Towards realistic simulations of lava dome growth using the level set method

The level set method has been implemented in a computational volcanology context. New techniques are presented to solve the advection equation and the reinitialisation equation. These techniques are based upon an algorithm developed in the finite difference context, but are modified to take advantage of the robustness of the finite element method. The resulting algorithm is tested on a well documented Rayleigh–Taylor instability benchmark [19], and on an axisymmetric problem where the analytical solution is known. Finally, the algorithm is applied to a basic study of lava dome growth.

On the construction of nearest neighbour balanced row-column designs

Nearest–neighbour balance is considered a desirable property for an experiment to possess in situations where experimental units are influenced by their neighbours. This paper introduces a measure of the degree of nearest–neighbour balance of a design. The measure is used in an algorithm which generates nearest–neighbour balanced designs and is readily modified to obtain designs with various types of nearest–neighbour balance. Nearest–neighbour balanced designs are produced for a wide class of parameter settings, and in particular for those settings for which such designs cannot be found by existing direct combinatorial methods. In addition, designs with unequal row and column sizes, and designs with border plots are constructed using the approach presented here.

An improved seeded region growing algorithm

Recently Adams and Bischof (1994) proposed a novel region growing algorithm for segmenting intensity images. The inputs to the algorithm are the intensity image and a set of seeds - individual points or connected components - that identify the individual regions to be segmented. The algorithm grows these seed regions until all of the image pixels have been assimilated. Unfortunately the algorithm is inherently dependent on the order of pixel processing. This means, for example, that raster order processing and anti-raster order processing do not, in general, lead to the same tessellation. In this paper we propose an improved seeded region growing algorithm that retains the advantages of the Adams and Bischof algorithm fast execution, robust segmentation, and no tuning parameters - but is pixel order independent. (C) 1997 Elsevier Science B.V.

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.

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.

The Modified Card Sorting Test: Test-retest stability and relationships with demographic variables in a healthy older adult sample

Objectives. To investigate the test-retest stability of a standardized version of Nelson's (1976) Modified Card Sorting Test (MCST) and its relationships with demographic variables in a sample of healthy older adults. Design. A standard card order and administration were devised for the MCST and administered to participants at an initial assessment, and again at a second session conducted a minimum of six months later in order to examine its test-retest stability. Participants were also administered the WAIS-R at initial assessment in order to provide a measure of psychometric intelligence. Methods. Thirty-six (24 female, 12 male) healthy older adults aged 52 to 77 years with mean education 12.42 years (SD = 3.53) completed the MCST on two occasions approximately 7.5 months (SD = 1.61) apart. Stability coefficients and test-retest differences were calculated for the range of scores. The effect of gender on MCST performance was examined. Correlations between MCST scores and age, education and WAIS-R IQs were also determined. Results. Stability coefficients ranged from .26 for the percent perseverative errors measure to .49 for the failure to maintain set measure. Several measures were significantly correlated with age, education and WAIS-R IQs, although no effect of gender on MCST performance was found. Conclusions. None of the stability coefficients reached the level required for clinical decision making. The results indicate that participants' age, education, and intelligence need to be considered when interpreting MCST performance. Normative studies of MCST performance as well as further studies with patients with executive dysfunction are needed.

Comparison of carbohydrate-deficient transferrin, immunoglobulin A antibodies reactive with acetaldehyde-modified protein and acetaldehyde-modified albumin with conventional markers of alcohol consumption

Carbohydrate-deficient transferrin (CDT) has emerged as the best new marker for alcohol abuse. Recently plasma immunoglobulin A (IgA) reactivity with acetaldehyde (AcH)-modified proteins, or the modified proteins per se, have been proposed as a markers for high levels of alcohol consumption. In this study, we have compared CDT, IgA reactivity with AcH adducts (IgA ASR), and AcH-modified albumin with conventional markers of high alcohol intake in groups with well-defined drinking histories, The plasma activity of ALT, AST, and gamma-glutamyltransferase increased steadily with increasing alcohol consumption, CDT and AcH-modified albumin showed a similar pattern, whereas IgA ASR appeared only to be elevated after a threshold level of consumption had been reached, Neither CDT IgA ASR or AcH-modified albumin correlated strongly with any of the conventional markers or each other. This study shows that CDT, IgA ASR, AcH-modified albumin, and the conventional markers are not related, but suggests that the concurrent use of CDT and IgA ASR may lead to better identification of high alcohol intake.

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.

Protein sequence threading, the alignment problem, and a two-step strategy

Conventionally, protein structure prediction via threading relies on some nonoptimal method to align a protein sequence to each member of a library of known structures. We show how a score function (force field) can be modified so as to allow the direct application of a dynamic programming algorithm to the problem. This involves an approximation whose damage can be minimized by an optimization process during score function parameter determination. The method is compared to sequence to structure alignments using a more conventional pair-wise score function and the frozen approximation. The new method produces results comparable to the frozen approximation, but is faster and has fewer adjustable parameters. It is also free of memory of the template's original amino acid sequence, and does not suffer from a problem of nonconvergence, which can be shown to occur with the frozen approximation. Alignments generated by the simplified score function can then be ranked using a second score function with the approximations removed. (C) 1999 John Wiley & Sons, Inc.

