BioSMACK: a Linux Live CD for genome-wide association analyses

( Chang Bum Hong ),( Young Jin Kim ),( Sang Hoon Moon ),( Young Ah Shin ),( Min Jin Go ),( Dong Joon Kim ),( Jong Young Lee ),( Yoon Shin Cho ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2012 BMB Reports Vol.45 No.1

Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc. go.kr/biosmack. [BMB reports 2012; 45(1): 44-46]

鹽化物含有 콘크리트의 透水係數와 鐵筋腐蝕 性狀

김영수,진유동,문양고 釜山大學校生産技術硏究所` 1998 生産技術硏究所論文集 Vol.54 No.-

염화물함유 콘크리트의 투수성과 철근부식에 미치는 영향을 규명하기 위해 염화물 함유량을 0, 0.3, 0.6㎏/㎥으로 변화시키고 W/C비를 0.4, 0.45, 0.5, 0.6으로 변화시킨 상태에서 투수계수, 철근 부식면적율, 압축강도, 슬럼프, S.E.M에 의한 미세구조를 보통 콘크리트, fly ash 혼입 콘크리트, AE 혼입 콘크리트와 비교하여 다음과 같은 결론을 얻었다. 1) 콘크리트 투수계수는 W/C비 또는 염화물 함유량이 클수록 증가하였다. W/C비 0.5까지는 투수계수의 증가폭이 크지 않으나 W/C비 0.65에서는 염화물 혼입 및 보통 콘크리트의 투수계수가 크게 증가하여 W/C비가 염화물 함유량 보다는 특수성에 더 큰 영향인자임을 알 수 있었다. 2) 철근부식 면적율은 투수계수와 마찬가지로 W/C비 또는 염화물 함유량이 클수록 증가하였다. W/C비 0.65에서 보통 콘크리트의 투수계수는 염화물 혼입시와 유사하나 철근부식 면적율은 현격히 작은 결과를 나타내 투수계수의 증가에 따라 철근부식 면적율이 반드시 비례하여 커지는 것은 아님을 알 수 있었다. 3) 플라이애쉬 및 AE감수제를 혼입하면 콘크리트 투수계수 및 철근부식 면적율이 크게 감소하여 밀실화 효과가 우수하였으며, 피복두께를 2㎝에서 3㎝로 증가 시키면 염화물 및 혼화재 혼입 유무에 관계없이 철근부식 면적율은 모두 감소하였다. The purpose of this paper is to investigate the coeffecient of permeability and the properties of corrosion of steel in concrete containing chloride. For this purpose, the experiments for the permeability and the rate of corrosion area by selecting factors and levels such as chloride content, W/C and admixture were executed. The major results are as follows. 1) The coefficient of permeability was increased with increasing chloride is higher than that of plain concrete. 3) The permeability and the rate of corrosion area in concrete containing fly ash and AE water reducer is lower than that of plain concrete and concrete containing chloride at the same W/C 4) The rate of corrosion area was decreased with increasing covering depth from 2㎝ to 3㎝.

양어용 사료첨가제로서 감귤발효액(EM-Fermented Orange)의 항산화특성

이준백,문상욱,이영돈,고유봉 제주대학교 해양연구소 2000 해양과환경연구소 연구논문집 Vol.24 No.-

Mandarine orange (Citrus unshiu Marc.) only added with sugar was fermented by effective microorganisms (EM) called "EM-fermented orange". EM was mainly composed of lactic acid bacteria, phototrophic bacteria and feast. As pH of EM-fermented orange reached 3.5 to 4.0 in the course of fermentation, the incubation was stopped. and then. EM-fermented orange was preservable at room temperature for about 6 months. Composition and concentration of free amino acids in EM-fermented orange were analyzed. Concentration of total amino acids was 167mg/l, and the relative content of carnosine (β-alanyl-L-histidine) which was well known as a kind of antioxidant materials was very high. 41%. In addition. crude extract showing antioxidant activity could be obtained from EM-fermented orange using some organic solvents. The antioxidant activity of the crude extract was equivalent to about 9% of that of vitamin E by the use of 1.1-diphenyl-2-picrylhydrazyl (DPPH) method. It was suggested that EM-fermented orange having antioxidant characteristics could promote the health of fish.

