Chmelnitsky, Elly G; Ferguson, Steven H

2012-06-01

Classification of animal vocalizations is often done by a human observer using aural and visual analysis but more efficient, automated methods have also been utilized to reduce bias and increase reproducibility. Beluga whale, Delphinapterus leucas, calls were described from recordings collected in the summers of 2006-2008, in the Churchill River, Manitoba. Calls (n=706) were classified based on aural and visual analysis, and call characteristics were measured; calls were separated into 453 whistles (64.2%; 22 types), 183 pulsed∕noisy calls (25.9%; 15 types), and 70 combined calls (9.9%; seven types). Measured parameters varied within each call type but less variation existed in pulsed and noisy call types and some combined call types than in whistles. A more efficient and repeatable hierarchical clustering method was applied to 200 randomly chosen whistles using six call characteristics as variables; twelve groups were identified. Call characteristics varied less in cluster analysis groups than in whistle types described by visual and aural analysis and results were similar to the whistle contours described. This study provided the first description of beluga calls in Hudson Bay and using two methods provides more robust interpretations and an assessment of appropriate methods for future studies.

Analysis of the Pre-stack Split-Step Migration Operator Using Ritz Values

NASA Astrophysics Data System (ADS)

Kaplan, S. T.; Sacchi, M. D.

2009-05-01

The Born approximation for the acoustic wave-field is often used as a basis for developing algorithms in seismic imaging (migration). The approximation is linear, and, as such, can be written as a matrix-vector multiplication (Am=d). In the seismic imaging problem, d is seismic data (the recorded wave-field), and we aim to find the seismic reflectivity m (a representation of earth structure and properties) so that Am=d is satisfied. This is the often studied inverse problem of seismic migration, where given A and d, we solve for m. This can be done in a least-squares sense, so that the equation of interest is, AHAm = AHd. Hence, the solution m is largely dependent on the properties of AHA. The imaging Jacobian J provides an approximation to AHA, so that J-1AHA is, in a broad sense, better behaved then AHA. We attempt to quantify this last statement by providing an analysis of AHA and J-1AHA using their Ritz values, and for the particular case where A is built using a pre-stack split-step migration algorithm. Typically, one might try to analyze the behaviour of these matrices using their eigenvalue spectra. The difficulty in the analysis of AHA and J-1AHA lie in their size. For example, a subset of the relatively small Marmousi data set makes AHA a complex valued matrix with, roughly, dimensions of 45 million by 45 million (requiring, in single-precision, about 16 Peta-bytes of computer memory). In short, the size of the matrix makes its eigenvalues difficult to compute. Instead, we compute the leading principal minors of similar tridiagonal matrices, Bk=Vk-1AHAVk and Ck = Uk-1 J-1 AHAUk. These can be constructed using, for example, the Lanczos decomposition. Up to some value of k it is feasible to compute the eigenvalues of Bk and Ck which, in turn, are the Ritz values of, respectively, AHA and J-1 AHA, and may allow us to make quantitative statements about their behaviours.

Four dimensional variational inversion of atmospheric chemical sources in WRFDA

NASA Astrophysics Data System (ADS)

Guerrette, J. J.

Atmospheric aerosols are known to affect health, weather, and climate, but their impacts on regional scales are uncertain due to heterogeneous source, transport, and transformation mechanisms. The Weather Research and Forecasting model with chemistry (WRF-Chem) can account for aerosol-meteorology feedbacks as it simultaneously integrates equations of dynamical and chemical processes. Here we develop and apply incremental four dimensional variational (4D-Var) data assimilation (DA) capabilities in WRF-Chem to constrain chemical emissions (WRFDA-Chem). We develop adjoint (ADM) and tangent linear (TLM) model descriptions of boundary layer mixing, emission, aging, dry deposition, and advection of black carbon (BC) aerosol. ADM and TLM model performance is verified against finite difference derivative approximations. A second order checkpointing scheme is used to reduce memory costs and enable simulations longer than six hours. We apply WRFDA-Chem to constraining anthropogenic and biomass burning sources of BC throughout California during the 2008 Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) field campaign. Manual corrections to the prior emissions and subsequent inverse modeling reduce the spread in total emitted BC mass between two biomass burning inventories from a factor of x10 to only x2 across three days of measurements. We quantify posterior emission variance using an eigendecomposition of the cost function Hessian matrix. We also address the limited scalability of 4D-Var, which traditionally uses a sequential optimization algorithm (e.g., conjugate gradient) to approximate these Hessian eigenmodes. The Randomized Incremental Optimal Technique (RIOT) uses an ensemble of TLM and ADM instances to perform a Hessian singular value decomposition. While RIOT requires more ensemble members than Lanczos requires iterations to converge to a comparable posterior control vector, the wall-time of RIOT is x10 shorter since the ensemble is executed in parallel. This work demonstrates that RIOT improves the scalability of 4D-Var for high-dimensional nonlinear problems. Overall, WRFDA-Chem and RIOT provide a framework for air quality forecasting, campaign planning, and emissions constraint that can be used to refine our understanding of the interplay between atmospheric chemistry, meteorology, climate, and human health.

Psychological traits underlying different killing methods among Malaysian male murderers.

PubMed

Kamaluddin, Mohammad Rahim; Shariff, Nadiah Syariani; Nurfarliza, Siti; Othman, Azizah; Ismail, Khaidzir H; Mat Saat, Geshina Ayu

2014-04-01

Murder is the most notorious crime that violates religious, social and cultural norms. Examining the types and number of different killing methods that used are pivotal in a murder case. However, the psychological traits underlying specific and multiple killing methods are still understudied. The present study attempts to fill this gap in knowledge by identifying the underlying psychological traits of different killing methods among Malaysian murderers. The study adapted an observational cross-sectional methodology using a guided self-administered questionnaire for data collection. The sampling frame consisted of 71 Malaysian male murderers from 11 Malaysian prisons who were selected using purposive sampling method. The participants were also asked to provide the types and number of different killing methods used to kill their respective victims. An independent sample t-test was performed to establish the mean score difference of psychological traits between the murderers who used single and multiple types of killing methods. Kruskal-Wallis tests were carried out to ascertain the psychological trait differences between specific types of killing methods. The results suggest that specific psychological traits underlie the type and number of different killing methods used during murder. The majority (88.7%) of murderers used a single method of killing. Multiple methods of killing was evident in 'premeditated' murder compared to 'passion' murder, and revenge was a common motive. Examples of multiple methods are combinations of stabbing and strangulation or slashing and physical force. An exception was premeditated murder committed with shooting, when it was usually a single method, attributed to the high lethality of firearms. Shooting was also notable when the motive was financial gain or related to drug dealing. Murderers who used multiple killing methods were more aggressive and sadistic than those who used a single killing method. Those who used multiple methods or slashing also displayed a higher level of minimisation traits. Despite its limitations, this study has provided some light on the underlying psychological traits of different killing methods which is useful in the field of criminology.

Evaluation of an Automated Touch Typing System

ERIC Educational Resources Information Center

Diercks, Caroll J.

1977-01-01

Examines an alternative method for teaching typewriting skills--the Automated Instruction Touch Typing System, an individualized self-paced instructional method using the principles of response conditioning. (Author/RK)

Comparison effectiveness of cooperative learning type STAD with cooperative learning type TPS in terms of mathematical method of Junior High School students

NASA Astrophysics Data System (ADS)

Wahyuni, A.

2018-05-01

This research is aimed to find out whether the model of cooperative learning type Student Team Achievement Division (STAD) is more effective than cooperative learning type Think-Pair-Share in SMP Negeri 7 Yogyakarta. This research was a quasi-experimental research, using two experimental groups. The population of research was all students of 7thclass in SMP Negeri 7 Yogyakarta that consists of 5 Classes. From the population were taken 2 classes randomly which used as sample. The instrument to collect data was a description test. Measurement of instrument validity use content validity and construct validity, while measuring instrument reliability use Cronbach Alpha formula. To investigate the effectiveness of cooperative learning type STAD and cooperative learning type TPS on the aspect of student’s mathematical method, the datas were analyzed by one sample test. Comparing the effectiveness of cooperative learning type STAD and TPS in terms of mathematical communication skills by using t-test. Normality test was not conducted because the sample of research more than 30 students, while homogeneity tested by using Kolmogorov Smirnov test. The analysis was performed at 5% confidence level.The results show as follows : 1) The model of cooperative learning type STAD and TPS are effective in terms of mathematical method of junior high school students. 2). STAD type cooperative learning model is more effective than TPS type cooperative learning model in terms of mathematical methods of junior high school students.

Improvement of the Owner Distinction Method for Healing-Type Pet Robots

NASA Astrophysics Data System (ADS)

Nambo, Hidetaka; Kimura, Haruhiko; Hara, Mirai; Abe, Koji; Tajima, Takuya

In order to decrease human stress, Animal Assisted Therapy which applies pets to heal humans is attracted. However, since animals are insanitary and unsafe, it is difficult to practically apply animal pets in hospitals. For the reason, on behalf of animal pets, pet robots have been attracted. Since pet robots would have no problems in sanitation and safety, they are able to be applied as a substitute for animal pets in the therapy. In our previous study where pet robots distinguish their owners like an animal pet, we used a puppet type pet robot which has pressure type touch sensors. However, the accuracy of our method was not sufficient to practical use. In this paper, we propose a method to improve the accuracy of the distinction. The proposed method can be applied for capacitive touch sensors such as installed in AIBO in addition to pressure type touch sensors. Besides, this paper shows performance of the proposed method from experimental results and confirms the proposed method has improved performance of the distinction in the conventional method.

Evaluation of AISI Type 304 stainless steel as a suitable surface material for evaluating the efficacy of peracetic acid-based disinfectants against Clostridium difficile spores.

PubMed

Black, Elaine; Owens, Krista; Staub, Richard; Li, Junzhong; Mills, Kristen; Valenstein, Justin; Hilgren, John

2017-01-01

Disinfectants play an important role in controlling microbial contamination on hard surfaces in hospitals. The effectiveness of disinfectants in real life can be predicted by laboratory tests that measure killing of microbes on carriers. The modified Quantitative Disk Carrier Test (QCT-2) is a standard laboratory method that employs American Iron and Steel Institute (AISI) Type 430 stainless steel carriers to measure hospital disinfectant efficacy against Clostridium difficile spores. The formation of a rust-colored precipitate was observed on Type 430 carriers when testing a peracetic acid (PAA)-based disinfectant with the QCT-2 method. It was hypothesized that the precipitate was indicative of corrosion of the Type 430 carrier, and that corrosion could impact efficacy results. The objective of this study was to compare the suitability of AISI Type 430 to Type 304 stainless steel carriers for evaluating PAA-based disinfectants using the QCT-2 method. Type 304 is more corrosion-resistant than Type 430, is ubiquitous in healthcare environments, and is used in other standard methods. Suitability of the carriers was evaluated by comparing their impacts on efficacy results and PAA degradation rates. In efficacy tests with 1376 ppm PAA, reductions of C. difficile spores after 5, 7 and 10 minutes on Type 430 carriers were at least about 1.5 log10 lower than reductions on Type 304 carriers. In conditions simulating a QCT-2 test, PAA concentration with Type 430 carriers was reduced by approximately 80% in 10 minutes, whereas PAA concentration in the presence of Type 304 carriers remained stable. Elemental analyses of residues on each carrier type after efficacy testing were indicative of corrosion on the Type 430 carrier. Use of Type 430 stainless steel carriers for measuring the efficacy of PAA-based disinfectants should be avoided as it can lead to an underestimation of real life sporicidal efficacy. Type 304 stainless steel carriers are recommended as a suitable alternative.

Evaluation of AISI Type 304 stainless steel as a suitable surface material for evaluating the efficacy of peracetic acid-based disinfectants against Clostridium difficile spores

PubMed Central

Owens, Krista; Staub, Richard; Li, Junzhong; Mills, Kristen; Valenstein, Justin; Hilgren, John

2017-01-01

Disinfectants play an important role in controlling microbial contamination on hard surfaces in hospitals. The effectiveness of disinfectants in real life can be predicted by laboratory tests that measure killing of microbes on carriers. The modified Quantitative Disk Carrier Test (QCT-2) is a standard laboratory method that employs American Iron and Steel Institute (AISI) Type 430 stainless steel carriers to measure hospital disinfectant efficacy against Clostridium difficile spores. The formation of a rust-colored precipitate was observed on Type 430 carriers when testing a peracetic acid (PAA)-based disinfectant with the QCT-2 method. It was hypothesized that the precipitate was indicative of corrosion of the Type 430 carrier, and that corrosion could impact efficacy results. The objective of this study was to compare the suitability of AISI Type 430 to Type 304 stainless steel carriers for evaluating PAA-based disinfectants using the QCT-2 method. Type 304 is more corrosion-resistant than Type 430, is ubiquitous in healthcare environments, and is used in other standard methods. Suitability of the carriers was evaluated by comparing their impacts on efficacy results and PAA degradation rates. In efficacy tests with 1376 ppm PAA, reductions of C. difficile spores after 5, 7 and 10 minutes on Type 430 carriers were at least about 1.5 log10 lower than reductions on Type 304 carriers. In conditions simulating a QCT-2 test, PAA concentration with Type 430 carriers was reduced by approximately 80% in 10 minutes, whereas PAA concentration in the presence of Type 304 carriers remained stable. Elemental analyses of residues on each carrier type after efficacy testing were indicative of corrosion on the Type 430 carrier. Use of Type 430 stainless steel carriers for measuring the efficacy of PAA-based disinfectants should be avoided as it can lead to an underestimation of real life sporicidal efficacy. Type 304 stainless steel carriers are recommended as a suitable alternative. PMID:29065168

Flow Cytometric Human Leukocyte Antigen-B27 Typing with Stored Samples for Batch Testing

PubMed Central

Seo, Bo Young

2013-01-01

Background Flow cytometry (FC) HLA-B27 typing is still used extensively for the diagnosis of spondyloarthropathies. If patient blood samples are stored for a prolonged duration, this testing can be performed in a batch manner, and in-house cellular controls could easily be procured. In this study, we investigated various methods of storing patient blood samples. Methods We compared four storage methods: three methods of analyzing lymphocytes (whole blood stored at room temperature, frozen mononuclear cells, and frozen white blood cells [WBCs] after lysing red blood cells [RBCs]), and one method using frozen platelets (FPLT). We used three ratios associated with mean fluorescence intensities (MFI) for HLAB27 assignment: the B27 MFI ratio (sample/control) for HLA-B27 fluorescein-5-isothiocyanate (FITC); the B7 MFI ratio for HLA-B7 phycoerythrin (PE); and the ratio of these two ratios, B7/B27 ratio. Results Comparing the B27 MFI ratios of each storage method for the HLA-B27+ samples and the B7/B27 ratios for the HLA-B7+ samples revealed that FPLT was the best of the four methods. FPLT had a sensitivity of 100% and a specificity of 99.3% for HLA-B27 assignment in DNA-typed samples (N=164) when the two criteria, namely, B27 MFI ratio >4.0 and B7/B27 ratio <1.5, were used. Conclusions The FPLT method was found to offer a simple, economical, and accurate method of FC HLA-B27 typing by using stored patient samples. If stored samples are used, this method has the potential to replace the standard FC typing method when used in combination with a complementary DNA-based method. PMID:23667843

Discriminative power of Campylobacter phenotypic and genotypic typing methods.

PubMed

Duarte, Alexandra; Seliwiorstow, Tomasz; Miller, William G; De Zutter, Lieven; Uyttendaele, Mieke; Dierick, Katelijne; Botteldoorn, Nadine

2016-06-01

The aim of this study was to compare different typing methods, individually and combined, for use in the monitoring of Campylobacter in food. Campylobacter jejuni (n=94) and Campylobacter coli (n=52) isolated from different broiler meat carcasses were characterized using multilocus sequence typing (MLST), flagellin gene A restriction fragment length polymorphism typing (flaA-RFLP), antimicrobial resistance profiling (AMRp), the presence/absence of 5 putative virulence genes; and, exclusively for C. jejuni, the determination of lipooligosaccharide (LOS) class. Discriminatory power was calculated by the Simpson's index of diversity (SID) and the congruence was measured by the adjusted Rand index and adjusted Wallace coefficient. MLST was individually the most discriminative typing method for both C. jejuni (SID=0.981) and C. coli (SID=0.957). The most discriminative combination with a SID of 0.992 for both C. jejuni and C. coli was obtained by combining MLST with flaA-RFLP. The combination of MLST with flaA-RFLP is an easy and feasible typing method for short-term monitoring of Campylobacter in broiler meat carcass. Copyright © 2016 Elsevier B.V. All rights reserved.

The TASS Method for Scoring Production Work

ERIC Educational Resources Information Center

Orsborn, Karen J.

1977-01-01

Describes and recommends to typing teachers the Time and Speed Scoring (TASS) method for testing typewriting production and figuring production rates. This method measures speed and quality as two separate items, because proficiency in production typewriting should reflect the student's skill in typing both accurately and quickly. (MF)

Using rate of divergence as an objective measure to differentiate between voice signal types based on the amount of disorder in the signal

PubMed Central

Calawerts, William M; Lin, Liyu; Sprott, JC; Jiang, Jack J

2016-01-01

Objective/Hypothesis The purpose of this paper is to introduce rate of divergence as an objective measure to differentiate between the four voice types based on the amount of disorder present in a signal. We hypothesized that rate of divergence would provide an objective measure that can quantify all four voice types. Study Design 150 acoustic voice recordings were randomly selected and analyzed using traditional perturbation, nonlinear, and rate of divergence analysis methods. ty Methods We developed a new parameter, rate of divergence, which uses a modified version of Wolf’s algorithm for calculating Lyapunov exponents of a system. The outcome of this calculation is not a Lyapunov exponent, but rather a description of the divergence of two nearby data points for the next three points in the time series, followed in three time delayed embedding dimensions. This measure was compared to currently existing perturbation and nonlinear dynamic methods of distinguishing between voice signals. Results There was a direct relationship between voice type and rate of divergence. This calculation is especially effective at differentiating between type 3 and type 4 voices (p<0.001), and is equally effective at differentiating type 1, type 2, and type 3 signals as currently existing methods. Conclusion The rate of divergence calculation introduced is an objective measure that can be used to distinguish between all four voice types based on amount of disorder present, leading to quicker and more accurate voice typing as well as an improved understanding of the nonlinear dynamics involved in phonation. PMID:26920858

Bypass diode for a solar cell

DOEpatents

Rim, Seung Bum; Kim, Taeseok; Smith, David D; Cousins, Peter J

2013-11-12

Methods of fabricating bypass diodes for solar cells are described. In once embodiment, a method includes forming a first conductive region of a first conductivity type above a substrate of a solar cell. A second conductive region of a second conductivity type is formed on the first conductive region. In another embodiment, a method includes forming a first conductive region of a first conductivity type above a substrate of a solar cell. A second conductive region of a second conductivity type is formed within, and surrounded by, an uppermost portion of the first conductive region but is not formed in a lowermost portion of the first conductive region.

Sensitive typing of reverse ABO blood groups with a waveguide-mode sensor.

PubMed

Uno, Shigeyuki; Tanaka, Torahiko; Ashiba, Hiroki; Fujimaki, Makoto; Tanaka, Mutsuo; Hatta, Yoshihiro; Takei, Masami; Awazu, Koichi; Makishima, Makoto

2018-07-01

Portable, on-site blood typing methods will help provide life-saving blood transfusions to patients during an emergency or natural calamity, such as significant earthquakes. We have previously developed waveguide-mode (WM) sensors for forward ABO and Rh(D) blood typing and detection of antibodies against hepatitis B virus and hepatitis C virus. In this study, we evaluated a WM-sensor for reverse ABO blood typing. Since reverse ABO blood typing is a method for detection of antibodies against type A and type B oligosaccharide antigens on the surface of red blood cells (RBCs), we fixed a synthetic type A or type B trisaccharide antigen on the sensor chip of the WM sensor. We obtained significant changes in the reflectance spectra from a WM sensor on type A antigen with type B plasma and type O plasma and on type B antigen with type A plasma and type O plasma, and no spectrum changes on type A antigen or type B antigen with type AB plasma. Signal enhancement with the addition of a peroxidase reaction failed to increase the sensitivity for detection on oligosaccharide chips. By utilizing hemagglutination detection using regent type A and type B RBCs, we successfully determined reverse ABO blood groups with higher sensitivity compared to a method using oligosaccharide antigens. Thus, functionality of a portable device utilizing a WM sensor can be expanded to include reverse ABO blood typing and, in combination with forward ABO typing and antivirus antibody detection, may be useful for on-site blood testing in emergency settings. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

SYBR Green Real-Time PCR Method To Detect Clostridium botulinum Type A▿

PubMed Central

Fenicia, Lucia; Anniballi, Fabrizio; De Medici, Dario; Delibato, Elisabetta; Aureli, Paolo

2007-01-01

Botulinum toxins (BoNTs) are classically produced by Clostridium botulinum but rarely also from neurotoxigenic strains of Clostridium baratii and Clostridium butyricum. BoNT type A (BoNT/A), BoNT/B, BoNT/E, and very rarely BoNT/F are mainly responsible for human botulism. Standard microbiological methods take into consideration only the detection of C. botulinum. The presumptive identification of the toxigenic strains together with the typing of BoNT has to be performed by mouse bioassay. The development of PCR-based methods for the detection and typing of BoNT-producing clostridia would be an ideal alternative to the mouse bioassay. The objective of this study was to develop a rapid and robust real-time PCR method for detecting C. botulinum type A. Four different techniques for the extraction and purification of DNA from cultured samples were initially compared. Of the techniques used, Chelex 100, DNeasy tissue kit, InstaGene matrix DNA, and boiling, the boiling technique was significantly less efficient than the other three. These did not give statistically different results, and Chelex 100 was chosen because it was less expensive than the others. In order to eliminate any false-negative results, an internal amplification control was synthesized and included in the amplification mixture according to ISO 22174. The specificity of the method was tested against 75 strains of C. botulinum type A, 4 strains of C. botulinum type Ab, and 101 nontarget strains. The detection limit of the reaction was less than 6 × 101 copies of C. botulinum type A DNA. The robustness of the method was confirmed using naturally contaminated stool specimens to evaluate the tolerance of inhibitor substances. SYBR green real-time PCR showed very high specificity for the detection of C. botulinum types A and Ab (inclusivity and exclusivity, 100%). PMID:17369349

Analyses of Crime Patterns in NIBRS Data Based on a Novel Graph Theory Clustering Method: Virginia as a Case Study

PubMed Central

Nolan, Jim

2014-01-01

This paper suggests a novel clustering method for analyzing the National Incident-Based Reporting System (NIBRS) data, which include the determination of correlation of different crime types, the development of a likelihood index for crimes to occur in a jurisdiction, and the clustering of jurisdictions based on crime type. The method was tested by using the 2005 assault data from 121 jurisdictions in Virginia as a test case. The analyses of these data show that some different crime types are correlated and some different crime parameters are correlated with different crime types. The analyses also show that certain jurisdictions within Virginia share certain crime patterns. This information assists with constructing a pattern for a specific crime type and can be used to determine whether a jurisdiction may be more likely to see this type of crime occur in their area. PMID:24778585

System and method employing a minimum distance and a load feature database to identify electric load types of different electric loads

DOEpatents

Lu, Bin; Yang, Yi; Sharma, Santosh K; Zambare, Prachi; Madane, Mayura A

2014-12-23

A method identifies electric load types of a plurality of different electric loads. The method includes providing a load feature database of a plurality of different electric load types, each of the different electric load types including a first load feature vector having at least four different load features; sensing a voltage signal and a current signal for each of the different electric loads; determining a second load feature vector comprising at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the different electric loads; and identifying by a processor one of the different electric load types by determining a minimum distance of the second load feature vector to the first load feature vector of the different electric load types of the load feature database.

