Applications and efficiencies of the first cat 63K DNA array

The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array\u2019s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50\u20131,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations

A Pre-Landing Assessment of Regolith Properties at the InSight Landing Site

This article discusses relevant physical properties of the regolith at the Mars InSight landing site as understood prior to landing of the spacecraft. InSight will land in the northern lowland plains of Mars, close to the equator, where the regolith is estimated to be ≥3--5 m thick. These investigations of physical properties have relied on data collected from Mars orbital measurements, previously collected lander and rover data, results of studies of data and samples from Apollo lunar missions, laboratory measurements on regolith simulants, and theoretical studies. The investigations include changes in properties with depth and temperature. Mechanical properties investigated include density, grain-size distribution, cohesion, and angle of internal friction. Thermophysical properties include thermal inertia, surface emissivity and albedo, thermal conductivity and diffusivity, and specific heat. Regolith elastic properties not only include parameters that control seismic wave velocities in the immediate vicinity of the Insight lander but also coupling of the lander and other potential noise sources to the InSight broadband seismometer. The related properties include Poisson’s ratio, P- and S-wave velocities, Young’s modulus, and seismic attenuation. Finally, mass diffusivity was investigated to estimate gas movements in the regolith driven by atmospheric pressure changes. Physical properties presented here are all to some degree speculative. However, they form a basis for interpretation of the early data to be returned from the InSight mission.Additional co-authors: Nick Teanby and Sharon Keda

Thomson scattering stray light reduction techniques using a CCD camera

The DIII-D Thomson scattering system has been expanded to measure divertor plasma temperatures from 1-500 eV and densities from 0.05 to 8 X 10{sup 20} m{sup -3}. To complete this system, a difficult stray light problem was overcome to allow for an accurate Rayleigh scattering density calibration. The initial stray light levels were over 500 times higher than the expected Rayleigh scattered signal. Using a CCD camera, various portions of the vessel interior were examined while the laser was fired through the vessel in air at atmospheric pressure. Image relaying, exit window tilting, entrance and exit baffle modifications, and a beam polarizer were then used to reduce the stray light to acceptable levels. The CCD camera gave prompt feedback on the effectiveness of each modification, without the need to re-establish vacuum conditions required when using the normal avalanche Photodiode detectors (APD). Once the stray light was sufficiently reduced, the APD detectors provided the signal time history to more accurately identify the source location. We have also found that certain types of high reflectance dielectric coatings produce 10 to 15 times more scatter than other types of more conventional coatings. By using low-scatter mirror coatings and these new stray light reduction techniques, we now have more flexibility in the design of complex Thomson scattering configurations required to probe the central core and the new radiative divertor regions of the DIII-D vessel

Broad-band soft x-ray diagnostic instruments at the LLNL Novette laser facility

Complementary broad-band instruments have been developed to measure time dependent, absolute soft x-ray spectra at the Lawrence Livermore National Laboratory (LLNL) Nd glass laser irradiation facilities. Absolute flux measurements of x rays emitted from laser-produced plasmas are important for understanding laser absorption and energy transport. We will describe two new 10-channel XRD systems that have been installed at the LLNL Novette facility for use in the 0.15- to 1.5-keV range. Since XRD channel time response is limited by available oscilloscope performance to 120 ps, a soft x-ray streak camera has been developed for better time resolution (20 ps) and greater dynamic range (approx.10/sup 3/) in the same x-ray energy region. Using suitable filters, grazing incidence mirrors, and a gold or cesium-iodide transmission cathode, this streak camera instrument has been installed at Novette to provide one broad and four relatively narrow channels. It can also be used in a single channel, spatially discriminating mode by means of pinhole imaging. The complementary nature of these instruments has been enhanced by locating them in close proximity and matching their channel energy responses. As an example of the use of these instruments, we present results from Novette 2..omega..(0.53 ..mu..m) gold disk irradiations at 1 ns and 10/sup 14/ to 10/sup 15/ W/cm/sup 2/

A tangentially viewing VUV TV system for the DIII-D divertor

A video camera system capable of imaging VUV emission in the 120--160 nm wavelength range, from the entire divertor region in the DIII-D tokamak, was designed. The new system has a tangential view of the divertor similar to an existing tangential camera system which has produced two dimensional maps of visible line emission (400--800 nm) from deuterium and carbon in the divertor region. However, the overwhelming fraction of the power radiated by these elements is emitted by resonance transitions in the ultraviolet, namely the C IV line at 155.0 nm and Ly-{alpha} line at 121.6 nm. To image the ultraviolet light with an angular view including the inner wall and outer bias ring in DIII-D, a 6-element optical system (f/8.9) was designed using a combination of reflective and refractive optics. This system will provide a spatial resolution of 1.2 cm in the object plane. An intermediate UV image formed in a secondary vacuum is converted to the visible by means of a phosphor plate and detected with a conventional CID camera (30 ms framing rate). A single MgF{sub 2} lens serves as the vacuum interface between the primary and secondary vacuums; a second lens must be inserted in the secondary vacuum to correct the focus at 155 nm. Using the same tomographic inversion method employed for the visible TV, they reconstruct the poloidal distribution of the UV divertor light. The grain size of the phosphor plate and the optical system aberrations limit the best focus spot size to 60 {micro}m at the CID plane. The optical system is designed to withstand 350 C vessel bakeout, 2 T magnetic fields, and disruption-induced accelerations of the vessel