Browsing by Author "Yang, Y"

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    Bayesian crack detection in ultra high resolution multimodal images of paintings
    (2013 18th International Conference on Digital Signal Processing, DSP 2013, 2013-12-06) Cornelis, B; Yang, Y; Vogelstein, JT; Dooms, A; Daubechies, I; Dunson, D
    The preservation of our cultural heritage is of paramount importance. Thanks to recent developments in digital acquisition techniques, powerful image analysis algorithms are developed which can be useful non-invasive tools to assist in the restoration and preservation of art. In this paper we propose a semi-supervised crack detection method that can be used for high-dimensional acquisitions of paintings coming from different modalities. Our dataset consists of a recently acquired collection of images of the Ghent Altarpiece (1432), one of Northern Europe's most important art masterpieces. Our goal is to build a classifier that is able to discern crack pixels from the background consisting of non-crack pixels, making optimal use of the information that is provided by each modality. To accomplish this we employ a recently developed non-parametric Bayesian classifier, that uses tensor factorizations to characterize any conditional probability. A prior is placed on the parameters of the factorization such that every possible interaction between predictors is allowed while still identifying a sparse subset among these predictors. The proposed Bayesian classifier, which we will refer to as conditional Bayesian tensor factorization or CBTF, is assessed by visually comparing classification results with the Random Forest (RF) algorithm. © 2013 IEEE.
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    Genetic variants in the TEP1 gene are associated with prostate cancer risk and recurrence.
    (Prostate Cancer Prostatic Dis, 2015-12) Gu, C; Li, Q; Zhu, Y; Qu, Y; Zhang, G; Wang, M; Yang, Y; Wang, J; Jin, L; Wei, Q; Ye, D
    BACKGROUND: Telomere-related genes play an important role in carcinogenesis and progression of prostate cancer (PCa). It is not fully understood whether genetic variations in telomere-related genes are associated with development and progression in PCa patients. METHODS: Six potentially functional single-nucleotide polymorphisms (SNPs) of three key telomere-related genes were evaluated in 1015 PCa cases and 1052 cancer-free controls, to test their associations with risk of PCa. Among 426 PCa patients who underwent radical prostatectomy (RP), the prognostic significance of the studied SNPs on biochemical recurrence (BCR) was also assessed using the Kaplan-Meier analysis and Cox proportional hazards regression model. The relative telomere lengths (RTLs) were measured in peripheral blood leukocytes using real-time PCR in the RP patients. RESULTS: TEP1 rs1760904 AG/AA genotypes were significantly associated with a decreased risk of PCa (odds ratio (OR): 0.77, 95% confidence interval (CI): 0.64-0.93, P=0.005) compared with the GG genotype. By using median RTL as a cutoff level, RP patients with TEP1 rs1760904 AG/AA genotypes tended to have a longer RTL than those with the GG genotype (OR: 1.55, 95% CI: 1.04-2.30, P=0.031). A significant interaction between TEP1 rs1713418 and age in modifying PCa risk was observed (P=0.005). After adjustment for clinicopathologic risk factors, the presence of heterozygotes or rare homozygotes of TEP1 rs1760904 and TNKS2 rs1539042 were associated with BCR in the RP cohorts (hazard ratio: 0.53, 95% CI: 0.36-0.79, P=0.002 and hazard ratio: 1.67, 95% CI: 1.07-2.48, P=0.017, respectively). CONCLUSIONS: These data suggest that genetic variations in the TEP1 gene may be biomarkers for risk of PCa and BCR after RP.
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    Interpreting Incidentally Identified Variants in Genes Associated With Catecholaminergic Polymorphic Ventricular Tachycardia in a Large Cohort of Clinical Whole-Exome Genetic Test Referrals.
