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At least 343 records · Page 19Linked to original sources

PubMed2004

Constructing sequence alignments from a Markov decision model with estimated parameter values.

Current methods for aligning biological sequences are based on dynamic programming algorithms. If large numbers of sequences or a number of long sequences are to be aligned, the required computations are expensive in memory and central processing unit (CPU) time. In an attempt to bring the tools of large-scale linear programming (LP) methods to bear on this problem, we formulate the alignment process as a controlled Markov chain and construct a suggested alignment based on policies that minimise the expected total cost of the alignment. We discuss the LP associated with the total expected discounted cost and show the results of a solution of the problem based on a primal-dual interior point method. Model parameters, estimated from aligned sequences, along with cost function parameters are used to construct the objective and constraint conditions of the LP problem. This article concludes with a discussion of some alignments obtained from the LP solutions of problems with various cost function parameter values.

Algorithms↗

PubMed2004

Minimax design of optically transparent and reflective coatings.

We consider the design problem of creating coatings that are either highly reflective or highly transparent. The goal is to create an optical element, consisting of planar dielectric layers, that reflects (or transmits) energy over a given range of wavelengths and angles of incidence. The approach that we take is to formulate the problem as a minimax optimization problem. We demonstrate that the approach can be effective in producing coatings of a few layers with desirable properties.

Journal Article↗

PubMedDate not supplied

kappa Nearest neighbors QSAR modeling as a variational problem: theory and applications.

Variable selection k Nearest Neighbor (kNN) QSAR is a popular nonlinear methodology for building correlation models between chemical descriptors of compounds and biological activities. The models are built by finding a subspace of the original descriptor space where activity of each compound in the data set is most accurately predicted as the averaged activity of its k nearest neighbors in this subspace. We have formulated the problem of searching for the optimized kNN QSAR models with the highest predictive power as a variational problem. We have investigated the relative contribution of several model parameters such as the selection of variables, the number (k) of nearest neighbors, and the shape of the weighting function used to evaluate the contributions of k nearest neighbor compound activities to the predicted activity of each compound. We have derived the expression for the weighting function which maximizes the model performance. This optimization methodology was applied to several experimental data sets divided into the training and test sets. We report a significant improvement of both the leave-one-out cross-validated R(2) (q(2)) for the training sets and predictive R(2) of the test sets in all cases. Depending on the data set, the average improvements in the prediction accuracy (prediction R(2)) for the test sets ranged between 1.1% and 94% and for the training sets (q(2)) between 3.5% and 118%. We also describe a modified computational procedure for model building based on the use of relational databases to store descriptors and calculate compounds' similarities, which simplifies calculations and increases their efficiency.

Models, Molecular↗

PubMed2003

Film flow of a suspension down an inclined plane.

A method is developed for simulating the film flow of a suspension of rigid particles with arbitrary shapes down an inclined plane in the limit of vanishing Reynolds number. The problem is formulated in terms of a system of integral equations of the first and second kind for the free-surface velocity and the traction distribution along the particle surfaces involving the a priori unknown particle linear velocity of translation and angular velocity of rotation about designated centres. The problem statement is completed by introducing scalar constraints that specify the force and torque exerted on the individual particles. A boundary-element method is implemented for solving the governing equations for the case of a two-dimensional periodic suspension. The system of linear equations arising from numerical discretization is solved using a preconditioner based on a particle-cluster iterative method recently developed by Pozrikidis (2000 Engng Analysis Bound. Elem. 25, 19-30). Numerical investigations show that the generalized minimal residual (GMRES) method with this preconditioner is significantly more efficient than the plain GMRES method used routinely in boundary-element implementations. Extensive numerical simulations for solitary particles and random suspensions illustrate the effect of the particle shape, size and aspect ratio in semi-finite shear flow, and the effect of free-surface deformability in film flow.

Computer Simulation↗

PubMedDate not supplied

Resolving and avoiding conflict with the professional staff.

The professional staff perspective radically diverges from that of management. Whereas the professional staff sees the hospital in terms of its providing quality health care to each individual patient, hospital executives see the hospital in terms of its financial and systemwide performance. Unless these divergent perspectives are effectively integrated to solve problems and formulate hospital policies, chronic conflict between hospital management and the professional staff is inevitable.

Conflict, Psychological↗

PubMedDate not supplied

[Category of needs in its general biological and psychosomatic aspects].

