Data for Genetic Analysis Workshop 16 Problem 1, Association Analysis of Rheumatoid Arthritis Data

For Genetic Analysis Workshop 16 Problem 1, we provided data for genome-wide association analysis of rheumatoid arthritis. Single-nucleotide polymorphism (SNP) genotype data were provided for 868 cases and 1194 controls that had been assayed using an Illumina 550 k platform. In addition, phenotypic data were provided from genotyping DRB1 alleles, which were classified according to the rheumatoid arthritis shared epitope, levels of anti-cyclic citrullinated peptide, and levels of rheumatoid factor IgM. Several questions could be addressed using the data, including analysis of genetic associations using single SNPs or haplotypes, as well as gene-gene and genetic analysis of SNPs for qualitative and quantitative factors

Phase-matched multi-layer based polarisation-independent spot-size converter for silicon nanowire

The efficient coupling of optical power from a silicon nanowire (NW) to an optical fibre is challenging for both the quasi-TE and quasi-TM polarisations. Here, we propose a polarisation-independent spot-size converter (PI-SSC) based on phase-matched multi-layer waveguides for efficient coupling between a silicon NW and an optical fibre for both the polarisations. The fabrication process of the proposed PI-SSC is compatible with the complementary metal-oxide-semiconductor (CMOS) process. The optimisation for the proposed PI-SSC is studied by using a numerically efficient algorithm, combining a rigorous H-field based full-vectorial finite element method (VFEM) and the least squares boundary residual (LSBR) method. The simulation results show that using an eleven-layer based PI-SSC, the coupling losses between a silicon NW and a lensed fibre of radius 2 μm can be reduced to only 0.34 dB and 0.25 dB for the quasi-TE and quasi-TM polarisations, respectively. Furthermore, the output multi-layer is horizontally tapered, which further reduces the coupling loss for both the polarisations and the end face is easy to be polished

Multi-scale physical properties of NGC 6334 as revealed by local relative orientations between magnetic fields, density gradients, velocity gradients, and gravity

We present ALMA dust polarization and molecular line observations toward 4 clumps (I(N), I, IV, and V) in the massive star-forming region NGC 6334. In conjunction with large-scale dust polarization and molecular line data from JCMT, Planck, and NANTEN2, we make a synergistic analysis of relative orientations between magnetic fields ($\theta_{\mathrm{B}}$), column density gradients ($\theta_{\mathrm{NG}}$), local gravity ($\theta_{\mathrm{LG}}$), and velocity gradients ($\theta_{\mathrm{VG}}$) to investigate the multi-scale (from $\sim$30 pc to 0.003 pc) physical properties in NGC 6334. We find that the relative orientation between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ changes from statistically more perpendicular to parallel as column density ($N_{\mathrm{H_2}}$) increases, which is a signature of trans-to-sub-Alfv\'{e}nic turbulence at complex/cloud scales as revealed by previous numerical studies. Because $\theta_{\mathrm{NG}}$ and $\theta_{\mathrm{LG}}$ are preferentially aligned within the NGC 6334 cloud, we suggest that the more parallel alignment between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ at higher $N_{\mathrm{H_2}}$ is because the magnetic field line is dragged by gravity. At even higher $N_{\mathrm{H_2}}$, the angle between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ or $\theta_{\mathrm{LG}}$ transits back to having no preferred orientation or statistically slightly more perpendicular, suggesting that the magnetic field structure is impacted by star formation activities. A statistically more perpendicular alignment is found between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{VG}}$ throughout our studied $N_{\mathrm{H_2}}$ range, which indicates a trans-to-sub-Alfv\'{e}nic state at small scales as well. The normalised mass-to-flux ratio derived from the polarization-intensity gradient (KTH) method increases with $N_{\mathrm{H_2}}$.Comment: 35 pages, 18 figures. Accepted by Ap

Morphology and Nanomechanics of Sensory Neurons Growth Cones following Peripheral Nerve Injury