Advantages of a validated UPLC-MS/MS standard addition method for the quantification of A-type dimeric and trimeric proanthocyanidins in cranberry extracts in comparison with well-known quantification methods.

PubMed

van Dooren, Ines; Foubert, Kenn; Theunis, Mart; Naessens, Tania; Pieters, Luc; Apers, Sandra

2018-01-30

The berries of Vaccinium macrocarpon, cranberry, are widely used for the prevention of urinary tract infections. This species contains A-type proanthocyanidins (PACs), which intervene in the initial phase of the development of urinary tract infections by preventing the adherence of Escherichia coli by their P-type fimbriae to uroepithelial cells. Unfortunately, the existing clinical studies used different cranberry preparations, which were poorly standardized. Because of this, the results were hard to compare, which led sometimes to conflicting results. Currently, PACs are quantified using the rather non-specific spectrophotometric 4-dimethylaminocinnamaldehyde (DMAC) method. In addition, a normal phase HPTLC-densitometric method, a HPLC-UV method and three LC-MS/MS methods for quantification of procyanidin A2 were recently published. All these methods contain some shortcomings and errors. Hence, the development and validation of a fast and sensitive standard addition LC-MS/MS method for the simultaneous quantification of A-type dimers and trimers in a cranberry dry extract was carried out. A linear calibration model could be adopted for dimers and, after logaritmic transformation, for trimers. The maximal interday and interconcentration precision was found to be 4.86% and 4.28% for procyanidin A2, and 5.61% and 7.65% for trimeric PACs, which are all acceptable values for an analytical method using LC-MS/MS. In addition, twelve different cranberry extracts were analyzed by means of the newly validated method and other widely used methods. There appeared to be an enormous variation in dimeric and trimeric PAC content. Comparison of these results with LC-MS/MS analysis without standard addition showed the presence of matrix effects for some of the extracts and proved the necessity of standard addition. A comparison of the well-known and widely used DMAC method, the butanol-HCl assay and this newly developed LC-MS/MS method clearly indicated the need for a reliable method able to quantify A-type PACs, which are considered to be the pharmacologically active constituents of cranberry, since neither the DMAC or butanol-HCl assays are capable of distinguishing between A and B-type PACs and therefore cannot detect adulterations with, for example, extracts with a high B-type PAC content. Hence, the combination of the DMAC method or butanol-HCl assay with this more specific LC-MS/MS assay could overcome these shortcomings. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of coupling between time-delay systems from time series

NASA Astrophysics Data System (ADS)

Prokhorov, M. D.; Ponomarenko, V. I.

2005-07-01

We propose a method for estimation of coupling between the systems governed by scalar time-delay differential equations of the Mackey-Glass type from the observed time series data. The method allows one to detect the presence of certain types of linear coupling between two time-delay systems, to define the type, strength, and direction of coupling, and to recover the model equations of coupled time-delay systems from chaotic time series corrupted by noise. We verify our method using both numerical and experimental data.

Frozen Elephant Trunk and Antegrade Visceral Debranching in the Surgical Treatment of Type B Aortic Dissection: An Alternative Method

PubMed Central

Tuncer, Altug; Akbulut, Mustafa; Adademir, Taylan; Tas, Serpil; Ak, Adnan; Arslan, Özgür; Erden, Benay; Şişmanoğlu, Mesut

2016-01-01

Intervention is inevitable in complicated Type B aortic dissections. Classical surgical procedures and endovascular interventions are far from ideal treatments due to their high risk of periprocedural complications and mortality. There is often a need for alternative method in cases of difficult anatomy. We present the combined use of frozen elephant trunk and antegrade visceral debranching methods in the treatment of a 54-year-old male patient with complicated Type B aortic dissection. PMID:28516092

Comparison of a gel column blood typing method and a point-of-care cartridge for dog erythrocyte antigen 1.1.

PubMed

Blois, Shauna L; Richardson, Danielle M; Abrams-Ogg, Anthony C G

2013-01-01

Blood typing for the presence of Dog Erythrocyte Antigen (DEA) 1.1 is recommended in all donor and recipient dogs prior to transfusion of blood products. The objective of this study was to determine if a point-of-care DEA 1.1 blood typing cartridge could be used in place of the gel column typing method. Detection of DEA 1.1 was performed using a laboratory-based gel column method and a point-of-care cartridge. A convenience sample of 30 healthy blood donors, 13 dogs with immune-mediated hemolytic anemia (IMHA) (3 of which had concurrent immune-mediated thrombocytopenia [IMT]), and 44 dogs with other diseases was included in the study. Agreement was observed between the tests for normal dogs and dogs with nonimmune-mediated disease in 74/74 cases. Two dogs in the IMHA group had indeterminate gel column blood typing results; 1 dog in this group had a negative gel column test result but a positive cartridge test result. There was good agreement between the 2 methods for normal dogs and dogs with nonimmune-mediated disease. Blood typing methods in dogs with IMHA should be further investigated. © Veterinary Emergency and Critical Care Society 2013.

Spectral embedding finds meaningful (relevant) structure in image and microarray data

PubMed Central

Higgs, Brandon W; Weller, Jennifer; Solka, Jeffrey L

2006-01-01

Background Accurate methods for extraction of meaningful patterns in high dimensional data have become increasingly important with the recent generation of data types containing measurements across thousands of variables. Principal components analysis (PCA) is a linear dimensionality reduction (DR) method that is unsupervised in that it relies only on the data; projections are calculated in Euclidean or a similar linear space and do not use tuning parameters for optimizing the fit to the data. However, relationships within sets of nonlinear data types, such as biological networks or images, are frequently mis-rendered into a low dimensional space by linear methods. Nonlinear methods, in contrast, attempt to model important aspects of the underlying data structure, often requiring parameter(s) fitting to the data type of interest. In many cases, the optimal parameter values vary when different classification algorithms are applied on the same rendered subspace, making the results of such methods highly dependent upon the type of classifier implemented. Results We present the results of applying the spectral method of Lafon, a nonlinear DR method based on the weighted graph Laplacian, that minimizes the requirements for such parameter optimization for two biological data types. We demonstrate that it is successful in determining implicit ordering of brain slice image data and in classifying separate species in microarray data, as compared to two conventional linear methods and three nonlinear methods (one of which is an alternative spectral method). This spectral implementation is shown to provide more meaningful information, by preserving important relationships, than the methods of DR presented for comparison. Tuning parameter fitting is simple and is a general, rather than data type or experiment specific approach, for the two datasets analyzed here. Tuning parameter optimization is minimized in the DR step to each subsequent classification method, enabling the possibility of valid cross-experiment comparisons. Conclusion Results from the spectral method presented here exhibit the desirable properties of preserving meaningful nonlinear relationships in lower dimensional space and requiring minimal parameter fitting, providing a useful algorithm for purposes of visualization and classification across diverse datasets, a common challenge in systems biology. PMID:16483359

Epigenome-wide association studies without the need for cell-type composition.

PubMed

Zou, James; Lippert, Christoph; Heckerman, David; Aryee, Martin; Listgarten, Jennifer

2014-03-01

In epigenome-wide association studies, cell-type composition often differs between cases and controls, yielding associations that simply tag cell type rather than reveal fundamental biology. Current solutions require actual or estimated cell-type composition--information not easily obtainable for many samples of interest. We propose a method, FaST-LMM-EWASher, that automatically corrects for cell-type composition without the need for explicit knowledge of it, and then validate our method by comparison with the state-of-the-art approach. Corresponding software is available from http://www.microsoft.com/science/.

Semi-supervised learning for photometric supernova classification

NASA Astrophysics Data System (ADS)

Richards, Joseph W.; Homrighausen, Darren; Freeman, Peter E.; Schafer, Chad M.; Poznanski, Dovi

2012-01-01

We present a semi-supervised method for photometric supernova typing. Our approach is to first use the non-linear dimension reduction technique diffusion map to detect structure in a data base of supernova light curves and subsequently employ random forest classification on a spectroscopically confirmed training set to learn a model that can predict the type of each newly observed supernova. We demonstrate that this is an effective method for supernova typing. As supernova numbers increase, our semi-supervised method efficiently utilizes this information to improve classification, a property not enjoyed by template-based methods. Applied to supernova data simulated by Kessler et al. to mimic those of the Dark Energy Survey, our methods achieve (cross-validated) 95 per cent Type Ia purity and 87 per cent Type Ia efficiency on the spectroscopic sample, but only 50 per cent Type Ia purity and 50 per cent efficiency on the photometric sample due to their spectroscopic follow-up strategy. To improve the performance on the photometric sample, we search for better spectroscopic follow-up procedures by studying the sensitivity of our machine-learned supernova classification on the specific strategy used to obtain training sets. With a fixed amount of spectroscopic follow-up time, we find that, despite collecting data on a smaller number of supernovae, deeper magnitude-limited spectroscopic surveys are better for producing training sets. For supernova Ia (II-P) typing, we obtain a 44 per cent (1 per cent) increase in purity to 72 per cent (87 per cent) and 30 per cent (162 per cent) increase in efficiency to 65 per cent (84 per cent) of the sample using a 25th (24.5th) magnitude-limited survey instead of the shallower spectroscopic sample used in the original simulations. When redshift information is available, we incorporate it into our analysis using a novel method of altering the diffusion map representation of the supernovae. Incorporating host redshifts leads to a 5 per cent improvement in Type Ia purity and 13 per cent improvement in Type Ia efficiency. A web service for the supernova classification method used in this paper can be found at .

Effectual switching filter for removing impulse noise using a SCM detector

NASA Astrophysics Data System (ADS)

Yuan, Jin-xia; Zhang, Hong-juan; Ma, Yi-de

2012-03-01

An effectual method is proposed to remove impulse noise from corrupted color images. The spiking cortical model (SCM) is adopted as a noise detector to identify noisy pixels in each channel of color images, and detected noise pixels are saved in three marking matrices. According to the three marking matrices, the detected noisy pixels are divided into two types (type I and type II). They are filtered differently: an adaptive median filter is used for type I and an adaptive vector median for type II. Noise-free pixels are left unchanged. Extensive experiments show that the proposed method outperforms most of the other well-known filters in the aspects of both visual and objective quality measures, and this method can also reduce the possibility of generating color artifacts while preserving image details.

Assessing and Evaluating Multidisciplinary Translational Teams: A Mixed Methods Approach

PubMed Central

Wooten, Kevin C.; Rose, Robert M.; Ostir, Glenn V.; Calhoun, William J.; Ameredes, Bill T.; Brasier, Allan R.

2014-01-01

A case report illustrates how multidisciplinary translational teams can be assessed using outcome, process, and developmental types of evaluation using a mixed methods approach. Types of evaluation appropriate for teams are considered in relation to relevant research questions and assessment methods. Logic models are applied to scientific projects and team development to inform choices between methods within a mixed methods design. Use of an expert panel is reviewed, culminating in consensus ratings of 11 multidisciplinary teams and a final evaluation within a team type taxonomy. Based on team maturation and scientific progress, teams were designated as: a) early in development, b) traditional, c) process focused, or d) exemplary. Lessons learned from data reduction, use of mixed methods, and use of expert panels are explored. PMID:24064432

[Metabolic surgery in treatment of diabetes mellitus of type II].

PubMed

Sedov, V M; Fishman, M B

2013-01-01

Nowadays, according to data of WHO, the diabetes mellitus was diagnosed in more than 280 million people. The diabetes mellitus type II had 90% patients. The applied methods of conservative therapy seldom lead to euglycemia condition of patients. Last years the treatment of diabetes mellitus was carried out by the method of different bariatic interventions. Good results was obtained, they should be analyzed and investigate. The results of treatment of 142 patients from 628 patients (with type II) were estimated. The patients were undergone by different bariatic interventions. Modern laparoscopic operations were performed on all the patients. Controlled bandage of stomach had 81 of patients. Gastric resection was performed in 28. Gastric bypass surgery was carried out in 22 of patients and biliopancreatic diversion - in 11. The improvement of control of leukemia level was obtained. Diabetes type II could be treated by surgical methods. The best results were obtained after combined operations, which potentially could present an alternative method of treatment of type II diabetes.

Quantifying the Performance of P-Type Transparent Conducting Oxides by Experimental Methods

PubMed Central

Fleischer, Karsten; Norton, Emma; Mullarkey, Daragh; Caffrey, David; Shvets, Igor V.

2017-01-01

Screening for potential new materials with experimental and theoretical methods has led to the discovery of many promising candidate materials for p-type transparent conducting oxides. It is difficult to reliably assess a good p-type transparent conducting oxide (TCO) from limited information available at an early experimental stage. In this paper we discuss the influence of sample thickness on simple transmission measurements and how the sample thickness can skew the commonly used figure of merit of TCOs and their estimated band gap. We discuss this using copper-deficient CuCrO2 as an example, as it was already shown to be a good p-type TCO grown at low temperatures. We outline a modified figure of merit reducing thickness-dependent errors, as well as how modern ab initio screening methods can be used to augment experimental methods to assess new materials for potential applications as p-type TCOs, p-channel transparent thin film transistors, and selective contacts in solar cells. PMID:28862695

Aeronautic Instruments. Section V : Power Plant Instruments

NASA Technical Reports Server (NTRS)

Washburn, G E; Sylvander, R C; Mueller, E F; Wilhelm, R M; Eaton, H N; Warner, John A C

1923-01-01

Part 1 gives a general discussion of the uses, principles, construction, and operation of airplane tachometers. Detailed description of all available instruments, both foreign and domestic, are given. Part 2 describes methods of tests and effect of various conditions encountered in airplane flight such as change of temperature, vibration, tilting, and reduced air pressure. Part 3 describes the principal types of distance reading thermometers for aircraft engines, including an explanation of the physical principles involved in the functioning of the instruments and proper filling of the bulbs. Performance requirements and testing methods are given and a discussion of the source of error and results of tests. Part 4 gives methods of tests and calibration, also requirements of gauges of this type for the pressure measurement of the air pressure in gasoline tanks and the engine oil pressure on airplanes. Part 5 describes two types of gasoline gauges, the float type and the pressure type. Methods of testing and calibrating gasoline depth gauges are given. The Schroeder, R. A. E., and the Mark II flowmeters are described.

Price of gasoline: forecasting comparisons. [Box-Jenkins, econometric, and regression methods

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

Bopp, A.E.; Neri, J.A.

Gasoline prices are simulated using three popular forecasting methodologies: A Box--Jenkins type method, an econometric method, and a regression method. One-period-ahead and 18-period-ahead comparisons are made. For the one-period-ahead method, a Box--Jenkins type time-series model simulated best, although all do well. However, for the 18-period simulation, the econometric and regression methods perform substantially better than the Box-Jenkins formulation. A rationale for and implications of these results ae discussed. 11 references.

Peptide and protein biomarkers for type 1 diabetes mellitus

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

Zhang, Qibin; Metz, Thomas O.

A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

Mechanical treatment methods in the pinon-juniper type

Treesearch

Brent J. Racher

2008-01-01

(Please note, this is an abstract only) Mechanical treatments in the pinon-juniper type are driven by the objectives of the treatment. Objectives of restoring meadows or grassland from encroachment or returning to a savanna can require a different method of treatment than thinning pinon-juniper woodlands. Often these types of objectives are intermingled within a...

Peptide and protein biomarkers for type 1 diabetes mellitus

DOEpatents

Zhang, Qibin; Metz, Thomas O.

2014-06-10

A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

What's in a Name? A Comparison of Methods for Classifying Predominant Type of Maltreatment

ERIC Educational Resources Information Center

Lau, A.S.; Leeb, R.T.; English, D.; Graham, J.C.; Briggs, E.C.; Brody, K.E.; Marshall, J.M.

2005-01-01

Objective:: The primary aim of the study was to identify a classification scheme, for determining the predominant type of maltreatment in a child's history that best predicts differences in developmental outcomes. Method:: Three different predominant type classification schemes were examined in a sample of 519 children with a history of alleged…

Comparative Efficiency of the Fenwick Can and Schuiling Centrifuge in Extracting Nematode Cysts from Different Soil Types

PubMed Central

Bellvert, Joaquim; Crombie, Kieran; Horgan, Finbarr G.

2008-01-01

The Fenwick can and Schuiling centrifuge are widely used to extract nematode cysts from soil samples. The comparative efficiencies of these two methods during cyst extraction have not been determined for different soil types under different cyst densities. Such information is vital for statutory laboratories that must choose a method for routine, high-throughput soil monitoring. In this study, samples of different soil types seeded with varying densities of potato cyst nematode (Globodera rostochiensis) cysts were processed using both methods. In one experiment, with 200 ml samples, recovery was similar between methods. In a second experiment with 500 ml samples, cyst recovery was higher using the Schuiling centrifuge. For each method and soil type, cyst extraction efficiency was similar across all densities tested. Extraction was efficient from pure sand (Fenwick 72%, Schuiling 84%) and naturally sandy soils (Fenwick 62%, Schuiling 73%), but was significantly less efficient from clay-soil (Fenwick 42%, Schuiling 44%) and peat-soil with high organic matter content (Fenwick 35%, Schuiling 33%). Residual moisture (<10% w/w) in samples prior to analyses reduced extraction efficiency, particularly for sand and sandy soils. For each soil type and method, there were significant linear relationships between the number of cysts extracted and the numbers of cysts in the samples. We discuss the advantages and disadvantages of each extraction method for cyst extraction in statutory soil laboratories. PMID:19259516

Comparison of rangeland vegetation sampling techniques in the Central Grasslands

USGS Publications Warehouse

Stohlgren, T.J.; Bull, K.A.; Otsuki, Yuka

1998-01-01

Maintaining native plant diversity, detecting exotic species, and monitoring rare species are becoming important objectives in rangeland conservation. Four rangeland vegetation sampling techniques were compared to see how well they captured local pant diversity. The methods tested included the commonly used Parker transects, Daubenmire transects as modified by the USDA Forest Service, a new transect and 'large quadrat' design proposed by the USDA Agricultural Research Service, and the Modified-Whittaker multi-scale vegetation plot. The 4 methods were superimposed in shortgrass steppe, mixed grass prairie, northern mixed prairie, and tallgrass prairie in the Central Grasslands of the United States with 4 replicates in each prairie type. Analysis of variance tests showed significant method effects and prairie type effects, but no significant method X type interactions for total species richness, the number of native species, the number of species with less than 1 % cover, and the time required for sampling. The methods behaved similarly in each prairie type under a wide variety of grazing regimens. The Parker, large quadrat, and Daubenmire transects significantly underestimated the total species richness and the number of native species in each prairie type, and the number of species with less than 1 % cover in all but the tallgrass prairie type. The transect techniques also consistently missed half the exotic species, including noxious weeds, in each prairie type. The Modified-Whittaker method, which included an exhaustive search for plant species in a 20 x 50 m plot, served as the baseline for species richeness comparisons. For all prairie types, the Modified-Whittaker plot captured an average of 42. (?? 2.4; 1 S.E.) plant species per site compared to 15.9 (?? 1.3), 18.9 (?? 1.2), and 22.8 (?? 1.6) plant species per site using the Parker, large quadrat, and Daubenmire transect methods, respectively. The 4 methods captured most of the dominant species at each site and thus produced similar results for total foliar cover and soil cover. The detection and measurement of exotic plant species were greatly enhanced by using ten 1 m2 subplots in a multi-scale sampling design and searching a larger area (1,000 m2) at each site. Even with 4 replicate sites, the transect methods usually captured, and thus would monitor, 36 to 66 % of the plant species at each site. To evaluate the status and trends of common, rare, and exotic plant species at local, regional, and national scales, innovative, multi-scale methods must replace the commonly used transect methods to the past.

