Diffusion of Mn interstitials in (Ga,Mn)As epitaxial layers

Magnetic properties of thin (Ga,Mn)As layers improve during annealing by out-diffusion of interstitial Mn ions to a free surface. Out-diffused Mn atoms participate in the growth of a Mn-rich surface layer and a saturation of this layer causes an inhibition of the out-diffusion. We combine high-resolution x-ray diffraction with x-ray absorption spectroscopy and a numerical solution of the diffusion problem for the study of the out-diffusion of Mn interstitials during a sequence of annealing steps. Our data demonstrate that the out-diffusion of the interstitials is substantially affected by the internal electric field caused by an inhomogeneous distribution of charges in the (Ga,Mn)As layer.Comment: 11 pages, 5 figure

A model study of the January 2006 low total ozone episode over Western Europe and comparison with ozone sonde data

Total column and stratospheric ozone levels at mid-latitudes often reveal strong fluctuations on time scales of days caused by dynamic processes. In some cases the total ozone column is distinctly reduced below climatological values. Here, a very low total ozone episode around 19 January 2006 over Western Europe is investigated when the observed total ozone column over Uccle (BE), measured by a Brewer spectrophotometer, reached a daily minimum of 200 DU, the lowest recorded value at this station. In order to investigate the mechanisms leading to the ozone minimum, the present study used data from (i) six ozone sounding stations in Western and Middle Europe, (ii) ECMWF meteorological fields, (iii) a simulation of the CLaMS model for January 2006, (iv) a multi-year run of the chemistry transport model KASIMA, and (v) a six-year run of the climate chemistry model ECHAM5/MESSy1. The ozone decrease at different heights was quantified and it was determined to what extent different transport mechanisms, and instantaneous, in-situ chemical ozone depletion contributed to the event. All three models reproduced the evolution and formation of the event. The ozone column decrease between Theta=300 and 750K was strongest at Uccle (BE) and De Bilt (NL) with 108 and 103 DU, respectively, and somewhat lower at Hohenpeissenberg (DE), Payerne (CH), Prague (CZ) and Lerwick (UK) with 85, 84, 83 and 74 DU, respectively. This analysis demonstrated that mainly the displacement of the ozone depleted polar vortex contributed to the ozone column decrease. Advection of ozone-poor low-latitude air masses was important in the UTLS region. The vertical displacement of isentropes connected with divergence of air out of the column was found to be of minor importance compared to the horizontal transport processes. Severe low total ozone episodes seem to occur when the mentioned mechanisms are superimposed. Instantaneous, in-situ chemical ozone depletion accounted for only 2+/-1% of the overall total ozone decrease at the sounding stations

Properties of permutation-based gene tests and controlling type 1 error using a summary statistic based gene test

Background: The advent of genome-wide association studies has led to many novel disease-SNP associations, opening the door to focused study on their biological underpinnings. Because of the importance of analyzing these associations, numerous statistical methods have been devoted to them. However, fewer methods have attempted to associate entire genes or genomic regions with outcomes, which is potentially more useful knowledge from a biological perspective and those methods currently implemented are often permutation-based. Results: One property of some permutation-based tests is that their power varies as a function of whether significant markers are in regions of linkage disequilibrium (LD) or not, which we show from a theoretical perspective. We therefore develop two methods for quantifying the degree of association between a genomic region and outcome, both of whose power does not vary as a function of LD structure. One method uses dimension reduction to “filter” redundant information when significant LD exists in the region, while the other, called the summary-statistic test, controls for LD by scaling marker Z-statistics using knowledge of the correlation matrix of markers. An advantage of this latter test is that it does not require the original data, but only their Z-statistics from univariate regressions and an estimate of the correlation structure of markers, and we show how to modify the test to protect the type 1 error rate when the correlation structure of markers is misspecified. We apply these methods to sequence data of oral cleft and compare our results to previously proposed gene tests, in particular permutation-based ones. We evaluate the versatility of the modification of the summary-statistic test since the specification of correlation structure between markers can be inaccurate. Conclusion: We find a significant association in the sequence data between the 8q24 region and oral cleft using our dimension reduction approach and a borderline significant association using the summary-statistic based approach. We also implement the summary-statistic test using Z-statistics from an already-published GWAS of Chronic Obstructive Pulmonary Disorder (COPD) and correlation structure obtained from HapMap. We experiment with the modification of this test because the correlation structure is assumed imperfectly known

