Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data

Sequencing family DNA samples provides an attractive alternative to population based designs to identify rare variants associated with human disease due to the enrichment of causal variants in pedigrees. Previous studies showed that genotype calling accuracy can be improved by modeling family relatedness compared to standard calling algorithms. Current family-based variant calling methods use sequencing data on single variants and ignore the identity-by-descent (IBD) sharing along the genome. In this study we describe a new computational framework to accurately estimate the IBD sharing from the sequencing data, and to utilize the inferred IBD among family members to jointly call genotypes in pedigrees. Through simulations and application to real data, we showed that IBD can be reliably estimated across the genome, even at very low coverage (e.g. 2X), and genotype accuracy can be dramatically improved. Moreover, the improvement is more pronounced for variants with low frequencies, especially at low to intermediate coverage (e.g. 10X to 20X), making our approach effective in studying rare variants in cost-effective whole genome sequencing in pedigrees. We hope that our tool is useful to the research community for identifying rare variants for human disease through family-based sequencing

Effect of Ultra-high Pressure Treatment on the Chemical Properties, Colour and Sensory Quality of Young Red Wine

The effects of ultra-high pressure (UHP) treatment on the chemical properties, colour and sensory qualityof young red wine were studied. UHP did not significantly affect the alcohol content, and the methanolcontent was higher than that of the control, with the latter first increasing and then decreasing with theincrease in the pressure or period of treatment. The glycerol content was also markedly changed by UHP,although without a regular pattern. The pH value was not markedly changed by the treatments, and thecontents of total acids and volatile acids were scarcely affected. The fructose and glucose contents wereclearly changed according to the different treatment conditions. The tartaric acid, citric acid and lacticacid levels showed evident changes, whereas the malic acid level was not changed by UHP treatment. Thetrend of these changes was similar to what occurs during natural ageing. As the pressure of the treatmentwas increased to 200 MPa, the chroma value increased, followed by a decline upon higher pressuretreatments. The hue of the wine was significantly changed by treatment at different pressures, reachingthe highest value after treatment at 400 MPa and then decreasing with increasing pressure. The chromaand hue values of the wine were changed significantly according to the duration of the UHP. After UHP, theappearance, aroma and taste of the wine was improved, with the score for appearance obviously increased.When the wine was treated at 500 MPa for 30 min, its sensory quality received the highest score

Evaluation and Application of Remotely Sensed Soil Moisture Products

Whereas in-situ measurements of soil moisture are very accurate, achieving accurate regional soil moisture estimates derived solely from point measurements is difficult because of the dependence upon the density of the gauge network and the proper upkeep of these instruments, which can be costly. Microwave remote sensing is the only technology capable of providing timely direct measurements of regional soil moisture in areas that are lacking in-situ networks. Soil moisture remote sensing technology is well established has been successfully applied in many fashions to Earth Science applications. Since the microwave emission from the soil surface has such a high dependency upon the moisture content within the soil, we can take advantage of this relationship and combined with physically-based models of the land surface, derive accurate regional estimates of the soil column water content from the microwave brightness temperature observed from satellite-based remote sensing instruments. However, there still remain many questions regarding the most efficient methodology for evaluating and applying satellite-based soil moisture estimates. As discussed below, we to use satellite-based estimates of soil moisture dynamics to improve the predictive capability of an optimized hydrologic model giving more accurate root-zone soil moisture estimates

Two-Speed DCT Electric Powertrain Shifting Control and Rig Testing

Dual clutch transmissions (DCTs) are recognized as being suitable for electric drive applications as they can drive with high efficiency and achieve good shifting comfort. A two-speed DCT electric drivetrain is described in this paper, comprised of only two gear pairs and a final drive gear in the two-speed gearbox. The fundamental shifting control algorithm is provided. On the testing rig of University of Technology, Sydney (UTS) powertrain lab, shifting controls and some driving cycle controls were realized. The results demonstrated that the control algorithm functioned well both in transient shifting control process and in the driving cycle conditions

The Effects of Ultra-high Pressure Treatment on the Phenolic Composition of Red Wine

Wine is usually aged in oak barrels. In this study, young red wines were treated with ultra-high pressure(UHP) to stimulate the ageing process. Changes in phenolic acids, flavan-3-ols and proanthocyanidinswere determined by reverse-phase high pressure liquid chromatography (RP-HPLC). The concentrationof phenolic acids increased, while the levels of flavan-3-ols decreased. The content and structure ofproanthocyanidins also changed and the tendency was similar to that of natural ageing

Endothelial Cell Cortactin Phosphorylation by Src Contributes to Polymorphonuclear Leukocyte Transmigration In Vitro

