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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

Reliability Enhanced Multi-objective Economic Dispatch Strategy for Hybrid Renewable Energy System with Storage

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Journal of the Operations Research Society of China 2023年第1期11卷 51-81页

作者： Anongpun Man-im Weerakorn Ongsakul Nimal Madhu Department of Energy Environment and Climate ChangeSchool of EnvironmentResources and DevelopmentAsian Institute of TechnologyKlong LuangPathumthani12120Thailand

An optimal dispatch strategy for the economic operation of hybrid renewable energy system with storage is presented in this paper. Solar photovoltaic (PV), Wind and Battery Storage are the prime components of interest constituting the hybrid system. In addition to the economic aspect of the systems, the formulation focuses on renewable prioritized operation, system reliability and environmental sustainability enhancement. Being a multi-objective (MO) problem, a modified non-dominated sorting particle swarm optimization is used for solving the problem, considering operational cost, pollutant emission, and expected energy not served as operational objectives. The non-dominated sorting particle swarm optimization (NSPSO) is augmented with crowding distance technique, stochastic weight trade-off and chaotic mutation approaches, to control the exploration of global and particle bests, alleviating premature convergence, and enhancing solution search capability. A two-stage approach is used to derive the best solution. A modified IEEE 30-bus test system is used to demonstrate the results. By using the proposed approach, a lower and wider Pareto front is obtained, in comparison with prominent optimization approaches.

关键词： Multi-objective economic dispatch Emission reduction Particle swarm optimization Hybrid energy system Expected energy not served Battery energy storage

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

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npj Computational Materials 2021年第1期7卷 205-219页

作者： Krishan Kanhaiya Seonghan Kim Wonpil im Hendrik Heinz Department of Chemical and Biological Engineering University of Colorado at BoulderBoulderCO 80301USA Departments of Biological Sciences Chemistryand BioengineeringLehigh UniversityBethlehemPA 18015USA

The earlier integration of validated Lennard–Jones(LJ)potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields,for example,metal–electrolyte interfaces,recognition of biomolecules,colloidal assembly of metal nanostructures,alloys,and *** we introduce 12-6 and 9-6 LJ parameters for classical all-atom simulations of 10 further fcc metals(Ac,Ca(α),Ce(γ),Es(β),Fe(γ),Ir,Rh,Sr(α),Th(α),Yb(β))and stainless *** parameters reproduce lattice constants,surface energies,water interfacial energies,and interactions with(bio)organic molecules in 0.1 to 5%agreement with experiment,as well as qualitative mechanical properties under standard *** are reduced up to a factor of one hundred in comparison to earlier Lennard–Jones parameters,embedded atom models,and density functional *** also explain a quantitative correlation between atomization energies from experiments and surface energies that supports parameter *** models are computationally very efficient and applicable to an exponential space of *** with a wide range of force fields such as the Interface force field(IFF),AMBER,CHARMM,COMPASS,CVFF,DREIDING,OPLS-AA,and PCFF enables reliable simulations of nanostructures up to millions of atoms and microsecond time ***-friendly model building and input generation are available in the CHARMM-GUI Nanomaterial *** a limitation,deviations in mechanical properties vary and are comparable to DFT *** discuss the incorporation of reactivity and features of the electronic structure to expand the range of applications and further increase the accuracy.

关键词： steel metals qualitative

Al-incorporation into Li7La3Zr2O12 solid electrolyte keeping stabilized cubic phase for all-solid-state Li batteries

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Journal of Energy Chemistry 2018年第5期27卷 1501-1508页

作者： Changbin im Dongwon Park Hosung Kim Jaeyoung Lee Chemical Energy Storage and Transformation Center (CHESS) Research Institute for Solar and Sustainable Energies (RISE) Gwangju Institute of Science and Technology (GIST)Gwangju 500-712 South Korea Ertl Center for Electrochemistry and Catalysis GIST Research Institute GIST Gwangju 500-712 South Korea Electrochemical Reaction and Technology Laboratory School of Earth Scieences and Environmental Engineering GIST Cwangju 500-712 South Korea Gwangju Research Center Korea Institute of Industrial Technology (KITECH) Gwangju 61012 South Korea

We observe the influence of AI occupancies in Li sites on the formation process of the garnet solid elec- trolyte of Li_7La_3Zr_2O_12 （LLZO）. A direct incorporation of AI is first promoted in a Li-insufficient garnet solid electrolyte during the calcination process of 850 ℃ and then the cubic phase of LLZO is obtained after successive annealing step of 1000 ℃. Comparing to pristine LLZO, AI incorporated LLZO shows less formation of Li_2CO_3, keeping crystallographic and physicochemical properties. This AI incorporation im- proves both the ionic conductivity and interfacial resistance to poisoning procedure.

