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mySyntenyPortal: an application package to construct websites for synteny block analysis
Lee, Jongin,Lee, Daehwan,Sim, Mikang,Kwon, Daehong,Kim, Juyeon,Ko, Younhee,Kim, Jaebum BioMed Central 2018 BMC bioinformatics Vol.19 No.-
<P><B>Background</B></P><P>Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks.</P><P><B>Results</B></P><P>To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements.</P><P><B>Conclusions</B></P><P>mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data.</P>
Indirect Photon-counting Detector (PCD) for Transmission Imaging
Daehong Kim,Hakjae Lee,Seung-Jae Lee 한국자기학회 2020 Journal of Magnetics Vol.25 No.4
Photon-counting detectors (PCDs) are replacing energy integrating detectors in electromagnetic wave transmission imaging to achieve high performance. The purpose of this study was to develop an indirect PCD system for transmission imaging. The detector module is a combination of scintillator and SiPM, the SiPM is insensitive to magnetic field and operating at low voltage. A 2D array of a GAGG coupled with SiPM, positioning logic circuit, and preamplifier were enclosed in housing that sealed from light. A channel reduction circuit was used to identify the channel from the positioning logic circuit, and then output an analog pulse signal corresponding to the valid channel. The pulse signal measurements were performed using a oscilloscope. The profile analysis of the flood map confirmed that each point was distinct in both the center and peripheral regions. Additionally, the letters engraved on the phantom in the images were confirmed. Therefore, the indirect PCD system has potential for transmission imaging. Our future work will design an indirect PCD for low-energy photon detection and multi-energy imaging.
The Effectiveness of Ferritin as a Contrast Agent for Cell Tracking MRI in Mouse Cancer Models
Lee, Chan Wha,Choi, Sun Il,Lee, Sang Jin,Oh, Young Taek,Park, Gunwoo,Park, Na Yeon,Yoon, Kyoung-Ah,Kim, Sunshin,Kim, Daehong,Kim, Yun-Hee,Suh, Jin-Suck Yonsei University College of Medicine 2017 Yonsei medical journal Vol.48 No.5
<P><B>Purpose</B></P><P>We aimed to investigate the effectiveness of ferritin as a contrast agent and a potential reporter gene for tracking tumor cells or macrophages in mouse cancer models.</P><P><B>Materials and Methods</B></P><P>Adenoviral human ferritin heavy chain (Ad-hFTH) was administrated to orthotopic glioma models and subcutaneous colon cancer mouse models using U87MG and HCT116 cells, respectively. Brain MR images were acquired before and daily for up to 6 days after the intracranial injection of Ad-hFTH. In the HCT116 tumor model, MR examinations were performed before and at 6, 24, and 48 h after intratumoral injection of Ad-hFTH, as well as before and every two days after intravenous injection of ferritin-labeled macrophages. The contrast effect of ferritin <I>in vitro</I> was measured by MR imaging of cell pellets. MRI examinations using a 7T MR scanner comprised a T1-weighted (T1w) spin-echo sequence, T2-weighted (T2w) relaxation enhancement sequence, and T2*-weighted (T2*w) fast low angle shot sequence.</P><P><B>Results</B></P><P>Cell pellet imaging of Ad-hFTH <I>in vitro</I> showed a strong negatively enhanced contrast in T2w and T2*w images, presenting with darker signal intensity in high concentrations of Fe. T2w images of glioma and subcutaneous HCT116 tumor models showed a dark signal intensity around or within the Ad-hFTH tumor, which was distinct with time and apparent in T2*w images. After injection of ferritin-labeled macrophages, negative contrast enhancement was identified within the tumor.</P><P><B>Conclusion</B></P><P>Ferritin could be a good candidate as an endogenous MR contrast agent and a potential reporter gene that is capable of maintaining cell labeling stability and cellular safety.</P>
Kwon, Daehong,Lee, Daehwan,Kim, Juyeon,Lee, Jongin,Sim, Mikang,Kim, Jaebum Oxford University Press 2018 Nucleic acids research Vol.46 No.w1
<P><B>Abstract</B></P><P>Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.</P>
이재원(Jaewon Lee),임대홍(Daehong Lim),이형원(Hyungwon Lee),서성현(Seonghyeon Seo),강상훈(Sang Hun Kang) 한국추진공학회 2016 한국추진공학회 학술대회논문집 Vol.2016 No.5
가스 다이내믹 공진 점화 (GIS : Gas-dynamic Ignition System)에서 공진에 의한 가열 효과에 영향을 미치는 여러 인자 중 공진 관 입구의 각도의 변화와 공진관과 노즐 사이의 거리가 가열효과에 미치는 영향을 확인하기 위한 연구를 수행하였다. 기존에 설계된 형상에서 공진관 입구의 각도를 변경하여 생성한 격자계에 대하여 전산해석을 실시하였다. 이를 통하여 공진관 입구의 각도, 노즐과의 거리에 따른 공진관으로 유입되는 유동 특성과 열 공진 현상 메커니즘을 파악하였으며, 어느 정도의 각도가 공진관의 형상으로서 적합한지 확인하였다. In this study, effects of the angle of resonance tube and the distance of nozzle and the cavity on the heating characteristics of gas dynamic resonance ignitor are investigated. Analysis of the various angles of resonance tube and distance of nozzle and cavity grid system are conducted using numerical analysis. In the results, fluid dynamic characteristics and heating mechanisms of a resonance tube are found. Appropriate angle of the resonance tube is determined as well.
Kihong Son,Seunghyung Lee,Hyobin Lee,Yejin Lee,Dongwook Son,Seunghyeon Myeong,Minjoo Chang,Daehong Kim,Myung-Ae Chung 한국자기학회 2023 Journal of Magnetics Vol.28 No.4
This simulation study aims to differentiate between contrast media and calcification in blood vessel using the effective atomic number (EAN) extraction method in electromagnetic X-ray computed tomography (CT) imaging. Calibration was performed on six tissue-equivalent materials, three contrast medium, and one calcium solution. The Hounsfield unit (HU) values at 80 kV and 140 ㎸ with electromagnetic spectrum using dualenergy computed tomography (DECT) facilitated this calibration. EAN from the polynomial method was then compared with that from the Stoichiometric method. In 120 ㎸ vascular imaging, when the HU of calcium and iodine contrast media were alike, EAN provided a more pronounced contrast than HU. The iodine contrast agent’s enhancement in EAN was approximately 30.0 %, and in HU, it was 13.0 % relative to calcium. This indicates EAN’s potential to better differentiate contrast media from calcification in clinical contexts.