A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Elemental unbiased estimators for the Generalized Pareto tail

Unbiased location- and scale-invariant `elemental' estimators for the GPD tail parameter are constructed. Each involves three log-spacings. The estimators are unbiased for finite sample sizes, even as small as N=3. It is shown that the elementals form a complete basis for unbiased location- and scale-invariant estimators constructed from linear combinations of log-spacings. Preliminary numerical evidence is presented which suggests that elemental combinations can be constructed which are consistent estimators of the tail parameter for samples drawn from the pure GPD family.

Sources of variability in the free-ball micro-scale abrasion test

In the 'free-ball' version of the micro-scale abrasion or ball-cratering test the rotating ball rests against a tilted sample and a grooved drive shaft. Tests under nominally identical conditions with different apparatus commonly show small but significant differences in measured wear rate. An indirect method has been developed and demonstrated for continuous on-line measurement of the coefficient of friction in the free-ball test. Experimental investigation of the effects of sample tilt angle and drive shaft groove width shows that both these factors influence the stability of the rotation of the ball, and the shape of the abrasive slurry pool, which in turn affect the coefficient of friction in the wear scar area and the measured wear rate. It is suggested that in order to improve the reproducibility of this method the geometry of the apparatus should be specified. For the apparatus used in this work with a steel ball of 25 mm diameter, a sample tilt angle of 60-75° and a shaft groove width of about 10mm provided the most stable ball motion and a wear rate which showed least variability. © 2004 Elsevier B.V. All rights reserved.

Bayesian two-sample tests

In this paper, we present two classes of Bayesian approaches to the two-sample problem. Our first class of methods extends the Bayesian t-test to include all parametric models in the exponential family and their conjugate priors. Our second class of methods uses Dirichlet process mixtures (DPM) of such conjugate-exponential distributions as flexible nonparametric priors over the unknown distributions.

A comparison of different failure assessment methodologies applied to the NESC-1 test

Predictions for a 75x205mm surface semi-elliptic defect in the NESC-1 spinning cylinder test have been made using BS PD 6493:1991, the R6 procedure, non-linear cracked body finite element analysis techniques and the local approach to fracture. All the techniques agree in predicting ductile tearing near the inner surface of the cylinder followed by cleavage initiation. However they differ in the amount of ductile tearing, and the exact location and time of any cleavage event. The amount of ductile tearing decreases with increasing sophistication in the analysis, due to the drop in peak crack driving force and more explicit consideration of constraint effects. The local approach predicts a high probability of cleavage in both HAZ and base material after 190s, while the other predictions suggest that cleavage is unlikely in the HAZ due to constraint loss, but likely in the underlying base material. The timing of this event varies from ∼150s for R6 predictions to ∼250-300s using non-linear cracked body analysis.

An investigation into the residual stresses in an aluminium 2024 test weld

This paper uses finite element (FE) analysis to examine the residual stresses generated during the TIG welding of aluminium aerospace alloys. It also looks at whether such an approach could be useful for evaluating the effectiveness of various residual stress control techniques. However, such simulations cannot be founded in a vacuum. They require accurate measurements to refine and validate them. The unique aspect of this work is that two powerful engineering techniques are combined: FE modelling and neutron diffraction. Weld trials were performed and the direct measurement of residual strain made using the ENGIN neutron diffraction strain scanning facility. The predicted results show an excellent agreement with experimental values. Finally this model is used to simulate a weld made using a "Low Stress No Distortion" (LSND) technique. Although the stress reduction predicted is only moderate, the study suggests the approach to be a quick and efficient means of optimising such techniques.

Estimating material elasticity by spherical indentation load-relaxation tests on viscoelastic samples of finite thickness

A two-step viscoelastic spherical indentation method is proposed to compensate for 1) material relaxation and 2) sample thickness. In the first step, the indenter is moved at a constant speed and the reaction force is measured. In the second step, the indenter is held at a constant position and the relaxation response of the material is measured. Then the relaxation response is fit with a multi-exponential function which corresponds to a three-branch general Maxwell model. The relaxation modulus is derived by correcting the finite ramp time introduced in the first step. The proposed model takes into account the sample thickness, which is important for applications in which the sample thickness is less than ten times the indenter radius. The model is validated numerically by finite element simulations. Experiments are carried out on a 10% gelatin phantom and a chicken breast sample with the proposed method. The results for both the gelatin phantom and the chicken breast sample agree with the results obtained from a surface wave method. Both the finite element simulations and experimental results show improved elasticity estimations by incorporating the sample thickness into the model. The measured shear elasticities of the 10% gelatin sample are 6.79 and 6.93 kPa by the proposed finite indentation method at sample thickness of 40 and 20 mm, respectively. The elasticity of the same sample is estimated to be 6.53 kPa by the surface wave method. For the chicken breast sample, the shear elasticity is measured to be 4.51 and 5.17 kPa by the proposed indentation method at sample thickness of 40 and 20 mm, respectively. Its elasticity is measured by the surface wave method to be 4.14 kPa. © 2011 IEEE.

