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

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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

Interfacial modulation of bifunctional electrolyte additive engineering for dendrite-free and robust lithium metal anode

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Journal of Energy Chemistry 2024年第10期97卷 120-127,I0003页

作者： Mahammad Rafi Shaik Yongmin Park Young-Kwang jung Won Bin im Division of Materials Science and Engineering Hanyang University222Wangsimni-roSeongdongguSeoul 0473Republic of Kor Department of Chemical Engineering and Biotechnology University of CambridgeCambridge CB3 OASUK

Anode materials for rechargeable electric car batteries are obtained from Li-metal owing to their extremely high specific capacity and low redox ***,safety concerns related to dendrite formation on the anode surface caused by the uneven distribution of Li-ions during the discharge process interfere with the use of Li-metal in industrial *** this study,methyl vinyl sulfone(MVS),a sulfone-based functional electrolyte additive,is used in an additive engineering strategy to control Lielectrolyte interactions and address the aforementioned *** dendrite growth may be restricted,and transition metal degradation on the surface of the cathode can be reduced by the MVS-derived functional electrolyte additive interfacial *** electrochemical performance of an ethylene carbonate/dimethyl carbonate(EC/DMC)+1 wt% MVS Li-metal anode of a Li||Li symmetric cell exhibits remarkable cycle stability,maintaining a low overvoltage for over 750 h at 1 mA cm^(-2),and capacity of 1 mA h cm^(-2).Additionally,LiNi_(0.8)Co_(0.1)Mn_(0.1)O_(2)(NCM811) full cells with the MVS additive exhibit enhanced electrochemical stability for 250 cycles at a current density of 100 mA g^(-1).This study provides an innovative approach for stabilizing the metal-electrolyte interfacial layer that may be used for practical applications in metal-based rechargeable batteries.

关键词： Lithium rechargeable battery Dendrite-free Electrolyte additive Bifunctional electrolyte Interfacial layer

Trap and 1/f-noise effects at the surface and core of GaN nanowire gateall-around FET structure

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Nano Research 2019年第4期12卷 809-814页

作者： Mallem Siva Pratap Reddy Ki-Sik im jung-Hee Lee Raphael Caulmione Sorin Cristoloveanu School of Electronics Engineering Kyungpook National University Daegu 41566 Republic of Korea Advanced Material Research Center Kumoh National Institute of Technology Gumi 39177 Republic of Korea SOITEC Bernin 38190 France Institute of Microelectronics Electromagnetism and Photonics Grenoble Polytechnic Institute Minatec Grenoble 38016 France

Using capacitance,conductance and noise measurements,we investigate the trapping behavior at the surface and in the core of triangular-shaped one-dimensional (1 D) array of GaN nanowire gate-all-around field effect transistor (GAA FET),fabricated via a top-down *** surface traps in such a low dimensional device play a crucial role in determining the device *** estimated surface trap density rapidly decreases with increasing frequency,ranging from 6.07 × 1012 cm-2·eV-1 at 1 kHz to 1.90 × 1011 cm-2·eV-1 at 1 MHz,*** noise results reveal that the power spectral density increases with gate voltage and clearly exhibits 1/f-noise signature in the accumulation region (Vgs > Vth =3.4 V) for all *** the surface depletion region (1.5 V ime,the electron trapping/detrapping process through deep traps expands into the totally depleted nanowire core and the G-R noise prevails in the entire nanowire channel.

关键词： gate-all-around field effect transistor (FET) nanowire GaN trap 1/f-noise

Lentinula edodes extract inhibits matrix metalloproteinase expression and increases typeⅠprocollagen expression via the p38 MAPK/c-Fos signaling pathway in ultraviolet A and B-irradiated HaCaT keratinocytes

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Asian Pacific Journal of Tropical Biomedicine 2021年第4期11卷 164-173页

作者： jung im Lee jung Hwan Oh Fatih Karadeniz So Young Park Hye Ran Kim Hyun Jin Jo Kyung im jung Byung-Jin Jeon Chang-Suk Kong Marine Biotechnology Center for Pharmaceuticals and Foods Silla UniversityBusan 46958Korea Department of Food and Nutrition College of Medical and Life SciencesSilla UniversityBusan 46958Korea Ocean Fisheries and Bio Center Busan technoparkBusan 46048Korea

