202 research outputs found

    Semisupervised Kernel Marginal Fisher Analysis for Face Recognition

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    Dimensionality reduction is a key problem in face recognition due to the high-dimensionality of face image. To effectively cope with this problem, a novel dimensionality reduction algorithm called semisupervised kernel marginal Fisher analysis (SKMFA) for face recognition is proposed in this paper. SKMFA can make use of both labelled and unlabeled samples to learn the projection matrix for nonlinear dimensionality reduction. Meanwhile, it can successfully avoid the singularity problem by not calculating the matrix inverse. In addition, in order to make the nonlinear structure captured by the data-dependent kernel consistent with the intrinsic manifold structure, a manifold adaptive nonparameter kernel is incorporated into the learning process of SKMFA. Experimental results on three face image databases demonstrate the effectiveness of our proposed algorithm

    Multiview Discriminative Geometry Preserving Projection for Image Classification

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    In many image classification applications, it is common to extract multiple visual features from different views to describe an image. Since different visual features have their own specific statistical properties and discriminative powers for image classification, the conventional solution for multiple view data is to concatenate these feature vectors as a new feature vector. However, this simple concatenation strategy not only ignores the complementary nature of different views, but also ends up with “curse of dimensionality.” To address this problem, we propose a novel multiview subspace learning algorithm in this paper, named multiview discriminative geometry preserving projection (MDGPP) for feature extraction and classification. MDGPP can not only preserve the intraclass geometry and interclass discrimination information under a single view, but also explore the complementary property of different views to obtain a low-dimensional optimal consensus embedding by using an alternating-optimization-based iterative algorithm. Experimental results on face recognition and facial expression recognition demonstrate the effectiveness of the proposed algorithm

    A Roughness Study of Ytterbium-Doped Potassium Yttrium Tungstate (YB: KYW) Thin-Disk Femtosecond Ablated Dentin

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    Introduction: The aim of this study was to evaluate the morphological changes and quantitatively assess the roughness of dentin after the ablation with a Ytterbium-Doped Potassium Yttrium Tungstate (YB: KYW) thin-disk femtosecond pulsed laser of different fluences, scanning speeds and scanning distances.Method: Twelve extracted human premolars were sectioned into crowns and roots along the cementum-enamel junction, and then the crowns were cut longitudinally into sheets about 1.5 mm thick with a cutting machine. The dentin samples were fixed on a stage at focus plane. The laser beam was irradiated onto the samples through a galvanometric scanning system, so rectangular movement could be achieved. After ablation, the samples were examined with a scanning electron microscope and laser three-dimensional profile measurement microscope for morphology and roughness study.With increasing laser fluence, dentin samples exhibited more melting and resolidification of dentin as well as debris-like structure and occluded parts of dentinal tubules.Results: When at the scanning speed of 2400mm/s and scanning distance of 24μm, the surface roughness of dentin ablated with femtosecond pulsed laser decreased significantly and varied between values of dentin surface roughness grinded with two kinds of diamond burs with different grits. When at the scanning speed of 1200mm/s and scanning distance of 12μm, the surface roughness decreased slightly, and the surface roughness of dentin ablated with femtosecond pulsed laser was almost equal to that grinded with a low grit diamond bur.Conclusion: This study showed that increased laser influence may lead to more collateral damage and lower dentin surface roughness, while scanning speed and scanning distance were also negatively correlated with surface roughness. Adequate parameters should be chosen to achieve therapeutic benefits, and different parameters can result in diverse ablation results

    Regression-based approach for testing the association between multi-region haplotype configuration and complex trait

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    <p>Abstract</p> <p>Background</p> <p>It is quite common that the genetic architecture of complex traits involves many genes and their interactions. Therefore, dealing with multiple unlinked genomic regions simultaneously is desirable.</p> <p>Results</p> <p>In this paper we develop a regression-based approach to assess the interactions of haplotypes that belong to different unlinked regions, and we use score statistics to test the null hypothesis of non-genetic association. Additionally, multiple marker combinations at each unlinked region are considered. The multiple tests are settled via the <it>minP </it>approach. The <it>P </it>value of the "best" multi-region multi-marker configuration is corrected via Monte-Carlo simulations. Through simulation studies, we assess the performance of the proposed approach and demonstrate its validity and power in testing for haplotype interaction association.</p> <p>Conclusion</p> <p>Our simulations showed that, for binary trait without covariates, our proposed methods prove to be equal and even more powerful than htr and hapcc which are part of the FAMHAP program. Additionally, our model can be applied to a wider variety of traits and allow adjustment for other covariates. To test the validity, our methods are applied to analyze the association between four unlinked candidate genes and pig meat quality.</p

