• Genomics & Informatics
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• v.9 no.1
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• pp.39-43
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• 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

• Journal of Information Processing Systems
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• v.6 no.4
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• pp.609-620
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• 2010

In order to provide a tailored education for learners within the ubiquitous environment, it is critical to undertake an analysis of the learning activities of learners. For this purpose, SCORM (Sharable Contents Object Reference Model), IMS LD (Instructional Management System Learning Design) and other standards provide learning design support functions, such as, progress checks. However, in order to apply these types of standards, contents packaging is required, and due to the complicated standard dimensions, the facilitation level is lower than the work volume when developing the contents and this requires additional work when revision becomes necessary. In addition, since the learning results are managed by the server there is the problem of the OS being unable to save data when the network is cut off. In this study, a system is realized to manage the actions of learners through the event interception of a web-browser by using event hooking. Through this technique, all HTMLbased contents can be facilitated again without additional work and saving and analysis of learning results are available to improve the problems following the application of standards. Furthermore, the ubiquitous learning environment can be supported by tracking down learning results when the network is cut off.

• Journal of Physiology & Pathology in Korean Medicine
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• v.19 no.2
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• pp.426-428
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• 2005

This study was conducted to investigate the effects of black raspberry wine which was administered per os on estrogen levels in Splague-Dawley(SD) rats. Black raspberry wine containing 13% alcohol(v/v) was prepared from ripe fruits of Rubus coreanus fermented with Saccharomyces cervisiae. The rats were divided into 2 groups(A and B): The group A received black raspberry wine and the group B received saline for 7 weeks. All animals were bi weekly monitored for estrogen levels by radioimmunoassay using $125^I$ labeled anti-estrogen monospecific antibody. There was a significant(2.02 fold) increase in estrogen levels in the group A with a peak at the 7th week post administration of black raspberry wine. There was no significant change in estrogen levels of the rats in the group B. These data point to uncharacterized phytoestrogenic bioactivity of black raspberry wine that appears to be a useful phytoestrogenic herbal remedy for human health.

• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• Journal of The Korean Society of Grassland and Forage Science
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• v.40 no.4
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• pp.285-290
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• 2020

To understand the role of small heat shock protein (sHSPs) in rice plant response to various stresses such as the heat and oxidative stresses, a cDNA encoding a 24.1 kDa mitochondrial small HSP (Oshsp24.1) was isolated from rice by rapid amplification of cDNA ends (RACE) PCR. The deduced amino acid sequence shows very high similarity with other plant small HSPs. DNA gel blot analysis suggests that the rice genome contains more than one copy of Oshsp24.1. High level of expression of Oshsp24.1 transcript was observed in rice seedlings in response to heat, methyl viologen, hydrogen peroxide, ozone, salt and heavy metal stresses. Recombinant OsHSP24.1 protein was produced in E. coli cells for biochemical assay. The protein formed oligomeric complex when incubated with Sulfo-EGS (ethylene glycol bis (succinimidyl succinate)). Our results shows that Oshsp24.1 has an important role in abiotic stress response and have potential for developing stress-tolerant plants.

• Proceedings of the Korea Information Processing Society Conference
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• 2013.05a
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• pp.148-150
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• 2013

최근 TCP/IP에서 세션을 통하여 노드들 간의 통신을 연결하는 방식에서 현재는 하나의 채널을 통해 고속의 I/O가 가능하도록 하는 인피니밴드 같은 기술이 많이 연구되고 있다. 인피니밴드는 프로세싱 노드와 입출력 장치 사이의 통신, 프로세스간 통신에 대한 산업 표준이 되고 있고 프로세싱 노드와 입출력 장치를 연결하기 위해 스위치 기반의 상호 연결은 전통적인 버스 입출력을 대체하는 새로운 입출력 방식이다. 또한 인피니밴드에서는 현재 이슈가 되고 있는 RDMA 방식을 이용해 원격지 서버들간에 직접 메모리 접근 방식을 통해 CPU와 OS의 로드를 최소화하고 있다. 본 논문에서는 인피니밴드 네트워크를 이용하는 저장장치 접근 프로토콜인 iSER(iSCSI Extension RDMA Protocol)와 기존 이더넷망에서 사용되는 iSCSI(Internet SCSI) 프로토콜을 이용하여 서버와 저장장치 간의 IOPS 와 초당 데이터 전송량에 대한 성능을 평가한다. 우리는 성능평가를 위해 Intel에서 제공하는 저장장치 I/O 성능평가 도구인 IO meter를 이용했다.

• Radiation Oncology Journal
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• v.28 no.4
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• pp.193-204
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• 2010

