Browsing by Author "Yang, H"

Now showing 1 - 16 of 16
  • Thumbnail Image
    ItemOpen Access
    Antiviral inhibitory capacity of CD8+ T cells predicts the rate of CD4+ T-cell decline in HIV-1 infection.
    (J Infect Dis, 2012-08-15) Yang, H; Wu, H; Hancock, G; Clutton, G; Sande, N; Xu, X; Yan, H; Huang, X; Angus, B; Kuldanek, K; Fidler, S; Denny, TN; Birks, J; McMichael, A; Dorrell, L
    BACKGROUND: Rare human immunodeficiency virus type 1 (HIV-1)-infected individuals who maintain control of viremia without therapy show potent CD8+ T-cell-mediated suppression of viral replication in vitro. Whether this is a determinant of the rate of disease progression in viremic individuals is unknown. METHODS: We measured CD8+ T-cell-mediated inhibition of a heterologous HIV-1 isolate in 50 HIV-1-seropositive adults with diverse progression rates. Linear mixed models were used to determine whether CD8+ T-cell function could explain variation in the rate of CD4+ T-cell decline. RESULTS: There was a significant interaction between CD8+ T-cell antiviral activity in vitro and the rate of CD4+ T-cell decline in chronically infected individuals (P < .0001). In a second prospective analysis of recently infected subjects followed for up to 3 years, CD8+ T-cell antiviral activity strongly predicted subsequent CD4+ T-cell decline (P < .0001) and explained up to 73% of the interindividual variation in the CD4+ T-cell slope. In addition, it was inversely associated with viral load set point (r = -0.68 and P = .002). CONCLUSIONS: The antiviral inhibitory capacity of CD8+ T cells is highly predictive of CD4+ T-cell loss in early HIV-1 infection. It has potential as a benchmark of effective immunity in vaccine evaluation.
  • Thumbnail Image
    ItemOpen Access
    Colloidal quantum dot absorption enhancement in flexible Fano filters
    (Applied Physics Letters, 2010-03-12) Chen, L; Yang, H; Qiang, Z; Pang, H; Sun, L; Ma, Z; Pate, R; Stiff Roberts, A; Gao, S; Xu, J; Brown, GJ; Zhou, W
    We report here modified absorption property of colloidal quantum dots (CQDs) inside flexible Fano filters-made of patterned single crystalline silicon nanomembrane transferred onto flexible plastic substrates. Enhanced optical absorption was obtained both experimentally and theoretically, when the CQD absorption peak spectrally overlaps with Fano resonance peak. On the other hand, suppressed absorption was observed when the Fano resonance has no spectral overlap with the CQD absorption bands. © 2010 American Institute of Physics.
  • Thumbnail Image
    ItemOpen Access
    Combining 2D synchrosqueezed wave packet transform with optimization for crystal image analysis
    (Journal of the Mechanics and Physics of Solids, 2016-04-01) Lu, J; Wirth, B; Yang, H
    © 2016 Elsevier Ltd. All rights reserved.We develop a variational optimization method for crystal analysis in atomic resolution images, which uses information from a 2D synchrosqueezed transform (SST) as input. The synchrosqueezed transform is applied to extract initial information from atomic crystal images: crystal defects, rotations and the gradient of elastic deformation. The deformation gradient estimate is then improved outside the identified defect region via a variational approach, to obtain more robust results agreeing better with the physical constraints. The variational model is optimized by a nonlinear projected conjugate gradient method. Both examples of images from computer simulations and imaging experiments are analyzed, with results demonstrating the effectiveness of the proposed method.
  • Thumbnail Image
    ItemOpen Access
    Crystal image analysis using 2D synchrosqueezed transforms
    (Multiscale Modeling and Simulation, 2015-01-01) Yang, H; Lu, J; Ying, L
    © 2015 Society for Industrial and Applied Mathematics.We propose efficient algorithms based on a band-limited version of 2D synchrosqueezed transforms to extract mesoscopic and microscopic information from atomic crystal images. The methods analyze atomic crystal images as an assemblage of nonoverlapping segments of 2D general intrinsic mode type functions, which are superpositions of nonlinear wave-like components. In particular, crystal defects are interpreted as the irregularity of local energy; crystal rotations are described as the angle deviation of local wave vectors from their references; the gradient of a crystal elastic deformation can be obtained by a linear system generated by local wave vectors. Several numerical examples of synthetic and real crystal images are provided to illustrate the efficiency, robustness, and reliability of our methods.
  • Thumbnail Image
    ItemOpen Access
    ELSI: A Unified Software Interface for Kohn-Sham Electronic Structure Solvers
    (2017-07-01) Yu, VWZ; Corsetti, F; García, A; Huhn, WP; Jacquelin, M; Jia, W; Lange, B; Lin, L; Lu, J; Mi, W; Seifitokaldani, A; Vázquez-Mayagoitia, Á; Yang, C; Yang, H; Blum, V
    Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.
  • Thumbnail Image
    ItemOpen Access
    GxE interactions between FOXO genotypes and drinking tea are significantly associated with prevention of cognitive decline in advanced age in China.
