• Mass Spectrometry Letters
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• v.13 no.4
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• pp.177-183
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• 2022

The monomer and dimer structures of the amyloid fragment Aβ(1-16) sequence formed in H₂O were investigated using electrospray ionization mass spectrometry (MS) and tandem MS (MS/MS). Aβ16 monomers and dimers were indicated by signals representing multiple proton adduct forms, [monomer+zH]ⁿ⁺ (=M^z+, z = charge state) and [dimer+zH]^z+ (=D^z+), in the MS spectrum. Fragment ions of monomers and dimers were observed using collision-induced dissociation MS/MS. Peptide bond dissociation was mostly observed in the D1-D7 and V11-K16 regions of the MS/MS spectra for the monomer (or dimer), regardless of the monomer (or dimer) charge state. Both covalent and non-covalent bond dissociation processes were indicated by the MS/MS results for the dimers. During the non-covalent bond dissociation process, the D³⁺ dimer complex was separated into two components: the M¹⁺ and M²⁺ subunits. During the covalent bond dissociation of the D³⁺ dimer complex, the b and y fragment ions attached to the monomer, (M+b_10-15)^z+ and (M+y_9-15)^z+, were thought to originate from the dissociation of the M²⁺ monomer component of the (M¹⁺+M²⁺) complex. Two different D³⁺ complex geometries exist; two distinguished interaction geometries resulting from interactions between the M¹⁺ monomer and two different regions of M²⁺ (the N-terminus and C-terminus) are proposed. Intricate fragmentation patterns were observed in the MS/MS spectrum of the D⁵⁺ complex. The complicated nature of the MS/MS spectrum is attributable to the coexistence of two D⁵⁺ configurations, (M¹⁺+M⁴⁺) and (M²⁺M³⁺), in the Aβ16 solution.

• Tuberculosis and Respiratory Diseases
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• v.43 no.1
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• pp.69-74
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• 1996

Background: The diagnosis of pulmonary embolism (PE) based on clinical findings is often elusive and therefore requires confirmative diagnostic method. Pulmonary angiography, though the gold standard for the diagnosis of pulmonary embolism, is an invasive method and requires trained personnel and special equipment. Lung V/Q scan, on the other hand, is a noninvasive method but the diagnostic specificity and sensitivity arc not satisfactory in case that the results are either intermediate or low probability scan. Plasma D-dimer is generated when a thrombus is fibrinolysed by plasmin and is known to be increased in various thrombotic disorders. The aim of this study was to investigate the value of the determination of plasma D-dimer level in the diagnosis of pulmonary embolism. Methods: Pulmonary angiography was performed in 17 patients who were clinically suspected to have pulmonary embolism. 9 patients(PE, $56{\pm}13.4$ yrs, M:F=8:1) were diagnosed to have pulmonary embolism by pulmonary angiography. The control group were the 8 patients with negative pulmonary angiography and 13 orthopedic patients with no evidence of pulmonary embolism on scintigraphic and impedance plethysmographic studies(n=21) (non-PE, $54.5{\pm}11.1$ yrs, M:F=11:10). Plasma D-dimer was measured by latex agglutination method in study subjects and the results were analyzed according to the presence or absence of pulmonary embolism. Results: 1) The increased level of plasma D-dimer was more frequently observed in the patients with pulmonary embolism than in the controls(>0.5 mg/L, 8 in PE, 10 in non-PE; <0.5 mg/L, 1 in PE, 11 in non-PE, p=0.049). 2) The diagnostic value of plasma D-dimer level higher than 0.5 mg/L were as follows: sensitivity 88.9%(8/9), specificity 52.4%(11/21), positive predictive value 44.4%(8/18), and negative predictive value 91.7%(11/12). Conclusion: Plasma D-dimer determination showed high sensitivity and negative predictive value in the diagnosis of pulmonary embolism and is therefore thought to be useful in excluding the possibility of pulmonary embolism.

