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Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling

  • Lim, Jong-Sung;Choi, Beom-Soon;Lee, Jeong-Soo;Shin, Chan-Seok;Yang, Tae-Jin;Rhee, Jae-Sung;Lee, Jae-Seong;Choi, Ik-Young
    • Genomics & Informatics
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    • v.10 no.1
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    • pp.1-8
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    • 2012
  • Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

Metabolic Syndrome and Bone Mineral Density among Elderly Korean Women (여성 노인의 대사증후군과 골밀도의 관련성 조사연구)

  • Lee, Hae-Young;ChoiKwon, Smi
    • Journal of Korean Biological Nursing Science
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    • v.13 no.2
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    • pp.134-141
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    • 2011
  • Purpose: Although the risk factors of metabolic syndrome have been extensively studied, the association between osteoporosis and metabolic syndrome has remained unclear in Korean elderly women. Yet to be determined are the effect of risk factors of metabolic syndrome on osteoporosis in these subjects. The purpose of this study was to investigate how the risk factors of metabolic syndrome affect the bone mineral density in Korean elderly women. Methods: One hundred twenty one elderly women from a community center in Seoul elderly welfare center participated in this study. A structured questionnare was used to assess their demographics and lifestyles. Participants' anthropometric information was also obtained by measuring heights, weights, and waist circumferences. The blood samples were also obtained to measure blood glucoses and blood lipids. Bone mineral density was measured with the use of ultra sono. Results: The prevalence of metabolic syndrome in our subjects was 58%. In multivariate regression analysis, fasting plasma glucose level (p=.036) and triglycerides (p=.006) were significant factors predicting bone mineral density after adjusting age and other factors of metabolic syndrome. In age-adjusted analysis, women with metabolic syndrome had significantly higher bone mineral density as compared to those without metabolic syndrome (p=.026). Conclusion: Bone mineral density among elderly Korean women is associated with the level of blood glucose and triglycerides.

Color Difference Characterization on Nickel Silicides (니켈실리사이드의 색차분석)

  • Jung Youngsoon;Song Ohsung;Kim Dugjoong;Choi Yongyun;Kim Chongjun
    • Journal of Surface Science and Engineering
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    • v.38 no.1
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    • pp.44-48
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    • 2005
  • We prepared nickel silicide layers from p-Si(l00)/SiO₂(2000 Å)/poly-Si(700 Å)/Ni(400 Å) structures, feasible for gates in MOSFETs, by annealing them from 500℃~900℃ for 30 minutes. We measured the color coordination in visible range, cross sectional micro-structure, and surface topology with annealing temperature by an UV-VIS-IR spectrometer, field effect scanning electron microscope(FE-SEM), and scanning probe micro-scope respectively. We conclude that we may identify the nickel silicide by color difference of 0.90 and predict the silicide process reliability by color coordination measurement. The nickel silicide layers showed similar thickness while the columnar grains size and surface roughness increased as annealing temperature increased.

LEE SANG GAK TELESCOPE (LSGT): A REMOTELY OPERATED ROBOTIC TELESCOPE FOR EDUCATION AND RESEARCH AT SEOUL NATIONAL UNIVERSITY

  • IM, MYUNGSHIN;CHOI, CHANGSU;KIM, KIHYUN
    • Journal of The Korean Astronomical Society
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    • v.48 no.4
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    • pp.207-212
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    • 2015
  • We introduce the Lee Sang Gak Telescope (LSGT), a remotely operated, robotic 0.43-meter telescope. The telescope was installed at the Siding Spring Observatory, Australia, in 2014 October, to secure regular and exclusive access to the dark sky and excellent atmospheric conditions in the southern hemisphere from the Seoul National University (SNU) campus. Here, we describe the LSGT system and its performance, present example images from early observations, and discuss a future plan to upgrade the system. The use of the telescope includes (i) long-term monitoring observations of nearby galaxies, active galactic nuclei, and supernovae; (ii) rapid follow-up observations of transients such as gamma-ray bursts and gravitational wave sources; and (iii) observations for educational activities at SNU. Based on observations performed so far, we find that the telescope is capable of providing images to a depth of R = 21:5 mag (point source detection) at 5-σ with 15 min total integration time under good observing conditions.

A Study of Non-destructive Indentation and Small Punch Tests for Monitoring Materials Reliability (소재의 안전전단을 위한 비파괴 압입 및 소형펀치 시험법 연구)

  • Ok Myoung-Ryul;Ju Jang-Bog;Lee Jeong-Hwan;Ahn Jeong-Hoon;Nahm Seung Hoon;Lee Hae-Moo;Kwon Dongil
    • 한국가스학회:학술대회논문집
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    • 1997.09a
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    • pp.78-85
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    • 1997
  • Indentation and small punch tests are very powerful methods to monitor the materials reliability since they are very simple, easy and almost non-destructive. First, recently-developed continuous indentation test can provide the more material properties such as hardness, elastic modulus, yield strength, work-hardening exponent, etc., than the conventional hardness test. In our study, the true stress-strain curve was derived from the indentation load-depth curve for spherical indentation. In detail, the strain was able to be obtained from plastic depth/contact radius ratio, and the flow stress was from mean contact pressure through the analysis of elastic-plastic indentation stress field. Secondly, the small punch test was studied to evaluate the fracture toughness and defomation properties such as elastic modulus and yield strength. Like the indentation test, this test can be applied without severe damage of the target structure.