    (J Gerontol A Biol Sci Med Sci, 2015-04) Zeng, Y; Chen, H; Ni, T; Ruan, R; Feng, L; Nie, C; Cheng, L; Li, Y; Tao, W; Gu, J; Land, KC; Yashin, A; Tan, Q; Yang, Z; Bolund, L; Yang, H; Hauser, E; Willcox, DC; Willcox, BJ; Tian, X; Vaupel, JW
    Logistic regression analysis based on data from 822 Han Chinese oldest old aged 92+ demonstrated that interactions between carrying FOXO1A-266 or FOXO3-310 or FOXO3-292 and tea drinking at around age 60 or at present time were significantly associated with lower risk of cognitive disability at advanced ages. Associations between tea drinking and reduced cognitive disability were much stronger among carriers of the genotypes of FOXO1A-266 or FOXO3-310 or FOXO3-292 compared with noncarriers, and it was reconfirmed by analysis of three-way interactions across FOXO genotypes, tea drinking at around age 60, and at present time. Based on prior findings from animal and human cell models, we postulate that intake of tea compounds may activate FOXO gene expression, which in turn may positively affect cognitive function in the oldest old population. Our empirical findings imply that the health benefits of particular nutritional interventions, including tea drinking, may, in part, depend upon individual genetic profiles.
  • Thumbnail Image
    ItemOpen Access
    Interaction Between the FOXO1A-209 Genotype and Tea Drinking Is Significantly Associated with Reduced Mortality at Advanced Ages.
    (Rejuvenation Res, 2016-06) Zeng, Y; Chen, H; Ni, T; Ruan, R; Nie, C; Liu, X; Feng, L; Zhang, F; Lu, J; Li, J; Li, Y; Tao, W; Gregory, SG; Gottschalk, W; Lutz, MW; Land, KC; Yashin, A; Tan, Q; Yang, Z; Bolund, L; Ming, Q; Yang, H; Min, J; Willcox, DC; Willcox, BJ; Gu, J; Hauser, E; Tian, X; Vaupel, JW
    On the basis of the genotypic/phenotypic data from Chinese Longitudinal Healthy Longevity Survey (CLHLS) and Cox proportional hazard model, the present study demonstrates that interactions between carrying FOXO1A-209 genotypes and tea drinking are significantly associated with lower risk of mortality at advanced ages. Such a significant association is replicated in two independent Han Chinese CLHLS cohorts (p = 0.028-0.048 in the discovery and replication cohorts, and p = 0.003-0.016 in the combined dataset). We found the associations between tea drinking and reduced mortality are much stronger among carriers of the FOXO1A-209 genotype compared to non-carriers, and drinking tea is associated with a reversal of the negative effects of carrying FOXO1A-209 minor alleles, that is, from a substantially increased mortality risk to substantially reduced mortality risk at advanced ages. The impacts are considerably stronger among those who carry two copies of the FOXO1A minor allele than those who carry one copy. On the basis of previously reported experiments on human cell models concerning FOXO1A-by-tea-compounds interactions, we speculate that results in the present study indicate that tea drinking may inhibit FOXO1A-209 gene expression and its biological functions, which reduces the negative impacts of FOXO1A-209 gene on longevity (as reported in the literature) and offers protection against mortality risk at oldest-old ages. Our empirical findings imply that the health outcomes of particular nutritional interventions, including tea drinking, may, in part, depend upon individual genetic profiles, and the research on the effects of nutrigenomics interactions could potentially be useful for rejuvenation therapies in the clinic or associated healthy aging intervention programs.
  • Thumbnail Image
    ItemOpen Access
  • Thumbnail Image
    ItemOpen Access
    Multidimensional Butterfly Factorization
    (Applied and Computational Harmonic Analysis) Li, Y; Yang, H; Ying, L
  • Thumbnail Image
    ItemOpen Access
  • Thumbnail Image
    ItemOpen Access
  • No Thumbnail Available
    ItemMetadata only
  • Thumbnail Image
    ItemOpen Access
    Removal of Canvas Patterns in Digital Acquisitions of Paintings
    (IEEE Transactions on Image Processing) Cornelis, B; Yang, H; Goodfriend, A; Ocon, N; Lu, J; Daubechies, I
  • Thumbnail Image
    ItemOpen Access
  • Thumbnail Image
    ItemOpen Access
    Statistical analysis of synchrosqueezed transforms
    (Applied and Computational Harmonic Analysis, 2014-10-24) Yang, H
    © 2017 Elsevier Inc.Synchrosqueezed transforms are non-linear processes for a sharpened time-frequency representation of wave-like components. They are efficient tools for identifying and analyzing wave-like components from their superposition. This paper is concerned with the statistical properties of compactly supported synchrosqueezed transforms for wave-like components embedded in a generalized Gaussian random process in multidimensional spaces. Guided by the theoretical analysis of these properties, new numerical implementations are proposed to reduce the noise fluctuations of these transforms on noisy data. A MATLAB package SynLab together with several heavily noisy examples is provided to support these theoretical claims.
  • Thumbnail Image
    ItemOpen Access
    The antiviral inhibitory capacity of CD8+T cells predicts the rate of CD4+cell decline in HIV-1 infection
    (HIV MEDICINE, 2012-04) Yang, H; Wu, H; Hancock, G; Clutton, G; Sande, N; Xu, X; Yan, H-P; Huang, X; Angus, B; Kuldanek, K; Fidler, S; Denny, T; Birks, J; McMichael, A; Dorrell, L