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Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
Lee, Soohyun,Seo, Chae Hwa,Lim, Byungho,Yang, Jin Ok,Oh, Jeongsu,Kim, Minjin,Lee, Sooncheol,Lee, Byungwook,Kang, Changwon,Lee, Sanghyuk Oxford University Press 2011 Nucleic acids research Vol.39 No.2
<P>We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. Quantitative RT–PCR based on 27 randomly selected genes in two human cell lines and computer simulation experiments demonstrated superior accuracy of NEUMA over other recently developed methods. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (‘consistency coefficient’) for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. We propose that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data.</P>
Choi, Hyeongsu,Lee, Jeongsu,Shin, Seokyoon,Lee, Juhyun,Lee, Seungjin,Park, Hyunwoo,Kwon, Sejin,Lee, Namgue,Bang, Minwook,Lee, Seung-Beck,Jeon, Hyeongtag IOP Pub 2018 Nanotechnology Vol.29 No.21
<P>Representative tin sulfide compounds, tin monosulfide (SnS) and tin disulfide (SnS<SUB>2</SUB>) are strong candidates for future nanoelectronic devices, based on non-toxicity, low cost, unique structures and optoelectronic properties. However, it is insufficient for synthesizing of tin sulfide thin films using vapor phase deposition method which is capable of fabricating reproducible device and securing high quality films, and their device characteristics. In this study, we obtained highly crystalline SnS thin films by atomic layer deposition and obtained highly crystalline SnS<SUB>2</SUB> thin films by phase transition of the SnS thin films. The SnS thin film was transformed into SnS<SUB>2</SUB> thin film by annealing at 450 °C for 1 h in H<SUB>2</SUB>S atmosphere. This phase transition was confirmed by x-ray diffractometer and x-ray photoelectron spectroscopy, and we studied the cause of the phase transition. We then compared the film characteristics of these two tin sulfide thin films and their switching device characteristics. SnS and SnS<SUB>2</SUB> thin films had optical bandgaps of 1.35 and 2.70 eV, and absorption coefficients of about 10<SUP>5</SUP> and 10<SUP>4</SUP> cm<SUP>−1</SUP> in the visible region, respectively. In addition, SnS and SnS<SUB>2</SUB> thin films exhibited p-type and n-type semiconductor characteristics. In the images of high resolution-transmission electron microscopy, SnS and SnS<SUB>2</SUB> directly showed a highly crystalline orthorhombic and hexagonal layered structure. The field effect transistors of SnS and SnS<SUB>2</SUB> thin films exhibited on–off drain current ratios of 8.8 and 2.1 × 10<SUP>3</SUP> and mobilities of 0.21 and 0.014 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP>, respectively. This difference in switching device characteristics mainly depends on the carrier concentration because it contributes to off-state conductance and mobility. The major carrier concentrations of the SnS and SnS<SUB>2</SUB> thin films were 6.0?×?10<SUP>16</SUP> and 8.7?×?10<SUP>13</SUP> cm<SUP>−3</SUP>, respectively, in this experiment.</P>
A scaling law for the lift of hovering insects
Lee, Jeongsu,Choi, Haecheon,Kim, Ho-Young Cambridge University Press 2015 Journal of fluid mechanics Vol.782 No.-
<P>Insect hovering is one of the most fascinating acrobatic flight modes in nature, and its aerodynamics has been intensively studied, mainly through computational approaches. While the numerical analyses have revealed detailed vortical structures around flapping wings and resulting forces for specific hovering conditions, theoretical understanding of a simple unified mechanism enabling the insects to be airborne is still incomplete. Here, we construct a scaling law for the lift of hovering insects through relatively simple scaling arguments of the strength of the leading edge vortex and the momentum induced by the vortical structure. Comparison of our theory with the measurement data of 35 species of insects confirms that the scaling law captures the essential physics of lift generation of hovering insects. Our results offer a simple yet powerful guideline for biologists who seek the evolutionary direction of the shape and kinematics of insect wings, and for engineers who design flapping-based micro air vehicles.</P>
Hydrodynamic advantages of a low aspect-ratio flapping foil
Lee, Jeongsu,Park, Yong-Jai,Cho, Kyu-Jin,Kim, Daegyoum,Kim, Ho-Young Academic Press 2017 Journal of Fluids and Structures Vol. No.