Objective:To determine the effect of Lentinula edodes extract on ultraviolet(UV)A and UVB-induced changes in matrix metalloproteinase(MMP)and type I procollagen expression using human immortalized HaCaT ***:Lentinula edodes ethanol extract(LEE)was obtained by extraction with 80%ethanol for 4 h at 80℃.Effect of LEE on UVinduced alteration on the expression and production of MMPs and type I procollagen in keratinocytes was investigated using ELISA,RT-PCR,and Western blotting *** determine the underlying mechanism of LEE-mediated effects,mitogen-activated protein kinase(MAPK)and activator protein 1 signaling pathways were analysed by Western blotting ***:LEE significantly inhibited the expression of MMP-1 and MMP-9 and increased the expression of type I procollagen in UVA and UVB-irradiated HaCaT *** phosphorylation levels of p38 were significantly inhibited by LEE whereas it did not affect c-Jun N-terminal kinase and extracellular signal-regulated kinase *** of p38 phosphorylation was also accompanied by downregulation of UVA and UVB-induced increase in ***:LEE effectively inhibits the expression of MMP-1 and MMP-9 and increases type I procollagen production through the p38 MAPK/c-Fos signaling pathway in UVA and UVB-irradiated HaCaT *** findings suggest that Lentinula edodes may be developed as a cosmetic material to suppress UV exposuremediated skin aging.

关键词： Lentinula edodes Ultraviolet Matrix metalloproteinases TypeⅠprocollagen Ha Ca T

Anti-MMP-2 and MMP-9 activity of Salsola komarovii Iljin extract and its solvent fractions

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Asian Pacific Journal of Tropical Biomedicine 2020年第10期10卷 460-469页

作者： jung-Ha Kil Fatih Karadeniz Ga Hyun Yu Hojun Kim Junse Kim jung Hwan Oh jung im Lee Chang-SukKong Youngwan Seo Marine Biotechnology Center for Pharmaceuticals and Foods Silla UniversityBaegyang-daero 700 beon-gil 140Sasang-guBusan 46958Korea Department of Food and Nutrition College of Medical and Life SciencesSilla UniversityBaegyang-daero 700 beon-gil 140Sasang-guBusan 46958Korea Division of Marine Bioscience Korea Maritime and Ocean UniversityBusan 49112Korea

Objective: To investigate matrix metalloproteinases(MMP)-2 and MMP-9 inhibitory effect of Salsola komarovii Iljin, an edible halophyte with health beneficial ***: Salsola komarovii crude extracts(SKI), and solvent(n-hexane, 85% aq. MeOH, n-BuOH, and H2O) fractionated extracts of SKI were prepared. Gelatin zymography was carried out to observe MMP enzymatic activity. The release of the MMP enzymes was measured by enzyme-linked immunosorbent assay. Expression of MMPs in m RNA and protein level were investigated by polymerase chain reaction analysis and immunoblotting, ***: SKI and SKI fractions inhibited active MMP-2 and MMP-9 amount in the treated cell culture medium. Also, SKI suppressed the release of MMP-2 and MMP-9 from stimulated HT1080 human fibrosarcoma cells. Furthermore, SKI suppressed the m RNA and protein expression of MMP-2 and MMP-9. SKI fractions showed parallel effects except for H2O fraction which did not yield any significant MMP inhibitory effect. Among fractions, 85% aq. Me OH was the most active fraction to inhibit both the enzymatic effect and expression of MMP-2 and ***: SKI may contain potential MMP release inhibitory compounds. Salsola komarovii is a promising source of compounds against MMP and could be utilized in the development of antitumor agents.

关键词： release utilized effect

Identification of differentially expressed miRNAs associated with chronic kidney disease-mineral bone disorder

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Frontiers of Medicine 2017年第3期11卷 378-385页

作者： Kyung im Kim Sohyun Jeong Nayoung Han jung Mi Oh Kook-Hwan Oh In-Wha Kim College of Pharmacy Korea University Sejong 30019 Republic of Korea College of Pharmacy and Research Institute of Pharmaceutical Sciences -Seoul National University Seoui 08826 Republic of Korea Divisionof-Nephrology Department of Internai Medicine Seoul National University Hospital Seoul 03080 Republic of Korea

The purpose of this study is to characterize a meta-signature of differentially expressed mRNA in chronic kidney disease （CKD） to predict putative microRNA （miRNA） in CKD-mineral bone disorder （CKD- MBD） and confirm the changes in these genes and miRNA expression under uremic conditions by using a cell culture system. PubMed searches using MeSH terms and keywords related to CKD, uremia, and mRNA arrays were conducted. Through a computational analysis, a meta-signature that characterizes the significant intersection of differentially expressed mRNA and expected miRNAs associated with CKD-MBD was determined. Additionally, changes in gene and miRNA expressions under uremic conditions were confirmed with human Saos-2 osteoblast-like cells. A statistically significant mRNA meta-signature of upregulated and downregulated mRNA levels was identified. Furthermore, miRNA expression profiles were inferred, and computational anaIyses were performed with the imputed mieroRNA regulation based on weighted ranked expression and putative microRNA targets （imRE） method to identify miRNAs associated with CKD occurrence. TLR4 and miR-146b levels were significantly associated with CKD-MBD. TLR4 levels were significantly downregulated, whereas pri- miR-146b and miR-146b were upregulated in the presence of uremic toxins in human Saos-2 osteoblast-like cells. Differentially expressed miRNAs associated with CKD-MBD were identified through a computational analysis, and changes in gene and miRNA expressions were confirmed with an in vitro cell culture system.