Comparison of Genomic Methods for Differentiating Strains of Enterococcus faecium: Assessment Using Clinical Epidemiologic Data

PubMed Central

Savor, Connie; Pfaller, Michael A.; Kruszynski, Julie A.; Hollis, Richard J.; Noskin, Gary A.; Peterson, Lance R.

1998-01-01

Genomic DNA extracted from 45 vancomycin-resistant Enterococcus faecium (VRE) isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis. The ability of this method (restriction endonuclease analysis [REA]) to distinguish strains at the subspecies level was compared with results previously determined by pulsed-field gel electrophoresis (PFGE). Chart reviews were performed to provide a clinical correlation of possible epidemiologic relatedness. A likely clinical association was found for 29 patients as part of two outbreaks. REA found 21 of 21 isolates were the same type in the first outbreak, with PFGE calling 19 strains the same type. In the second outbreak with eight patient isolates, HindIII found six were the same type and two were unique types. HaeIII found three strains were the same type, two strains were a separate type, and three more strains were unique types, while PFGE found three were the same type and five were unique types. No single “ideal” method can be used without clinical epidemiologic investigation, but any of these techniques is helpful in providing focus to infection control practitioners assessing possible outbreaks of nosocomial infection. PMID:9774587

Type I and II β-turns prediction using NMR chemical shifts.

PubMed

Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

2014-07-01

A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of Cο, Cα, H(N), and N(H) chemical shifts were generally (i + 1) > (i + 2). The mean values of Cβ and Hα chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2% with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.

On the optimization of a mixed speaker array in an enclosed space using the virtual-speaker weighting method

NASA Astrophysics Data System (ADS)

Peng, Bo; Zheng, Sifa; Liao, Xiangning; Lian, Xiaomin

2018-03-01

In order to achieve sound field reproduction in a wide frequency band, multiple-type speakers are used. The reproduction accuracy is not only affected by the signals sent to the speakers, but also depends on the position and the number of each type of speaker. The method of optimizing a mixed speaker array is investigated in this paper. A virtual-speaker weighting method is proposed to optimize both the position and the number of each type of speaker. In this method, a virtual-speaker model is proposed to quantify the increment of controllability of the speaker array when the speaker number increases. While optimizing a mixed speaker array, the gain of the virtual-speaker transfer function is used to determine the priority orders of the candidate speaker positions, which optimizes the position of each type of speaker. Then the relative gain of the virtual-speaker transfer function is used to determine whether the speakers are redundant, which optimizes the number of each type of speaker. Finally the virtual-speaker weighting method is verified by reproduction experiments of the interior sound field in a passenger car. The results validate that the optimum mixed speaker array can be obtained using the proposed method.

Linear and non-linear regression analysis for the sorption kinetics of methylene blue onto activated carbon.

PubMed

Kumar, K Vasanth

2006-10-11

Batch kinetic experiments were carried out for the sorption of methylene blue onto activated carbon. The experimental kinetics were fitted to the pseudo first-order and pseudo second-order kinetics by linear and a non-linear method. The five different types of Ho pseudo second-order expression have been discussed. A comparison of linear least-squares method and a trial and error non-linear method of estimating the pseudo second-order rate kinetic parameters were examined. The sorption process was found to follow a both pseudo first-order kinetic and pseudo second-order kinetic model. Present investigation showed that it is inappropriate to use a type 1 and type pseudo second-order expressions as proposed by Ho and Blanachard et al. respectively for predicting the kinetic rate constants and the initial sorption rate for the studied system. Three correct possible alternate linear expressions (type 2 to type 4) to better predict the initial sorption rate and kinetic rate constants for the studied system (methylene blue/activated carbon) was proposed. Linear method was found to check only the hypothesis instead of verifying the kinetic model. Non-linear regression method was found to be the more appropriate method to determine the rate kinetic parameters.

Changing practice: red blood cell typing by molecular methods for patients with sickle cell disease.

PubMed

Casas, Jessica; Friedman, David F; Jackson, Tannoa; Vege, Sunitha; Westhoff, Connie M; Chou, Stella T

2015-06-01

Extended red blood cell (RBC) antigen matching is recommended to limit alloimmunization in patients with sickle cell disease (SCD). DNA-based testing to predict blood group phenotypes has enhanced availability of antigen-negative donor units and improved typing of transfused patients, but replacement of routine serologic typing for non-ABO antigens with molecular typing for patients has not been reported. This study compared the historical RBC antigen phenotypes obtained by hemagglutination methods with genotype predictions in 494 patients with SCD. For discrepant results, repeat serologic testing was performed and/or investigated by gene sequencing for silent or variant alleles. Seventy-one typing discrepancies were identified among 6360 antigen comparisons (1.1%). New specimens for repeat serologic testing were obtained for 66 discrepancies and retyping agreed with the genotype in 64 cases. One repeat Jk(b-) serologic phenotype, predicted Jk(b+) by genotype, was found by direct sequencing of JK to be a silenced allele, and one N typing discrepancy remains under investigation. Fifteen false-negative serologic results were associated with alleles encoding weak antigens or single-dose Fy(b) expression. DNA-based RBC typing provided improved accuracy and expanded information on RBC antigens compared to hemagglutination methods, leading to its implementation as the primary method for extended RBC typing for patients with SCD at our institution. © 2015 AABB.

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.

PubMed

Niu, Liang; Xu, Zongli; Taylor, Jack A

2016-09-01

The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes-Infinium I (type I) and Infinium II (type II)-in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis. Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html). niulg@ucmail.uc.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis.

PubMed

Gurtler, Volker; Grando, Danilla; Mayall, Barrie C; Wang, Jenny; Ghaly-Derias, Shahbano

2012-09-01

In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with predictable instability based on recombination and concerted evolution of the rrn operon that will complement existing typing methods. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Alaska: Beaufort Sea

Atmospheric Science Data Center

2014-05-15

... Imaging SpectroRadiometer (MISR), illustrate different methods that may be used to assess sea ice type. Sea ice in the Beaufort Sea ... March 19, 2001 - Illustration of different methods to assess sea ice type. project:  MISR ...

Lie symmetry analysis, Bäcklund transformations, and exact solutions of a (2 + 1)-dimensional Boiti-Leon-Pempinelli system

NASA Astrophysics Data System (ADS)

Zhao, Zhonglong; Han, Bo

2017-10-01

In this paper, the Lie symmetry analysis method is employed to investigate the Lie point symmetries and the one-parameter transformation groups of a (2 + 1)-dimensional Boiti-Leon-Pempinelli system. By using Ibragimov's method, the optimal system of one-dimensional subalgebras of this system is constructed. Truncated Painlevé analysis is used for deriving the Bäcklund transformation. The method of constructing lump-type solutions of integrable equations by means of Bäcklund transformation is first presented. Meanwhile, the lump-type solutions of the (2 + 1)-dimensional Boiti-Leon-Pempinelli system are obtained. The lump-type wave is one kind of rogue wave. The fusion-type N-solitary wave solutions are also constructed. In addition, this system is integrable in terms of the consistent Riccati expansion method.

Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec.

PubMed

Vincent, Caroline; Usongo, Valentine; Berry, Chrystal; Tremblay, Denise M; Moineau, Sylvain; Yousfi, Khadidja; Doualla-Bell, Florence; Fournier, Eric; Nadon, Céline; Goodridge, Lawrence; Bekal, Sadjia

2018-08-01

Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evolution of Query Optimization Methods

NASA Astrophysics Data System (ADS)

Hameurlain, Abdelkader; Morvan, Franck

Query optimization is the most critical phase in query processing. In this paper, we try to describe synthetically the evolution of query optimization methods from uniprocessor relational database systems to data Grid systems through parallel, distributed and data integration systems. We point out a set of parameters to characterize and compare query optimization methods, mainly: (i) size of the search space, (ii) type of method (static or dynamic), (iii) modification types of execution plans (re-optimization or re-scheduling), (iv) level of modification (intra-operator and/or inter-operator), (v) type of event (estimation errors, delay, user preferences), and (vi) nature of decision-making (centralized or decentralized control).

Adjusting for multiple prognostic factors in the analysis of randomised trials

PubMed Central

2013-01-01

Background When multiple prognostic factors are adjusted for in the analysis of a randomised trial, it is unclear (1) whether it is necessary to account for each of the strata, formed by all combinations of the prognostic factors (stratified analysis), when randomisation has been balanced within each stratum (stratified randomisation), or whether adjusting for the main effects alone will suffice, and (2) the best method of adjustment in terms of type I error rate and power, irrespective of the randomisation method. Methods We used simulation to (1) determine if a stratified analysis is necessary after stratified randomisation, and (2) to compare different methods of adjustment in terms of power and type I error rate. We considered the following methods of analysis: adjusting for covariates in a regression model, adjusting for each stratum using either fixed or random effects, and Mantel-Haenszel or a stratified Cox model depending on outcome. Results Stratified analysis is required after stratified randomisation to maintain correct type I error rates when (a) there are strong interactions between prognostic factors, and (b) there are approximately equal number of patients in each stratum. However, simulations based on real trial data found that type I error rates were unaffected by the method of analysis (stratified vs unstratified), indicating these conditions were not met in real datasets. Comparison of different analysis methods found that with small sample sizes and a binary or time-to-event outcome, most analysis methods lead to either inflated type I error rates or a reduction in power; the lone exception was a stratified analysis using random effects for strata, which gave nominal type I error rates and adequate power. Conclusions It is unlikely that a stratified analysis is necessary after stratified randomisation except in extreme scenarios. Therefore, the method of analysis (accounting for the strata, or adjusting only for the covariates) will not generally need to depend on the method of randomisation used. Most methods of analysis work well with large sample sizes, however treating strata as random effects should be the analysis method of choice with binary or time-to-event outcomes and a small sample size. PMID:23898993

Evaluation of Fourier transform infrared (FT-IR) spectroscopy and chemometrics as a rapid approach for sub-typing Escherichia coli O157:H7 isolates.

PubMed

Davis, R; Paoli, G; Mauer, L J

2012-09-01

The importance of tracking outbreaks of foodborne illness and the emergence of new virulent subtypes of foodborne pathogens have created the need for rapid and reliable sub-typing methods for Escherichia coli O157:H7. Fourier transform infrared (FT-IR) spectroscopy coupled with multivariate statistical analyses was used for sub-typing 30 strains of E. coli O157:H7 that had previously been typed by multilocus variable number tandem repeat analysis (MLVA) and pulsed field gel electrophoresis (PFGE). Hierarchical cluster analysis (HCA) and canonical variate analysis (CVA) of the FT-IR spectra resulted in the clustering of the same or similar MLVA types and separation of different MLVA types of E. coli O157:H7. The developed FT-IR method showed better discriminatory power than PFGE in sub-typing E. coli O157:H7. Results also indicated the spectral relatedness between different outbreak strains. However, the grouping of some strains was not in complete agreement with the clustering based on PFGE and MLVA. Additionally, HCA of the spectra differentiated the strains into 30 sub-clusters, indicating the high specificity and suitability of the method for strain level identification. Strains were also classified (97% correct) based on the type of Shiga toxin present using CVA of the spectra. This study demonstrated that FT-IR spectroscopy is suitable for rapid (≤16 h) and economical sub-typing of E. coli O157:H7 with comparable accuracy to MLVA typing. This is the first report of using an FT-IR-based method for sub-typing E. coli O157:H7. Copyright © 2012 Elsevier Ltd. All rights reserved.

Resistance to densification, tensile strength and capsule-filling performance of some pharmaceutical diluents.

PubMed

Nikolakakis, I; Aragon, O B; Malamataris, S

1998-07-01

The purpose of this study was to compare some indicators of capsule-filling performance, as measured by tapped density under different conditions, and elucidate possible quantitative relationships between variation of capsule fill-weight (%CV) and gravitational and inter-particle forces (attractive or frictional) derived from measurements of particle size, true density, low compression and tensile strength. Five common pharmaceutical diluents (lactose, maize starch, talc, Emcocel and Avicel) were investigated and two capsule-filling methods (pouring powder and dosator nozzle) were employed. It was found that for the pouring-type method the appropriateness of Hausner's ratio (HR), Carr's compressibility index (CC%) and Kawakita's constant (alpha) as indicators of capsule fill-weight variation decreases in the order alpha > CC% > HR; the appropriateness of these indicators also decreases with increasing cylinder size and with impact velocity during tapping. For the dosator-type method the appropriateness of the indicators decreases in the order HR > CC% > alpha, the opposite of that for the pouring-type method; the appropriateness of the indicators increases with decreasing cylinder size and impact velocity. The relationship between %CV and the ratio of inter-particle attractive to gravitational forces calculated from measurements of particle size and true density (Fvdw/Wp) was more significant for the pouring-type capsule-filling method. For the dosator-type method a significant relationship (1% level) was found between %CV and the product of Fvdw/Wp and a function expressing the increase, with packing density (p(f)), in the ratio of frictional to attractive inter-particle forces derived from compression (P) and tensile-strength (T) testing, d(log(P/T))/d(p(f)). The value of tapped density in predictions of capsule-filling performance is affected by the testing conditions in a manner depending on the filling method applied. For the pouring-type method predictions can be based on the ratio of attractive (inter-particle) to gravitational forces, whereas for the dosator-type method the contribution of frictional and attractive forces should, because of packing density change, also be taken into account.

Fetal ECG extraction via Type-2 adaptive neuro-fuzzy inference systems.

PubMed

Ahmadieh, Hajar; Asl, Babak Mohammadzadeh

2017-04-01

We proposed a noninvasive method for separating the fetal ECG (FECG) from maternal ECG (MECG) by using Type-2 adaptive neuro-fuzzy inference systems. The method can extract FECG components from abdominal signal by using one abdominal channel, including maternal and fetal cardiac signals and other environmental noise signals, and one chest channel. The proposed algorithm detects the nonlinear dynamics of the mother's body. So, the components of the MECG are estimated from the abdominal signal. By subtracting estimated mother cardiac signal from abdominal signal, fetal cardiac signal can be extracted. This algorithm was applied on synthetic ECG signals generated based on the models developed by McSharry et al. and Behar et al. and also on DaISy real database. In environments with high uncertainty, our method performs better than the Type-1 fuzzy method. Specifically, in evaluation of the algorithm with the synthetic data based on McSharry model, for input signals with SNR of -5dB, the SNR of the extracted FECG was improved by 38.38% in comparison with the Type-1 fuzzy method. Also, the results show that increasing the uncertainty or decreasing the input SNR leads to increasing the percentage of the improvement in SNR of the extracted FECG. For instance, when the SNR of the input signal decreases to -30dB, our proposed algorithm improves the SNR of the extracted FECG by 71.06% with respect to the Type-1 fuzzy method. The same results were obtained on synthetic data based on Behar model. Our results on real database reflect the success of the proposed method to separate the maternal and fetal heart signals even if their waves overlap in time. Moreover, the proposed algorithm was applied to the simulated fetal ECG with ectopic beats and achieved good results in separating FECG from MECG. The results show the superiority of the proposed Type-2 neuro-fuzzy inference method over the Type-1 neuro-fuzzy inference and the polynomial networks methods, which is due to its capability to capture the nonlinearities of the model better. Copyright © 2017 Elsevier B.V. All rights reserved.

A Method for Calculating Fermi Energy and Carrier Concentrations in Semiconducts

ERIC Educational Resources Information Center

Gaylord, T. K.; Linxwiler, J. N., Jr.

1976-01-01

An efficient numerical method for calculating the Fermi energy, the free electron and free hole concentrations, and the ionized impurity conductors in a semiconductor material is described. The method allows freedom with respect to type of material, temperature, and amount and type of donor and acceptor impurities. (Author/CP)

[DNA quantification of blood samples pre-treated with pyramidon].

PubMed

Zhu, Chuan-Hong; Zheng, Dao-Li; Ni, Rao-Zhi; Wang, Hai-Sheng; Ning, Ping; Fang, Hui; Liu, Yan

2014-06-01

To study DNA quantification and STR typing of samples pre-treated with pyramidon. The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.

Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

PubMed Central

Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

2015-01-01

Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

Enhanced Deforestation Mapping in North Korea using Spatial-temporal Image Fusion Method and Phenology-based Index

NASA Astrophysics Data System (ADS)

Jin, Y.; Lee, D.

2017-12-01

North Korea (the Democratic People's Republic of Korea, DPRK) is known to have some of the most degraded forest in the world. The characteristics of forest landscape in North Korea is complex and heterogeneous, the major vegetation cover types in the forest are hillside farm, unstocked forest, natural forest, and plateau vegetation. Better classification of types in high spatial resolution of deforested areas could provide essential information for decisions about forest management priorities and restoration of deforested areas. For mapping heterogeneous vegetation covers, the phenology-based indices are helpful to overcome the reflectance value confusion that occurs when using one season images. Coarse spatial resolution images may be acquired with a high repetition rate and it is useful for analyzing phenology characteristics, but may not capture the spatial detail of the land cover mosaic of the region of interest. Previous spatial-temporal fusion methods were only capture the temporal change, or focused on both temporal change and spatial change but with low accuracy in heterogeneous landscapes and small patches. In this study, a new concept for spatial-temporal image fusion method focus on heterogeneous landscape was proposed to produce fine resolution images at both fine spatial and temporal resolution. We classified the three types of pixels between the base image and target image, the first type is only reflectance changed caused by phenology, this type of pixels supply the reflectance, shape and texture information; the second type is both reflectance and spectrum changed in some bands caused by phenology like rice paddy or farmland, this type of pixels only supply shape and texture information; the third type is reflectance and spectrum changed caused by land cover type change, this type of pixels don't provide any information because we can't know how land cover changed in target image; and each type of pixels were applied different prediction methods. Results show that both STARFM and FSDAF predicted in low accuracy in second type pixels and small patches. Classification results used spatial-temporal image fusion method proposed in this study showed overall classification accuracy of 89.38%, with corresponding kappa coefficients of 0.87.

Combined use of ribotyping, PFGE typing and IS431 typing in the discrimination of nosocomial strains of methicillin-resistant Staphylococcus aureus.

PubMed

Yoshida, T; Kondo, N; Hanifah, Y A; Hiramatsu, K

1997-01-01

We have previously reported the phenotypic characterization of methicillin-resistant Staphylococcus aureus (MRSA) clinical strains isolated in Malaya University Hospital in the period 1987 to 1989 using antibiogram, coagulase typing, plasmid profiles, and phage typing. Here, we report the analysis of the same strains with three genotyping methods; ribotyping, pulsed-field gel electrophoresis (PFGE) typing, and IS431 typing (a restriction enzyme fragment length polymorphism analysis using an IS431 probe). Ribotyping could discriminate 46 clinical MRSA strains into 5 ribotypes, PFGE typing into 22 types, and IS431 typing into 15 types. Since the differences of the three genotyping patterns from strain to strain were quite independent from one another, the combined use of the three genotyping methods could discriminate 46 strains into 39 genotypes. Thus, the powerful discriminatory ability of the combination was demonstrated.

Automatic 3D kidney segmentation based on shape constrained GC-OAAM

NASA Astrophysics Data System (ADS)

Chen, Xinjian; Summers, Ronald M.; Yao, Jianhua

2011-03-01

The kidney can be classified into three main tissue types: renal cortex, renal medulla and renal pelvis (or collecting system). Dysfunction of different renal tissue types may cause different kidney diseases. Therefore, accurate and efficient segmentation of kidney into different tissue types plays a very important role in clinical research. In this paper, we propose an automatic 3D kidney segmentation method which segments the kidney into the three different tissue types: renal cortex, medulla and pelvis. The proposed method synergistically combines active appearance model (AAM), live wire (LW) and graph cut (GC) methods, GC-OAAM for short. Our method consists of two main steps. First, a pseudo 3D segmentation method is employed for kidney initialization in which the segmentation is performed slice-by-slice via a multi-object oriented active appearance model (OAAM) method. An improved iterative model refinement algorithm is proposed for the AAM optimization, which synergistically combines the AAM and LW method. Multi-object strategy is applied to help the object initialization. The 3D model constraints are applied to the initialization result. Second, the object shape information generated from the initialization step is integrated into the GC cost computation. A multi-label GC method is used to segment the kidney into cortex, medulla and pelvis. The proposed method was tested on 19 clinical arterial phase CT data sets. The preliminary results showed the feasibility and efficiency of the proposed method.

Deep Learning Method for Denial of Service Attack Detection Based on Restricted Boltzmann Machine.

PubMed

Imamverdiyev, Yadigar; Abdullayeva, Fargana

2018-06-01

In this article, the application of the deep learning method based on Gaussian-Bernoulli type restricted Boltzmann machine (RBM) to the detection of denial of service (DoS) attacks is considered. To increase the DoS attack detection accuracy, seven additional layers are added between the visible and the hidden layers of the RBM. Accurate results in DoS attack detection are obtained by optimization of the hyperparameters of the proposed deep RBM model. The form of the RBM that allows application of the continuous data is used. In this type of RBM, the probability distribution of the visible layer is replaced by a Gaussian distribution. Comparative analysis of the accuracy of the proposed method with Bernoulli-Bernoulli RBM, Gaussian-Bernoulli RBM, deep belief network type deep learning methods on DoS attack detection is provided. Detection accuracy of the methods is verified on the NSL-KDD data set. Higher accuracy from the proposed multilayer deep Gaussian-Bernoulli type RBM is obtained.

Development of a Thiolysis HPLC Method for the Analysis of Procyanidins in Cranberry Products.