• Tuberculosis and Respiratory Diseases
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• v.59 no.6
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• pp.651-655
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• 2005

Background : Diagnosing a pulmonary embolism is difficult because its presenting symptoms are nonspecific and there are limitations with all of the objective tests. The D-dimer is known to be a marker of the lysis of intravascular cross-linked fibrin as a result of the activation of the endogenous fibrinolytic pathways, and the D-dimer assay is these an objective method for diagnosing a pulmonary embolism. This study assessed the benefits of the D-dimer test for diagnosing a pulmonary embolism using semiquantitative latex agglutination. Methods : The latex agglutination results of 185 patients were retrospectively reviewed. The D-dimer test was performed at the time a pulmonary embolism was suspected. Ninety patients(group I) were diagnosis with PE through spiral chest CT or a chest CT angiogram, perfusion/ventilation scans, and/or pulmonary angiogram. Ninety-five patients (group II) were found not to have a pulmonary embolism through the above tests. Results : The male to female ratio and mean age in groups I and II was 37:55, and 57 years old to 50:45 and 52 years old, respectively. When the cut off value for a positive D-dimer assay was set to $500{\mu}g$, the sensitivity, positive predictive value, negative predictive value and specificity was 86.7%, 61.4%, 79.3%, and 48.4%, respectively. Conclusion : The semiquantitative latex agglutination method in the D-dimer test has a lower sensitivity and negative predictive value than the well known ELISA test particularly for small emboli. Therefore, this test is not a suitable screening test for excluding a pulmonary embolism.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.301-301
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• 2011

We present theoretical investigations of the self-assembled growth of one-dimensional (1D) molecular lines directed across the dimer rows on the H-terminated Si(001) surface [1]. Based on density-functional theory calculations, a new growth mechanism of the 1D acetylacetone line is proposed [2], which involves the radical chain reaction initiated at two dangling-bond sites on one side of two adjacent Si dimers. It is also enabled that, if an H-free Si dimer were employed as the initial reaction site, a 1D acetylacetone line can grow along the dimer row. Our findings represent the first insight into the growth of 1D molecular lines not only across but also along the dimer rows on the H-terminated Si(001) surface.

• Proceedings of the Korean Society of Propulsion Engineers Conference
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• 2010.11a
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• pp.797-799
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• 2010

In preparation of NBD dimer, one of the industrially useful multicyclic hydrocarbon compound, various catalyst, solvent and byproducts were included in reaction product at the end of dimerization reaction. In order to increase the yield of NBD dimer mixture, first of all, effective separation process development was required. The research for improvement of NBD dimer yield were performed by use of eco-friendly and recyclable separation solvent.

• Bulletin of the Korean Chemical Society
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• v.21 no.5
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• pp.510-514
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• 2000

Molecular hydrogen dimer, ($H_2)_2$ is a weakly bound van der Waals complex. The configuration of two hydrogen molecules and the potential well structure of the dimer have been the subjects of various studies among chemists and astrophysicists. In this study, we used DFT, MCG2, and MCG3 methods to determine the structure and energy of the molecular hydrogen dimer. We compared the results with previously reported ab initio method results. The ab initio results were also recalculated for comparison. All optimized geometries obtained from the MP2 and DFT methods are T-shaped. The H-H bond lengths for the dimer are almost the same as those of monomer. The center-to-center distance depeds on the levels of theory and the size of the basis sets. The bond lengths of the $H_2$ molecule from the MCG2 and MCG3 methods are shown to be in excellent agreement with the experimental value. The geometry of optimized dimer is T-shaped, and the well depths for the dimerization potential are very small, being 23 $cm-^1$ and 27 $cm-^1$ at the MCG2 and MCG3 levels, respectively. In general the MP2 level of theory predicts stronger van der Waals than the DFT, and agrees better with the MCG2 and MCG3 theories.

