Comparison of methods for library construction and short read annotation of shellfish viral metagenomes

Hong‑Ying Wei,Sheng Huang,Jiang‑Yong Wang,Fang Gao,Jing‑Zhe Jiang 한국유전학회 2018 Genes & Genomics Vol.40 No.3

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI’s NR and Uniprot’s Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

빔 구조물의 손상평가를 위한 임피던스 기술의 응용

홍동표,홍용,왕고평,김병진,김영문,이재정,김재열 한국공작기계학회 2006 한국공작기계학회 추계학술대회논문집 Vol.2006 No.-

This paper presents a primary study for a new method of enhancing measurement using impedance analysis method, which is widely used for structure health monitoring. Many of skyscrapers, bridges, tunnels, which have been built up several years, and nearly reached their operating life due to aging crack, material deterioration, and so on. therefore, the health monitoring technique has obtained considerable attention. The goal of this research is to show basic information to evaluate structural health condition using piezoelectric sensors. The piezoelectric materials have various merits. It is easy to shape various forms and can be embedded on the materials more conveniently. Moreover, the excitation frequency can be changed and the piezoelectric sensors cost less. All these features make the piezoelectric-based system applicable to structural healthy monitoring. This work presents a study for the development of a practical and quantitative technique for assessment of the structural health condition by piezoelectric impedance-based technique associated with longitudinal wave propagation. To estimate the damage condition numerically, we suggest the evaluation method Cov (Covariance) and CC (Correlation Coefficient) in this paper.

Steel Bridge Construction of Hong Kong–Zhuhai–Macao Bridge

Wen-bo Gao,Quan-ke Su,Jin-wen Zhang,Hong-bing Xie,Feng Wen,Fang Li,Ji-zhu Liu 한국강구조학회 2020 International Journal of Steel Structures Vol.20 No.5

The 55-km-long Hong Kong–Zhuhai–Macao Bridge (HZMB) is the world’s longest sea-crossing bridge, connecting Hong Kong with Zhuhai and Macao at the mouth of the Pearl River Estuary in China, comprising 22.9-km-long steel bridges. HZMB is the leading steel bridge in China, with top-level manufacturing and installation technology. This paper outlines the steel bridge construction experiences of HZMB to provide comparisons for the construction of other long sea-crossing steel bridges at home or abroad. The main considerations of construction constraints, scheme selection, structural and aesthetic design of HZMB are presented, and the following points related to new strategies in the steel bridge construction of HZMB are elaborated: (1) construction quality assurance, (2) automatic manufacturing technology, (3) large segment off shore installation, (4) eco-friendly paint (content limitation of volatile organic compounds) and new multifunctional inspection gantry, and (5) Guss Mastic Asphalt steel deck pavement system. The successful implementation of those strategies shows that the steel bridge construction of HZMB promotes improvement in the overall construction and management level of the Chinese bridge industry. The advanced experience of HZMB has opened up broad prospects for the design and construction of off shore bridge engineering in China.

Langmuir Aggregation of Fluorescein Isothiocyanate (FITC) on Cetyl Trimethylammonium Bromide (CTAB) and Application to Determination of Anionic Detergent in Sewage

Gao, Hong-Wen,Zhou, De-Yan Korean Chemical Society 2002 Bulletin of the Korean Chemical Society Vol.23 No.1

The microphase adsorption - spectral correction (MPASC) technique was described and applied to study the interaction of fluorescein isothiocyanate (FITC) with cetyl trimethylammonium bromide (CTAB). The synergism mechanism of micelle was analyzed and discussed. The aggregation of FITC on CTAB obeys the Langmuir monolayer adsorption. Results showed that the monomer and micellar aggregate is $FITC-CTAB_3$ and $(FITC-CTAB_3)_{29}$, respectively at pH 9.62. The adsorption constant of the CTAB-FITC aggregate was determined to be $2.10{\times}10^5$. Interestingly, it was observed for the addition of an anionic surfactant to desorb FITC from its CTAB aggregate and this has been applied to the quantitative determination of trace amounts of anionic detergent (AD) in sewage.

Spectrophotometric Investigation of Cu and Fe Complexes with o-Chlorophenylfluorone and Selective Competition Coordination Determination of Iron Traces

Gao, Hong-Wen Korean Chemical Society 2002 Bulletin of the Korean Chemical Society Vol.23 No.7

The two reactions between iron ion (Fe3+ ) and o-chlorophenylfluorone (o-CPF) and copper ion (Cu2+ ) and o-CPF are sensitive at pH 6 in the presence of Triton X-100. We have determined the formation constants of the complexes by the spectral correction technique. Because of the poor selectivity of o-CPF to metals, the competition coordination of only the iron ion from the Cu-o-CPF complex was found and applied to the selective detection of iron traces by the Selective Competition Coordination Determination (SCCD) approach.The analysis of several samples shows that the relative standard deviations are less than 5.0% and the recovery of iron ions between 94.5% and 106%.

