MSIQ: Joint Modeling of Multiple RNA-seq Samples for Accurate Isoform Quantification

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling us to better understand the regulation of gene expression and fundamental biological processes. Accurate isoform quantification from RNA-seq data is challenging due to the information loss in sequencing experiments. A recent accumulation of multiple RNA-seq data sets from the same tissue or cell type provides new opportunities to improve the accuracy of isoform quantification. However, existing statistical or computational methods for multiple RNA-seq samples either pool the samples into one sample or assign equal weights to the samples when estimating isoform abundance. These methods ignore the possible heterogeneity in the quality of different samples and could result in biased and unrobust estimates. In this article, we develop a method, which we call "joint modeling of multiple RNA-seq samples for accurate isoform quantification" (MSIQ), for more accurate and robust isoform quantification by integrating multiple RNA-seq samples under a Bayesian framework. Our method aims to (1) identify a consistent group of samples with homogeneous quality and (2) improve isoform quantification accuracy by jointly modeling multiple RNA-seq samples by allowing for higher weights on the consistent group. We show that MSIQ provides a consistent estimator of isoform abundance, and we demonstrate the accuracy and effectiveness of MSIQ compared with alternative methods through simulation studies on D. melanogaster genes. We justify MSIQ's advantages over existing approaches via application studies on real RNA-seq data from human embryonic stem cells, brain tissues, and the HepG2 immortalized cell line

Flow and Heat Transfer in Jet Cooling Rolling Bearing

The real flow field inside a jet cooling ball bearing is an air-oil two-phase flow since the air entrainment in the lubricant is ineluctable. The flow heat transfer characteristics are thought to have significant impacts in cooling effect forecast and temperature control. To this end, the fluid flow and heat transfer characteristics of the air-oil two-phase flow inside a jet cooling rolling bearing have been investigated by simulation and experiment herein. A multiphase VOF numerical method for the flow field calculation has been proposed. The temperature distributions of the bearing system have been measured, and the flow pattern under different operation speeds has also been captured. The parameter effects on the jet cooling rolling bearing flow field and temperature distribution have been revealed accordingly. The research findings can be used for the structural optimization and the precise lubrication design of the rolling bearing

2-Eth­oxy­ethyl (Z)-2-cyano-3-[(N-phenyl­carbamo­yl)amino]­prop-2-enoate

The crystal structure of the title compound, C15H17N3O4, is stabilized by inter­molecular N—H⋯N hydrogen bonds. An intra­molecular N—H⋯O hydrogen bond also occurs

Spatio-temporal variations and influencing factors of polycyclic aromatic hydrocarbons in atmospheric bulk deposition along a plain-mountain transect in western China

Ten atmospheric bulk deposition (the sum of wet and dry deposition) samplers for polycyclic aromatic hydrocarbons (PAHs) were deployed at a plain-mountain transect (namely PMT transect, from Daying to Qingping) in Chengdu Plain, West China from June 2007 to June 2008 in four consecutive seasons (about every three months). The bulk deposition fluxes of ∑15-PAHs ranged from 169.19 μg m−2 yr−1 to 978.58 μg m−2 yr−1 with geometric mean of 354.22 μg m−2 yr−1. The most prevalent PAHs were 4-ring (39.65%) and 3-ring (35.56%) PAHs. The flux values were comparable to those in rural areas. Higher fluxes of total PAHs were observed in the middle of PMT transect (SL, YX and JY, which were more urbanized than other sites). The seasonal deposition fluxes in the sampling profile indicated seasonality of the contaminant source was an important factor in controlling deposition fluxes. PAHs bulk deposition was negatively correlated with meteorological parameters (temperature, wind speed, humidity, and precipitation). No significant correlations between soil concentrations and atmospheric deposition were found along this transect. PAHs in soil samples had combined sources of coal, wood and petroleum combustion, while a simple source of coal, wood and grass combustion for bulk deposition. There were significant positive correlation relationship (p < 0.05) between annual atmospheric bulk deposition and local PAHs emission, with biomass burning as the major contribution to the total emission of PAHs. This transect acts as an important PAHs source rather than being a sink according to the ratio of deposition/emission. Mountain cold trap effect existed in this transect where the altitude was higher than 1000 m. Long-range transport had an impact on the bulk deposition in summer. And this transect was a source to Tibetan only in summer. The forward trajectory analysis showed most air masses did not undergo long-range transport due to the blocking effect of surrounding mountains. Only a few air masses (<10%) arrived at the eastern and northern region of China or farther regions via long-range transport