3D 광학 스캐너를 이용한 인체모형 팬텀 표면 데이터 획득 및 X-ray 에너지의 몬테카를로 시뮬레이션(MCs)을 이용한 팬텀 선량 평가와 영상구현

신준봉(Jun-Bong Shin),이도희(Do-Heui Lee),윤경준(Kyoung-Jun Yoon),박민재(Min-Jae Park),고영문(Young-Moon Go),김성우(Sung-Woo Kim),홍승모(Seung-Mo Hong),이현철(Hyun-Cheol Lee),이의섭(Ui-Seob Lee),노선영(Seon-Yeong No),강석윤(Seok-Yoon 대한영상의학기술학회 2021 대한영상의학기술학회 논문지 Vol.2021 No.-

목 적:본 연구의 목적은 기존 컴퓨터단층촬영(Computed tomography, 이하 CT) 스캔 방법 대신 3D 광학 스캐너 (3D optical scanner)를 이용하여 인체모형 팬텀의 표면 데이터를 획득하고 기존 CT 스캔 표면 데이터와 3D 광학 스캔 표면 데이터 차이를 비교 분석하는 것이며, 3D 광학 스캔 표면 데이터를 몬테카를로 시뮬레이션(Monte Carlo Simulation, MCs)에 적용하여 일반 촬영 에너지조건으로 팬텀 선량 평가와 영상 구현을 연구하는 것입니다. 연구방법: 일반촬영의 선량 평가를 위해 환자 표면 데이터를 얻을 때 3D 광학 스캐너를 활용할 것을 제안합니다. 우리는 3D 광학 스캐너(Go!SCAN SPARKTM, CREAFORM) 사용하여 기존 CT 스캔 방법을 대신해 인체모형 팬텀의 표면 데이터를 얻었습니다. 3D 스캔 표면 데이터를 정렬하고 편집하기 위해 Meshlab 프로그램을 이용하였으며, 3D slicer 프로그램을 이용하여 CT 스캔 표면 데이터와 3D 스캔 표면 데이터 차이를 정량적으로 비교분석 하였습니다. 또한 3D 스캔 표면 데이터 분석 프로그램(VXelements, CREAFORM)을 사용하여 인체 모형 팬텀의 재현성을 평가 하였습니다. SpekCalc 프로그램을 이용하여 X-ray beam 에너지 스펙트럼을 계산하고 Geant4 기반의 MCs인 TOPAS를 이용하여 X-ray Beam을 모델링 하였습니다. 인체모형 팬텀을 MCs에 적용 하여 일반촬영 에너지 조건으로 팬텀 선량을 평가하고 Phase space data 통해 영상을 구현을 연구 하였습니다. 결 과:3D slicer를 이용한 CT 스캔 표면 데이터와 3D 광학 스캔 표면 데이터의 정량적 비교 분석에서 Hounsdroff distance는 Average 2.45 mm, Dice coefficient는 0.97로 나타나 CT 스캔 표면 데이터와 3D 스캔 표면 데이터가 거의 일치하는 것을 확인할 수 있었습니다. 또한 인체모형 팬텀 재현성 평가에서 인체모형 팬텀의 AP position, RAO position, LAO position 기준으로 팔이 있는 팬텀의 error distribution은 2 mm 오차 범위에서 평균 89.78%가, 4 mm 오차 범위에서 96.05%가 일치하는 것으로 나타났으며, 팔을 제외한 경우 error distribution은 2 mm 오차 범위에서 평균 96.48%가, 4 mm 오차 범위에서 99.45%가 일치하는 것으로 나타나 3D 광학 스캐너의 표면 데이터 재현성이 우수한 것으로 나타났습니다. 인체모형 팬텀을 이용한 3D 스캔 표면 데이터를 MCs에 적용하여 전신일반촬영 에너지 조건으로 팬텀선량 평가가 가능하며, Phase space data 통해 영상을 구현할 수 있다는 것을 확인 하였습니다. 결 론:본 연구에서 3D 광학 스캐너를 사용한 인체모형 팬텀 데이터 획득은 기존 CT scan 방식보다 간편하고 방사선 노출 없이 다양한 위치와 균일한 표면 구조의 정보를 정밀하게 얻을 수 있으며 MCs을 이용한 선량계산이 가능하며, Phase space data 통해 영상을 구현이 가능함에 따라 앞으로 일반촬영 분야의 활용과 선량평가에 매우 유용할 것으로 생각 됩니다. Purpose:The purpose of this work is to acquire surface data of anthropromophic phantom using 3D optical scanner instead of conventional computed tomography (CT) scanning methods and to compare the differences between existing CT scan surface data and 3D optical scan surface data. also it is to apply 3D optical scan surface data to Monte Carlo simulations (MCs) to study whether phantom dose evaluation and image implementation are possible under general shooting energy conditions. Targets and Methods:We suggest utilizing a 3D optical scanner when obtaining patient surface data for dose evaluation of normal photography. We obtained surface data of anthropromophic phantom instead of conventional CT scanning methods using 3D optical scanners (Go!SCAN SPARKTM, CREAFORM). The Meshlab program was used to sort and edit 3D scan surface data, and the CT scan surface data and 3D scan surface data differences were quantitatively compared using the 3D slicer program. The reproducibility of the dummy phantom was also evaluated using the 3D Scan Surface Data Analysis Program (VXelements, CREAFORM). Using the SpekCalc program, the X-ray beam energy spectrum was calculated and the X-ray beam was modeled using TOPAS, a Geant4-based MCs. We applied the anthropromophic phantom to MCs evaluate the phantom dose in X-ray energy conditions and study whether the image can be implemented through phase space data. Result:Quantitative comparative analysis of CT scan surface data and 3D optical scan surface data using 3D slicer showed that Hounsdroff distance was Average 2.45 mm and Dice coefficient was 0.97, indicating a close match between CT scan surface data and 3D scan surface data. In addition, the anthropromophic phantom reproducibility assessment shows that the error distribution of the phantom with arms by AP position, RAO position, and LAO position of the anthropromophic phantom averaged 89.78% in the 2 mm error range and 96.05% in the 4 mm error range. MCs using anthropromophic phantom confirmed that 3D scan surface data can be applied to Monte Carlo simulation to evaluate phantom dose under X-ray energy conditions through phase space data. Conclusion:In this study, anthropromophic phan tom data acquisition using 3D optical scanners is simpler than conventional CT scan methods, provides precise information of various locations and uniform surface structures without radiation exposure, enables dosing using MCs, and enables image implementation through phase space data.