    (Circulation. Arrhythmia and electrophysiology, 2017-04) Landstrom, AP; Dailey-Schwartz, AL; Rosenfeld, JA; Yang, Y; McLean, MJ; Miyake, CY; Valdes, SO; Fan, Y; Allen, HD; Penny, DJ; Kim, JJ
    BACKGROUND:The rapid expansion of genetic testing has led to increased utilization of clinical whole-exome sequencing (WES). Clinicians and genetic researchers are being faced with assessing risk of disease vulnerability from incidentally identified genetic variants which is typified by variants found in genes associated with sudden death-predisposing catecholaminergic polymorphic ventricular tachycardia (CPVT). We sought to determine whether incidentally identified variants in genes associated with CPVT from WES clinical testing represent disease-associated biomarkers. METHODS AND RESULTS:CPVT-associated genes RYR2 and CASQ2 variants were identified in one of the world's largest collections of clinical WES referral tests (N=6517, Baylor Miraca Genetics Laboratories) and compared with a control cohort of ostensibly healthy individuals (N=60 706) and a case cohort of CPVT cases (N=155). Within the WES cohort, the rate of rare variants in CPVT-associated genes was 8.8% compared with 6.0% among controls and 60.0% among cases. There was a predominance of variants of undetermined significance (97.7%). After protein topology mapping, WES variants colocalized more frequently to residues with variants found in controls compared with cases. Retrospective clinical evaluation of individuals referred to our institution with WES-positive variants demonstrated no evidence of clinical CPVT in individuals with a low pretest clinical suspicion for CPVT. CONCLUSIONS:The prevalence of incidentally identified CPVT-associated variants is ≈9% among WES tests. Variants of undetermined significances in CPVT-associated genes in WES genetic testing, in the absence of clinical suspicion for CPVT, are unlikely to represent markers of CPVT pathogenicity.
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    Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
    (Nature, 2011-11-23) McLellan, JS; Pancera, M; Carrico, C; Gorman, J; Julien, JP; Khayat, R; Louder, R; Pejchal, R; Sastry, M; Dai, K; O'Dell, S; Patel, N; Shahzad ul Hussan, S; Yang, Y; Zhang, B; Zhou, T; Zhu, J; Boyington, JC; Chuang, GY; Diwanji, D; Georgiev, I; Kwon, YD; Lee, D; Louder, MK; Moquin, S; Schmidt, SD; Yang, ZY; Bonsignori, M; Crump, JA; Kapiga, SH; Sam, NE; Haynes, BF; Burton, DR; Koff, WC; Walker, LM; Phogat, S; Wyatt, R; Orwenyo, J; Wang, LX; Arthos, J; Bewley, CA; Mascola, JR; Nabel, GJ; Schief, WR; Ward, AB; Wilson, IA; Kwong, PD
    Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.
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    Ultraviolet-Visible Plasmonic Properties of Gallium Nanoparticles Investigated by Variable-Angle Spectroscopic and Mueller Matrix Ellipsometry
    (ACS Photonics, 2014-07-16) Yang, Y; Akozbek, N; Kim, TH; Sanz, JM; Moreno, F; Losurdo, M; Brown, AS; Everitt, HO
    © 2014 American Chemical Society.Self-assembled, irregular ensembles of hemispherical Ga nanoparticles (NPs) were deposited on sapphire by molecular beam epitaxy. These samples, whose constituent unimodal or bimodal distribution of NP sizes was controlled by deposition time, exhibited localized surface plasmon resonances tunable from the ultraviolet to the visible (UV/vis) spectral range. The optical response of each sample was characterized using a variable-angle spectroscopic ellipsometer, and the dielectric response of the ensemble of NPs on each sample was parametrized using Lorentz oscillators. From this, a relationship was found between NP size and the deduced Lorentzian parameters (resonant frequency, damping, oscillator strength) for most unimodal and bimodal samples at most frequencies and angles of incidence. However, for samples with a bimodal size distribution, Mueller matrix ellipsometry revealed nonspecular scattering at particular frequencies and angles, suggesting a resonant interparticle coupling effect consistent with recently observed strong local field enhancements in the ultraviolet. (Graph presented).