Analysis of psychoemotional stress which directly affects the health of the population shows that progress in studying stress and in prevention of its unfavourable consequences depends a great deal on the understanding of the human needs problem. At the same time the problem of the origin, evolution and transformation of needs is a subject of theoretical biology, since the dynamics of needs is the basis of self-development of the live nature, the specific (essential) force of live systems, the drive and aim of their active behaviour. The paper formulates the problems of further study of needs by theoretical biology, the science of human higher nervous activity and other adjacent spheres of science.

Emotions↗

PubMed1999

Measuring and modelling pollution for risk analysis.

The great scale and complexity of environmental risk analysis offers major methodological challenges to those engaged in policymaking. In this paper we describe some of those challenges from the perspective gained through our work at the University of British Columbia (UBC). We describe some of our experiences with respect to the difficult problems of formulating environmental standards and developing abatement strategies. A failed but instructive attempt to find support for experiments on a promising method of reducing acid rain will be described. Then we describe an approach to scenario analysis under hypothetical new standards. Even with measurements of ambient environmental conditions in hand the problem of inferring actual human exposures remains. For example, in very hot weather people will tend to stay inside and population levels of exposure to e.g. ozone could be well below those predicted by the ambient measurements. Setting air quality criteria should ideally recognize the discrepancies likely to arise. Computer models that incorporate spatial random pollution fields and predict actual exposures from ambient levels will be described. From there we turn to the statistical issues of measurement and modelling and some of the contributions in these areas by the UBC group and its partners elsewhere. In particular we discuss the problem of measurement error when non-linear regression models are used. We sketch our approach to imputing unmeasured predictors needed in such models, deferring details to references cited below. We describe in general terms how those imputed measurements and their errors can be accommodated within the framework of health impact analysis.

Air Pollution↗

PubMed2005

A nonparametric statistical method for image segmentation using information theory and curve evolution.

In this paper, we present a new information-theoretic approach to image segmentation. We cast the segmentation problem as the maximization of the mutual information between the region labels and the image pixel intensities, subject to a constraint on the total length of the region boundaries. We assume that the probability densities associated with the image pixel intensities within each region are completely unknown a priori, and we formulate the problem based on nonparametric density estimates. Due to the nonparametric structure, our method does not require the image regions to have a particular type of probability distribution and does not require the extraction and use of a particular statistic. We solve the information-theoretic optimization problem by deriving the associated gradient flows and applying curve evolution techniques. We use level-set methods to implement the resulting evolution. The experimental results based on both synthetic and real images demonstrate that the proposed technique can solve a variety of challenging image segmentation problems. Futhermore, our method, which does not require any training, performs as good as methods based on training.

Algorithms↗

PubMed2002

Testing model fit in longitudinal data analysis against alternatives with omitted covariates.

Several types of common model misspecifications can be re-formulated as problems of omitted covariates. These include situations with unmeasured confounders, measurement errors in observed covariates and informative censoring. Longitudinal data present special opportunities for detecting omitted covariates that are related to the observed ones differently across time than across individuals. This situation arises with period and cohort effects, as well as with usual formulations of classical measurement error in observed covariates. In this article we focus on testing for the existence of omitted covariates in longitudinal data analysis when models are fit by generalized estimation equations. When omitted covariates are present, specification of the correct link function conditionally on only observed covariates under the alternative usually involves complicated numerical integration. We propose a quasi-score test statistic that avoids the need to fit such alternative models. The statistic is asymptotically chi-square distributed under the null hypothesis of no omitted covariates with degrees of freedom determined by the assumed alternative structure. We study the significance level and the power of the quasi-score test in linear and logistic regression models. The test is then applied to an analysis of excessive daytime sleepiness.

Cohort Studies↗

PubMed1967

Cell growth and division. I. A mathematical model with applications to cell volume distributions in mammalian suspension cultures.

A mathematical model is formulated for the development of a population of cells in which the individual members may grow and divide or die. A given cell is characterized by its age and volume, and these parameters are assumed to determine the rate of volume growth and the probability per unit time of division or death. The initial value problem is formulated, and it is shown that if cell growth rate is proportional to cell volume, then the volume distribution will not converge to a time-invariant shape without an added dispersive mechanism. Mathematical simplications which are possible for the special case of populations in the exponential phase or in the steady state are considered in some detail. Experimental volume distributions of mammalian cells in exponentially growing suspension cultures are analyzed, and growth rates and division probabilities are deduced. It is concluded that the cell volume growth rate is approximately proportional to cell volume and that the division probability increases with volume above a critical threshold. The effects on volume distribution of division into daughter cells of unequal volumes are examined in computer models.

Animals↗

PubMed1982

Quality circles as a management tool for hospital pharmacy.