Applying spatial regression to evaluate risk factors for microbiological contamination of urban groundwater sources in Juba, South Sudan

This study developed methodology for statistically assessing groundwater contamination mechanisms. It focused on microbial water pollution in low-income regions. Risk factors for faecal contamination of groundwater-fed drinking-water sources were evaluated in a case study in Juba, South Sudan. The study was based on counts of thermotolerant coliforms in water samples from 129 sources, collected by the humanitarian aid organisation M,decins Sans FrontiSres in 2010. The factors included hydrogeological settings, land use and socio-economic characteristics. The results showed that the residuals of a conventional probit regression model had a significant positive spatial autocorrelation (Moran\u27s I = 3.05, I-stat = 9.28); therefore, a spatial model was developed that had better goodness-of-fit to the observations. The most significant factor in this model (p-value 0.005) was the distance from a water source to the nearest Tukul area, an area with informal settlements that lack sanitation services. It is thus recommended that future remediation and monitoring efforts in the city be concentrated in such low-income regions. The spatial model differed from the conventional approach: in contrast with the latter case, lowland topography was not significant at the 5% level, as the p-value was 0.074 in the spatial model and 0.040 in the traditional model. This study showed that statistical risk-factor assessments of groundwater contamination need to consider spatial interactions when the water sources are located close to each other. Future studies might further investigate the cut-off distance that reflects spatial autocorrelation. Particularly, these results advise research on urban groundwater quality

‘Location, Location, Location’: a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate

Motivation: For the analysis of rare variants in sequence data, numerous approaches have been suggested. Fixed and flexible threshold approaches collapse the rare variant information of a genomic region into a test statistic with reduced dimensionality. Alternatively, the rare variant information can be combined in statistical frameworks that are based on suitable regression models, machine learning, etc. Although the existing approaches provide powerful tests that can incorporate information on allele frequencies and prior biological knowledge, differences in the spatial clustering of rare variants between cases and controls cannot be incorporated. Based on the assumption that deleterious variants and protective variants cluster or occur in different parts of the genomic region of interest, we propose a testing strategy for rare variants that builds on spatial cluster methodology and that guides the identification of the biological relevant segments of the region. Our approach does not require any assumption about the directions of the genetic effects. Results: In simulation studies, we assess the power of the clustering approach and compare it with existing methodology. Our simulation results suggest that the clustering approach for rare variants is well powered, even in situations that are ideal for standard methods. The efficiency of our spatial clustering approach is not affected by the presence of rare variants that have opposite effect size directions. An application to a sequencing study for non-syndromic cleft lip with or without cleft palate (NSCL/P) demonstrates its practical relevance. The proposed testing strategy is applied to a genomic region on chromosome 15q13.3 that was implicated in NSCL/P etiology in a previous genome-wide association study, and its results are compared with standard approaches. Availability: Source code and documentation for the implementation in R will be provided online. Currently, the R-implementation only supports genotype data. We currently are working on an extension for VCF files. Contact: [email protected]

Social media use and impact during the holiday travel planning process

Through an empirical study among holiday travellers, residing in the Former Soviet Union Republics, this paper presents a comprehensive view of role and impact of social media on the whole holiday travel planning process: Before, during and after the trip, providing insights on usage levels, scope of use, level of influence and trust. Findings suggest that social media are predominantly used after holidays for experience sharing. It is also shown that there is a strong correlation between perceived level of influence from social media and changes made in holiday plans prior to final decisions. Moreover, it is revealed that user-generated content is perceived as more trustworthy when compared to official tourism websites, travel agents and mass media advertising