Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus

Summary: Often in human genetic analysis, multiple tables of single nucleotide polymorphism (SNP) statistics are shown alongside a Haploview style correlation plot. Readers are then asked to make inferences that incorporate knowledge across these multiple sets of results. To better facilitate a collective understanding of all available data, we developed a Ruby-based web application, LD-Plus, to generate figures that simultaneously display physical location of SNPs, binary SNP attributes (such as coding/non-coding or presence on genotyping platforms), common haplotypes and their frequencies and continuously scaled values (such as Fst, minor allele frequency, genotyping efficiency or P-values), all in the context of the D′ and r2 linkage disequilibrium structures. Combining these results into one comprehensive figure reduces dereferencing between figures and tables, and can provide unique insights into genetic features that are not clearly seen when results are partitioned across multiple figures and tables

Randomized placebo controlled trials of n-acetyl cysteine as adjunct therapy for schizophrenia and bipolar disorder

Glutathione is the principal antioxidant of the brain. There is evidence of oxidative stress, lowered brain glutathione and genetic linkage involve glutathione metabolic genes in schizophrenia and bipolar disorder. N-acetyl cysteine (NAC) is a safe, orally bioavailable, precursor of glutathione. NAC has been shown to reverse animal models of oxidative stress, and raises brain glutathione levels.<br /

Extensive infrared spectroscopic study of CuO: signatures of strong spin-phonon interaction and structural distortion

Optical properties of single-crystal monoclinic CuO in the range 70 - 6000 \cm were studied at temperatures from 7 to 300 K. Normal reflection spectra were obtained from the (001) and (010) crystal faces thus giving for the first time separate data for the $A_{u}$ and $B_{u}$ phonon modes excited in the purely transverse way (TO modes). Mode parameters, including polarizations of the $B_{u}$ modes not determined by the crystal symmetry, were extracted by the dispersion analysis of reflectivity curves as a function of temperature. Spectra of all the components of the optical conductivity tensor were obtained using the Kramers-Kronig method recently extended to the case of the low-symmetry crystals. The number of strong phonon modes is in agreement with the factor-group analysis for the crystal structure, currently accepted for the CuO. However, several "extra" modes of minor intensity are detected. Comparison of frequencies of "extra" modes with the available phonon dispersion curves points to possible "diagonal" doubling of the unit cell \{{\bf a}, {\bf b}, {\bf c}\} $\to$ \{{\bf a}+{\bf c}, {\bf b}, {\bf a}-{\bf c}\} and formation of the superlattice. The previously reported softening of the $A^{3}_{u}$ mode ($\sim$ 400 \cm) with cooling at $T_{N}$ is found to be $\sim$ 10 % for the TO mode. The mode is very broad at high temperatures and strongly narrows in the AFM phase. We attribute this effect to strong resonance coupling of this mode to optical or acoustic bi-magnons and reconstruction of the magnetic excitations spectrum at the N\'eel point. A significant anisotropy of $\epsilon^{\infty}$ is observed: it was found to be 5.9 along the {\bf b}-axis, 6.2 along the {[}101{]} chains and 7.8 the {[}10$\bar{1}${]} chains. The "transverse" effective charge is value is about 2 electrons.Comment: 23 pages, 14 figures, REVTeX, submitted to PR

Partial coalescence of soap bubbles

We present the results of an experimental investigation of the merger of a soap bubble with a planar soap film. When gently deposited onto a horizontal film, a bubble may interact with the underlying film in such a way as to decrease in size, leaving behind a smaller daughter bubble with approximately half the radius of its progenitor. The process repeats up to three times, with each partial coalescence event occurring over a time scale comparable to the inertial-capillary time. Our results are compared to the recent numerical simulations of Martin and Blanchette [“Simulations of surfactant effects on the dynamics of coalescing drops and bubbles,” Phys. Fluids 27, 012103 (2015)] and to the coalescence cascade of droplets on a fluid bath

Sensitivity of Cross Sections for Elastic Nucleus-Nucleus Scattering to Halo Nucleus Density Distributions

