OncoDB: An interactive online database for analysis of gene expression and viral infection in cancer

Large-scale multi-omics datasets, most prominently from the TCGA consortium, have been made available to the public for systematic characterization of human cancers. However, to date, there is a lack of corresponding online resources to utilize these valuable data to study gene expression dysregulation and viral infection, two major causes for cancer development and progression. To address these unmet needs, we established OncoDB, an online database resource to explore abnormal patterns in gene expression as well as viral infection that are correlated to clinical features in cancer. Specifically, OncoDB integrated RNA-seq, DNA methylation, and related clinical data from over 10 000 cancer patients in the TCGA study as well as from normal tissues in the GTEx study. Another unique aspect of OncoDB is its focus on oncoviruses. By mining TCGA RNA-seq data, we have identified six major oncoviruses across cancer types and further correlated viral infection to changes in host gene expression and clinical outcomes. All the analysis results are integratively presented in OncoDB with a flexible web interface to search for data related to RNA expression, DNA methylation, viral infection, and clinical features of the cancer patients. OncoDB is freely accessible at http://oncodb.org

Active Flow Control of a Three-Element Airfoil in Unbounded Flow and in Ground Effect

Multi-element high lift devices are used in aircraft wings to have higher lift at low speed during take-off and landing. 30P30N is a three-element airfoil developed by NASA/McDonnell Douglas for which high quality flow field data is available. As a result, it has been a subject of many Computational Fluid Dynamics (CFD) simulations in the literature. In this research, CFD simulations are performed using commercial CFD solver ANSYS Fluent. Reynolds-Averaged Navier-Stokes (RANS) equations are solved in conjunction with the Spalart-Allmaras (SA) turbulence model. Mesh generation is accomplished by ICEM in ANSYS. First the CFD solution is validated against the experimental data. The validated code is then used to determine the relationship between the flap deflection angle and the lift coefficient for the 30P30N airfoil both in unbounded flow and in ground effect for various flight heights. The airfoil flow field is then subjected to Active Flow Control (AFC) by injecting a uniform jet or by including a synthetic jet near the leading edge of the flap to change the momentum in the boundary layer on the flap. The goal is to enhance lift by reducing separation on the flap at higher flap angles. The results show that in unbounded flow, the flow on the flap separates when the flap deflection angle is greater xii than 45 degrees, and in ground effect the flow separates when the flap deflection angle is greater than 40 degrees. After AFC is employed, the lift coefficient is enhanced sharply using both flow control methods compared to the lift coefficient without flow control in unbounded flow as well as in ground effect. The stall flap deflection angle increases to 50 degrees for both the uniform blowing control and the synthetic jet control. In unbounded flow, the lift coefficient is enhanced sharply by synthetic jet flow control and the stall flap deflection angle increases to 50 degrees; however for the uniform blowing control, the effect on lift enhancement is relatively smaller