PubMed

Gao, Chi; Cunningham, David G; Liu, Haiyan; Khoo, Christina; Gu, Liwei

2018-03-07

The objective of this study was to develop a thiolysis HPLC method to quantify total procyanidins, the ratio of A-type linkages, and A-type procyanidin equivalents in cranberry products. Cysteamine was utilized as a low-odor substitute of toluene-α-thiol for thiolysis depolymerization. A reaction temperature of 70 °C and reaction time of 20 min, in 0.3 M of HCl, were determined to be optimum depolymerization conditions. Thiolytic products of cranberry procyanidins were separated by RP-HPLC and identified using high-resolution mass spectrometry. Standards curves of good linearity were obtained on thiolyzed procyanidin dimer A2 and B2 external standards. The detection and quantification limits, recovery, and precision of this method were validated. The new method was applied to quantitate total procyanidins, average degree of polymerization, ratio of A-type linkages, and A-type procyanidin equivalents in cranberry products. Results showed that the method was suitable for quantitative and qualitative analysis of procyanidins in cranberry products.

Multisensor data fusion for physical activity assessment.

PubMed

Liu, Shaopeng; Gao, Robert X; John, Dinesh; Staudenmayer, John W; Freedson, Patty S

2012-03-01

This paper presents a sensor fusion method for assessing physical activity (PA) of human subjects, based on support vector machines (SVMs). Specifically, acceleration and ventilation measured by a wearable multisensor device on 50 test subjects performing 13 types of activities of varying intensities are analyzed, from which activity type and energy expenditure are derived. The results show that the method correctly recognized the 13 activity types 88.1% of the time, which is 12.3% higher than using a hip accelerometer alone. Also, the method predicted energy expenditure with a root mean square error of 0.42 METs, 22.2% lower than using a hip accelerometer alone. Furthermore, the fusion method was effective in reducing the subject-to-subject variability (standard deviation of recognition accuracies across subjects) in activity recognition, especially when data from the ventilation sensor were added to the fusion model. These results demonstrate that the multisensor fusion technique presented is more effective in identifying activity type and energy expenditure than the traditional accelerometer-alone-based methods.

Novel Intersection Type Recognition for Autonomous Vehicles Using a Multi-Layer Laser Scanner.

PubMed

An, Jhonghyun; Choi, Baehoon; Sim, Kwee-Bo; Kim, Euntai

2016-07-20

There are several types of intersections such as merge-roads, diverge-roads, plus-shape intersections and two types of T-shape junctions in urban roads. When an autonomous vehicle encounters new intersections, it is crucial to recognize the types of intersections for safe navigation. In this paper, a novel intersection type recognition method is proposed for an autonomous vehicle using a multi-layer laser scanner. The proposed method consists of two steps: (1) static local coordinate occupancy grid map (SLOGM) building and (2) intersection classification. In the first step, the SLOGM is built relative to the local coordinate using the dynamic binary Bayes filter. In the second step, the SLOGM is used as an attribute for the classification. The proposed method is applied to a real-world environment and its validity is demonstrated through experimentation.

Novel Intersection Type Recognition for Autonomous Vehicles Using a Multi-Layer Laser Scanner

PubMed Central

An, Jhonghyun; Choi, Baehoon; Sim, Kwee-Bo; Kim, Euntai

2016-01-01

There are several types of intersections such as merge-roads, diverge-roads, plus-shape intersections and two types of T-shape junctions in urban roads. When an autonomous vehicle encounters new intersections, it is crucial to recognize the types of intersections for safe navigation. In this paper, a novel intersection type recognition method is proposed for an autonomous vehicle using a multi-layer laser scanner. The proposed method consists of two steps: (1) static local coordinate occupancy grid map (SLOGM) building and (2) intersection classification. In the first step, the SLOGM is built relative to the local coordinate using the dynamic binary Bayes filter. In the second step, the SLOGM is used as an attribute for the classification. The proposed method is applied to a real-world environment and its validity is demonstrated through experimentation. PMID:27447640

A Review of the Reliability and Validity of Likert-Type Scales for People with Intellectual Disability

ERIC Educational Resources Information Center

Hartley, S. L.; MacLean, W. E., Jr.

2006-01-01

Background: Likert-type scales are increasingly being used among people with intellectual disability (ID). These scales offer an efficient method for capturing a wide range of variance in self-reported attitudes and behaviours. This review is an attempt to evaluate the reliability and validity of Likert-type scales in people with ID. Methods:…

A Method for Determining Job Types for Low Aptitude Airmen.

ERIC Educational Resources Information Center

Mayo, Clyde C.

An opinion survey method for identifying low aptitude job types was developed and used in a study of 11 Air Force career ladders. Lists of low aptitude tasks were defined by technical advisers. These tasks were then rated on nine factors by Air Force instructors who also described low aptitude job types and gave their opinion concerning the…

On the exact solutions of high order wave equations of KdV type (I)

NASA Astrophysics Data System (ADS)

Bulut, Hasan; Pandir, Yusuf; Baskonus, Haci Mehmet

2014-12-01

In this paper, by means of a proper transformation and symbolic computation, we study high order wave equations of KdV type (I). We obtained classification of exact solutions that contain soliton, rational, trigonometric and elliptic function solutions by using the extended trial equation method. As a result, the motivation of this paper is to utilize the extended trial equation method to explore new solutions of high order wave equation of KdV type (I). This method is confirmed by applying it to this kind of selected nonlinear equations.

Method of mechanical quadratures for solving singular integral equations of various types

NASA Astrophysics Data System (ADS)

Sahakyan, A. V.; Amirjanyan, H. A.

2018-04-01

The method of mechanical quadratures is proposed as a common approach intended for solving the integral equations defined on finite intervals and containing Cauchy-type singular integrals. This method can be used to solve singular integral equations of the first and second kind, equations with generalized kernel, weakly singular equations, and integro-differential equations. The quadrature rules for several different integrals represented through the same coefficients are presented. This allows one to reduce the integral equations containing integrals of different types to a system of linear algebraic equations.

Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii.

PubMed

Tanigawa, Kana; Watanabe, Koichi

2011-03-01

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080(T), was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

Comparison of direct measurement methods for headset noise exposure in the workplace

PubMed Central

Nassrallah, Flora G.; Giguère, Christian; Dajani, Hilmi R.; Ellaham, Nicolas N.

2016-01-01

The measurement of noise exposure from communication headsets poses a methodological challenge. Although several standards describe methods for general noise measurements in occupational settings, these are not directly applicable to noise assessments under communication headsets. For measurements under occluded ears, specialized methods have been specified by the International Standards Organization (ISO 11904) such as the microphone in a real ear and manikin techniques. Simpler methods have also been proposed in some national standards such as the use of general purpose artificial ears and simulators in conjunction with single number corrections to convert measurements to the equivalent diffuse field. However, little is known about the measurement agreement between these various methods and the acoustic manikin technique. Twelve experts positioned circum-aural, supra-aural and insert communication headsets on four different measurement setups (Type 1, Type 2, Type 3.3 artificial ears, and acoustic manikin). Fit-refit measurements of four audio communication signals were taken under quiet laboratory conditions. Data were transformed into equivalent diffuse-field sound levels using third-octave procedures. Results indicate that the Type 1 artificial ear is not suited for the measurement of sound exposure under communication headsets, while Type 2 and Type 3.3 artificial ears are in good agreement with the acoustic manikin technique. Single number corrections were found to introduce a large measurement uncertainty, making the use of the third-octave transformation preferable. PMID:26960783

Analyzing the photonic band gaps in two-dimensional plasma photonic crystals with fractal Sierpinski gasket structure based on the Monte Carlo method

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

Zhang, Hai-Feng, E-mail: hanlor@163.com; Key Laboratory of Radar Imaging and Microwave Photonics; Liu, Shao-Bin

2016-08-15

In this paper, the properties of photonic band gaps (PBGs) in two types of two-dimensional plasma-dielectric photonic crystals (2D PPCs) under a transverse-magnetic (TM) wave are theoretically investigated by a modified plane wave expansion (PWE) method where Monte Carlo method is introduced. The proposed PWE method can be used to calculate the band structures of 2D PPCs which possess arbitrary-shaped filler and any lattice. The efficiency and convergence of the present method are discussed by a numerical example. The configuration of 2D PPCs is the square lattices with fractal Sierpinski gasket structure whose constituents are homogeneous and isotropic. The type-1more » PPCs is filled with the dielectric cylinders in the plasma background, while its complementary structure is called type-2 PPCs, in which plasma cylinders behave as the fillers in the dielectric background. The calculated results reveal that the enough accuracy and good convergence can be obtained, if the number of random sampling points of Monte Carlo method is large enough. The band structures of two types of PPCs with different fractal orders of Sierpinski gasket structure also are theoretically computed for a comparison. It is demonstrate that the PBGs in higher frequency region are more easily produced in the type-1 PPCs rather than in the type-2 PPCs. Sierpinski gasket structure introduced in the 2D PPCs leads to a larger cutoff frequency, enhances and induces more PBGs in high frequency region. The effects of configurational parameters of two types of PPCs on the PBGs are also investigated in detail. The results show that the PBGs of the PPCs can be easily manipulated by tuning those parameters. The present type-1 PPCs are more suitable to design the tunable compacted devices.« less

Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method.

PubMed

Lager, Malin; Mernelius, Sara; Löfgren, Sture; Söderman, Jan

2016-01-01

Healthcare-associated infections caused by Escherichia coli and antibiotic resistance due to extended-spectrum beta-lactamase (ESBL) production constitute a threat against patient safety. To identify, track, and control outbreaks and to detect emerging virulent clones, typing tools of sufficient discriminatory power that generate reproducible and unambiguous data are needed. A probe based real-time PCR method targeting multiple single nucleotide polymorphisms (SNP) was developed. The method was based on the multi locus sequence typing scheme of Institute Pasteur and by adaptation of previously described typing assays. An 8 SNP-panel that reached a Simpson's diversity index of 0.95 was established, based on analysis of sporadic E. coli cases (ESBL n = 27 and non-ESBL n = 53). This multi-SNP assay was used to identify the sequence type 131 (ST131) complex according to the Achtman's multi locus sequence typing scheme. However, it did not fully discriminate within the complex but provided a diagnostic signature that outperformed a previously described detection assay. Pulsed-field gel electrophoresis typing of isolates from a presumed outbreak (n = 22) identified two outbreaks (ST127 and ST131) and three different non-outbreak-related isolates. Multi-SNP typing generated congruent data except for one non-outbreak-related ST131 isolate. We consider multi-SNP real-time PCR typing an accessible primary generic E. coli typing tool for rapid and uniform type identification.

Development of an irradiation method with lateral modulation of SOBP width using a cone-type filter for carbon ion beams.

PubMed

Ishizaki, Azusa; Ishii, Keizo; Kanematsu, Nobuyuki; Kanai, Tatsuaki; Yonai, Shunsuke; Kase, Yuki; Takei, Yuka; Komori, Masataka

2009-06-01

Passive irradiation methods deliver an extra dose to normal tissues upstream of the target tumor, while in dynamic irradiation methods, interplay effects between dynamic beam delivery and target motion induced by breathing or respiration distort the dose distributions. To solve the problems of those two irradiation methods, the authors have developed a new method that laterally modulates the spread-out Bragg peak (SOBP) width. By reducing scanning in the depth direction, they expect to reduce the interplay effects. They have examined this new irradiation method experimentally. In this system, they used a cone-type filter that consisted of 400 cones in a grid of 20 cones by 20 cones. There were five kinds of cones with different SOBP widths arranged on the frame two dimensionally to realize lateral SOBP modulation. To reduce the number of steps of cones, they used a wheel-type filter to make minipeaks. The scanning intensity was modulated for each SOBP width with a pair of scanning magnets. In this experiment, a stepwise dose distribution and spherical dose distribution of 60 mm in diameter were formed. The nonflatness of the stepwise dose distribution was 5.7% and that of the spherical dose distribution was 3.8%. A 2 mm misalignment of the cone-type filter resulted in a nonflatness of more than 5%. Lateral SOBP modulation with a cone-type filter and a scanned carbon ion beam successfully formed conformal dose distribution with nonflatness of 3.8% for the spherical case. The cone-type filter had to be set to within 1 mm accuracy to maintain nonflatness within 5%. This method will be useful to treat targets moving during breathing and targets in proximity to important organs.

Automatic Detection and Recognition of Craters Based on the Spectral Features of Lunar Rocks and Minerals

NASA Astrophysics Data System (ADS)

Ye, L.; Xu, X.; Luan, D.; Jiang, W.; Kang, Z.

2017-07-01

Crater-detection approaches can be divided into four categories: manual recognition, shape-profile fitting algorithms, machine-learning methods and geological information-based analysis using terrain and spectral data. The mainstream method is Shape-profile fitting algorithms. Many scholars throughout the world use the illumination gradient information to fit standard circles by least square method. Although this method has achieved good results, it is difficult to identify the craters with poor "visibility", complex structure and composition. Moreover, the accuracy of recognition is difficult to be improved due to the multiple solutions and noise interference. Aiming at the problem, we propose a method for the automatic extraction of impact craters based on spectral characteristics of the moon rocks and minerals: 1) Under the condition of sunlight, the impact craters are extracted from MI by condition matching and the positions as well as diameters of the craters are obtained. 2) Regolith is spilled while lunar is impacted and one of the elements of lunar regolith is iron. Therefore, incorrectly extracted impact craters can be removed by judging whether the crater contains "non iron" element. 3) Craters which are extracted correctly, are divided into two types: simple type and complex type according to their diameters. 4) Get the information of titanium and match the titanium distribution of the complex craters with normal distribution curve, then calculate the goodness of fit and set the threshold. The complex craters can be divided into two types: normal distribution curve type of titanium and non normal distribution curve type of titanium. We validated our proposed method with MI acquired by SELENE. Experimental results demonstrate that the proposed method has good performance in the test area.

Analysis of focusing error signals by differential astigmatic method under off-center tracking in the land-groove-type optical disk

NASA Astrophysics Data System (ADS)

Shinoda, Masahisa; Nakatani, Hidehiko

2015-04-01

We theoretically calculate the behavior of the focusing error signal in the land-groove-type optical disk when the objective lens traverses on out of the radius of the optical disk. The differential astigmatic method is employed instead of the conventional astigmatic method for generating the focusing error signals. The signal behaviors are compared and analyzed in terms of the gain difference of the slope sensitivity of the focusing error signals from the land and the groove. In our calculation, the format of digital versatile disc-random access memory (DVD-RAM) is adopted as the land-groove-type optical disk model, and advantageous conditions for suppressing the gain difference are investigated. The calculation method and results described in this paper will be reflected in the next generation land-groove-type optical disks.

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

PubMed Central

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution. PMID:28045981

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

PubMed

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael; Ambur, Ole Herman

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

The application of digital image analysis for blood typing: the comparison of anti-A and anti-B monoclonal antibodies activity with standard hemagglutinating sera

NASA Astrophysics Data System (ADS)

Medvedeva, Maria F.; Doubrovski, Valery A.

2017-03-01

The resolution of the acousto-optical method for blood typing was estimated experimentally by means of two types of reagents: monoclonal antibodies and standard hemagglutinating sera. The peculiarity of this work is the application of digital photo images processing by pixel analysis previously proposed by the authors. The influence of the concentrations of reagents, of blood sample, which is to be tested, as well as of the duration of the ultrasonic action on the biological object upon the resolution of acousto-optical method were investigated. The optimal experimental conditions to obtain maximum of the resolution of the acousto-optical method were found, it creates the prerequisites for a reliable blood typing. The present paper is a further step in the development of acousto-optical method for determining human blood groups.

A One-Step Immunostaining Method to Visualize Rodent Muscle Fiber Type within a Single Specimen

PubMed Central

Sawano, Shoko; Komiya, Yusuke; Ichitsubo, Riho; Ohkawa, Yasuyuki; Nakamura, Mako; Tatsumi, Ryuichi; Ikeuchi, Yoshihide; Mizunoya, Wataru

2016-01-01

In this study, we present a quadruple immunostaining method for rapid muscle fiber typing of mice and rats using antibodies specific to the adult myosin heavy chain (MyHC) isoforms MyHC1, 2A, 2X, and 2B, which are common marker proteins of distinct muscle fiber types. We developed rat monoclonal antibodies specific to each MyHC isoform and conjugated these four antibodies to fluorophores with distinct excitation and emission wavelengths. By mixing the four types of conjugated antibodies, MyHC1, 2A, 2X, and 2B could be distinguished within a single specimen allowing for facile delineation of skeletal muscle fiber types. Furthermore, we could observe hybrid fibers expressing MyHC2X and MyHC2B together in single longitudinal muscle sections from mice and rats, that was not attained in previous techniques. This staining method is expected to be applied to study muscle fiber type transition in response to environmental factors, and to ultimately develop techniques to regulate animal muscle fiber types. PMID:27814384

System and method employing a self-organizing map load feature database to identify electric load types of different electric loads

DOEpatents

Lu, Bin; Harley, Ronald G.; Du, Liang; Yang, Yi; Sharma, Santosh K.; Zambare, Prachi; Madane, Mayura A.

2014-06-17

A method identifies electric load types of a plurality of different electric loads. The method includes providing a self-organizing map load feature database of a plurality of different electric load types and a plurality of neurons, each of the load types corresponding to a number of the neurons; employing a weight vector for each of the neurons; sensing a voltage signal and a current signal for each of the loads; determining a load feature vector including at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the loads; and identifying by a processor one of the load types by relating the load feature vector to the neurons of the database by identifying the weight vector of one of the neurons corresponding to the one of the load types that is a minimal distance to the load feature vector.

Application of unweighted pair group methods with arithmetic average (UPGMA) for identification of kinship types and spreading of ebola virus through establishment of phylogenetic tree

NASA Astrophysics Data System (ADS)

Andriani, Tri; Irawan, Mohammad Isa

2017-08-01

Ebola Virus Disease (EVD) is a disease caused by a virus of the genus Ebolavirus (EBOV), family Filoviridae. Ebola virus is classifed into five types, namely Zaire ebolavirus (ZEBOV), Sudan ebolavirus (SEBOV), Bundibugyo ebolavirus (BEBOV), Tai Forest ebolavirus also known as Cote d'Ivoire ebolavirus (CIEBOV), and Reston ebolavirus (REBOV). Identification of kinship types of Ebola virus can be performed using phylogenetic trees. In this study, the phylogenetic tree constructed by UPGMA method in which there are Multiple Alignment using Progressive Method. The results concluded that the phylogenetic tree formation kinship ebola virus types that kind of Tai Forest ebolavirus close to Bundibugyo ebolavirus but the layout state ebola epidemic spread far apart. The genetic distance for this type of Bundibugyo ebolavirus with Tai Forest ebolavirus is 0.3725. Type Tai Forest ebolavirus similar to Bundibugyo ebolavirus not inuenced by the proximity of the area ebola epidemic spread.

Bovine Papillomavirus in Brazil: Detection of Coinfection of Unusual Types by a PCR-RFLP Method

PubMed Central

Carvalho, R. F.; Sakata, S. T.; Giovanni, D. N. S.; Mori, E.; Brandão, P. E.; Richtzenhain, L. J.; Pozzi, C. R.; Arcaro, J. R. P.; Miranda, M. S.; Mazzuchelli-de-Souza, J.; Melo, T. C.; Comenale, G.; Assaf, S. L. M. R.; Beçak, W.; Stocco, R. C.

2013-01-01

Bovine papillomavirus (BPV) is recognized as a causal agent of benign and malignant tumors in cattle. Thirteen types of BPV are currently characterized and classified into three distinct genera, associated with different pathological outcomes. The described BPV types as well as other putative ones have been demonstrated by molecular biology methods, mainly by the employment of degenerated PCR primers. Specifically, divergences in the nucleotide sequence of the L1 gene are useful for the identification and classification of new papillomavirus types. On the present work, a method based on the PCR-RFLP technique and DNA sequencing was evaluated as a screening tool, allowing for the detection of two relatively rare types of BPV in lesions samples from a six-year-old Holstein dairy cow, chronically affected with cutaneous papillomatosis. These findings point to the dissemination of BPVs with unclear pathogenic potential, since two relatively rare, new described BPV types, which were first characterized in Japan, were also detected in Brazil. PMID:23865043

Molecular typing of Vibrio parahaemolyticus isolated from seafood harvested along the south-west coast of India.

PubMed

Bhowmick, P P; Khushiramani, R; Raghunath, P; Karunasagar, I; Karunasagar, I

2008-02-01

Evaluation of protein profiling for typing Vibrio parahaemolyticus using 71 strains isolated from different seafood and comparison with other molecular typing techniques such as random amplified polymorphic DNA analysis (RAPD) and enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR. Three molecular typing methods were used for the typing of 71 V. parahaemolyticus isolates from seafood. RAPD had a discriminatory index (DI) of 0.95, while ERIC-PCR showed a DI of 0.94. Though protein profiling had less discriminatory power, use of this method can be helpful in identifying new proteins which might have a role in establishment in the host or virulence of the organism. The use of protein profiling in combination with other established typing methods such as RAPD and ERIC-PCR generates useful information in the case of V. parahaemolyticus associated with seafood. The study demonstrates the usefulness of nucleic acid and protein-based studies in understanding the relationship between various isolates from seafood.

Method for identifying type I diabetes mellitus in humans

DOEpatents

Metz, Thomas O [Kennewick, WA; Qian, Weijun [Richland, WA; Jacobs, Jon M [Pasco, WA; Smith, Richard D [Richland, WA

2011-04-12

A method and system for classifying subject populations utilizing predictive and diagnostic biomarkers for type I diabetes mellitus. The method including determining the levels of a variety of markers within the serum or plasma of a target organism and correlating this level to general populations as a screen for predisposition or progressive monitoring of disease presence or predisposition.

