• Genomics & Informatics
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• v.15 no.1
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• pp.51-53
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• 2017

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.

• Childhood Kidney Diseases
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• v.15 no.1
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• pp.38-48
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• 2011

Purpose: Focal segmental glomerulosclerosis (FSGS) is the most common glomerulopathy causing pediatric renal failure. Since specific treatment targeting the etiology and pathophysiology of primary FSGS is yet elusive, the authors explored the pathophysiology of FSGS by transcriptome analysis of the disease using an animal model. Methods: FGS/kist strain, a mouse model of primary FSGS, and RFM/kist strain, as control and the parent strain of FGS/kist, were used. Kidney tissues were harvested and isolated renal cortex was used to extract mRNA, which was run on AB 1700 mouse microarray chip after reverse transcription to get the transcriptome profile. Results: Sixty two genes were differentially expressed in FGS/kist kidney tissue compared to the control. Those genes were related to cell cycle/cell death, immune reaction, and lipid metabolism/vasculopathy, and the key molecules of their networks were TNF, IL-6/4, IFN${\gamma}$, TP53, and PPAR${\gamma}$. Conclusion: This study confirmed that renal cell death, immune system activation with subsequent fibrosis, and lipid metabolism-related early vasculopathy were involved in the pathophysiology of FSGS. In addition, the relevance of methodology used in this study, namely transcriptome profiling, and Korean animal model of FGS/kist was validated. Further study would reveal novel pathophysiology of FSGS for new therapeutic targets.

• Journal of the Korean Association of Geographic Information Studies
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• v.4 no.1
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• pp.18-26
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• 2001

Landsat TM band ratio algorithms were made by in-water optical measurement data of each sampling points for water quality monitoring of coastal area using Landsat TM satellite data. The algorithm was derived from in-water optical reflectance data which was measuring by the PRR(profiling reflectance radiometer). And, in-water optical reflectance data were applied to Landsat TM bands. Relationship between in-water optical reflectance and pigments proposed by the ratio of TM band 1 and band 2 showed to as follows; $Y=3.8352{\times}(R(band\;1)/R(band\;2))^{-2.1978}$ ($R^2$=0.7069) and, relationship of the ratio of TM band 1 and band 3 as follows; $Y=23.288{\times}(R(band\;1)/R(band\;3))^{-1.5243}$ ($R^2$=0.8062). Calculated the upwelling radiance of water surface and radiance of TM showed the ratio of atmospheric effect. In the coastal area Rayleigh and Mie scattering of atmosphere is to make over 80% of normalized radiance of Landsat TM. In order to apply in-water algorithm obtained by PRR, we had to calculate the atmospheric effects at sampling site. And, the quantitative analysis of in-water components using Landsat TM data need the calibration of in-water algorithm and effective method of atmospheric correction.

• Journal of Digital Convergence
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• v.20 no.4
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• pp.367-376
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• 2022

In traditional criminal cases, there is a limit to information collection because information on the subject of investigation is provided only with personal information held by the national organization of legal. Surface web-based OSINT(Open Source Intelligence), including SNS and portal sites that can be searched by general search engines, can be used for meaningful profiling for criminal investigations. The Korean-style OSINT workflow can effectively profile based on OSINT, but in the case of individuals, OSINT that can be collected is limited because it begins with "name", and the reliability is limited, such as collecting information of the persons with the same name. In order to overcome these limitations, this paper defines information related to individuals, i.e., equivalent information, and enables efficient and accurate information collection based on this. Therefore, we present an improved workflow that can extract information related to a specific person, ie., equivalent information, from OSINT. For this purpose, different workflows are presented according to the person's profile. Through this, effective profiling of a person (individuals) is possible, thereby increasing reliability in collecting investigation information. According to this study, in the future, by developing a system that can automate the analysis process of information collected using artificial intelligence technology, it can lay the foundation for the use of OSINT in criminal investigations and contribute to diversification of investigation methods.

• BMB Reports
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• v.42 no.9
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• pp.611-616
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• 2009

We investigated the expression pattern of dehydration responsive element-binding protein-3 in tomato under different abiotic stresses. Full length LeDREB3 cDNA was isolated from tomato plant, followed by phylogenetic analysis based on deduced amino acid sequences that revealed significant sequence similarity to DREB proteins belonging to diverse families of plant species. Southern blot analysis showed duplicate copies of LeDREB3 in the tomato genome while organ-specific expression profiling indicated constitutive expression of LeDREB3 in all tested organs, which was particularly strong in flower. LeDREB3 expression was significantly induced by Nacl, drought, low temperature and $H_2O_2$. Moreover, LeDREB3 was slightly regulated by treatment with ABA and MV. These observations suggest that the LeDREB3 gene may be involved in the response of the tomato plant to stress.