A prior peripheral nerve injury in vivo, promotes a rapid elongated mode of sensory neurons neurite regrowth in vitro. This in vitro model of conditioned axotomy allows analysis of the cellular and molecular mechanisms leading to an improved neurite re-growth. Our differential interference contrast microscopy and immunocytochemistry results show that conditioned axotomy, induced by sciatic nerve injury, did not increase somatic size of adult lumbar sensory neurons from mice dorsal root ganglia sensory neurons but promoted the appearance of larger neurites and growth cones. Using atomic force microscopy on live neurons, we investigated whether membrane mechanical properties of growth cones of axotomized neurons were modified following sciatic nerve injury. Our data revealed that neurons having a regenerative growth were characterized by softer growth cones, compared to control neurons. The increase of the growth cone membrane elasticity suggests a modification in the ratio and the inner framework of the main structural proteins

Combining microscopic and macroscopic probes to untangle the single-ion anisotropy and exchange energies in an S=1 quantum antiferromagnet

The magnetic ground state of the quasi-one-dimensional spin-1 antiferromagnetic chain is sensitive to the relative sizes of the single-ion anisotropy (D) and the intrachain (J) and interchain (J') exchange interactions. The ratios D/J and J'/J dictate the material's placement in one of three competing phases: a Haldane gapped phase, a quantum paramagnet and an XY-ordered state, with a quantum critical point at their junction. We have identified [Ni(HF)2(pyz)_2]SbF6, where pyz = pyrazine, as a rare candidate in which this behavior can be explored in detail. Combining neutron scattering (elastic and inelastic) in applied magnetic fields of up to 10~tesla and magnetization measurements in fields of up to 60~tesla with numerical modeling of experimental observables, we are able to obtain accurate values of all of the parameters of the Hamiltonian [D = 13.3(1)~K, J = 10.4(3)~K and J' = 1.4(2)~K], despite the polycrystalline nature of the sample. Density-functional theory calculations result in similar couplings (J = 9.2~K, J' = 1.8~K) and predict that the majority of the total spin population resides on the Ni(II) ion, while the remaining spin density is delocalized over both ligand types. The general procedures outlined in this paper permit phase boundaries and quantum-critical points to be explored in anisotropic systems for which single crystals are as yet unavailable

Supplement: "Going the Distance: Mapping Host Galaxies of LIGO and Virgo Sources in Three Dimensions Using Local Cosmography and Targeted Follow-up" (2016, ApJL, 829, L15)

This is a supplement to the Letter of Singer et al., in which we demonstrated a rapid algorithm for obtaining joint 3D estimates of sky location and luminosity distance from observations of binary neutron star mergers with Advanced LIGO and Virgo. We argued that combining the reconstructed volumes with positions and redshifts of possible host galaxies can provide large-aperture but small field of view instruments with a manageable list of targets to search for optical or infrared emission. In this Supplement, we document the new HEALPix-based file format for 3D localizations of gravitational-wave transients. We include Python sample code to show the reader how to perform simple manipulations of the 3D sky maps and extract ranked lists of likely host galaxies. Finally, we include mathematical details of the rapid volume reconstruction algorithm

Data for Genetic Analysis Workshop (GAW) 15 Problem 2, Genetic Causes of Rheumatoid Arthritis and Associated Traits

For Genetic Analysis Workshop 15 Problem 2, we organized data from several ongoing studies designed to identify genetic and environmental risk factors for rheumatoid arthritis. Data were derived from the North American Rheumatoid Arthritis Consortium (NARAC), collaboration among Canadian researchers, the European Consortium on Rheumatoid Arthritis Families (ECRAF), and investigators from Manchester, England. All groups used a common standard for defining rheumatoid arthritis, but NARAC also further selected for a more severe phenotype in the probands. Genotyping and family structures for microsatellite-based linkage analysis were provided from all centers. In addition, all centers but ECRAF have genotyped families for linkage analysis using SNPs and these data were additionally provided. NARAC also had additional data from a dense genotyping analysis of a region of chromosome 18 and results from candidate gene studies, which were provided. Finally, smoking influences risk for rheumatoid arthritis, and data were provided from the NARAC study on this behavior as well as some additional phenotypes measuring severity. Several questions could be evaluated using the data that were provided. These include comparing linkage analysis using single-nucleotide polymorphisms versus microsatellites and identifying credible regions of linkage outside the HLA region on chromosome 6p13, which has been extensively documented; evaluating the joint effects of smoking with genetic factors; and identifying more homogenous subsets of families for whom genetic susceptibility might be stronger, so that linkage and association studies may be more efficiently conducted