Efficient Storage Scheme for Microarray Data using Structural Similarity

Jonghan Yun,Dongkyoo Shin,Dongil Shin,Sanghoon Song 대한전자공학회 2008 ICEIC:International Conference on Electronics, Inf Vol.1 No.1

As one of typical techniques for acquiring bioinformation, gene microarray was solidly entrenched. However microarray experiments create very complex and huge amount of data and many researchers were being pinched at managing microarray data. Microarray was standardized by MGED group and MAGE-ML is established as a format expressed for MAGE-OM by XML. As establishing this standard, database design for microarray data has gained interest in bioinformatics area. However it has no consideration for efficient storage construction. In this paper, we propose strategies that efficiently convert complex structure of MAGE-ML into relatively compact structure in RDBMS based on the structural similarity of MAGE-ML element. The model induces fewer numbers of joins from database.

RDBMS 기반의 효율적인 MAGE-ML 데이터의 저장 기법

윤종한(Jonghan Yun),신동규(Dongkyu Shin),신동일(Dongil Shin) 한국정보과학회 2009 한국정보과학회 학술발표논문집 Vol.36 No.1

마이크로어레이(microarray) 실험은 생명정보학(bioinformatics)의 발전에 많은 기여를 하면서 유전자연구에 적합한 도구로 확립되었다. 그러나 마이크로어레이 실험으로 생성되는 데이터는 형태가 다양하고 복잡한 형태를 갖기 때문에 저장이나 공유에서 많은 어려움이 있다. 이러한 문제점을 해결하기위한 방안으로 마이크로어레이의 표준 객체 모델이 발표 되었고 MAGE-ML(Microarray Gene Expression Markup Language)은 그것을 XML의 형식으로 표현한 것이다. MAGE-ML은 마이크로어레이 데이터의 교환에 많은 기여를 한다. 또한 MAGE-ML문서는 관계형 테이블에 분산되어 있는 정보를 연속된 형태로 나타내므로 하나의 실험에 대한 정보를 효율적으로 처리할 수 있다는 장점이 있다. 본 논문에서는 MAGE-ML의 형태로 교환이 이루어지는 마이크로어레이 데이터를 좀더 효율적으로 저장하는 앙상블 기법을 제안한다. 이 앙상블 기법은 Shared Inlining 기법과 MAGE-ML의 엘리먼트들의 구조적 유사성을 이용하여 분류하는 기법을 동시에 사용한다.

구조적 유사성을 이용한 마이크로어레이 데이터의 효율적인 저장을 위한 기법의 설계 및 구현

윤종한(Jonghan Yun),신동규(Dongkyu Shin),신동일(Dongil Shin) 한국정보과학회 2008 한국정보과학회 학술발표논문집 Vol.35 No.1

생명정보 대량 획득기술의 하나인 마이크로어레이(microarray)는 DNA와 각종 유적자 연구에 사용되는 도구로서 확립되면서, 생명정보학(bioinformatics)분야의 발전에 크게 기여하였다. 그러나 마이크로어레이는 생명정보학분야의 핵심기술 중 하나로 발전하였음에도 불구하고 마이크로어레이 실험으로 생성되는 데이터는 형태가 다양하고 매우 복잡한 형태를 갖기 때문에 데이터의 공유나 저장에서 많은 어려움을 겪는 것이 사실이다. 따라서 마이크로어레이 실험결과 분석을 위한 최소한의 컨텐츠가 정의되고 표준화 되었다. MIAME 데이터, MAGE-OM/ML과 같은 표준화된 공개 저장소는 전문 생물학 연구단체에게 과거부터 지금까지 주요 관심사가 되어왔다. 하지만 많은 공개저장소의 설립되었지만 마이크로어레이 데이터의 구조적 특징을 고려하여 효과적인 설계를 하지 않은 것이 사실이다. 본 논문은 표준을 따르는 동시에 마이크로어 레이 데이터의 구조적 빈발 패턴이 반복되는 계층적 특징을 반영하는 전략을 제안한다. 이를 통하여 복잡한 데이터의 구조를 객체들의 빈발 패턴을 파악하여 그 계층을 줄임으로서 복잡도를 줄일 수 있었다. 이 과정에서 관계형 데이터베이스 기반의 공개저장소의 성능에 영향을 주는 관계 테이블(join-table)의 숫자는 줄어든다. 이에 따라, 성능은 개선된다. 이 전략을 통하여 생성된 테이블의 숫자는 원본 데이터를 단순 매핑시켜 저장하는 방법에 비하여 약 31%줄어든다. 결국 MAGE-ML 데이터의 저장과 로딩 시간은 이 논문에서 제시하는 전략을 적용하지 않은 방법에 비해 60%에서 65%를 줄일 수 있었다.

