Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Real - time prediction of rainfall induced instability of residual soil slopes associated with deep cracks

The early warning based on real-time prediction of rain-induced instability of natural residual slopes helps to minimise human casualties due to such slope failures. Slope instability prediction is complicated, as it is influenced by many factors, including soil properties, soil behaviour, slope geometry, and the location and size of deep cracks in the slope. These deep cracks can facilitate rainwater infiltration into the deep soil layers and reduce the unsaturated shear strength of residual soil. Subsequently, it can form a slip surface, triggering a landslide even in partially saturated soil slopes. Although past research has shown the effects of surface-cracks on soil stability, research examining the influence of deep-cracks on soil stability is very limited. This study aimed to develop methodologies for predicting the real-time rain-induced instability of natural residual soil slopes with deep cracks. The results can be used to warn against potential rain-induced slope failures. The literature review conducted on rain induced slope instability of unsaturated residual soil associated with soil crack, reveals that only limited studies have been done in the following areas related to this topic: - Methods for detecting deep cracks in residual soil slopes. - Practical application of unsaturated soil theory in slope stability analysis. - Mechanistic methods for real-time prediction of rain induced residual soil slope instability in critical slopes with deep cracks. Two natural residual soil slopes at Jombok Village, Ngantang City, Indonesia, which are located near a residential area, were investigated to obtain the parameters required for the stability analysis of the slope. A survey first identified all related field geometrical information including slope, roads, rivers, buildings, and boundaries of the slope. Second, the electrical resistivity tomography (ERT) method was used on the slope to identify the location and geometrical characteristics of deep cracks. The two ERT array models employed in this research are: Dipole-dipole and Azimuthal. Next, bore-hole tests were conducted at different locations in the slope to identify soil layers and to collect undisturbed soil samples for laboratory measurement of the soil parameters required for the stability analysis. At the same bore hole locations, Standard Penetration Test (SPT) was undertaken. Undisturbed soil samples taken from the bore-holes were tested in a laboratory to determine the variation of the following soil properties with the depth: - Classification and physical properties such as grain size distribution, atterberg limits, water content, dry density and specific gravity. - Saturated and unsaturated shear strength properties using direct shear apparatus. - Soil water characteristic curves (SWCC) using filter paper method. - Saturated hydraulic conductivity. The following three methods were used to detect and simulate the location and orientation of cracks in the investigated slope: (1) The electrical resistivity distribution of sub-soil obtained from ERT. (2) The profile of classification and physical properties of the soil, based on laboratory testing of soil samples collected from bore-holes and visual observations of the cracks on the slope surface. (3) The results of stress distribution obtained from 2D dynamic analysis of the slope using QUAKE/W software, together with the laboratory measured soil parameters and earthquake records of the area. It was assumed that the deep crack in the slope under investigation was generated by earthquakes. A good agreement was obtained when comparing the location and the orientation of the cracks detected by Method-1 and Method-2. However, the simulated cracks in Method-3 were not in good agreement with the output of Method-1 and Method-2. This may have been due to the material properties used and the assumptions made, for the analysis. From Method-1 and Method-2, it can be concluded that the ERT method can be used to detect the location and orientation of a crack in a soil slope, when the ERT is conducted in very dry or very wet soil conditions. In this study, the cracks detected by the ERT were used for stability analysis of the slope. The stability of the slope was determined using the factor of safety (FOS) of a critical slip surface obtained by SLOPE/W using the limit equilibrium method. Pore-water pressure values for the stability analysis were obtained by coupling the transient seepage analysis of the slope using finite element based software, called SEEP/W. A parametric study conducted on the stability of an investigated slope revealed that the existence of deep cracks and their location in the soil slope are critical for its stability. The following two steps are proposed to predict the rain-induced instability of a residual soil slope with cracks. (a) Step-1: The transient stability analysis of the slope is conducted from the date of the investigation (initial conditions are based on the investigation) to the preferred date (current date), using measured rainfall data. Then, the stability analyses are continued for the next 12 months using the predicted annual rainfall that will be based on the previous five years rainfall data for the area. (b) Step-2: The stability of the slope is calculated in real-time using real-time measured rainfall. In this calculation, rainfall is predicted for the next hour or 24 hours and the stability of the slope is calculated one hour or 24 hours in advance using real time rainfall data. If Step-1 analysis shows critical stability for the forthcoming year, it is recommended that Step-2 be used for more accurate warning against the future failure of the slope. In this research, the results of the application of the Step-1 on an investigated slope (Slope-1) showed that its stability was not approaching a critical value for year 2012 (until 31st December 2012) and therefore, the application of Step-2 was not necessary for the year 2012. A case study (Slope-2) was used to verify the applicability of the complete proposed predictive method. A landslide event at Slope-2 occurred on 31st October 2010. The transient seepage and stability analyses of the slope using data obtained from field tests such as Bore-hole, SPT, ERT and Laboratory tests, were conducted on 12th June 2010 following the Step-1 and found that the slope in critical condition on that current date. It was then showing that the application of the Step-2 could have predicted this failure by giving sufficient warning time.

