Progressive effects of single-nucleotide polymorphisms on 16 Phenotypic Traits based on Longitudinal Data

Donghe Li,Hahn Kang,Sanghun Lee,Sungho Won 한국유전학회 2020 Genes & Genomics Vol.42 No.4

Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ( h2snp ) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ( h2snp = 0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR , P = 3.2 × 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes

Donghe Li,원성호 한국유전체학회 2016 Genomics & informatics Vol.14 No.4

Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named “BOolean Operation-based Screening and Testing” (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.

Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes

Li, Donghe,Wo, Sungho Korea Genome Organization 2016 Genomics & informatics Vol.14 No.4

Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named "BOolean Operation-based Screening and Testing" (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.

Cytoprotective Effect of Taurine against Hydrogen Peroxide- Induced Oxidative Stress in UMR-106 Cells through the Wnt/β- Catenin Signaling Pathway

( Jing Lou ),( Donghe Han ),( Huihui Yu ),( Guang Yu ),( Meihua Jin ),( Sung-jin Kim ) 한국응용약물학회 2018 Biomolecules & Therapeutics(구 응용약물학회지) Vol.26 No.6

Osteoporosis development is closely associated with oxidative stress and reactive oxygen species (ROS). Taurine has potential antioxidant effects, but its role in osteoblasts is not clearly understood. The aim of this study was to determine the protective effects and mechanisms of actions of taurine on hydrogen peroxide (H₂O₂)-induced oxidative stress in osteoblast cells. UMR-106 cells were treated with taurine prior to H₂O₂ exposure. After treatment, cell viability, apoptosis, intracellular ROS production, malondialdehyde content, and alkaline phosphate (ALP) activity were measured. We also investigated the protein levels of β-catenin, ERK, CHOP and NF-E2-related factor 2 (Nrf2) along with the mRNA levels of Nrf2 downstream antioxidants. The results showed that pretreatment of taurine could reverse the inhibition of cell viability and suppress the induced apoptosis in a dose-dependent manner: taurine significantly reduced H₂O₂-induced oxidative damage and expression of CHOP, while it induced protein expression of Nrf2 and β-catenin and activated ERK phosphorylation. DKK1, a Wnt/β-catenin signaling inhibitor, significantly suppressed the taurine-induced Nrf2 signaling pathway and increased CHOP. Activation of ERK signaling mediated by taurine in the presence of H₂O₂ was significantly inhibited by DKK1. These data demonstrated that taurine protects osteoblast cells against oxidative damage via Wnt/β-catenin-mediated activation of the ERK signaling pathway.

Cytoprotective Effect of Taurine against Hydrogen Peroxide-Induced Oxidative Stress in UMR-106 Cells through the Wnt/β-Catenin Signaling Pathway

Lou, Jing,Han, Donghe,Yu, Huihui,Yu, Guang,Jin, Meihua,Kim, Sung-Jin The Korean Society of Applied Pharmacology 2018 Biomolecules & Therapeutics(구 응용약물학회지) Vol.26 No.6

Osteoporosis development is closely associated with oxidative stress and reactive oxygen species (ROS). Taurine has potential antioxidant effects, but its role in osteoblasts is not clearly understood. The aim of this study was to determine the protective effects and mechanisms of actions of taurine on hydrogen peroxide ($H_2O_2$)-induced oxidative stress in osteoblast cells. UMR-106 cells were treated with taurine prior to $H_2O_2$ exposure. After treatment, cell viability, apoptosis, intracellular ROS production, malondialdehyde content, and alkaline phosphate (ALP) activity were measured. We also investigated the protein levels of ${\beta}-catenin$, ERK, CHOP and NF-E2-related factor 2 (Nrf2) along with the mRNA levels of Nrf2 downstream antioxidants. The results showed that pretreatment of taurine could reverse the inhibition of cell viability and suppress the induced apoptosis in a dose-dependent manner: taurine significantly reduced $H_2O_2$-induced oxidative damage and expression of CHOP, while it induced protein expression of Nrf2 and ${\beta}-catenin$ and activated ERK phosphorylation. DKK1, a Wnt/${\beta}-catenin$ signaling inhibitor, significantly suppressed the taurine-induced Nrf2 signaling pathway and increased CHOP. Activation of ERK signaling mediated by taurine in the presence of $H_2O_2$ was significantly inhibited by DKK1. These data demonstrated that taurine protects osteoblast cells against oxidative damage via Wnt/${\beta}-catenin$-mediated activation of the ERK signaling pathway.

