Spectral gene set enrichment (SGSE)

Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. Results: We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes the statistical association between gene sets and principal components (PCs) using our principal component gene set enrichment (PCGSE) method. The overall statistical association between each gene set and the spectral structure of the data is then computed by combining the PC-level p-values using the weighted Z-method with weights set to the PC variance scaled by Tracey-Widom test p-values. Using simulated data, we show that the SGSE algorithm can accurately recover spectral features from noisy data. To illustrate the utility of our method on real data, we demonstrate the superior performance of the SGSE method relative to standard cluster-based techniques for testing the association between MSigDB gene sets and the variance structure of microarray gene expression data. Availability: http://cran.r-project.org/web/packages/PCGSE/index.html Contact: [email protected] or [email protected]

Principal component gene set enrichment (PCGSE)

Motivation: Although principal component analysis (PCA) is widely used for the dimensional reduction of biomedical data, interpretation of PCA results remains daunting. Most existing methods attempt to explain each principal component (PC) in terms of a small number of variables by generating approximate PCs with few non-zero loadings. Although useful when just a few variables dominate the population PCs, these methods are often inadequate for characterizing the PCs of high-dimensional genomic data. For genomic data, reproducible and biologically meaningful PC interpretation requires methods based on the combined signal of functionally related sets of genes. While gene set testing methods have been widely used in supervised settings to quantify the association of groups of genes with clinical outcomes, these methods have seen only limited application for testing the enrichment of gene sets relative to sample PCs. Results: We describe a novel approach, principal component gene set enrichment (PCGSE), for computing the statistical association between gene sets and the PCs of genomic data. The PCGSE method performs a two-stage competitive gene set test using the correlation between each gene and each PC as the gene-level test statistic with flexible choice of both the gene set test statistic and the method used to compute the null distribution of the gene set statistic. Using simulated data with simulated gene sets and real gene expression data with curated gene sets, we demonstrate that biologically meaningful and computationally efficient results can be obtained from a simple parametric version of the PCGSE method that performs a correlation-adjusted two-sample t-test between the gene-level test statistics for gene set members and genes not in the set. Availability: http://cran.r-project.org/web/packages/PCGSE/index.html Contact: [email protected] or [email protected]

Analysis of vibration induced error in turbulence velocity measurements from an aircraft wing tip boom

The effect of rolling motion of a wing on the magnitude of error induced due to the wing vibration when measuring atmospheric turbulence with a wind probe mounted on the wing tip was investigated. The wing considered had characteristics similar to that of a B-57 Cambera aircraft, and Von Karman's cross spectrum function was used to estimate the cross-correlation of atmospheric turbulence. Although the error calculated was found to be less than that calculated when only elastic bendings and vertical motions of the wing are considered, it is still relatively large in the frequency's range close to the natural frequencies of the wing. Therefore, it is concluded that accelerometers mounted on the wing tip are needed to correct for this error, or the atmospheric velocity data must be appropriately filtered

Doppler lidar signal and turbulence study

Wind fields were measured with the ground-based NASA/MSFC lidar are compared with the in situ NASA RB-57 aircraft measurements. The mean wind fields, the turbulence intensities, and the turbulence spectra determined from measurements by both systems are in very good agreement. Turbulence intensities and spectra were calculated from the fluctuations with time in the radial wind speed component. The second moment or Doppler frequency spectral width of the lidar measurements was also compared with turbulence intensities measured by the aircraft. These second moments could only be resolved at the very low altitudes (in three range bins). Turbulence intensities estimated from the spectral width data were an order of magnitude higher than those measured by the aircraft. An interesting boundary layer evolved during the progress of the experiment. The breakup of a stable boundary layer resulted in winds blowing in one direction above 600 m msl and in the opposite direction below that level. Both the aircraft and the lidar systems clearly identified this unusual boundary layer flow and showed the identical trends

Test results of modified electrical charged particle generator for application to fog dispersal