Weight analysis of mastectomy specimens and abdominal flaps used for breast reconstruction in Koreans

Yun, Jiyoung,Jeong, Hyung Hwa,Cho, Jonghan,Kim, Eun Key,Eom, Jin Sup,Han, Hyun Ho Korean Society of Plastic and Reconstructive Surge 2018 Archives of Plastic Surgery Vol.45 No.3

Background Slim patients or those with large breasts may be ineligible for breast reconstruction with an abdominal flap, as the volume of the flap may be insufficient. This study aimed to establish that abdominal tissue-based breast reconstruction can be well suited for Korean patients, despite their thin body habitus. Methods A total of 252 patients who underwent postmastectomy breast reconstruction with an abdominal flap from October 2006 to May 2013 were retrospectively reviewed. The patients' age and body mass index were analyzed, and a correlation analysis was performed between the weight of the mastectomy specimen and that of the initial abdominal flap. Results The average weights of the mastectomy specimen and initial abdominal flap were 451.03 g and 644.95 g, respectively. The ratio of the weight of the mastectomy specimen to that of the initial flap was $0.71{\pm}0.23$. There was a strong positive linear relationship between the weight of the mastectomy specimen and that of the initial flap (Pearson correlation coefficient, 0.728). Thirty nulliparous patients had a final-to-initial flap weight ratio of $0.66{\pm}0.11$. The 25 patients who underwent a contralateral procedure had a ratio of $0.96{\pm}0.30$. The adjusted ratio of the final flap weight to the initial flap weight was $0.66{\pm}0.12$. Conclusions Breast weight had a strong positive relationship with abdominal flap weight in Koreans. Abdominal flaps provided sufficient soft tissue for breast reconstruction in most Korean patients, including nulliparous patients. However, when the mastectomy weight is estimated to be >700 g, a contralateral reduction procedure may be considered.

4세대 오창 원형방사광가속기 소개

원종한(Jonghan Won),윤형중(Hyung Joong Yun),고경태(Kyung-Tae Ko),안득순(Deuk Soon Ahn),이주한(Jouhahn Lee) 대한지질학회 2021 대한지질학회 학술대회 Vol.2021 No.10

빛은 질량이 없는 입자의 흐름으로 보는 입자성과 공간을 통해 전파하는 전자파 특성의 이중성을 가지며 적외선으로부터 경 X-선, 감마선에 이르는 넓은 파장을 아우른다. 방사광가속기는 광범위한 파장 영역의 빛을 인공적으로 만들어 내는 “빛공장”으로 알려져 있다. 방사광가속기는 크게 전자총, 가속기, 저장링, 빔라인으로 구성이 되어져 있으며, 입자충돌용 가속기에서 엑스선을 뽑아 사용한 1세대 방사광가속기, 방사광 발생·사용을 주목적으로 구축된 2세대 방사광가속기, 휨자석(bending magnet) 대신 주기적으로 배열된 자석구조물로 전자빔이 자석배열을 통과하면서 경로를 여러 번 바꿔 더 밝은 방사광을 발생하게 만들어주는 삽입장치(wiggler or undulator)를 사용한 3세대 방사광가속기, 그리고 MBA 격자(multi-bend achromat lattice)를 사용하여 기존의 3세대 보다 전자빔의 에미턴스(빔크기)를 100~1000분의 1 정도 수준으로 줄이고 휘도(밝기) 및 결맞음을 약 100배까지 개선시킨 4세대 방사광가속기로 구분된다. 현재 충청북도 오창에 건설 예정인(2022년~2028년) 다목적 방사광가속기는 전자빔 에너지 4 GeV, 에미턴스 <100 pm·rad의 세계적 수준의 4세대 원형 방사광가속기이다. 총 빔라인 40개 여개를 수용할 수 있으며, 바이오에서 최첨단 신소재까지 다양한 분야를 연구를 할 수 있는 초대형 국가연구 기반시설이 될 것이다. 본 발표에서는 2021년 하반기부터 본격적으로 착수할 다목적 방사광가속기의 기획부터 가속기의 사양 및 활용에 이르는 전반적인 사항을 설명할 예정이다.

