• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• Journal of the Korean Society of Safety
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• v.35 no.1
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• pp.107-115
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• 2020

This paper introduces the first vital area identification (VAI) process for the physical protection of nuclear power plants (NPPs) during low power and shutdown (LPSD) operation. This LPSD VAI is based on the 3rd generation VAI method which very efficiently utilizes probabilistic safety assessment (PSA) event trees (ETs). This LPSD VAI process was implemented to the virtual NPP during LPSD operation in this study. Korea Atomic Energy Research Institute (KAERI) had developed the 2nd generation full power VAI method that utilizes whole internal and external (fire and flooding) PSA results of NPPs during full power operation. In order to minimize the huge burden of the 2nd generation full power VAI method, the 3rd generation full power VAI method was developed, which utilizes ETs and minimal PSA fault trees instead of using the whole PSA fault tree. In the 3rd generation full power VAI method, (1) PSA ETs are analyzed, (2) minimal mitigation systems for avoiding core damage are selected from ETs by calculating system-level target sets and prevention sets, (3) relatively small sabotage fault tree that has the systems in the shortest system-level prevention set is composed, (4) room-level target sets and prevention sets are calculated from this small sabotage fault tree, and (5) the rooms in the shortest prevention set are defined as vital areas that should be protected. Currently, the 3rd generation full power VAI method is being employed for the VAI of Korean NPPs. This study is the first development and application of the 3rd generation VAI method to the LPSD VAI of NPP. For the LPSD VAI, (1) many LPSD ETs are classified into a few representative LPSD ETs based on the functional similarity of accident scenarios, (2) a few representative LPSD ETs are simplified with some VAI rules, and then (3) the 3rd generation VAI is performed as mentioned in the previous paragraph. It is well known that the shortest room-level prevention sets that are calculated by the 2nd and 3rd generation VAI methods are identical.

• Korean Journal of Food Science and Technology
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• v.48 no.4
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• pp.361-365
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• 2016

This study was conducted to isolate and identify a microorganism that increases tricin-O-(threo-${\beta}$-guaiacylglyceryl) ether (TTGE) content in the hulls of rice (Oryza sativa L.). Bacteria from germinated rice were isolated by enrichment cultivation using yeast mold, luria bertani, potato dextrose and mannitol egg york polymyxin broths. The highest increase in TTGE content ($339.30{\mu}g/g$) was achieved by a microorganism isolated by PDA enrichment cultivation. On the basis of 16S RNA sequence homology and phylogenetic analysis, the isolated bacterium was identified to have 100% similarity with Burkholderia vietnamiensis. The isolated bacteria were short rods, negative for the Gram stain, and positive for the catalase test. The highest TTGE level was $435.86{\mu}g/g$ in 72-h fermented samples, representing a 2.5x increase compared with the control ($175.65{\mu}g/g$). In conclusion, the bacterium isolated from germinated rice extract was Burkholderia vietnamiensis, and the optimum fermentation period to maximize TTGE levels was 72 h. These findings might help in developing functional materials using rice hulls, a waste product of rice milling.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.71-77
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• 2010

The time, yield, and related genes expression of PHB accumulation of Acidiphilium cryptum DX1-1 were investigated under four different initial C/N ratios, 1.2, 2.4, 7.5, and 24. The results of time and yield of poly-$\beta$-hydroxybutyrate (PHB) accumulation show that the initial C/N ratio of 2.4 was optimum for strain DX1-1 to accumulate PHB, but both higher and lower initial C/N ratios did not favor that process. Based on the genome of Acidiphilium cryptum JF-5, 13 PHB accumulation related genes in strain JF-5 were chosen and successfully cloned from strain DX1-1. The differential expressions of the 13 functional genes, in different C/N ratios as cited above, were then studied by real-time PCR. The results show that all the 13 genes were most upregulated when the initial C/N ratio was 2.4, and among which the gene Acry_3030 encoding poly-$\beta$-hydroxybutyrate polymerase and Aery_0626 encoding acetyl-CoA synthetase were much more upregulated than the other genes, which proved that they play the most important role for PHB accumulation, and acetate is the main initial substance for PHB accumulation for strain DX1-1. Potential regulatory motifs analysis showed that the genes related to PHB accumulation are regulated by different promoters and that the motif had weak similarity to the model promoters, suggesting that PHB metabolism in Acidiphilium cryptum may be mediated by a different mechanism.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.12 no.1
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• pp.294-300
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• 2011

This study was performed to examine the presence of dysphagia and analyze characteristics of the symptoms in cerebrovascular accident(CVA) patients without awareness of dysphagia. A questionnaire for this study was given to CVA patients who had visited P rehabilitation medical center in Busan. Eleven patients (4 males and 7 females) who answered no awareness of dysphasia were given to VFSS, functional dysphasia scale, and NCSE. Descriptive statistics and Pearson correlation analysis were performed by SPSS 12.0. All of subjects without awareness of dysphasia showed characteristics of dysphasia symptoms. Prominent dysfunctions were problems in oral phase and delay of swallowing reflex in pharyngeal phase. For the aspect of cognition, they showed lower score in construction, memory, and similarity than other NCSE items. There was highly significant correlation between orientation, judgment and delay of swallowing reflex. Verbal comprehension and residual materials in oral cavity showed closed correlation. CVA patients without awareness had dysphagia with high probability. The early evaluation of dysphagia should be performed in CVA patients in order to prevent complications due to CVA, so it is necessary to increase the effectiveness of rehabilitation therapy.