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Synthesis of Novel Quinacridone Dyes and Their Photovoltaic Performances in Organic Dye-sensitized Solar Cells

  • SaKong, Chun;Kim, Se-Hun;Yuk, Sim-Bum;Kim, Jeong-Yun;Park, Se-Woong;Ko, Min-Jae;Kim, Jae-Pil
    • Bulletin of the Korean Chemical Society
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    • v.32 no.8
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    • pp.2553-2559
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    • 2011
  • Two novel quinacridone (QNC) dyes with thiophene or benzene-conjugated bridge and cyanoacrylic acid acceptor were first designed and synthesized for use in dye-sensitized solar cells (DSSCs). The absorption spectra, electrochemical and photovoltaic properties of these dyes were investigated. Under simulated AM 1.5G irradiation conditions, the solar cell based on the quinacridone dye containing thiophene as a bridge unit had a short-circuit photocurrent density of 8.51 $mA{\cdot}cm^{-2}$, an open-circuit voltage of 643.6 mV, and a fill factor of 0.70, corresponding to an overall conversion efficiency of 3.86%.

High Impedance Fault Detection on 22.9kV Multigrounded Distribution System (22.9kV 이중접지 배전선로 고저항 지락 검출)

  • Park, Young-Moon;Lee, Ki-Won;Lim, Ju-Il;Yoon, Man-Chul;Yoo, Myeong-Ho
    • Proceedings of the KIEE Conference
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    • 1987.11a
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    • pp.463-468
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    • 1987
  • In this paper, a high impedance fault detection on 22.9kV multigrounded distribution system that has been very difficult by any existing conventional protective relaying systems is studied. Because the fault current is very low, it cannot be distinguished from neutral current caused by load unvalanced on multigrounded distribution system. We developed the new and best algorithms of high impedance ground fault detection. This algorithms are 'the even order power method, even order ratio method', 'and even order ratio varience method'. Using this algorithms, a detection device for high impedance faults is constructed and tested in the laboratory. And continually, it is installed and has been tested in KEPCO substations.

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Dynamic Mechanical Behavior of Ultra-High Molecular Weight Polyethylene Irradiated with Gamma Rays

  • Lee, Choon-Soo;Jho, Jae-Young;Park, Kuiwon;Hwang, Tae-Won
    • Macromolecular Research
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    • v.12 no.1
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    • pp.141-143
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    • 2004
  • We have investigated the dynamic mechanical behavior of ultra-high molecular weight polyethylene (UHMWPE) irradiated with varying doses of gamma rays. A relaxation peak in the loss factor curve, which has not been reported previously in the literature, is observed at a temperature above the crystal melting temperature. The peak is unique to UHMWPE and appears to be related to the high degree of entanglement. Because the temperature and intensity of the peak are reduced by irradiation-induced chain scission and crosslinking, respectively, we believe that the peak is associated with disentanglement relaxation. The behavior of the storage modulus in the melt state agrees with the classical theory of rubber elasticity.

The Optimal Distribution Feeder Reconfiguration Using Knowledge Base (지식베이스를 이용한 배전계통의 최적재구성)

  • Cho, S.H.;Choi, B.Y.;Kim, S.H.;Lee, J.K.
    • Proceedings of the KIEE Conference
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    • 1993.07a
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    • pp.99-101
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    • 1993
  • This paper presents an approach to feeder reconfiguration in order to achieve an efficient operation of distribution systems utilizing knowledge base. The optimal feeder reconfiguration in this study eliminates various abnormal states which will create feeder overloads and feeder constraint problems. and will also accomplish minimum power loss of the distribution systems under normal operating condition by means of branch exchanges to change the status of sectionalizing switches with experiences of the experts. For an effective implementation of feeder reconfiguration, a best-first tree searching strategy based on heuristics is employed to evaluate the various alternatives of load transfer. The heuristic exchange of branches results in reduction of the search space as a means of implementing the best-first searching strategy.

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Infiltrative Lipoma Invading the Anal Sac in a Dog: A Rare Case Report

  • Junyoung Kim;Dai Jung Chung;Jihye Choi;Junghee Yoon
    • Journal of Veterinary Clinics
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    • v.40 no.2
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    • pp.147-151
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    • 2023
  • A 6-year-old female Chihuahua was presented to the Animal Medical Center for surgical resection of a perineal mass that had recently increased in size. Ultrasonography revealed a large, homogeneous fatty mass with irregular margins between the surrounding muscle layers due to infiltrating fatty tissues. Cytological findings from fine-needle aspirates revealed numerous sheets and clusters of adipocytes, which was consistent with the fatty mass. Based on ultrasonographic and cytological findings, an infiltrative lipoma was suspected. During the surgery, the perineal mass was found to be non-encapsulated, irregularly marginated, and extensively distributed into the surrounding muscles. The mass extended inside the pelvic cavity and left anal sac. The perineal mass was surgically removed and submitted for histopathologic examination. Histopathology confirmed that the mass was an infiltrative lipoma invading into the anal sac and surrounding muscles. The present report was an unusual presentation of infiltrative lipoma that invaded the anal sac in the perineum.