• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.65-74
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• 2021

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

• Genomics & Informatics
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• v.20 no.4
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• pp.45.1-45.7
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• 2022

Food security will be affected by climate change worldwide, particularly in the developing world, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and food quality. Auxin is a hormone that plays a critical role in improving plants' tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes in plants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promoters of five auxin-responsive genes in Zea mays. We applied a data fusion approach based on the combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a direct impact on cell membrane proteins. The short-term auxin response may be represented by the regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopeptidase (POP) in Z. mays and the 3-fold overexpression of this gene under auxin treatment for 30 min indicated the role of POP in maize auxin response. POP is regulated by auxin to perform stress adaptation. In addition, the detection of two AuxRE TGTCTC motifs in the upstream sequence of the bx1 gene suggests that bx1 can be regulated by auxin. Auxin may also be involved in the regulation of dehydration-responsive element-binding and some members of the protein kinase superfamily.

• Molecules and Cells
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• v.47 no.1
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• pp.100005.1-100005.15
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• 2024

Amyotrophic lateral sclerosis is a devastating neurodegenerative disease with a complex genetic basis, presenting both in familial and sporadic forms. The hexanucleotide (G₄C₂) repeat expansion in the C9orf72 gene, which triggers distinct pathogenic mechanisms, has been identified as a major contributor to familial and sporadic Amyotrophic lateral sclerosis cases. Animal models have proven pivotal in understanding these mechanisms; however, discrepancies between models due to variable transgene sequence, expression levels, and toxicity profiles complicate the translation of findings. Herein, we provide a systematic comparison of 7 publicly available Drosophila transgenes modeling the G₄C₂ expansion under uniform conditions, evaluating variations in their toxicity profiles. Further, we tested 3 previously characterized disease-modifying drugs in selected lines to uncover discrepancies among the tested strains. Our study not only deepens our understanding of the C9orf72 G₄C₂ mutations but also presents a framework for comparing constructs with minute structural differences. This work may be used to inform experimental designs to better model disease mechanisms and help guide the development of targeted interventions for neurodegenerative diseases, thus bridging the gap between model-based research and therapeutic application.

• Journal of Korea Water Resources Association
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• v.53 no.7
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• pp.493-505
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• 2020

The rainfall-runoff model has been generally adopted to obtain a consistent runoff sequence with the use of the long-term ground-gauged based precipitation data. The Thiessen polygon is a commonly applied approach for estimating the mean areal rainfall from the ground-gauged precipitation by assigning weight based on the relative areas delineated by a polygon. However, spatial bias is likely to increase due to a sparse network of the rain gauge. This study aims to generate continuous runoff sequences with the mean areal rainfall obtained from radar rainfall estimates through a PRMS rainfall-runoff model. Here, the systematic error of radar rainfall is corrected by applying the G/R Ratio. The results showed that the estimated runoff using the corrected radar rainfall estimates are largely similar and comparable to that of the Thiessen. More importantly, one can expect that the mean areal rainfall obtained from the radar rainfall estimates are more desirable than that of the ground in terms of representing rainfall patterns in space, which in turn leads to significant improvement in the estimation of runoff.

• Journal of the Korean Association of Geographic Information Studies
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• v.18 no.2
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• pp.1-15
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• 2015

Urban flooding threatens human beings and facilities with chemical and physical hazards since the beginning of human civilization. Recent studies have emphasized the integration of data and models for effective urban flood inundation modeling. However, the model set-up process is tend to be time consuming and to require a high level of data processing skill. Furthermore, in spite of the use of high resolution grid data, inundation depth and velocity are varied with building treatment methods in 2-D inundation model, because undesirable grids are generated and resulted in the reliability decline of the simulation results. Thus, it requires building generalization process or enhancing building orthogonality to minimize the distortion of building before converting building footprint into grid data. This study aims to develop building generalization method for 2-dimensional inundation analysis to enhance the model reliability, and to investigate the effect of building generalization method on urban inundation in terms of geographical engineering and hydraulic engineering. As a result to improve the reliability of 2-dimensional inundation analysis, the building generalization method developed in this study should be adapted using Digital Building Model(DBM) before model implementation in urban area. The proposed building generalization sequence was aggregation-simplification, and the threshold of the each method should be determined by considering spatial characteristics, which should not exceed the summation of building gap average and standard deviation.

• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.234-243
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• 2018

The Antarctic Ocean contains numerous microorganisms that produce novel biocatalysts that can have applications in various industries. We screened various psychrophilic bacterial strains isolated from the Ross Sea and found that a Croceibacter atlanticus strain (Stock No. 40-F12) showed high lipolytic activity on a tributyrin plate. We isolated the corresponding lipase gene (lipCA) by shotgun cloning and expressed the LipCA enzyme in Escherichia coli cells. Homology modeling of LipCA was carried out using the Spain Arreo lake metagenome alpha/beta hydrolase as a template. According to the model, LipCA has an ${\alpha}/{\beta}$ hydrolase fold, Gly-X-Ser-X-Glymotif, and lid sequence, indicating that LipCA is a typical lipase enzyme. Active LipCA enzyme was purified fromthe cell-free extract by ammonium sulfate precipitation and gel filtration chromatography. We determined its enzymatic properties including optimum temperature and pH, stability, substrate specificity, and organic solvent stability. LipCA was immobilized by the cross-linked enzyme aggregate (CLEA) method and its enzymatic properties were compared to those of free LipCA. After cross-linking, temperature, pH, and organic solvent stability increased considerably, whereas substrate specificities did not changed. The LipCA CLEA was recovered by centrifugation and showed approximately 40% activity after 4th recovery. This is the first report of the expression, characterization, and immobilization of a C. atlanticus lipase, and this lipase could have potential industrial application.