The underlying mechanisms that regulate leukocyte transendothelial migration through the vascular endothelium remain unclear. Cortactin is a substrate of Src tyrosine kinases and a regulator of cytoskeletal dynamics. Previous studies demonstrated a role for Src phosphorylation of cortactin in clustering of E-selectin and intercellular cell adhesion molecule-1 around adherent leukocytes. In the current study, we used an in vitro flow model to investigate the role of Src-induced cortactin phosphorylation in endothelium during polymorphonuclear leukocyte (PMN) transmigration through human umbilical vein endothelium (HUVEC) monolayers preactivated with tumor necrosis factor-{alpha}. Inhibition of Src in HUVEC using Src kinase inhibitors PP2 and SU6656 reduced PMN transmigration by 45±8% and 36±6%, respectively. Live cell imaging of green fluorescent protein–tagged cortactin in HUVEC revealed redistribution of cortactin in the region surrounding transmigrating PMN. Knockdown of cortactin in HUVEC by small interfering RNA also impaired transmigration to a similar degree, and this phenotype was rescued by reexpression of wild-type cortactin. Analysis of the location of initial arrest and locomotion of PMN adherent to HUVEC demonstrated that inhibition of Src tyrosine kinases or pretreatment with cortactin small interfering RNA reduced PMN transmigration at endothelial cell-to-cell junctions and not adhesion. Tyrosine phosphorylation of cortactin was important for transmigration, because expression of a mutant, in which the tyrosine phosphorylation sites were mutated to phenylalanine (cortactin3F), failed to rescue PMN transmigration. Moreover, expression of cortactin3F alone partially blocked PMN transmigration. These data suggest a model whereby tyrosine phosphorylation of cortactin by Src family kinases regulates PMN transmigratio

Effect of Suspension Freeze-concentration Technology on the Quality of Wine

One of the factors that inhibits the development of the Chinese wine industry is that the sugar content ofthe grape feedstock is insufficient. In order to produce wine with better qualities using these materials,concentrating the grape juice could be a good alternative to adding sugars. In this study, suspension freezeconcentrationtechnology was applied to concentrating grape juice with a low sugar content. The freezeconcentratedgrape juice was made into red and white wines separately. In the control group, red andwhite wines were made from chaptalized (sugar-enriched) grape juice. The physical and chemical indexes,sensory evaluation results and polyphenolic content of the wine were analysed to evaluate the practicalityof applying the freeze-concentration technology in the wine industry. The results show that, after removingice every 30 min for approximately 14 h with a -18°C coolant, grape juice with an initial sugar content of14°Brix reached 23°Brix. Both the red wines and white wines made from freeze-concentrated grape juicewere of a higher quality than the wines made from chaptalised grape juice. Moreover, the phenolic contentwas concentrated, which may provide health benefits. Thus, suspension freeze-concentration technology isa promising alternative to traditional chaptalisation technology

Probing Spin-Flip Scattering in Ballistic Nanosystems

Because spin-flip length is longer than the electron mean-free path in a metal, past studies of spin-flip scattering are limited to the diffusive regime. We propose to use a magnetic double barrier tunnel junction to study spin-flip scattering in the nanometer sized spacer layer near the ballistic limit. We extract the voltage and temperature dependence of the spin-flip conductance Gs in the spacer layer from magnetoresistance measurements. In addition to spin scattering information including the mean-free path (70 nm) and the spin-flip length (1:0–2:6 m) at 4.2 K, this technique also yields information on the density of states and quantum well resonance in the spacer laye

An independent test of the photometric selection of white dwarf candidates using LAMOST DR3

In Gentile Fusillo et al. (2015) we developed a selection method for white dwarf candidates which makes use of photometry, colours and proper motions to calculate a probability of being a white dwarf (Pwd). The application of our method to the Sloan Digital Sky Survey (SDSS) data release 10 resulted in nearly 66,000 photometrically selected objects with a derived Pwd, approximately 21000 of which are high confidence white dwarf candidates. Here we present an independent test of our selection method based on a sample of spectroscopically confirmed white dwarfs from the LAMOST (Large Sky Area Multi-Fiber Spectroscopic Telescope) survey. We do this by cross matching all our $\sim$66,000 SDSS photometric white dwarf candidates with the over 4 million spectra available in the third data release of LAMOST. This results in 1673 white dwarf candidates with no previous SDSS spectroscopy, but with available LAMOST spectra. Among these objects we identify 309 genuine white dwarfs. We find that our Pwd can efficiently discriminate between confirmed LAMOST white dwarfs and contaminants. Our white dwarf candidate selection method can be applied to any multi-band photometric survey and in this work we conclusively confirm its reliability in selecting white dwarfs without recourse to spectroscopy. We also discuss the spectroscopic completeness of white dwarfs in LAMOST, as well as deriving effective temperatures, surface gravities and masses for the hydrogen-rich atmosphere white dwarfs in the newly identified LAMOST sample.Comment: 10 pages, 7 figures. Accepted for publication in MNRAS. The full catalogue presented in table 4 is available at http://www2.warwick.ac.uk/fac/sci/physics/research/astro/catalogues/SDSS_WD_candidates_with_LAMOST_spectra.cs