The beta modified Weibull distribution

A five-parameter distribution so-called the beta modified Weibull distribution is defined and studied. The new distribution contains, as special submodels, several important distributions discussed in the literature, such as the generalized modified Weibull, beta Weibull, exponentiated Weibull, beta exponential, modified Weibull and Weibull distributions, among others. The new distribution can be used effectively in the analysis of survival data since it accommodates monotone, unimodal and bathtub-shaped hazard functions. We derive the moments and examine the order statistics and their moments. We propose the method of maximum likelihood for estimating the model parameters and obtain the observed information matrix. A real data set is used to illustrate the importance and flexibility of the new distribution.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Matrix elements of U(2n) generators in a multishell spin-orbit basis. I. The del-operator MEs in a two-shell composite Gelfand-Paldus basis

This is the first in a series of three articles which aimed to derive the matrix elements of the U(2n) generators in a multishell spin-orbit basis. This is a basis appropriate to many-electron systems which have a natural partitioning of the orbital space and where also spin-dependent terms are included in the Hamiltonian. The method is based on a new spin-dependent unitary group approach to the many-electron correlation problem due to Gould and Paldus [M. D. Gould and J. Paldus, J. Chem. Phys. 92, 7394, (1990)]. In this approach, the matrix elements of the U(2n) generators in the U(n) x U(2)-adapted electronic Gelfand basis are determined by the matrix elements of a single Ll(n) adjoint tensor operator called the del-operator, denoted by Delta(j)(i) (1 less than or equal to i, j less than or equal to n). Delta or del is a polynomial of degree two in the U(n) matrix E = [E-j(i)]. The approach of Gould and Paldus is based on the transformation properties of the U(2n) generators as an adjoint tensor operator of U(n) x U(2) and application of the Wigner-Eckart theorem. Hence, to generalize this approach, we need to obtain formulas for the complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. The nonzero shift coefficients are uniquely determined and may he evaluated by the methods of Gould et al. [see the above reference]. In this article, we define zero-shift adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis which are appropriate to the many-electron problem. By definition, these are proportional to the corresponding two-shell del-operator matrix elements, and it is shown that the Racah factorization lemma applies. Formulas for these coefficients are then obtained by application of the Racah factorization lemma. The zero-shift adjoint reduced Wigner coefficients required for this procedure are evaluated first. All these coefficients are needed later for the multishell case, which leads directly to the two-shell del-operator matrix elements. Finally, we discuss an application to charge and spin densities in a two-shell molecular system. (C) 1998 John Wiley & Sons.

Matrix elements of U(2n) generators in a multishell spin-orbit basis. II. The two-shell nonzero shift ACCs and U(2n) generator MEs

This is the second in a series of articles whose ultimate goal is the evaluation of the matrix elements (MEs) of the U(2n) generators in a multishell spin-orbit basis. This extends the existing unitary group approach to spin-dependent configuration interaction (CI) and many-body perturbation theory calculations on molecules to systems where there is a natural partitioning of the electronic orbital space. As a necessary preliminary to obtaining the U(2n) generator MEs in a multishell spin-orbit basis, we must obtain a complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. The zero-shift coefficients were obtained in the first article of the series. in this article, we evaluate the nonzero shift adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis. We then demonstrate that the one-shell versions of these coefficients may be obtained by taking the Gelfand-Tsetlin limit of the two-shell formulas. These coefficients,together with the zero-shift types, then enable us to write down formulas for the U(2n) generator matrix elements in a two-shell spin-orbit basis. Ultimately, the results of the series may be used to determine the many-electron density matrices for a partitioned system. (C) 1998 John Wiley & Sons, Inc.