• Current Photovoltaic Research
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• v.8 no.3
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• pp.94-101
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• 2020

This study was trying to focus on achieving high efficiency of multi junction solar cell with thin film silicon solar cells. The proposed thin film Si-Ge/c-Si tandem junction solar cell concept with a combination of low-cost thin-film silicon solar cell technology and high-efficiency c-Si cells in a monolithically stacked configuration. The tandem junction solar cells using amorphous silicon germanium (a-SiGe:H) as an absorption layer of upper sub-cell were simulated through ASA (Advanced Semiconductor Analysis) simulator for acquiring the optimum structure. Graded Ge composition - effect of E_g profiling and inserted buffer layer between absorption layer and doped layer showed the improved current density (J_sc) and conversion efficiency (η). 13.11% conversion efficiency of the tandem junction solar cell was observed, which is a result of showing the possibility of thin film Si-Ge/c-Si tandem junction solar cell.

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.222-230
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• 2007

Some drugs may be limited in their clinical application due to their propensity towards their adverse effects. Toxicogenomic technology represents a useful approach for evaluating the toxic properties of new drug candidates early in the drug discovery process. Nitrofurantoin (NF) is clinical chemotherapeutic agent and antimicrobial and used to treatment of urinary tract infections. However, NF has been shown to result in pulmonary toxic effects. In this research, we revealed the changing expression gene profiles in BEAS-2B, human bronchial epithelial cell line, exposed to NF by using human oligonucleotide chip. Through the clustering analysis of gene expression profiles, we identified 136 up-regulated genes and 379 down-regulated genes changed by more than 2-fold by NF. This study identifies several interesting targets and functions in relation to NF-induced toxicity through a gene ontology analysis method including biological process, cellular components, molecular function and KEGG pathway.

• Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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• v.33 no.6
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• pp.537-546
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• 2015

This paper deals with the retrieval of integrated water vapor (IWV) from the zenith tropospheric delay estimated by precisely processing GPS observations at IEODO ocean research station in the East China Sea. A comparison of GPS-IWV with the radiosonde profiling from June and November in 2014 was made to confirm the method and the procedure, adopted for the IWV determination. A series of analysis of these IWV values was performed to capture characteristics of their seasonal and diurnal variations. Furthermore, the troposphere around the ocean research station during typhoon events was spatiotemporally analyzed by including thirteen GPS sites over the Korean Peninsula, indicating correlation between the typhoon location and the tropospheric density.

• Journal of the Korean Magnetic Resonance Society
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• v.15 no.2
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• pp.90-103
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• 2011

Cornus officinalis (Cornaceae) is primarily grown in Asian countries. The pericarp of C. officinalis (Corni Fructus) is a well-known traditional medicine with tonic, analgesic, and diuretic properties. We analyzed methanolic extracts of Corni Fructus (grown in Korea and China) by $^1H$ NMR spectroscopy. Metabolite profiling was performed to characterize the metabolic difference between different Corni Fructus origins (Korea or China). Principal components analysis revealed significant separation between Comus Fructus from different origins. The metabolites responsible for differences were identified using loading plots, coefficients plots, and variable influence on projection followed by t-tests. As a result, 16 metabolites were identified and quantified; tyrosine, acetate, sucrose, and malate differed the most between origins. These data suggest that NMR-based metabolomics can be used to identify differences between Corni Fructus samples obtained from different regions.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.2
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• pp.115-122
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• 2007

As the genome of B.mori is available in GenBank and the EST database of B.mori is expanding, identification of novel genes of B.mori is conceivable by data-mining techniques. We used the in silico cloning method to get the vacuolar-type $H^+-ATP$ synthetase (V-ATPase) c subunit (16 kDa proteolipid subunit) gene of B.mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and sequencing. The V-ATPase c subunit cDNA contains a 468 bp ORF. The ORF encoded a 155-residue protein that showed extensive homology with V-ATPase c subunits from other 15 species and contained four membrane-spanning helices. Tissue expression pattern analysis revealed that V-ATPase c expressed strongly in Malpighian tubules, not in fat body. This gene has been registered in GenBank under the accession number EU082222.