A pharmacy department's experience with a quality circle program is described. The quality circle is a type of participative management where a group of employees within a department voluntarily meets on a regular basis to identify and research departmental problems and formulate alternative solutions for management. The pharmacy department formed one of the first five circles at the hospital. Each circle meets for one hour weekly on hospital time. The pharmacy quality circle includes three staff pharmacists, two support staff, and a pharmacy supervisor who serves as the leader. Through brainstorming sessions, the circle has identified problems within the department. The circle collects data to help define the problems, and specific solutions are presented to management. Among the solutions recommended have been: assigning a clerk as a receptionist at the pharmacy front window so that the pharmacist would not be interrupted; widening the front window to accommodate separate lines for inpatient and outpatient prescriptions; and instituting a double-ticket procedure to help retrieve employee prescriptions. Management accepted and instituted all of the circle's proposals. The quality circle has been a successful management tool in this pharmacy department.

Attitude of Health Personnel↗

PubMed2004

Bayesian model averaging in EEG/MEG imaging.

In this paper, the Bayesian Theory is used to formulate the Inverse Problem (IP) of the EEG/MEG. This formulation offers a comparison framework for the wide range of inverse methods available and allows us to address the problem of model uncertainty that arises when dealing with different solutions for a single data. In this case, each model is defined by the set of assumptions of the inverse method used, as well as by the functional dependence between the data and the Primary Current Density (PCD) inside the brain. The key point is that the Bayesian Theory not only provides for posterior estimates of the parameters of interest (the PCD) for a given model, but also gives the possibility of finding posterior expected utilities unconditional on the models assumed. In the present work, this is achieved by considering a third level of inference that has been systematically omitted by previous Bayesian formulations of the IP. This level is known as Bayesian model averaging (BMA). The new approach is illustrated in the case of considering different anatomical constraints for solving the IP of the EEG in the frequency domain. This methodology allows us to address two of the main problems that affect linear inverse solutions (LIS): (a) the existence of ghost sources and (b) the tendency to underestimate deep activity. Both simulated and real experimental data are used to demonstrate the capabilities of the BMA approach, and some of the results are compared with the solutions obtained using the popular low-resolution electromagnetic tomography (LORETA) and its anatomically constraint version (cLORETA).

Artifacts↗

PubMed2006

Multibody grouping by inference of multiple subspaces from high-dimensional data using oriented-frames.

Recently, subspace constraints have been widely exploited in many computer vision problems such as multibody grouping. Under linear projection models, feature points associated with multiple bodies reside in multiple subspaces. Most existing factorization-based algorithms can segment objects undergoing independent motions. However, intersections among the correlated motion subspaces will lead most previous factorization-based algorithms to erroneous segmentation. To overcome this limitation, in this paper, we formulate the problem of multibody grouping as inference of multiple subspaces from a high-dimensional data space. A novel and robust algorithm is proposed to capture the configuration of the multiple subspace structure and to find the segmentation of objects by clustering the feature points into these inferred subspaces, no matter whether they are independent or correlated. In the proposed method, an Oriented-Frame (OF), which is a multidimensional coordinate frame, is associated with each data point indicating the point's preferred subspace configuration. Based on the similarity between the subspaces, novel mechanisms of subspace evolution and voting are developed. By filtering the outliers due to their structural incompatibility, the subspace configurations will emerge. Compared with most existing factorization-based algorithms that cannot correctly segment correlated motions, such as motions of articulated objects, the proposed method has a robust performance in both independent and correlated motion segmentation. A number of controlled and real experiments show the effectiveness of the proposed method. However, the current approach does not deal with transparent motions and motion subspaces of different dimensions.

Algorithms↗

PubMed1990

Gas absorption in pulmonary airways at low Peclet number.

A mathematical model is presented that investigates the mass transport of a diffusible and soluble gas contaminant through a liquid-lined tube when the Peclet number is small. The transport is determined by four dimensionless parameters: lambda, the tube aspect ratio; d, the relative difference in end concentrations; gamma, the radial transport coefficient; and Pe, the Peclet number. The problem is formulated for arbitrary gamma, but in the case of ozone and nitrous oxides the value of gamma is small. An asymptotic analysis for Pe much less than 1 and gamma much less than 1 is presented which yields the concentration field and transport characteristics we seek. It also provides a low Peclet number analysis for the conjugate problem of mass and heat transfer that is not currently available in the literature. The application to transport in the small airways of the lung is discussed, particularly the radial absorption differences in inspiratory and expiratory flow. Depending on the relative sizes of gamma and Pe, fractional uptake decreases with increasing Pe during inspiration but can increase during expiration.

