NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

족저압력분포 측정장비를 이용한 골프 스윙시 족저압 분석

이동기,이중숙,이범진,이훈식,김용재,박승범,주종필 한국운동역학회 2005 한국운동역학회지 Vol.15 No.1

D. K. LEE, J. S. LEE, B. J. LEE, H. S. LEE, Y. J. KIM, S. B. PARK, J. P. JOO. PIantar foot pressure analysis during golf swing motion using plantar foot pressure measurement system. Korean Journal of Sport Biomechanics, Vol. 15, No. 1, pp. 75-89, 2005. In this study, weight carrying pattern analysis and comparison method of four foot region were suggested. We used three types of club(driver, iron7, pitching wedge). This analysis method can compare between top class golfer and beginner. And the comparison data can be used to correct the swing pose of trainee. If motion analysis system, which can measure the swing speed and instantaneous acceleration at the point of hitting a ball, is combined with this plantar foot force analysis method, new design development of golf shoes to increase comfort and ball flight distance will be available. 1. Address acting, forces concentrated in rare foot regions and lateral foot of right foot. Back swing top acting, relatively high force occurred in medial forefoot region of left foot and forefoot region of right foot. Impact acting, high force value observed in the lateral rarefoot region of left foot and medial forefoot region of right foot. Finish acting, force concentration observed on the lateral region and rarefoot region of left foot. 2. Forces were increased in address of right foot with clubs length increased. All clubs, back swing top acting, high force value observed in the lateral forefoot region of right foot. All clubs, in impact, high force value observed in the lateral rarefoot region of left foot and medial forefoot region of right foot. Finish acting, force concentration observed on the rarefoot region in driver and lateral foot region in iron on left foot. 3. Right foot forces distribution were increased in address, back swing top and left foot force distribution were increased in impact, finnish

진도(전라남도, 진도군)의 거미상

김주필(Joo Pil Kim),지승환(Seung Hwan Ji),이형민(Hyung Min Lee),이형진(Hyung Jin Lee),이현동(Hyun Dong Lee) 한국거미연구소 2017 한국거미 Vol.33 No.1

2016년 7월 6일부터 8일까지 전라남도 진도군 일대를 한국거미연구회 회원인 김주필, 지승환, 이형민, 이형진, 이현동 등이 채집 조사한 결과 19과 47속 62종의 거미가 조사 연구되어 이에 보고하는 바이다. The author investigated the spiders of Jin island in July 06~08.2016. In the present paper 62 species of 47 genera belongs to 19 families were identified. These specimens are deposited at the Joo-Pil Spider Museum, Namyangju-Si, Gyeonggi-Do.

서초동(서울시 서초구)의 거미상

김주필(Joo Pil Kim),정혜리(Hye ri Jeong),김대희(Dae Hee Kim),박동우(Dong Woo Park),서재웅(Jae Woong Seo),이현우(Hyun woo Lee) 한국거미연구소 2017 한국거미 Vol.33 No.1

2016년 3월 31일부터 7월 31일까지 서울특별시 서초구 서초동에 위치한 서울고등학교 교정 일대를 서울고등학교 환경생물부 부원들이 채집 조사한 결과 20과 43속 53종의 거미가 조사 연구되어 이에 보고하는 바이다. From March 31st to July 31st in 2016, members of an environmental biology club at Seoul High School located in Seocho-gu, Seoul, Dae-Hee Kim, Dong-Woo Park, Jae-Woong Seo and Hyun-woo Lee, collected 20 families 43 genera 53 species of spiders and report the result of the study here.

유착성 관절낭염 치료에 있어서 한방 치료와 양방 치료의 임상적 고찰 : 동서협진 모델 개발을 위한 기초 연구를 중심으로

남동우,정인태,김주희,박유선,임사비나,이두익,이재동,이윤호,최도영 경희대학교 동서의학연구소 2006 東西醫學硏究所 論文集 Vol.2006 No.-

Objectives : To observe the effect of acupuncture treatment and western medical treatment on frozen shoulder patients. Methods : 39 voluntary patients were randomly assigned to the Eastern treatment group(E group, n=22) and the Western treatment group(W group, n=17). The E group received acupuncture treatment on LI15, TE14, GB21 and Master Dong's acupuncture points, Shin-gwan and Gyun-joong, twice a week for 4 weeks. The W group received suprascapular nerve block, subacromial injection and trigger point injection, twice a week for 4 weeks. Both groups were instructed to practice self exercise during their daily lives. Evaluations were made before treatment and after treatment using Constant Shoulder Assessment(CSA), Shoulder Pain and Disability Index(SPADI) and the patient's satisfaction concerning the treatment was measured by Visual Analogue Scale(VAS). The obtained data were analyzed and compared. Results : The E group showed significant improvement(p<0.05) according to the CSA and SPADI. The patient's satisfaction scored 5.67 on a scale of 10. The W group showed significant improvement(p<0.05) according to the CSA and SPADI. The patient's satisfaction scored 7.73. But the difference between the two groups were insignificant according to CSA and SPADI. Conclusion : Both acupuncture and nerve block treatment significantly improved frozen shoulder. But the difference of the two treatments was insignificant.

