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A case of maternal uniparental disomy of chromosome 20 detected during 1,000 high risk Korean NIPT
( Sohyun Shim ),( Junnam Lee ),( Youngjoo Jeon ),( Yongwook Jung ),( Jahyun Jang ),( Taeheon Lee ),( Eunhae Cho ),( Donghyun Cha ) 대한산부인과학회 2016 대한산부인과학회 학술대회 Vol.102 No.-
Chromosomal loss in trisomy to generate a disomic fetus can cause confined placental mosaicism and/or fetoplacental mosaicism. After trisomy rescue event, there is a risk of fetal uniparental disomy (UPD). The phenotypic consequences of UPD for several chromosomes are still unknown or poorly understood. In this study, we performed whole genome sequencing based NIPT (G-NIPTä) in 1,000 high risk Korean pregnancies and we have detected five cases of other chromosomal trisomies except chromosomes 21, 18 and 13. Chromosomes involved were 7 (1case), 8 (1 case), 16 (1 case) and 20 (2 cases). All three trisomy cases involving chromosomes 7 and 20 were investigated invasively for the presence of UPD. One case of trisomy 7 and one case of trisomy 20 showed normal karyotype at amniocentesis, respectively. However, 1 case of trisomy 20 revealed to have low level of mosaicism of trisomy 20 (47,XX,+20[2]/46,XX[40]) at amniocentesis. To rule out UPD, we performed chromosomal microarray from both amniotic fluid and maternal gDNA in all the three cases. We found 30Mb homozygosity spanning the centeromere in amniocentesis of the low level mosaic 20 case. This finding suggests nondisjunction error happened at meiosis. Then, by comparing all the SNPs of involved chromosomes between mother and fetus, maternal or paternal UPD can be decided. The low level mosaic 20 case can be diagnosed to have maternal UPD 20 and others didn't show any UPD pattern. Recently, maternal UPD 20 has been suggested as a new imprinting disorder with intrauterine growth restriction, short stature and prominent feeding difficulties with failure to thrive. To best of our knowledge, two cases of UPD were detected by following discordant NIPT and invasive testing which were a case of UPD 21 and a case of UPD 15 with fetal mosaicism. From this study, we showed the potential use of NIPT for the detection of UPD, especially when the trisomies of specific chromosomes with imprinting syndromes are detected by NIPT.
포인트 클라우드 기반 콘크리트 변형 정보 추출 기법 개발
심소현(Shim, Sohyun),이태민(Lee, Taemin),최하진(Choi, Hajin) 한국콘크리트학회 2021 한국콘크리트학회 학술대회 논문집 Vol.33 No.2
이 연구는 기존 구조물 변형 계측의 한계를 개선하기 위해 포인트 클라우드 기반 콘크리트 구조물의 변형 정보 추출 기법을 개발하는데 그 목적을 두었다. 포인트 클라우드 기반 3차원 공간좌표정보로면의 형성과 법선벡터 추출이 가능하며, 법선벡터의 변화를 계측할 수 있다. 압축강도 공시체 대상으로 검증한 결과, 3차원 공간좌표에서 재구성한 면의 변형을 1초 간격으로 30프레임씩 확인 가능했고 RoI 6,566 ㎟ 내에서 최소 간격 0.1 mm 해상도의 정확도를 확인할 수 있었다. The objective of this research is to improve the limitations of existing structural strain measurement methods. Point cloud based 3D deformation of concrete elements was extracted. As a result of the experimental verification, the deformation of the reconstructed surface in 3D spatial coordinates could be checked at 30 frames per second, and the accuracy of the resolution of the minimum interval of 0.1 mm within the RoI area 6,566 ㎟ was confirmed.
