Multichannel surface EMG decomposition based on measurement correlation and LMMSE

A method based on measurement correlation (MC) and linear minimum mean square error (LMMSE) for multichannel surface electromyography (sEMG) signal decomposition was developed in this study. This MC-LMMSE method gradually and iteratively increases the correlation between an optimized vector and a reconstructed matrix that is correlated with the measurement matrix. The performance of the proposed MC-LMMSE method was evaluated with both simulated and experimental sEMG signals. Simulation results show that the MC-LMMSE method can successfully reconstruct up to 53 innervation pulse trains with a true positive rate greater than 95%. The performance of the MC-LMMSE method was also evaluated using experimental sEMG signals collected with a 64-channel electrode array from the first dorsal interosseous muscles of three subjects at different contraction levels. A maximum of 16 motor units were successfully extracted from these multichannel experimental sEMG signals. The performance of the MC-LMMSE method was further evaluated with multichannel experimental sEMG data by using the “two sources” method. The large population of common MUs extracted from the two independent subgroups of sEMG signals demonstrates the reliability of the MC-LMMSE method in multichannel sEMG decomposition

Identification and Nearly Full-Length Genome Characterization of Novel Porcine Bocaviruses

The genus bocavirus includes bovine parvovirus (BPV), minute virus of canines (MVC), and a group of human bocaviruses (HBoV1-4). Using sequence-independent single primer amplification (SISPA), a novel bocavirus group was discovered with high prevalence (12.59%) in piglet stool samples. Two nearly full-length genome sequences were obtained, which were approximately 5,100 nucleotides in length. Multiple alignments revealed that they share 28.7–56.8% DNA sequence identity with other members of Parvovirinae. Phylogenetic analyses indicated their closest neighbors were members of the genus bocavirus. The new viruses had a putative non-structural NP1 protein, which was unique to bocaviruses. They were provisionally named porcine bocavirus 1 and 2 (PBoV1, PBoV2). PBoV1 and PBoV2 shared 94.2% nucleotide identity in NS1 gene sequence, suggesting that they represented two different bocavirus species. Two additional samples (6V, 7V) were amplified for 2,407 bp and 2,434 bp products, respectively, including a partial NP1 gene and the complete VP1 gene; Phylogenetic analysis indicated that 6Vand 7V grouped with PBoV1 and PBoV2 in the genus of bocavirus, but were in the separate clusters. Like other parvoviruses, PBoV1, PBoV2, 6Vand 7V also contained a putative secretory phospholipase A2 (sPLA2) motif in the VP1 unique region, with a conserved HDXXY motif in the catalytic center. The conserved motif YXGXF of the Ca2+-binding loop of sPLA2 identified in human bocavirus was also found in porcine bocavirus, which differs from the YXGXG motif carried by most other parvoviruses. The observation of PBoV and potentially other new bocavirus genus members may aid in molecular and functional characterization of the genus bocavirus

3-[(3,5-Di-tert-butyl-2-hydroxy­benzyl­idene)methyl­eneamino]benzonitrile

The mol­ecule of the title compound, C22H26N2O, displays a trans configuration with respect to the C=N double bond. The dihedral angle between the planes of the two aromatic rings is 26.30 (15)°. There is a strong intra­molecular O—H⋯N hydrogen bond between the imine and hydroxyl groups

Genome size variation within species of Chinese jujube (Ziziphus jujuba Mill.) and its wild ancestor sour jujube (Z. acidojujuba Cheng et Liu)

One of the most important attributes of a genome is genome size, which can to a large extent reflect the evolutionary history and diversity of a plant species. However, studies on genome size diversity within a species are still very limited. This study aims to clarify the variation in genome sizes of Chinese jujube and sour jujube, and to characterize if there exists an association between genome sizes and geographical variation. We measured the genome sizes of 301 cultivars of Chinese jujube and 81 genotypes of sour jujube by flow cytometry. Ten fruit traits, including weight, vertical diameter, horizontal diameter, size, total acids, total sugar, monosaccharide, disaccharide, soluble solids, and ascorbic acid were measured in 243 cultivars of Chinese jujube. The estimated genome sizes of Chinese jujube cultivars ranged from 300.77 Mb to 640.94 Mb, with an average of 408.54 Mb, with the highest number of cultivars (20.93%) falling in the range of 334.787 to 368.804 Mb. The genome size is somewhat different with geographical distribution. The results showed weakly significant positive correlation (p \u3c 0.05) between genome size and fruit size, vertical diameter, horizontal diameter, and weight in the Chinese jujube. The estimated sour jujube genome sizes ranged from 346.93 Mb to 489.44 Mb, with the highest number of genotypes (24.69%) falling in the range of 418.185 to 432.436 Mb. The average genome size of sour jujube genotypes is 423.55 Mb, 15 Mb larger than that of Chinese jujube. There exists a high level of variation in genome sizes within both Chinese jujube cultivars and sour jujube genotypes. Genome contraction may have been occurred during the domestication of Chinese jujube. This study is the first large-scale investigation of genome size variation in both Chinese jujube and sour jujube, which has provided useful resources and data for the characterization of genome evolution within a species and during domestication in plants

In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans

BACKGROUND: Currently available vaccines against leptospirosis are of low efficacy, have an unacceptable side-effect profile, do not induce long-term protection, and provide no cross-protection against the different serovars of pathogenic leptospira. The current major focus in leptospirosis research is to discover conserved protective antigens that may elicit longer-term protection against a broad range of Leptospira. There is a need to screen vaccine candidate genes in the genome of Leptospira interrogans. RESULTS: Bioinformatics, comparative genomic hybridization (CGH) analysis and transcriptional analysis were used to identify vaccine candidates in the genome of L. interrogans serovar Lai strain #56601. Of a total of 4727 open reading frames (ORFs), 616 genes were predicted to encode surface-exposed proteins by P-CLASSIFIER combined with signal peptide prediction, α-helix transmembrane topology prediction, integral β-barrel outer membrane protein and lipoprotein prediction, as well as by retaining the genes shared by the two sequenced L. interrogans genomes and by subtracting genes with human homologues. A DNA microarray of L. interrogans strain #56601 was constructed for CGH analysis and transcriptome analysis in vitro. Three hundred and seven differential genes were identified in ten pathogenic serovars by CGH; 1427 genes had high transcriptional levels (Cy3 signal ≥ 342 and Cy5 signal ≥ 363.5, respectively). There were 565 genes in the intersection between the set encoding surface-exposed proteins and the set of 307 differential genes. The number of genes in the intersection between this set of 565 and the set of 1427 highly transcriptionally active genes was 226. These 226 genes were thus identified as putative vaccine candidates. The proteins encoded by these genes are not only potentially surface-exposed in the bacterium, but also conserved in two sequenced L. interrogans. Moreover, these genes are conserved among ten epidemic serovars in China and have high transcriptional levels in vitro. CONCLUSION: Of the 4727 ORFs in the genome of L. interrogans, 226 genes were identified as vaccine candidates by bioinformatics, CGH and transcriptional analysis on the basis of the theory of reverse vaccinology. The proteins encoded by these genes might be useful as vaccine candidates as well as for diagnosis of leptospirosis