A simplified approach for calculating the moments of action for linear reaction-diffusion equations

The mean action time is the mean of a probability density function that can be interpreted as a critical time, which is a finite estimate of the time taken for the transient solution of a reaction-diffusion equation to effectively reach steady state. For high-variance distributions, the mean action time under-approximates the critical time since it neglects to account for the spread about the mean. We can improve our estimate of the critical time by calculating the higher moments of the probability density function, called the moments of action, which provide additional information regarding the spread about the mean. Existing methods for calculating the nth moment of action require the solution of n nonhomogeneous boundary value problems which can be difficult and tedious to solve exactly. Here we present a simplified approach using Laplace transforms which allows us to calculate the nth moment of action without solving this family of boundary value problems and also without solving for the transient solution of the underlying reaction-diffusion problem. We demonstrate the generality of our method by calculating exact expressions for the moments of action for three problems from the biophysics literature. While the first problem we consider can be solved using existing methods, the second problem, which is readily solved using our approach, is intractable using previous techniques. The third problem illustrates how the Laplace transform approach can be used to study coupled linear reaction-diffusion equations.

Traffic density estimation of signalised arterials with stop line detector and probe data

This research aims to develop a reliable density estimation method for signalised arterials based on cumulative counts from upstream and downstream detectors. In order to overcome counting errors associated with urban arterials with mid-link sinks and sources, CUmulative plots and Probe Integration for Travel timE estimation (CUPRITE) is employed for density estimation. The method, by utilizing probe vehicles’ samples, reduces or cancels the counting inconsistencies when vehicles’ conservation is not satisfied within a section. The method is tested in a controlled environment, and the authors demonstrate the effectiveness of CUPRITE for density estimation in a signalised section, and discuss issues associated with the method.

Analysis and prediction of the critical current density across [001]-tilt YBa2Cu3O7- grain boundaries of arbitrary misorientation angles

A qualitative analysis of the expected dilatation strain field in the vicinity of an array of grain-boundary (GB) dislocations is presented. The analysis provides a basis for the prediction of the critical current densities (jc) across low-angle YBa2Cu3O7- (YBCO) GBs as a function of their energy. The introduction of the GB energy allows the extension of the analysis to high-angle GBs using established models which predict the GB energy as a function of misorientation angle. The results are compared to published data for jc across [001]-tilt YBCO GBs for the full range of misorientations, showing a good fit. Since the GB energy is directly related to the GB structure, the analysis may allow a generalization of the scaling behavior of jc with the GB energy. © 1995 The American Physical Society.

Enhancing the current density of electrodeposited ZnO--Cu2O solar cells by engineering their heterointerfaces

Using ZnO seed layers, an efficient approach for enhancing the heterointerface quality of electrodeposited ZnO–Cu2O solar cells is devised. We introduce a sputtered ZnO seed layer followed by the sequential electrodeposition of ZnO and Cu2O films. The seed layer is employed to control the growth and crystallinity and to augment the surface area of the electrodeposited ZnO films, thereby tuning the quality of the ZnO–Cu2O heterointerface. Additionally, the seed layer also assists in forming high quality ZnO films, with no pin-holes, in a high pH electrolyte solution. X-ray electron diffraction patterns, scanning electron and atomic force microscopy images, as well as photovoltaic measurements, clearly demonstrate that the incorporation of certain seed layers results in the alteration of the heterointerface quality, a change in the heterojunction area and the crystallinity of the films near the junction, which influence the current density of photovoltaic devices.

Finite element analysis of hollow flange beams with web stiffeners

A new cold-formed and resistance welded section known as the Hollow Flange Beam (HFB) has been developed recently in Australia. In contrast to the common lateral torsional buckling mode of I-beams, this unique section comprising two stiff triangular flanges and a slender web is susceptible to a lateral distortional buckling mode of failure involving lateral deflection, twist, and cross-section change due to web distortion. This lateral distortional buckling behavior has been shown to cause significant reduction of the available flexural capacity of HFBs. An investigation using finite element analyses and large scale experiments was carried out into the use of transverse web plate stiffeners to improve the lateral buckling capacity of HFBs. This paper presents the details of the finite element model and analytical results. The experimental procedure and results are outlined in a companion paper at this conference.

Finite-element analysis of hollow flange beams with web stiffeners

A new cold-formed and resistance-welded section known as the hollow flange beam (HFB) has been developed recently in Australia. In contrast to the common lateral-torsional buckling mode of I-beams, this unique section comprising two stiff triangular flanges and a slender web is susceptible to a lateral-distortional buckling mode of failure involving lateral deflection, twist, and cross-section change due to web distortion. This lateral-distortional buckling behavior has been shown to cause significant reduction of the available flexural capacity of HFBs. An investigation using finite-element analyses and large-scale experiments was carried out into the use of transverse web plate stiffeners to improve the lateral buckling capacity of HFBs. This paper presents the details of the finite-element model and analytical results. The experimental procedure and results are outlined in a companion paper.