Minimally invasive procedures in severe acute pancreatitis treatment – assessment of benefits and possibilities of use

PubMed Central

Jackowski, Marek

2014-01-01

Introduction Acute pancreatitis (AP) consists of an extremely varied complex of pathological symptoms and clinical conditions, ranging from mild gastric complaints to multi-organ failure resulting in death. Aim To present the authors’ own experience regarding surgical treatment for pancreatic necrosis complicated by infection using different methods, including classic and laparoscopic methods as well as those combined with percutaneous techniques. Material and methods In the period 2007–2010, 34 patients with the diagnosis of severe AP were treated at the Department of General, Gastroenterological and Oncological Surgery, Collegium Medicum, Nicolaus Copernicus University. In 7 patients classic necrosectomy with repeated peritoneal flushing was performed (type 1), in 5 patients laparotomy with active drainage (type 2), in 12 video-assisted retroperitoneal debridement (type 3), and in 10 only percutaneous drainage methods (type 4). Results Total duration of hospitalisation was from 10 to 192 days. The highest death rate was observed for type 1 procedures. Significant differences with regard to the absolute number of postoperative complications between different groups were not observed; however, their quality varied. Classic methods were used in patients whose general and local condition was more severe. Conclusions When AP and its complications are diagnosed, a suitable method of surgical treatment has to be selected extremely precisely and in an individualised way. Minimally invasive methods used in selected patients provide better outcomes and higher safety superseding classic, open techniques of surgical treatment. PMID:25097683

Comparability among four invertebrate sampling methods, Fountain Creek Basin, Colorado, 2010-2012

USGS Publications Warehouse

Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.; Brown, Krystal D.

2014-01-01

The U.S. Geological Survey, in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, designed a study to determine if sampling method and sample timing resulted in comparable samples and assessments of biological condition. To accomplish this task, annual invertebrate samples were collected concurrently using four sampling methods at 15 U.S. Geological Survey streamflow gages in the Fountain Creek basin from 2010 to 2012. Collectively, the four methods are used by local (U.S. Geological Survey cooperative monitoring program) and State monitoring programs (Colorado Department of Public Health and Environment) in the Fountain Creek basin to produce two distinct sample types for each program that target single-and multiple-habitats. This study found distinguishable differences between single-and multi-habitat sample types using both community similarities and multi-metric index values, while methods from each program within sample type were comparable. This indicates that the Colorado Department of Public Health and Environment methods were compatible with the cooperative monitoring program methods within multi-and single-habitat sample types. Comparisons between September and October samples found distinguishable differences based on community similarities for both sample types, whereas only differences were found for single-habitat samples when multi-metric index values were considered. At one site, differences between September and October index values from single-habitat samples resulted in opposing assessments of biological condition. Direct application of the results to inform the revision of the existing Fountain Creek basin U.S. Geological Survey cooperative monitoring program are discussed.

Automatic classification of bottles in crates

NASA Astrophysics Data System (ADS)

Aas, Kjersti; Eikvil, Line; Bremnes, Dag; Norbryhn, Andreas

1995-03-01

This paper presents a statistical method for classification of bottles in crates for use in automatic return bottle machines. For the automatons to reimburse the correct deposit, a reliable recognition is important. The images are acquired by a laser range scanner coregistering the distance to the object and the strength of the reflected signal. The objective is to identify the crate and the bottles from a library with a number of legal types. The bottles with significantly different size are separated using quite simple methods, while a more sophisticated recognizer is required to distinguish the more similar bottle types. Good results have been obtained when testing the method developed on bottle types which are difficult to distinguish using simple methods.

Charting improvements in US registry HLA typing ambiguity using a typing resolution score.

PubMed

Paunić, Vanja; Gragert, Loren; Schneider, Joel; Müller, Carlheinz; Maiers, Martin

2016-07-01

Unrelated stem cell registries have been collecting HLA typing of volunteer bone marrow donors for over 25years. Donor selection for hematopoietic stem cell transplantation is based primarily on matching the alleles of donors and patients at five polymorphic HLA loci. As HLA typing technologies have continually advanced since the beginnings of stem cell transplantation, registries have accrued typings of varied HLA typing ambiguity. We present a new typing resolution score (TRS), based on the likelihood of self-match, that allows the systematic comparison of HLA typings across different methods, data sets and populations. We apply the TRS to chart improvement in HLA typing within the Be The Match Registry of the United States from the initiation of DNA-based HLA typing to the current state of high-resolution typing using next-generation sequencing technologies. In addition, we present a publicly available online tool for evaluation of any given HLA typing. This TRS objectively evaluates HLA typing methods and can help define standards for acceptable recruitment HLA typing. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Evaluation of two sets of immunohistochemical and Western blot confirmatory methods in the detection of typical and atypical BSE cases

USDA-ARS?s Scientific Manuscript database

Aims: To compare the ability of the Italian and the U.S. bovine spongiform encephalopathy (BSE) confirmatory protocols in the detection of classical (C-) and atypical - low (L-) and high (H-) type- BSE forms. Methods and Results: Obex samples from U.S. and Italian C-type BSE cases, a U.S. H-type and...

[Detection of constitutional types of EEG using the orthogonal decomposition method].

PubMed

Kuznetsova, S M; Kudritskaia, O V

1987-01-01

The authors present an algorithm of investigation into the processes of brain bioelectrical activity with the help of an orthogonal decomposition device intended for the identification of constitutional types of EEGs. The method has helped to effectively solve the task of the diagnosis of constitutional types of EEGs, which are determined by a variable degree of hereditary predisposition for longevity or cerebral stroke.

Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system.

PubMed

Kiro, Ruth; Shitrit, Dror; Qimron, Udi

2014-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.

On conjugate gradient type methods and polynomial preconditioners for a class of complex non-Hermitian matrices

NASA Technical Reports Server (NTRS)

Freund, Roland

1988-01-01

Conjugate gradient type methods are considered for the solution of large linear systems Ax = b with complex coefficient matrices of the type A = T + i(sigma)I where T is Hermitian and sigma, a real scalar. Three different conjugate gradient type approaches with iterates defined by a minimal residual property, a Galerkin type condition, and an Euclidian error minimization, respectively, are investigated. In particular, numerically stable implementations based on the ideas behind Paige and Saunder's SYMMLQ and MINRES for real symmetric matrices are proposed. Error bounds for all three methods are derived. It is shown how the special shift structure of A can be preserved by using polynomial preconditioning. Results on the optimal choice of the polynomial preconditioner are given. Also, some numerical experiments for matrices arising from finite difference approximations to the complex Helmholtz equation are reported.

Preliminary study of urine metabolism in type two diabetic patients based on GC-MS

PubMed Central

Zhang, Ning; Geng, Fang; Hu, Zhong-Hua; Liu, Bin; Wang, Ye-Qiu; Liu, Jun-Cen; Qi, Yong-Hua; Li, Li-Jing

2016-01-01

Objective: Comparative study of type 2 diabetes and healthy controls by metabolomics methods to explore the pathogenesis of Type II diabetes. Methods: Gas chromatography - mass spectrometry (GC-MS) with a variety of multivariate statistical analysis methods to the healthy control group 58 cases, 68 cases of Type II diabetes group were analyzed. Chromatographic conditions: DB-5MS column; the carrier gas He; flow rate of 1 mL·min-1, the injection volume 1 uL; split ratio is 100: 1. MS conditions: electron impact (EI) ion source, an auxiliary temperature of 280°C, the ion source 230°C, quadrupole 150°C; mass scan range 30~600 mAu. Results: Established analytical method based on urine metabolomics GC-MS of Type II diabetes, determine the urine succinic acid, L-leucine, L-isoleucine, tyrosine, slanine, acetoace acid, mannose, L-isoleucine, L-threonine, Phenylalanine, fructose, D-glucose, palmi acid, oleic acid and arachidonic acid were significantly were significantly changed. Conclusion: Based on metabolomics of GC-MS detection and analysis metabolites can be found differences between type 2 diabetes and healthy control group, PCA diagram can effectively distinguish Type II diabetes and healthy control group, with load diagrams and PLS-DA VIP value metabolite screening, the resulting differences in metabolic pathways involved metabolites, including amino acid metabolism, lipid metabolism, glucose metabolism and energy metabolism. PMID:27508010

What influences the choice of assessment methods in health technology assessments? Statistical analysis of international health technology assessments from 1989 to 2002.

PubMed

Draborg, Eva; Andersen, Christian Kronborg

2006-01-01

Health technology assessment (HTA) has been used as input in decision making worldwide for more than 25 years. However, no uniform definition of HTA or agreement on assessment methods exists, leaving open the question of what influences the choice of assessment methods in HTAs. The objective of this study is to analyze statistically a possible relationship between methods of assessment used in practical HTAs, type of assessed technology, type of assessors, and year of publication. A sample of 433 HTAs published by eleven leading institutions or agencies in nine countries was reviewed and analyzed by multiple logistic regression. The study shows that outsourcing of HTA reports to external partners is associated with a higher likelihood of using assessment methods, such as meta-analysis, surveys, economic evaluations, and randomized controlled trials; and with a lower likelihood of using assessment methods, such as literature reviews and "other methods". The year of publication was statistically related to the inclusion of economic evaluations and shows a decreasing likelihood during the year span. The type of assessed technology was related to economic evaluations with a decreasing likelihood, to surveys, and to "other methods" with a decreasing likelihood when pharmaceuticals were the assessed type of technology. During the period from 1989 to 2002, no major developments in assessment methods used in practical HTAs were shown statistically in a sample of 433 HTAs worldwide. Outsourcing to external assessors has a statistically significant influence on choice of assessment methods.

spa typing for epidemiological surveillance of Staphylococcus aureus.

PubMed

Hallin, Marie; Friedrich, Alexander W; Struelens, Marc J

2009-01-01

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

Automatic identification of bacterial types using statistical imaging methods

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Greenspan, Hayit; Tepper, Gapi; Abboud, Shimon

2003-05-01

The objective of the current study is to develop an automatic tool to identify bacterial types using computer-vision and statistical modeling techniques. Bacteriophage (phage)-typing methods are used to identify and extract representative profiles of bacterial types, such as the Staphylococcus Aureus. Current systems rely on the subjective reading of plaque profiles by human expert. This process is time-consuming and prone to errors, especially as technology is enabling the increase in the number of phages used for typing. The statistical methodology presented in this work, provides for an automated, objective and robust analysis of visual data, along with the ability to cope with increasing data volumes.

Dual Contraceptive Method Use Among Youth in Alternative Schools.

PubMed

Coyle, Karin K; Peterson, Amy J; Franks, Heather M; Anderson, Pamela M; Glassman, Jill R

2016-12-01

Dual contraceptive method use, or using a highly effective contraceptive method plus a barrier method like condoms, is gaining attention as a strategy for preventing unplanned pregnancy and sexually transmitted diseases. We investigated rates of dual method use among a sample of youth in urban alternative schools, and explored the relationship between dual method use and sexual partner type. The study analyzed data from 765 students enrolled in 11 district-run continuation high schools in northern California. We explored the association between dual method use and sexual partner type (steady only, a mix of steady and non-steady, and non-steady only) using logistic regression. Differences in dual rates by partner type were statistically significant, with higher rates of dual methods use reported among young people reporting non-steady sexual partners only, as compared to those with steady partners only. The data illustrate that young people in alternative school settings could gain from further intervention on the benefits, skills, and challenges of using two methods of contraception as opposed to one with both steady and non-steady sexual partners.

New Eudesmane-Type Sesquiterpenoids from the Mangrove-Derived Endophytic Fungus Penicillium sp. J-54.

PubMed

Qiu, Liuming; Wang, Pei; Liao, Ge; Zeng, Yanbo; Cai, Caihong; Kong, Fandong; Guo, Zhikai; Proksch, Peter; Dai, Haofu; Mei, Wenli

2018-03-28

Four new eudesmane-type sesquiterpenoids, penicieudesmol A-D ( 1 - 4 ), were isolated from the fermentation broth of the mangrove-derived endophytic fungus Penicillium sp. J-54. Their structures were determined by spectroscopic methods, the in situ dimolybdenum CD method, and modified Mosher's method. The bioassays results showed that 2 exhibited weak cytotoxicity against K-562 cells.

77 FR 35573 - World Trade Center Health Program; Addition of Certain Types of Cancer to the List of WTC-Related...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-13

... following methods: Federal eRulemaking Portal: http://www.regulations.gov . Follow the instructions for.... Methods Used by the Administrator to Determine Whether to Add Cancer or Types of Cancer to the List of WTC... cancers The Administrator developed a hierarchy of methods (detailed in section III.D of this preamble...

Graphical Methods: A Review of Current Methods and Computer Hardware and Software. Technical Report No. 27.

ERIC Educational Resources Information Center

Bessey, Barbara L.; And Others

Graphical methods for displaying data, as well as available computer software and hardware, are reviewed. The authors have emphasized the types of graphs which are most relevant to the needs of the National Center for Education Statistics (NCES) and its readers. The following types of graphs are described: tabulations, stem-and-leaf displays,…

Identification of rat serum alkaline phosphatase isoenzyme by means of wheat germ agglutinin.

PubMed

Wada, H; Niwa, N; Hayakawa, T; Tsuge, H

1997-01-01

Wheat germ agglutinin (WGA) precipitates bone type serum alkaline phosphatase (sALP) isoenzyme specifically. The precipitates are composed of the macromolecules of WGA and "bone type sALP" (WGA-ALP complex). In order to use bone type sALP as a marker in polyacrylamide gel electrophoresis (PAGE), a method to separate "bone type sALP" from the "WGA-ALP complex" was established by using N-acetyl-D-glucosamine (GlcNAc)-Sepharose 6E column chromatography. It was concluded that this method is useful for clinical examination in the rat.

Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods.

PubMed

Rodriguez, C; Van Broeck, J; Taminiau, B; Delmée, M; Daube, G

2016-08-01

Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined. Copyright © 2016 Elsevier Ltd. All rights reserved.

HLA Type Inference via Haplotypes Identical by Descent

NASA Astrophysics Data System (ADS)

Setty, Manu N.; Gusev, Alexander; Pe'Er, Itsik

The Human Leukocyte Antigen (HLA) genes play a major role in adaptive immune response and are used to differentiate self antigens from non self ones. HLA genes are hyper variable with nearly every locus harboring over a dozen alleles. This variation plays an important role in susceptibility to multiple autoimmune diseases and needs to be matched on for organ transplantation. Unfortunately, HLA typing by serological methods is time consuming and expensive compared to high throughput Single Nucleotide Polymorphism (SNP) data. We present a new computational method to infer per-locus HLA types using shared segments Identical By Descent (IBD), inferred from SNP genotype data. IBD information is modeled as graph where shared haplotypes are explored among clusters of individuals with known and unknown HLA types to identify the latter. We analyze performance of the method in a previously typed subset of the HapMap population, achieving accuracy of 96% in HLA-A, 94% in HLA-B, 95% in HLA-C, 77% in HLA-DR1, 93% in HLA-DQA1 and 90% in HLA-DQB1 genes. We compare our method to a tag SNP based approach and demonstrate higher sensitivity and specificity. Our method demonstrates the power of using shared haplotype segments for large-scale imputation at the HLA locus.

The impact of loss to follow-up on hypothesis tests of the treatment effect for several statistical methods in substance abuse clinical trials.

PubMed

Hedden, Sarra L; Woolson, Robert F; Carter, Rickey E; Palesch, Yuko; Upadhyaya, Himanshu P; Malcolm, Robert J

2009-07-01

"Loss to follow-up" can be substantial in substance abuse clinical trials. When extensive losses to follow-up occur, one must cautiously analyze and interpret the findings of a research study. Aims of this project were to introduce the types of missing data mechanisms and describe several methods for analyzing data with loss to follow-up. Furthermore, a simulation study compared Type I error and power of several methods when missing data amount and mechanism varies. Methods compared were the following: Last observation carried forward (LOCF), multiple imputation (MI), modified stratified summary statistics (SSS), and mixed effects models. Results demonstrated nominal Type I error for all methods; power was high for all methods except LOCF. Mixed effect model, modified SSS, and MI are generally recommended for use; however, many methods require that the data are missing at random or missing completely at random (i.e., "ignorable"). If the missing data are presumed to be nonignorable, a sensitivity analysis is recommended.

Molecular Typing and Epidemiology of Human Listeriosis Cases, Denmark, 2002-2012.

PubMed

Jensen, Anne Kvistholm; Björkman, Jonas T; Ethelberg, Steen; Kiil, Kristoffer; Kemp, Michael; Nielsen, Eva Møller

2016-04-01

Denmark has a high incidence of invasive listeriosis (0.9 cases/100,000 population in 2012). We analyzed patient data, clinical outcome, and trends in pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) of Listeria monocytogenes strains isolated in Denmark during 2002-2012. We performed 2-enzyme PFGE and serotyping on 559 isolates and MLST on 92 isolates and identified some correlation between molecular type and clinical outcome and patient characteristics. We found 178 different PFGE types, but isolates from 122 cases belonged to just 2 closely related PFGE types, clonal complex 8 and sequence type 8. These 2 types were the main cause of a peak in incidence of invasive listeriosis during 2005-2009, possibly representing an outbreak or the presence of a highly prevalent clone. However, current typing methods could not fully confirm these possibilities, highlighting the need for more refined discriminatory typing methods to identify outbreaks within frequently occurring L. monocytogenes PFGE types.

Molecular Typing and Epidemiology of Human Listeriosis Cases, Denmark, 2002–20121

PubMed Central

Björkman, Jonas T.; Ethelberg, Steen; Kiil, Kristoffer; Kemp, Michael; Nielsen, Eva Møller

2016-01-01

Denmark has a high incidence of invasive listeriosis (0.9 cases/100,000 population in 2012). We analyzed patient data, clinical outcome, and trends in pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) of Listeria monocytogenes strains isolated in Denmark during 2002–2012. We performed 2-enzyme PFGE and serotyping on 559 isolates and MLST on 92 isolates and identified some correlation between molecular type and clinical outcome and patient characteristics. We found 178 different PFGE types, but isolates from 122 cases belonged to just 2 closely related PFGE types, clonal complex 8 and sequence type 8. These 2 types were the main cause of a peak in incidence of invasive listeriosis during 2005–2009, possibly representing an outbreak or the presence of a highly prevalent clone. However, current typing methods could not fully confirm these possibilities, highlighting the need for more refined discriminatory typing methods to identify outbreaks within frequently occurring L. monocytogenes PFGE types. PMID:26982714

Blind identification of image manipulation type using mixed statistical moments

NASA Astrophysics Data System (ADS)

Jeong, Bo Gyu; Moon, Yong Ho; Eom, Il Kyu

2015-01-01

We present a blind identification of image manipulation types such as blurring, scaling, sharpening, and histogram equalization. Motivated by the fact that image manipulations can change the frequency characteristics of an image, we introduce three types of feature vectors composed of statistical moments. The proposed statistical moments are generated from separated wavelet histograms, the characteristic functions of the wavelet variance, and the characteristic functions of the spatial image. Our method can solve the n-class classification problem. Through experimental simulations, we demonstrate that our proposed method can achieve high performance in manipulation type detection. The average rate of the correctly identified manipulation types is as high as 99.22%, using 10,800 test images and six manipulation types including the authentic image.

An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing.

PubMed

Quintelas, Cristina; Ferreira, Eugénio C; Lopes, João A; Sousa, Clara

2018-01-01

The sustained emergence of new declared bacterial species makes typing a continuous challenge for microbiologists. Molecular biology techniques have a very significant role in the context of bacterial typing, but they are often very laborious, time consuming, and eventually fail when dealing with very closely related species. Spectroscopic-based techniques appear in some situations as a viable alternative to molecular methods with advantages in terms of analysis time and cost. Infrared and mass spectrometry are among the most exploited techniques in this context: particularly, infrared spectroscopy emerged as a very promising method with multiple reported successful applications. This article presents a systematic review on infrared spectroscopy applications for bacterial typing, highlighting fundamental aspects of infrared spectroscopy, a detailed literature review (covering different taxonomic levels and bacterial species), advantages, and limitations of the technique over molecular biology methods and a comparison with other competing spectroscopic techniques such as MALDI-TOF MS, Raman, and intrinsic fluorescence. Infrared spectroscopy possesses a high potential for bacterial typing at distinct taxonomic levels and worthy of further developments and systematization. The development of databases appears fundamental toward the establishment of infrared spectroscopy as a viable method for bacterial typing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New method to incorporate Type B uncertainty into least-squares procedures in radionuclide metrology.

PubMed

Han, Jubong; Lee, K B; Lee, Jong-Man; Park, Tae Soon; Oh, J S; Oh, Pil-Jei

2016-03-01

We discuss a new method to incorporate Type B uncertainty into least-squares procedures. The new method is based on an extension of the likelihood function from which a conventional least-squares function is derived. The extended likelihood function is the product of the original likelihood function with additional PDFs (Probability Density Functions) that characterize the Type B uncertainties. The PDFs are considered to describe one's incomplete knowledge on correction factors being called nuisance parameters. We use the extended likelihood function to make point and interval estimations of parameters in the basically same way as the least-squares function used in the conventional least-squares method is derived. Since the nuisance parameters are not of interest and should be prevented from appearing in the final result, we eliminate such nuisance parameters by using the profile likelihood. As an example, we present a case study for a linear regression analysis with a common component of Type B uncertainty. In this example we compare the analysis results obtained from using our procedure with those from conventional methods. Copyright © 2015. Published by Elsevier Ltd.

Comparability among four invertebrate sampling methods and two multimetric indexes, Fountain Creek Basin, Colorado, 2010–2012

USGS Publications Warehouse

Bruce, James F.; Roberts, James J.; Zuellig, Robert E.