Absorption↗

PubMed2005

Generalized optical theorem for scattering in inhomogeneous media.

The scattering of scalar waves by objects embedded in an inhomogeneous medium contained by a bounded volume is discussed using the method of pseudopotentials. The scattering amplitude for the object in an extended uniform medium is assumed known and used as input. The scattering process is described by using an expansion of the scattering amplitude in terms of spherical harmonics. An appropriate multipole decomposition of the Green function in the bounded medium is developed and the effective scattering amplitude in this environment is defined. The generalized optical theorem obeyed by this effective scattering amplitude is obtained and analyzed. The scattering problem is formulated entirely and explicitly in terms of the bounded medium's Green functions. This approach is thus very flexible in regards to the choice of incident field. In the case of waveguides the connection between propagation and scattering is explicit. At the same time it still allows for independent computation of the propagation and scattering aspects of the problem. This is the main advantage of using as input the scattering amplitude in an extended uniform medium.

Algorithms↗

PubMed1993

Simulation studies of biomagnetic computed tomography.

The reconstruction of planar and three-dimensional current distributions from measured biomagnetic signals is a new field of research, known as biomagnetic computed tomography. This noninvasive imaging technique promises to provide precise, millimeter-sized resolution images of the electrical currents in tissues or organs. We performed simulation studies on phantom models of electrical sources. As a first step towards the development of an imaging algorithm, we addressed a simplified problem to identify the shape and direction of current flow in a planar surface. The problem was formulated by identifying a space in which the image was to be reconstructed. The space was segmented into a grid. Each grid space represented a current element. The magnetic field at a sampling point due to the current elements was computed using the Biot-Savart law. Since there were many more current elements than sample points, the problem was undetermined and had an uncountable number of solutions. The projection theorem was used to define an analytic solution for the magnitude and orientation of the current elements in the grid space. The solution required the inversion of large matrices in double precision. Such arrays were preprocessed on a mainframe computer, which permitted them to be rendered on any workstation. The accuracy of the image was determined by comparing it with the known location of the sources. Our results show that shape of the filamentary current flow can be imaged with our techniques. The resolution of images based on the sampling of the field, number of voxels in the reconstruction space, and noise is also analyzed.

Computer Simulation↗

PubMedDate not supplied

Efficient and accurate computation of the electric fields of excitable cells.

The numerical computation of the electric fields produced by excitable cells is important in many applications. Traditionally, a potential formulation was used. An integral formulation based on the differentiation of Green's theorem, which solves directly for the electric field, is presented herein. This is desirable because the electric field is proportional to current density, which can be calculated on the cell membrane. Fredholm equations of the second kind are produced, which are more appropriate than are those of the first kind (produced by formulations based on potential). Analytic formulae are presented to calculate the required matrix entries for zeroth order triangular elements that are generally used for field computations in boundary element methods. Results indicated that significantly more accurate answers may be obtained with significantly less computation by formulating the problem directly in terms of electric field as opposed to potential. This approach has the additional advantage that, for equal intracellular and extracellular conductivities, only one matrix must be generated, and no system of simultaneous equations must be solved; this drastically reduces storage and computation requirements. Examples are given to illustrate this technique and to compare the electric field formulation with the potential formulation.

Cell Membrane↗

PubMed1984

A study of rotational brain injury.

Of concern in the paper is an investigation on brain injuries which may occur owing to an input angular acceleration of the head. The study is based on the use of an improved mathematical model for the cranium. The eccentricity of the braincase is incorporated through the consideration of a prolate spheroidal shell as the representative of the skull. Also the dissipative mechanical behaviour of the brain material (as per the observations of experimenters) has been accounted for by considering the material contained in the shell as viscoelastic. The problem is formulated in terms of prolate spheroidal coordinates. The singularities of the governing equations of motion (when expressed in the prolate coordinate system) are removed by a suitable transformation of the concerned dependent variable, viz. the one that stands for the angular displacement of a representative point of the system. In the first place the solution of the boundary value problem is sought in the Laplace transform space, by employing a finite difference technique. Use of the alternating-direction-implicit method together with Thomas algorithm was made for obtaining the angular acceleration in the transformed space. The Laplace inversion is also carried out with the help of numerical procedures (Gauss quadrature formula is used for this purpose). The results of the parametric study are presented through graphs. The plots illustrate the shear stresses and strains in the brain medium. A meaningful comparison of the computational results with those of previous investigations indicate that the eccentricity of the braincase plays a significant role in causing injury to the brain.

Animals↗