<P>A high aspect-ratio foil is known to be advantageous in terms of both thrust and efficiency in flapping propulsion. However, many species of fish have evolved a low aspect-ratio hydrofoil, which naturally leads one to search for its physical advantages in locomotion. Here we study the flow physics of a hydrofoil in angular reciprocating motion with negligible free-stream velocity to reveal the effects of an aspect ratio on hydrodynamic performance. By establishing a scaling law for the thrust of a foil of general shapes and corroborating it experimentally, we find that the thrust of an angularly reciprocating foil is maximized at a low aspect ratio of 0.7 while hydromechanical efficiency continuously increases with an aspect ratio. This result suggests that a low aspect-ratio foil can improve thrust produced by the foil when they start from rest, but at the expense of efficiency. (C) 2017 Elsevier Ltd. All rights reserved.</P>
이정수(Jeongsu Lee),이영철(Young chul Lee) 대한기계학회 2021 대한기계학회 춘추학술대회 Vol.2021 No.11
Die-casting is one of the most representative mass production processes widely used for various industrial areas including automotive, shipbuilding, mechanical, and electronics. Although its wide usage in diverse industries, the manufacturing environment of the die-casting industry is limited to the traditional level resulting in high failure rates. In this study, we proposed a novel die-casting fault detection technology based on unsupervised deep learning. The proposed deep-learning approach consists of the time-series image transformation termed fingerprinting and self-labeled training based on a geometric transformation of transformed images. The evaluation with the die-casting manufacturing data suggests that the proposed approach exhibited outstanding performance compared to state-of-the-art deep-learning-based anomaly detection algorithms when trained with the unlabeled dataset.
Jang, Jeongsu,Lee, Yangjin,Yoon, Jun-Yeong,Yoon, Hoon Hahn,Koo, Jahyun,Choe, Jeongheon,Jeon, Sungho,Sung, Jongbaek,Park, Jungwon,Lee, Won Chul,Lee, Hoonkyung,Jeong, Hu Young,Park, Kibog,Kim, Kwanpyo American Chemical Society 2018 Nano letters Vol.18 No.10
<P>The van der Waals epitaxy of functional materials provides an interesting and efficient way to manipulate the electrical properties of various hybrid two-dimensional (2D) systems. Here we show the controlled epitaxial assembly of semiconducting one-dimensional (1D) atomic chains, AuCN, on graphene and investigate the electrical properties of 1D/2D van der Waals heterostructures. AuCN nanowire assembly is tuned by different growth conditions, although the epitaxial alignment between AuCN chains and graphene remains unchanged. The switching of the preferred nanowire growth axis indicates that diffusion kinetics affects the nanowire formation process. Semiconducting AuCN chains endow the 1D/2D hybrid system with a strong responsivity to photons with an energy above 2.7 eV, which is consistent with the bandgap of AuCN. A large UV response (responsivity ∼10<SUP>4</SUP> A/W) was observed under illumination using 3.1 eV (400 nm) photons. Our study clearly demonstrates that 1D chain-structured semiconductors can play a crucial role as a component in multifunctional van der Waals heterostructures.</P> [FIG OMISSION]</BR>
Seunghee Lee,Kichang Lee,Hyeona Kim,Jeongsu An,Junho Han,Taekwon Lee,Hogyun Jeong,Youngkwon Cho 대한수의학회 2020 Journal of Veterinary Science Vol.21 No.5
Background: Dental diseases are common in dogs and cats, and accurate measurements of dentoalveolar structure are important for planning of treatment. The information that the comparison computed tomography (CT) with dental radiography (DTR) is not yet reported in veterinary medicine. Objectives: The purpose of this study was to compare the DTR with CT of dentoalveolar structures in healthy dogs and cats, and to evaluate the CT images of 2 different slice thicknesses (0.5 and 1.0 mm). Methods: We included 6 dogs (2 Maltese and 1 Spitz, Beagle, Pomeranian, mixed, 1 to 8 years, 4 castrated males, and 2 spayed female) and 6 cats (6 domestic short hair, 8 months to 3 years, 4 castrated male, and 2 spayed female) in this study. We measured the pulp cavity to tooth width ratio (P/T ratio) and periodontal space of maxillary and mandibular canine teeth, maxillary fourth premolar, mandibular first molar, maxillary third premolar and mandibular fourth premolar. Results: P/T ratio and periodontal space in the overall dentition of both dogs and cats were smaller in DTR compared to CT. In addition, CT images at 1.0 mm slice thickness was generally measured to be greater than the images at 0.5 mm slice thickness. Conclusions: The results indicate that CT with thin slice thickness provides more accurate information on the dentoalveolar structures. Additional DTR, therefore, may not be required for evaluating dental structure in small-sized dogs and cats.