2018-05-24

The U.S. Geological Survey (USGS), in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, analyzed previously collected invertebrate data to determine the comparability among four sampling methods and two versions (2010 and 2017) of the Colorado Benthic Macroinvertebrate Multimetric Index (MMI). For this study, annual macroinvertebrate samples were collected concurrently (in space and time) at 15 USGS surface-water gaging stations in the Fountain Creek Basin from 2010 to 2012 using four sampling methods. The USGS monitoring project in the basin uses two of the methods and the Colorado Department of Public Health and Environment recommends the other two. These methods belong to two distinct sample types, one that targets single habitats and one that targets multiple habitats. The study results indicate that there are significant differences in MMI values obtained from the single-habitat and multihabitat sample types but methods from each program within each sample type produced comparable values. This study also determined that MMI values calculated by different versions of the Colorado Benthic Macroinvertebrate MMI are indistinguishable. This indicates that the Colorado Department of Public Health and Environment methods are comparable with the USGS monitoring project methods for single-habitat and multihabitat sample types. This report discusses the direct application of the study results to inform the revision of the existing USGS monitoring project in the Fountain Creek Basin.

[Comparison of MPure-12 Automatic Nucleic Acid Purification and Chelex-100 Method].

PubMed

Shen, X; Li, M; Wang, Y L; Chen, Y L; Lin, Y; Zhao, Z M; Que, T Z

2017-04-01

To explore the forensic application value of MPure-12 automatic nucleic acid purification （MPure-12 Method） for DNA extraction by extracting and typing DNA from bloodstains and various kinds of biological samples with different DNA contents. Nine types of biological samples, such as bloodstains, semen stains, and saliva were collected. DNA were extracted using MPure-12 method and Chelex-100 method, followed by PCR amplification and electrophoresis for obtaining STR-profiles. The samples such as hair root, chutty, butt, muscular tissue, saliva stain, bloodstain and semen stain were typed successfully by MPure-12 method. Partial alleles were lacked in the samples of saliva, and the genotyping of contact swabs was unsatisfactory. Additional, all of the bloodstains （20 μL, 15 μL, 10 μL, 5 μL, 1 μL） showed good typing results using Chelex-100 method. But the loss of alleles occurred in 1 μL blood volume by MPure-12 method. MPure-12 method is suitable for DNA extraction of a certain concentration blood samples．Chelex-100 method may be better for the extraction of trace blood samples．This instrument used in nucleic acid extraction has the advantages of simplicity of operator, rapidity, high extraction efficiency, high rate of reportable STR-profiles and lower man-made pollution. Copyright© by the Editorial Department of Journal of Forensic Medicine

P-type gallium nitride

DOEpatents

Rubin, M.; Newman, N.; Fu, T.; Ross, J.; Chan, J.

1997-08-12

Several methods have been found to make p-type gallium nitride. P-type gallium nitride has long been sought for electronic devices. N-type gallium nitride is readily available. Discovery of p-type gallium nitride and the methods for making it will enable its use in ultraviolet and blue light-emitting diodes and lasers. pGaN will further enable blue photocathode elements to be made. Molecular beam epitaxy on substrates held at the proper temperatures, assisted by a nitrogen beam of the proper energy produced several types of p-type GaN with hole concentrations of about 5{times}10{sup 11} /cm{sup 3} and hole mobilities of about 500 cm{sup 2} /V-sec, measured at 250 K. P-type GaN can be formed of unintentionally-doped material or can be doped with magnesium by diffusion, ion implantation, or co-evaporation. When applicable, the nitrogen can be substituted with other group III elements such as Al. 9 figs.

P-type gallium nitride

DOEpatents

Rubin, Michael; Newman, Nathan; Fu, Tracy; Ross, Jennifer; Chan, James

1997-01-01

Several methods have been found to make p-type gallium nitride. P-type gallium nitride has long been sought for electronic devices. N-type gallium nitride is readily available. Discovery of p-type gallium nitride and the methods for making it will enable its use in ultraviolet and blue light-emitting diodes and lasers. pGaN will further enable blue photocathode elements to be made. Molecular beam epitaxy on substrates held at the proper temperatures, assisted by a nitrogen beam of the proper energy produced several types of p-type GaN with hole concentrations of about 5.times.10.sup.11 /cm.sup.3 and hole mobilities of about 500 cm.sup.2 /V-sec, measured at 250.degree. K. P-type GaN can be formed of unintentionally-doped material or can be doped with magnesium by diffusion, ion implantation, or co-evaporation. When applicable, the nitrogen can be substituted with other group III elements such as Al.

Development of an ELA-DRA gene typing method based on pyrosequencing technology.

PubMed

Díaz, S; Echeverría, M G; It, V; Posik, D M; Rogberg-Muñoz, A; Pena, N L; Peral-García, P; Vega-Pla, J L; Giovambattista, G

2008-11-01

The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throughput genotyping of major histocompatibility complex genes in horses and other animal species, making this system interesting as a rapid screening method for animal genotyping of immune-related genes.

A new serotyping method for Klebsiella species: evaluation of the technique.

PubMed Central

Riser, E; Noone, P; Bonnet, M L

1976-01-01

A new indirect fluorescent typing method for Klebsiella species is compared with an established method, capsular swelling. The fluorescent antibody (FA) technique was tested with standards and unknowns, and the results were checked by capsular swelling. Several unknowns were sent away for confirmation of typing, by capsular swelling. The FA method was also tried by a technician in the routine department for blind identification of standards. Fluorescence typing gives close correlation with the established capsular swelling technique but has greater sensitivity; allows more econimical use of expensive antisera; possesses greater objectivity as it requires less operator skill in the reading of results; resolves most of the cross reactions observed with capsular swelling; and has a higher per cent success rate in identification. PMID:777043

Optimization of complex slater-type functions with analytic derivative methods for describing photoionization differential cross sections.

PubMed

Matsuzaki, Rei; Yabushita, Satoshi

2017-05-05

The complex basis function (CBF) method applied to various atomic and molecular photoionization problems can be interpreted as an L2 method to solve the driven-type (inhomogeneous) Schrödinger equation, whose driven term being dipole operator times the initial state wave function. However, efficient basis functions for representing the solution have not fully been studied. Moreover, the relation between their solution and that of the ordinary Schrödinger equation has been unclear. For these reasons, most previous applications have been limited to total cross sections. To examine the applicability of the CBF method to differential cross sections and asymmetry parameters, we show that the complex valued solution to the driven-type Schrödinger equation can be variationally obtained by optimizing the complex trial functions for the frequency dependent polarizability. In the test calculations made for the hydrogen photoionization problem with five or six complex Slater-type orbitals (cSTOs), their complex valued expansion coefficients and the orbital exponents have been optimized with the analytic derivative method. Both the real and imaginary parts of the solution have been obtained accurately in a wide region covering typical molecular regions. Their phase shifts and asymmetry parameters are successfully obtained by extrapolating the CBF solution from the inner matching region to the asymptotic region using WKB method. The distribution of the optimized orbital exponents in the complex plane is explained based on the close connection between the CBF method and the driven-type equation method. The obtained information is essential to constructing the appropriate basis sets in future molecular applications. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Automated classification of dolphin echolocation click types from the Gulf of Mexico.

PubMed

Frasier, Kaitlin E; Roch, Marie A; Soldevilla, Melissa S; Wiggins, Sean M; Garrison, Lance P; Hildebrand, John A

2017-12-01

Delphinids produce large numbers of short duration, broadband echolocation clicks which may be useful for species classification in passive acoustic monitoring efforts. A challenge in echolocation click classification is to overcome the many sources of variability to recognize underlying patterns across many detections. An automated unsupervised network-based classification method was developed to simulate the approach a human analyst uses when categorizing click types: Clusters of similar clicks were identified by incorporating multiple click characteristics (spectral shape and inter-click interval distributions) to distinguish within-type from between-type variation, and identify distinct, persistent click types. Once click types were established, an algorithm for classifying novel detections using existing clusters was tested. The automated classification method was applied to a dataset of 52 million clicks detected across five monitoring sites over two years in the Gulf of Mexico (GOM). Seven distinct click types were identified, one of which is known to be associated with an acoustically identifiable delphinid (Risso's dolphin) and six of which are not yet identified. All types occurred at multiple monitoring locations, but the relative occurrence of types varied, particularly between continental shelf and slope locations. Automatically-identified click types from autonomous seafloor recorders without verifiable species identification were compared with clicks detected on sea-surface towed hydrophone arrays in the presence of visually identified delphinid species. These comparisons suggest potential species identities for the animals producing some echolocation click types. The network-based classification method presented here is effective for rapid, unsupervised delphinid click classification across large datasets in which the click types may not be known a priori.

Automated classification of dolphin echolocation click types from the Gulf of Mexico

PubMed Central

Roch, Marie A.; Soldevilla, Melissa S.; Wiggins, Sean M.; Garrison, Lance P.; Hildebrand, John A.

2017-01-01

Delphinids produce large numbers of short duration, broadband echolocation clicks which may be useful for species classification in passive acoustic monitoring efforts. A challenge in echolocation click classification is to overcome the many sources of variability to recognize underlying patterns across many detections. An automated unsupervised network-based classification method was developed to simulate the approach a human analyst uses when categorizing click types: Clusters of similar clicks were identified by incorporating multiple click characteristics (spectral shape and inter-click interval distributions) to distinguish within-type from between-type variation, and identify distinct, persistent click types. Once click types were established, an algorithm for classifying novel detections using existing clusters was tested. The automated classification method was applied to a dataset of 52 million clicks detected across five monitoring sites over two years in the Gulf of Mexico (GOM). Seven distinct click types were identified, one of which is known to be associated with an acoustically identifiable delphinid (Risso’s dolphin) and six of which are not yet identified. All types occurred at multiple monitoring locations, but the relative occurrence of types varied, particularly between continental shelf and slope locations. Automatically-identified click types from autonomous seafloor recorders without verifiable species identification were compared with clicks detected on sea-surface towed hydrophone arrays in the presence of visually identified delphinid species. These comparisons suggest potential species identities for the animals producing some echolocation click types. The network-based classification method presented here is effective for rapid, unsupervised delphinid click classification across large datasets in which the click types may not be known a priori. PMID:29216184

Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types.

PubMed

Cornish, Alex J; Filippis, Ioannis; David, Alessia; Sternberg, Michael J E

2015-09-01

Each cell type found within the human body performs a diverse and unique set of functions, the disruption of which can lead to disease. However, there currently exists no systematic mapping between cell types and the diseases they can cause. In this study, we integrate protein-protein interaction data with high-quality cell-type-specific gene expression data from the FANTOM5 project to build the largest collection of cell-type-specific interactomes created to date. We develop a novel method, called gene set compactness (GSC), that contrasts the relative positions of disease-associated genes across 73 cell-type-specific interactomes to map genes associated with 196 diseases to the cell types they affect. We conduct text-mining of the PubMed database to produce an independent resource of disease-associated cell types, which we use to validate our method. The GSC method successfully identifies known disease-cell-type associations, as well as highlighting associations that warrant further study. This includes mast cells and multiple sclerosis, a cell population currently being targeted in a multiple sclerosis phase 2 clinical trial. Furthermore, we build a cell-type-based diseasome using the cell types identified as manifesting each disease, offering insight into diseases linked through etiology. The data set produced in this study represents the first large-scale mapping of diseases to the cell types in which they are manifested and will therefore be useful in the study of disease systems. Overall, we demonstrate that our approach links disease-associated genes to the phenotypes they produce, a key goal within systems medicine.

A reliable combination method to identification and typing of epidemic and endemic clones among clinical isolates of Acinetobacter baumannii.

PubMed

Piran, Arezoo; Shahcheraghi, Fereshteh; Solgi, Hamid; Rohani, Mahdi; Badmasti, Farzad

2017-10-01

The multi-drug resistant (MDR) Acinetobacter baumannii as an important nosocomial pathogen has emerged a global health concern in recent years. In this study, we applied three easier, faster, and cost-effective methods including PCR-based open reading frames (ORFs) typing, sequence typing of bla OXA-51-like and RAPD-PCR method to rapid typing of A. baumannii strains. Taken together in the present study the results of ORFs typing, PCR-sequencing of bla OXA-51-like genes and MLST sequence typing revealed there was a high prevalence (62%, 35/57) of ST2 as international and successful clone which detected among clinical isolates of multi-drug resistant A. baumannii with ORF pattern B and bla OXA-66 gene. Only 7% (4/57) of MDR isolates belonged to ST1 with ORF pattern A and bla OXA-69 gene. Interestingly, we detected singleton ST513 (32%, 18/57) that encoded bla OXA-90 and showed the ORF pattern H as previously isolated in Middle East. Moreover, our data showed RAPD-PCR method can detect divergent strains of the STs. The Cl-1, Cl-2, Cl-3, Cl-4, Cl-10, Cl-11, Cl-12, Cl-13 and Cl-14 belonged to ST2. While the Cl-6, Cl-7, Cl-8 and Cl-9 belonged to ST513. Only Cl-5 belonged to ST1. It seems that the combination of these methods have more discriminatory than any method separately and could be effectively applied to rapid detection of the clonal complex (CC) of A. baumannii strains without performing of MLST or PFGE. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of the Volumes of the Posterior Cranial Fossa, Cerebellum, and Herniated Tonsils Using the Stereological Methods in Patients with Chiari Type I Malformation

PubMed Central

Vurdem, Ümit Erkan; Acer, Niyazi; Ertekin, Tolga; Savranlar, Ahmet; İnci, Mehmet Fatih

2012-01-01

Objective. The aim of this study was to determine the posterior cranial fossa volume, cerebellar volume, and herniated tonsillar volume in patients with chiari type I malformation and control subjects using stereological methods. Material and Methods. These volumes were estimated retrospectively using the Cavalieri principle as a point-counting technique. We used magnetic resonance images taken from 25 control subjects and 30 patients with chiari type I malformation. Results. The posterior cranial fossa volume in patients with chiari type I malformation was significantly smaller than the volume in the control subjects (P < 0.05). In the chiari type I malformation group, the cerebellar volume was smaller than the control group, but this difference was not statistically significant (P > 0.05). In the chiari type I malformation group, the ratio of cerebellar volume to posterior cranial fossa volume was higher than in the control group. We also found a positive correlation between the posterior cranial fossa volume and cerebellar volume for each of the groups (r = 0.865, P < 0.001). The mean (±SD) herniated tonsillar volume and length were 0.89 ± 0.50 cm3 and 9.63 ± 3.37 mm in the chiari type I malformation group, respectively. Conclusion. This study has shown that posterior cranial fossa and cerebellum volumes can be measured by stereological methods, and the ratio of these measurements can contribute to the evaluation of chiari type I malformation cases. PMID:22629166

Calculation Method of Lateral Strengths and Ductility Factors of Constructions with Shear Walls of Different Ductility

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

Yamaguchi, Nobuyoshi; Nakao, Masato; Murakami, Masahide

2008-07-08

For seismic design, ductility-related force modification factors are named R factor in Uniform Building Code of U.S, q factor in Euro Code 8 and Ds (inverse of R) factor in Japanese Building Code. These ductility-related force modification factors for each type of shear elements are appeared in those codes. Some constructions use various types of shear walls that have different ductility, especially for their retrofit or re-strengthening. In these cases, engineers puzzle the decision of force modification factors of the constructions. Solving this problem, new method to calculate lateral strengths of stories for simple shear wall systems is proposed andmore » named 'Stiffness--Potential Energy Addition Method' in this paper. This method uses two design lateral strengths for each type of shear walls in damage limit state and safety limit state. Two lateral strengths of stories in both limit states are calculated from these two design lateral strengths for each type of shear walls in both limit states. Calculated strengths have the same quality as values obtained by strength addition method using many steps of load-deformation data of shear walls. The new method to calculate ductility factors is also proposed in this paper. This method is based on the new method to calculate lateral strengths of stories. This method can solve the problem to obtain ductility factors of stories with shear walls of different ductility.« less

Maternal T-Cell Engraftment Interferes With Human Leukocyte Antigen Typing in Severe Combined Immunodeficiency.

PubMed

Liu, Chang; Duffy, Brian; Bednarski, Jeffrey J; Calhoun, Cecelia; Lay, Lindsay; Rundblad, Barrett; Payton, Jacqueline E; Mohanakumar, Thalachallour

2016-02-01

To report the laboratory investigation of a case of severe combined immunodeficiency (SCID) with maternal T-cell engraftment, focusing on the interference of human leukocyte antigen (HLA) typing by blood chimerism. HLA typing was performed with three different methods, including sequence-specific primer (SSP), sequence-specific oligonucleotide, and Sanger sequencing on peripheral blood leukocytes and buccal cells, from a 3-month-old boy and peripheral blood leukocytes from his parents. Short tandem repeat (STR) testing was performed in parallel. HLA typing of the patient's peripheral blood leukocytes using the SSP method demonstrated three different alleles for each of the HLA-B and HLA-C loci, with both maternal alleles present at each locus. Typing results from the patient's buccal cells showed a normal pattern of inheritance for paternal and maternal haplotypes. STR enrichment testing of the patient's CD3+ T lymphocytes and CD15+ myeloid cells confirmed maternal T-cell engraftment, while the myeloid cell profile matched the patient's buccal cells. Maternal T-cell engraftment may interfere with HLA typing in patients with SCID. Selection of the appropriate typing methods and specimens is critical for accurate HLA typing and immunologic assessment before allogeneic hematopoietic stem cell transplantation. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tissue type determination by impedance measurement: A bipolar and monopolar comparison

PubMed Central

Sharp, Jack; Bouazza-Marouf, Kaddour; Noronha, Dorita; Gaur, Atul

2017-01-01

Background: In certain medical applications, it is necessary to be able to determine the position of a needle inside the body, specifically with regards to identifying certain tissue types. By measuring the electrical impedance of specific tissue types, it is possible to determine the type of tissue the tip of the needle (or probe) is at. Materials and Methods: Two methods have been investigated for electric impedance detection; bipolar and monopolar. Commercially available needle electrodes are of a monopolar type. Although many patents exist on the bipolar setups, these have not as yet been commercialized. This paper reports a comparison of monopolar and bipolar setups for tissue type determination. In vitro experiments were carried out on pork to compare this investigation with other investigations in this field. Results: The results show that both monopolar and bipolar setups are capable of determining tissue type. However, the bipolar setup showed slightly better results; the difference between the different soft tissue type impedances was greater compared to the monopolar method. Conclusion: Both monopolar and bipolar electrical impedance setups work very similarly in inhomogeneous volumes such as biological tissue. There is a clear potential for clinical applications with impedance-based needle guidance, with both the monopolar and bipolar setups. It is, however, worth noting that the bipolar setup is more versatile. PMID:28217047

New Eudesmane-Type Sesquiterpenoids from the Mangrove-Derived Endophytic Fungus Penicillium sp. J-54

PubMed Central

Qiu, Liuming; Wang, Pei; Liao, Ge; Zeng, Yanbo; Cai, Caihong; Kong, Fandong; Guo, Zhikai; Proksch, Peter; Dai, Haofu; Mei, Wenli

2018-01-01

Four new eudesmane-type sesquiterpenoids, penicieudesmol A–D (1–4), were isolated from the fermentation broth of the mangrove-derived endophytic fungus Penicillium sp. J-54. Their structures were determined by spectroscopic methods, the in situ dimolybdenum CD method, and modified Mosher’s method. The bioassays results showed that 2 exhibited weak cytotoxicity against K-562 cells. PMID:29597304

Multistage morphological segmentation of bright-field and fluorescent microscopy images

NASA Astrophysics Data System (ADS)

Korzyńska, A.; Iwanowski, M.

2012-06-01

This paper describes the multistage morphological segmentation method (MSMA) for microscopic cell images. The proposed method enables us to study the cell behaviour by using a sequence of two types of microscopic images: bright field images and/or fluorescent images. The proposed method is based on two types of information: the cell texture coming from the bright field images and intensity of light emission, done by fluorescent markers. The method is dedicated to the image sequences segmentation and it is based on mathematical morphology methods supported by other image processing techniques. The method allows for detecting cells in image independently from a degree of their flattening and from presenting structures which produce the texture. It makes use of some synergic information from the fluorescent light emission image as the support information. The MSMA method has been applied to images acquired during the experiments on neural stem cells as well as to artificial images. In order to validate the method, two types of errors have been considered: the error of cell area detection and the error of cell position using artificial images as the "gold standard".

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2)

PubMed Central

de Oliveira, Gilberto Santos; Kawahara, Rebeca; Rosa-Fernandes, Livia; Avila, Carla Cristi; Teixeira, Marta M. G.; Larsen, Martin R.

2018-01-01

Background Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2. Methods/Principal findings The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms. Conclusions and significance This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method allows T. cruzi strain typing using MS/MS spectra as discriminatory features and allows the differentiation of TcI-TcVI DTUs. Similar to genomic-based strategies, the Tc-STAMS2 method allows identification of strains within DTUs. Its robustness towards different experimental and biological variables makes it a valuable complementary strategy to the current T. cruzi genotyping assays. Moreover, this method can be used to identify DTU-specific features correlated with the strain phenotype. PMID:29608573

Structural dynamics and vibrations of damped, aircraft-type structures

NASA Technical Reports Server (NTRS)

Young, Maurice I.