Experimental and numerical study of grout injections in silty soils

Compensation grouting is increasingly employed as a mitigation technique of settlements induced by tunnelling and its effectiveness both in clayey and sandy soils is reported in a wide number of case histories. However, the results are highly dependent on grout properties, injection characteristics and soil properties. An experimental study was conducted to investigate the parameters that control grout injections in silty soils. The results from one injection test in a large sample of silty soil show that the compensation efficiency, defined as the ratio of the volume of heave obtained at ground surface and the injected grout volume, is much lower than one and tends to decrease with time, while the initial volume of grout lost due to pressure filtration is small. Finally, results from finite elements back analyses of the laboratory test show that a good agreement with the experimental data can be obtained if the development of large strains is taken into account. © 2012 Taylor & Francis Group.

3D modeling of high-T c superconductors by finite element software

A three-dimensional (3D) numerical model is proposed to solve the electromagnetic problems involving transport current and background field of a high-T c superconducting (HTS) system. The model is characterized by the E-J power law and H-formulation, and is successfully implemented using finite element software. We first discuss the model in detail, including the mesh methods, boundary conditions and computing time. To validate the 3D model, we calculate the ac loss and trapped field solution for a bulk material and compare the results with the previously verified 2D solutions and an analytical solution. We then apply our model to test some typical problems such as superconducting bulk array and twisted conductors, which cannot be tackled by the 2D models. The new 3D model could be a powerful tool for researchers and engineers to investigate problems with a greater level of complicity.

Deformation and fracture of impulsively loaded sandwich panels

Light metal sandwich panel structures with cellular cores have attracted interest for multifunctional applications which exploit their high bend strength and impact energy absorption. This concept has been explored here using a model 6061-T6 aluminum alloy system fabricated by friction stir weld joining extruded sandwich panels with a triangular corrugated core. Micro-hardness and miniature tensile coupon testing revealed that friction stir welding reduced the strength and ductility in the welds and a narrow heat affected zone on either side of the weld by approximately 30%. Square, edge clamped sandwich panels and solid plates of equal mass per unit area were subjected to localized impulsive loading by the impact of explosively accelerated, water saturated, sand shells. The hydrodynamic load and impulse applied by the sand were gradually increased by reducing the stand-off distance between the test charge and panel surfaces. The sandwich panels suffered global bending and stretching, and localized core crushing. As the pressure applied by the sand increased, face sheet fracture by a combination of tensile stretching and shear-off occurred first at the two clamped edges of the panels that were parallel with the corrugation and weld direction. The plane of these fractures always lay within the heat affected zone of the longitudinal welds. For the most intensively loaded panels additional cracks occurred at the other clamped boundaries and in the center of the panel. To investigate the dynamic deformation and fracture processes, a particle-based method has been used to simulate the impulsive loading of the panels. This has been combined with a finite element analysis utilizing a modified Johnson-Cook constitutive relation and a Cockcroft-Latham fracture criterion that accounted for local variation in material properties. The fully coupled simulation approach enabled the relationships between the soil-explosive test charge design, panel geometry, spatially varying material properties and the panel's deformation and dynamic failure responses to be explored. This comprehensive study reveals the existence of a strong instability in the loading that results from changes in sand particle reflection during dynamic evolution of the panel's surface topology. Significant fluid-structure interaction effects are also discovered at the sample sides and corners due to changes of the sand reflection angle by the edge clamping system. © 2012 Elsevier Ltd. All rights reserved.

MgB2 sample tests for possible applications of superconducting fault current limiters

Cheap to make and easy to shape, Magnesium Diboride (MgB2) throws the field of applied superconductivity wide open. Great efforts have been made to develop a super-conducting fault current limiter (SFCL) using MgB 2. With a superconducting transition temperature of 39 K, MgB 2 can be conveniently cooled with commercial cryocoolers. A cryogenic desktop test system, an ac pulse generation system and a real time data acquisition program in LabView/DAQmx were developed to investigate the quench behavior of MgB2 wires under pulse overcurrents at 25 K in self-field conditions. The experimental results on the current limitation behavior show the possibilities for using MgB2 for future SFCL applications. © 2007 IEEE.