Robot Manipulator Visual Servoing via Kalman Filter- Optimized Extreme Learning Machine and Fuzzy Logic

Zhiyu Zhou,Yanjun Hu,Jiangfei Ji,Yaming Wang,Zefei Zhu,Donghe Yang,Ji Chen 한국인터넷정보학회 2022 KSII Transactions on Internet and Information Syst Vol.16 No.8

Visual servoing (VS) based on the Kalman filter (KF) algorithm, as in the case of KF-based image-based visual servoing (IBVS) systems, suffers from three problems in uncalibrated environments: the perturbation noises of the robot system, error of noise statistics, and slow convergence. To solve these three problems, we use an IBVS based on KF, African vultures optimization algorithm enhanced extreme learning machine (AVOA-ELM), and fuzzy logic (FL) in this paper. Firstly, KF online estimation of the Jacobian matrix. We propose an AVOA-ELM error compensation model to compensate for the sub-optimal estimation of the KF to solve the problems of disturbance noises and noise statistics error. Next, an FL controller is designed for gain adaptation. This approach addresses the problem of the slow convergence of the IBVS system with the KF. Then, we propose a visual servoing scheme combining FL and KF-AVOA-ELM (FL-KF-AVOA-ELM). Finally, we verify the algorithm on the 6-DOF robotic manipulator PUMA 560. Compared with the existing methods, our algorithm can solve the three problems mentioned above without camera parameters, robot kinematics model, and target depth information. We also compared the proposed method with other KF-based IBVS methods under different disturbance noise environments. And the proposed method achieves the best results under the three evaluation metrics.

Multimodal Fusion and Data Augmentation for 3D Semantic Segmentation

Dong He,Furqan Abid,Jong-Hwan Kim 제어로봇시스템학회 2022 제어로봇시스템학회 국제학술대회 논문집 Vol.2022 No.11

Since modern autonomous driving (AD) platforms offer a variety of sensors, it is intuitive to leverage complementary data from multimodal sensors to produce reliable 3D semantic segmentation. However, due to the information loss and the sub-optimized fusion in multimodal fusion methods, LiDAR-only methods currently occupy the top positions in the leaderboard of datasets. In this paper, we focus on two aspects to improve the LiDAR-camera fusion semantic segmentation performance, namely data augmentation and fusion strategy. First, we propose an novel data augmentation by refining point-image patches. Second, we design an attention fusion block for the dual-branch segmentation network by considering the modality gap between LiDAR and RGB camera. Experiments on nuScences indicate that our proposed method outperforms the baseline methods on key classes.

A Comparative Study of Request Strategies between Native and Non-Native Speakers of English

Donghee Son(Donghee Son) 한국사회언어학회 2023 사회언어학 Vol.31 No.1

This paper aims to investigate Korean EFL learners’ pragmatic performance in request speech acts in comparison with native speakers of English. Written discourse completion tasks (WDCT) are used to examine how native and non-native speakers request in terms of request strategies, internal modifications, and external modifications. The results show that first, Korean learners had a higher frequency of inappropriate strategies than native speakers. Second, they lacked the quantity and variety of internal modifications both lexically and syntactically. However, regarding external modifications, their use of supportive moves was similar to that of natives in frequency and order. In addition, this study identified newly emergent supportive moves that are Korean-specific and detrimental to communication goals. The findings shed light on pragmatic instruction in the Korean EFL situation by providing research-informed data. Several pedagogical implications are suggested for application in teaching.

Evaluation of Shielding Thickness of Transport Cask for Transporting Co-60 Source Rods Produced Using PWRs

Donghee Lee,Yongdeog Kim,Kiyoung Kim 한국방사성폐기물학회 2022 한국방사성폐기물학회 학술논문요약집 Vol.20 No.1

The Co-60 is a radioactive material widely used in domestic and foreign medical, industrial, health and research fields. Currently, world market for the Co-60 is about 80 MCi/yr and is expected to grow to 150 MCi/yr by 2025. For the Co-60, Nordion of Canada occupies about 80% of the world market. In the case of Korea, a small amount of sources with relatively low radioactivity intensity are produced using research reactors, but most of the Co-60 is entirely dependent on imports. Accordingly, although the technical feasibility of the Co-60 production technology using the PHWR was evaluated, it was evaluated as a negative result on the additional construction of a hot cell, core management, safety analysis and economic feasibility. Canada, the main producer of the Co-60, is also conducting research on the Co-60 production technology using PWR with GE-Hitachi and Westinghouse as the number of PHWR is expected to decrease. In Korea, it is necessary to preoccupy the Co-60 production technology and auxiliary technology using the PWR by utilizing excellent technology, and active research is being conducted to secure unique nuclear power technology that does not depend on foreign countries. Therefore, in this study, the thickness and weight of the radioactive shielding required for handling (transport) of Co-60 produced using the PWR were calculated.

Comparison of Results According to the Number of Measured Faces in Burnup Measurement of Spent Fuel

Donghee Lee 한국방사성폐기물학회 2023 한국방사성폐기물학회 학술논문요약집 Vol.21 No.1

The burnup of spent fuel is one of the important management items that must be managed before storing the fuel in dry storage facilities, as well as for transportation and disposal in the future. Currently, the burnup of spent fuel is managed by calculating the design burnup at the time of design and measuring the real burnup using in-reactor measurement devices. Furthermore, to ensure the reliability of such data, the burnup of spent fuel can be measured using burnup measurement equipment to compare and analyze the data. In fact, KHNP is measuring the burnup of spent fuel using the burnup measurement equipment (SICOM-NG-FA) developed by ENUSA in Spain. The burnup measurement equipment analyzes the axial burnup profile of spent fuel using gamma and neutron detectors. Burnup measurement is performed by moving the spent fuel up and down inside the measurement equipment and measuring the burnup of the fuel surface facing the gamma and neutron detectors. This paper aims to compare the results of measuring the burnup of spent fuel on two sides versus four sides using the burnup measurement equipment.