GWAB: a web server for the network-based boosting of human genome-wide association data
Shim, Jung Eun,Bang, Changbae,Yang, Sunmo,Lee, Tak,Hwang, Sohyun,Kim, Chan Yeong,Singh-Blom, U. Martin,Marcotte, Edward M.,Lee, Insuk Oxford University Press 2017 Nucleic acids research Vol.45 No.w1
<P><B>Abstract</B></P><P>During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part to limited statistical power, most studies identify only small numbers of candidate genes that pass the conventional significance thresholds (e.g. <I>P</I> ≤ 5 × 10<SUP>−8</SUP>). This limitation can be partly overcome by increasing the sample size, but this comes at a higher cost. Alternatively, weak association signals can be boosted by incorporating independent data. Previously, we demonstrated the feasibility of boosting GWAS disease associations using gene networks. Here, we present a web server, GWAB (www.inetbio.org/gwab), for the network-based boosting of human GWAS data. Using GWAS summary statistics (<I>P</I>-values) for SNPs along with reference genes for a disease of interest, GWAB reprioritizes candidate disease genes by integrating the GWAS and network data. We found that GWAB could more effectively retrieve disease-associated reference genes than GWAS could alone. As an example, we describe GWAB-boosted candidate genes for coronary artery disease and supporting data in the literature. These results highlight the inherent value in sub-threshold GWAS associations, which are often not publicly released. GWAB offers a feasible general approach to boost such associations for human disease genetics.</P>
고추밭 토양 중 잔류농약 추정을 위한 GLEAMS 모형 적용
진소현 ( Sohyun Jin ),윤광식 ( Kwangsik Yoon ),최우정 ( Woojung Choi ),심재한 ( Jaehan Shim ),최우영 ( Wooyoung Choi ),임상선 ( Sangsun Lim ),김상돈 ( Sangdon Kim ),최동호 ( Dongho Choi ),박지연 ( Jiyeon Park ) 한국농공학회 2010 한국농공학회 학술대회초록집 Vol.2010 No.-
농촌에서 생산량 증가를 위한 농약의 시용량이 급증하면서 토양에 처리된 잔류농약이 강우나 토양유실 등을 통하여 수질이나 동·식물체로 이행되기 때문에 농경지 토양의 잔류농약평가는 중요하다 할 수 있다. 토양 중 잔류농약을 평가하는데 있어 GLEAMS와 같은 모형은 이미 세계적으로 많이 이용되고 있지만 국내의 적용 사례는 찾기 힘들다. 본 연구에서는 토양중 잔류농약을 추정하기 위해 고추밭에서 살포된 농약 성분을 분석하고 GLEAMS 모형을 이용하여 잔류농약을 산정하고 비교분석하여 각 농약에 적합한 매개변수를 산정하였다. 고추밭 토양의 잔류농약을 실측하기 위해서 전남대학교 실험온실에서 농약 시용량 관행구와 관행의 2배구로 나누어 3반복하여 실험하였으며, 농약은 Alachlor, Cypermethrin, Fenvalerate, Endosulfan 총 4종류를 살포하였다. GLEAMS 모형에 고추밭 실험조건을 적용하여 모의발생 한 뒤 실측값과 비교하여 KOC(유기탄소흡착계수)와 같은 매개변수를 보정하였다. 각 농약별 토양중 반감기는 endosulfan(50days) >fenvalerate(35days) > cypermethrin(30days) > alachlor(15days)의 순서였고, GLEAMS 모의 발생 결과도 비슷한 경향을 보였으며 시용량 관행구에 비해서 2배구에서 잔류농약이 많이 검출되었다. GLEAMS 모형에서도 cypermethrin을 제외하고 시용량 차이에 따른 잔류농약 효과를 잘 나타내었고 국내 토양중 잔류농약을 평가하는데 GLEAMS 모형의 적용이 큰 것으로 판단된다.
