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RORγt and RORα are transcription factors of the RAR-related orphan nuclear receptor (ROR) family. They are expressed in Th17 cells and have been suggested to play a role in Th17 differentiation. Although RORγt signature genes have been characterized in mouse Th17 cells, detailed information on its transcriptional control in human Th17 cells is limited and even less is known about RORα signature genes which have not been reported in either human or mouse T cells. In this study, global gene expression of human CD4 T cells activated under Th17 skewing conditions was profiled by RNA sequencing. RORγt and RORα signature genes were identified in these Th17 cells treated with specific siRNAs to knock down RORγt or RORα expression. We have generated selective small molecule RORγt modulators and they were also utilized as pharmacological tools in RORγt signature gene identification. Our results showed that RORγt controlled the expression of a very selective number of genes in Th17 cells and most of them were regulated by RORα as well albeit a weaker influence. Key Th17 genes including IL-17A, IL-17F, IL-23R, CCL20 and CCR6 were shown to be regulated by both RORγt and RORα. Our results demonstrated an overlapping role of RORγt and RORα in human Th17 cell differentiation through regulation of a defined common set of Th17 genes. RORγt as a drug target for treatment of Th17 mediated autoimmune diseases such as psoriasis has been demonstrated recently in clinical trials. Our results suggest that RORα could be involved in same disease mechanisms and gene signatures identified in this report could be valuable biomarkers for tracking the pharmacodynamic effects of compounds that modulate RORγt or RORα activities in patients. [ABSTRACT FROM AUTHOR]

RNA-seq technology has become an important tool for quantifying the gene and transcript expression in transcriptome study. The two major difficulties for the gene and transcript expression quantification are the read mapping ambiguity and the overdispersion of the read distribution along reference sequence. Many approaches have been proposed to deal with these difficulties. A number of existing methods use Poisson distribution to model the read counts and this easily splits the counts into the contributions from multiple transcripts. Meanwhile, various solutions were put forward to account for the overdispersion in the Poisson models. By checking the similarities among the variation patterns of read counts for individual genes, we found that the count variation is exon-specific and has the conserved pattern across the samples for each individual gene. We introduce Gamma-distributed latent variables to model the read sequencing preference for each exon. These variables are embedded to the rate parameter of a Poisson model to account for the overdispersion of read distribution. The model is tractable since the Gamma priors can be integrated out in the maximum likelihood estimation. We evaluate the proposed approach, PGseq, using four real datasets and one simulated dataset, and compare its performance with other popular methods. Results show that PGseq presents competitive performance compared to other alternatives in terms of accuracy in the gene and transcript expression calculation and in the downstream differential expression analysis. Especially, we show the advantage of our method in the analysis of low expression. [ABSTRACT FROM AUTHOR]

Arid areas play a significant role in the global nitrogen cycle. Dry and wet deposition of inorganic nitrogen (N) species were monitored at one urban (SDS) and one suburban (TFS) site at Urumqi in a semi-arid region of central Asia. Atmospheric concentrations of NH3, NO2, HNO3, particulate ammonium and nitrate (pNH4+ and pNO3−) concentrations and NH4-N and NO3-N concentrations in precipitation showed large monthly variations and averaged 7.1, 26.6, 2.4, 6.6, 2.7 µg N m−3 and 1.3, 1.0 mg N L−1 at both SDS and TFS. Nitrogen dry deposition fluxes were 40.7 and 36.0 kg N ha−1 yr−1 while wet deposition of N fluxes were 6.0 and 8.8 kg N ha−1 yr−1 at SDS and TFS, respectively. Total N deposition averaged 45.8 kg N ha−1 yr−1at both sites. Our results indicate that N dry deposition has been a major part of total N deposition (83.8% on average) in an arid region of central Asia. Such high N deposition implies heavy environmental pollution and an important nutrient resource in arid regions. [ABSTRACT FROM AUTHOR]

Effective video monitoring systems require optimization of camera and road network coverage, to exploit fully the hardware and software solutions in smart city traffic applications. Monitoring requirements have grown increasingly diverse as scenes are becoming increasingly complex, thereby transforming the camera and road network coverage optimization issue into a nonlinear, high-dimension, and multi-objective problem. Previous research on this topic however, has focused on a single, specific optimization objective, which may result in invalid optimization results in actual applications. To extend this research, we propose a multi-objective scheduling optimization algorithm for a camera network that addresses the problem of directional road network coverage. In this solution, we incorporate an expanding parameter of main optical axes into particle swarm optimization algorithm. Our new strategy divides the range of main optical axes of all the cameras to control the scheduling number, achieving collaborative optimization of multiple objectives. In a simulated camera and road network, an experiment was designed for evaluating the effectiveness of the proposed method, comparing the distribution of optimization results with the global and local optimal solutions of the true value. A second experiment compared the distribution, performance and running time of the optimization results with different values of expanding parameter of main optical axes. A third experiment compared the performance of the optimization solutions with different values of camera parameters. The results showed that the proposed method can adapt to user application preference, and is effective and robust to schedule and allocate monitoring resources in different scenarios. [ABSTRACT FROM AUTHOR]