关键词： chronic kidney disease microRNA mineral bone disorder uremia

In vivo analysis of post-joint-preserving surgery fracture of 3D-printed Ti-6Al-4V implant to treat bone cancer

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Bio-Design and Manufacturing 2021年第4期4卷 879-888页

作者： Jong Woong Park Ye Chan Shin Hyun Guy Kang Sangeun Park Eunhyeok Seo Hyokyung Sung im Doo jung Division of Convergence Technology National Cancer CenterGoyang 10408Republic of Korea Orthopaedic Oncology Clinic National Cancer CenterGoyang 10408Republic of Korea Department of Materials Engineering and Convergence Technology Gyeongsang National UniversityJin-Ju 52828Republic of Korea Department of Mechanical Engineering Ulsan National Institute of Science and TechnologyUNIST-Gil 50Ulsan 44919Republic of Korea

Cancer growth in the bone due to its random shape disables bone strength and thus changes its capacity to support body weight or muscles,which can crucially affect the quality of human life in terms of normal walking or daily *** successful patient recovery,it is necessary to remove the cancer-affected minimal bone area and quickly replace it with a biocompatible metal implant within less than 2 *** electron beam-melted Ti-6Al-4V implant was designed and applied in a patient to preserve the natural knee joint close to the bone *** developed implant fits the bone defect well,and the independent ambulatory function of the natural knee joint was restored in the patient within six weeks after surgery.A delayed fracture occurred six months after the successful replacement of cancer-affected bone with Ti-6Al-4V implant at the proximal meshed junction of the implant because of a minor downward ***,mechanical,and computational analyses were conducted for the fractured area to find the main reason for the delayed *** findings pertaining to the mechanical and material investigation can help realize the safe implantation of the three-dimensionally printed titanium implant to preserve the natural joints of patients with massive bone defects of the extremities.

关键词： 3D printing Bone cancer Titanium alloy implant Electron beam melting Fracture analysis

Clostridium difficile infection aggravates colitis in interleukin 10-deficient mice

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World Journal of Gastroenterology 2014年第45期20卷 17084-17091页

作者： Mi Na Kim Seong-Joon Koh jung Mogg Kim Jong Pil im Hyun Chae jung Joo Sung Kim Seoul National University Healthcare System Gangnam Center Seoul National University Hospital Department of Internal Medicine Seoul National University Boramae Hospital Seoul National University College of Medicine Department of Microbiology Hanyang University College of Medicine Department of Internal Medicine Liver Research Institute Seoul National University College of Medicine

Aim: To investigate the effect of Clostridium difficile (C. difficile) infection in an interleukin 10-deficient (IL-10-/-) mouse model of inflammatory bowel disease.

关键词： Clostridium difficile Inflammatory bowel disease Interleukin 10-deficient mice Interferon-γ Colitis

Structure-activity relationship of lysophosphatidylcholines in HL-60 human leukemia cells

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Acta Pharmacologica Sinica 2004年第11期 137-140页

作者： Eun-hee LEE,Jee H jung,Dong-soon im Laboratories of Pharmacology and Marine Natural Product Laboratories of Pharmacology and Marine Natural Product Laboratories of Pharmacology and Marine Natural Product College of Pharmacy Pusan National University Busan 609-735 Korea College of Pharmacy Pusan National University Busan 609-735 Korea College of Pharmacy Pusan National University Busan 609-735 Korea

Aim: To explore the structure-activity relationship of lysophosphatidylcholine (LPC) and lysolipid molecules from a marine sponge and ladybirds. METHODS: We tested three synthetic LPCs and four natural lysolipids on Ca2+ mobilization in HL-60 human leukemia cells. RESULTS: We observed lysolipid-mediated Ca2+ mobilization. The activity was the same in both ester- and ether-linked lysolipids, and introduction of a double bond or methoxy group on the alkyl chain did not significantly modulate the activity. However, replacement of trimethylammonium moiety in the choline structure with ammonium moiety reduced the activity. Furthermore, change of the alkyl chain length influenced the Ca2+ response. CONCLUSION: LPC-induced Ca2+ mobilization might be dependent on the length of alkyl chain and the presence of choline moiety in HL-60 leukemia cells.

关键词： lysophosphatidylcholines leukemia calcium signaling structure-activity relationship platelet activating factor