Global particle simulations of the lower hybrid (LH) waves have been carried out using fully kinetic ions and drift kinetic electrons with a realistic electron-to-ion mass ratio. The LH wave frequency, mode structure, and electron Landau damping from the electrostatic simulations agree very well with the analytic theory. Linear simulation of the propagation of a LH wave-packet in the toroidal geometry shows that the wave propagates faster in the high field side than the low field side, in agreement with a ray tracing calculation. This poloidal asymmetry arises from the non-conservation of the poloidal mode number due to the non-uniform magnetic field. In contrast, the poloidal mode number is conserved in the cylindrical geometry with the uniform magnetic field. © 2014 IOP Publishing Ltd.

The gyrokinetic toroidal code has been upgraded for global simulations by coupling the core and scrape-off layer regions across the separatrix with field-aligned particle-grid interpolations. A fully kinetic particle pusher for high frequency waves (ion cyclotron frequency and beyond) and a guiding center pusher for low frequency waves have been implemented using cylindrical coordinates in a global toroidal geometry. The two integrators correctly capture the particle orbits and agree well with each other, conserving energy and canonical angular momentum. As a verification and application of this new capability, ion guiding center simulations have been carried out to study ion orbit losses at the edge of the DIII-D tokamak for single null magnetic separatrix discharges. The ion loss conditions are examined as a function of the pitch angle for cases without and with a radial electric field. The simulations show good agreement with past theoretical results and with the experimentally observed feature in which high energy ions flow out along the ion drift orbits and then hit the divertor plates. A measure of the ion direct orbit loss fraction shows that the loss fraction increases with the ion energy for DIII-D in the initial velocity space. Finally, as a further verification of the capability of the new code, self-consistent simulations of zonal flows in the core region of the DIII-D tokamak were carried out. All DIII-D simulations were performed in the absence of turbulence.

The cornea is the outermost layer of the eye and is a vital component of focusing incoming light on the retina. Central corneal thickness (CCT) is now recognized to have a significant role in ocular health and is a risk factor for various ocular diseases, such as keratoconus and primary open angle glaucoma. Most previous genetic studies utilized European and Asian subjects to identify genetic loci associated with CCT. Minority populations, such as Latinos, may aid in identifying additional loci and improve our understanding of the genetic architecture of CCT. In this study, we conducted a genome-wide association study (GWAS) in Latinos, a traditionally understudied population in genetic research, to further identify loci contributing to CCT. Study participants were genotyped using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). All study participants were 40 years of age and older. We assessed the association between individual single nucleotide polymorphisms (SNPs) and CCT using linear regression, adjusting for age, gender and principal components of genetic ancestry. To expand genomic coverage and to interrogate additional SNPs, we imputed SNPs from the 1000 Genomes Project reference panels. We identified a novel SNP, rs10453441 (P = 6.01E-09), in an intron of WNT7B that is associated with CCT. Furthermore, WNT7B is expressed in the human cornea. We also replicated 11 previously reported loci, including IBTK, RXRA-COL5A1, COL5A1, FOXO1, LRRK1 and ZNF469 (P < 1.25E-3). These findings provide further insight into the genetic architecture of CCT and illustrate that the use of minority groups in GWAS will help identify additional loci.

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.