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CORE:Common Region Extension Based Multiple Protein Structure Alignment for Producing Multiple Solution

Journal of Computer Science & Technology 2013年第4期28卷 647-656页

作者： Woo-Cheol kim Sanghyun Park Jung-Im won College of Information Sciences and Technology The Pennsylvania State University University Park Department of Computer Science Yonsei University Research Center of Information and Electronic Engineering Hallym University Chuncheon

Over the past several decades, biologists have conducted numerous studies examining both general and specific functions of proteins. Generally, if similarities in either the structure or sequence of amino acids exist for two proteins, then a common biological function is expected. Protein function is determined primarily based on the structure rather than the sequence of amino acids. The algorithm for protein structure alignment is an essential tool for the research. The quality of the algorithm depends on the quality of the similarity measure that is used, and the similarity measure is an objective function used to determine the best alignment because of their individual strength and weakness However, none of existing similarity measures became golden standard They require excessive filtering to find a single alignment. In this paper, we introduce a new strategy that finds not a single alignment, but multiple alignments with different lengths. This method has obvious benefits of high quality alignment. However, this novel method leads to a new problem that the running time for this method is considerably longer than that for methods that find only a single alignment. To address this problem~ we propose algorithms that can locate a common region （CORE） of multiple alignment candidates, and can then extend the CORE into multiple alignments. Because the CORE can be defined from a final alignment, we introduce CORE＊ that is similar to CORE and propose an algorithm to identify the CORE＊. By adopting CORE＊ and dynamic programming, our proposed method produces multiple alignments of various lengths with higher accuracy than previous methods. In the experiments, the alignments identified by our algorithm are longer than those obtained by TM-align by 17% and 15.48%, on average, when the comparison is conducted at the level of super-family and fold, respectively.

关键词： structure alignment similarity search protein structure

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Effects of multi-dopants （Zn and Ho） in stabilizing spinel structure for cathode materials in lithium rechargeable batteries-Novel chelated sol-gel synthesis

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Particuology 2016年第1期14卷 87-95页

作者： R. Thirunakaran Taewhan kim won-Sub Yoon CSIR-Central Electrochemical Research Institute Karaikudi 630 006 Tamil Nadu India Department of Energy Science Sungkyunkwan University Suwon 440-746 South Korea

Multi-doped spinels, namely LiMn204 and LiZnxHoyMn2 x yO4 （x=0.10-0.18; y= 0.02-0.10）, for use as cathode materials for lithium-ion rechargeable batteries were synthesized via sol-gel method, using lauric acid as the chelating agent, to obtain micron-sized particles. The physical properties of the synthesized samples were investigated using differential thermal analysis, Fourier-transform infrared spectroscopy, X-ray diffraction （XRD）, scanning electron microscopy （SEM）, transmission electron microscopy, energy-dispersive X-ray analysis, and electrochemical methods. XRD showed that LiMn204 and LiZnxHoyMn2_x y04 have high degrees of crystallinity and good phase purities. The SEM images of LiMn204 showed an ice-cube morphology with particles of size 1 μm. Charge-discharge studies showed that undoped LiMn2 O4 delivered the discharge capacity of 124 mA h/g with coulombic efficiency of 95% during the first cycle, whereas doped spinels delivered discharge capacities of 125, 120, and 127 mA h/g in the first cycle with coulombic efficiencies of 96%, 91%, and 91%, respectively.

关键词： Holmium Zinc Lauric acid Sol-gel Spinel cathode Lithium-ion battery

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Effect of Radiant Spectral Characteristics on Performance of a Near-Infra-Red Heating Module

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Journal of Thermal Science 2011年第6期20卷 510-515页

作者： Ju-Hyun kim won-Taek Choi Minsub Han School of Mechanical System Engineering University of Incheon Araytech IncheonKorea

We simulated the heat transfer phenomena of the heating module that is primarily based on the radiant energy in the near-infra-red(NIR) *** the module,the power emitted by the lamp filament is distributed to the lamp glass,reflector,and the target medium,which are cooled by an air *** radiant heat transfer is simulated by using the ray-tracing scheme,in which the spectral characteristics of the emission and the materials are *** heat transport from the lamp glass to the cooling air is analyzed by using the finite volume *** the lamp-filament temperature rises in the range of 3000-3400K,the NIR radiant power on the target medium ***,the lamp-glass temperature also rises,and the proportion of the NIR power to the entire radiation has a peak in the temperature *** spectral distributions of the absorbed energies in all the components in the module are highly non-uniform,and a monochromatic model of the radiant heat transfer may result in a significant discrepancy.