Matrix elements of U(2n) generators in a multishell spin-orbit basis. III. General formulas

This is the third and final article in a series directed toward the evaluation of the U(2n) generator matrix elements (MEs) in a multishell spin/orbit basis. Such a basis is required for many-electron systems possessing a partitioned orbital space and where spin-dependence is important. The approach taken is based on the transformation properties of the U(2n) generators as an adjoint tensor operator of U(n) x U(2) and application of the Wigner-Eckart theorem. A complete set of adjoint coupling coefficients for the two-shell composite Gelfand-Paldus basis (which is appropriate to the many-electron problem) were obtained in the first and second articles of this series. Ln the first article we defined zero-shift coupling coefficients. These are proportional to the corresponding two-shell del-operator matrix elements. See P. J. Burton and and M. D. Gould, J. Chem. Phys., 104, 5112 (1996), for a discussion of the del-operator and its properties. Ln the second article of the series, the nonzero shift coupling coefficients were derived. Having obtained all the necessary coefficients, we now apply the formalism developed above to obtain the U(2n) generator MEs in a multishell spin-orbit basis. The methods used are based on the work of Gould et al. (see the above reference). (C) 1998 John Wiley & Sons, Inc.

A study of the stability of subcycling algorithms in structural dynamics

Algorithms for explicit integration of structural dynamics problems with multiple time steps (subcycling) are investigated. Only one such algorithm, due to Smolinski and Sleith has proved to be stable in a classical sense. A simplified version of this algorithm that retains its stability is presented. However, as with the original version, it can be shown to sacrifice accuracy to achieve stability. Another algorithm in use is shown to be only statistically stable, in that a probability of stability can be assigned if appropriate time step limits are observed. This probability improves rapidly with the number of degrees of freedom in a finite element model. The stability problems are shown to be a property of the central difference method itself, which is modified to give the subcycling algorithm. A related problem is shown to arise when a constraint equation in time is introduced into a time-continuous space-time finite element model. (C) 1998 Elsevier Science S.A.

Reliability and validity of scores on scales to measure managerial aspirations

The present investigation assessed the reliability and validity of the scores of a subjective measure of desired aspirations and a behavioral measure of enacted aspirations. A sample of 5,655 employees was randomly split into two halves. Principal components analysis on Sample 1, followed by confirmatory factor analysis on Sample 2, confirmed the desired and enacted scales as distinct but related measures of managerial aspirations. The desired and enacted scales had satisfactory levels of internal consistency and temporal stability over a 1-year period. Relationships between the measures of desired and enacted managerial aspirations and both attitudinal and behavioral criteria, measured concurrently and 1 year later, provided preliminary support for convergent and discriminant validity for our sample. Desired aspirations demonstrated stronger validity than enacted aspirations. Although further examination of the psychometric properties of the scales is warranted, the present findings provide promising support for their validity and reliability for our sample.

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Subcycling first- and second-order generalizations of the trapezoidal rule

Subcycling algorithms which employ multiple timesteps have been previously proposed for explicit direct integration of first- and second-order systems of equations arising in finite element analysis, as well as for integration using explicit/implicit partitions of a model. The author has recently extended this work to implicit/implicit multi-timestep partitions of both first- and second-order systems. In this paper, improved algorithms for multi-timestep implicit integration are introduced, that overcome some weaknesses of those proposed previously. In particular, in the second-order case, improved stability is obtained. Some of the energy conservation properties of the Newmark family of algorithms are shown to be preserved in the new multi-timestep extensions of the Newmark method. In the first-order case, the generalized trapezoidal rule is extended to multiple timesteps, in a simple way that permits an implicit/implicit partition. Explicit special cases of the present algorithms exist. These are compared to algorithms proposed previously. (C) 1998 John Wiley & Sons, Ltd.

A note on extension variances in IR2

Matheron (1971) proposed an approximation of the extension variance in IR. We propose in this note an extension of this formula in IR2, based on a MacLaurin formula. Its application is shown in an example, the estimation of the maximum depressional storage of a soil surface.