A computer image analysis system for microvessel density measurement in solid tumours

Microvessel density (MVD) is a widely used surrogate measure of angiogenesis in pathological specimens and tumour models. Measurement of MVD can be achieved by several methods. Automation of counting methods aims to increase the speed, reliability and reproducibility of these techniques. The image analysis system described here enables MVD measurement to be carried out with minimal expense in any reasonably equipped pathology department or laboratory. It is demonstrated that the system translates easily between tumour types which are suitably stained with minimal calibration. The aim of this paper is to offer this technique to a wider field of researchers in angiogenesis.

Local stress-strain distribution and load transfer across cartilage matrix at micro-scale using combined microscopy-based finite element method

Articular cartilage is the load-bearing tissue that consists of proteoglycan macromolecules entrapped between collagen fibrils in a three-dimensional architecture. To date, the drudgery of searching for mathematical models to represent the biomechanics of such a system continues without providing a fitting description of its functional response to load at micro-scale level. We believe that the major complication arose when cartilage was first envisaged as a multiphasic model with distinguishable components and that quantifying those and searching for the laws that govern their interaction is inadequate. To the thesis of this paper, cartilage as a bulk is as much continuum as is the response of its components to the external stimuli. For this reason, we framed the fundamental question as to what would be the mechano-structural functionality of such a system in the total absence of one of its key constituents-proteoglycans. To answer this, hydrated normal and proteoglycan depleted samples were tested under confined compression while finite element models were reproduced, for the first time, based on the structural microarchitecture of the cross-sectional profile of the matrices. These micro-porous in silico models served as virtual transducers to produce an internal noninvasive probing mechanism beyond experimental capabilities to render the matrices micromechanics and several others properties like permeability, orientation etc. The results demonstrated that load transfer was closely related to the microarchitecture of the hyperelastic models that represent solid skeleton stress and fluid response based on the state of the collagen network with and without the swollen proteoglycans. In other words, the stress gradient during deformation was a function of the structural pattern of the network and acted in concert with the position-dependent compositional state of the matrix. This reveals that the interaction between indistinguishable components in real cartilage is superimposed by its microarchitectural state which directly influences macromechanical behavior.

Second-order elastic finite element analysis of steel structures using a single element per member

Finite element frame analysis programs targeted for design office application necessitate algorithms which can deliver reliable numerical convergence in a practical timeframe with comparable degrees of accuracy, and a highly desirable attribute is the use of a single element per member to reduce computational storage, as well as data preparation and the interpretation of the results. To this end, a higher-order finite element method including geometric non-linearity is addressed in the paper for the analysis of elastic frames for which a single element is used to model each member. The geometric non-linearity in the structure is handled using an updated Lagrangian formulation, which takes the effects of the large translations and rotations that occur at the joints into consideration by accumulating their nodal coordinates. Rigid body movements are eliminated from the local member load-displacement relationship for which the total secant stiffness is formulated for evaluating the large member deformations of an element. The influences of the axial force on the member stiffness and the changes in the member chord length are taken into account using a modified bowing function which is formulated in the total secant stiffness relationship, for which the coupling of the axial strain and flexural bowing is included. The accuracy and efficiency of the technique is verified by comparisons with a number of plane and spatial structures, whose structural response has been reported in independent studies.

Inelastic finite element analysis of composite beams on the basis of the plastic hinge approach

This paper emphasizes material nonlinear effects on composite beams with recourse to the plastic hinge method. Numerous combinations of steel and concrete sections form arbitrary composite sections. Secondly, the material properties of composite beams vary remarkably across its section from ductile steel to brittle concrete. Thirdly, concrete is weak in tension, so composite section changes are dependent on load distribution. To this end, the plastic zone approach is convenient for inelastic analysis of composite sections that can evaluate member resistance, including material nonlinearities, by routine numerical integration with respect to every fiber across the composite section. As a result, many researchers usually adopt the plastic zone approach for numerical inelastic analyses of composite structures. On the other hand, the plastic hinge method describes nonlinear material behaviour of an overall composite section integrally. Consequently, proper section properties for use in plastic hinge spring stiffness are required to represent the material behaviour across the arbitrary whole composite section. In view of numerical efficiency and convergence, the plastic hinge method is superior to the plastic zone method. Therefore, based on the plastic hinge approach, how to incorporate the material nonlinearities of the arbitrary composite section into the plastic hinge stiffness formulation becomes a prime objective of the present paper. The partial shear connection in this paper is by virtue of the effective flexural rigidity as AISC 1993 [American Institute of Steel Construction (AISC). Load and resistance factor design specifications. 2nd ed., Chicago; 1993]. Nonlinear behaviour of different kinds of composite beam is investigated in this paper, including two simply supported composite beams, a cantilever and a two span continuous composite beam.