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Kim Doyun,Bak Myeong Seong,Park Haney,Baek In Seon,Chung Geehoon,박재현,Ahn Sora,Park Seon-Young,배현수,Park Hi-Joon,김선광 한국뇌신경과학회 2023 Experimental Neurobiology Vol.32 No.3
Quantification of tyrosine hydroxylase (TH)-positive neurons is essential for the preclinical study of Parkinson’s disease (PD). However, manual analysis of immunohistochemical (IHC) images is labor-intensive and has less reproducibility due to the lack of objectivity. Therefore, several automated methods of IHC image analysis have been proposed, although they have limitations of low accuracy and difficulties in practical use. Here, we developed a convolutional neural network-based machine learning algorithm for TH+ cell counting. The developed analytical tool showed higher accuracy than the conventional methods and could be used under diverse experimental conditions of image staining intensity, brightness, and contrast. Our automated cell detection algorithm is available for free and has an intelligible graphical user interface for cell counting to assist practical applications. Overall, we expect that the proposed TH+ cell counting tool will promote preclinical PD research by saving time and enabling objective analysis of IHC images.
Kim, Jiseon,Min, Jee Sun,Kim, Doyun,Zheng, Yu Fen,Mailar, Karabasappa,Choi, Won Jun,Lee, Choongho,Bae, Soo Kyung Elsevier 2017 Journal of pharmaceutical and biomedical analysis Vol.134 No.-
<P><B>Abstract</B></P> <P>In this study, a simple and sensitive liquid chromatography-tandem mass spectrometry (LC–MS/MS) method for the quantification of <I>trans</I>-ε-viniferin in small volumes (10μl) of mouse plasma using chlorpropamide as an internal standard was developed and validated. Plasma samples were precipitated with acetonitrile and separated using an Eclipse Plus C<SUB>18</SUB> column (100×4.6mm, 1.8-μm) with a mobile phase consisting of 0.1% formic acid in acetonitrile and 0.1% formic acid in water (60:40v/v) at a flow rate of 0.5ml/min. A triple quadrupole mass spectrometer operating in positive ion mode with selected reaction-monitoring mode was used to determine <I>trans</I>-ε-viniferin and chlorpropamide transitions of 455.10→215.05 and 277.00→111.00, respectively. The lower limit of quantification was 5ng/ml with a linear range of 5–2500ng/ml (<I>r</I> ≥0.9949). All validation data, including the selectivity, precision, accuracy, recovery, dilution integrity, and stability, conformed to the acceptance requirements. No matrix effects were observed. The developed method was successfully applied to pharmacokinetic studies of <I>trans</I>-ε-viniferin following intravenous (2.5mg/kg), intraperitoneal (2.5, 5 and 10mg/kg), and oral (40mg/kg) administration in mice. This is the first report on the pharmacokinetic properties of <I>trans</I>-ε-viniferin. The results provide a meaningful basis for evaluating the pre-clinical or clinical applications of <I>trans</I>-ε-viniferin.</P> <P><B>Highlights</B></P> <P> <UL> <LI> First LC–MS/MS method for <I>trans</I>-ε-viniferin quantification in mouse plasma. </LI> <LI> A simple protein precipitation that allowed for efficient/reproducible recovery yields was used. </LI> <LI> The small plasma volume (10μl) supports the ability to examine pharmacokinetics in mice. </LI> </UL> </P>
Explicit CFD Analysis Model Validation for Dry Cask Simulator
Doyun Kim,Ju-chan Lee,Seunghwan Yu 한국방사성폐기물학회 2023 한국방사성폐기물학회 학술논문요약집 Vol.21 No.1
Spent nuclear fuels should be safely stored until being disposed and dry storage system is predominantly used to retain the fuels. During long-term storage, there are several mechanisms that could result in the degradation of spent nuclear fuels, and the temperature is the most important parameter to predict and estimate the degradation behaviors. Therefore, thermal analysis to estimate temperatures of spent nuclear fuel and the storage system should be performed to evaluate whether the temperatures exceed safety limit. Recently, thermal hydraulic analysis with CFD codes is widely used to investigate the temperature of spent nuclear fuel in dry storage. Herein, Explicit CFD analysis model is introduced and validated by estimating the thermal hydraulic response of the dry storage system that is Dry Cask Simulator (DCS). Extended Storage Collaborating Program (ESCP) led by the Electric Power Research Institute (EPRI) is organized to assess degradation effects of spent nuclear fuel during long-term dry storage, and DCS is the first phase of the program. The dry storage system, containing a single BWR assembly in a canister, was designed to produce validation-quality data for thermal analysis model. ANSYS FLUENT is used to simulate DCS, and the test condition of 0.5 kW decay heat and 100 kPa helium pressure was investigated in this study. In case of peak cladding temperature (PCT), PCT from the experiment was 376 K while that of CFD was 374 K. It implies CFD simulation gives good agreement with experimental measurement. Peak temperatures of channel can, basket, canister and shell predicted by CFD simulation also show good prediction and the discrepancies were less than 7 K while measurements uncertainty was 7 K.