• Korean journal of communication and information
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• v.38
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• pp.40-72
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• 2007

Amid the rapid growth in use of portal news, this study examined whether portal news would substitute traditional news media, in particular newspapers and television news. To answer the research question, this study attempted to investigate how the decrease in use of traditional news media was associated with online news use, reliance on, and motivations for portal news. First, this study found that there was a negative and significant relationship between the Internet use and television news viewing, suggesting that those who are more likely to use the Internet are less likely to watch television news programs. Also, portal news was negatively associated with time spent with newspaper reading, while it was not related to television news viewing. Second, this study found that convenience/information-seeking needs appeared as the major motivations for using portal news, which were negatively and significantly associated with the decreased time spent with watching television news programs. In other words, those who used portal news for convenience/information-seeking needs are less likely to watch television news programs, which may indicate that portal news could be a substitute for television news in terms of convenience/information-seeking motivations. In addition, the result of this study showed that there was a complementary relationship between portal news and newspapers in terms of surveillance needs. Those findings could be explained by the concept of "functional similarity" in the process of media substitution. Based on the findings, implications of this study were discussed.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.180-192
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• 2017

The purpose of this study is to investigate the antioxidative and antimicrobial activities of sourdough fermented with the lactic acid bacteria (LAB) isolated from sliced radish kimchi. According to 16S rRNA gene sequence analysis, the isolated lactic acid bacteria were categorized as Leuconostoc dextranicum SRK03, Lactobacillus brevis SRK15, Pediococcus halophilus SRK22, Lactobacillus acidophilus SRK30, Lactobacillus plantarum SRK38, Leuconostoc citreum SRK 42, and Lactobacillus delbrueckii SRK60 with sequence similarity of 99%. After fermentation with L. dextranicum SRK03, L. acidophilus SRK30, L. plantarum SRK38 or L. delbrueckii SRK60 and Saccharomyces cerevisiae KCTC 7246 at $30^{\circ}C$ for 24 h LAB and yeast in sourdough were present at levels of $10^9$ and $10^7CFU/g$, respectively. In particular, the titratable acidity and ethanol and exopolysaccharide contents of sourdough fermented with L. dextranicum SRK03 were also significantly (P < 0.05) higher than those of sourdough fermented with L. acidophilus SRK30, L. plantarum SRK38, or L. delbrueckii SRK60. The sourdough fermented with L. dextranicum SRK03 and L. acidophilus SRK30 showed not only good DPPH radical-scavenging capacity but anti-lipid peroxidation activity. In addition, the viable counts of Bacillus cereus ATCC 11778 and Staphylococcus aureus ATCC 6538 in sourdough during storage for 5 days at $25^{\circ}C$ were significantly (P < 0.05) lower than those of pathogenic bacteria in the control group due to the organic acids and bacteriocin produced by L. acidophilus SRK30 strain.

• Tuberculosis and Respiratory Diseases
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• v.65 no.2
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• pp.147-151
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• 2008

Non-resolving or slowly resolving pulmonary infiltrates in spite of administering adequate antimicrobial therapy are a clinical diagnostic challenge for physicians. The rate of radiographic resolution varies with the patients' age, the underlying comorbidities, the extent of radiographic involvement, the functional status and the causal pathogens. It is important to differentiate non-resolving or slowly resolving bacterial pneumonia from other uncommon infectious pneumonias or malignancies that require invasive diagnostic techniques to confirm the diagnosis. Bronchioloalveolar carcinoma can present with various clinical and radiographic features. Unfortunately, the radiographic similarity of consolidative BAC to pneumonia often leads to an incorrect diagnosis of pneumonia and possibly significant delays in obtaining appropriate diagnostic studies. We describe here a case of a mixed adenocarcinoma and bronchioloalveolar carcinoma that was initially diagnosed as pneumonia due to the consolidation pattern on the radiography and the patient's initial improvement with antibiotic treatment.

• Communications of Mathematical Education
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• v.32 no.3
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• pp.407-433
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• 2018

In order to analyze textbooks from a discursive approach, the purpose of this study is to structuralize an analytic framework based on previous literature review and apply it to analyzing the meanings and their syntheses developed by words and visual mediators appeared in the definition of graph in first-year middle school textbooks. The discursive approach consists of the communicational approach developed by Sfard(2008) and the systemic functional linguistics developed by Halliday(1985/2004). In this study, ideational meta-functions for ideational meanings and interpersonal meta-functions for interpersonal meanings were employed to analyze the meanings produced by words and visual mediators in textbooks, whereas textual meta-functions for textual meanings were used for analyzing the synthesized relationships between words and visual mediators. Results show that first, density in mathematical discourse was very high and subjects in mathematical activities were ambiguous in the ideational meanings of words, and behavior aspect was more emphasized than thinking aspect in the interpersonal meanings of words which request student participations. In the case of ideational meanings of visual mediators, there was a lack of narrative diagrams, whereas there were qualitative differences in the case of offer. Second, there was a need for promoting a wide range of diverse synthetic relationships between words and visual mediators for developing enriched mathematical meanings through the varying uses like specification, explanation, similarity, and complement. These results are so important that they provide a new analytic framework from a discursive approach to textbook analysis because not only words, but also visual mediators are analyzed as tools for producing meanings in mathematics textbooks and their synthetic relationships are also examined.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.