1992-01-01

Engineering preliminary design methods for approximating and predicting the effects of viscous or equivalent viscous-type damping treatments on the free and forced vibration of lightly damped aircraft-type structures are developed. Similar developments are presented for dynamic hysteresis viscoelastic-type damping treatments. It is shown by both engineering analysis and numerical illustrations that the intermodal coupling of the undamped modes arising from the introduction of damping may be neglected in applying these preliminary design methods, except when dissimilar modes of these lightly damped, complex aircraft-type structures have identical or nearly identical natural frequencies. In such cases, it is shown that a relatively simple, additional interaction calculation between pairs of modes exhibiting this 'modal response' phenomenon suffices in the prediction of interacting modal damping fractions. The accuracy of the methods is shown to be very good to excellent, depending on the normal natural frequency separation of the system modes, thereby permitting a relatively simple preliminary design approach. This approach is shown to be a natural precursor to elaborate finite element, digital computer design computations in evaluating the type, quantity, and location of damping treatment.

Forest Pest Control. Bulletin 759.

ERIC Educational Resources Information Center

Coleman, V. Rodney

This manual describes the major forest types, the major species, seed orchards, and tree nurseries. Methods of identifying forest insect pests and diseases are given. The most common types of insecticides, fungicides, and herbicides are described. Both sprayer and granular applicator methods are discussed. Environmental considerations are…

Descriptive Question Answering with Answer Type Independent Features

NASA Astrophysics Data System (ADS)

Yoon, Yeo-Chan; Lee, Chang-Ki; Kim, Hyun-Ki; Jang, Myung-Gil; Ryu, Pum Mo; Park, So-Young

In this paper, we present a supervised learning method to seek out answers to the most frequently asked descriptive questions: reason, method, and definition questions. Most of the previous systems for question answering focus on factoids, lists or definitional questions. However, descriptive questions such as reason questions and method questions are also frequently asked by users. We propose a system for these types of questions. The system conducts an answer search as follows. First, we analyze the user's question and extract search keywords and the expected answer type. Second, information retrieval results are obtained from an existing search engine such as Yahoo or Google. Finally, we rank the results to find snippets containing answers to the questions based on a ranking SVM algorithm. We also propose features to identify snippets containing answers for descriptive questions. The features are adaptable and thus are not dependent on answer type. Experimental results show that the proposed method and features are clearly effective for the task.

P and n-type microcrystalline semiconductor alloy material including band gap widening elements, devices utilizing same

DOEpatents

Guha, Subhendu; Ovshinsky, Stanford R.

1988-10-04

An n-type microcrystalline semiconductor alloy material including a band gap widening element; a method of fabricating p-type microcrystalline semiconductor alloy material including a band gap widening element; and electronic and photovoltaic devices incorporating said n-type and p-type materials.

48 CFR 16.104 - Factors in selecting contract types.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Factors in selecting... CONTRACTING METHODS AND CONTRACT TYPES TYPES OF CONTRACTS Selecting Contract Types 16.104 Factors in selecting contract types. There are many factors that the contracting officer should consider in selecting and...

48 CFR 16.104 - Factors in selecting contract types.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Factors in selecting... CONTRACTING METHODS AND CONTRACT TYPES TYPES OF CONTRACTS Selecting Contract Types 16.104 Factors in selecting contract types. There are many factors that the contracting officer should consider in selecting and...

48 CFR 1516.303-73 - Types of cost-sharing.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., cost matching, or other in-kind contributions. (b) In-kind contributions represent non-cash... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Types of cost-sharing. 1516... CONTRACTING METHODS AND CONTRACT TYPES TYPES OF CONTRACTS Cost-Reimbursement Contracts 1516.303-73 Types of...

Application of ride quality technology to predict ride satisfaction for commuter-type aircraft

NASA Technical Reports Server (NTRS)

Jacobson, I. D.; Kuhlthau, A. R.; Richards, L. G.

1975-01-01

A method was developed to predict passenger satisfaction with the ride environment of a transportation vehicle. This method, a general approach, was applied to a commuter-type aircraft for illustrative purposes. The effect of terrain, altitude and seat location were examined. The method predicts the variation in passengers satisfied for any set of flight conditions. In addition several noncommuter aircraft were analyzed for comparison and other uses of the model described. The method has advantages for design, evaluation, and operating decisions.

A taxonomy of adolescent health: development of the adolescent health profile-types.

PubMed

Riley, A W; Green, B F; Forrest, C B; Starfield, B; Kang, M; Ensminger, M E

1998-08-01

The aim of this study was to develop a taxonomy of health profile-types that describe adolescents' patterns of health as self-reported on a health status questionnaire. The intent was to be able to assign individuals to mutually exclusive and exhaustive groups that characterize the important aspects of their health and need for health services. Cluster analytic empirical methods and clinically based conceptual methods were used to identify patterns of health in samples of adolescents from schools and from clinics that serve adolescents with chronic conditions and acute illnesses. Individuals with similar patterns of scores across multiple domains were assigned to the same profile-type. Results from the empirical and conceptually based methods were integrated to produce a practical system for assigning youths to profile-types. Four domains of health (Satisfaction, Discomfort, Risks and Resilience) were used to group individuals into 13 distinct profile-types. The profile-types were characterized primarily by the number of domains in which health is poor, identifying the unique combinations of problems that characterize different subgroups of adolescents. This method of reporting the information available on health status surveys is potentially a more informative way of identifying and classifying the health needs of subgroups in the population than is available from global scores or multiple scale scores. The reliability and validity of this taxonomy of health profile-types for the purposes of planning and evaluating health services must be demonstrated. That is the purpose of the accompanying study.

Genotypic and phenotypic characteristics of Methicillin-resistant Staphylococcus aureus (MRSA) strains, isolated on three different geography locations.

PubMed

Ostojić, Maja; Hukić, Mirsada

2015-08-04

Staphylococcus aureus is a major cause of hospital-acquired infections worldwide. Increased frequency of methicillin-resistant Staphylococcus aureus (MRSA) in hospitalized patients and possibility of vancomycin resistance requires rapid and reliable characterization of isolates and control of MRSA spread in hospitals. Typing of isolates helps to understand the route of a hospital pathogen spread. The aim of this study was to investigate and compare genotypic and phenotypic characteristics of MRSA samples on three different geography locations. In addition, our aim was to evaluate three different methods of MRSA typing: spa-typing, agr-typing and GenoType MRSA.  We included 104 samples of MRSA, isolated in 3 different geographical locations in clinical hospitals in Zagreb, Mostar, and Heidelberg, during the period of six months. Genotyping and phenotyping were done by spa-typing, agr-typing and dipstick assay GenoType MRSA. We failed to type all our samples by spa-typing.  The most common spa-type in clinical hospital Zagreb was t041, in Mostar t001, and in Heidelberg t003.We analyzed 102/104 of our samples by agr-typing method. We did not find any agr-type IV in our locations. We analyzed all our samples by the dipstick assay GenoType MRSA. All isolates in our study were MRSA strains. In Zagreb there were no positive strains to PVL gene. In Mostar we have found 5/25 positive strains to PVL gene, in Heidelberg there was 1/49. PVL positive isolates were associated with spa-type t008 and agr-type I, thus, genetically, they were community-associated MRSA (CA-MRSA). Dipstick assay GenoType MRSA has demonstrated sufficient specificity, sensibility, simple performance and low cost, so we could introduce it to work in smaller laboratories. Using this method may expedite MRSA screening, thus preventing its spread in hospitals.

Capsule Typing of Haemophilus influenzae by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

PubMed

Månsson, Viktor; Gilsdorf, Janet R; Kahlmeter, Gunnar; Kilian, Mogens; Kroll, J Simon; Riesbeck, Kristian; Resman, Fredrik

2018-03-01

Encapsulated Haemophilus influenzae strains belong to type-specific genetic lineages. Reliable capsule typing requires PCR, but a more efficient method would be useful. We evaluated capsule typing by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Isolates of all capsule types (a-f and nontypeable; n = 258) and isogenic capsule transformants (types a-d) were investigated. Principal component and biomarker analyses of mass spectra showed clustering, and mass peaks correlated with capsule type-specific genetic lineages. We used 31 selected isolates to construct a capsule typing database. Validation with the remaining isolates (n = 227) showed 100% sensitivity and 92.2% specificity for encapsulated strains (a-f; n = 61). Blinded validation of a supplemented database (n = 50) using clinical isolates (n = 126) showed 100% sensitivity and 100% specificity for encapsulated strains (b, e, and f; n = 28). MALDI-TOF mass spectrometry is an accurate method for capsule typing of H. influenzae.

High voltage semiconductor devices and methods of making the devices

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

Matocha, Kevin; Chatty, Kiran; Banerjee, Sujit

A multi-cell MOSFET device including a MOSFET cell with an integrated Schottky diode is provided. The MOSFET includes n-type source regions formed in p-type well regions which are formed in an n-type drift layer. A p-type body contact region is formed on the periphery of the MOSFET. The source metallization of the device forms a Schottky contact with an n-type semiconductor region adjacent the p-type body contact region of the device. Vias can be formed through a dielectric material covering the source ohmic contacts and/or Schottky region of the device and the source metallization can be formed in the vias.more » The n-type semiconductor region forming the Schottky contact and/or the n-type source regions can be a single continuous region or a plurality of discontinuous regions alternating with discontinuous p-type body contact regions. The device can be a SiC device. Methods of making the device are also provided.« less

High voltage semiconductor devices and methods of making the devices

DOEpatents

Matocha, Kevin; Chatty, Kiran; Banerjee, Sujit

2017-02-28

A multi-cell MOSFET device including a MOSFET cell with an integrated Schottky diode is provided. The MOSFET includes n-type source regions formed in p-type well regions which are formed in an n-type drift layer. A p-type body contact region is formed on the periphery of the MOSFET. The source metallization of the device forms a Schottky contact with an n-type semiconductor region adjacent the p-type body contact region of the device. Vias can be formed through a dielectric material covering the source ohmic contacts and/or Schottky region of the device and the source metallization can be formed in the vias. The n-type semiconductor region forming the Schottky contact and/or the n-type source regions can be a single continuous region or a plurality of discontinuous regions alternating with discontinuous p-type body contact regions. The device can be a SiC device. Methods of making the device are also provided.

A Systematic Review of the Prevalence and Attribution of Human Papillomavirus Types Among Cervical, Vaginal and Vulvar Pre-cancers and Cancers in the United States

PubMed Central

Insinga, Ralph P.; Liaw, Kai-Li; Johnson, Lisa G.; Madeleine, Margaret M.

2008-01-01

Objectives To describe (1) prevalence and (2) estimated attribution of human papillomavirus (HPV) types in U.S. cervical, vaginal and vulvar precancers and cancers. Methods U.S. studies reporting HPV typing for cervical (CIN), vulvar (VIN) and vaginal (VaIN) intraepithelial neoplasias and/or invasive cancers of those sites were gathered from the PubMed database (http://www.ncbi.nlm.nih.gov/sites/entrez/). Selected studies had polymerase chain reaction testing data for ≥10 cases for a disease endpoint. Analytic methods augmented prior reviews of cervical disease with an updated and expanded analysis (including vulvar and vaginal disease), new selection criteria for specimens, and adjustment for histologic type, where possible, among pooled cancer cases. In addition, for analyses of estimated attribution of HPV types, we incorporated accounting methods for lesions infected with multiple HPV types. Results Data from 22 U.S. studies meeting review eligibility criteria were tabulated. Following adjustment for the presence of multiple HPV types in a single specimen, the top two HPV types contributing to disease were: CIN 1 (HPV 16/66) [15.3%], CIN 2/3 (16/31) [61.9%], cervical cancer (16/18) [79.2%], VIN 1 (6/11) [41.7%], VIN 3 (16/18) [84.0%], vulvar cancer (16/33) [55.5%], VaIN 3 (16/18) [65.1%], vaginal cancer (16/18) [72.7%]. Conclusions The HPV type distribution and proportion of cases testing positive for any HPV type were observed to vary among U.S. cervical, vulvar and vaginal neoplasias and by grade of disease. Adjustment for the presence of multi-type HPV infections can have an important impact on the estimated attribution of HPV types to disease, particularly for types other than HPV 16. PMID:18628412

Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

PubMed

Garcillán-Barcia, M Pilar; Ruiz del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

2015-01-01

Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. Copyright © 2014 Elsevier Inc. All rights reserved.

Method for isolating chromosomal DNA in preparation for hybridization in suspension

DOEpatents

Lucas, Joe N.

2000-01-01

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. Chromosomal DNA in a sample containing cell debris is prepared for hybridization in suspension by treating the mixture with RNase. The treated DNA can also be fixed prior to hybridization.

A comparative analysis of the effectiveness of cytogenetic and molecular genetic methods in the detection of Down syndrome.

PubMed

Mačkić-Đurović, Mirela; Projić, Petar; Ibrulj, Slavka; Cakar, Jasmina; Marjanović, Damir

2014-05-01

The goal of this study was to examine the effectiveness of 6 STR markers application (D21S1435, D21S11, D21S1270, D21S1411, D21S226 and IFNAR) in molecular genetic diagnostics of Down syndrome (DS) and to compare it with cytogenetic method. Testing was performed on 73 children, with the previously cytogenetically confirmed Down syndrome. DNA isolated from the buccal swab was used. Previously mentioned loci located on chromosome 21 were simultaneously amplified using quantitative fluorescence PCR (QF PCR). Using this method, 60 previously cytogenetically diagnosed DS with standard type of trisomy 21 were confirmed. Furthermore, six of eight children with mosaic type of DS were detected. Two false negative results for mosaic type of DS were obtained. Finally, five children with the translocation type of Down syndrome were also confirmed with this molecular test. In conclusion, molecular genetic analysis of STR loci is fast, cheap and simple method that could be used in detection of DS. Regarding possible false results detected for certain number of mosaic types, cytogenetic analysis should be used as a confirmatory test.

Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach.

PubMed

Abd El Aziz, Mohamed; Selim, I M; Xiong, Shengwu

2017-06-30

This paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.

[Research on fast classification based on LIBS technology and principle component analyses].

PubMed

Yu, Qi; Ma, Xiao-Hong; Wang, Rui; Zhao, Hua-Feng

2014-11-01

Laser-induced breakdown spectroscopy (LIBS) and the principle component analysis (PCA) were combined to study aluminum alloy classification in the present article. Classification experiments were done on thirteen different kinds of standard samples of aluminum alloy which belong to 4 different types, and the results suggested that the LIBS-PCA method can be used to aluminum alloy fast classification. PCA was used to analyze the spectrum data from LIBS experiments, three principle components were figured out that contribute the most, the principle component scores of the spectrums were calculated, and the scores of the spectrums data in three-dimensional coordinates were plotted. It was found that the spectrum sample points show clear convergence phenomenon according to the type of aluminum alloy they belong to. This result ensured the three principle components and the preliminary aluminum alloy type zoning. In order to verify its accuracy, 20 different aluminum alloy samples were used to do the same experiments to verify the aluminum alloy type zoning. The experimental result showed that the spectrum sample points all located in their corresponding area of the aluminum alloy type, and this proved the correctness of the earlier aluminum alloy standard sample type zoning method. Based on this, the identification of unknown type of aluminum alloy can be done. All the experimental results showed that the accuracy of principle component analyses method based on laser-induced breakdown spectroscopy is more than 97.14%, and it can classify the different type effectively. Compared to commonly used chemical methods, laser-induced breakdown spectroscopy can do the detection of the sample in situ and fast with little sample preparation, therefore, using the method of the combination of LIBS and PCA in the areas such as quality testing and on-line industrial controlling can save a lot of time and cost, and improve the efficiency of detection greatly.

New type of liquid rubber and compositions based on it.

PubMed

Semikolenov, S V; Nartova, A V; Voronchikhin, V D; Dubkov, K A

2014-11-01

The new method for producing the functionalized polymers and oligomers containing carbonyl C=O groups is developed. The method is based on the noncatalytic oxidation of unsaturated rubbers by nitrous oxide (N2O) at 180-230 °С. The proposed method allows obtaining the new type of functionalized rubbers-liquid unsaturated polyketones with regulated molecular weight and concentration of C=O groups. The influence of the liquid polyketone addition on properties of rubber-based composites is investigated. The study indicates good prospects of using the liquid polyketones for the improvement of properties and operating characteristics of the various types of rubbers and the rubber-cord systems.

Error analysis and correction of lever-type stylus profilometer based on Nelder-Mead Simplex method

NASA Astrophysics Data System (ADS)

Hu, Chunbing; Chang, Suping; Li, Bo; Wang, Junwei; Zhang, Zhongyu

2017-10-01

Due to the high measurement accuracy and wide range of applications, lever-type stylus profilometry is commonly used in industrial research areas. However, the error caused by the lever structure has a great influence on the profile measurement, thus this paper analyzes the error of high-precision large-range lever-type stylus profilometry. The errors are corrected by the Nelder-Mead Simplex method, and the results are verified by the spherical surface calibration. It can be seen that this method can effectively reduce the measurement error and improve the accuracy of the stylus profilometry in large-scale measurement.

New exact solutions of the Tzitzéica-type equations in non-linear optics using the expa function method

NASA Astrophysics Data System (ADS)

Hosseini, K.; Ayati, Z.; Ansari, R.

2018-04-01

One specific class of non-linear evolution equations, known as the Tzitzéica-type equations, has received great attention from a group of researchers involved in non-linear science. In this article, new exact solutions of the Tzitzéica-type equations arising in non-linear optics, including the Tzitzéica, Dodd-Bullough-Mikhailov and Tzitzéica-Dodd-Bullough equations, are obtained using the expa function method. The integration technique actually suggests a useful and reliable method to extract new exact solutions of a wide range of non-linear evolution equations.

Improving the quality of the ECG signal by filtering in wavelet transform domain

NASA Astrophysics Data System (ADS)

DzierŻak, RóŻa; Surtel, Wojciech; Dzida, Grzegorz; Maciejewski, Marcin

2016-09-01

The article concerns the research methods of noise reduction occurring in the ECG signals. The method is based on the use of filtration in wavelet transform domain. The study was conducted on two types of signal - received during the rest of the patient and obtained during physical activity. For each of the signals 3 types of filtration were used. The study was designed to determine the effectiveness of various wavelets for de-noising signals obtained in both cases. The results confirm the suitability of the method for improving the quality of the electrocardiogram in case of both types of signals.

Method Of Bonding A Metal Connection To An Electrode Including A Core Having A Fiber Or Foam Type Structure For An Electrochemical Cell, An

DOEpatents

Loustau, Marie-Therese; Verhoog, Roelof; Precigout, Claude

1996-09-24

A method of bonding a metal connection to an electrode including a core having a fiber or foam-type structure for an electrochemical cell, in which method at least one metal strip is pressed against one edge of the core and is welded thereto under compression, wherein, at least in line with the region in which said strip is welded to the core, which is referred to as the "main core", a retaining core of a type analogous to that of the main core is disposed prior to the welding.

High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform.

PubMed

Trembizki, Ella; Smith, Helen; Lahra, Monica M; Chen, Marcus; Donovan, Basil; Fairley, Christopher K; Guy, Rebecca; Kaldor, John; Regan, David; Ward, James; Nissen, Michael D; Sloots, Theo P; Whiley, David M

2014-06-01

Neisseria gonorrhoeae antimicrobial resistance (AMR) is a global problem heightened by emerging resistance to ceftriaxone. Appropriate molecular typing methods are important for understanding the emergence and spread of N. gonorrhoeae AMR. We report on the development, validation and testing of a Sequenom MassARRAY iPLEX method for multilocus sequence typing (MLST)-style genotyping of N. gonorrhoeae isolates. An iPLEX MassARRAY method (iPLEX14SNP) was developed targeting 14 informative gonococcal single nucleotide polymorphisms (SNPs) previously shown to predict MLST types. The method was initially validated using 24 N. gonorrhoeae control isolates and was then applied to 397 test isolates collected throughout Queensland, Australia in the first half of 2012. The iPLEX14SNP method provided 100% accuracy for the control isolates, correctly identifying all 14 SNPs for all 24 isolates (336/336). For the 397 test isolates, the iPLEX14SNP assigned results for 5461 of the possible 5558 SNPs (SNP call rate 98.25%), with complete 14 SNP profiles obtained for 364 isolates. Based on the complete SNP profile data, there were 49 different sequence types identified in Queensland, with 11 of the 49 SNP profiles accounting for the majority (n = 280; 77%) of isolates. AMR was dominated by several geographically clustered sequence types. Using the iPLEX14SNP method, up to 384 isolates could be tested within 1 working day for less than Aus$10 per isolate. The iPLEX14SNP offers an accurate and high-throughput method for the MLST-style genotyping of N. gonorrhoeae and may prove particularly useful for large-scale studies investigating the emergence and spread of gonococcal AMR. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The feasibility of using explicit method for linear correction of the particle size variation using NIR Spectroscopy combined with PLS2regression method

NASA Astrophysics Data System (ADS)

Yulia, M.; Suhandy, D.

2018-03-01

NIR spectra obtained from spectral data acquisition system contains both chemical information of samples as well as physical information of the samples, such as particle size and bulk density. Several methods have been established for developing calibration models that can compensate for sample physical information variations. One common approach is to include physical information variation in the calibration model both explicitly and implicitly. The objective of this study was to evaluate the feasibility of using explicit method to compensate the influence of different particle size of coffee powder in NIR calibration model performance. A number of 220 coffee powder samples with two different types of coffee (civet and non-civet) and two different particle sizes (212 and 500 µm) were prepared. Spectral data was acquired using NIR spectrometer equipped with an integrating sphere for diffuse reflectance measurement. A discrimination method based on PLS-DA was conducted and the influence of different particle size on the performance of PLS-DA was investigated. In explicit method, we add directly the particle size as predicted variable results in an X block containing only the NIR spectra and a Y block containing the particle size and type of coffee. The explicit inclusion of the particle size into the calibration model is expected to improve the accuracy of type of coffee determination. The result shows that using explicit method the quality of the developed calibration model for type of coffee determination is a little bit superior with coefficient of determination (R2) = 0.99 and root mean square error of cross-validation (RMSECV) = 0.041. The performance of the PLS2 calibration model for type of coffee determination with particle size compensation was quite good and able to predict the type of coffee in two different particle sizes with relatively high R2 pred values. The prediction also resulted in low bias and RMSEP values.

