Improved support vector clustering algorithm for color image segmentation

Color image segmentation has attracted more and more attention in various application fields during the past few years. Essentially speaking, color image segmentation problem is a process of clustering according to the color of pixels. But, traditional clustering methods do not scale well with the number of training sample, which limits the ability of handling massive data effectively. With the utilization of an improved approximate Minimum Enclosing Ball algorithm, this article develops an fast support vector clustering algorithm for computing the different clusters of given color images in kernel-introduced space to segment the color images. We prove theoretically that the proposed algorithm converges to the optimum within any given precision quickly. Compared to other popular algorithms, it has the competitive performances both on training time and accuracy. Color image segmentation experiments on both synthetic and real-world data sets demonstrate the validity of the proposed algorithm

SENP3-mediated host defense response contains HBV replication and restores protein synthesis

Certain organs are capable of containing the replication of various types of viruses. In the liver, infection of Hepatitis B virus (HBV), the etiological factor of Hepatitis B and hepatocellular carcinoma (HCC), often remains asymptomatic and leads to a chronic carrier state. Here we investigated how hepatocytes contain HBV replication and promote their own survival by orchestrating a translational defense mechanism via the stress-sensitive SUMO-2/3-specific peptidase SENP3. We found that SENP3 expression level decreased in HBV-infected hepatocytes in various models including HepG2-NTCP cell lines and a humanized mouse model. Downregulation of SENP3 reduced HBV replication and boosted host protein translation. We also discovered that IQGAP2, a Ras GTPase-activating-like protein, is a key substrate for SENP3-mediated de-SUMOylation. Downregulation of SENP3 in HBV infected cells facilitated IQGAP2 SUMOylation and degradation, which leads to suppression of HBV gene expression and restoration of global translation of host genes via modulation of AKT phosphorylation. Thus, The SENP3-IQGAP2 de-SUMOylation axis is a host defense mechanism of hepatocytes that restores host protein translation and suppresses HBV gene expression

Nonlinear beam fields simulation of a mixed wave and definition of nonlinearity parameter with diffraction correction

The acoustic nonlinearity parameter has been frequently measured for early detection of micro damage in various materials. The technique typically employs a toneburst signal of single frequency and measures the second harmonic generation during its propagation in through-transmission mode. In this work, we propose a two wave mixing technique and the use of difference frequency components in determining the nonlinearity parameter. One important advantage of this technique is to use difference frequency components apart from higher harmonics including the second harmonic, therefore effects of source nonlinearity can be minimized and low attenuating nonlinear signal can be acquired. Beam fields radiated from various configurations of radiating transducers are simulated. The fundamental and difference frequency waves are calculated using the multi-Gaussian beam model based on the quasilinear solution for the Westervelt equation. Explicit expressions for diffraction and attenuation corrections are derived, and the nonlinearity parameter is newly defined with these corrections included

Identification of transcriptome induced in roots of maize seedlings at the late stage of waterlogging

<p>Abstract</p> <p>Background</p> <p>Plants respond to low oxygen stress, particularly that caused by waterlogging, by altering transcription and translation. Previous studies have mostly focused on revealing the mechanism of the response at the early stage, and there is limited information about the transcriptional profile of genes in maize roots at the late stage of waterlogging. The genetic basis of waterlogging tolerance is largely unknown. In this study, the transcriptome at the late stage of waterlogging was assayed in root cells of the tolerant inbred line HZ32, using suppression subtractive hybridization (SSH). A forward SSH library using RNA populations from four time points (12 h, 16 h, 20 h and 24 h) after waterlogging treatment was constructed to reveal up-regulated genes, and transcriptional and linkage data was integrated to identify candidate genes for waterlogging tolerance.</p> <p>Results</p> <p>Reverse Northern analysis of a set of 768 cDNA clones from the SSH library revealed a large number of genes were up-regulated by waterlogging. A total of 465 ESTs were assembled into 296 unigenes. Bioinformatic analysis revealed that the genes were involved in complex pathways, such as signal transduction, protein degradation, ion transport, carbon and amino acid metabolism, and transcriptional and translational regulation, and might play important roles at the late stage of the response to waterlogging. A significant number of unigenes were of unknown function. Approximately 67% of the unigenes could be aligned on the maize genome and 63 of them were co-located within reported QTLs.</p> <p>Conclusion</p> <p>The late response to waterlogging in maize roots involves a broad spectrum of genes, which are mainly associated with two response processes: defense at the early stage and adaption at the late stage. Signal transduction plays a key role in activating genes related to the tolerance mechanism for survival during prolonged waterlogging. The crosstalk between carbon and amino acid metabolism reveals that amino acid metabolism performs two main roles at the late stage: the regulation of cytoplasmic pH and energy supply through breakdown of the carbon skeleton.</p

The FDA-approved natural product dihydroergocristine reduces the production of the Alzheimer's disease amyloid-beta peptides

Known gamma-secretase inhibitors or modulators display an undesirable pharmacokinetic profile and toxicity and have therefore not been successful in clinical trials for Alzheimer's disease (AD). So far, no compounds from natural products have been identified as direct inhibitors of gamma-secretase. To search for bioactive molecules that can reduce the amount of amyloid-beta peptides (A beta) and that have better pharmacokinetics and an improved safety profile, we completed a screen of similar to 400 natural products by using cell-based and cell-free gamma-secretase activity assays. We identified dihydroergocristine (DHEC), a component of an FDA-(Food and Drug Administration)-approved drug, to be a direct inhibitor of gamma-secretase. Micromolar concentrations of DHEC substantially reduced A beta levels in different cell types, including a cell line derived from an AD patient. Structure-activity relationship studies implied that the key moiety for inhibiting gamma-secretase is the cyclized tripeptide moiety of DHEC. A Surface Plasmon Resonance assay showed that DHEC binds directly to gamma-secretase and Nicastrin, with equilibrium dissociation constants (K-d) of 25.7 nM and 9.8 mu M, respectively. This study offers DHEC not only as a new chemical moiety for selectively modulating the activity of gamma-secretase but also a candidate for drug repositioning in Alzheimer's disease

Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events

Bud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by next generation sequencing (NGS), and we provide evidence that a long loss of heterozygosity (LOH) event may be responsible for this alteration in fruit shape. Moreover, compared to the reference genome, we identified 237,476 high quality single nucleotide polymorphisms (SNPs) in the wild-type and bud sport genomes. Using this SNP set, a long LOH event was identified at the distal end of scaffold Pp06 of the bud sport genome. Haplotypes from 155 additional peach accessions were phased, suggesting that the homozygous distal end of scaffold Pp06 of the bud sport was likely derived from only one haplotype of the wild-type flat peach. A genome-wide association study (GWAS) of 127 peach accessions was conducted to associate a SNP found at 26,924,482 bp of scaffold Pp06 to differences in fruit shape. All accessions with round-shaped fruit were found to have an A/A genotype, while those with A/T, or T/T genotypes had flat-shaped fruits. Finally, we also found that 236 peach accessions and 141 Prunus species with round-type fruit were found to have an A/A genotype at this SNP, while 22 flat peach accessions had an A/T genotype. Taken together, our results suggest that genes flanking this A/T polymorphism, and haplotyped carrying the T allele may determine flat fruit shape in this population. Furthermore, the LOH event resulting in the loss of the haplotype carrying the T allele may therefore be responsible for fruit shape alteration in wild-type flat peach

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Comparison of human, chimpanzee, and macaque brain transcriptomes reveals a significant developmental remodeling in the human prefrontal cortex, potentially shaped by microRNA