• Genomics & Informatics
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• v.13 no.3
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• pp.81-85
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• 2015

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

• Geophysics and Geophysical Exploration
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• v.14 no.1
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• pp.98-104
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• 2011

Numerical simulation in exploration geophysics provides important insights into subsurface wave propagation phenomena. Although elastic wave simulations take longer to compute than acoustic simulations, an elastic simulator can construct more realistic wavefields including shear components. Therefore, it is suitable for exploration of the responses of elastic bodies. To overcome the long duration of the calculations, we use a Graphic Processing Unit (GPU) to accelerate the elastic wave simulation. Because a GPU has many processors and a wide memory bandwidth, we can use it in a parallelised computing architecture. The GPU board used in this study is an NVIDIA Tesla C1060, which has 240 processors and a 102 GB/s memory bandwidth. Despite the availability of a parallel computing architecture (CUDA), developed by NVIDIA, we must optimise the usage of the different types of memory on the GPU device, and the sequence of calculations, to obtain a significant speedup of the computation. In this study, we simulate two- (2D) and threedimensional (3D) elastic wave propagation using the Finite-Difference Time-Domain (FDTD) method on GPUs. In the wave propagation simulation, we adopt the staggered-grid method, which is one of the conventional FD schemes, since this method can achieve sufficient accuracy for use in numerical modelling in geophysics. Our simulator optimises the usage of memory on the GPU device to reduce data access times, and uses faster memory as much as possible. This is a key factor in GPU computing. By using one GPU device and optimising its memory usage, we improved the computation time by more than 14 times in the 2D simulation, and over six times in the 3D simulation, compared with one CPU. Furthermore, by using three GPUs, we succeeded in accelerating the 3D simulation 10 times.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.11
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• pp.1529-1539
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• 2017

Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper${\times}$Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypomethylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion: In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

• Korean Journal of Occupational Health Nursing
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• v.13 no.1
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• pp.5-18
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• 2004

