A Self-Consistent Field Solution for Robust Common Spatial Pattern Analysis

The common spatial pattern analysis (CSP) is a widely used signal processing technique in brain-computer interface (BCI) systems to increase the signal-to-noise ratio in electroencephalogram (EEG) recordings. Despite its popularity, the CSP's performance is often hindered by the nonstationarity and artifacts in EEG signals. The minmax CSP improves the robustness of the CSP by using data-driven covariance matrices to accommodate the uncertainties. We show that by utilizing the optimality conditions, the minmax CSP can be recast as an eigenvector-dependent nonlinear eigenvalue problem (NEPv). We introduce a self-consistent field (SCF) iteration with line search that solves the NEPv of the minmax CSP. Local quadratic convergence of the SCF for solving the NEPv is illustrated using synthetic datasets. More importantly, experiments with real-world EEG datasets show the improved motor imagery classification rates and shorter running time of the proposed SCF-based solver compared to the existing algorithm for the minmax CSP

A Bi-level Nonlinear Eigenvector Algorithm for Wasserstein Discriminant Analysis

Much like the classical Fisher linear discriminant analysis, Wasserstein discriminant analysis (WDA) is a supervised linear dimensionality reduction method that seeks a projection matrix to maximize the dispersion of different data classes and minimize the dispersion of same data classes. However, in contrast, WDA can account for both global and local inter-connections between data classes using a regularized Wasserstein distance. WDA is formulated as a bi-level nonlinear trace ratio optimization. In this paper, we present a bi-level nonlinear eigenvector (NEPv) algorithm, called WDA-nepv. The inner kernel of WDA-nepv for computing the optimal transport matrix of the regularized Wasserstein distance is formulated as an NEPv, and meanwhile the outer kernel for the trace ratio optimization is also formulated as another NEPv. Consequently, both kernels can be computed efficiently via self-consistent-field iterations and modern solvers for linear eigenvalue problems. Comparing with the existing algorithms for WDA, WDA-nepv is derivative-free and surrogate-model-free. The computational efficiency and applications in classification accuracy of WDA-nepv are demonstrated using synthetic and real-life datasets

Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas

<p>Abstract</p> <p>Background</p> <p><it>Alu </it>methylation is correlated with the overall level of DNA methylation and recombination activity of the genome. However, the maintenance and methylation status of each CpG site within <it>Alu </it>elements (<it>Alu</it>) and its methylation status have not well characterized. This information is useful for understanding natural status of <it>Alu </it>in the genome and helpful for developing an optimal assay to quantify <it>Alu </it>hypomethylation.</p> <p>Methods</p> <p>Bisulfite clone sequencing was carried out in 14 human gastric samples initially. A <it>Cac</it>8I COBRA-DHPLC assay was developed to detect methylated-<it>Alu </it>proportion in cell lines and 48 paired gastric carcinomas and 55 gastritis samples. DHPLC data were statistically interpreted using SPSS version 16.0.</p> <p>Results</p> <p>From the results of 427 <it>Alu </it>bisulfite clone sequences, we found that only 27.2% of CpG sites within <it>Alu </it>elements were preserved (4.6 of 17 analyzed CpGs, A ~ Q) and that 86.6% of remaining-CpGs were methylated. Deamination was the main reason for low preservation of methylation targets. A high correlation coefficient of methylation was observed between <it>Alu </it>clones and CpG site J (0.963), A (0.950), H (0.946), D (0.945). Comethylation of the sites H and J were used as an indicator of the proportion of methylated-<it>Alu </it>in a <it>Cac</it>8I COBRA-DHPLC assay. Validation studies showed that hypermethylation or hypomethylation of <it>Alu </it>elements in human cell lines could be detected sensitively by the assay after treatment with 5-aza-dC and M.<it>Sss</it>I, respectively. The proportion of methylated-<it>Alu </it>copies in gastric carcinomas (3.01%) was significantly lower than that in the corresponding normal samples (3.19%) and gastritis biopsies (3.23%).</p> <p>Conclusions</p> <p>Most <it>Alu </it>CpG sites are deaminated in the genome. 27% of <it>Alu </it>CpG sites represented in our amplification products. 87% of the remaining CpG sites are methylated. <it>Alu </it>hypomethylation in primary gastric carcinomas could be detected with the <it>Cac</it>8I COBRA-DHPLC assay quantitatively.</p