Weight analysis of mastectomy specimens and abdominal flaps used for breast reconstruction in Koreans

Jiyoung Yun,Hyung Hwa Jeong,Jonghan Cho,김은기,엄진섭,한현호 대한성형외과학회 2018 Archives of Plastic Surgery Vol.45 No.3

Background Slim patients or those with large breasts may be ineligible for breast reconstruction with an abdominal flap, as the volume of the flap may be insufficient. This study aimed to establish that abdominal tissue–based breast reconstruction can be well suited for Korean patients, despite their thin body habitus. Methods A total of 252 patients who underwent postmastectomy breast reconstruction with an abdominal flap from October 2006 to May 2013 were retrospectively reviewed. The patients’ age and body mass index were analyzed, and a correlation analysis was performed between the weight of the mastectomy specimen and that of the initial abdominal flap. Results The average weights of the mastectomy specimen and initial abdominal flap were 451.03 g and 644.95 g, respectively. The ratio of the weight of the mastectomy specimen to that of the initial flap was 0.71±0.23. There was a strong positive linear relationship between the weight of the mastectomy specimen and that of the initial flap (Pearson correlation coefficient, 0.728). Thirty nulliparous patients had a final-to-initial flap weight ratio of 0.66±0.11. The 25 patients who underwent a contralateral procedure had a ratio of 0.96±0.30. The adjusted ratio of the final flap weight to the initial flap weight was 0.66±0.12. Conclusions Breast weight had a strong positive relationship with abdominal flap weight in Koreans. Abdominal flaps provided sufficient soft tissue for breast reconstruction in most Korean patients, including nulliparous patients. However, when the mastectomy weight is estimated to be >700 g, a contralateral reduction procedure may be considered.

InGaAs/GaAs quantum well intermixing using proton irradiation for non-absorbing mirror

Ye Seul Yun,SangHyeon Kim,Han-Youl Ryu,Min-Su Park,Hojin Jang,Jonghan Song,Weon Cheol Lim,Young Jun Chang,Won Jun Choi 한국물리학회 2016 Current Applied Physics Vol.16 No.9

We report a proton irradiation-induced intermixing on InGaAs/GaAs quantum well (QW) heterostructures with thick upper cladding layers. Proton irradiation was performed with different dose, followed with annealing. Proton irradiated and annealed sample shows the blue-shift of the photoluminescence (PL) spectra and the blue-shift energy was increased up to about 30 meV with increasing dose, but was insensitive to the annealing temperature. Finally, we calculated that the relative absorption coefficient at the laser wavelength for the irradiated sample with dose of 1 1016/cm2 was 0.045, suggesting such proton irradiation-induced intermixing is a promising approach for fabricating non-absorbing mirror.

Fermi-level depinning in metal/Ge interface using oxygen plasma treatment

Janardhanam, Vallivedu,Yun, Hyung-Joong,Jyothi, Inapagundla,Yuk, Shim-Hoon,Lee, Sung-Nam,Won, Jonghan,Choi, Chel-Jong Elsevier 2019 APPLIED SURFACE SCIENCE - Vol.463 No.-

