• Title/Summary/Keyword: bases

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Molecular Dynamics Simulation Study for Ionic Strength Dependence of RNA-host factor Interaction in Staphylococcus aureus Hfq

  • Lazar, Prettina;Lee, Yun-O;Kim, Song-Mi;Chandrasekaran, Meganathan;Lee, Keun-Woo
    • Bulletin of the Korean Chemical Society
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    • v.31 no.6
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    • pp.1519-1526
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    • 2010
  • The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

The New Urbanization Process and Changing Spatial Structure of Seoul (서울의 신도시화 과정과 공간구조의 변화)

  • 이경자;홍인옥;최병두
    • Journal of the Economic Geographical Society of Korea
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    • v.6 no.2
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    • pp.443-470
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    • 2003
  • This study is to consider economic, political, socio-cultural and environmental characteristics of the new urbanization process and its spatial structures and urban policy of Seoul in the 1990s. Some experimental findings which have been identified throughout this study can be summarized as follows. First of all, Seoul, the largest city in S.Korea has experienced a restructuring process of economy, which has been promoted by the development of producer services as well as knowledge- based or high tech industries. Secondly, the autonomy of Seoul has increased after the introduction of local self-government, with relatively higher self-management of local finance than other cities, strengthening the tendency of enterpreneurialism, empowering civil movements, and increasing the political participation of women. Thirdly, in the socio-cultural aspect, the material wants to gain a certain identity through consumption, using urban environments culturally, varying consuming attitudes and ways of leisure times in relation with the rapid development of transportation and information communication. Fourthly, in the environmental aspect, Seoul has tried to introduce the concept of sustainable development in terms of increasing wants on the quality of life, and to develop a pro-environmental eco-city with environmental rehabilitation, constructing green space and eco-park. Finally, in the spatial dimension, Seoul has shown a structuration of multi-centers, with highly spectacular urban landscapes and seemingly authentic urban planning. These results make us confirm that Seoul has been in the process of new urbanization which can be distinguished from the previous one.

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A Comparison of shear Bonding Strength with Polyacrylic acid and Phosphoric acid Enamel Surface Conditioning (폴리아크릴산과 인산으로 법랑질표면 처리후 전단결합강도의 비교)

  • Roh, Joung-Sub;Kim, Sang-Cheol
    • The korean journal of orthodontics
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    • v.32 no.1 s.90
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    • pp.51-57
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    • 2002
  • The purpose of this study was to compare in vitro shear bonding strength with three different enamel surface preparations (1) 30% sulfated polyacrylic acid with 0.3M lithium sulfate (2) 40% sulfated polyacrylic acid with 0.3M lithium sulfate (3) 37% phosphoric acid. 105 extracted human premolar teeth were divided into each three groups of 35. Metal brackets were bonded to teeth in the three groups. The same self curing resin was used for all groups. A shearing force was applied to the teeth. After debonding, bases of bracket and enamel surfaces were examined under steroscopic microscope to determine the failure modes. Statistical analysis of the data was carried out with one way ANOVA and Student t- test. The results were as follows. 1. Shear bond strength values for the 30% polyacrylic acid and 40% polyacrylic acid group were approximately two thirds of the phosphoric acid group. It maintains clinically acceptable but not enough bond strength. 2. There was no statistically significant difference in shear bond strengths between 30% and 40% polyacrylic acid group. 3. The failure modes of brackets had some differences. In polyacrylic acid groups, the percentage of adhesive/enamel failure was higher than that of adhesive/ bracket interface failure. On the contrary in phosphoric acid groups, the results were reversed. Further study of bond strength could be required. If polyacrylic acid enamel conditioning is used clinically.

Effect of tribochemical silica coating on the shear bond strength of rebonded monocrystalline ceramic brackets (단결정형 세라믹 브라켓의 재접착 시 tribochemical silica coating이 전단접착강도에 미치는 영향)