Doyun Kim,Woo-Jin Song,Sung-Soo Kim,Soyoung Jeong,Hyun Jeong Hong,Youngmin Yun 대한수의학회 2023 大韓獸醫學會誌 Vol.63 No.2
A 13-year-old neutered male Maltese dog presented to our hospital with lethargy and anorexia. Laboratory abnormalities included severe non-regenerative anemia (hematocrit, 12.9%; reticulocyte count 12.8 K/μL). The cytology of bone marrow revealed erythroid hypercellularity with mild myelofibrosis. Therefore, late-stage precursor-targeted immune-mediated anemia (PIMA) was diagnosed. Multimodal treatment including 2 immunosuppressant drugs (prednisolone and mycophenolate mofetil), antithrombic drug (clopidogrel), and blood transfusion was performed. The dog showed complete remission from PIMA, and the total duration of follow-up was 622 days. This is the first case report of canine PIMA managed successfully with prednisolone and mycophenolate mofetil in Korea.
Kim, Jiwoong,Kwon, Hanjung,Kim, Jae-Hee,Roh, Ki-Min,Shin, Doyun,Jang, Hee Dong Elsevier 2015 JOURNAL OF ALLOYS AND COMPOUNDS Vol.619 No.-
<P><B>Abstract</B></P> <P>The elastic properties and electronic structures of partially ordered and disordered Zr(C<SUB>1−</SUB> <I> <SUB>x</SUB> </I>N<I> <SUB>x</SUB> </I>) solid solution compounds were investigated using first principles calculations to understand the effects of nitrogen content and atomic distribution. To obtain a proper exchange–correlation energy, we used local density and generalized gradient approximations with Perdew–Burke–Ernzerhof (LDA and GGA-PBE) parametrization. Partially ordered and disordered structures of Zr(C<SUB>1−</SUB> <I> <SUB>x</SUB> </I>N<I> <SUB>x</SUB> </I>) compounds were expressed using unit cell and special quasi-random structure (SQS) models, respectively. We demonstrated that although the disordered models have P1 symmetry with different model sizes and cell shapes compared with ordered models, they reproduce the equilibrium structure and elastic properties of the Zr(C<SUB>1−</SUB> <I> <SUB>x</SUB> </I>N<I> <SUB>x</SUB> </I>) compounds with B1 (Fm-3m) symmetry. However, clear differences exist in the electronic structures. Therefore, the atomic configuration is essential for calculating the electronic structures of the Zr(C<SUB>1−</SUB> <I> <SUB>x</SUB> </I>N<I> <SUB>x</SUB> </I>) compounds.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Elastic and electronic properties of Zr(C<SUB>1−<I>x</I> </SUB>N<SUB> <I>x</I> </SUB>) compounds by first principles. </LI> <LI> We elucidate the effects of atomic configuration on compound properties. </LI> <LI> Ordered and disordered models are depicted by unit cell and special quasi-random structures. </LI> <LI> Disordered structures are suitable models to estimate compound elastic properties. </LI> <LI> The atomic configuration is essential to obtain accurate electronic structures. </LI> </UL> </P>
MRPrimerV: a database of PCR primers for RNA virus detection
Kim, Hyerin,Kang, NaNa,An, KyuHyeon,Kim, Doyun,Koo, JaeHyung,Kim, Min-Soo Oxford University Press 2017 Nucleic acids research Vol.45 No.d1
<P>Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.</P>