X-ray reflectivity measurement of interdiffusion in metallic multilayers during rapid heating

A technique for measuring interdiffusion in multilayer materials during rapid heating using X-ray reflectivity is described. In this technique the sample is bent to achieve a range of incident angles simultaneously, and the scattered intensity is recorded on a fast high-dynamic-range mixed-mode pixel array detector. Heating of the multilayer is achieved by electrical resistive heating of the silicon substrate, monitored by an infrared pyrometer. As an example, reflectivity data from Al/Ni heated at rates up to 200 K s^(−1) are presented. At short times the interdiffusion coefficient can be determined from the rate of decay of the reflectivity peaks, and it is shown that the activation energy for interdiffusion is consistent with a grain boundary diffusion mechanism. At longer times the simple analysis no longer applies because the evolution of the reflectivity pattern is complicated by other processes, such as nucleation and growth of intermetallic phases

Recovery of the crucian carp Carassius carassius (L.): Approach and early results of an English conservation project

Aquatic Conservation: Marine and Freshwater Ecosystems published by John Wiley & Sons Ltd The crucian carp Carassius carassius, a cyprinid fish characteristic of small ponds, is in decline throughout most of its European range, including in England where it is currently thought to be non-native. The present study, undertaken by the Norfolk Crucian Project, reports on reductions in pond populations of crucian carp in Norfolk, eastern England as well as the success of recent introduction/re-introduction efforts in terms of crucian survival, recruitment and growth over the last 10 years. A 72% decline in crucian carp distribution was observed between the 1950s–1980s and the 2010s. Of 18 crucian carp introductions/re-introductions to restored and suitable existing ponds, 17 were successful in terms of survival, increasing the number of current crucian sites in Norfolk by 37%. Recruitment of young crucian carp was demonstrated for 12 of the 18 stocked ponds, with apparent elevated juvenile growth relative to other English and European populations. Delays in, or a lack of, crucian recruitment in some ponds appeared to result from the presence of other fish species (especially threespine stickleback Gasterosteus aculeatus) with predation and interspecific competition possible contributory factors. This study shows that, through combinations of pond rehabilitation and stocking, it has been possible to achieve a substantial recovery of crucian carp populations in the study region. Although the crucian carp is currently presumed to be non-native within England, given other scientific studies that show a lack of adverse impacts of this species on native biota, and because it is greatly threatened in its native range, the call is sounded for more crucian carp conservation projects in other parts of England as well as in Europe more generally

Case management and Think First completion

“The final, definitive version of this article has been published in the Journal, Probation Journal, Vol 53 Issue 3, 2006, Copyright The Trade Union and Professional Association for Family Court and Probation Staff, by SAGE Publications Ltd at: http://prb.sagepub.com/ " DOI: 10.1177/0264550506066771This article considers the findings of a small-scale study of the practice of case managers supervising offenders required to attend the Think First Group. It explores the interface between one-to-one and group-based work within multi-modal programmes of supervision and seeks to identify those practices that support individuals in completing a group.Peer reviewe

Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction

A genetic algorithm based method for stringent haplotyping of family data

<p>Abstract</p> <p>Background</p> <p>The linkage phase, or haplotype, is an extra level of information that in addition to genotype and pedigree can be useful for reconstructing the inheritance pattern of the alleles in a pedigree, and computing for example Identity By Descent probabilities. If a haplotype is provided, the precision of estimated IBD probabilities increases, as long as the haplotype is estimated without errors. It is therefore important to only use haplotypes that are strongly supported by the available data for IBD estimation, to avoid introducing new errors due to erroneous linkage phases.</p> <p>Results</p> <p>We propose a genetic algorithm based method for haplotype estimation in family data that includes a stringency parameter. This allows the user to decide the error tolerance level when inferring parental origin of the alleles. This is a novel feature compared to existing methods for haplotype estimation. We show that using a high stringency produces haplotype data with few errors, whereas a low stringency provides haplotype estimates in most situations, but with an increased number of errors.</p> <p>Conclusion</p> <p>By including a stringency criterion in our haplotyping method, the user is able to maintain the error rate at a suitable level for the particular study; one can select anything from haplotyped data with very small proportion of errors and a higher proportion of non-inferred haplotypes, to data with phase estimates for every marker, when haplotype errors are tolerable. Giving this choice makes the method more flexible and useful in a wide range of applications as it is able to fulfil different requirements regarding the tolerance for haplotype errors, or uncertain marker-phases.</p

