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.

Protocols for conducting dolphin capture-release health assessment studies

Marine mammals, such as dolphins, can serve as key indicator species in coastal areas by reflecting the effects of natural and anthropogenic stressors. As such they are often considered sentinels of environmental and ecosystem health (Bossart 2006; Wells et al. 2004; Fair and Becker 2000). The bottlenose dolphin is an apex predator and a key component of many estuarine environments in the southeastern United States (Woodward-Clyde Consultants 1994; SCDNR 2005). Health assessments of dolphins are especially critical in areas where populations are depleted, show signs of epidemic disease and/or high mortality and/or where habitat is being altered or impacted by human activities. Recent assessments of environmental conditions in the Indian River Lagoon, Florida (IRL) and the estuarine waters surrounding Charleston, South Carolina (CHS) highlight the need for studies of the health of local bottlenose dolphins. While the condition of southeastern estuaries was rated as fair in the National Coastal Condition Report (U.S. EPA 2001), it was noted that the IRL was characterized by poorer than expected benthic communities, significant sediment toxicity and increased nutrient concentrations. Similarly, portions of the CHS estuary have sediment concentrations of aliphatic aromatic hydrocarbons, select inorganic metals, and some persistent pesticides far in excess of reported bioeffect levels (Hyland et al. 1998). Long-term trends in water quality monitoring and recent scientific research suggest that waste load assimilation, non-point source runoff impacts, contaminated sediments, and toxic pollutants are key issues in the CHS estuary system. Several ‘hot spots’ with high levels of heavy metals and organic compounds have been identified (Van Dolah et al. 2004). High concentrations of anthropogenic trace metals, polychlorinated biphenyls (PCB’s) and pesticides have been found in the sediments of Charleston Harbor, as well as the Ashley and Cooper Rivers (Long et al. 1998). Two superfund sites are located within the CHS estuary and the key contaminants of concern associated with these sites are: polycyclic aromatic hydrocarbons (PAH), lead, chromium, copper, arsenic, zinc and dioxin. Concerns related to the overall health of IRL dolphins and dermatologic disease observed in many dolphins in the area (Bossart et al. 2003) initiated an investigation of potential factors which may have impacted dolphin health. From May-August 2001, 35 bottlenose dolphins died in the IRL during an unusual mortality event (MMC 2003). Many of these dolphins were diagnosed with a variety of skin lesions including proliferative ulcerative dermatitis due to protozoa and fungi, dolphin pox and a vesicular dermatopathy of unknown etiology (Bossart et al. 2003). Multiple species from fish to dolphins in the IRL system have exhibited skin lesions of various known and unknown etiologies (Kane et al. 2000; Bossart et al. 2003; Reif et al. 2006). On-going photo-identification (photo-ID) studies have documented skin diseases in IRL dolphins (Mazzoil et al. 2005). In addition, up to 70% of green sea turtles in the IRL exhibit fibropapillomas, with the highest rates of occurrence being seen in turtles from the southern IRL (Hirama 2001).

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.

Fabrication of test structures for 4×4 InP/InGaAsP integrated optical matrix

A novel optical switching matrix measuring 1×2 mm2 in size is fabricated. The switching matrix is composed of waveguides, four 1×4 multimode interference (MMI) splitters, 32 total internal refraction mirrors and four 4×1 MMI combiners with the extremely compact size of 1×2 mm2. This integrated device are assessed and loss contribution measured from test structure is presented.

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.