Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries

Background: Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry. Results: We introduce the polygenic transcriptome risk score (PTRS), which is based on predicted transcript levels (rather than SNPs), and explore the portability of PTRS across populations using UK Biobank data. Conclusions: We show that PTRS has a significantly higher portability (Wilcoxon p=0.013) in the African-descent samples where the loss of performance is most acute with better performance than PRS when used in combination

Importance of implant technique on risk of major paravalvular leak (PVL) after St. Jude mechanical heart valve replacement: a report from the Artificial Valve Endocarditis Reduction Trial (AVERT)

Objective: To examine risk factors for major paravalvular leak (PVL) events after mechanical heart valve replacement. Methods: We analyzed outcome of 807 patients randomized into the Artificial Valve Endocarditis Reduction Trial (AVERT). The mean follow-up time was 30.6 months and 21 major PVL events were reported. Three additional major PVL events associated with endocarditis were excluded from analysis. All baseline medical history variables, as well as operative parameters (including use of pledgets and suture technique) were examined using Cox regression. Results: Major PVL was reported after 11 aortic, 9 mitral, and 1 double valve replacement. 6/404 (1.5%) patients with conventional valves experienced a major PVL event versus 15/403 (3.7%) in the Silzone group. 10/172 (5.8%) patients with valve suture technique without pledgets experienced a major PVL event versus 11/635 (1.7%) patients with pledgets. Final multivariable model showed that only suture technique without pledgets (p = 0.005) was an independent significant risk factor for major PVL events. Silzone cuff showed a strong trend (p = 0.055). Conclusions: Suture technique without pledgets is an independent significant risk factor for major PVL events. In this study, use of pledgets during valve replacement had a protective effect against subsequent paravalvular leak, supporting the use of buttress reinforcement for valve suture. The use of Silzone cuff, although not statistically significant, showed a strong trend as a risk facto

ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets

Variation in gene expression has been observed in natural populations and associated with complex traits or phenotypes such as disease susceptibility and drug response. Gene expression itself is controlled by various genetic and non-genetic factors. The binding of a class of small RNA molecules, microRNAs (miRNAs), to mRNA transcript targets has recently been demonstrated to be an important mechanism of gene regulation. Because individual miRNAs may regulate the expression of multiple gene targets, a comprehensive and reliable catalogue of miRNA-regulated targets is critical to understanding gene regulatory networks. Though experimental approaches have been used to identify many miRNA targets, due to cost and efficiency, current miRNA target identification still relies largely on computational algorithms that aim to take advantage of different biochemical/thermodynamic properties of the sequences of miRNAs and their gene targets. A novel approach, ExprTarget, therefore, is proposed here to integrate some of the most frequently invoked methods (miRanda, PicTar, TargetScan) as well as the genome-wide HapMap miRNA and mRNA expression datasets generated in our laboratory. To our knowledge, this dataset constitutes the first miRNA expression profiling in the HapMap lymphoblastoid cell lines. We conducted diagnostic tests of the existing computational solutions using the experimentally supported targets in TarBase as gold standard. To gain insight into the biases that arise from such an analysis, we investigated the effect of the choice of gold standard on the evaluation of the various computational tools. We analyzed the performance of ExprTarget using both ROC curve analysis and cross-validation. We show that ExprTarget greatly improves miRNA target prediction relative to the individual prediction algorithms in terms of sensitivity and specificity. We also developed an online database, ExprTargetDB, of human miRNA targets predicted by our approach that integrates gene expression profiling into a broader framework involving important features of miRNA target site predictions.</p

Enhanced greenhouse gas emission from exposed sediments along a hydroelectric reservoir during an extreme drought event

An active debate has been underway on the magnitude and duration of carbon (C) emissions from hydroelectric reservoirs, yet little attention has been paid to stochastic C emissions from reservoir sediments during extreme climatic events. A rare opportunity for field measurements of CO2 efflux from a hydroelectric reservoir in Korea during an extreme drought event was used to examine how prolonged droughts can affect microbial organic matter processing and the release of CO2, CH4 and N2O from exposed sediments. Chamber measurements of CO2 efflux along an exposed sediment transect, combined with high-frequency continuous sensor measurements of the partial pressure of CO2 (pCO(2)) in the reservoir surface water, exhibited extraordinary pulses of CO2 from exposed sediments and the turbulent inflowing water in contrast to a small CO2 sink in the main water body of the reservoir and a low efflux of CO2 from the flooded sediment. Significant increases in the production of CO2, CH4 and N2O observed in a laboratory incubation of sediments, together with enhanced activities of phenol oxidase and three hydrolases, indicate a temporary activation of microbial organic matter processing in the drying sediment. The results suggest that drought-triggered pulses of greenhouse gas emission from exposed sediments can offset the C accumulation in reservoir sediments over time scales of years to decades, reversing the trend of declining C emissions from aging reservoirsope

