Strategies for selection of subjects for sequencing after detection of a linkage peak

Linkage analysis has the potential to localize disease genes of interest, but the choice of which subjects to select for follow-up sequencing after identifying a linkage peak might influence the ability to find a disease gene. We compare nine different strategies for selection of subjects for follow-up sequencing using sequence data from the Genetic Analysis Workshop 17. We found that our more selective strategies, which included methods to identify case subjects more likely to be affected by genetic causes, out-performed sequencing all case and control subjects in linked pedigrees and required sequencing fewer individuals. We found that using genotype data from population control subjects had a higher benefit-cost ratio than sequencing control subjects selected as being the opposite extreme of the case subjects. We conclude that choosing case subjects for sequencing based on more selective strategies can be reliable and cost-effective

Promising Practices of Dairy, Horse, and Livestock Evaluation Career Development Event Coaches: A Mixed-Methods Study

The present study describes promising practices of successful dairy, horse, and livestock judging coaches. Expert coaches were interviewed regarding previous experience, coaching philosophy, coaching objectives, coaching style, and advice. Twenty-seven promising practices and eight themes were identified from the interviews. A questionnaire was sent to the accessible population of coaches to determine practice usage and relationship to youth performance. Influential and motivating practices were found to be most used by coaches. Youth performance was related to use of competitive and expectancy related promising practices. Findings suggest use of promising practices would facilitate greater coaching success in competition and youth development

Trauma histories of men and women in residential drug treatment: The Scottish evidence

This article focuses on self-reported child neglect and abuse in residential drug treatment drawing on data from clients in Scotland collected 1996-1999. It notes the lack of adoption of regular screening using validated tools of childhood trauma in men and women. The authors’ findings suggest that the prevalence of childhood abuse histories are higher in female drug users than male drug users but recognises that even with standardised tools there is a wealth of diverse categories of severity of abuse that warn against broad treatment plans for ‘the traumatised’

PedGenie: meta genetic association testing in mixed family and case-control designs

<p>Abstract</p> <p>Background-</p> <p>PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Carlo significance testing. Our aim is to demonstrate that PedGenie, a unique and flexible analysis tool freely available in Genie 2.4 software, is significantly enhanced by incorporating meta statistics for detecting genetic association with disease using data across multiple study groups.</p> <p>Methods-</p> <p>Meta statistics (chi-squared tests, odds ratios, and confidence intervals) were calculated using formal Cochran-Mantel-Haenszel techniques. Simulated data from unrelated individuals and individuals in families were used to illustrate meta tests and their empirically-derived p-values and confidence intervals are accurate, precise, and for independent designs match those provided by standard statistical software.</p> <p>Results-</p> <p>PedGenie yields accurate Monte Carlo p-values for meta analysis of data across multiple studies, based on validation testing using pedigree, nuclear family, and case-control data simulated under both the null and alternative hypotheses of a genotype-phenotype association.</p> <p>Conclusion-</p> <p>PedGenie allows valid combined analysis of data from mixtures of pedigree-based and case-control resources. Added meta capabilities provide new avenues for association analysis, including pedigree resources from large consortia and multi-center studies.</p

Searching for Gravitational Waves from Binary Inspirals with LIGO

We describe the current status of the search for gravitational waves from inspiralling compact binary systems in LIGO data. We review the result from the first scientific run of LIGO (S1). We present the goals of the search of data taken in the second scientific run (S2) and describe the differences between the methods used in S1 and S2.Comment: 9 pages, 2 figures. Published in proceedings of the 8th Gravitational Wave Data Analysis Workshop, Milwaukee, WI, USA, 17-20 December 200

Radiative Falloff in Neutron Star Spacetimes

We systematically study late-time tails of scalar waves propagating in neutron star spacetimes. We consider uniform density neutron stars, for which the background spacetime is analytic and the compaction of the star can be varied continously between the Newtonian limit 2M/R << 1 and the relativistic Buchdahl limit 2M/R = 8/9. We study the reflection of a finite wave packet off neutron stars of different compactions 2M/R and find that a Newtonian, an intermediate, and a highly relativistic regime can be clearly distinguished. In the highly relativistic regime, the reflected signal is dominated by quasi-periodic peaks, which originate from the wave packet bouncing back and forth between the center of the star and the maximum of the background curvature potential at R ~ 3 M. Between these peaks, the field decays according to a power-law. In the Buchdahl limit 2M/R -> 8/9 the light travel time between the center and the maximum or the curvature potential grows without bound, so that the first peak arrives only at infinitely late time. The modes of neutron stars can therefore no longer be excited in the ultra-relativistic limit, and it is in this sense that the late-time radiative decay from neutron stars looses all its features and gives rise to power-law tails reminiscent of Schwarzschild black holes.Comment: 10 pages, 7 figures, to appear in PR

A coherent triggered search for single spin compact binary coalescences in gravitational wave data

In this paper we present a method for conducting a coherent search for single spin compact binary coalescences in gravitational wave data and compare this search to the existing coincidence method for single spin searches. We propose a method to characterize the regions of the parameter space where the single spin search, both coincident and coherent, will increase detection efficiency over the existing non-precessing search. We also show example results of the coherent search on a stretch of data from LIGO's fourth science run but note that a set of signal based vetoes will be needed before this search can be run to try to make detections.Comment: 14 pages, 4 figure

Effects of Feeding a Novel Alfalfa Leaf Pellet Product (ProLEAF MAX) and Alfalfa Stems (ProFiber Plus) on Performance in the Feedlot and Carcass Quality of Beef Steers

Alfalfa is often included in the diets of beef animals; however, the nutrient content of alfalfa is variable depending on the region in which it is grown, climate, soil, and many other factors. The leaf portion of alfalfa has a less variable nutrient composition than the stem portion of the plant. The variability that is present in the alfalfa plant can make the development of total mixed rations of consistent nutrient content difficult. As such, the purpose of this study was to determine how the inclusion of fractionated alfalfa leaves and alfalfa stems impacts performance and carcass quality of finishing beef steers. Twenty-four steers were allocated to one of three treatments: a control group fed a typical finishing diet with alfalfa as the forage (CON; n = 8), a typical diet that replaced alfalfa with fractionated alfalfa leaf pellets and alfalfa stems (ProLEAF MAX™ + ProFiber Plus™; PLM+PFP; n = 8), or a typical diet that replaced alfalfa with alfalfa stems (PFP; n = 8) for 63 days. Steers were fed individually once daily, weighed every 14 days and ultrasound images were collected every 28 days. At the end of the feeding trial, steers were harvested at a commercial facility and carcass data was obtained. Analysis of dry matter intake demonstrated that steers receiving the PFP and CON diets consumed more feed (P \u3c 0.001) than steers consuming the PLM+PFP diet. Steers receiving the PLM+PFP diet gained less (P \u3c 0.001) weight than the steers receiving the other two dietary treatments. No differences (P \u3e 0.10) in feed efficiency or carcass characteristics were observed. Steers receiving the PFP diet had improved (P = 0.016) cost of gain ($0.93 per kg) when compared with steers receiving PLM+PFP ($1.08 per kg) diet. Overall, our findings demonstrate that the inclusion of PFP in place of alfalfa hay in a finishing diet has the potential to improve cost of gain, without negatively affecting growth, performance, or carcass characteristics of finishing feedlot steers

High quality and quantity Genome-wide germline genotypes from FFPE normal tissue

<p>Abstract</p> <p>Background</p> <p>Although collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes representing decades of stored samples, they have not typically been utilized to their full potential. Normal tissue from such samples would be extremely valuable for generation of genotype data for individuals who cannot otherwise provide a DNA sample.</p> <p>Findings</p> <p>We extracted DNA from normal tissue identified in FFPE tissue blocks from prostate surgery and obtained complete genome wide genotype data for over 500,000 SNP markers for these samples, and for DNA extracted from whole blood for 2 of the cases, for comparison.</p> <p>Four of the five FFPE samples of varying age and amount of tissue had identifiable normal tissue. We obtained good quality genotype data for between 89 and 99% of all SNP markers for the 4 samples from FFPE. Concordance rates of over 99% were observed for the 2 samples with DNA from both FFPE and from whole blood.</p> <p>Conclusions</p> <p>DNA extracted from normal FFPE tissue provides excellent quality and quantity genome-wide genotyping data representing germline DNA, sufficient for both linkage and association analyses. This allows genetic analysis of informative individuals who are no longer available for sampling in genetic studies.</p