Understanding service users’ and therapists’ experiences of pharmacological treatment for sexual preoccupation and/or hypersexuality in incarcerated sex offenders

This research comprises two qualitative studies understanding the experiences of 1) convicted sex offenders voluntarily receiving pharmacological treatment to reduce sexual preoccupation and 2) therapists working with these offenders. The studies form part of a research programme evaluating the use of pharmacological treatment with sexual offenders. In study one, semi-structured interviews were conducted with 13 sexual offenders receiving selective serotonin reuptake inhibitors (SSRIs). In study two, interviews were conducted with eight intervention staff with varying levels of experience of working with offenders taking anti-libidinals. Thematic analysis was used and in study one, two main themes emerged: (i) the impact of the pharmacological treatment on prisoners’ daily functioning; (ii) barriers to compliance/engagement. In study two, three main themes emerged: (i) offenders’ reluctance to engage with pharmacological treatment; (ii) challenges for therapists; (iii) pharmacology: ‘just another piece of the puzzle’. Findings are discussed in relation to practice and future research

A gene frequency model for QTL mapping using Bayesian inference

<p>Abstract</p> <p>Background</p> <p>Information for mapping of quantitative trait loci (QTL) comes from two sources: linkage disequilibrium (non-random association of allele states) and cosegregation (non-random association of allele origin). Information from LD can be captured by modeling conditional means and variances at the QTL given marker information. Similarly, information from cosegregation can be captured by modeling conditional covariances. Here, we consider a Bayesian model based on gene frequency (BGF) where both conditional means and variances are modeled as a function of the conditional gene frequencies at the QTL. The parameters in this model include these gene frequencies, additive effect of the QTL, its location, and the residual variance. Bayesian methodology was used to estimate these parameters. The priors used were: logit-normal for gene frequencies, normal for the additive effect, uniform for location, and inverse chi-square for the residual variance. Computer simulation was used to compare the power to detect and accuracy to map QTL by this method with those from least squares analysis using a regression model (LSR).</p> <p>Results</p> <p>To simplify the analysis, data from unrelated individuals in a purebred population were simulated, where only LD information contributes to map the QTL. LD was simulated in a chromosomal segment of 1 cM with one QTL by random mating in a population of size 500 for 1000 generations and in a population of size 100 for 50 generations. The comparison was studied under a range of conditions, which included SNP density of 0.1, 0.05 or 0.02 cM, sample size of 500 or 1000, and phenotypic variance explained by QTL of 2 or 5%. Both 1 and 2-SNP models were considered. Power to detect the QTL for the BGF, ranged from 0.4 to 0.99, and close or equal to the power of the regression using least squares (LSR). Precision to map QTL position of BGF, quantified by the mean absolute error, ranged from 0.11 to 0.21 cM for BGF, and was better than the precision of LSR, which ranged from 0.12 to 0.25 cM.</p> <p>Conclusions</p> <p>In conclusion given a high SNP density, the gene frequency model can be used to map QTL with considerable accuracy even within a 1 cM region.</p

Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

<p>Abstract</p> <p>Background</p> <p>A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study.</p> <p>Results</p> <p>The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28% across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters.</p> <p>Conclusions</p> <p>An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear.</p

Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance

The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased. The accuracy decreased more when QTL had different variance values than when all QTL had an equal variance. The accuracy of MEBV calculated with PLSR was affected neither by the number of QTL nor by the distribution of QTL variance. Additional simulations and analyses showed that these conclusions were not affected by the number of individuals in the training population, by the number of markers and by the heritability of the trait. Results of this study show that the effect of the number of QTL and distribution of QTL variance on the accuracy of MEBV depends on the method that is used to calculate MEBV