Finite element modelling of temperature gradient driven rock alteration and mineralization in porous rock masses

We present finite element simulations of temperature gradient driven rock alteration and mineralization in fluid saturated porous rock masses. In particular, we explore the significance of production/annihilation terms in the mass balance equations and the dependence of the spatial patterns of rock alteration upon the ratio of the roll over time of large scale convection cells to the relaxation time of the chemical reactions. Special concepts such as the gradient reaction criterion or rock alteration index (RAI) are discussed in light of the present, more general theory. In order to validate the finite element simulation, we derive an analytical solution for the rock alteration index of a benchmark problem on a two-dimensional rectangular domain. Since the geometry and boundary conditions of the benchmark problem can be easily and exactly modelled, the analytical solution is also useful for validating other numerical methods, such as the finite difference method and the boundary element method, when they are used to dear with this kind of problem. Finally, the potential of the theory is illustrated by means of finite element studies related to coupled flow problems in materially homogeneous and inhomogeneous porous rock masses. (C) 1998 Elsevier Science S.A. All rights reserved.

Effects of medium thermoelasticity on high Rayleigh number steady-state heat transfer and mineralization in deformable fluid-saturated porous media heated from below

In this paper, a solution method is presented to deal with fully coupled problems between medium deformation, pore-fluid flow and heat transfer in fluid-saturated porous media having supercritical Rayleigh numbers. To validate the present solution method, analytical solutions to a benchmark problem are derived for some special cases. After the solution method is validated, a numerical study is carried out to investigate the effects of medium thermoelasticity on high Rayleigh number steady-state heat transfer and mineralization in fluid-saturated media when they are heated from below. The related numerical results have demonstrated that: (1) medium thermoelasticity has a little influence on the overall pattern of convective pore-fluid flow, but it has a considerable effect on the localization of medium deformation, pore-fluid flow, heat transfer and mineralization in a porous medium, especially when the porous medium is comprised of soft rock masses; (2) convective pore-fluid flow plays a very important role in the localization of medium deformation, heat transfer and mineralization in a porous medium. (C) 1999 Elsevier Science S.A. All rights reserved.

A numerical study of pore-fluid, thermal and mass flow iu fluid-saturated porous rock basins

We present a numerical methodology for the study of convective pore-fluid, thermal and mass flow in fluid-saturated porous rock basins. lit particular, we investigate the occurrence and distribution pattern of temperature gradient driven convective pore-fluid flow and hydrocarbon transport in the Australian North West Shelf basin. The related numerical results have demonstrated that: (1) The finite element method combined with the progressive asymptotic approach procedure is a useful tool for dealing with temperature gradient driven pore-fluid flow and mass transport in fluid-saturated hydrothermal basins; (2) Convective pore-fluid flow generally becomes focused in more permeable layers, especially when the layers are thick enough to accommodate the appropriate convective cells; (3) Large dislocation of strata has a significant influence off the distribution patterns of convective pore;fluid flow, thermal flow and hydrocarbon transport in the North West Shelf basin; (4) As a direct consequence of the formation of convective pore-fluid cells, the hydrocarbon concentration is highly localized in the range bounded by two major faults in the basin.

A consistent point-searching algorithm for solution interpolation in unstructured meshes consisting of 4-node bilinear quadrilateral elements

To translate and transfer solution data between two totally different meshes (i.e. mesh 1 and mesh 2), a consistent point-searching algorithm for solution interpolation in unstructured meshes consisting of 4-node bilinear quadrilateral elements is presented in this paper. The proposed algorithm has the following significant advantages: (1) The use of a point-searching strategy allows a point in one mesh to be accurately related to an element (containing this point) in another mesh. Thus, to translate/transfer the solution of any particular point from mesh 2 td mesh 1, only one element in mesh 2 needs to be inversely mapped. This certainly minimizes the number of elements, to which the inverse mapping is applied. In this regard, the present algorithm is very effective and efficient. (2) Analytical solutions to the local co ordinates of any point in a four-node quadrilateral element, which are derived in a rigorous mathematical manner in the context of this paper, make it possible to carry out an inverse mapping process very effectively and efficiently. (3) The use of consistent interpolation enables the interpolated solution to be compatible with an original solution and, therefore guarantees the interpolated solution of extremely high accuracy. After the mathematical formulations of the algorithm are presented, the algorithm is tested and validated through a challenging problem. The related results from the test problem have demonstrated the generality, accuracy, effectiveness, efficiency and robustness of the proposed consistent point-searching algorithm. Copyright (C) 1999 John Wiley & Sons, Ltd.