• Genomics & Informatics
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• v.14 no.3
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• pp.112-124
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• 2016

Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism. In the current work, 64 genes and 23 miRNAs have been selected from literatures, whose deregulation is well established in seven types of solid cancer like lung, breast, prostate, pancreases, colorectal, stomach, and bladder cancer. In silico study reveals, miRNAs namely, miR-106a, miR-21, and miR-29b-2 have a strong binding affinity towards PTEN, TGFBR2, and VEGFA genes, respectively, suggested as important factors in RNA silencing mechanism. Furthermore, interaction between AGO protein (PDB ID-3F73, chain A) with selected miRNAs and with miRNAs-mRNAs duplex were studied computationally to understand their binding at molecular level. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding miRNAs based gene silencing mechanism in solid cancer.

• Journal of the Korean Chemical Society
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• v.19 no.2
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• pp.85-91
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• 1975

The crystal structure of piperidinothiosemicarbazide, $C_6H_{13}N_3S$, has been determined by single crystal X-ray analysis. The space group is P21/c with four molecules in the unit cell of dimensions $a=14.68{\pm}0.04,\;b=4.59{\pm}0.02,\;c=12.92{\pm}0.04{\AA}\;and\;{\beta}=109.4{\pm}0.2^{\circ}$. Three-dimensional photographic intensities were estimated visually. The structure has been solved by an interpretation of a Patterson synthesis and refined by block-diagonal least-squares methods to give a final R value of 0.14 for 378 observed independent reflections. There are two independent hydrogen bonds in the structure. One of them is of the type N-H${\ldots}$S with the length 3.28 and $3.39{\AA}$, and another is of the type N-H${\ldots}$N with the length $3.03{\AA}$. Apart from the hydrogen bonding system the molecules are held together in the crystal by van der Waals forces.

• Journal of Sensor Science and Technology
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• v.17 no.5
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• pp.369-374
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• 2008

A novel fiber optic surface plasmon resonance (SPR) sensor using cyclic olefin copolymer (COC) prism with the spectral modulation is presented. The SPR sensor chip is fabricated using the SU-8 photolithography, Ni-electroplating and COC injection molding process. The sidewall of the COC prism is partially deposited with Au/Cr (45/2.nm thickness) by e-beam evaporator, and the thermal bonding process is conducted for micro fluidic channels and optical fibers alignment. The SPR spectrum for a phosphate buffered saline (0.1.M PBS, pH.7.2) solution shows a distinctive dip at 1300.nm wavelength, which shifts toward longer wavelength with respect to the bovine serum albumin (BSA)concentrations. The sensitivity of the wavelength shift is $1.16\;nm{\cdot}{\mu}g^{-1}{\cdot}{\mu}l^{-1}$. From the wavelength of SPR dips, the refractive indices (RI) of the BSA solutions can be theoretically calculated using Kretchmann configuration, and the change rate of the RI was found to be $2.3{\times}10^{-5}RI{\cdot}{\mu}g^{-1}{\cdot}l^{-1}$. The realized fiber optic SPR sensor with a COC prism has clearly shown the feasibility of a new disposable, low cost and miniaturized SPR biosensor for biochemical molecular analyses.

• Polymer(Korea)
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• v.28 no.5
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• pp.433-443
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• 2004

The membranes of the blends of chitosan and polycaprolactarn (PA6) were prepared in formic acid. FT-IR data revealed that hydrogen bonding between amide and hydroxyl groups of chitosan and PA6, respectively, was formed. Thermogravimetric analysis demonstrated that the blend samples contain water. DMA results showed that the dissipation of water in the samples significantly reduced the storage modulus (E'). The mechanical loss tangent (tan $\delta$) data of the blend samples showed the $\beta$d loss peak around $0^{\circ}C$. The blend samples were completely dried in a vacuum and then exposed to high moisture to absorb water which would cause, so called, w-bridges between the molecules. The E' data of these regained samples increased abnormally and additional loss peak appeared on the shoulder of the peak around $50^{\circ}C$. Under dry condition, the samples with a blend ratio of 40/60 for chitosan/PA6 displayed a better miscibility between two components.

• Proceedings of the Korean Vacuum Society Conference
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• 2000.02a
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• pp.170-170
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• 2000

Synthetic polymers such as polyimide, polycarbonate, and poly(methyl methacrylate) are long chain molecules which consist of carbon, hydrogen, and heteroatom linked together chemically. Recently, polymer surface can be modified by using a high energy ion beam process. High energy ions are introduced into polymer structure with high velocity and provide a high degree of chemical bonding between molecular chains. In high energy beam process the modified polymers have the highly crosslinked three-dimensionally connected rigid network structure and they showed significant improvements in electrical conductivity, in hardness and in resistance to wear and chemicals. Polyimide films (Kapton, types HN) with thickness of 50~100${\mu}{\textrm}{m}$ were used for investigations. They were treated with two different surface modification techniques: Plasma Source Ion Implantation (PSII) and conventional Ion Implantation. Polyimide films were implanted with different ion species such as Ar+, N+, C+, He+, and O+ with dose from 1 x 1015 to 1 x 1017 ions/cm2. Ion energy was varied from 10keV to 60keV for PSII experiment. Polyimide samples were also implanted with 1 MeV hydrogen, oxygen, nitrogen ions with a dose of 1x1015ions/cm2. This work provides the possibility for inducing conductivity in polyimide films by ion beam bombardment in the keloelectronvolt to megaelectronvolt energy range. The electrical properties of implanted polyimide were determined by four-point probe measurement. Depending on ion energy, doses, and ion type, the surface resistivity of the film is reduced by several orders of magnitude. Ion bombarded layers were characterized by Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS), XPS, and SEM.

