A microchip optomechanical accelerometer

The monitoring of accelerations is essential for a variety of applications ranging from inertial navigation to consumer electronics. The basic operation principle of an accelerometer is to measure the displacement of a flexibly mounted test mass; sensitive displacement measurement can be realized using capacitive, piezo-electric, tunnel-current, or optical methods. While optical readout provides superior displacement resolution and resilience to electromagnetic interference, current optical accelerometers either do not allow for chip-scale integration or require bulky test masses. Here we demonstrate an optomechanical accelerometer that employs ultra-sensitive all-optical displacement read-out using a planar photonic crystal cavity monolithically integrated with a nano-tethered test mass of high mechanical Q-factor. This device architecture allows for full on-chip integration and achieves a broadband acceleration resolution of 10 \mu g/rt-Hz, a bandwidth greater than 20 kHz, and a dynamic range of 50 dB with sub-milliwatt optical power requirements. Moreover, the nano-gram test masses used here allow for optomechanical back-action in the form of cooling or the optical spring effect, setting the stage for a new class of motional sensors.Comment: 16 pages, 9 figure

Single-atom entropy squeezing for two two-level atoms interacting with a single-mode radiation field

In this paper we consider a system of two two-level atoms interacting with a single-mode quantized electromagnetic field in a lossless resonant cavity via $l$-photon-transition mechanism. The field and the atoms are initially prepared in the coherent state and the excited atomic states, respectively. For this system we investigate the entropy squeezing, the atomic variances, the von Neumann entropy and the atomic inversions for the single-atom case. We show that the more the number of the parties in the system the less the amounts of the nonclassical effects exhibited in the entropy squeezing. The entropy squeezing can give information on the corresponding von Neumann entropy. Also the nonclassical effects obtained form the asymmetric atoms are greater than those obtained form the symmetric atoms. Finally, the entropy squeezing gives better information than the atomic variances only for the asymmetric atoms.Comment: 15 pages, 4 figures, comments are most welcom

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.

Asthma is a common disease with a complex risk architecture including both genetic and environmental factors. We performed a meta-analysis of North American genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of European American, African American or African Caribbean, and Latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. We identified five susceptibility loci. Four were at previously reported loci on 17q21, near IL1RL1, TSLP and IL33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. In addition, we identified a new asthma susceptibility locus at PYHIN1, with the association being specific to individuals of African descent (P = 3.9 × 10(-9)). These results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma

Integration of multiple data sources to prioritize candidate genes using discounted rating system

Background: Identifying disease gene from a list of candidate genes is an important task in bioinformatics. The main strategy is to prioritize candidate genes based on their similarity to known disease genes. Most of existing gene prioritization methods access only one genomic data source, which is noisy and incomplete. Thus, there is a need for the integration of multiple data sources containing different information. Results: In this paper, we proposed a combination strategy, called discounted rating system (DRS). We performed leave one out cross validation to compare it with N-dimensional order statistics (NDOS) used in Endeavour. Results showed that the AUC (Area Under the Curve) values achieved by DRS were comparable with NDOS on most of the disease families. But DRS worked much faster than NDOS, especially when the number of data sources increases. When there are 100 candidate genes and 20 data sources, DRS works more than 180 times faster than NDOS. In the framework of DRS, we give different weights for different data sources. The weighted DRS achieved significantly higher AUC values than NDOS. Conclusion: The proposed DRS algorithm is a powerful and effective framework for candidate gene prioritization. If weights of different data sources are proper given, the DRS algorithm will perform better

How to deal with the early GWAS data when imputing and combining different arrays is necessary

Genotype imputation has become an essential tool in the analysis of genome-wide association scans. This technique allows investigators to test association at ungenotyped genetic markers, and to combine results across studies that rely on different genotyping platforms. In addition, imputation is used within long-running studies to reuse genotypes produced across generations of platforms. Typically, genotypes of controls are reused and cases are genotyped on more novel platforms yielding a case–control study that is not matched for genotyping platforms. In this study, we scrutinize such a situation and validate GWAS results by actually retyping top-ranking SNPs with the Sequenom MassArray platform. We discuss the needed quality controls (QCs). In doing so, we report a considerable discrepancy between the results from imputed and retyped data when applying recommended QCs from the literature. These discrepancies appear to be caused by extrapolating differences between arrays by the process of imputation. To avoid false positive results, we recommend that more stringent QCs should be applied. We also advocate reporting the imputation quality measure (RT2) for the post-imputation QCs in publications

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry

A Partial Loss-of-Function Variant in AKT2 is Associated with Reduced Insulin-Mediated Glucose Uptake in Multiple Insulin Sensitive Tissues: a Genotype-Based Callback Positron Emission Tomography Study

Rare fully penetrant mutations in AKT2 are an established cause of monogenic disorders of glucose metabolism. Recently, a novel partial loss-of-function AKT2 coding variant (p.Pro50Thr) was identified that is nearly specific to Finns (frequency 1.1%), with the low-frequency allele associated with an increase in fasting plasma insulin level and risk of type 2 diabetes. The effects of p.Pro50Thr on insulin-stimulated glucose uptake (GU) in the whole body and in different tissues have not previously been investigated.  We identified carriers (N=20) and matched non-carriers (N=25) for this allele in the population-based METSIM study and invited these individuals back for positron emission tomography study with [18F]-fluorodeoxyglucose during euglycemic hyperinsulinemia. When we compared p.P50T/AKT2 carriers to non-carriers, we found a 39.4% reduction in whole body GU (P=0.006) and a 55.6% increase in the rate of endogenous glucose production (P=0.038). We found significant reductions in GU in multiple tissues: skeletal muscle (36.4%), liver (16.1%), brown adipose (29.7%), and bone marrow (32.9%), and increases of 16.8-19.1% in 7 tested brain regions. These data demonstrate that the P50T substitution of AKT2 influences insulin-mediated GU in multiple insulin sensitive tissues, and may explain, at least in part, the increased risk of type 2 diabetes in p.P50T/AKT2 carriers.</p

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestr