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lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Park, Charny,Yu, Namhee,Choi, Ikjung,Kim, Wankyu,Lee, Sanghyuk Oxford University Press 2014 Bioinformatics Vol.30 No.17
<P><B>Motivation:</B> A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need.</P><P><B>Results:</B> We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein–lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface.</P><P><B>Availability and implementation:</B> lncRNAtor is available at http://lncrnator.ewha.ac.kr/.</P><P><B>Contact:</B> sanghyuk@ewha.ac.kr</P><P><B>Supplementary information:</B> Supplementary data are available at <I>Bioinformatics</I> online.</P>
Jang, Insu,Chang, Hyeshik,Jun, Yukyung,Park, Seongjin,Yang, Jin Ok,Lee, Byungwook,Kim, Wankyu,Kim, V. Narry,Lee, Sanghyuk Oxford University Press 2015 Bioinformatics Vol.31 No.4
<P><B>Summary:</B> Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase.</P><P><B>Availability and implementation:</B> miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr.</P><P><B>Contact:</B> sanghyuk@ewha.ac.kr</P>
A White-Light-Emitting Molecule: Frustrated Energy Transfer between Constituent Emitting Centers
Park, Sanghyuk,Kwon, Ji Eon,Kim, Se Hun,Seo, Jangwon,Chung, Kyeongwoon,Park, Sun-Young,Jang, Du-Jeon,Medina, Begoñ,a Miliá,n,Gierschner, Johannes,Park, Soo Young American Chemical Society 2009 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.131 No.39
<P>White-light-emitting single molecules are promising materials for use in a new generation of displays and light sources because they offer the possibility of simple fabrication with perfect color reproducibility and stability. To realize white-light emission at the molecular scale, thereby eliminating the detrimental concentration- or environment-dependent energy transfer problem in conventional fluorescent or phosphorescent systems, energy transfer between a larger band-gap donor and a smaller band-gap acceptor must be fundamentally blocked. Here, we present the first example of a concentration-independent ultimate white-light-emitting molecule based on excited-state intramolecular proton transfer materials. Our molecule is composed of covalently linked blue- and orange-light-emitting moieties between which energy transfer is entirely frustrated, leading to the production of reproducible, stable white photo- and electroluminescence.</P>
Detection and Classification of a Ballistic Missile in Ascent Phase
Sanghyuk Park,Jaehyeon Jeong,Chang-Kyung Ryoo,Keeyoung Choi 제어로봇시스템학회 2011 제어로봇시스템학회 국제학술대회 논문집 Vol.2011 No.10
In the boost phase, it is important to early detect and classify an enemy ballistic missile for a swift defense response. These tasks can be typically achieved by search radar which is generally operated at a low data gathering rate of 6 and 12rpm. Moreover, detection altitude is limited by the elevation angle of an antenna. For these reasons, the number of radar measurement is about only 10 to 20 until the ballistic missile in the ascent phase reaches to the maximum detection altitude of the search radar. Such a low data update rate makes detection and classification of a ballistic missile difficult. But, fortunately, a ballistic missile has special features that make it distinguish from other aerial vehicles. In this paper, contrary to general algorithm using the characteristics of the radar signal, we suggest an algorithm using the dynamic characteristics of a ballistic missile for a detection and classification of a ballistic missile in ascent phase.
수산화칼슘 적용에 따른 상아질 접착제의 접착강도 변화에 관한 연구
박노훈,박상혁,최기운,박상진 대한치과보존학회 2007 Restorative Dentistry & Endodontics Vol.32 No.3
본 연구는 다양한 접착 과정과 기전을 지닌 4종의 상아질 접착제를 이용하여 수산화칼슘의 사용 여부 및 그 적용 기간이 접착강도에 미치는 영향을 측정 및 평가하고 주사전자현미경을 이용한 접착 계면의 관찰을 통해 복합레진 수복이나 레진 시멘트를 이용한 수복물 접착 시에 적절한 상아질 접착제의 선택과 사용방법을 알아보고자 시행하였다. 치수강에 근접한 상이질 표면을 노출시킨 후, Ca(OH)_(2)를 생리식염수와 혼합하여 실험군 치아 24개의 상아질 표면에 적용한 후, IRM (Intermediate Restorative Material, Dentsply Caulk, Milford, USA)으로 적용된 수산화칼슘 및 변연 부위의 상아질과 법랑질 모두를 밀폐하여 36.5℃ 증류수에서 실험기간 (7일 및 30일) 동안 보관하였다. Scotchbond Multipurpose, Single Bond, SE Bond and Prompt L-Pop 등 4종의 상아질 접착제를 제조사의 지시에 따라 적용하고 복합 레진을 3회에 나누어 총 5 mm 높이로 적충한 뒤 각 층마다 20초씩 광조사를 시행하였다. Universal testing machine을 이용하여 1 mm/min의 crosshead speed로 하중을 가하여 미세인장 접착 강도를 측정하고 파단면을 주사전자현미경으로 관찰하였다. 이상의 연구 결과에서 단기간 (7일 또는 30일간)의 수산화칼슘 적용은 상아질 접착제의 접착 과정의 차이에 따른 변화를 나타내지 않는 것으로 평가되었다 The purpose of this study was to investigate the effect of calcium hydroxide on dentin bonding strength of various dentin bonding systems as a function of time in composite resin restoration. Dentin adhesives used in this study were Scotchbond Multipurpose, Single Bond, SE Bond and Prompt L-Pop. Flat dentin surfaces adjacent to pulp chamber were created, then Ca(OH)_(2) and saline were mixed and applied on dentin surface of experimental group, then IRM was used to cover the mixture on dentin surface and the specimens were stored at 36.5℃ for experiment period (7 days, 30 days). After removing IRM and Ca(OH)_(2), each dentin adhesives were treated on dentin surfaces. Composite resin (Z-250, 3M) was placed with 5 mm height and was light-cured for 20 seconds. After stored in distilled water for 24 hours, each dentin-composite bonded spicemen was embedded in epoxy resin and sectioned into 1.0×1.0 ㎟ cross section composite-dentin beams. Specimen was mounted on zig of Universal testing machine and μTBS test was performed. SEM analysis was performed to examine the fractured surfaces. The results suggested that applying calcium hydroxide did not show significant difference in dentin bonding strength. [J Kor Acad Cons Dent 32(3):198-207, 2007]
Wind and Airspeed Error Estimation with GPS and Pitot-static System for Small UAV
Sanghyuk Park 한국항공우주학회 2017 International Journal of Aeronautical and Space Sc Vol.18 No.2
This paper presents a method to estimate steady wind and airspeed bias error using an aircraft with GPS and airspeed sensor. The estimation uses the vector relation between the inertial, air, and wind velocities through a novel design of an extended Kalman filter. The observability analysis is also presented to show that the aircraft is required to keep changing its flight direction for the desired observability. The feasibility and performance of the proposed algorithm is demonstrated through simulations and flight experiments.
Real-Time Selection of Waypoints in the Sense of Survivability Enhancement
SanghyUk Park,Chang-Kyung Ryoo 한국산업정보학회 2014 한국산업정보학회 학술대회논문집 Vol.2014 No.1
This paper proposes a real-time determination of waypoints that should be passed by an aerospace system such as unmanned aerial vehicle and cruise missile. In the very initial stage, anti-air threats are regarded as the points occupying the domains that are divided by Voronoi lines. The Voronoi vertices are the candidates of the waypoints. Each waypoint is then sequentially optimized to maximize the survivability while the adjacent waypoints are fixed during the optimization until converged. It takes less than a second to find optimal waypoints on the path of interest.