关键词： Computational Fluid Dynamics(CFD) Curing Drying Coating process

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Improvement of hydrogen embrittlement and stress corrosion cracking by annealing for Al-4.4Mg-0.6Mn alloy

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Transactions of Nonferrous Metals Society of China 2011年第A01期21卷 17-22页

作者： Seong-Jong kim Min-Su HAN Seong-Kweon kim Seok-ki JANG Division of Marine Engineering Mokpo National Maritime University Media Engineering Seoul National University of Technology

With no annealing treatment, cathodic polarization trends in 5083F A1 alloy revealed concentration polarization and activation polarization. However, the annealed specimens have lower current densities at corrosion protection potential compared to the non-annealed specimen. The results of SSRTs conducted in seawater at the applied potential range of-l.8 V to -0.5 V indicated that the maximum tensile strength, elongation, and time-to-fracture had high values at applied potentials of -0.7 to -1.4 V. The maximum tensile strength, elongation, and time-to-f？acture decreased when the potential values were beyond this range in either anodic or cathodic direction. In general, the increased shear lip caused by annealing treatment indicates elongation. Time-to-fracture would likely increase with elongation. Potentials between -0.5 V to -0.6 V were found to be in the region of stress corrosion cracking. The corrosion protection zone was determined to be -0.7 V to -J,4 V because these potential ranges produced good mechanical properties. Potential less than -1.4 V produced a fractured surface with a mixture of dimples （ductile fractures） and a quasi-cleavage pattern resulting from the effects of hydrogen gas.

关键词： annealing 5083F A1-Mg alloy corrosion seawater slow strain rate tests

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Effects of humic acid on phytodegradation of petroleum hydrocarbons in soil simultaneously contaminated with heavy metals

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Journal of Environmental Sciences 2011年第12期23卷 2034-2041页

作者： Soyoung Park ki Seob kim Jeong-Tae kim Daeseok Kang kijune Sung Department of Ocean Engineering Pukyong National University Busan 608-737 Korea Department of Ecological Engineering Pukyong National University Busan 608-737 Korea

The use of humic acid （HA） to enhance the efficiency of phytodegradation of petroleum hydrocarbons in soil contaminated with diesel fuel was evaluated in this study. A sample of soil was artificially contaminated with commercially available diesel fuel to an initial total petroleum hydrocarbons （TPH） concentration of 2300 mg/kg and four heavy metals with concentrations of 400 mg/kg for Pb, 200 mg/kg for Cu, 12 mg/kg for Cd, and 160 mg/kg for Ni. Three plant species, Brassica campestris, Festuca arundinacea, and Helianthus annuus, were selected for the phytodegradation experiment. Percentage degradation of TPH in the soil in a control pot supplemented with HA increased to 45% from 30% without HA. The addition of HA resulted in an increases in the removal of TPH from the soil in pots planted with B. campestris, F. arundinacea, and H. annuus, enhancing percentage degradation to 86%, 64%, and 85% from 45%, 54%, and 66%, respectively. The effect of HA was also observed in the degradation of n-alkanes within 30 days. The rates of removal of n-alkanes in soil planted with B. campestris and H. annuus were high for n-alkanes in the range of C11–C28. A dynamic increase in dehydrogenase activity was observed during the last 15 days of a 30-day experimental period in all the pots amended with HA. The enhanced biodegradation performance for TPHs observed might be due to an increase in microbial activities and bioavailable TPH in soils caused by combined effects of plants and HA. The results suggested that HA could act as an enhancing agent for phytodegradation of petroleum hydrocarbons in soil contaminated with diesel fuel and heavy metals.

关键词： phytodegradation TPHs humic acid n-alkanes DHA combined effects

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High-frequency acoustic backscattering characteristics for acoustic detection of the red tide species Akashiwo sanguinea and Alexandrium affine

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Journal of Oceanology and Limnology 2019年第4期37卷 1268-1276页

作者： kim Hansoo KANG Donhyug JUNG Seung won kim Mira Maritime Security and Safety Research Center Korea Institute of Ocean Science & Technology (KIOST) Busan 49111 Korea Department of Ocean System Engineering Jeju National University Jeju 63243 Korea Library of Marine Samples Korea Institute of Ocean Science & Technology (KIOST) Geoje 53201 Korea

Harmful algal blooms (HABs), caused by the overgrowth of certain phytoplankton species, have negative effects on marine environments and coastal fisheries. In addition to cell-counting methods using phytoplankton nets, a hydroacoustic technique based on acoustic backscattering has been proposed for the detection of phytoplankton blooms. However, little is known of the acoustic properties of HAB species. In this study, as essential data to support this technique, we measured the acoustic properties of two HAB species, Akashiwo sanguinea and Alexandrium affine, which occur in the South Sea off the coast of Korea. Due to the small size of the target, we used ultrasound for the measurements. Experiments were conducted under laboratory and field conditions. In the laboratory experiment, the acoustic signal received from each species was directly proportional to the cell abundance. We derived a relationship between the cell abundance and acoustic signal received for each species. The measured signals were compared to predictions of a fluid sphere scattering model. When A. sanguinea blooms appeared at an abundance greater than 3 500 cells/mL, the acoustic signals varied with cell abundance, showing a good correlation. These results confirm that acoustic measurements can be used to detect HAB species.

