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.

중·한 교육 현황 및 개혁 동향의 비교

황현옥,정홍섭 新羅大學校 2003 論文集 Vol.52 No.-

There are a lot of similarities between China and Korea in their cultural and historical background. Both countries have adopted the 6:3:3:4 pattern for their elementary school, junior high school, senior high school and college education. Their difference lies in the fact that most schools in China are public schools but the schools in Korea are both private and public ones. Korea is superior to China in teachers' quality, teaching facilities and ratio of high school students who can enter colleges and universities. But Korea is not as good as China in the quality of higher education owing to its over-reliance on private school education and students' tuition fees. In recent years both China and Korea have made great efforts in reformation of education. For example, they have given more financial support to education, changed their college entrance examination from purely written examination to comprehensive evaluation, and decentralized their control over education. But China falls behind Korea in financial support, reform of teaching methodology and introduction of market economy into education. At present, China is trying to put the idea of market economy into the development of private schools and the decision on the amount of tuition fees. Korean government, on the other hand, is giving more support to its private schools. This paper holds that China should learn from Korea in private school management, teachers' training and occupational education whereas Korea should learn from China in improving the quality of tertiary education.

Differential Bidirectional Transceiver for On-chip Long Wires

Hong-Yi Huang,Ruei-Iun Pu 대한전자공학회 2006 ITC-CSCC :International Technical Conference on Ci Vol.2006 No.3

Petri Nets Based Coordination Component for CSCW Environment

Huang Hong Zhong,Zhou Feng,Zu Xu The Korean Society of Mechanical Engineers 2005 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.19 No.5

In view of the lack of efficient coordination of interdependent task in the collaborative design system, the mechanisms for temporal and resource coordination problems are established based on Petri Nets, respectively. Both of the mechanisms are encapsulated and implemented in the coordination component so as to increase the flexibility and acceptability of the system. We model the CSCW system based on Petri Nets for simulation, analysis and optimization. A case study on the overhead traveling crane is given to demonstrate and validate our theory.

CFD analysis of ventilation efficiency around an elevated highway using visitation frequency and purging flow rate

Huang, Hong,Kato, Shinsuke,Ooka, Ryozo,Jiang, Taifeng Techno-Press 2006 Wind and Structures, An International Journal (WAS Vol.9 No.4

The concentration of air pollution along roads is higher than the surrounding area because ventilation efficiency has decreased due to the high-density use of space along roads in recent years. In this study, ventilation efficiency around a heavily traffic road covered by an elevated highway and hemmed in along its side by buildings is evaluated using Visitation Frequency (VF, the frequency for pollutant to return to the objective domain) and Purging Flow Rate (PFR, the air flow rate for defining the local domain-averaged concentration). These are analyzed using Computational Fluid Dynamics (CFD) based on the standard $k-{\varepsilon}$ model. The VF and PFR characteristics of four objective domains are analyzed in terms of the changes in wind direction and arrangements of the fencing dividing up and down direction in the road center under the elevated highway. The resulting VFs are more than 1.0 for all cases, which means that pollutants return to the objective domain restricted by the elevated highway and side buildings. The influence of the arrangement of the buildings around the objective domain and the structure in the domain on the VF is substantial. In cases where there are no obstacles under the elevated highway, the local air exchange rate in the domain tends to be improved. Using these indices, the urban ventilation efficiencies between different urban areas can be compared easily.

A GENERALIZATION OF OSTROWSKI-TYPE INEQUALITY

Hong, Huang The Kangwon-Kyungki Mathematical Society 2018 한국수학논문집 Vol.26 No.4

A generalization of Ostrowski-type inequality involving functions of two independent variables is given.