• BMB Reports
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• v.56 no.11
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• pp.606-611
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• 2023

The main protease (Mpro) of SARS-CoV-2 cleaves 11 sites of viral polypeptide chains and generates essential non-structural proteins for viral replication. Mpro is an important drug target against COVID-19. In this study, we developed a real-time fluorometric turn-on assay system to evaluate Mpro proteolytic activity for a substrate peptide between NSP4 and NSP5. It produced reproducible and reliable results suitable for HTS inhibitor assays. Thus far, most inhibitors against Mpro target the active site for substrate binding. Mpro exists as a dimer, which is essential for its activity. We investigated the potential of the Mpro dimer interface to act as a drug target. The dimer interface is formed of domain II and domain III of each protomer, in which N-terminal ten amino acids of the domain I are bound in the middle as a sandwich. The N-terminal part provides approximately 39% of the dimer interface between two protomers. In the real-time fluorometric turn-on assay system, peptides of the N-terminal ten amino acids, N10, can inhibit the Mpro activity. The dimer interface could be a prospective drug target against Mpro. The N-terminal sequence can help develop a potential inhibitor.

• Korean Journal of Microbiology
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• v.34 no.1_2
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• pp.58-63
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• 1998

Fragment assembly problem is to reconstruct DNA sequence contigs from a collection of fragment sequences. We have developed an efficient X-window program, XFAP, for assembling DNA fragments. In the XFAP, the dimer frequency comparison method is used to quickly eliminate pairs of fragments that can not overlap. This method takes advantage of the difference of dimer frequencies within the minimum acceptable overlap length in each fragment pair. Hirschberg algorithm is applied to compute the maximal-scoring overlapping alignment in linear space. The perfomance of XFAP was tested on a set of DNA fragment sequences extracted from long DNA sequences of GenBank by a fragmentation program and showed a great improvement in execution time, especially as the number of fragments increases.

• KSBB Journal
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• v.19 no.4
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• pp.315-320
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• 2004

We examined the culture conditions and degrading characteristics of styrene dimer (endocrine disrupter) using microorganism. The isolated microbe were consisted of 3 kinds of strain. The strains were identified to Pseudomonas sp. and Klebsiella pneumoniae by API 20E kit, but one was not identified. Single strain was not grown on the C-medium containing styrene dimer. However the complex strain YH3 could grow and we confirmed it by the broth color and O.D$_{660nm}$ (optical density 660 nm). The optimal culture conditions of complex strain YH3 were 35$^{\circ}C$, 1,000 ppm (v/v) of styrene dimer and pH 7.0, respectively. In tolerance test against the organic solvents, the complex strain YH3 could grow above log P=3.1, and could degrade ethyl benzene and 2,4-D, one kind of herbicide. As a result of TLC (Thin Layer Chromatography) analysis, we confirmed that the metabolite of styrene dimer was created by YH3 after 5th day, but not at control samples.

• Journal of the Semiconductor & Display Technology
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• v.8 no.2
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• pp.55-58
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• 2009

Density functional theory was used to investigate the adsorption and reaction of $HfCl_4$ with two hydroxyls on Si (001)-$2{\times}1$ surface in atomic layer deposition (ALD) process. We prepared a reasonable Si substrate which consisted of six inter-dimer dissociated $H_2O$ molecules and two intra-dimer dissociated $H_2O$ molecules. The $HfCl_4$must react with two hydroxyls to be a bulk-like structure. When $HfCl_4$ was adsorbed on a hydroxyl, there was energy benefit of -0.55 eV. Though there was energy loss for $HfCl_4$ to react with H of hydroxyl, thermal energy of ALD chamber would be enough to pass the energy barriers. There were five reaction pathways for $HfCl_4$ to react with two hydroxyls; inter-dimer, intra-dimer, cross-dimer, inter-row, and cross-row. Inter-row, inter-dimer and intra-dimer were relatively favorable among the five reaction pathways based on the energy difference. The electron densities between O and Hf in these three reactions were higher than the others and they had shorter Hf-O and O-O bond lengths than the other two reaction pathways.