Therapeutic Effect of Total Ginseng Saponin on Skin Wound Healing

Young Soo Kim,Ik-Hyun Cho,Moon-Jin Jeong,Soon-Jeong Jeong,Seung Yeol Nah,Young-Sik Cho,Seung Hyun Kim,Ara Go,Se Eun Kim,Seong Soo Kang,Chang Jong Moon,Jong Choon Kim,Sung Ho Kim,Chun Sik Bae 고려인삼학회 2011 Journal of Ginseng Research Vol.35 No.3

In this study, we investigated the effects of total ginseng saponin (TGS) on the cutaneous wound healing process using histological analysis. A total of 24 ICR mice, 5-weeks-old, were used for all in vivo experiments. Mice were divided into control and TGS-treated groups and four equidistant 1-cm full-thickness dorsal incisional wounds were created. The wounds were extracted at days 1, 3, 5, and 7 post-injury for histomorphometrical analysis including wound area and contracture measurements, keratinocyte migration rate, and calculation of infiltrating inflammatory cells. The results showed that the wound area was smaller and keratinocyte migration rate was higher in the TGS-treated group than that of the control group from days 3 to 7. Inflammatory cells in the TGS-treated group at days 1 and 3 were reduced compared to the control group. Wound contraction in the TGS-treated group was greater than in the control group on days 3 to 5, and collagen deposition in the TGS-treated group was higher than in the control group during wound healing. The results indicate a beneficial effect of TGS when used to treat skin wounds.