Production of higher-fidelity digital elevation models is important; as such models are indispensable components of space data infrastructure. However, loss of terrain features is a constant problem for grid digital elevation models, although these models have already been defined in such a way that their distinct usage as data sources in terrain modeling processing is prohibited. Therefore, in this study, the novel concept-terrain semanteme is proposed to define local space terrain features, and a new process for generating grid digital elevation models based on this new concept is designed. A prototype system is programmed to test the proposed approach; the results indicate that terrain semanteme can be applied in the process of grid digital elevation model generation, and that usage of this new concept improves the digital elevation model fidelity. Moreover, the terrain semanteme technique can be applied for recovery of distorted digital elevation model regions containing terrain semantemes, with good recovery efficiency indicated by experiments. [ABSTRACT FROM AUTHOR]

Objective: Severe mental illness (SMI) represents major social and public health problem in China, especially in low- or middle-income regions. We aim to assess the prevalence and distribution of SMI in Hunan province in central China. Methods: Multistage stratified random sampling methods were used to select qualified subjects in 123 districts and counties in Hunan province. 89465 individuals were randomly identified, and 72999 (81.6%) completed the supplemental 12-Item General Health Questionnaire (GHQ-12) and Cue questionnaire of psychiatric abnormal behaviors. 6082 suspected individuals having high or moderate risk, or psychiatric cues, were administered the Structured Clinical Interview for DSM-IV Axis I disorders (SCID-I) by psychiatrists. Results: 720 respondents were definitely diagnosed as SMI. The 1-month and lifetime prevalence was 9.35‰ and 10.10‰, respectively. The most frequent SMI was schizophrenia, followed by bipolar disorder, intellectual disability, epileptic mental disorder, paranoid psychosis and schizoaffective disorders, with 1-month prevalence ranging from 0.11‰ to 6.50‰ and lifetime prevalence ranging from 0.24‰ to 6.86‰. Multivariate logistic regression analysis revealed that lower education, farmer occupation, retirees or jobless/unemployed, unmarried or divorced and age of 30–64 years old were major factors that associated with the increased risk of SMI. In addition, only 33.3% of 528 patients who completed questionnaire sought help in psychiatric institutions, and up to 51.7% of 720 patients were not referred to the SMI management system in Hunan province. Conclusions: These findings provided a large-scale prevalence data of SMI in a provincial sample of China. The psychiatric disorders brought economical and psychological burden for family and society, which may shed light on the significance of scaling up province-wide mental health service and strengthening the SMI management. [ABSTRACT FROM AUTHOR]