This study aims to investigate the use state of the health service computerization system in the occupational nursing field and the occupational nursers' satisfaction level, and provide basic data to promote the development of the health service computerization system for the nursing field. For this study, a questionnaire was provided to 118 occupational nurses who belong to Busan and Gyeongnam branches of KAOHN(Korean Association of Occupational Health Nurses) for 2 months (from Dec. 1, 2002 to Jan. 31, 2003). A tool of Choi Yong-Heui(2000) was used to investigate the satisfaction level of using the health service computerization system. The collected materials were analyzed in real number and percentage, average and standard deviation, t-test and ANOVA by using the SPSS WIN 10.0 program. This study is summarized as follows: 1. The average age was $31.99{\pm}5.58$ old in this study. The married were 54.2%. Participants who graduated from a junior college was 76.9%. The average service period was $4.48{\pm}4.68$ years. In service types, 79.7% of participants served in a health care center. The average service period was $3.22{\pm}2.89$ years. The service place which had 1000 workers or more was 35.6%. 2. Only 20.3% of participants in this study had a computer use education. 3. The field who participants used mostly was communication/internet, $3.29{\pm}.85$ hours in average. 4. 97.1% of occupational fields had computers and peripheral devices: 71.4% in pentium computer, 42.8% in the hard disk capacity of 20-29GB, 60.0% in 15 inch monitors, 86.2% in printers, 18.1% in digital cameras, 12.4% in LAN, and 9.5% in scanners. 80.1% of the occupational fields which were objects of study could use communication. 5. The occupational fields which did not introduced the health service computerization system were 62.8%. The main cause was attributable to entrepreneurs' insufficient recognition 66.6%. 51.5% of the entrepreneurs did not have an introduction plan. 37.2% of participating companies had the health service computerization system. 56.4% of them introduced it since the year 2000. 81.6% of the introduction motivation aimed to the efficiency of health service. The most issue upon introduction was insufficient understanding of a person in charge - 25.6%. The in-house development of the system covered 56.4%. 61.5% of the participants accepted their demands from the first stage of development. The direct effect of computerization showed the increase of 25.9% in the quickness and continuity of service treatment, and 25.9% in the serviceability of statistical treatment. 6. 22.0% of the participants had a computerization system use education. 69.2% of them had a in-house education. An educational method by nurses who used the computerization system was 76.9%. 92.3% of the education was helpful for practical duties. 7. An analysis of the computer use by health service fields showed that the medicine management in a health management field was 15.9%. the work environment measuring management in a work environment filed was 32.9%. the employment. general and special examination management in a heal th management field was 61.1 %. the various reports management in an administrative field was 64%. the health education data preparation management in an educational field was 58.0%. and the medicine and expendables management in an equipment management field was 51.6%. An analysis of the computerization system use showed that the various statistical data manage in a health management field was 13.0%. the work environment measuring management in a health management field was 34.8%. the personal disease management in a health management field was 51.9%. the heal education data preparation management in an educational field was 54.5%. and the equipment management of health care centers in an equipment management field was 52.6%. 8. 31.6% of the participants wanted that health service computerization system would include the generals of health services. 42.4% of the participants thought that first of all. the aggressive interest and investment of employers were required to build the health service computerization system. 9. The participants' satisfaction level on the computerization system use was $3.51{\pm}.57$ points. An analysis by each factor showed $3.62{\pm}.68$ points in a service change factor. $3.15{\pm}.63$ points in a computer program use factor, and $3.45{\pm}.71$ points in a continuous computerization use factor. 10. An analysis of the computerization system use by general characteristics of participants showed that the married (p = .022) had the satisfaction level higher than the unmarried. 11. The satisfaction level of the computerization system use by participants' computer use ability tended to be higher in proportion to the increase of computer use abilities in spreadsheet (F=2.606. p=.048). presentation (F=3.62. p=.012) and communication/internet(F=2.885. p=.0321. Based on the study results mentioned above. I will suggest as follows : The nationwide enlargement and repetition study is required for occupational nurses who serve in occupational nursing fields. The computerization system in a health service field is inferior comparing with other fields. The computerization system standard by business types and characteristics should be prepared through employers's aggressive participation and national support. Therefore various statistical data which occurs in occupational fields will be managed systematically and efficiently. A regular and systematic computer education plan for occupational nurses in charge of health services in the filed is urgently required to efficiently manage and improve the health of on-site workers.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.5
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• pp.842-847
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• 2012

This study was conducted to estimate the greenhouse gas emissions on local government levels from 1990 to 2010 using 2006 IPCC guideline methodology. To calculate greenhouse gas emissions based on the 16 local governments, emission factor and scaling factor were used with default value and activity data came from the food, agricultural, forestry and fisheries statistical yearbook of MIFAFF (Ministry for Food, Agriculture, Forestry, and Fisheries). The total emissions in crop sector gradually decreased from 1990 to 2010 due to a decline in agricultural land and nitrogen fertilizer usage. The annual average emission of greenhouse gas was the highest in Jeonnam (JN) with 1,698 Gg $CO_2$-eq and following Chungnam (CN), Gyungbuk (GB), Jeonbuk (JB) and Gyunggi (GG). The sum of top-six locals emission had occupied 83.4% of the total emission in cropland sector. The annual average emissions in 1990 by applying 2006 IPCC guideline were approximately 43% less than the national greenhouse gas inventory by 1996 IPCC guideline. Jeonnam (JN) province occupied also the highest results of greenhouse gas emission estimated by gas types (methane, nitrous oxide and carbon dioxide) and emission sources such as rice cultivation, agricultural soil, field burning of crop residue and urea fertilizer.

• Journal of Acupuncture Research
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• v.24 no.6
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• pp.1-14
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• 2007

