Sparsifying the Fisher Linear Discriminant by Rotation

Many high dimensional classification techniques have been proposed in the literature based on sparse linear discriminant analysis (LDA). To efficiently use them, sparsity of linear classifiers is a prerequisite. However, this might not be readily available in many applications, and rotations of data are required to create the needed sparsity. In this paper, we propose a family of rotations to create the required sparsity. The basic idea is to use the principal components of the sample covariance matrix of the pooled samples and its variants to rotate the data first and to then apply an existing high dimensional classifier. This rotate-and-solve procedure can be combined with any existing classifiers, and is robust against the sparsity level of the true model. We show that these rotations do create the sparsity needed for high dimensional classifications and provide theoretical understanding why such a rotation works empirically. The effectiveness of the proposed method is demonstrated by a number of simulated and real data examples, and the improvements of our method over some popular high dimensional classification rules are clearly shown.Comment: 30 pages and 9 figures. This paper has been accepted by Journal of the Royal Statistical Society: Series B (Statistical Methodology). The first two versions of this paper were uploaded to Bin Dong's web site under the title "A Rotate-and-Solve Procedure for Classification" in 2013 May and 2014 January. This version may be slightly different from the published versio

Fork head transcription factor is required for ovarian mature in the brown planthopper, Nilaparvata lugens (Stål)

<p>Abstract</p> <p>Background</p> <p>The brown planthopper (BPH), <it>Nilaparvata lugens</it>, is the most devastating rice pest in many areas throughout Asia. The reproductive system of female <it>N. lugens </it>consists of a pair of ovaries with 24-33 ovarioles per ovary in most individuals which determine its fecundity. The fork head (Fox) is a transcriptional regulatory molecule, which regulates and controls many physiological processes in eukaryotes. The Fox family has several subclasses and members, and several Fox factors have been reported to be involved in regulating fecundity.</p> <p>Results</p> <p>We have cloned a fork head gene in <it>N. lugens</it>. The full-length cDNA of <it>Nl</it>FoxA is 1789 bp and has an open reading frame of 1143 bp, encoding a protein of 380 amino acids. Quantitative real-time PCR (RT-qPCR) and Reverse Transcription- PCR (RT-PCR) analysis revealed that <it>NlFoxA </it>mRNA was mainly expressed in the fat body, midgut, cuticle and Malpighian tube, and was expressed continuously with little change during all the developmental stages. <it>Nl</it>FoxA belongs to the FoxA subfamily of the Fox transcription factors. Knockdown of <it>NlFoxA </it>expression by RNAi using artificial diet containing double-stranded RNA (dsRNA) significantly decreased the number of offspring and impacted the development of ovaries. ELISA and Western blot analyses showed that feeding-based RNAi of <it>NlFoxA </it>gene also resulted in decreased expression of vitellogenin (Vg) protein.</p> <p>Conclusion</p> <p><it>Nl</it>FoxA plays an important role in regulation of fecundity and development of ovaries in the BPH via regulating vitellogenin expression.</p

Virus-Host Mucosal Interactions During Early SIV Rectal Transmission

To deepen our understanding of early rectal transmission of HIV-1, we studied virus-host interactions in the rectal mucosa using simian immunodeficiency virus (SIV)-Indian rhesus macaque model and mRNA deep sequencing. We found that rectal mucosa actively responded to SIV as early as 3 days post-rectal inoculation (dpi) and mobilized more robust responses at 6 and 10 dpi. Our results suggests that the failure of the host to contain virus replication at the portal of entry is attributable to both a high-level expression of lymphocyte chemoattractant, proinflammatory and immune activation genes, which can recruit and activate viral susceptible target cells into mucosa; and a high-level expression of SIV accessory genes, which are known to be able to counter and evade host restriction factors and innate immune responses. This study provides new insights into the mechanism of rectal transmission

Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems

Solenoid-free current drive via ECRH in EXL-50 spherical torus plasmas

As a new spherical tokamak (ST) designed to simplify engineering requirements of a possible future fusion power source, the EXL-50 experiment features a low aspect ratio (A) vacuum vessel (VV), encircling a central post assembly containing the toroidal field coil conductors without a central solenoid. Multiple electron cyclotron resonance heating (ECRH) resonances are located within the VV to improve current drive effectiveness. Copious energetic electrons are produced and measured with hard X-ray detectors, carry the bulk of the plasma current ranging from 50kA to 150kA, which is maintained for more than 1s duration. It is observed that over one Ampere current can be maintained per Watt of ECRH power issued from the 28-GHz gyrotrons. The plasma current reaches Ip>80kA for high density (>5e18me-2) discharge with 150kW ECHR heating. An analysis was carried out combining reconstructed multi-fluid equilibrium, guiding-center orbits of energetic electrons, and resonant heating mechanisms. It is verified that in EXL-50 a broadly distributed current of energetic electrons creates smaller closed magnetic-flux surfaces of low aspect ratio that in turn confine the thermal plasma electrons and ions and participate in maintaining the equilibrium force-balance