  • Jeon, Young-Mi;Son, Woo-Sung;Kang, Sang-Wook
    • The korean journal of orthodontics
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    • v.40 no.3
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    • pp.184-194
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    • 2010
  • Objective: The purpose of this study was to investigate the effect of tribochemical silica coating on the shear bond strength (SBS) of rebonded ceramic brackets using nano-filled flowable composite resin. Methods: A total of 60 premolars were prepared and divided into 4 equal groups as follows: Tribochemical silica coating (TC) + Transbond XT (XT), TC + Transbond supreme LV (LV), Sandblast treatment (SA) + XT, SA + LV. Treated ceramic brackets were rebonded on the premolars using each adhesive. All samples were tested in shear mode on a universal testing machine. Results: SBS of silica coated groups were high enough for clinical usage (TCLV: 10.82 $\pm$ 1.82 MPa, TCXT: 11.50 $\pm$ 1.72 MPa). But, SBS of the sandblast treated groups had significantly lower values than the tribochemical silica coated groups (SALV, 1.23 $\pm$ 1.16 MPa; SAXT, 1.76 $\pm$ 1.39 MPa; p < 0.05). There was no difference between the shear bond strength by type of adhesive. In the silica coated groups, 77% of the samples showed bonding failure in the adhesive. In the sandblast treated group, all bonding failures occurred at the bracket-adhesive interface. Conclusions: The result of this study suggest that newly introduced nano-filled flowable composite resin and tribochemical silica coating application on debonded ceramic bracket bases can produce appropriate bond strengths for orthodontic bonding.

A CLINICAL STUDY ON THE RETENTION OF MAXILLARY COMPLETE DENTURE WITH DIFFERENT DENTURE BASE MATERIALS (의치상의 종류에 따른 상악 의치상의 유지력에 관한 임상적 연구)

  • Lee Jong-Hyuk;Lim Ju-Hwan;Cho In-Ho
    • The Journal of Korean Academy of Prosthodontics
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    • v.39 no.1
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    • pp.58-70
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    • 2001
  • For the successful treatment of complete denture, obtaining a good retention is essential. There are lots of factors affecting denture retention. Denture material, one of those factors affecting denture retention, was the subject of this study, and internal surface treatment also considered for the method of enhancing denture retention. Two resin(Lucitone $199^{(R)}$(heat cured resin) Vertex $CP^{(R)}$(self cured resin)) and two metal($Biosil^{(R)}$(Co-Cr alloy), $Vitallium^{(R)}$(Co-Cr alloy)) denture base materials were used for making test denture base. Newly developed device was used for measuring denture retention. After the retention was measured. We treated internal surface of test denture base with $50{\mu}m\;Al_2O_3$ powder, under 90psi, for 1 minute. Then the retention was measured again. The result was analyzed with K-S test, one-way ANOVA test and independent t-test to deter mine the significant differences as the 95% level of confidence. The results are as follows : In cases of without internal surface treatment, the retention was increased in order of $Vitallium^{(R)},\;Biosil^{(R)},\;Vertex CP^{(R)}$ and Lucitone $199^{(R)}$. Except between Vertex $CP^{(R)}$ and $Biosil^{(R)}$, retention of the other materials was significantly different (p<0.05). After the treatment of internal surface, the retention was increased in order of $Vitallium^{(R)},\;Biosil^{(R)},\;Lucno\;199^{(R)},\;Vertex\;CP^{(R)}$. Except between Lucitone $199^{(R)}$ and Vertex $CP^{(R)}$, $Vitallium^{(R)}$ and $Biosil^{(R)}$ the retention of remaining groups was significantly different each other (p<0.05). In the matter of each material, after the internal surface treatment the retention was increased with Vertex $CP^{(R)},\;Biosil^{(R)}\;and\;Vitallium^{(R)}$ and the value of differences were statistically significant. When we compare the retention of resin and metal denture base, the retention of both denture bases increased significantly with internal surface treatment, and resin denture base showed better retention. As the results show, selecting denture base material could be an important choice of complete denture treatment. To increase denture retention, internal surface treatment can be considered as a possible method.

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Development of an SWRL-based Backward Chaining Inference Engine SMART-B for the Next Generation Web (차세대 웹을 위한 SWRL 기반 역방향 추론엔진 SMART-B의 개발)

  • Song Yong-Uk;Hong June-Seok;Kim Woo-Ju;Lee Sung-Kyu;Youn Suk-Hee
    • Journal of Intelligence and Information Systems
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    • v.12 no.2
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    • pp.67-81
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    • 2006
  • While the existing Web focuses on the interface with human users based on HTML, the next generation Web will focus on the interaction among software agents by using XML and XML-based standards and technologies. The inference engine, which will serve as brains of software agents in the next generation Web, should thoroughly understand the Semantic Web, the standard language of the next generation Web. As abasis for the service, the W3C (World Wide Web Consortium) has recommended SWRL (Semantic Web Rule Language) which had been made by compounding OWL (Web Ontology Language) and RuleML (Rule Markup Language). In this research, we develop a backward chaining inference engine SMART-B (SeMantic web Agent Reasoning Tools -Backward chaining inference engine), which uses SWRL and OWL to represent rules and facts respectively. We analyze the requirements for the SWRL-based backward chaining inference and design analgorithm for the backward chaining inference which reflects the traditional backward chaining inference algorithm and the requirements of the next generation Semantic Web. We also implement the backward chaining inference engine and the administrative tools for fact and rule bases into Java components to insure the independence and portability among different platforms under the environment of Ubiquitous Computing.