Backgrounds : Rheumatoid Arthritis(RA) is known as the chronic inflammatory diseasethat induces persistent inflammation in the joint cavity. The destruction of cartilage occurs as the result of bones destoyed by pannus, several influential cytokines induced by the synovial capsulitis, varieties of proteinases, $O_2$ radicals, and the secondary degenerative changes of articular cartilage. The type 2 collagen-induced arthritis model is used in recent experimental research on rheumatoid arthritis. Cervus elaphus sibiricus (Nockyong) has the effect of relieving pain by nourishing the muscles, joints, and bones. It is also known to be efficacious in promoting and enhancing the immune system. The objective of this study was to investigate the effect of Cervus elaphus sibiricus herbal acupuncture to inhibit the generation of proinflammatory enzyme on type 2 collagen-induced arthritis. I investigated the inhibition of mRNA transcription of MIF(macrophage migration inhibitory factor), $TNF-{\alpha}$(Tumor necrosis $factor-{\alpha}$) and MMP-9 (matrix metalloproteinase-9) of Cervus elaphus sibiricus herbal acupuncture using an in vitro test. Also investigated was the inhibition of differentiation of Th 1 cells and activation of cytokines(MIF, $TNF-{\alpha}$, IL-6, MMP-9), which are known to cause initial RA ,and are also related to the morphology of the synovial membranes of the joint capsule, by an in vivo test, using CIA(collagen induced arthritis) model mice. Materials & methods : The laboratory animals used in this experiment were 4 week-old DBA female mice, weighing approximately 20 grams, and adjusted to the laboratory environment. The experiment was divided into the normal group(NOR)-no treated group, control group(CON)-CIA induced group, and sample group(SAM)-Cervus elaphus sibiricus herbal acupuncture treated group. RA was induced in the mice via injection of $50{\mu}{\ell}$ C II mixed CFA. The Cervus elaphus sibiricus herbal acupuncture solution was applied on $GB_{35}$(陽陵泉) for 26 days from the 3rd day of RA inducement. The concentration of the solution was determined via a MTT assay. To research the effect on the expression of MIF, $TNF-{\alpha}$ and MMP-9 mRNA, RT-PCR was performed on synovial membrane cells from the knee joint of CIA mice. C II induced RA knee joint's histo-chemical synovial membrane was observed using a specimen model via the Hematoxilin and Eosin dying technique. Results : The expression of mRNA of RA-related cytokines such as MIF, $TNF-{\alpha}$, and MMP-9 dosedependently decreased in the cell from the synovial membranes of the joint, which is treated with Cervus elaphus sibiricus herbal acupuncture solution. In mice treated with Cervus elaphus sibiricusherbal acupuncture, the damage of synovial membranes of the joint was lessened, and differentiation of Th 1 cells was suppressed. The activation of RA-related cytokines such as MIF was suppressed, and the generation of $TNF-{\alpha}$ and MMP-9 showed a statistically significant decreas. Conclusions : It is speculated that Cervus elaphus sibiricus herbal acupuncture has the therapeutic effect of palliating the damage of the tissue impaired by RA by inhibition of the initial RA progression and by regulating excessive differentiation of Th 1 cell as it suppresses the generation of RA-related cytokines during the highest stage of RA by acting on pro-inflammatory enzymes.

• Pediatric Infection and Vaccine
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• v.10 no.2
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• pp.208-214
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• 2003

Purpose : We performed a retrospective study on bacterial meningitis in children, pertaining to the causative organisms, bacterial resistance to antibiotics and the effect of recent introduction of Haemophilus influenzae type b(Hib) vaccine. Methods : We analysed the forty-three cases of bacterial meningitis which had been treated at the Inha University Hospital from June 1996 to June 2003. Results : Nineteen cases(44.2%) of them were infants younger than 2 months of age, and 29 cases(67.5%) younger than 1 year of age. The common causative organisms under 2 months of age were group B streptococcus(GBS)(47.4%), E. coli(21.1%), and Klebsiella pneumoniae(21.1%). In the age group beyond 2 months of age, S. pneumoniae were seen in 50 %, H. influenzae in 16.7% and N. meningitidis in 16.7%. All of the five cases of Hib meningitis had not been vaccinated for Hib. There has been no Hib meningitis cases since 2001. Overall fatality rate was 4.5%, and complication occurred in 39%. Complications was significantly less frequent in patients resumed to be treated within 48 hours after onset compared to after 48 hours after onset. Penicillin resistance of S. pneumoniae and GBS isolated among bacterial meningitis cases was high. Conclusion : Timing of treatment after the onset of the disease appeared the most important factor for prognosis of bacterial meningitis. The cases of H. influenzae meningitis have decreased probably due to Hib vaccination.