SNL-EFDC를 이용한 군산항 유사퇴적고 계산의 비교 연구

이동주 ( Dong-joo Lee ),송상현 ( Sang-hyun Song ) 한국환경기술학회 2015 한국환경기술학회지 Vol.16 No.4

본 논문은 Ziegler, Lick, and Jones에 의해 개발된 SEDZLJ라 부르는 유사역학 알고리즘이 계산되는 SNL-EFDC 모델을 이용하여 군산항의 퇴적고 계산에 관하여 연구하였다. SEDZLJ모듈은 SEDflume 이나 Annular flumes로부터 얻은 현장 침식률 및 침식 한계전단응력 자료를 직접 결합할 필요가 있다. 군산항에서는 SEDflume 자료를 구할 수 없기 때문에 Ryu와 Yim에 의한 Annular flumes 실험으로부터 얻은 현장 침식률 및 침식 한계전단응력 자료를 이용하였다. SNL-EFDC 모델이 군산항의 유사퇴적고를 계산하기 위해 적용되었고 관측된 부유사 농도와 퇴적고를 사용하여 검증되었다. 유사 퇴적고 계산에 대한 모델의 적용성은 NSEC가 0.72로 침식과 퇴적의 물리적 변화가 적절하게 재현됨이 입증되었다. 부가적으로 검증된 모델은 저면 활성층두께에 대한 매개변수 α값의 영향을 조사하기 위해 사용되었고, Lee와 Park에 의해 수행된 SEDTM을 이용한 유사이동 계산의 결과와 비교하기 위해 사용되었다. 그 결과, 매개변수 α값의 변화는 유사퇴적고 계산에 미미한 영향이 미치는 것으로 나타났다. SEDZLJ에 의한 결과를 SEDTM의 것과 비교할 때 SEDZLJ모듈이 군산항에서 SEDTM 보다 NSEC가 0.03향상 되어 토사이송 과정을 재현함이 확인되었다. This paper was studied on the sediment deposition height computation at Gunsan port using recently advanced SNL-EFDC model which the sediment dynamics algorithm was called as SEDZLJ developed by Ziegler, Lick and Jones. SEDZLJ module needs to directly incorporate site-specific erosion rate and critical shear stress data from SEDflume or Annularflumes. Here this model attempted to use site-specific erosion rate and critical shear stress data from Annular flumes experiment by Ryu and Yim instead of unavailable SEDflume data at Gunsan port. SNL-EFDC was applicated to calculate deposition height at Gunsan port and verified using observed values for suspended sediment concentration and sediment deposition height. The model applicability for sediment deposition height computation was evaluated as NSEC 0.72 and verified that it reproduced the physical variations of erosion and deposition. In addition, the verified model was used to investigate the effect of parameter “α” on the active bed layer thickness and used to compare with the result of sediment transport computation using SEDTM done by Lee and Park. As a result, it was found that the change of parameter “α” value has a negligible effect on sediment deposition height computation. As results of SEDZLJ are compared with those of SEDTM, it was identified that SEDZLJ module reproduces the sediment transport process more appropriately than SEDTM at Gunsan port with advanced NSEC 0.03.

BEZ235 (PIK3/mTOR inhibitor) Overcomes Pazopanib Resistance in Patient-Derived Refractory Soft Tissue Sarcoma Cells

Kim, Hee Kyung,Kim, Sun Young,Lee, Su Jin,Kang, Mihyeon,Kim, Seung Tae,Jang, Jiryeon,Rath, Oliver,Schueler, Julia,Lee, Dong Woo,Park, Woong Yang,Kim, Sung Joo,Park, Se Hoon,Lee, Jeeyun Neoplasia Press 2016 Translational oncology Vol.9 No.3

