Fused inverse-normal method for integrated differential expression analysis of RNA-seq data

Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies. The proposed method generalizes the inverse-normal method without increase in computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expression in GBM compared to healthy controls of the oncogene RAD51, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM. The proposed method provides a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease

Numerical simulation of flow and heat transfer of continous cast steel slab under traveling magnetic field

A unified numerical model for simulating solidification transport phenomena (STP) of steel slab in electromagnetic continuous casting (EMCC) process was developed. In order to solve the multi-physics fields coupled problem conveniently, the complicated bidirectional coupled process between EM and STP was simplified as a unidirectional one, and a FEM/FVM-combined numerical simulation technique was adopted. The traveling magnetic fields (TMFs) applied to the EMCC process were calculated using the ANSYS11.0 software, and then the EM-data output by ANSYS were converted to FVM-format using a data-format conversion program developed previously. Thereafter, the governing equations were solved using a pressure-based Direct-SIMPLE algorithm. The simulation results of the STP in CC-process show that, due to the influences of Lorentz force and Joule heat, the two strong circulating flows and the temperature field can be obviously damped and changed once TMF with one pair of poles (1-POPs) or 2-POPs is applied, which would accordingly improve the quality of casting. It was found in the present research that the integrated actions of 2-POPs TMF are superior to 1-POPs. All the computations indicate that the present numerical model of EM-STP as well as the FEM/FVM-combined technique is successful

Plasma lensing with magnetic field and a small correction to the Faraday rotation measurement

Plasma lensing displays interesting characteristics that set it apart from gravitational lensing. The magnetised medium induces birefringence in the two polarisation modes. As the lensing deflection grows stronger, e.g. when images form near the critical curve, the geometric delay of the signal can cause rotation in linear polarisation, in addition to Faraday rotation. This rotation has a frequency dependence to the power of four. We study the geometric rotation of the lensed image in a Gaussian density model and find that it is necessary to take into account the geometric rotation when estimating magnetised media, especially in the under-dense lens. At frequencies of $\sim 1$ GHz or lower, the geometric rotation can dominate. We simulate the flux of lensed images and find that when the image forms near the lensing critical curve, the birefringence can convert the linear polarisation and un-polarisation pulse into a circular mode. The lensing magnification has the potential to increase the probability of detecting such events.Comment: MNRAS, 7 pages, comments welcom

Laboratory Evaluation of R407H for Commercial Refrigeration Applications

Recently, many types of low GWP refrigerants are being promoted to reduce global warming in the global HVAC/R market. As the optimal refrigerant for each application is different depending on application type, capacity and temperature range, and safety requirement, it is important to have diversity of refrigerant choice. Globally and in the US the commercial refrigeration industry is in a transition to refrigerants below a global warming potential of 1500 to meet regulatory requirements. A new Class A1 refrigerant blend in the R407 series was developed, R407H, to meet this requirement for commercial refrigeration applications. To evaluate the performance of the blend in medium and low temperature conditions a comparison was performed at Creative Thermal Solutions (Urbana, IL) utilizing a refrigeration laboratory. The laboratory was instrumented to ASHRAE 72 standard requirements and consists of varying capacity, VFD controlled, tandem scroll compressors, coupled with a controlled condenser and running a set of 5 cases with a combined LT load of 2.98kW and combined medium temperature load of 7.86kW. The equipment selected was standard R22/R404A equipment. The system was controlled by an Emerson E2 in combination with LabVIEW and HP Datalogging. The system was baselined with R22 and a comparison was made to R404A and R407H. As the test is ongoing, R407A and R448A final data will be avaliable during the presentation. The system was analyzed both as a nominal “Drop-In” and with minor optimizations. System effects due to glide, such as frosting, condenser and evaporator efficiency were analyzed and potential control parameters proposed and evaluated. In conclusion it was determined that R407H utilizing traditional R407 refrigerant chemistry without any additional HFO, Hydrocarbon or CO2 components is suitable as a replacement for existing R22 and R404A systems reaching expected efficiency targets while providing the benefits associated with well studied chemistries at the target GWP

Changes of lake organic carbon sinks from closed basins since the Last Glacial Maximum and quantitative evaluation of human impacts

Background Closed basins occupy 21% of the world's land area and can substantially affect global carbon budgets. Conventional understanding suggests that the terminal areas of closed basins collect water and carbon from throughout the entire basin, and changes in lake organic carbon sinks are indicative of basin-wide organic carbon storages. However, this hypothesis lacks regional and global validation. Here, we first validate the depositional process of organic carbon in a typical closed-basin region of northwest China using organic geochemical proxies of both soil and lake sediments. Then we estimate the organic carbon sinks and human impacts in extant closed-basin lakes since the Last Glacial Maximum (LGM). Results Results show that 80.56 Pg organic carbon is stored in extant closed-basin lakes mainly found in the northern mid-latitudes. Carbon accumulation rates vary from 17.54 g C m(-2) yr(-1) during modern times, 6.36 g C m(-2) yr(-1) during the mid-Holocene and 2.25 g C m(-2) yr(-1) during the LGM. Then, we evaluated the influence by human activities during the late Holocene (in the past three thousand years). The ratio of human impacts on lake organic carbon storage in above closed basins is estimated to be 22.79%, and human-induced soil organic carbon emissions in the past three thousand years amounted to 207 Pg. Conclusions While the magnitude of carbon storage is not comparable to those in peatland, vegetation and soil, lake organic carbon sinks from closed basins are significant to long-term terrestrial carbon budget and contain information of climate change and human impact from the whole basins. These observations improve our understanding of carbon sinks in closed basins at various time scales, and provide a basis for the future mitigation policies to global climate change.Peer reviewe