Group Additive Regression Models for Genomic Data Analysis

One important problem in genomic research is to identify genomic features such as gene expression data or DNA single nucleotide polymorphisms (SNPs) that are related to clinical phenotypes. Often these genomic data can be naturally divided into biologically meaningful groups such as genes belonging to the same pathways or SNPs within genes. In this paper, we propose group additive regression models and a group gradient descent boosting procedure for identifying groups of genomic features that are related to clinical phenotypes. Our simulation results show that by dividing the variables into appropriate groups, we can obtain better identification of the group features that are related to the phenotypes. In addition, the prediction mean square errors are also smaller than the component-wise boosting procedure. We demonstrate the application of the methods to pathway-based analysis of microarray gene expression data of breast cancer and gene-based genetic association analysis of type 1 diabetes. Results from analysis of two breast cancer data sets indicate that the pathways of Metalloendopeptidases (MMPs) and MMP inhibitors, as well as cell proliferation, cell growth and maintenance are important to breast cancer relapse and survival. Results from analysis of a set of nonsynonymous SNPs on chromosome 6 confirmed a few genes that are associated with type 1 diabetes

Experimental Study on Uplift Capacity of Purlins considering Restraints from Standing Seam Roof Systems

A total of 32 specimens of single-span purlin roof assemblies considering uplift wind load were tested to investigate the structural behavior of cold-formed steel purlins with one flange fastened to standing seam roofs. Failure modes and failure loads of purlins with different parameters were obtained. Full finite element models, incorporate purlins, clips and standing seam roof panels, were developed, and the analysis results were consistent to a high degree with the test results. Using the same element type and material model, the rotational restraint of test roof systems and corresponding influence factors were investigated by finite element models. Finally, using the rotational restraint rigidities and comparing with the test results, the lateral restraint of test roof systems were also studied through a simple finite element model incorporates pure the purlin and presents the rotational restraints and lateral restraints by rotational and lateral springs. It is shown that the standing seam roofs do provide some extent of rotational restraints and lateral restraints to purlins at the connection points, especially for purlins without sag rod

Saikosaponins induced hepatotoxicity in mice via lipid metabolism dysregulation and oxidative stress: a proteomic study

Background Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury. Methods Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice. Serum and liver total triglyceride and cholesterol were used to indicate lipid metabolism homeostasis. Liver ROS, GSH, MDA and iNOS were used to examine the oxidative stress level after SS administration. Western blot was used to detect CYP2E1 expression. A 8-Plex iTRAQ Labeling Coupled with 2D LC - MS/MS technique was applied to analyze the protein expression profiles in livers of mice administered with different doses of SS for different time periods. Gene ontology analysis, cluster and enrichment analysis were employed to elucidate potential mechanism involved. HepG2 cells were used to identify our findings in vitro. Results SS dose- and time-dependently induced liver injury in mice, indicated by increased serum AST, ALT and LDH levels. According to proteomic analysis, 487 differentially expressed proteins were identified in mice administrated with different dose of SS for different time periods. Altered proteins were enriched in pathways such as lipid metabolism, protein metabolism, macro molecular transportation, cytoskeleton structure and response to stress. SS enhanced CYP2E1 expression in a time and dose dependent manner, and induced oxidative stress both in vivo and in vitro. Conclusion Our results identified hepatotoxicity and established dose-time course-liver toxicity relationship in mice model of SS administration and suggested potential mechanisms, including impaired lipid and protein metabolism and oxidative stress. The current study provides experimental evidence for clinical safe use of RB, and also new insights into understanding the mechanism by which SS and RB induced liver injury

Inwardly rectifying potassium channels in Drosophila

Inwardly rectifying potassium channels (Kir) are a special subset of potassium selective ion channels which pass potassium more easily into rather than out of the cell. These channels mediate a variety of cellular functions, including control of membrane resting potential, maintenance of potassium homeostasis and regulation of cellular metabolism. Given the existence of fifteen Kir genes in mammals, current genetic studies using mutant animals that lack a single channel may have missed many important physiological functions of these channels due to gene redundancy. This issue can be circumvented by using a simple model organism like Drosophila, whose genome encodes only 3 Kir proteins. The sophisticated genetic approaches of Drosophila may also provide powerful tools to identify additional regulation mechanisms of Kir channels. Here we provide an overview of the progress made in elucidating the function of Drosophila Kir channels. The knowledge of Drosophila Kir channels may lead us to uncover novel functions and regulation mechanisms of human Kir channels and help on pathological studies of related diseases