<P><I>BACKGROUND:</I> Although pazopanib treatment has become the standard chemotherapy in salvage setting for metastatic sarcoma patients, most patients progress after pazopanib treatment in 4 to 6 months. After failure to pazopanib, patients have limited options for treatment. Therefore, subsequent therapy in patients who failed to pazopanib is urgently needed and the use of patient derived cells or patient derived tumors for accompanying testing with various pharmacological inhibitors could offer additional treatment options for these patients. <I>METHODS:</I> Patient derived tumor cells were collected from ascites at the time of progression to pazopanib and a 13-drug panel was tested for drug sensitivity. We confirmed the results using <I>in vitro</I> cell viability assay and immunoblot assay. We also performed the genomic profiling of PDX model. <I>RESULTS:</I> The growth of patient derived tumor cells was significantly reduced by exposure to 1.0 μM AZD2014 compared with control (control versus AZD2014, mean growth = 100.0% vs 16.04%, difference = 83.96%, 95% CI = 70.01% to 97.92%, <I>P</I> = .0435). Similarly, 1.0 μM BEZ235 profoundly inhibited tumor cell growth <I>in vitro</I> when compared to control (control versus BEZ235, mean growth = 100.0% vs 7.308%, difference = 92.69%, 95% CI = 78.87% to 106.5%, <I>P</I> < .0001). Despite the presence of CDK4 amplification in the patient-derived tumor cells, LEE011 did not considerably inhibit cell proliferation when compared with control (control vs LEE011, mean growth = 100.0% vs 80.23%, difference = 19.77%, 95% CI = 1.828% to 37.72%, <I>P</I> = .0377). The immunoblot analysis showed that BEZ235 treatment decreased pAKT, pmTOR and pERK whereas AZD2014 decreased only pmTOR. <I>CONCLUSION:</I> Taken together, upregulation of mTOR/AKT pathway in sarcoma patient derived cells was considerably inhibited by the treatment of AZD2014 and BEZ235 with downregulation of AKT pathway (greater extent for BEZ235). These molecules may be considered as treatment option in STS patient who have failed to pazopanib in the context of clinical trials.</P>

소포제 종류 및 혼입률에 따른 초속경 라텍스개질 모르타르의 역학적 특성

이봉학,홍창우,이주형,김동호 江原大學校 産業技術硏究所 2001 産業技術硏究 Vol.21 No.B

The purpose of this study was to remove the excessive air foaming which was produced in mixing the RSLMC(latex-modified concrete with rapid-setting cement) by choosing the best antifoam agent type. A series of RSLMM(latex-modified mortar with rapid-setting cement) experiments were carried out as a basic experiments for RSLMC with the main experimental variables such as antifiamer types (A, B, C, D), antifoamer contents(0, 1, 2, 3%), and latex contents(10, 15%). Air content test and compressive strength tests were carried out to measure the improved properties of RSLMM. SEM analysis, also, was carried to observe the formation of latex film. The results of RSLMM showed that the decrease of 50% air content was obtained by admixturing an antifoam agent by 1%. This made the strength enhanced and the workability be within the purposed. The best properties of compressive strengths was obtained at latex content of 15% and D antifoam agent of 1%. compressive strength increased about 32.6%. The analysis of SEM results no difference in a formation of later film.

여성 스포츠 소비자 증대를 위한 커뮤니케이션 형태 연구

이상봉,노영태,이영덕,전동호,박병주,박철준 釜山大學校 附設 體育科學硏究所 1997 體育科學硏究所 論文集 Vol.13 No.-

This study was executed in order to gauge the possibility of the strategy of marketing communication, which was for an increase of female consumer' participation in sports. It was conducted among a random sample of 1.346 women over the age of 18 in Pusan area, and its contents of survey was the shape of leisure activity and preferation of mass media, the aspects of their watching TV. 1. The form of leisure activity seemed to be most favoured as spectators.. Meanwhile sports-type leisure activity appeared to be more favoured by people out of work compared to people in work. 2. It was shown in the most people that they got the media of the use of commercial sports institution by their family or friends. 3. It was shown that female magazines was the most favoured among periodical magazines. 4. In daily newspapers, they prefer local one to central one. Meanwhile sports-newspaper was the worst favoured. 5. TV news was the most preferred, that is in case of the married against the unmarried. 6. It was the most shown that sports program was watched during suitable hours. But a few people answered that they hardly watch that. 7. It was shown that cultural program was watched generally during suitable hours, yet the unmarried scarcely watch that. 8. It was the most shown that comedy program was watched during suitable hours. But a few people answered that they hardly watch that. 9. It was the most shown that dramatic series and movie program were occasionally watched by them.

전산유체역학을 이용한 싸이클론형 전기집진기 고도 설계 연구

이은주,장동순,나혜령,김혜숙 忠南大學校 環境問題硏究所 1995 環境硏究 Vol.13 No.-

A computer program is developed in order to figure out the physical insight of the combined dust removal equipment, that is, cyclonic electrostatic precipitator. The computer program employs Patankar's control-volume based finite-difference method, in which SIMPLEC algorithm is used for the resolution of pressure-linked momentum equation. Further two equation k-ε model is incorperated for Reynolds stresses and many empirical formulae are employed for dust charging and electric resistivity. A series of extensive parametric investigations are performed in terms of tangential velocity(swirl intensity), applied voltage across two electrodes, and particulate diameters, etc. It is found that the electrostatic force gives much more strong effect, expecially for small particulate, on the dust removal than the centrifugal force. Other calculated results are physically acceptable and consistent.