In order to clear up the sensitivity of the nucleus-nucleus scattering to the nuclear matter distributions of exotic halo nuclei, we have calculated differential cross sections for elastic scattering of the $^6$He and $^{11}$Li nuclei on several nuclear targets at the energy of 0.8 GeV/nucleon with different assumed nuclear density distributions in $^6$He and $^{11}$Li.Comment: 10 pages, 7 figures. Submitted to Proceedings of the 61 International Conference "Nucleus-2011" on the Problems of the Nuclear Spectroscopy and the Atomic Nuclear Structure, Sarov Nijzegorodskaya district, October 10-14, 201

Employing the Precautionary Principle to Evaluate the Use of E-Cigarettes

Electronic cigarettes (e-cigarettes) have emerged onto the public market as an alternative to tobacco cigarettes; however, science is inconclusive as e-cigarettes have not been thoroughly investigated, including their short- and long-term risks and benefits (1, 2). The question arises of whether e-cigarettes will become the future tobacco crisis. This paper connects the precautionary principle to the use of e-cigarettes in an effort to guide decision-makers in the prevention of adverse health outcomes and societal costs

Parasite infections in a social carnivore: Evidence of their fitness consequences and factors modulating infection load

There are substantial individual differences in parasite composition and infection load in wildlife populations. Few studies have investigated the factors shaping this heterogeneity in large wild mammals or the impact of parasite infections on Darwinian fitness, particularly in juveniles. A host's parasite composition and infection load can be shaped by factors that determine contact with infective parasite stages and those that determine the host's resistance to infection, such as abiotic and social environmental factors, and age. Host–parasite interactions and synergies between coinfecting parasites may also be important. We test predictions derived from these different processes to investigate factors shaping infection loads (fecal egg/oocyte load) of two energetically costly gastrointestinal parasites: the hookworm Ancylostoma and the intracellular Cystoisospora, in juvenile spotted hyenas (Crocuta crocuta) in the Serengeti National Park, in Tanzania. We also assess whether parasite infections curtail survival to adulthood and longevity. Ancylostoma and Cystoisospora infection loads declined as the number of adult clan members increased, a result consistent with an encounter‐reduction effect whereby adults reduced encounters between juveniles and infective larvae, but were not affected by the number of juveniles in a clan. Infection loads decreased with age, possibly because active immune responses to infection improved with age. Differences in parasite load between clans possibly indicate variation in abiotic environmental factors between clan den sites. The survival of juveniles (<365 days old) to adulthood decreased with Ancylostoma load, increased with age, and was modulated by maternal social status. High‐ranking individuals with low Ancylostoma loads had a higher survivorship during the first 4 years of life than high‐ranking individuals with high Ancylostoma loads. These findings suggest that high infection loads with energetically costly parasites such as hookworms during early life can have negative fitness consequences

Improving radiation hardness in space-based Charge-Coupled Devices through the narrowing of the charge transfer channel

Charge-Coupled Devices (CCDs) have been the detector of choice for imaging and spectroscopy in space missions for several decades, such as those being used for the Euclid VIS instrument and baselined for the SMILE SXI. Despite the many positive properties of CCDs, such as the high quantum efficiency and low noise, when used in a space environment the detectors suffer damage from the often-harsh radiation environment. High energy particles can create defects in the silicon lattice which act to trap the signal electrons being transferred through the device, reducing the signal measured and effectively increasing the noise. We can reduce the impact of radiation on the devices through four key methods: increased radiation shielding, device design considerations, optimisation of operating conditions, and image correction. Here, we concentrate on device design operations, investigating the impact of narrowing the charge-transfer channel in the device with the aim of minimising the impact of traps during readout. Previous studies for the Euclid VIS instrument considered two devices, the e2v CCD204 and CCD273, the serial register of the former having a 50 μm channel and the latter having a 20 μm channel. The reduction in channel width was previously modelled to give an approximate 1.6× reduction in charge storage volume, verified experimentally to have a reduction in charge transfer inefficiency of 1.7×. The methods used to simulate the reduction approximated the charge cloud to a sharp-edged volume within which the probability of capture by traps was 100%. For high signals and slow readout speeds, this is a reasonable approximation. However, for low signals and higher readout speeds, the approximation falls short. Here we discuss a new method of simulating and calculating charge storage variations with device design changes, considering the absolute probability of capture across the pixel, bringing validity to all signal sizes and readout speeds. Using this method, we can optimise the device design to suffer minimum impact from radiation damage effects, here using detector development for the SMILE mission to demonstrate the process