Trial-of-antibiotic algorithm for the diagnosis of tuberculosis in a district hospital in a developing country with high HIV prevalence

OBJECTIVE: To evaluate a diagnostic algorithm for pulmonary tuberculosis based on smear microscopy and objective response to trial of antibiotics. SETTING: Adult medical wards, Hlabisa Hospital, South Africa, 1996-1997. METHODS: Adults with chronic chest symptoms and abnormal chest X-ray had sputum examined for Ziehl-Neelsen stained acid-fast bacilli by light microscopy. Those with negative smears were treated with amoxycillin for 5 days and assessed. Those who had not improved were treated with erythromycin for 5 days and reassessed. Response was compared with mycobacterial culture. RESULTS: Of 280 suspects who completed the diagnostic pathway, 160 (57%) had a positive smear, 46 (17%) responded to amoxycillin, 34 (12%) responded to erythromycin and 40 (14%) were treated as smear-negative tuberculosis. The sensitivity (89%) and specificity (84%) of the full algorithm for culture-positive tuberculosis were high. However, 11 patients (positive predictive value [PPV] 95%) were incorrectly diagnosed with tuberculosis, and 24 cases of tuberculosis (negative predictive value [NPV] 70%) were not identified. NPV improved to 75% when anaemia was included as a predictor. Algorithm performance was independent of human immunodeficiency virus status. CONCLUSION: Sputum smear microscopy plus trial of antibiotic algorithm among a selected group of tuberculosis suspects may increase diagnostic accuracy in district hospitals in developing countries.

Characterization of the structural and surface properties of chemically modified MCM-41 material

Mesoporous Mobil catalytic materials of number 41 (MCM-41) silica was chemically modified using both inorganic and organic precursors and characterized using the techniques, XRD, XPS, MAS NMR, FTIR, W-Vis, and physical adsorption of nitrogen, hydrocarbons (hexane, benzene, acetone, and methanol) and water vapor. Modification using organic reagents was found to result in a significant loss in porosity and a shape change of surface properties (increased hydrophobicity and decreased acidity). With inorganic modifying reagents, the decrease in porosity was also observed while the surface properties were not significantly altered as reflected by the adsorption isotherms of organics and water vapors. Chemical modifications can greatly improve the hydrothermal stability of MCM-41 material because of the enhanced surface hydrophobicity (with organic modifiers) or increased pore wall thickness (with inorganic modifiers). (C) 2000 Elsevier Science B.V. All rights reserved.

Minimum-order stable recursive filter design via the genetic algorithm approach

In this paper, the minimum-order stable recursive filter design problem is proposed and investigated. This problem is playing an important role in pipeline implementation sin signal processing. Here, the existence of a high-order stable recursive filter is proved theoretically, in which the upper bound for the highest order of stable filters is given. Then the minimum-order stable linear predictor is obtained via solving an optimization problem. In this paper, the popular genetic algorithm approach is adopted since it is a heuristic probabilistic optimization technique and has been widely used in engineering designs. Finally, an illustrative example is sued to show the effectiveness of the proposed algorithm.

Long-term quantification of the release of monomers from dental resin composites and a resin-modified glass ionomer cement

This study quantified the release of monomers from polymerized specimens of four commercially available resin composites and one glass ionomer cement immersed in water:ethanol solutions. Individual standard curves were prepared from five monomers: (1) triethylene glycol dimethacrylate (TEGDMA), (2) 2-hydroxy-ethyl methacrylate (HEMA), (3) urethane dimethacrylate (UDMA), (4) bisphenol A glycidyl dimethacrylate (BISGMA), and (5) bisphenol A. The concentration of the monomers was determined at Days 1, 7, 30, and 90 with the use of electrospray ionization/mass spectrometry. Data were expressed in mean mumol per mm(2) surface area of specimen and analyzed with Scheffe's test (P < 0.05). The following monomers were found in water: monomers (1) and (2) from Delton sealant, monomer (5) from ScotchBond Multipurpose Adhesive and Delton sealant, monomer (3) from Definite and monomer (4) from Fuji II LC, ScotchBond Multipurpose Adhesive, Synergy and Definite. All these monomers increased in concentration over time, with the exception of monomer (1) from Delton sealant. Monomers (3) and (5) were found in extracts of materials despite their absence from the manufacturer's published composition. All monomers were released in significantly higher concentrations in water:ethanol solutions than in water. The greatest release of monomers occurred in the first day. The effect of the measured concentrations of monomers (1-5) on human genes, cells, or tissues needs to be considered with the use of a biological model. (C) 2002 Wiley Periodicals, Inc.

An equivalent algorithm for simulating thermal effects of magma intrusion problems in porous rocks

An equivalent algorithm is proposed to simulate thermal effects of the magma intrusion in geological systems, which are composed of porous rocks. Based on the physical and mathematical equivalence, the original magma solidification problem with a moving boundary between the rock and intruded magma is transformed into a new problem without the moving boundary but with a physically equivalent heat source. From the analysis of an ideal solidification model, the physically equivalent heat source has been determined in this paper. The major advantage in using the proposed equivalent algorithm is that the fixed finite element mesh with a variable integration time step can be employed to simulate the thermal effect of the intruded magma solidification using the conventional finite element method. The related numerical results have demonstrated the correctness and usefulness of the proposed equivalent algorithm for simulating the thermal effect of the intruded magma solidification in geological systems. (C) 2003 Elsevier B.V. All rights reserved.

A spectral clustering algorithm for manufacturing cell formation

A graph clustering algorithm constructs groups of closely related parts and machines separately. After they are matched for the least intercell moves, a refining process runs on the initial cell formation to decrease the number of intercell moves. A simple modification of this main approach can deal with some practical constraints, such as the popular constraint of bounding the maximum number of machines in a cell. Our approach makes a big improvement in the computational time. More importantly, improvement is seen in the number of intercell moves when the computational results were compared with best known solutions from the literature. (C) 2009 Elsevier Ltd. All rights reserved.