The 3′ UTR Variants in the GRP78 Are Not Associated with Overall Survival in Resectable Hepatocellular Carcinoma

Background: Elevated glucose-regulated protein 78 (GRP78) levels in tissues have been known to be related with poor prognosis in hepatocellular carcinoma (HCC) patients. Though the variants in the 3′ untranslated region (UTR) of GRP78 gene were not associated with HCC risk, we wonder whether these polymorphisms affect survival of HCC patients. Methodology/Principal Findings: Blood samples of HCC patients were maintained in our specimen bank between 1996 to 2003. DNA from 576 unrelated and resectable patients with HCC was typed for rs16927997 (T>C), rs1140763 (T>C) and rs12009 (T>C) by TaqMan assays. The Kaplan-Meier method and log-rank test were used to estimate overall survival. Linkage disequilibrium (LD) analysis identified a total of 3 haplotypes and 6 diplotypes in this region. The distribution of haplotype was not related to the clinical characteristics. Univariate analysis showed that the allele, genotype, haplotype and diplotype did not effect the survival. None of the clinical features show a significant association (P correced>0.05) with overall patient outcome in multiple comparisons. Conclusions/Significance: There is no noteworthy influence of 3′ UTR variants in the GRP78 on prognosis of resectable HCC in the Chinese population. © 2011 Zhu et al.published_or_final_versio

DCs Pulsed with Novel HLA-A2-Restricted CTL Epitopes against Hepatitis C Virus Induced a Broadly Reactive Anti-HCV-Specific T Lymphocyte Response

OBJECTIVE: To determine the capacity of dendritic cells (DCs) loaded with single or multiple-peptide mixtures of novel hepatitis C virus (HCV) epitopes to stimulate HCV-specific cytotoxic T lymphocyte (CTL) effector functions. METHODS: A bioinformatics approach was used to predict HLA-A2-restricted HCV-specific CTL epitopes, and the predicted peptides identified from this screen were synthesized. Subsequent IFN-γ ELISPOT analysis detected the stimulating function of these peptides in peripheral blood mononuclear cells (PBMCs) from both chronic and self-limited HCV infected subjects (subjects exhibiting spontaneous HCV clearance). Mature DCs, derived in vitro from CD14(+) monocytes harvested from the study subjects by incubation with appropriate cytokine cocktails, were loaded with novel peptide or epitope peptide mixtures and co-cultured with autologous T lymphocytes. Granzyme B (GrB) and IFN-γ ELISPOT analysis was used to test for epitope-specific CTL responses. T-cell-derived cytokines contained in the co-cultured supernatant were detected by flow cytometry. RESULTS: We identified 7 novel HLA-A2-restricted HCV-specific CTL epitopes that increased the frequency of IFN-γ-producing T cells compared to other epitopes, as assayed by measuring spot forming cells (SFCs). Two epitopes had the strongest stimulating capability in the self-limited subjects, one found in the E2 and one in the NS2 region of HCV; five epitopes had a strong stimulating capacity in both chronic and self-limited HCV infection, but were stronger in the self-limited subjects. They were distributed in E2, NS2, NS3, NS4, and NS5 regions of HCV, respectively. We also found that mDCs loaded with novel peptide mixtures could significantly increase GrB and IFN-γ SFCs as compared to single peptides, especially in chronic HCV infection subjects. Additionally, we found that DCs pulsed with multiple epitope peptide mixtures induced a Th1-biased immune response. CONCLUSIONS: Seven novel and strongly stimulating HLA-A2-restricted HCV-specific CTL epitopes were identified. Furthermore, DCs loaded with multiple-epitope peptide mixtures induced epitope-specific CTLs responses

Towards a General Prediction System for the Primary Delay in Urban Railways

Nowadays a large amount of data is collected from sensor devices across the cyber-physical networks. Accurate and reliable primary delay predictions are essential for rail operations management and planning. However, very few existing \u27big data\u27 methods meet the specific needs in railways. We propose a comprehensive and general data-driven Primary Delay Prediction System (PDPS) framework, which combines General Transit Feed Specification (GTFS), Critical Point Search (CPS), and deep learning models to leverage the data fusion. Based on this framework, we have also developed an open source data collection and processing tool that reduces the barrier to the use of the different open data sources. Finally, we demonstrate an advanced deep learning model, the novel ConvLSTM Encoder-Decoder model with CPS for better primary delay predictions