Purpose: To analyze the treatment outcomes, complications, prognostic factors after a long-term follow-up of patients with nasopharyngeal carcinoma treated with radiation therapy (RT) alone or concurrent chemoradiation therapy (CCRT). Materials and Methods: Between December 1981 and December 2006, 190 eligible patients with non-metastatic nasopharyngeal carcinoma were treated at our department with a curative intent. Of these patients, 103 were treated with RT alone and 87 patients received CCRT. The median age was 49 years (range, 8~78 years). The distributions of clinical stage according to the AJCC 6th edition included I: 7 (3.6%), IIA: 8 (4.2%), IIB: 33 (17.4%), III: 82 (43.2%), IVA: 31 (16.3%), IVB: 29 (15.3%). The accumulated radiation doses to the primary tumor ranged from 66.6~87.0 Gy (median, 72 Gy). Treatment outcomes and prognostic factors were retrospectively analyzed. Acute and late toxicities were assessed using the RTOG criteria. Results: A total of 96.8% (184/190) of patients completed the planned treatment. With a mean follow-up of 73 months (range, 2~278 months; median, 52 months), 93 (48.9%) patients had relapses that were local 44 (23.2%), nodal 13 (6.8%), or distant 49 (25.8%). The 5- and 10-year overall survival (OS), disease-free survival (DFS), and disease-specific survival (DSS) rates were 55.6% and 44.5%, 54.8% and 51.3%, in addition to 65.3% and 57.4%, respectively. Multivariate analyses revealed that CCRT, age, gender, and stage were significant prognostic factors for OS. The CCRT and gender were independent prognostic factors for both DFS and DSS. There was no grade 4 or 5 acute toxicity, but grade 3 mucositis and hematologic toxicity were present in 42 patients (22.1%) and 18 patients (9.5%), respectively. During follow-up, grade 3 hearing loss in 9 patients and trismus in 6 patients were reported. Conclusion: The results of our study were in accordance with findings of previous studies and we confirmed that CCRT, low stage, female gender, and young age were related to improvement in OS. However, there are limitations in the locoregional control that can be achieved by CCRT with 20 conventional radiation therapy. This observation has led to further studies on clarifying the efficacy of concurrent chemotherapy by intensity modulated radiation therapy.

• Radiation Oncology Journal
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• v.31 no.3
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• pp.155-161
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• 2013

Purpose: To evaluate the treatment outcomes of preoperative versus postoperative concurrent chemoradiotherapy (CRT) on locally advanced rectal cancer. Materials and Methods: Medical data of 114 patients with locally advanced rectal cancer treated with CRT preoperatively (54 patients) or postoperatively (60 patients) from June 2003 to April 2011 was analyzed retrospectively. 5-Fluorouracil (5-FU) or a precursor of 5-FU-based concurrent CRT (median, 50.4 Gy) and total mesorectal excision were conducted for all patients. The median follow-up duration was 43 months (range, 16 to 118 months). The primary end point was disease-free survival (DFS). The secondary end points were overall survival (OS), locoregional control, toxicity, and sphincter preservation rate. Results: The 5-year DFS rate was 72.1% and 48.6% for the preoperative and postoperative CRT group, respectively (p = 0.05, the univariate analysis; p = 0.10, the multivariate analysis). The 5-year OS rate was not significantly different between the groups (76.2% vs. 69.0%, p = 0.23). The 5-year locoregional control rate was 85.2% and 84.7% for the preoperative and postoperative CRT groups (p = 0.98). The sphincter preservation rate of low-lying tumor showed significant difference between both groups (58.1% vs. 25.0%, p = 0.02). Pathologic tumor and nodal down-classification occurred after the preoperative CRT (53.7% and 77.8%, both p < 0.001). Acute and chronic toxicities were not significantly different between both groups (p=0.10 and p = 0.62, respectively). Conclusion: The results confirm that preoperative CRT can be advantageous for improving down-classification rate and the sphincter preservation rate of low-lying tumor in rectal cancer.

• Restorative Dentistry and Endodontics
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• v.32 no.4
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• pp.365-376
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• 2007

The purpose of this study was to evaluate the effect of different etching times on microtensile bond strength (${\mu}TBS$) to dentin both initial and after thermocycling with 3 different types of total-etching adhesives. Fifty four teeth were divided into 18 groups by etching times (5, 15, 25 sec), adhesives types (Scotchbond Multipurpose (SM), Single Bond (SB), One-Step (OS)) and number of thermocycling (0, 2,000 cycles). Flat dentin surfaces were prepared on mid-coronal dentin of extracted third molars. After exposed fresh dentin surfaces were polished with 600-grit SiC papers, each specimen was acid-etched with 35% phosphoric acid (5, 15, 25 sec) and bonded with 3 different types of total etching adhesives respectively. Then, hybrid composite Z-250 was built up. Half of them were not thermocycled (control group) and the ethers were subjected to 2,000 thermocycle (experimental group). They were sectioned occluso-gingivally into $1.0\;{\times}\;1.0\;mm^2$ composite-dentin beams and tested with universal testing machine at a crosshead speed of 1.0 mm/min. Within limited data of this study, the results were as follows 1. There was no statistically significant difference in ${\mu}TBS$ between the thermocycled and non-thermocycled groups, except for both SM and SB etched for 25 sec. 2. In thermocycled SM and SB groups, bond strength decreased by extended etching time. In total etching systems, adhesive durability for dentin could be affected by type of solvents in adhesive and etching time. Especially, extended etching time may cause deteriorate effects on bond strength when ethanol-based adhesive was used.

• Journal of Mushroom
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• v.11 no.1
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• pp.15-20
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• 2013

This study was performed to obtain the scientific data an artificial culture of ear mushroom(Auricularia auricula). Liquid cultural of Auricularia auricula. mycelium was characterized with respect to temperature, pH, compositions of inorganic, carbon and nitrogen. The its optimum temperature and media pH were at $25^{\circ}C$ and pH 5.0~6.0 on the mycelial growth, respectively. The optimum inorganic compositions and concentration for mycelial growth were $MgSO_4$ 0.05%(w/v) and $KH_2PO_4$ 0.1%(w/v), respectively. The optimum carbon sources and nitrogen sources were black-sugar 2%(w/v) and soybean powder at 0.3~0.5%(w/v) with7 days optimum culture time.