关键词： Li_7La_3Zr_2O_12 AI incorporation Garnet solid electrolyte Cubic phase

Perception and attitude of theatre staff to preoperative HIV testing at the University of Port Harcourt Teaching Hospital

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Asian Pacific Journal of Tropical Medicine 2010年第2期3卷 145-147页

作者： Odigie JO Siminialayi im Department of Pharmacology and Toxicology College of Health SciencesUniversity of Port Harcourt

Objective:To elucidate the awareness and approach to pre-operative human immunodeficiency virus(HIV) testing and emphasis on the attendant components of HIV ***: The study was conducted at the theatres of the University of Port Harcourt Teaching Hospital among 123 nursing,anaesthetic,and operating staff.A descriptive cross sectional design was adopted with stratified *** study instrument was a structured,self administered pro ***:All respondents were all aware of HIV infection and all had transmission through infected blood and tissues(100.0%).88.6%had infection through needle stick injuries, 62.6%through vertical transmission,and 98.4%through blood *** three percent of respondents correctly knew what preoperative testing was,while 58.5%were aware of the preoperative testing policy of the *** respondents favoured the policy of preoperative *** values to seropositive patients were not very different as 72.4%of respondents claimed they treated every patient as high risk,and all respondents used personal protective ***:Routine HIV testing now represents a conventional means providing patients with knowledge of their HIV *** testing should be accompanied by informed consent,counselling,confidentiality,protection,and access to treatment.

关键词： Human immunodeficiency virus Pre operative HIV testing University of Port Harcourt Teaching Hospital

EP4 agonist alleviates indomethacin-induced gastric lesions and promotes chronic gastric ulcer healing

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World Journal of Gastroenterology 2009年第41期15卷 5149-5156页

作者： Wha Bin im Yariv Donde Larry A Wheeler Department of Biological Sciences and Medical Chemistry Herbert Research Center Allergan Inc. Irvine California CA 92612 United States

Aim： To investigate EP4-selective agonist effect on indomethacin-induced gastric lesions and on the spontaneous healing of chronic gastric ulcers. METHODS： In a mouse model of gastric bleeding with high dose of indomethacin （20 mg/kg）, an EP4-selective agonist was administered orally. Stomach lesions and gastric mucous regeneration were monitored. In a mouse model of chronic gastric ulcer induced by acetic acid, EP4 agonist effect on the healing of chronic gastric ulcer was evaluated in the presence or absence of low dose indomethadn （3 mg/kg）. In cultured human gastric mucous cells, EP4 agonist effect on indomethacin- induced apoptosis was assessed by flow cytometry. RESULTS： The EP4-selective agonist reduced high dose indomethacin-induced acute hemorrhagic damage and promoted mucous epithelial regeneration. Low-dose indomethacin aggravated ulcer bleeding and inflammation, and delayed the healing of the established chronic gastric ulcer. The EP4 agonist, when applied locally, not only offset indomethacin-induced gastric bleeding and inflammation, but also accelerated ulcer healing. In the absence of indomethacin, the EP4 agonist even accelerated chronic gastric ulcer healing and suppressed inflammatory cell infiltration in the granulation tissue. In vitro, the EP4 agonist protected human gastric mucous cells from indomethacin-induced ***： EP4-selective agonist may prevent indomethacin-induced gastric lesions and promote healing of existing and i ulcers, via promoting mucous epithelial cells. proliferation and survival of mucous epithelial cells.