Self-Assembly Modification of Perfluorosulfonic Acid Membranes for the Application to Direct Methanol Fuel Cells

Go Young Moon,Ji Won Rhim 한국고분자학회 2008 Macromolecular Research Vol.16 No.6

Genome-wide Survey of Copy Number Variants Associated with Blood Pressure and Body Mass Index in a Korean Population

Moon, Sang-Hoon,Kim, Young-Jin,Kim, Yun-Kyoung,Kim, Dong-Joon,Lee, Ji-Young,Go, Min-Jin,Shin, Young-Ah,Hong, Chang-Bum,Kim, Bong-Jo Korea Genome Organization 2011 Genomics & informatics Vol.9 No.4

Hypertension is the major factor of most death and high blood pressure (BP) can lead to stroke, myocardial infarction and cardiac failure. Moreover, hypertension is strongly correlated with body mass index (BMI). Although the exact causes of hypertension are still unclear, some of genetic loci were discovered from genome-wide association study (GWAS). Therefore, it is essential to study genetic variation for finding more genetic factor affecting hypertension. The purpose of our study is to conduct a CNV association study for hypertension-related traits, BP and BMI, in Korean individuals. We identified 2,206 CNV regions from 3,274 community-based Korean participants using the Affymetrix Genome-Wide Human SNP Array 6.0 platform and performed a logistic regression analysis of CNVs with two hypertension-related traits, BP and BMI. Moreover, the 4,692 participants in an independent cohort were selected for respective replication analyses. GWAS of CNV identified two loci encompassing previously known hypertension-related genes: LPA (lipoprotein) on 6q26, and JAK2 (Janus kinase 2) on 9p24, with suggestive p-values (0.0334 for LPA and 0.0305 for JAK2 ). These two positive findings, however, were not evaluated in the replication stage. Our result confirmed the conclusion of CNV study from the WTCCC suggesting weak association with common diseases. This is the first study of CNV association study with BP and BMI in Korean population and it provides a state of CNV association study with common human diseases using SNP array.

Micro Fuel Cells for the Portable Applications

Moon, Go-Young,Lee, Won-Ho The Membrane Society of Korea 2003 Korean Membrane Journal Vol.5 No.1

Due to the increasing intelligence, the increasing connectivity, and always-on characteristics energy needs for the portable electronics cannot be managed by the state-of-art battery technology. Micro fuel cell fuelled by aqueous methanol is gaining lots of interest from the new energy storage developers since it has the potential to offer the longer operation time to the portable electronic devices. Although the technical barriers to the commercialization exit, it is expected that the micro fuel cell technology bring huge benefits to the current energy storage market once it matures. In the article, benefits, challenges and market players of the direct methanol fuel cell arena is briefly reviewed.

Sulfonated PEEK Ion Exchange Membranes for Direct Methanol Fuel Cell Applications

Moon, Go-Young,Rhim, Ji-Won The Polymer Society of Korea 2007 Macromolecular Research Vol.15 No.4

Sulfonation of polyetheretherketones (PEEK) was carried out in order to fabricate commercial perfluorosulfonic acid membrane alternatives, which were characterized in terms of their ion exchange capacity, ionic conductivity, water swelling, methanol crossover and electrochemical performance in their direct application as a methanol fuel cell. A high ion exchange capacity, 1.88, was achieved with a sulfonation reaction time of 8 h, with a significantly low methanol crossover low compared to that of Nafion. However, the morphological stability was found to deteriorate for membranes with sulfonation reaction times exceeding 8 h. Electrochemical cell tests suggested that the fabrication parameters of the membrane electrode assembly based on the sulfonated PEEK membranes should be optimized with respect to the physicochemical properties of the newly prepared membranes.

Sulfonated PEEK Ion Exchange Membranes for Direct Methanol Fuel Cell Applications

Go Young Moon,Ji Won Rhim 한국고분자학회 2007 Macromolecular Research Vol.15 No.4