The Spectrum of Benign Esophageal Lesions: Imaging Findings

Benign esophageal lesions occur in various diseases. Barium studies are useful for the evaluation of mucosal surface lesions but provide little information about the extramucosal extent of disease. Computed tomography and magnetic resonance imaging, on the other hand, permit the assessment of wall thickness, mediastinal involvement, adjacent lymphadenopathy, and distant spread. In diseases such as fibrovascular polyps, duplication cysts, scleroderma, trauma, caustic esophagitis, hiatal hernia, esophageal diverticulum, achalasia, and paraesophageal varices, the findings of imaging studies are specific, obviating the need for further invasive diagnostic work-up. The advent of helical computed tomography and its volume data set allows the acquisition of multiplanar images, and magnetic resonance imaging is useful both for this and for tissue characterization. Thus, multiplanar cross-sectional imaging further extends the role of imaging modalities to the evaluation of benign esophageal lesions. Through an awareness of the multiplanar cross-sectional appearances of various benign esophageal lesions, the radiologist can play an important role in the detection, diagnosis, further diagnostic planning, and treatment of the diseases in which they occur

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential new diagnoses. Using our reference estimates from GTEx data, ANEVA-DOT can be incorporated in rare disease diagnostic pipelines to use RNA-sequencing data more effectively

A Pilot Study for the Neuroprotective Effect of Gongjin-dan on Transient Middle Cerebral Artery Occlusion-Induced Ischemic Rat Brain

In this study, we investigated whether gongjin-dan improves functional recovery and has neuroprotective effects on reducing the infarct volume after transient middle cerebral artery occlusion (MCAo). Infarct volume was measured using TTC staining and glucose utilization by F-18 FDG PET. Functional improvement was evaluated with the Rota-rod, treadmill, Garcia score test, and adhesive removal test. At 14 days after MCAo, neuronal cell survival, astrocytes expansion, and apoptosis were assessed by immunohistofluorescence staining in the peri-infarct region. Also, the expression of neurotrophic factors and inflammatory cytokines such as VEGF, BDNF, Cox-2, TNF-α, IL-1β, and IL-1α was measured in ischemic hemisphere regions. The gongjin-dan-treated group showed both reduced infarct volume and increased glucose utilization. Behavior tests demonstrated a significant improvement compared to the control. Also in the gongjin-dan treated group, NeuN-positive cells were increased and number of astrocytes, microglia, and apoptotic cells was significantly decreased compared with the control group in the ischemic peri-infarct area. Furthermore, the expression of VEGF and BDNF was increased and level of Cox-2, TNF-α, IL-1β, and IL-1α was decreased. These results suggest that gongjin-dan may improve functional outcome through the rapid restoration of metabolism and can be considered as a potential neuroprotective agent

Strain-Mediated Interlayer Coupling Effects on the Excitonic Behaviors in an Epitaxially Grown MoS2/WS2 van der Waals Heterobilayer.

van der Waals heterostructures composed of two different monolayer crystals have recently attracted attention as a powerful and versatile platform for studying fundamental physics, as well as having great potential in future functional devices because of the diversity in the band alignments and the unique interlayer coupling that occurs at the heterojunction interface. However, despite these attractive features, a fundamental understanding of the underlying physics accounting for the effect of interlayer coupling on the interactions between electrons, photons, and phonons in the stacked heterobilayer is still lacking. Here, we demonstrate a detailed analysis of the strain-dependent excitonic behavior of an epitaxially grown MoS2/WS2 vertical heterostructure under uniaxial tensile and compressive strain that enables the interlayer interactions to be modulated along with the electronic band structure. We find that the strain-modulated interlayer coupling directly affects the characteristic combined vibrational and excitonic properties of each monolayer in the heterobilayer. It is further revealed that the relative photoluminescence intensity ratio of WS2 to MoS2 in our heterobilayer increases monotonically with tensile strain and decreases with compressive strain. We attribute the strain-dependent emission behavior of the heterobilayer to the modulation of the band structure for each monolayer, which is dictated by the alterations in the band gap transitions. These findings present an important pathway toward designing heterostructures and flexible devices

Overexpression of arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhance

Indole-3-acetic acid (IAA), a major plant auxin, is produced in both tryptophan-dependent and tryptophanindependent pathways. A major pathway in Arabidopsis thaliana generates IAA in two reactions from tryptophan. Step one converts tryptophan to indole-3-pyruvic acid (IPA) by tryptophan aminotransferases followed by a rate-limiting step converting IPA to IAA catalyzed by YUCCA proteins. We identified eight putative StYUC (Solanum tuberosum YUCCA) genes whose deduced amino acid sequences share 50%-70% identity with those of Arabidopsis YUCCA proteins. All include canonical, conserved YUCCA sequences: FATGY motif, FMO signature sequence, and FAD-binding and NADPbinding sequences. In addition, five genes were found with ~50% amino acid sequence identity to Arabidopsis tryptophan aminotransferases. Transgenic potato (Solanum tuberosum cv. Jowon) constitutively overexpressing Arabidopsis AtYUC6 displayed high-auxin phenotypes such as narrow downward-curled leaves, increased height, erect stature, and longevity. Transgenic potato plants overexpressing AtYUC6 showed enhanced drought tolerance based on reduced water loss. The phenotype was correlated with reduced levels of reactive oxygen species in leaves. The results suggest a functional YUCCA pathway of auxin biosynthesis in potato that may be exploited to alter plant responses to the environment. © 2012 The Author