fgui: A Method for Automatically Creating Graphical User Interfaces for Command-Line R Packages

The fgui R package is designed for developers of R packages, to help rapidly, and sometimes fully automatically, create a graphical user interface for a command line R package. The interface is built upon the Tcl/Tk graphical interface included in R. The package further facilitates the developer by loading in the help files from the command line functions to provide context sensitive help to the user with no additional effort from the developer. Passing a function as the argument to the routines in the fgui package creates a graphical interface for the function, and further options are available to tweak this interface for those who want more flexibility.

Running coupling and mass anomalous dimension of SU(3) gauge theory with two flavors of symmetric-representation fermions

We have measured the running coupling constant of SU(3) gauge theory coupled to Nf=2 flavors of symmetric representation fermions, using the Schrodinger functional scheme. Our lattice action is defined with hypercubic smeared links which, along with the larger lattice sizes, bring us closer to the continuum limit than in our previous study. We observe that the coupling runs more slowly than predicted by asymptotic freedom, but we are unable to observe fixed point behavior before encountering a first order transition to a strong coupling phase. This indicates that the infrared fixed point found with the thin-link action is a lattice artifact. The slow running of the gauge coupling permits an accurate determination of the mass anomalous dimension for this theory, which we observe to be small, gamma_m < 0.6, over the range of couplings we can reach. We also study the bulk and finite-temperature phase transitions in the strong coupling region.Comment: 17 pages, 16 figures. Substantial modifications to explain why the fat-link result for the beta function supersedes our thin-link result; also updated the phase diagram to reflect additional numerical work. Added references. Final versio

A large multi-ethnic genome-wide association study identifies novel genetic loci for intraocular pressure.

Elevated intraocular pressure&nbsp;(IOP) is a major risk factor for glaucoma, a leading cause of blindness. IOP heritability has been estimated to up to 67%, and to date only 11 IOP loci have been reported, accounting for 1.5% of IOP variability. Here, we conduct a genome-wide association study of IOP in 69,756 untreated individuals of European, Latino, Asian, and African ancestry. Multiple longitudinal IOP measurements were collected through electronic health records and, in total, 356,987 measurements were included. We identify 47 genome-wide significant IOP-associated loci (P &lt; 5 × 10-8); of the 40 novel loci, 14 replicate at Bonferroni significance in an external genome-wide association study analysis of 37,930 individuals of European and Asian descent. We further examine their effect on the risk of glaucoma within our discovery sample. Using longitudinal IOP measurements from electronic health records improves our power to identify new variants, which together explain 3.7% of IOP variation

Adiposity, Cardiometabolic Risk, and Vitamin D Status: The Framingham Heart Study

OBJECTIVE: Because vitamin D deficiency is associated with a variety of chronic diseases, understanding the characteristics that promote vitamin D deficiency in otherwise healthy adults could have important clinical implications. Few studies relating vitamin D deficiency to obesity have included direct measures of adiposity. Furthermore, the degree to which vitamin D is associated with metabolic traits after adjusting for adiposity measures is unclear. RESEARCH DESIGN AND METHODS: We investigated the relations of serum 25-hydroxyvitamin D (25[OH]D) concentrations with indexes of cardiometabolic risk in 3,890 nondiabetic individuals; 1,882 had subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) volumes measured by multidetector computed tomography (CT). RESULTS: In multivariable-adjusted regression models, 25(OH)D was inversely associated with winter season, waist circumference, and serum insulin (P < 0.005 for all). In models further adjusted for CT measures, 25(OH)D was inversely related to SAT (−1.1 ng/ml per SD increment in SAT, P = 0.016) and VAT (−2.3 ng/ml per SD, P < 0.0001). The association of 25(OH)D with insulin resistance measures became nonsignificant after adjustment for VAT. Higher adiposity volumes were correlated with lower 25(OH)D across different categories of BMI, including in lean individuals (BMI <25 kg/m2). The prevalence of vitamin D deficiency (25[OH]D <20 ng/ml) was threefold higher in those with high SAT and high VAT than in those with low SAT and low VAT (P < 0.0001). CONCLUSIONS: Vitamin D status is strongly associated with variation in subcutaneous and especially visceral adiposity. The mechanisms by which adiposity promotes vitamin D deficiency warrant further study.National Institutes of Health's National Heart, Lung, and Blood Institute (N01-HC-25195, R01-DK-80739): American Heart Associatio

The impact of adjusting for baseline in pharmacogenomic genome-wide association studies of quantitative change.

