A Method of Protein Model Classification and Retrieval Using Bag-of-Visual-Features

In this paper we propose a novel visual method for protein model classification and retrieval. Different from the conventional methods, the key idea of the proposed method is to extract image features of proteins and measure the visual similarity between proteins. Firstly, the multiview images are captured by vertices and planes of a given octahedron surrounding the protein. Secondly, the local features are extracted from each image of the different views by the SURF algorithm and are vector quantized into visual words using a visual codebook. Finally, KLD is employed to calculate the similarity distance between two feature vectors. Experimental results show that the proposed method has encouraging performances for protein retrieval and categorization as shown in the comparison with other methods

Mechanisms of Stress Tolerance in Xerophyte \u3cem\u3eZygophyllum xanthoxylum\u3c/em\u3e and Their Application in Genetic Improvement of Legume Forages

Xerophytes, naturally growing in desert areas, have evolved multiple protective mechanisms to survive and grow well in harsh environments. Zygophyllum xanthoxylum, a succulent xerophyte with excellent adaptability to adverse arid environments and a fodder shrub with high palatability and nutrient value, colonizes arid areas in China and Mongolia. In this study, we found that Z. xanthoxylum grew better responding to salt condition with a typical feature for halophytes and became more tolerant to drought in the presence of moderate salinity (50 mM NaCl); 50 mM NaCl alleviated deleterious impacts of drought on the growth of Z. xanthoxylum by improving the relative water content, inducing a significant drop in leaf water potential and, concomitantly, increasing leaf turgor pressure and chlorophyll concentrations resulting in an enhancement of overall plant photosynthetic activity. Subsequently, co-expression of genes encoding the tonoplast Na+/H+ antiporter (ZxNHX) and H+-PPase (ZxVP1-1) which involve in leaf Na+ accumulation under stress condition by compartmentalizing Na+ into vacuoles in Z. xanthoxylum significantly improved both drought and salt tolerance in legume forages, Lotus corniculatus L. and Medicago sativa L

Cellular immune responses in patients with hepatitis B surface antigen seroclearance induced by antiviral therapy

<p>Abstract</p> <p>Background</p> <p>The mechanisms by which chronic hepatitis B is completely resolved through antiviral therapy are unknown, and the contribution of acquired T cell immunity to hepatitis B surface antigen (HBsAg) seroclearance has not been investigated. Therefore, we measured the T-cell responses to core and envelope antigens in patients with HBsAg seroclearance.</p> <p>Methods</p> <p>Fourteen subjects with HBsAg seroclearance following antiviral treatment for chronic hepatitis B, 7 HBeAg-positive immunotolerant HBV carriers and 9 HBeAg-negative inactive HBsAg carriers were recruited. HBV-specific T-cell responses to recombinant HBV core (rHBcAg) and envelope (rHBsAg) proteins and pools of core and envelope peptides were measured using an ELISPOT assay detecting interferon-gamma and intracellular cytokine staining (ICS) assays detecting interferon-gamma or interleukin 2.</p> <p>Results</p> <p>Interferon-gamma ELISPOT assays showed a low frequency of weak responses to the rHBsAg and S peptide pool in the HBsAg seroclearance group, and the response frequency to the rHBcAg and the C peptide pool was higher than to the rHBsAg (<it>P </it>< 0.001) and S peptide pool (<it>P </it>= 0.001) respectively. A higher response frequency to C than S peptide pools was confirmed in the interferon-gamma ICS assays for both CD4+ (<it>P </it>= 0.033) and CD8+ (<it>P </it>= 0.040) T cells in the HBsAg seroclearance group. The responses to C and S antigens in the inactive carriers were similar.</p> <p>Conclusions</p> <p>There was a low frequency of CD4+ and CD8+ T cell immune responses to envelope antigens in Chinese subjects with HBsAg seroclearance following antiviral therapy. It is unlikely that these immune responses are responsible for HBsAg seroclearance in these subjects.</p

Effect of temperature on betacyanins synthesis and the transcriptome of Suaeda salsa