• Molecules and Cells
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• v.43 no.9
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• pp.784-792
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• 2020

Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna (DmAK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in DmAK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of DmAK.

• Restorative Dentistry and Endodontics
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• v.38 no.3
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• pp.134-140
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• 2013

Objectives: There has been a growing interest in glass ceramic systems with good esthetics, high fracture resistance and bonding durability, and simplified fabrication techniques using CAD/CAM. The aim of this study is to compare flexural strength before and after heat treatment of two lithium disilicate CAD/CAM blocks, IPS e.max CAD (Ivoclar Vivadent) and Rosetta SM (Hass), and to observe their crystalline structures. Materials and Methods: Biaxial flexural strength was tested according to ISO 6872 with 20 disc form specimens sliced from each block before and after heat treatment. Also, the crystalline structures were observed using field-emission scanning microscopy (FE-SEM, Hitachi) and x-ray diffraction (XRD, Rigaku) analysis. The mean values of the biaxial flexural strength were analyzed by the Mann-Whitney U test at a significance level of p = 0.05. Results: There were no statistically significant differences in flexural strength between IPS e.max CAD and Rosetta SM either before heat treatment or after heat treatment. For both ceramics, the initial flexural strength greatly increased after heat treatment, with significant differences (p < 0.05). The FE-SEM images presented similar patterns of crystalline structure in the two ceramics. In the XRD analysis, they also had similar patterns, presenting high peak positions corresponding to the standard lithium metasilicate and lithium disilicate at each stage of heat treatment. Conclusions: IPS e.max CAD and Rosetta SM showed no significant differences in flexural strength. They had a similar crystalline pattern and molecular composition.

• Journal of the Korean Chemical Society
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• v.64 no.6
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• pp.350-353
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• 2020

The validity of the calculation method based on the local mode in hydrogen-bonded water molecules was investigated by comparing the frequencies of the local and normal modes of OH stretching vibration in water molecules. By calculating a monomer, dimer, and trimer of water molecules using a quantum chemical ab initio theory, we examined how the frequencies of the local and normal modes and the anharmonicity of local modes vary with molecular cluster size. It was shown that, as the number of molecules increases from monomer to trimer, the anharmonicity of OH bonds increases and the difference between local and normal mode frequencies decreases. This confirms that local-mode-based calculations that can easily handle the anharmonicity can be appropriate for the calculation of the OH stretching frequency of water molecules in the condensed phase.

• Journal of the Korean Chemical Society
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• v.37 no.5
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• pp.473-476
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• 1993

Dipropargyldiphenylmetane, $C_{19}H_{16}, crystallizes in a monoclinic space group $C2/_c$$ with a = 11304(3), b = 20.799(5), c = 6.622(2)${\AA}$, ${\beta} = 112.8(3)^{\circ}$, Z = 4, V = 1435.3${\AA}^3,\;F(000)\;=\;520,\;D_c\;=\;1.14g{\cdot}cm^{-3}$ and ${\mu}\;=\;0.32\;cm^{-1}$. The structure was solved by direct methods and all non-H atoms were identified in the E-map. The final refinement gave R = 0.055 from 1328 unique observed reflections with I $\geq$ -1.0 $\sigma(I).$ The molecule belongs to the point group $C_2$ of Symmetry by possessing the 2-fold axis which coincides witeh the crystallographic symmetry axis in the unit cell. The linear propargyl moiety is nearly $perpendicular(94.2)^{\circ}$ to the molecular plane of the benzene ring. The internal angle of methane carbon atoms in $108.1(1)^{\circ}$, bonding to the benzene and the propargyl moiety with the bond lengths of 1.530(2) and $1.560(2)\AA$, respectively. The shortest contant between the molecules is $3.538(2)\AA$ between C(9) and C(9) (-x, y, -1/2-z).

• Journal of the Korean Chemical Society
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• v.26 no.5
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• pp.265-273
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• 1982

The effect of ${\pi}$ bonds on the calculated dipole moments for square planar and tetrahedral [M(II)$O_2S_2$]] type complexes has been investigated by two different approaches. One is the approximate molecular orbital method based on the assumption that the mixing coefficient CM of the valence basis sets for the central metal ion and the appropriate ligand orbitals is equal for all ${\sigma}$ and ${\pi}$ bonding molecular orbitals. The other is the more refined calculation based on the semiempirical LCAO-MO method. If ${\sigma}$ bonds only are assumed to be formed, the calculated dipole moments for square planar and tetrahedral complexes are lower than those of the experimental values. If the contribution of ${\pi}$ bonds to the calculated dipole moments are fully considered, the calculated dipole moments for both square planar and tetrahedral [M(II)$O_2S_2$]] type complexes are higher than the experimental values. However if ${\pi}$ bonds are assumed to be delocalzed, the calculated dipole moments for tetrahedral [M(II$O_2S_2$]] type complexes fall in the range of the experimental values, but those for square planar complexes deviate from the experimental values. These results suggest that [M(II)$O_2S_2$]] type complexes may have the tetrahedral structure in inert solvent solution. This structure is in agreement with the experimental one. The calculated dipole moments for tetrahedral [M(II)$O_2S_2$]] type complexes indicate that the contribution of ${\pi}$ bonds to the calculated dipole moments may not be neglected.