Microwave hydrothermal synthesis of tobermorite for the solidification of iron

Iron is one of the heavy metals that present in industrial wastewater and domestic waste which damage agricultural production as well as the landscape if there is no proper treatment. One popular method was to introduce the heavy metal ions into the raw material for the synthesis of tobermorite, as the main cement component. However, the conventional hydrothermal synthesis was time and intense energy consuming. Therefore, microwave hydrothermal synthesis of tobermorite was evaluated by comparing with the conventional method. The experimental results showed that the dominant products were Fe-tobermorite/ tobermorite via conventional method, whilst it turned to be Fe-containing hydrogarnet under microwave hydrothermal synthesis when the Fe/Si ratio was 0.15/0.2, which were found to be more stable, thus enhancing the safety of the solidification. Both methods exhibited 100 % of solidification of iron, and the microwave hydrothermal synthesis consumed a much shorter time than conventional method. Therefore, present work has demonstrated that microwave hydrothermal synthesis of tobermorite is an effective alternative to conventional method for the solidification of iron.</p

miR-17-5p and miR-106a are involved in the balance between osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells

AbstractMesenchymal stem cells (MSCs) can differentiate into several distinct cell types, including osteoblasts and adipocytes. The balance between osteogenic and adipogenic differentiation is disrupted in several osteogenic-related disorders, such as osteoporosis. So far, little is known about the molecular mechanisms that drive final lineage commitment of MSCs. In this study, we revealed that miR-17-5p and miR-106a have dual functions in the modulation of human adipose-derived mesenchymal stem cells (hADSCs) commitment by gain- and loss-of-function assays. They could promote adipogenesis and inhibit osteogenesis. Luciferase reporter assay, western blot and ELISA suggested BMP2 was a direct target of miR-17-5p and miR-106a. Downregulation of endogeneous BMP2 by RNA interference suppressed osteogenesis and increased adipogenesis, similar to the effect of miR-17-5p and miR-106a upregulation. Moreover, the inhibitory effects of miR-17-5p on osteogenic and adipogenic differentiation of hADSCs could be reversed by BMP2 RNA interference. In conclusion, miR-17-5p and miR-106a regulate osteogenic and adipogenic lineage commitment of hADSCs by directly targeting BMP2, and subsequently decreased osteogenic TAZ, MSX2 and Runx2, and increased adipogenic C/EBPα and PPARγ

Isolation and Characterization of Equine Influenza Viruses (H3N8) from China, 2010~2011

Two equine influenza virus (EIV) strains were isolated during two restricted outbreaks from Heilongjiang Province, China in 2010 and 2011. Phylogenetic analysis of HA1 (hemagglutinin 1) gene revealed that the isolates belonged to Florida 2 sublineage of American lineage. Further analysis of the putative antigenic sites located in HA1 subunit protein revealed each isolate had a unique amino acid change. Analysis of antigenic sites between Chinese EIV and vaccine strains indicated equine influenza (EI) vaccines containing Richmond/1/07-like antigen seemed to have an optimum effect in China. Meanwhile, the Ohio/03 vaccine strain contained in updated ProteqFlu had the most closely genetically relationship with recent EIV isolates in China. China has not its own commercially available EI vaccine and most horses are still unvaccinated. Therefore, to monitor antigenic variation of circulating EIVs and give considerable suggestions on selection of vaccine candidate plays an important role in preventing and controlling EIV in China