Prolactin Inhibits BCL6 Expression in Breast Cancer Cells through a MicroRNA-339-5p-Dependent Pathway

Hong Yan,Min Zhao,Shan Huang,Ping Chen,Wen-yong Wu,Jin Huang,Zheng-sheng Wu,Qiang Wu 한국유방암학회 2016 Journal of breast cancer Vol.19 No.1

Purpose: Prolactin (PRL) plays a critical role in breast cancer progression by activating its cognate receptor and promotes the growth and differentiation of breast cancer cells. Studies have shown that B-cell lymphoma 6 (BCL6) is the target gene of microRNA- 339-5p (miR-339-5p) and that BCL6 expression contributes to breast cancer progression. Herein, we identified PRL as a potent suppressor of BCL6 expression in human breast cancer cells. Methods: Western blotting and quantitative reverse transcription-polymerase chain reaction were used to investigate molecular mechanisms underlying miR-339-5p expression and BCL6 manipulation in MCF-7, T47D, and SKBR3 breast cancer cells. Phenotypic changes in these breast cancer cell lines were assessed by performing cell viability (MTT), colony formation, migration, and invasion assays. Results: PRL suppressed BCL6 protein and mRNA expression and upregulated miR-339-5p expression in MCF-7 and T47D breast cancer cells. Selective downregulation of miR-339-5p expression significantly reversed PRL-induced suppression of BCL6 mRNA and protein expression. Exogenous PRL stimulation significantly decreased the proliferation, colony formation, migration, and invasion of breast cancer cells, and suppression of miR-339-5p expression reversed these processes in vitro. Conclusion: These results indicated that PRL inhibited BCL6 expression and regulated breast cancer progression through a miR-339-5p-dependent pathway.

Robust Reliability Analysis of Vibration Components

Hong-Zhong Huang,Yong-Hua Li,Ming J. Zuo 한국신뢰성학회 2004 International Journal of Reliability and Applicati Vol.5 No.2

Posbist Reliability Analysis of Typical Systems

Huang, Hong-Zhong,Tong, X.,He, L.P. The Korean Reliability Society 2007 International Journal of Reliability and Applicati Vol.8 No.2

Posbist reliability of typical systems is preliminarily discussed in Cai (1991). In this paper, we focus on the posbist reliability analysis of some typical systems in depth. First, the lifetime of the system is dealt as a fuzzy variable defined on the possibility space (U, ${\phi}$, $P_{oss}$) and the universe of discourse is expanded from (0, $+{\infty}$) to ($-{\infty},\;+{\infty}$). Then, a concrete possibility distribution function of the fuzzy variable is given, i.e., a Gaussian fuzzy variable. Finally, posbist reliability of typical systems (series, parallel, series-parallel, parallel-series, cold redundant system) is deduced. The expansion makes the proofs of some theorems straightforward and allows us to easily obtain the posbist reliability of typical systems. To illustrate the method a numerical example is given.

Concept Optimization for Mechanical Product Using Genetic Algorithm

Huang Hong Zhong,Bo Rui Feng,Fan Xiang Feng The Korean Society of Mechanical Engineers 2005 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.19 No.5

Conceptual design is the first step in the overall process of product design. Its intrinsic uncertainty, imprecision, and lack of information lead to the fact that current conceptual design activities in engineering have not been computerized and very few CAD systems are available to support conceptual design. In most of the current intelligent design systems, approach of principle synthesis, such as morphology matrix, bond graphic, or design catalogues, is usually adopted to deal with the concept generation, in which optional concepts are generally combined and enumerated through function analysis. However, as a large number of concepts are generated, it is difficult to evaluate and optimize these design candidates using regular algorithm. It is necessary to develop a new approach or a tool to solve the concept generation. Generally speaking, concept generation is a problem of concept synthesis. In substance, this process of developing design candidate is a combinatorial optimization process, viz., the process of concept generation can be regarded as a solution for a state-place composed of multi-concepts. In this paper, genetic algorithm is utilized as a feasible tool to solve the problem of combinatorial optimization in concept generation, in which the encoding method of morphology matrix based on function analysis is applied, and a sequence of optimal concepts are generated through the search and iterative process which is controlled by genetic operators, including selection, crossover, mutation, and reproduction in GA. Several crucial problems on GA are discussed in this paper, such as the calculation of fitness value and the criteria for heredity termination, which have a heavy effect on selection of better concepts. The feasibility and intellectualization of the proposed approach are demonstrated with an engineering case. In this work concept generation is implemented using GA, which can facilitate not only generating several better concepts, but also selecting the best concept. Thus optimal concepts can be conveniently developed and design efficiency can be greatly improved.