关键词： acoustic backscattering Akashiwo sanguinea Alexandrium affine fluid-sphere scattering model harmful algal blooms (HABs) red tide

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Offshore Structural Control Considering Fluid Structure Interaction

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China Ocean Engineering 2006年第2期20卷 259-268页

作者： Ju Myung kim Dong Hyawn kim Gyu won LEE Department of Civil Engineering Chonbuk National University Jeoh Ju Jeonbuk 561-156 Korea Department of Ocean System Engineering Kunsan National University KunsanJeonbuk 573-701 Korea

Tuned Mass Damper （TMD） was applied to an offshore structure to control ocean wave-induced vibration, In the analysis of the dynamic response of the offshore structure, fluid-structure interaction is considered and the errors, which occur in the linearization of the interaction, are investigated. For the investigation of the performance of TMD in controlling the vibration, both regular waves with different periods and irregular waves with different significant wave heights are used. Based on the numerical analysis it is concluded that the fluid-structure interaction should be considered in the evaluation of the capability of TMD in vibration control of offshore structures.

关键词： offshore structure tuned mass damper vibration control fluid-structure interaction nonlinear Morison equation

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Complete resection of a huge hypervascular inflammatory myofibroblastic tumor in right hemithorax after embolization

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World Journal of Pediatrics 2016年第4期12卷 498-500页

作者： Kyu-Nam kim Dong-won kim Department of Anesthesiology and Pain Medicine Hanyang University HospitalRepublic of Korea

Background:Inflammatory myofibroblastic tumor(IMT)is a rare and mostly benign tumor that has the possibility of malignant ***:Radiological findings revealed a huge mass that filled most of the right hemithorax of a 17-month-old female *** extirpation was stopped due to massive bleeding and limited exposure of the *** was conducted to obstruct the arteries feeding the *** resection was ***:Histopathologic examination led to the diagnosis of *** recovery was ***:Hypervascularity of IMT should be *** embolization can be effective to reduce intraoperative blood loss and facilitate the surgical procedure.

关键词： embolization granuloma mediastinal neoplasms plasma cell

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Nanomaterials for the abatement of cadmium (Ⅱ) ions from water/ wastewater

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Nano Research 2019年第7期12卷 1489-1507页

作者： Kumar Vikrant Vanish Kumar Kowsalya Vellingiri ki-Hyun kim Department of Civil and Environmental Engineering Hanyang University222 Wangsimni-roSeoul 04763Republic of Korea National Agri-Food Biotechnology Institute (NABI) S.A.S. NagarPunjab 140306India Environmental and Water Resources Engineering Division Department of Civil Engineering IIT MadrasChennai 600036India

The rapid rise of modern industry is the source of unchecked effluents containing many pernicious heavy metals (e.g.,cadmium).To rehabilitate the ecology,food resources,and health of humans and animals,various conventional methodologies are being used in wastewater treatment facilities for the abatement of ***,the development of advanced,economical,and efficient adsorbents is needed because of the many shortcomings of conventional methods (e.g.,high cost,intensive operation,and inefficiency).Recent advancements in materials science and chemistry have introduced the use of nanomaterials,which possess very high specific surface areas and multiple functionalities,for the removal of specific targets such as *** review explores the recent developments and trends in nanomaterial adsorption technology for the mitigation of *** paper further surveys the present obstacles and future opportunities for the advancement of nanomaterial-based technologies in the area of water treatment.

关键词： nanomaterials cadmium adsorption pollution control water purification heavy metal

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Evidence from a familial case suggests maternal inheritance of primary biliary cholangitis

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World Journal of Gastroenterology 2017年第39期23卷 7191-7197页

作者： Saeam Shin In Ho Moh Young Sik Woo Sung won Jung Jin Bae kim Ji won Park ki Tae Suk Hyoung Su kim Mineui Hong Sang Hoon Park Myung Seok Lee Department of Laboratory Medicine Kangnam Sacred Heart Hospital Hallym University College of Medicine Division of Gastroenterology and Hepatology Department of Internal Medicine Kangnam Sacred Heart Hospital Hallym University College of Medicine Department of Pathology Kangnam Sacred Heart Hospital Hallym University College of Medicine

Primary biliary cholangitis(PBC) is an idiopathic autoimmune liver disease characterized by chronic cholestasis and destruction of the intrahepatic bile ducts. Similar to other autoimmune diseases, the pathogenesis of PBC is considered to be a complex etiologic phenomenon involving the interaction of genetic and environmental factors. Although a number of common variants associated with PBC have been reported from genome-wide association studies, a precise genetic mechanism underlying PBC has yet to be identified. Here, we describe a family with four sisters who were diagnosed with PBC. After the diagnosis of the index patient who was in an advanced stage of PBC, one sister presented with acute hepatitis, and two sisters were subsequently diagnosed with PBC. Notably, one half-sister with a different mother exhibited no evidence of PBC following clinical investigation. Our report suggests the possibility of a maternal inheritance of PBC susceptibility. Moreover, judging from the highpenetrance of the disease observed in this family, we inferred that a pathogenic genetic variant might be the cause of PBC development. We describe a family that exhibited diverse clinical presentations of PBC that included asymptomatic stages with mildly increased liver enzyme levels and symptomatic stages with acute hepatitis or advanced liver fibrosis. Additional studies are needed to investigate the role of genetic factors in the pathogenesis of this rare autoimmune disease.

关键词： Primary biliary cholangitis Family history Genetic susceptibility

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