    Genome-Wide and Trait-Specific Markers: A Perspective in Designing Conservation Programs

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    Nowadays, breed conservation has entered the genomics era and it is imperative to develop novel theory to design the breeding schemes of the conservation populations by using the genomic information. The genome-wide markers have been regarded as a useful strategy to maintain genetic diversity. However, using the genome-wide SNPs to optimize diversity might not be optimal for some specific loci associated with specific-traits. Using the sequencing data of the conserved population of the Saba pig breed, we demonstrated that the conservation program designed by using the genome-wide SNPs might result in the loss of the genetic diversity of the reproduction trait. We suggested an idea of using phylogenetic tree to select valuable individuals for conservation program based on the genome-wide and trait-specific makers. The selection rule was to make the selected samples to be widely distributed as much as possible in both the genome-wide and trait-specific phylogenetic trees

    Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

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    Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1–5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome

    An H5N1 M2e-based multiple antigenic peptide vaccine confers heterosubtypic protection from lethal infection with pandemic 2009 H1N1 virus

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    Background. A 2009 global influenza pandemic caused by a novel swine-origin H1N1 influenza A virus has posted an increasing threat of a potential pandemic by the highly pathogenic avian influenza (HPAI) H5N1 virus, driving us to develop an influenza vaccine which confers cross-protection against both H5N1 and H1N1 viruses. Previously, we have shown that a tetra-branched multiple antigenic peptide (MAP) vaccine based on the extracellular domain of M2 protein (M2e) from H5N1 virus (H5N1-M2e-MAP) induced strong immune responses and cross-protection against different clades of HPAI H5N1 viruses. In this report, we investigated whether such M2e-MAP presenting the H5N1-M2e consensus sequence can afford heterosubtypic protection from lethal challenge with the pandemic 2009 H1N1 virus. Results. Our results demonstrated that H5N1-M2e-MAP plus Freund's or aluminum adjuvant induced strong cross-reactive IgG antibody responses against M2e of the pandemic H1N1 virus which contains one amino acid variation with M2e of H5N1 at position 13. These cross-reactive antibodies may maintain for 6 months and bounced back quickly to the previous high level after the 2nd boost administered 2 weeks before virus challenge. H5N1-M2e-MAP could afford heterosubtypic protection against lethal challenge with pandemic H1N1 virus, showing significant decrease of viral replications and obvious alleviation of histopathological damages in the challenged mouse lungs. 100% and 80% of the H5N1-M2e-MAP-vaccinated mice with Freund's and aluminum adjuvant, respectively, survived the lethal challenge with pandemic H1N1 virus. Conclusions. Our results suggest that H5N1-M2e-MAP has a great potential to prevent the threat from re-emergence of pandemic H1N1 influenza and possible novel influenza pandemic due to the reassortment of HPAI H5N1 virus with the 2009 swine-origin H1N1 influenza virus. © 2010 Zhao et al; licensee BioMed Central Ltd.published_or_final_versio

    Comparison of genetic impact on growth and wood traits between seedlings and clones from the same plus trees of Pinus koraiensis

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    To evaluate the relationships among clones and open pollinated families from the same plus trees and to select elite breeding materials, growth, and wood characteristics of 33-year-old Pinus koraiensis clones and families were measured and analyzed. The results show that growth and wood characters varied significantly. The variation due to clonal effects was higher than that of family effects. The ratio of genetic to phenotypic coefficient of variation of clones in growth and wood traits was above 90%, and the repeatability of these characteristics was more than 0.8, whereas the ratio of genetic to phenotypic coefficient of variation of families was above 90%. The broad-sense heritability of all characteristics exceeded 0.4, and the narrow-sense family heritability of growth traits was less than 0.3. Growth characteristics were positively correlated with each other, but most wood properties were weakly correlated in both clones and families. Fiber length and width were positively correlated between clones and families. Using the membership function method, eleven clones and four families were selected as superior material for improved diameter growth and wood production, and two families from clonal and open-pollinated trees showed consistently better performance. Generally, selection of the best clones is an effective alternative to deployment of families as the repeatability estimates from clonal trees were higher than narrow-sense heritability estimates from open pollinated families. The results provide valuable insight for improving P. koraiensis breeding programs and subsequent genetic improvement
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