A statistical approach to high-throughput screening of predicted orthologs

Orthologs are genes in different species that have diverged from a common ancestral gene after speciation. In contrast, paralogs are genes that have diverged after a gene duplication event. For many comparative analyses, it is of interest to identify orthologs with similar functions. Such orthologs tend to support species divergence (ssd-orthologs) in the sense that they have diverged only due to speciation, to the same relative degree as their species. However, due to incomplete sequencing or gene loss in a species, predicted orthologs can sometimes be paralogs or other non-ssd-orthologs. To increase the specificity of ssd-ortholog prediction, Fulton et al. [Fulton, D., Li, Y., Laird, M., Horsman, B., Roche, F., Brinkman, F., 2006. Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics 7 (1), 270] developed Ortholuge, a bioinformatics tool that identifies predicted orthologs with atypical genetic divergence. However, when the initial list of putative orthologs contains a non-negligible number of non-ssd-orthologs, the cut-off values that Ortholuge generates for orthology classification are difficult to interpret and can be too high, leading to decreased specificity of ssd-ortholog prediction. Therefore, we propose a complementary statistical approach to determining cut-off values. A benefit of the proposed approach is that it gives the user an estimated conditional probability that a predicted ortholog pair is unusually diverged. This enables the interpretation and selection of cut-off values based on a direct measure of the relative composition of ssd-orthologs versus non-ssd-orthologs. In a simulation comparison of the two approaches, we find that the statistical approach provides more stable cut-off values and improves the specificity of ssd-ortholog prediction for low-quality data sets of predicted orthologs.     

Localized coarsening of conforming all-hexahedral meshes

Finite element mesh adaptation methods can be used to improve the efficiency and accuracy of solutions to computational modeling problems. In many applications involving hexahedral meshes, localized modifications which preserve a conforming all-hexahedral mesh are desired. Effective hexahedral refinement methods that satisfy these criteria have recently become available; however, due to hexahedral mesh topology constraints, little progress has been made in the area of hexahedral coarsening. This paper presents a new method to locally coarsen conforming all-hexahedral meshes. The method works on both structured and unstructured meshes and is not based on undoing previous refinement. Building upon recent developments in quadrilateral coarsening, the method utilizes hexahedral sheet and column operations, including pillowing, column collapsing, and sheet extraction. A general algorithm for automated coarsening is presented and examples of models that have been coarsened with this new algorithm are shown. While results are promising, further work is needed to improve the automated process.     

Front‐projection optical‐system design for reflective LCoS technology

Abstract— Optical designs for three‐panel LCoS projection systems are reviewed. The impact of polarization aberrations in prism‐based systems is discussed and a simple model to analyze the sensitivity of contrast to thermal gradients in prisms is presented. To eliminate stress birefringence in LCoS projection systems, we have developed a projection optical system that does not require the use of polarizing prisms. An improved off‐axis design has been designed that simplifies manufacture and reduces cost. The performance of systems based on this architecture will be discussed.     

Identification and sizing of the entirely visible rocks from a 3D surface data segmentation of laboratory rock piles

Once segmentation of 3D surface data of a rock pile has been performed, the next task is to determine the visibility of the surface rocks. A region boundary-following algorithm that accommodates irregularly spaced 3D coordinate data is presented for determining this visibility. We examine 3D surface segmentations of laboratory rock piles and determine which regions in the segmentation correspond to entirely visible rocks, and which correspond to overlapped or partially visible rocks. This is a significant distinction as it allows accurate size determination of entirely visible rocks, separate handling of partially visible rocks, and prevents erroneous bias resulting from mishandling partially visible rocks as smaller entirely visible rocks. Literature review indicates that other rock pile sizing techniques fail to make this distinction. The rock visibility results are quantified by comparison to manual surface classifications of the laboratory piles and the size results are quantified by comparison to the sieve size.     

A methodology for measuring in situ lattice strain of bulk polycrystalline material under cyclic load

The material response of polycrystalline materials under cyclic loading is not fully understood. Even during uniaxial loading, individual grains embedded within the polycrystalline material can experience complicated strain histories. By quantifying the deformation state at the crystal level, we can begin to understand the conditions that lead to fatigue failure. An in situ powder diffraction method was developed and employed at the Cornell High Energy Synchrotron Source to measure the aggregate crystal response at various points in a material's life using synchrotron x ray. A set of experiments was conducted using a load frame capable of exerting cyclic uniaxial loads on a specimen. A high speed x-ray shutter was developed to synchronize the x-ray beam and the loading cycle. Using the high speed shutter, the evolution of the lattice strains for the families of crystallographic planes was measured while the aggregate was under cyclic uniaxial loading, thus monitoring a live evolution of lattice strain in a cyclically loaded specimen. The methodology is demonstrated using uniaxial cyclic specimens machined from oxygen free conductivity (OFHC) copper sheet.     

Mild body cooling impairs attention via distraction from skin cooling

Many contemporary workers are routinely exposed to mild cold stress, which may compromise mental function and lead to accidents. A study investigated the effect of mild body cooling of 1.0 degree C rectal temperature (Tre) on vigilance (i.e. sustained attention) and the orienting of spatial attention (i.e. spatially selective processing of visual information). Vigilance and spatial attention tests were administered to 14 healthy males and six females at four stages (pre-immersion, deltaTre = 0, -0.5 and - 1.0 degree C ) of a gradual, head-out immersion cooling session (18-25 deltaC water), and in four time-matched stages of a contrast session, in which participants sat in an empty tub and no cooling took place. In the spatial attention test, target discrimination times were similar for all stages of the contrast session, but increased significantly in the cooling phase upon immersion (deltaTre = 0 degrees C), with no further increases at deltaTre = -0.5 and - 1.0 degree C. Despite global response slowing, cooling did not affect the normal pattern of spatial orienting. In the vigilance test, the variability of detection time was adversely affected in the cooling but not the contrast trials: variability increased at immersion but did not increase further with additional cooling. These findings suggest that attentional impairments are more closely linked to the distracting effects of cold skin temperature than decreases in body core temperature.     

Exploring the Interaction between Java's Implicitly Thrown Exceptions and Instruction Scheduling

The frequent occurrence of implicitly thrown exceptions poses one of the challenges present in a Java compiler. Not only do these implicitly thrown exceptions directly affect the performance by requiring explicit checks, they also indirectly impact the performance by restricting code movement in order to satisfy the precise exception model in Java. In particular, instruction scheduling is one transformation that is restricted by implicitly thrown exceptions due to the heavy reliance on reordering instructions to exploit maximum hardware performance. The goal of this study is two-fold: first, investigate the degree to which implicitly thrown exceptions in Java hinder instruction scheduling, and second, find new techniques for allowing more efficient execution of Java programs containing implicitly thrown exceptions. Experimental results show that with aggressive scheduling techniques, such as superblock scheduling, the negative performance impact can be greatly reduced.     

A SWAT evaluation of the effect of climate change on the hydrology of the Volta River basin

The SWAT (Soil and Water Assessment Tool) was used to evaluate the impacts of a climate scenario based on IPCC A1B emissions on flows in the Volta River basin in West Africa for 2021–2050 and 2071–2100, using 1983–2012 as the reference period. Overall, the simulation indicates increased variability and a decrease of up to 40% in river flow as a consequence of decreasing rainfall and increasing temperature. In particular, the analysis shows smaller absolute but greater relative changes in the hydrology of the northern (upper) part of the basin, particularly at the end of the century.