진소현 ( Sohyun Jin ),윤광식 ( Kwangsik Yoon ),최우정 ( Woojung Choi ),심재한 ( Jaehan Shim ),최우영 ( Wooyoung Choi ),임상선 ( Sangsun Lim ),김상돈 ( Sangdon Kim ),최동호 ( Dongho Choi ),박지연 ( Jiyeon Park ) 한국농공학회 2010 한국농공학회 학술대회초록집 Vol.2010 No.-
영농활동 중 농약과 같은 인축과 환경생물에 독성을 갖는 물질이 수계환경에 노출빈도가 높은 논에 살포됨으로서 농약의 유출을 제어하는데 어려움이 있다. 이러한 농약의 유출을 제어하고자 국외에서는 수계환경중 농약 노출농도를 예측하는 모형을 활용하여 적용하고 있으나 국내에서는 이에 대한 연구가 라이시미터와 같은 제한적인 실험을 통해 농약의 위해성을 평가하고 있어 농약의 유출을 예측하고 평가하기 위한 모형의 개발 및 적용이 필요하다. 본 연구에서는 RICEWQ(Pesticide Runoff Model for Rice Crops) 모형을 이용하여 국내 관개지구 논 포장에서 주요 농약 5종(butachlor, chlorpyrifos-me, diazinon, isoprothiolane, oxadiazon)의 유출율을 모의발생하여 산정하였다. 유출율 산정을 위해 함평군 엄다면 소재 학야지구에 위치한 유역면적이 13.69 ha인 논을 대상으로 실험을 하였으며 수문조건 보정을 위해 필요한 강수량, 관개량, 유출량, 증발산량, 침투량을 실험지구에서 실측하였다. 관측치와 수문조건이 근접하도록 보정한 뒤 농약과 관련된 매개변수를 입력하여 구동하였고 이에 필요한 농약관련 매개변수는 현장에서 검출되는 농약의 모니터링이 어렵기 때문에 항온실험 결과를 이용하였다. 논에서 농약 이동을 모의하기위해 개발된 RICEWQ 모형을 통해 추정된 배수농도와 유량을 곱하여 농약 부하량을 산정한 뒤 유출율을 산정하였다.
Bae, Sohyun,Shim, So Hee,Park, Chae Woon,Son, Hye Kyung,Lee, Hyun Ju,Son, Ji Young,Jeon, Choonju,Kim, Hoeon Mary Ann Liebert, Inc 2011 STEM CELLS AND DEVELOPMENT Vol.20 No.2
<P>Mesenchymal stem cells (MSCs) are promising for cell therapy and regenerative medicine; but their lack of specific markers renders the cell culture at potential contamination risk with other cell types, in particular, fibroblasts. In this study, we mapped 2 differential transcriptome data of MSCs compared, one to mononuclear cells and the other to fibroblasts, onto the membrane proteome data, the analysis of which led to an identification of transmembrane 4 L6 family member 1 (TM4SF1) as a surface protein marker candidate that could discriminate MSCs simultaneously from blood cells and fibroblasts. Our analyses confirmed that TM4SF1 was abundantly expressed on MSCs but neither on other blood/tissue cells nor on fibroblasts. TM4SF1 immunoselection from bone marrow and adipose tissues yielded homogeneous cell populations that were highly similar to MSCs, in terms of morphology, immunophenotype, and differentiation potential. These findings indicate that TM4SF1 can serve as a surface protein marker which singly identifies MSCs from diverse cell sources, in particular, fibroblast-rich connective tissues.</P>
TRP14 Inhibits Osteoclast Differentiation via Its Catalytic Activity
Hong, Sohyun,Huh, Jeong-Eun,Lee, Soo Young,Shim, Jae-Kyung,Rhee, Sue Goo,Jeong, Woojin American Society for Microbiology 2014 Molecular and cellular biology Vol.34 No.18
<P>We previously reported the inhibitory role of thioredoxin-related protein of 14 kDa (TRP14), a novel disulfide reductase, in nuclear factor-κB (NF-κB) activation, but its biological function has remained to be explored. Here, we evaluated the role of TRP14 in the differentiation and function of osteoclasts (OCs), for which NF-κB and cellular redox regulation have been known to be crucial, using RAW 264.7 macrophage cells expressing wild-type TRP14 or a catalytically inactive mutant, as well as its small interfering RNA. TRP14 depletion enhanced OC differentiation, actin ring formation, and bone resorption, as well as the accumulation of reactive oxygen species (ROS). TRP14 depletion promoted the activation of NF-κB, c-Jun NH<SUB>2</SUB>-terminal kinase, and p38, the expression of c-Fos, and the consequent induction of nuclear factor of activated T cell, cytoplasmic 1 (NFATc1), a key determinant of osteoclastogenesis. However, pretreatment with <I>N</I>-acetylcysteine or diphenylene iodonium significantly reduced the OC differentiation, as well as the ROS accumulation and NF-κB activation, that were enhanced by TRP14 depletion. Furthermore, receptor activator of NF-κB ligand (RANKL)-induced ROS accumulation, NF-κB activation, and OC differentiation were inhibited by the ectopic expression of wild-type TRP14 but not by its catalytically inactive mutant. These results suggest that TRP14 regulates OC differentiation and bone resorption through its catalytic activity and that enhancing TRP14 may present a new strategy for preventing bone resorption diseases.</P>