Apodization technique for fiber grating fabrication with a halftone transmission amplitude mask

Experimental results of fiber Bragg gratings fabricated with halftone amplitude transmission masks and 10-cm-long phase masks are presented for the first time to our knowledge. The performance of the devices is evaluated in terms of their spectral characteristics and deviation from linear group delay. Good out-of-band sidelobe suppression of -27 dB and group-delay ripple of ?9.5 ps is achieved for fully apodized grating devices

Fabrication of electron beam generated, chirped, phase mask (1070 . 11 – 1070 . 66 nm) for fiber Bragg grating dispersion compensator

We report on the fabrication of a chirped, phase mask that was used to create a fiber Bragg grating(FBG)device for the compensation of chromatic dispersion in longhaul optical transmission networks.Electron beamlithography was used to expose the grating onto a resist-coated quartz plate. After etching, this phase mask was used to holographically expose an index grating into the fiber core [K. O. Hill, F. Bilodeau, D. C. Johnson, and J. Albert, Appl. Phys. Lett.62, 1035 (1993)]. The linear increase in the grating period, “chirp,” is only 0.55 nm over the 10 cm grating. This is too small to be defined by computer aided design and a digital deflection system. Instead, the chirp was incorporated by repeatedly rescaling the analog electronics used for field size calibration. Special attention must be paid to minimize any field stitching and exposure artifacts. This was done by using overlapping fields in a “voting” method. As a result, each grating line is exposed by the accumulation of three overlapping exposures at 1/3 dose. This translates any abrupt stitching error into a small but uniform change in the line-to-space ratio of the grating. The phase mask was used with the double-exposure photoprinting technique [K. O. Hill, F. Bilodeau, B. Malo, T. Kitagawa, S. Thériault, D. C. Johnson, J. Albert, and K. Takiguchi, Opt. Lett. 19, 1314 (1994)]: a KrF excimer laser holograp

Comparison of fiber Bragg grating dispersion-compensators made with holographic and E-beam written phase masks

Experimental results of time delay ripples in dispersion compensating fiber Bragg gratings fabricated with either holographic or electron-beam written 10-cm-long phase masks are presented. Deviations from linear phase delay are dependent upon UV exposure uniformity and phase mask errors

Temperature insensitive refractometer using core and cladding modes in open-top ridge waveguide

In order to overcome the well-known limitation of temperature instability in Bragg grating waveguide sensors, a temperature insensitive open-top ridge waveguide refractometer is developed by using a cladding mode resonance as a temperature reference. The relative shift of the core mode resonance to cladding mode resonance is used to measure the refractive index of substances under test. Specifically, the device fabricated here produces a relative resonance shift of 1 pm for every 5 × 10-4 of measured index change, with a temperature sensitivity ∼ 0.5 pm/°C

1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function.

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10(-8) previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples

Identification of common genetic risk variants for autism spectrum disorder

Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD.Peer reviewe

Corrigendum: 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function.

This corrects the article DOI: 10.1038/srep45040

1000 Genomes-based metaanalysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-Analysis of kidney function based on the estimated glomerular filtration rate (EGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, wh

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape : A Large-Scale Genome-Wide Interaction Study

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to similar to 2.8M SNPs with BMI and WHRadjBMI in four strata (men 50y, women 50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR= 50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may providefurther insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.Peer reviewe

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns

Epigenetic processes, including DNA methylation (DNAm), are among the mechanisms allowing integration of genetic and environmental factors to shape cellular function. While many studies have investigated either environmental or genetic contributions to DNAm, few have assessed their integrated effects. Here we examine the relative contributions of prenatal environmental factors and genotype on DNA methylation in neonatal blood at variably methylated regions (VMRs) in 4 independent cohorts (overall n = 2365). We use Akaike’s information criterion to test which factors best explain variability of methylation in the cohort-specific VMRs: several prenatal environmental factors (E), genotypes in cis (G), or their additive (G + E) or interaction (GxE) effects. Genetic and environmental factors in combination best explain DNAm at the majority of VMRs. The CpGs best explained by either G, G + E or GxE are functionally distinct. The enrichment of genetic variants from GxE models in GWAS for complex disorders supports their importance for disease risk