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The hierarchical structures of cause-and-effect relationships on the profit factors in overseas construction projects (해외건설공사 수익성 영향인자의 계층구조 및 사레적용에 관한 연구)

  • Han, Seung-Heon;Sun, Seung-Min;Park, Sang-Hyuk;Jung, Do-Young
    • Korean Journal of Construction Engineering and Management
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    • v.7 no.5
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    • pp.64-76
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    • 2006
  • Korea's overseas construction industry has been rather depressed by the weakened profitability as well as the sharp decrease of the market shares due to the lack of international competitiveness and the declined international market. There exist a lot of various risks in performing the overseas construction, and especially EPC projects, which entail complicated process from different parts, also require a sophisticated procurement and management skill. Subsequently, to survive in the competitive international market, we need to establish strategies to select potentially profitable projects at the initial stage of bidding process and to mitigate the high degree of risk exposure through contract negotiation and its adjustment. This research discusses the trend of environment in international construction markets. Then, it identifies the key factors that affect the profitability significantly through the structured surveys from 59 actual overseas projects, and it analyzes the key factors by using statistical methods. This research provides the profitability evaluation bases, with which overseas construction participants can forecast and analyze the risk more systematically, by eliciting profit-influencing factors using the result of statistical analysis, literature review and structuring their cause-and-effect relationships. The profitability casual hierarchy structure describes the profitability factors' hierarchy in details and their interrelationships. It also enables us to find out critical factors directly related to profitability aggravation through a qualitative and quantitative analysis. Ultimately, with this hierarchy structure as the base, the research will suggest how to develop the quantitative profitability forecasting model.

Synthesis, Potentiometric, Spectral Characterization and Microbial Studies of Transition Metal Complexes with Tridentate Ligand (세자리 리간드의 전이금속 착물에 대한 합성과 전위차 및 분광학적 확인 그리고 미생물학적 연구)

  • Jadhav, S.M.;Munde, A.S.;Shankarwar, S.G.;Patharkar, V.R.;Shelke, V.A.;Chondhekar, T.K.
    • Journal of the Korean Chemical Society
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    • v.54 no.5
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    • pp.515-522
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    • 2010
  • A relation between antimicrobial activities and the formation constants of solid complexes of Cu(II), Ni(II), Co(II), Mn(II) and Fe(III) with tridentate Schiff base ligand, 4-hydroxy-3(1-{2-(benzylideneamino)-phenylimino}-ethyl)-6-methyl-2Hpyran-2-one (HL) derived from o-phenylene diamines, dehydroacetic acid (DHA) and p-chloro benzaldehyde have been studied. The ligand and metal complexes were characterized by elemental analysis, conductivity, magnetic susceptibility, thermal analysis, X-ray diffraction, IR, $^1H$-NMR, UV-vis and mass spectra. From the analytical data, the stiochiometry of the complexes was found to be 1:2 (metal:ligand) with octahedral geometry. The molar conductance values suggest the nonelectrolytic nature of metal complexes. The X-ray diffraction data suggests monoclinic crystal system for Ni(II) and orthorhombic crystal system for Cu(II) and Co(II) complexes. The IR spectral data suggest that the ligand behaves as tridentate ligand with ONN donor atoms sequence towards central metal ion. Thermal behavior (TG/DTA) and kinetic parameters calculated by Coats-Redfern method suggests more ordered activated state in complex formation. The protonation constants of the complexes were determined potentiometrically in THF:water (60:40) medium at $25^{\circ}C$ and ionic strength ${\mu}=0.1\;M$ ($NaClO_4$). Antibacterial activities in vitro were performed against Staphylococcus aureu and Escherichia coli. Antifungal activities were studied against Aspergillus Niger and Trichoderma. The effect of the metal ions and stabilities of complexes on antimicrobial activities are discussed.