Regularity for Very Weak Solutions of A-Harmonic Equation with Weight

Gao, Hong-Ya,Zhang, Yu,Chu, Yu-Ming Department of Mathematics 2009 Kyungpook mathematical journal Vol.49 No.2

This paper deals with very weak solutions of the A-harmonic equation $divA(x,{\nabla}u)$ = 0 (*) with the operator $A:{\Omega}{\times}R^n{\rightarrow}R^n$ satisfies some coercivity and controllable growth conditions with Muckenhoupt weight. By using the Hodge decomposition with weight, a regularity property is proved: There exists an integrable exponent $r_1=r_1({\lambda},n,p)$ < p, such that every very weak solution $u{\in}W_{loc}^{1,r}({\Omega},{\omega})$ with $r_1$ < r < p belongs to $W_{loc}^{1,p}({\Omega},{\omega})$. That is, u is a weak solution to (*) in the usual sense.

Evaluating the electric property of different crystal faces and enhancing the Raman scattering of Cu2O microcrystal by depositing Ag on the surface

Hong Gao,Junying Zhang,Min Li,Kejia Liu,Dong Guo,Yue Zhang 한국물리학회 2013 Current Applied Physics Vol.13 No.5

The surface electric property of Cu2O microcrystal affects the interaction of facets with substance in the aqueous solution, and hence plays a key role in determining the photocatalytic activity. In this paper, the capability of Cu2O microcrystals with exclusive {111}, {110} or both lattice surfaces in reducing Agþ to Ag0were investigated. Ag particles selectively deposited on {111} surfaces of Cu2O, while not on {110} surfaces. The different behaviors of the two surfaces are mainly attributed to their different electric properties:negatively-charged {111} surfaces absorb Agþ ions while positively-charged {110} surfaces repel them. Raman scattering of Cu2O {111} surfaces was enhanced by the photo-deposition of Ag particles.

Name and Maintain Topological Faces in Rotating and Scanning Features

Gao Xue-Yao,Li Jia-Qi,Guo Hao,Gao Yun-Feng,Liu Yu-Hong 보안공학연구지원센터 2016 International Journal of Grid and Distributed Comp Vol.9 No.3

Features created in rotating and scanning operations are very complex. Naming and identifying their topological faces is an important problem in CAD fields. In this paper, a new method of coding topological faces in rotating and scanning features is proposed. Firstly, contour segments are numbered. Secondly, an angle between contour segment and rotating axis is computed. Thirdly, all topological faces are named based on contour segments’ numbers, rotating axis and other information. When a face splits and several subfaces merge, a method of processing their codes is given. The proposed method is applied to HUST-CAID feature modeling system. Experimental results show that it can name and identify topological faces effectively in operations.

Improvement of Tracking Performance Using Prediction-Based Algorithms for a Maneuvering Target

Hong Ping Gao,유창호,최재원,서태일 제어·로봇·시스템학회 2011 International Journal of Control, Automation, and Vol.9 No.3

This paper presents a study involving prediction of a complicated maneuvering target, with the aim of improving the tracking performance of a fire control system (FCS). In this study, we predict the position of a complicated maneuvering target 5 s in advance using the information up to the current time. Because of the large error caused by the complicated maneuvers and the long prediction time in-terval, the mechanical system of the fire control system will take a heavy load. In order to cope with this problem, several approaches to decreasing the prediction error have been proposed including the prediction algorithms based on the multiple model(MM) filter, interacting multiple model (IMM) filter, and variable dimension with input estimation (VDIE) filter. Finally, comparative simulation results are presented to verify the performance of the filters.

Constituents from Zhuyeqing Liquor with hepatoprotective effect on alcohol-induced HepaG 2 toxicity

Hong-Ying Gao,Guo-Yu Li,Hang-Yu Wang,Jian Huang,Xiao-Wei Du,Ying Han,Li-Fei Wang,Jin-Hui Wang 대한약학회 2015 Archives of Pharmacal Research Vol.38 No.5

An unprecedented new skeleton compound (1R,10R, 11S)-10,11-dimethyl-4-formyl-2,9-dioxa-bicyclo [5.4.0]undeca-4,6-dien-3-one (1), monoterpenoids and monoterpeneglycoside picrocrocinic ester (2), epijasminoside B (3) and 60 -O-(3-methoxyl-4-hydroxyl-coumaroyl)-epijasminoside B (4),along with 26 known compounds, were obtained fromZhuyeqing Liquor. These compounds were identified mainlyby analyzing their NMR, HR-ESI–MS and CD data. The isolatedcompounds were screened against alcohol induced HepaG2 toxicity for hepatoprotective assay. Compounds 10, 19,21 and 26 displayed the highest potency against alcoholinduced HepaG 2 toxicity with the cell viability ratio 41.21,56.91, 67.69 and 70.32 % respectively.