In pharmacogenomic studies of quantitative change, any association between genetic variants and the pretreatment (baseline) measurement can bias the estimate of effect between those variants and drug response. A putative solution is to adjust for baseline. We conducted a series of genome-wide association studies (GWASs) for low-density lipoprotein cholesterol (LDL-C) response to statin therapy in 34,874 participants of the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort as a case study to investigate the impact of baseline adjustment on results generated from pharmacogenomic studies of quantitative change. Across phenotypes of statin-induced LDL-C change, baseline adjustment identified variants from six loci meeting genome-wide significance (SORT/CELSR2/PSRC1, LPA, SLCO1B1, APOE, APOB, and SMARCA4/LDLR). In contrast, baseline-unadjusted analyses yielded variants from three loci meeting the criteria for genome-wide significance (LPA, APOE, and SLCO1B1). A genome-wide heterogeneity test of baseline versus statin on-treatment LDL-C levels was performed as the definitive test for the true effect of genetic variants on statin-induced LDL-C change. These findings were generally consistent with the models not adjusting for baseline signifying that genome-wide significant hits generated only from baseline-adjusted analyses (SORT/CELSR2/PSRC1, APOB, SMARCA4/LDLR) were likely biased. We then comprehensively reviewed published GWASs of drug-induced quantitative change and discovered that more than half (59%) inappropriately adjusted for baseline. Altogether, we demonstrate that (1) baseline adjustment introduces bias in pharmacogenomic studies of quantitative change and (2) this erroneous methodology is highly prevalent. We conclude that it is critical to avoid this common statistical approach in future pharmacogenomic studies of quantitative change

Green-diode-pumped femtosecond Ti:Sapphire laser with up to 450 mW average power

We investigate power-scaling of green-diode-pumped Ti:Sapphire lasers in continuous-wave (CW) and mode-locked operation. In a first configuration with a total pump power of up to 2 W incident onto the crystal, we achieved a CW power of up to 440 mW and self-starting mode-locking with up to 200 mW average power in 68-fs pulses using semiconductor saturable absorber mirror (SESAM) as saturable absorber. In a second configuration with up to 3 W of pump power incident onto the crystal, we achieved up to 650 mW in CW operation and up to 450 mW in 58-fs pulses using Kerr-lens mode-locking (KLM). The shortest pulse duration was 39 fs, which was achieved at 350 mW average power using KLM. The mode-locked laser generates a pulse train at repetition rates around 400 MHz. No complex cooling system is required: neither the SESAM nor the Ti:Sapphire crystal is actively cooled, only air cooling is applied to the pump diodes using a small fan. Because of mass production for laser displays, we expect that prices for green laser diodes will become very favorable in the near future, opening the door for low-cost Ti:Sapphire lasers. This will be highly attractive for potential mass applications such as biomedical imaging and sensing

Experimentally verified pulse formation model for high-power femtosecond VECSELs

Optically pumped vertical-external-cavity surface-emitting lasers (OP-VECSELs), passively modelocked with a semiconductor saturable absorber mirror (SESAM), have generated the highest average output power from any sub-picosecond semiconductor laser. Many applications, including frequency comb synthesis and coherent supercontinuum generation, require pulses in the sub-300-fs regime. A quantitative understanding of the pulse formation mechanism is required in order to reach this regime while maintaining stable, high-average-power performance. We present a numerical model with which we have obtained excellent quantitative agreement with two recent experiments in the femtosecond regime, and we have been able to correctly predict both the observed pulse duration and the output power for the first time. Our numerical model not only confirms the soliton-like pulse formation in the femtosecond regime, but also allows us to develop several clear guidelines to scale the performance toward shorter pulses and higher average output power. In particular, we show that a key VECSEL design parameter is a high gain saturation fluence. By optimizing this parameter, 200-fs pulses with an average output power of more than 1 W should be possible