IntroductionSuaeda salsa (Linn.) Pall. is an important tourist resource and ecological restoration species in coastal wetlands. Environmental factors such as low temperature, darkness, phytohormone, salt stress and seawater flflooding, and light can induce betalain synthesis in S. salsa, which plays an important role in plant adaptation to abiotic stress processes and in shaping the beautiful “red beach” landscape.MethodsIn this study, Illumina sequencing was used to profifile the transcriptome sequence (RNA-Seq) of S. salsa leaves at different temperatures (5° C, 10°C, 15°C, 20°C, 25°C, and 30°C) and to validate differentially expressed genes (DEGs) indicated by real-time PCR (RT-qPCR).ResultsThe betacyanin content was highest in S. salsa leaves at 15°C. Transcription group data showed that compared to the control group (15°C), the “betacyanin biosynthesis pathway” was signifificantly enriched in the fifive different temperature groups. KEGG analysis showed that the DEGs were mainly involved in pathways of phenylpropanoid biosynthesis, carbon fifixation in photosynthetic organisms, flflavonoid biosynthesis, and betacyanin biosynthesis. Among the key enzymes involved in biosynthesis of betacyanin, genes for tyrosinase, CYP76AD1 and 4,5-DOPA dioxygenase were signifificantly upregulated and most abundantly expressed at 15°C. It is possible that the gene for betacyanin synthesis from S. salsa is primarily regulated by the MYB1R1 and MYB1 transcription factor. Four DEGs were randomly selected for quantitative PCR analysis, and DEG expression was generally consistent with the RNA-Seq data, verifying the validity of the transcriptome sequencing data.DiscussionRelative to other temperatures, 15°C was optimum for S. salsa betacyanin synthesis, and this provides a theoretical reference for coastal wetland ecological remediation, reveals mechanisms of S. salsa discoloration, and further mines its potential application for landscape vegetation

Molecular epidemiology of measles viruses in China, 1995–2003

This report describes the genetic characterization of 297 wild-type measles viruses that were isolated in 24 provinces of China between 1995 and 2003. Phylogenetic analysis of the N gene sequences showed that all of the isolates belonged to genotype H1 except 3 isolates, which were genotype A. The nucleotide sequence and predicted amino acid homologies of the 294-genotype H1 strains were 94.7%–100% and 93.3%–100%, respectively. The genotype H1 isolates were divided into 2 clusters, which differed by approximately 2.9% at the nucleotide level. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Even though other measles genotypes have been detected in countries that border China, this report shows that genotype H1 is widely distributed throughout the country and that China has a single, endemic genotype. This important baseline data will help to monitor the progress of measles control in China

Genome Wide Association Study Identifies Genetic Variants Associated With Early And Sustained Response To (Peg)Interferon In Chronic Hepatitis B Patients: The GIANT-B Study

(Peg)interferon ((Peg)IFN) therapy leads to response in a minority of chronic hepatitis B (CHB) patients. Host genetic determinants of response are therefore in demand

PVRAR: Point-View Relation Neural Network Embedded with Both Attention Mechanism and Radon Transform for 3D Shape Recognition

Owing to the favorable performance of deep neural networks for 3D shape recognition, an increasing number of researchers are interested in designing novel 3D shape descriptors. However, the relationship between multiple views and point clouds needs to be further elucidated. We propose a multimodal method that combines the features of point clouds and multiple views, i.e., point-view relation neural network embedded with both attention mechanism and Radon transform, to obtain better descriptors. First, a two-dimensional linear Radon transform is performed to investigate linear and color features in multiple views, and the features are used as the input of our network to enable significant distinctions between different views. Moreover, a convolutional block attention module is adopted to enhance the features of point clouds and hence improve the expression ability of feature descriptors. The effectiveness of the proposed method is verified using ModelNet40 and ModelNet10 datasets. Experimental results show that our method can effectively improve the capability of feature extraction and expression as well as achieve state-of-the-art performance on two well-known 3D datasets