Modifications to a charged particle generator for use in fog dispersal applications were made and additional testing carried out. The modified nozzle, however, did not work as planned, and reported results are the unmodified nozzle. The addition of a positive displacement pump to supply the liquid water was highly successful. Measurements of the generator output current were made with a cylindrical collector system as well as with the needle probe used in previous studies. Measurements with the cylindrical collector and the needle probe showed identical agreement within the variability of the experiment. A high-voltage prove was purchased, and measurements of the corona voltage as well as the voltage variation in the charged particle jet were made. Electric fields in the vertical direction on the order of 1,000,000 v/m were measured. The voltage distribution along the centerline of the jet was compared with the numerical solutions of the Poisson equation and showed very good agreement. Velocity measurements using a pitot tube were made. The resulting measurements were compared with theoretical and other reported experimental results. The measured data showed the appropriate trends and agreed well with reported results. Based on the measured current-to-mass ratio from the charged particle generator, a calculation of the average droplet size was made. Droplet sizes were estimated to range between 0.8 and 0.4 microns. Using measured data, an analysis of the height to which the droplet can be dispersed by the charged particle generator was made. Although the mathematical model is highly simplified, the results indicated that particles would achieve heights on the order of 80 m

Effects of fog droplets on wake vortex decay rate

A simple model for the motion of particles in a laminar line vortex is discussed. The energy required to accelerate a set of these particles was determined and shown to be only a small fraction of the energy content of the vortex flow. It is shown that this energy transfer is unlikely to be sufficient to significantly modify the vortex decay rate. It is further argued that the effect of the particle on the viscous properties of the resulting two phase fluid leads to a slower decay rate than in single phase air flow. However, this conclusion may not necessarily follow for turbulence flows. Results show that the migration of particles to the outer flow results in a redistribution of the velocity profile in the vortex and in a non-uniform two phase viscosity across the core. It is suggested that these effects may accelerate vortex bursting

Responses of a bacterial pathogen to phosphorus limitation of its aquatic invertebrate host

Host nutrition is thought to affect the establishment, persistence, and severity of pathogenic infections. Nutrient-deficient foods possibly benefit pathogens by constraining host immune function or benefit hosts by limiting parasite growth and reproduction. However, the effects of poor elemental food quality on a host's susceptibility to infection and disease have received little study. Here we show that the bacterial microparasite Pasteuria ramosa is affected by the elemental nutrition of its aquatic invertebrate host, Daphnia magna. We found that high food carbon : phosphorus (C: P) ratios significantly reduced infection rates of Pasteuria in Daphnia and led to lower within-host pathogen multiplication. In addition, greater virulent effects of bacterial infection on host reproduction were found in Daphnia-consuming P-deficient food. Poor Daphnia elemental nutrition thus reduced the growth and reproduction of its bacterial parasite, Pasteuria. The effects of poor host nutrition on the pathogen were further evidenced by Pasteuria's greater inhibition of reproduction in P-limited Daphnia. Our results provide strong evidence that elemental food quality can significantly influence the incidence and intensity of infectious disease in invertebrate hosts

Using meta-ethnography to understand the emotional impact of caring for people with increasing cognitive impairment.

The definitive version is available at www.blackwell-synergy.comThe majority of people with degenerative neurological conditions are cared for within their own families. Cognitive impairment can be a significant and increasing symptom of these conditions. In this article we report how a team of experienced researchers carried out a meta-ethnography of qualitative research articles focusing on the impact of caring for a loved one with cognitive impairment. We followed the seven-step process outlined by Noblit and Hare. Synthesized findings from 31 papers suggest emotional impact is complex and uncertain and varies from day to day. The benefit of using meta-ethnography is that the results represent a larger sample size and a reinterpretation of multiple studies can hold greater application for practice. The results of this study offer an opportunity for nurses to be aware of both the positive and negative sides of caring and being cared for. This knowledge can be used to discuss with patients and carers how best to prepare for decreasing cognition and still maintain a worthwhile quality of life

The thinking line: defining drawing

Curated exhibition of works from the British Council collection alongside Canterbury Christ Church university staff and alumni