Kv1.3 is a voltage-gated potassium channel expressed on T cells that plays an important role in T cell activation. Previous studies have shown that blocking Kv1.3 channels in human T cells during activation results in reduced calcium entry, cytokine production, and proliferation. The aim of the present study was to further explore the effects of Kv1.3 blockers on the response of different human T cell subsets under various stimulation conditions. Our studies show that, unlike the immune suppressor cyclosporine A, the inhibitory effect of Kv1.3 blockers was partial and stimulation strength dependent, with reduced inhibitory efficacy on T cells under strengthened anti-CD3/CD28 stimulations. T cell responses to allergens including house dust mites and ragweed were partially reduced by Kv1.3 blockers. The effect of Kv1.3 inhibition was dependent on T cell subsets, with stronger effects on CCR7- effector memory compared to CCR7+ central memory CD4 T cells. Calcium entry studies also revealed a population of CD4 T cells resistant to Kv1.3 blockade. Activation of CD4 T cells was accompanied with an increase in Kv1.3 currents but Kv1.3 transcripts were found to be reduced, suggesting a posttranscriptional mechanism in the regulation of Kv1.3 activities. In summary, Kv1.3 blockers inhibit T cell activation in a manner that is highly dependent on the T cell identity and stimulation strength, These findings suggest that Kv1.3 blockers inhibit T cells in a unique, conditional manner, further refining our understanding of the therapeutic potential of Kv1.3 blockers. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the value of prospective ECG-gated high-pitch 128-slice dual-source CT (DSCT) angiography in the diagnosis of congenital extracardiac vascular anomalies in infants and children in comparison with transthoracic echocardiography (TTE). Methods: Eighty consecutive infants or children clinically diagnosed of congenital heart disease and suspected with extracardiac vascular anomaly were enrolled, and 75 patients were finally included in this prospective study. All patients underwent prospective ECG-gated high-pitch DSCT angiography after TTE with an interval of 1–7 days. The diagnostic accuracy and sensitivity of high-pitch DSCT angiography and TTE were compared according to the surgical/CCA findings. The image quality of DSCT was assessed using a five-point scale. The effective radiation dose (ED) was calculated. Results: A total of 17 congenital heart diseases and 162 separate extracardiac vascular anomalies were confirmed by surgical/CCA findings in 75 patients. The diagnostic accuracy of high-pitch DSCT angiography and TTE was 99.67% and 97.89%, respectively. The sensitivity of high-pitch DSCT angiography and TTE was 97.53% and 79.62%, respectively. There was significant difference regarding to the diagnostic accuracy and the sensitivity between high-pitch DSCT angiography and TTE (χ2 = 23.561 and 28.013, P<0.05). The agreement on the image quality scoring of DSCT between the two observers was excellent (κ = 0.81), and the mean score of image quality was 4.1±0.7. The mean ED of DSCT was 0.29±0.08 mSv. Conclusions: Prospective ECG-gated high-pitch 128-slice DSCT angiography with low radiation dose and high diagnostic accuracy has higher sensitivity compared to TTE in the detection of congenital extracardiac vascular anomalies in infants and children. [ABSTRACT FROM AUTHOR]

Currently, the purity of hybrid seed is a crucial limiting factor when developing hybrid japonica rice (Oryza sativa L.). To chemically control hybrid seed purity, we transferred an improved atrazine chlorohydrolase gene (atzA) from Pseudomonas ADP into hybrid japonica parental lines (two maintainers, one restorer), and Nipponbare, by using Agrobacterium-mediated transformation. We subsequently selected several transgenic lines from each genotype by using PCR, RT-PCR, and germination analysis. In the presence of the investigated atrazine concentrations, particularly 150 µM atrazine, almost all of the transgenic lines produced significantly larger seedlings, with similar or higher germination percentages, than did the respective controls. Although the seedlings of transgenic lines were taller and gained more root biomass compared to the respective control plants, their growth was nevertheless inhibited by atrazine treatment compared to that without treatment. When grown in soil containing 2 mg/kg or 5 mg/kg atrazine, the transgenic lines were taller, and had higher total chlorophyll contents than did the respective controls; moreover, three of the strongest transgenic lines completely recovered after 45 days of growth. After treatment with 2 mg/kg or 5 mg/kg of atrazine, the atrazine residue remaining in the soil was 2.9–7.0% or 0.8–8.7% respectively, for transgenic lines, and 44.0–59.2% or 28.1–30.8%, respectively, for control plants. Spraying plants at the vegetative growth stage with 0.15% atrazine effectively killed control plants, but not transgenic lines. Our results indicate that transgenic atzA rice plants show tolerance to atrazine, and may be used as parental lines in future hybrid seed production. [ABSTRACT FROM AUTHOR]

To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both RNA-Seq and microarray analyses were performed on RNA samples from a human T cell activation experiment. In contrast to other reports, our analyses focused on the difference, rather than similarity, between RNA-Seq and microarray technologies in transcriptome profiling. A comparison of data sets derived from RNA-Seq and Affymetrix platforms using the same set of samples showed a high correlation between gene expression profiles generated by the two platforms. However, it also demonstrated that RNA-Seq was superior in detecting low abundance transcripts, differentiating biologically critical isoforms, and allowing the identification of genetic variants. RNA-Seq also demonstrated a broader dynamic range than microarray, which allowed for the detection of more differentially expressed genes with higher fold-change. Analysis of the two datasets also showed the benefit derived from avoidance of technical issues inherent to microarray probe performance such as cross-hybridization, non-specific hybridization and limited detection range of individual probes. Because RNA-Seq does not rely on a pre-designed complement sequence detection probe, it is devoid of issues associated with probe redundancy and annotation, which simplified interpretation of the data. Despite the superior benefits of RNA-Seq, microarrays are still the more common choice of researchers when conducting transcriptional profiling experiments. This is likely because RNA-Seq sequencing technology is new to most researchers, more expensive than microarray, data storage is more challenging and analysis is more complex. We expect that once these barriers are overcome, the RNA-Seq platform will become the predominant tool for transcriptome analysis. [ABSTRACT FROM AUTHOR]