<P><B>Abstract</B></P> <P>Oxygen (O<SUB>2</SUB>) plasma treatment on germanium (Ge) surface was employed to depin Fermi-level in Al/n-type Ge interface. The Al contact to n-type Ge without and with O<SUB>2</SUB> plasma treatments for 1 and 2 min showed rectifying characteristics despite the low work function of Al, which could be associated with the Fermi-level pinning. An increase in O<SUB>2</SUB> plasma treatment time resulted in a decrease in Schottky barrier height along with the improvement of the homogeneity of Schottky interface. On the other hand, Al contact to O<SUB>2</SUB> plasma-treated n-type Ge for 3 min exhibited Ohmic behavior, implying the depinning of Fermi-level in Al/n-type Ge interface. A transition from rectifying to Ohmic behavior observed in Al/n-type Ge contact with O<SUB>2</SUB> plasma treatment for 3 min could be attributed to the more homogenous and stoichiometric formation of Ge-oxide layer. Such a high quality Ge-oxide layer effectively passivated unsatisfied surface states in Ge, which could be responsible for Fermi-level depinning of Ge.</P> <P><B>Highlights</B></P> <P> <UL> <LI> O<SUB>2</SUB> plasma treatment on Ge surface was employed to depin Fermi-level of Ge interface. </LI> <LI> Transition from Schottky to Ohmic behavior was observed in Al/n-type Ge with O<SUB>2</SUB> plasma treatment for 3 min. </LI> <LI> An increase in O<SUB>2</SUB> plasma treatment time led to the improved homogeneity of Schottky interface. </LI> <LI> More homogenous and stoichiometric Ge-oxide layer was formed after O<SUB>2</SUB> plasma treatment for 3 min. </LI> <LI> Ge surface passivation through Ge-oxide layer could be a main cause of depinning the Fermi-level of Ge. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Outcomes of Take-Back Operations in Breast Reconstruction with Free Lower Abdominal Flaps

Yim, Ji Hong,Yun, Jiyoung,Lee, Taik Jong,Kim, Eun Key,Cho, Jonghan,Eom, Jin Sup Korean Society of Plastic and Reconstructive Surge 2015 Archives of Plastic Surgery Vol.42 No.6

Background Microvascular complications after free-flap breast reconstructions are potentially devastating problems that can increase patient morbidity and lead to flap loss. To date, no comprehensive study has examined the rates of salvage and the methods of microvascular revision in breast reconstruction. We reviewed the treatment of microvascular complications of free-flap breast reconstruction procedures over a seven-year period. Methods A retrospective review of all patients who underwent microvascular breast reconstruction at our institution between April 2006 and December 2013 was conducted. Based on their surgical records, all patients who required emergency re-exploration were identified, the rate of flap salvage was determined, the factors associated with flap salvage were evaluated, and the causes and methods of revision were reviewed. Results During the review period, 605 breast reconstruction procedures with a free lower abdominal flap were performed. Seventeen of these flaps were compromised by microvascular complications, and three flaps were lost. The overall salvage rate was 82.35%. No significant differences between the salvaged group and the failed group were observed with regard to age, BMI, axillary dissection, number of anastomotic arteries and veins, recipient vessel types, or use of the superficial inferior epigastric vein in the revision operation. Successful salvage of the flap was associated with a shorter time period between recognizing the signs of flap compromise and the take-back operation. Conclusions The salvage rate of compromised lower abdominal flaps was high enough to warrant attempting re-exploration. Immediate intervention after the onset of flap compromise signs is as important as vigilant postoperative monitoring.

가속기를 이용한 활용 연구

안득순(Deuk Soon Ahn),원종한(Jonghan Won),윤형중(Hyung Joong Yun),고경태(Kyung-Tae Ko),이주한(Jouhahn Lee) 대한지질학회 2021 대한지질학회 학술대회 Vol.2021 No.10

선도적 기초원천연구 및 산업 연구개발 지원을 위해 세계 최고 수준의 다목적 방사광가속기 구축사업이 본격적으로 추진될 예정이다. 방사광가속기는 반도체, 소재, 바이오, 물리, 화학뿐만 아니라 지질환경과학 분야에도 많이 활용되고 있다. 본 발표에서는 방사광가속기를 활용한 다양한 연구분야의 소개와 함께 지질환경과학 분야의 국내외 연구 사례 등에 대해 소개하고자 한다. 또한, 방사광가속기 뿐만 아니라, 중이온가속기, 양성자가속기 등의 대형가속기를 활용한 국내외 연구 사례 및 다양한 활용 연구 분야 등에 대해서도 소개하고자 한다.