Cloning and Phylogenetic Analysis of Sid-1-Like Genes from Aphids

The sid-1 (systemic interference defective) gene encodes a transmembrane protein that is an important participator in the systemic RNAi pathway and has been reported in several organisms. In insects, sid-1-like genes were described from Tribolium castaneum, Apis mellifera, Bombyx mori and Schistocerca americana, but were not found in Drosophila melanogaster and Anopheles gambiae. To investigate whether this gene occurs in aphid species, RT-PCRs were performed using degenerate primers designed using the conserved motif of sid-1-like genes. An sid-1-like full-length transcript was amplified from the cotton/melon aphid, Aphis gossypii Glover (Homopera: Aphididae), and a fragment was amplified from the grain aphid, Sitobion avenae (F.). The trancript from A. gossypii was 3067 bp long, with an open reading frame encoding 766 amino acids. Sequence analysis indicated that this transcript shares highest similarity with the reported sid-1-like gene in Schistocerca americana (53%, fragment), followed by A. mellifera (44%), T. castaneum (32–44%), B. mori (38–42%) and Caenorhabditis elegans (25%). Analysis of the transmembrane protein topological structure indicated that the protein encoded by this gene has a similar structure to SID-1 of C. elegans. A phylogenetic tree with all available sid-1-like genes suggests that sid-1-like genes may have had a long evolutionary history. Considering its importance in the RNAi pathway, the absence of a sid-1-like gene in D. melanogaster and A. gambiae is worthy of further investigation

A multi-layer genome mining and phylogenomic analysis to construct efficient and autonomous efflux system for medium chain fatty acids

Medium-chain fatty acids (MCFAs) are important components for food, pharmaceutical and fuel industries. Nevertheless, engineering microorganisms to produce MCFAs often induces toxicity and stresses towards host strains, which could be alleviated via accelerating the export of MCFAs from cells. However, current secretory systems are inefficient and require inducible promoters. Here, a multi-layer genome mining and phylogenomic analysis was developed to identify efficient efflux transporters. Firstly, based on the genomic mining of 397 strains throughout various representative species, the evolutionary history of efflux transporters was recapitulated, and further experimental analysis revealed that acrE from Citrobacter exhibited the best performance. Secondly, according to the further mining of 797 Citrobacter genomes and 1084 Escherichia genomes, a detailed phylogenomic analysis of efflux transporter-centric genomic vicinities was performed. This led to the identification of efficient efflux pump combination acrE and acrF. These efflux pumps were then combined with the quorum-sensing circuit from Enterococcus faecalis to regulate MCFA efflux in an autonomous manner, which achieved a 4.9-fold boost in MCFA production and firstly demonstrated the efficient and autonomous efflux pump specially for MCFAs. The integrative omics technologies described here are enabling the utilization of the increasingly large database and the effective mining of target gene diversities

A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case

Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Uncertainty still exists, partly because of the limited number of cases analysed. In this study, a full autopsy including 5 organ systems was conducted on a confirmed H5N1 human fatal case (male, 42 years old) within 18 hours of death. In addition to the respiratory system (lungs, bronchus and trachea), virus was isolated from cerebral cortex, cerebral medullary substance, cerebellum, brain stem, hippocampus ileum, colon, rectum, ureter, aortopulmonary vessel and lymph-node. Real time RT-PCR evidence showed that matrix and hemagglutinin genes were positive in liver and spleen in addition to positive tissues with virus isolation. Immunohistochemistry and in-situ hybridization stains showed accordant evidence of viral infection with real time RT-PCR except bronchus. Quantitative RT-PCR suggested that a high viral load was associated with increased host responses, though the viral load was significantly different in various organs. Cells of the immunologic system could also be a target for virus infection. Overall, the pathogenesis of HPAI H5N1 virus was associated both with virus replication and with immunopathologic lesions. In addition, immune cells cannot be excluded from playing a role in dissemination of the virus in vivo

Full dimensional quantum mechanical calculations of the reaction probability of the H + NH 3 collision based on a mixed Jacobi and Radau description

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Eight-Dimensional Quantum Dynamics Study of CH4 and CD4 Dissociation on Ni(100) Surface

Methane dissociation on Ni(100) surface is one of the benchmark systems for exploring polyatomic molecular gas-surface reaction dynamics. We here present an eight-dimensional quantum dynamics study based on developing a highly accurate, 15-dimensional potential energy surface(PES). The CH4 interacting on a rigid Ni(100) surface is described with the methodology of neural network (NN) fit to plenty of ab initio configuration energy points. With the best-fitting NN(PES), we obtain the sticking probability S-0 of ground state (GS) CH4 and its isotopologue CD4 on a rigid Ni(100) from some direct quantum dynamics simulations. The promising azimuth-averaged and site averaged approaches are employed to treat the influence of surface impact sites. The improved nonlinear lattice-sudden model is considered for the surface temperature effect. The final S-0 of GS CH4 on Ni(100) surface at 475 K is in excellent agreement with two sets of available experiments. Furthermore, we calculate the So of GS CD4 on Ni(100) surface at 475 K. It is much lower than that GS CH4, which mainly contributes from the zero-point vibrational energy difference