• Journal of The Korean Association For Science Education
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• v.36 no.2
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• pp.295-302
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• 2016

In this study, we investigated a learning progression focusing on $5^{th}$ to $9^{th}$ graders' performances with dissolution and solution concepts using the construct modeling approach. We designed a construct map describing hypothetical pathways of the concept development of dissolution and solution by analyzing both National Science Curricula and related studies. A conceptions test consisting of ordered multiple-choice items was developed and administered to 826 students. A revised construct map was derived from analyses of the results based on the partial credit model, a branch of polytomous item response theory. The sequence of dissolution and solution concepts presented in the current science curriculum was found to correspond with the learning progression of the students. However, the lower anchor, the concept of the homogeneity of particles in solution, and the factors affecting solubility were not consistent with the expected levels of the construct map. After revising the construct map, we proposed a learning progression for dissolution and solution concepts with five levels: Students of level 1 (the lower anchor) recognize the particles in the solution but misunderstand various concepts; Students of level 2 understand the homogeneity of particles in solution; Students of level 3 understand solubility and the conservation of particles during dissolution; Students of level 4 partially understand the interaction between particles; and Students of level 5 (the upper anchor) understand the interaction between particles and the factors affecting solubility.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.11 no.3
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• pp.179-196
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• 1986

In this paper, the peformance of a statistical packet voice/data multiplexer is studied. In ths study we assume that in the packet voice/data multiplexer two separate finite queues are used for voice and data traffics, and that voice traffic gets priority over data. For the performance analysis we divide the output link of the multiplexer into a sequence of time slots. The voice signal is modeled as an (M+1) - state Markov process, M being the packet generation period in slots. As for the data traffic, it is modeled by a simple Poisson process. In our discrete time domain analysis, the queueing behavior of voice traffic is little affected by the data traffic since voice signal has priority over data. Therefore, we first analyze the queueing behavior of voice traffic, and then using the result, we study the queueing behavior of data traffic. For the packet voice multiplexer, both inpur state and voice buffer occupancy are formulated by a two-dimensional Markov chain. For the integrated voice/data multiplexer we use a three-dimensional Markov chain that represents the input voice state and the buffer occupancies of voice and data. With these models, the numerical results for the performance have been obtained by the Gauss-Seidel iteration method. The analytical results have been verified by computer simylation. From the results we have found that there exist tradeoffs among the number of voice users, output link capacity, voic queue size and overflow probability for the voice traffic, and also exist tradeoffs among traffic load, data queue size and oveflow probability for the data traffic. Also, there exists a tradeoff between the performance of voice and data traffics for given inpur traffics and link capacity. In addition, it has been found that the average queueing delay of data traffic is longer than the maximum buffer size, when the gain of time assignment speech interpolation(TASI) is more than two and the number of voice users is small.

• Journal of the Korean Society of Groundwater Environment
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• v.5 no.4
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• pp.192-202
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• 1998

We investigated the geochemistry and environmental isotopes of granite-bedrock groundwater in the Yeongcheon diversion tunnel which is located about 300 m below the land surface. The hydrochemistry of groundwaters belongs to the Ca-HCO$_3$type, and is controlled by flow systems and water-rock interaction in the flow conduits (fractures). The deuterium and oxygen-18 data are clustered along the meteoric water line, indicating that the groundwater are commonly of meteoric water origin and are not affected by secondary isotope effects such as evaporation and isotope exchange. Tritium data show that the groundwaters were mostly recharged before pre-thermonuclear period and have been mixed with younger surface water flowing down rapidly into the tunnel along fractured zones. Based on the mass balance and reaction simulation approaches, using both the hydrochemistry of groundwater and the secondary mineralogy of fracture-filling materials, we have modeled the low-temperature hydrogeochemical evolution of groundwater in the area. The results of geochemical simulation show that the concentrations of Ca$\^$2＋/, Na$\^$＋/ and HCO$_3$and pH of waters increase progressively owing to the dissolution of reactive minerals in flow paths. The concentrations of Mg$\^$2＋/ and K$\^$＋/ frist increase with the dissolution, but later decrease when montmorillonite and illitic material are precipitated respectively. The continuous adding of reactive minerals, namely the progressively larger degrees of water/rock interaction, causes the formation of secondary minerals with the following sequence: first hematite, then gibbsite, then kaolinite, then montmorillonite, then illtic material, and finally microcline. During the simulation all the gibbsite is consumed, kaolinite precipitates and then the continuous reaction converts the kaolinite to montmorillonite and illitic material. The reaction simulation results agree well with the observed, water chemistry and secondary mineralogy, indicating the successful applicability of this simulation technique to delineate the complex hydrogeochemistry of bedrock groundwaters.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.11
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• pp.2075-2082
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• 2006

This paper presents modeling and optimization techniques for hish efficiency solar cell process on single-crystalline float zone (FZ) wafers. Among a sequence of multiple steps of fabrication, the followings are the most sensitive steps for the contact formation: 1) Emitter formation by diffusion; 2) Anti-reflection-coating (ARC) with silicon nitride using plasma-enhanced chemical vapor deposition (PECVD); 3) Screen-printing for front and back metalization; and 4) Contact formation by firing. In order to increase the performance of solar cells in terms of efficiency, the contact formation process is modeled and optimized using neural networks and genetic algorithms, respectively. This paper utilizes the design of experiments (DOE) in contact formation to reduce process time and fabrication costs. The experiments were designed by using central composite design which consists of 24 factorial design augmented by 8 axial points with three center points. After contact formation process, the efficiency of the fabricated solar cell is modeled using neural networks. Established efficiency model is then used for the analysis of the process characteristics and process optimization for more efficient solar cell fabrication.