Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor

Propagation of leaky MHD waves at discontinuities with tilted magnetic field

We investigate the characteristics of magneto-acoustic surface waves propagating at a single density interface, in the presence of an inclined magnetic field. For linear wave propagation, the dispersion relation is obtained and analytical solutions are derived for small inclination angle. The inclination of the field renders the frequency of the waves complex, where the imaginary part describes wave attenuation, due to lateral energy leakage

Potential link of single nucleotide polymorphisms to virulence of vaccine‐associated field strains of lumpy skin disease virus in South Africa

South Africa is endemic for lumpy skin disease and is therefore reliant on various live attenuated vaccines for the control and prevention of the disease. In recent years, widespread outbreaks of vaccine‐like strains of lumpy skin disease virus (LSDV) were reported internationally, leading to an increase in the generation of full genome sequences from field isolates. In this study, the complete genomes of six LSDVs submitted during active outbreaks in the 1990s in South Africa were generated. Based on phylogenetic analysis, the six viruses clustered with vaccine strains in LSDV Subgroup 1.1 and are subsequently referred to as vaccine‐associated. The genetic differences between the phenotypically distinct vaccine and vaccine‐associated strains were 67 single nucleotide polymorphisms (SNPs). This study characterized the location and possible importance of each of these SNPs in their role during virulence and host specificity

Stories of change: five diseases, one vaccine: a boost for emerging livestock farmers in South Africa

Workshop report of IDRC Communications Workshop, NovemberSouth African and Canadian researchers are developing new generation livestock vaccines that are affordable, heat-stable and give long-term protection

Bluefin tuna (Thunnus thynnus) distribution in relation to sea surface temperature fronts in the Gulf of Maine (1994-96)

Fishery-linked aerial surveys for bluefin tuna (Thunnus thynnus) were conducted in the Gulf of Maine (GOM) from July through October, 1994-96. Each year, from 507 to 890 surface schools were detected and their locations examined in relation to oceanographic conditions. Correlations between bluefin tuna presence and environmental variables were explored for sea surface temperature (SST), distance to a SST front, frontal density (relative density of all SST fronts seen in a given 1 km area for 2 weeks prior to each tuna sighting), and bottom depth and slope. Mean SST associated with bluefin schools was 18.1degreesC (+/-2.8). Schools were located at a mean distance of 19.7 km (+/-19.6) from SST fronts, and in water masses with an average frontal density of 28.2 m km(-2) (+/-35.7). Mean bottom depth of detected schools was 139.0 m (+/-70.3), and mean bottom slope was 0.7% rise (+/-0.7). A binomial generalized linear model fit to these variables indicated that bluefin are seen closer to fronts than locations in which no tuna were seen. Using simple and partial Mantel tests, we investigated the spatial correlation between bluefin tuna presence and the environmental variables, controlling for spatial autocorrelation. For each day that schools were sighted, we performed 24 Mantel tests, on a combination of response and predictor variables. The spatial relationship between bluefin tuna and SST fronts was inconsistent. Our analysis identified significant spatial structure in the bluefin school locations that had no significant correlation with any of the measured environmental features, suggesting that other untested features, such as prey density, may be important predictors of bluefin distribution in the GOM.</p