Convergence to Diagonal Form of Block Jacobi-type Processes

NASA Astrophysics Data System (ADS)

Hari, Vjeran

2008-09-01

The main result of recent research on convergence to diagonal form of block Jacobi-type processes is presented. For this purpose, all notions needed to describe the result are introduced. In particular, elementary block transformation matrices, simple and non-simple algorithms, block pivot strategies together with the appropriate equivalence relations are defined. The general block Jacobi-type process considered here can be specialized to take the form of almost any known Jacobi-type method for solving the ordinary or the generalized matrix eigenvalue and singular value problems. The assumptions used in the result are satisfied by many concrete methods.

N-type droping of nanocrystalline diamond films with nitrogen and electrodes made therefrom

DOEpatents

Gruen, Dieter M [Downers Grove, IL; Krauss, Alan R [late of Naperville, IL; Auciello, Orlando H [Bolingbrook, IL; Carlisle, John A [Plainfield, IL

2004-09-21

An electrically conducting n-type ultrananocrystalline diamond (UNCD) having no less than 10.sup.19 atoms/cm.sup.3 of nitrogen is disclosed. A method of making the n-doped UNCD. A method for predictably controlling the conductivity is also disclosed.

48 CFR 35.006 - Contracting methods and contract type.

Code of Federal Regulations, 2011 CFR

2011-10-01

... indicated a high degree of probability that development is feasible and (2) the Government has determined... SPECIAL CATEGORIES OF CONTRACTING RESEARCH AND DEVELOPMENT CONTRACTING 35.006 Contracting methods and..., performance objectives, and specifications for the work can be defined will largely determine the type of...

Dispersive shock waves in systems with nonlocal dispersion of Benjamin-Ono type

NASA Astrophysics Data System (ADS)

El, G. A.; Nguyen, L. T. K.; Smyth, N. F.

2018-04-01

We develop a general approach to the description of dispersive shock waves (DSWs) for a class of nonlinear wave equations with a nonlocal Benjamin-Ono type dispersion term involving the Hilbert transform. Integrability of the governing equation is not a pre-requisite for the application of this method which represents a modification of the DSW fitting method previously developed for dispersive-hydrodynamic systems of Korteweg-de Vries (KdV) type (i.e. reducible to the KdV equation in the weakly nonlinear, long wave, unidirectional approximation). The developed method is applied to the Calogero-Sutherland dispersive hydrodynamics for which the classification of all solution types arising from the Riemann step problem is constructed and the key physical parameters (DSW edge speeds, lead soliton amplitude, intermediate shelf level) of all but one solution type are obtained in terms of the initial step data. The analytical results are shown to be in excellent agreement with results of direct numerical simulations.

Drug Resistance in Salmonella Typhimurium and its Implications*

PubMed Central

Anderson, E. S.

1968-01-01

A rise in Salmonella typhimurium infection was observed in calves in Britain during 1964–6, follwing the adoption of the intensive farming method. A single phage type of S. typhimurium, type 29, was incriminated as the major pathogen. Attempts to treat and control the disease with a range of antibiotics were ineffective, but resulted in the acquisition of transferable multiple drug resistance by type 29. The transmission of drug-resistant type 29, directly or indirectly, from bovines to man resulted in many human infections. Transferable drug resistance reaching man from enterobacteria of animal origin may ultimately enter specifically human pathogens. Infections such as that caused by type 29 can be eliminated, not by the massive use of antibiotics but by improvement in conditions of animal husbandry and reduction in the opportunities for the initiation and spread of the disease. A reappraisal is needed of the methods of using antibiotics to determine how these methods can be improved, in order to conserve the long-term efficacy of the antibiotics. PMID:4874171

Comparison of the DiversiLab Repetitive Element PCR System with spa Typing and Pulsed-Field Gel Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus▿

PubMed Central

Babouee, B.; Frei, R.; Schultheiss, E.; Widmer, A. F.; Goldenberger, D.

2011-01-01

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns. PMID:21307215

Multicenter Evaluation of Epidemiological Typing of Methicillin-Resistant Staphylococcus aureus Strains by Repetitive-Element PCR Analysis

PubMed Central

Deplano, Ariane; Schuermans, Annette; Van Eldere, Johan; Witte, Wolfgang; Meugnier, Hèléne; Etienne, Jerome; Grundmann, Hajo; Jonas, Daniel; Noordhoek, Gerda T.; Dijkstra, Jolanda; van Belkum, Alex; van Leeuwen, Willem; Tassios, Panayotis T.; Legakis, Nicholas J.; van der Zee, Anneke; Bergmans, Anneke; Blanc, Dominique S.; Tenover, Fred C.; Cookson, Barry C.; O'Neil, Gael; Struelens, Marc J.

2000-01-01

Rapid and efficient epidemiologic typing systems would be useful to monitor transmission of methicillin-resistant Staphylococcus aureus (MRSA) at both local and interregional levels. To evaluate the intralaboratory performance and interlaboratory reproducibility of three recently developed repeat-element PCR (rep-PCR) methods for the typing of MRSA, 50 MRSA strains characterized by pulsed-field gel electrophoresis (PFGE) (SmaI) analysis and epidemiological data were blindly typed by inter-IS256, 16S-23S ribosomal DNA (rDNA), and MP3 PCR in 12 laboratories in eight countries using standard reagents and protocols. Performance of typing was defined by reproducibility (R), discriminatory power (D), and agreement with PFGE analysis. Interlaboratory reproducibility of pattern and type classification was assessed visually and using gel analysis software. Each typing method showed a different performance level in each center. In the center performing best with each method, inter-IS256 PCR typing achieved R = 100% and D = 100%; 16S-23S rDNA PCR, R = 100% and D = 82%; and MP3 PCR, R = 80% and D = 83%. Concordance between rep-PCR type and PFGE type ranged by center: 70 to 90% for inter-IS256 PCR, 44 to 57% for 16S-23S rDNA PCR, and 53 to 54% for MP3 PCR analysis. In conclusion, the performance of inter-IS256 PCR typing was similar to that of PFGE analysis in some but not all centers, whereas other rep-PCR protocols showed lower discrimination and intralaboratory reproducibility. None of these assays, however, was sufficiently reproducible for interlaboratory exchange of data. PMID:11015358

Methods for estimating heterocyclic amine concentrations in cooked meats in the US diet.

PubMed

Keating, G A; Bogen, K T

2001-01-01

Heterocyclic amines (HAs) are formed in numerous cooked foods commonly consumed in the diet. A method was developed to estimate dietary HA levels using HA concentrations in experimentally cooked meats reported in the literature and meat consumption data obtained from a national dietary survey. Cooking variables (meat internal temperature and weight loss, surface temperature and time) were used to develop relationships for estimating total HA concentrations in six meat types. Concentrations of five individual HAs were estimated for specific meat type/cooking method combinations based on linear regression of total and individual HA values obtained from the literature. Using these relationships, total and individual HA concentrations were estimated for 21 meat type/cooking method combinations at four meat doneness levels. Reported consumption of the 21 meat type/cooking method combinations was obtained from a national dietary survey and the age-specific daily HA intake calculated using the estimated HA concentrations (ng/g) and reported meat intakes. Estimated mean daily total HA intakes for children (to age 15 years) and adults (30+ years) were 11 and 7.0 ng/kg/day, respectively, with 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) estimated to comprise approximately 65% of each intake. Pan-fried meats were the largest source of HA in the diet and chicken the largest source of HAs among the different meat types.

Thin film heterojunction photovoltaic cells and methods of making the same

DOEpatents

Basol, Bulent M.; Tseng, Eric S.; Rod, Robert L.

1983-06-14

A method of fabricating a thin film heterojunction photovoltaic cell which comprises depositing a film of a near intrinsic or n-type semiconductor compound formed of at least one of the metal elements of Class II B of the Periodic Table of Elements and at least tellurium and then heating said film at a temperature between about 250.degree. C. and 500.degree. C. for a time sufficient to convert said film to a suitably low resistivity p-type semiconductor compound. Such film may be deposited initially on the surface of an n-type semiconductor substrate. Alternatively, there may be deposited on the converted film a layer of n-type semiconductor compound different from the film semiconductor compound. The resulting photovoltaic cell exhibits a substantially increased power output over similar cells not subjected to the method of the present invention.

Study of travelling wave solutions for some special-type nonlinear evolution equations

NASA Astrophysics Data System (ADS)

Song, Junquan; Hu, Lan; Shen, Shoufeng; Ma, Wen-Xiu

2018-07-01

The tanh-function expansion method has been improved and used to construct travelling wave solutions of the form U={\\sum }j=0n{a}j{\\tanh }jξ for some special-type nonlinear evolution equations, which have a variety of physical applications. The positive integer n can be determined by balancing the highest order linear term with the nonlinear term in the evolution equations. We improve the tanh-function expansion method with n = 0 by introducing a new transform U=-W\\prime (ξ )/{W}2. A nonlinear wave equation with source terms, and mKdV-type equations, are considered in order to show the effectiveness of the improved scheme. We also propose the tanh-function expansion method of implicit function form, and apply it to a Harry Dym-type equation as an example.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

The Effects of Different Standard Setting Methods and the Composition of Borderline Groups: A Study within a Law Curriculum

ERIC Educational Resources Information Center

Dochy, Filip; Kyndt, Eva; Baeten, Marlies; Pottier, Sofie; Veestraeten, Marlies; Leuven, K. U.

2009-01-01

The aim of this study was to examine the effect of different standard setting methods on the size and composition of the borderline group, on the discrimination between different types of students and on the types of students passing with one method but failing with another. A total of 107 university students were classified into 4 different types…

Controlling Type I Error Rates in Assessing DIF for Logistic Regression Method Combined with SIBTEST Regression Correction Procedure and DIF-Free-Then-DIF Strategy

ERIC Educational Resources Information Center

Shih, Ching-Lin; Liu, Tien-Hsiang; Wang, Wen-Chung

2014-01-01

The simultaneous item bias test (SIBTEST) method regression procedure and the differential item functioning (DIF)-free-then-DIF strategy are applied to the logistic regression (LR) method simultaneously in this study. These procedures are used to adjust the effects of matching true score on observed score and to better control the Type I error…

Udzawa-type iterative method with parareal preconditioner for a parabolic optimal control problem

NASA Astrophysics Data System (ADS)

Lapin, A.; Romanenko, A.

2016-11-01

The article deals with the optimal control problem with the parabolic equation as state problem. There are point-wise constraints on the state and control functions. The objective functional involves the observation given in the domain at each moment. The conditions for convergence Udzawa's type iterative method are given. The parareal method to inverse preconditioner is given. The results of calculations are presented.

Development of a multiplex PCR-based rapid typing method for enterohemorrhagic Escherichia coli O157 strains.

PubMed

Ooka, Tadasuke; Terajima, Jun; Kusumoto, Masahiro; Iguchi, Atsushi; Kurokawa, Ken; Ogura, Yoshitoshi; Asadulghani, Md; Nakayama, Keisuke; Murase, Kazunori; Ohnishi, Makoto; Iyoda, Sunao; Watanabe, Haruo; Hayashi, Tetsuya

2009-09-01

Enterohemorrhagic Escherichia coli O157 (EHEC O157) is a food-borne pathogen that has raised worldwide public health concern. The development of simple and rapid strain-typing methods is crucial for the rapid detection and surveillance of EHEC O157 outbreaks. In the present study, we developed a multiplex PCR-based strain-typing method for EHEC O157, which is based on the variability in genomic location of IS629 among EHEC O157 strains. This method is very simple, in that the procedures are completed within 2 h, the analysis can be performed without the need for special equipment or techniques (requiring only conventional PCR and agarose gel electrophoresis systems), the results can easily be transformed into digital data, and the genes for the major virulence markers of EHEC O157 (the stx(1), stx(2), and eae genes) can be detected simultaneously. Using this method, 201 EHEC O157 strains showing different XbaI digestion patterns in pulsed-field gel electrophoresis (PFGE) analysis were classified into 127 types, and outbreak-related strains showed identical or highly similar banding patterns. Although this method is less discriminatory than PFGE, it may be useful as a primary screening tool for EHEC O157 outbreaks.

Push-Broom-Type Very High-Resolution Satellite Sensor Data Correction Using Combined Wavelet-Fourier and Multiscale Non-Local Means Filtering.

PubMed

Kang, Wonseok; Yu, Soohwan; Seo, Doochun; Jeong, Jaeheon; Paik, Joonki

2015-09-10

In very high-resolution (VHR) push-broom-type satellite sensor data, both destriping and denoising methods have become chronic problems and attracted major research advances in the remote sensing fields. Since the estimation of the original image from a noisy input is an ill-posed problem, a simple noise removal algorithm cannot preserve the radiometric integrity of satellite data. To solve these problems, we present a novel method to correct VHR data acquired by a push-broom-type sensor by combining wavelet-Fourier and multiscale non-local means (NLM) filters. After the wavelet-Fourier filter separates the stripe noise from the mixed noise in the wavelet low- and selected high-frequency sub-bands, random noise is removed using the multiscale NLM filter in both low- and high-frequency sub-bands without loss of image detail. The performance of the proposed method is compared to various existing methods on a set of push-broom-type sensor data acquired by Korean Multi-Purpose Satellite 3 (KOMPSAT-3) with severe stripe and random noise, and the results of the proposed method show significantly improved enhancement results over existing state-of-the-art methods in terms of both qualitative and quantitative assessments.

Push-Broom-Type Very High-Resolution Satellite Sensor Data Correction Using Combined Wavelet-Fourier and Multiscale Non-Local Means Filtering

PubMed Central

Kang, Wonseok; Yu, Soohwan; Seo, Doochun; Jeong, Jaeheon; Paik, Joonki

2015-01-01

In very high-resolution (VHR) push-broom-type satellite sensor data, both destriping and denoising methods have become chronic problems and attracted major research advances in the remote sensing fields. Since the estimation of the original image from a noisy input is an ill-posed problem, a simple noise removal algorithm cannot preserve the radiometric integrity of satellite data. To solve these problems, we present a novel method to correct VHR data acquired by a push-broom-type sensor by combining wavelet-Fourier and multiscale non-local means (NLM) filters. After the wavelet-Fourier filter separates the stripe noise from the mixed noise in the wavelet low- and selected high-frequency sub-bands, random noise is removed using the multiscale NLM filter in both low- and high-frequency sub-bands without loss of image detail. The performance of the proposed method is compared to various existing methods on a set of push-broom-type sensor data acquired by Korean Multi-Purpose Satellite 3 (KOMPSAT-3) with severe stripe and random noise, and the results of the proposed method show significantly improved enhancement results over existing state-of-the-art methods in terms of both qualitative and quantitative assessments. PMID:26378532

New well testing applications of the pressure derivative

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

Onur, M.

1989-01-01

This work presents new derivative type curves based on a new derivative group which is equal to the dimensionless pressure group divided by its logarithmic derivative with respect to dimensionless time group. One major advantage of these type curves is that the type-curve match of field pressure/pressure-derivative data with the new derivative type curves is accomplished by moving the field data plot in only the horizontal direction. This type-curve match fixes time match-point values. The pressure change versus time data is then matched with the dimensionless pressure solution to determine match-point values. Well/reservoir parameters can then be estimated in themore » standard way. This two step type-curve matching procedure increases the likelihood of obtaining a unique match. Moreover, the unique correspondence between the ordinate of the field data plot and the new derivative type curves should prove useful in determining whether given field data actually represents the well/reservoir model assumed by a selected type curve solution. It is also shown that the basic idea used in construction the type curves can be used to ensure that proper semilog straight lines are chosen when analyzing pressure data by semilog methods. Analysis of both drawdown and buildup data is considered and actual field cases are analyzed using the new derivative type curves and the semilog identification method. This work also presents new methods based on the pressure derivative to analyze buildup data obtained at a well (fracture or unfractured) produced to pseudosteady-state prior to shut-in. By using a method of analysis based on the pressure derivative, it is shown that a well's drainage area at the instant of shut-in and the flow capacity can be computed directly from buildup data even in cases where conventional semilog straight lines are not well-defined.« less

Method of junction formation for CIGS photovoltaic devices

DOEpatents

Delahoy, Alan E.

2006-03-28

Sulfur is used to improve the performance of CIGS devices prepared by the evaporation of a single source ZIS type compound to form a buffer layer on the CIGS. The sulfur may be evaporated, or contained in the ZIS type material, or both. Vacuum evaporation apparatus of many types useful in the practice of the invention are known in the art. Other methods of delivery, such as sputtering, or application of a thiourea solution, may be substituted for evaporation.

Method of junction formation for CIGS photovoltaic devices

DOEpatents

Delahoy, Alan E.

2010-01-26

Sulfur is used to improve the performance of CIGS devices prepared by the evaporation of a single source ZIS type compound to form a buffer layer on the CIGS. The sulfur may be evaporated, or contained in the ZIS type material, or both. Vacuum evaporation apparatus of many types useful in the practice of the invention are known in the art. Other methods of delivery, such as sputtering, or application of a thiourea solution, may be substituted for evaporation.

Using the Fusion Proximal Area Method and Gravity Method to Identify Areas with Physician Shortages

PubMed Central

Xiong, Xuechen; Jin, Chao; Chen, Haile; Luo, Li

2016-01-01

Objectives This paper presents a geographic information system (GIS)-based proximal area method and gravity method for identifying areas with physician shortages. The innovation of this paper is that it uses the appropriate methods to discover each type of health resource and then integrates all these methods to assess spatial access to health resources using population distribution data. In this way, spatial access to health resources for an entire city can be visualized in one neat package, which can help health policy makers quickly comprehend realistic distributions of health resources at a macro level. Methods First, classify health resources according to the trade areas of the patients they serve. Second, apply an appropriate method to each different type of health resource to measure spatial access to those resources. Third, integrate all types of access using population distribution data. Results In case study of Shanghai with the fusion method, areas with physician shortages are located primarily in suburban districts, especially in district junction areas. The result suggests that the government of Shanghai should pay more attention to these areas by investing in new or relocating existing health resources. Conclusion The fusion method is demonstrated to be more accurate and practicable than using a single method to assess spatial access to health resources. PMID:27695105

Type-2 fuzzy set extension of DEMATEL method combined with perceptual computing for decision making

NASA Astrophysics Data System (ADS)

Hosseini, Mitra Bokaei; Tarokh, Mohammad Jafar

2013-05-01

Most decision making methods used to evaluate a system or demonstrate the weak and strength points are based on fuzzy sets and evaluate the criteria with words that are modeled with fuzzy sets. The ambiguity and vagueness of the words and different perceptions of a word are not considered in these methods. For this reason, the decision making methods that consider the perceptions of decision makers are desirable. Perceptual computing is a subjective judgment method that considers that words mean different things to different people. This method models words with interval type-2 fuzzy sets that consider the uncertainty of the words. Also, there are interrelations and dependency between the decision making criteria in the real world; therefore, using decision making methods that cannot consider these relations is not feasible in some situations. The Decision-Making Trail and Evaluation Laboratory (DEMATEL) method considers the interrelations between decision making criteria. The current study used the combination of DEMATEL and perceptual computing in order to improve the decision making methods. For this reason, the fuzzy DEMATEL method was extended into type-2 fuzzy sets in order to obtain the weights of dependent criteria based on the words. The application of the proposed method is presented for knowledge management evaluation criteria.

Drug-target interaction prediction via class imbalance-aware ensemble learning.

PubMed

Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

2016-12-22

Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was able to predict many of the interactions successfully. Our proposed method has improved the prediction performance over the existing work, thus proving the importance of addressing problems pertaining to class imbalance in the data.

A Maze Game on Android Using Growing Tree Method

NASA Astrophysics Data System (ADS)

Hendrawan, Y. F.

2018-01-01

A maze is a type of puzzle games where a player moves in complex and branched passages to find a particular target or location. One method to create a maze is the Growing Tree method. The method creates a tree that has branches which are the paths of a maze. This research explored three types of Growing Tree method implementations for maze generation on Android mobile devices. The layouts produced could be played in first and third-person perspectives. The experiment results showed that it took 17.3 seconds on average to generate 20 cells x 20 cells dynamic maze layouts.

Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

PubMed

Scholz, Christian F P; Jensen, Anders

2017-01-01

The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

Methods and Materials for Entrepreneurship Education, Phase I. Final Report.

ERIC Educational Resources Information Center

Evans, Rupert N.; And Others

A study was conducted to compare the personality characteristics of two types of entrepreneurs, the craft-type and the opportunistic-type, which were described by Norman R. Smith. The craft-type entrepreneur is mainly interested in self-employment and owns a small business while the opportunistic-type, although interested in self-employment,…

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2).

PubMed

de Oliveira, Gilberto Santos; Kawahara, Rebeca; Rosa-Fernandes, Livia; Mule, Simon Ngao; Avila, Carla Cristi; Teixeira, Marta M G; Larsen, Martin R; Palmisano, Giuseppe

2018-04-01

Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2. The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms. This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method allows T. cruzi strain typing using MS/MS spectra as discriminatory features and allows the differentiation of TcI-TcVI DTUs. Similar to genomic-based strategies, the Tc-STAMS2 method allows identification of strains within DTUs. Its robustness towards different experimental and biological variables makes it a valuable complementary strategy to the current T. cruzi genotyping assays. Moreover, this method can be used to identify DTU-specific features correlated with the strain phenotype.