Analysis of Explanations and Examples of the Brønsted-Lowry Model Presented in Chemistry Textbooks Developed by 2009 Revised Curriculum (2009 개정교육과정의 화학교과서에 제시된 Brønsted-Lowry 모델에 관한 설명과 예시의 문제점 분석)

  • Choi, Hee;Park, Chul-Yong;Kim, Sungki;Paik, Seoung-Hey
    • Journal of the Korean Chemical Society
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    • v.62 no.4
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    • pp.279-287
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    • 2018
  • In this study, we analyzed the explanations and examples of Brønsted-Lowry model in Chemistry I and Chemistry II textbooks of the 2009 revised curriculum. In particular, the definition of the Brønsted-Lowry model, the examples, and the content of experiments were analyzed by the process perspective of chemical equilibrium, emergent process. The analyzed textbooks were 4 kinds of Chemistry I textbooks and 4 kinds of Chemistry II textbooks in 2009 revision curriculum. As a result, Chemical I textbooks did not adequately show the chemical equilibrium viewpoint when explaining the Brønsted-Lowry model. In the Chemistry II textbooks, the examples of Brønsted-Lowry model were not present emergent process viewpoint, and those were described as sequential viewpoint of Arrhenius model. In addition, examples of experiments to demonstrate the Brønsted-Lowry model of Chemistry II textbooks were insufficient. The experimental examples related to the definition of acid bases were at the level of classification by the color change of indicators. The experimental examples for explaining the strength of acid and base were to compare current intensity or amount of hydrogen gas generated from the reaction with metal. In addition, all textbooks presented the state of aqueous solution when describing the Brønsted-Lowry model, causing problems with differentiation from the Arrhenius model. Therefore, it is necessary to develop examples of experiments to help students understand Brønsted-Lowry model by presenting acid and base reaction in the non-aqueous solution state.

Growth responses of New Zealand Spinach [Tetragonia tetragonoides (Pall.) Kuntze] to different soil texture and salinity (신규 채소작물용 번행초의 토성 및 염도에 대한 생육 반응)

  • Kim, Sung-Ki;Kim, In-Kyung;Lee, Geung-Joo
    • Korean Journal of Agricultural Science
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    • v.38 no.4
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    • pp.631-639
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    • 2011
  • This research was conducted to investigate potential use of New Zealand spinach (Tetragonia tetragonoides) as a new vegetable crop which will be cultivating in salt-affected soils including reclaimed land. Traditionally New Zealand spinach has been studied to explore functional compound or salt removing potential. To cultivate the crop species in the salt-affected soil widely, it is essential to obtain salt and soil texture responses under the controlled environment. Fifty nine New Zealand spinach ecotypes native to Korean peninsula first collected over seashore areas, and primitive habitat soil environment was evaluated by analyzing soil chemical properties from 32 locations. Different textures of sandy, silt loam, and sandy loam soils were prepared from nearby sources of sea shore, upland and paddy soils, respectively. Target salinity levels of 16.0 dS/m, 27.5 dS/m, 39.9 dS/m, and 52.4 dS/m in electrical conductivity (ECw) were achieved by diluting of 25, 50, 75, 100% (v/v) sea water to tap water (control, 0.6 dS/m), respectively. Various measurements responding to soil texture and irrigation salinity included plant height, root length, fresh weight (FW), dry weight (DW), leaf parameters (leaf number, leaf length, leaf width), lateral branching, and inorganic ion content. was found to adapt to diverse habitats ranging various soil chemical properties including soil pH, organic matter, exchangeable bases, EC, and cation exchange capacity (CEC) in Korea. Responding to soil texture, New Zealand spinach grew better in silt loam and sandy loam soil than in sandy soil. Higher yield (FW and DW) seemed to be associated with branch number (r=0.99 and 0.99, respectively), followed by plant height (r=0.94 and 0.97, respectively) and leaf number (r=0.89 and 0.84, respectively). Plant height, FW, and DW of the New Zealand spinach accessions were decreased with increasing irrigation salinity, while root length was not significantly different compared to control. Based on previous report, more narrow spectrum of salinity range (up to 16 dS/m) needs to be further studied in order to obtain more accurate salinity responses of the plant. As expected, leaf Na content was increased significantly with increasing salinity, while K and Ca contents decreased. Growth responses to soil texture and irrigation salinity implied the potential use of New Zealand spinach as a leafy vegetable in salt-affected soil constructed with silt loam or sandy loam soils.