关键词： Prostaglandin E2 Non-steroidal anti-inflam- matory drugs Gastric bleeding Gastric ulcer EP4- subtype receptor

Silicon nanowire ratioed inverters on bendable substrates

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Nano Research 2018年第5期11卷 2586-2591页

作者： Jeongje Moon Yoonjoong Kim Doohyeok Lim Kyeungmin im Sangsig Kim Department of Electrical Engineering Korea University 145 Anam-ro Seongbuk-gu Seoul 02841 Republic of Korea LED PKG Development Group Samsung Electronics Co. Ltd. 1 Samsung-ro Yongin-si Gyeonggi-do 17113 Republic of Korea

In this study, we demonstrate the performance of silicon nanowire （SiNW） n-metal oxide semiconductor （MOS） and p-MOS ratioed inverters that are fabricated on bendable substrates. The electrical characteristics of the fabricated devices can be controlled by adjusting the load voltage. The logic swings of the n- and p-MOS ratioed inverters at a low supply voltage of 1V are 80% and 96%, respectively. The output voltage level of the p-MOS ratioed inverter is close to rail-to-rail operation. The device also exhibits stable characteristics with good fatigue properties. Our bendable SiNW ratioed inverters show promise as a candidate building block for future bendable electronics.

关键词： silicon nanowire ratioed inverter n-metal oxide semicon-ductor (MOS) inverter p-MOS inverter bendable substrate

Effect of shipping activity on warming trends in the Canadian Arctic

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Journal of Geographical Sciences 2021年第3期31卷 369-388页

作者： Mian Sabir HUSSAIN Inhye HEO Sujeong im Seungho LEE Climate Research Institute Konkuk UniversitySeoulKorea Department of Geography Konkuk UniversitySeoulKorea

This paper presents a detailed account of the effect of shipping activity on the increasing trends of air temperatures in the Canadian Arctic region for the period of 1980–*** trend of temperature has gained significant attention with respect to shipping activities and sea ice area in the Canadian ***,sea ice area and shipping traffic datasets were investigated,and simple linear regression analyses were conducted to predict the rate of change(per decade)of the average temperature,considering winter(January)and summer(July)*** results indicate that temperature generally increased over the studied *** warming trend was observed during July,with an increase of up to 1℃,for the Canadian Arctic *** increasing trend of temperature was observed during July from the lower to higher *** increase in temperature during July is speculated to increase the melting of *** also show a decline in sea ice area has a significant positive effect on the shipping traffic,and the numbers of marine vessel continue to increase in the *** increase in temperature causes the breaking of sea ice due to shipping activities over northern Arctic Canada.

关键词： shipping activity increasing trend of temperature sea ice area Canadian Arctic

Pattern and antibiogram of urinary tract infection at the University of Port Harcourt Teaching Hospital

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Asian Pacific Journal of Tropical Medicine 2010年第1期3卷 66-69页

作者： Wariso KT Siminialayi im Odigie JO Department of Medical Microbiology and Parasitology College of Health SciencesUniversity of Port Harcourt Department of Pharmacology and Toxicology College of Health SciencesUniversity of Port Harcourt

Objective:To explore the prevalence,pathogenicity,and antibiotic susceptibility patterns of urinary tract infections at the University of Port Harcourt Teaching ***:Samples from 400 patients with a presumptive diagnosis of urinary tract infection including 250 non pregnant females and 150 males were used for this *** were distributed into two groups: children aged 2 to 17(Croup A) and adults aged 18 to 75(Croup B).The standard wire loop and agar diffusion technique were employed for culture and susceptibility testing,*** obtained were analysed using SPSS,version ***:30.0%of Group A and 41.0%of Group B had significant bacteriuria with 66.7%and 79.3%as females,*** commonest isolates cultured were Escherichia coli(32.8%),Staphylococcus aureus(17.2%),and Klebsiella spp.(16.4%).About 76.6%of isolates were sensitive to the fluorinated quinolones,31.2%to the aminoglycosides,and 22.7%to the urinary antiseptic,*** isolates were nonsensitive to tetracycline(93.8%),cotrimoxazole(92.2%),and nalidixic acid(86.7%).Most isolates showed non-uniform sensitivity patterns to the cephaloporins(cefuroxime and ceftazidime). Pseudomonas *** were generally resistant to the fluorinated ***: Though the fluorinated quinolones are still largely effective for empirical therapy in urinary tract infections,the importance of prior sensitivity testing in checking the emergence of bacterial antibiotic resistance can not be overemphasized.

关键词： Urinary tract infection Bacterial susceptibility Antibiotic resistance Port Harcourt