• Journal of Digestive Cancer Research
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• v.5 no.1
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• pp.5-15
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• 2017

Hepatocellular carcinoma (HCC) is the sixth most common cancer and second leading cause of cancer-related death in the world. The aggressive but not always predictable pattern of HCC causes the limited treatment option and poorer outcome. Many researches had already proven the heterogeneity of HCC is one of the major challenges for treatment option and prognosis prediction. Molecular subtyping of HCC and selection of patient based on molecular profile can provide the optimization in the treatment and prognosis prediction. In this review, we have tried to summarize the molecular classification of HCC proposed by different valuable researches presented in the logistic way.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.60-66
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• 2005

To select the rapid and efficient molecular subtyping method for epidemiologic monitoring of Staphylococcus aureus (S. aureus) strains at clinical laboratory levels, a total 116 of S. aureus and MRSA (methicillin-resistant S. aureus) strains from diverse animal species [Korean cattle, goat, pig, dog, chicken, mouse] and also humans were analyzed. To evaluate the discriminatory ability (DA) of individual PCR methods, random amplified polymorphic of DNA [RAPD; 4M & RA primer], repetitive extragenic palindromic sequences PCR (REP-PCR), and enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) methods were conducted and then compared on their Simpson's index of diversity (SID) values based on the dendrogram patterns, which was produced by software program (BiolD2+ & GelCompar II). In first, RAPD using the 4M primer (SID 0.915) was expressed more higher SID value than that of RA primer (SID 0.874). 4M primer was expressed more powerful DA than RA. Both REP-PCR (SID 0.930) and ERIC-PCR (SID 0.929) methods showed much more higher DA than that of RAPD. According to the present results, both REP-PCR and ERIC-PCR among the tested analysis methods were found as the most reliable and discriminative molecular subtyping method, because they expressed the highest DA for the present S. aureus and MRSA strains.

• Korean Journal of Biological Psychiatry
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• v.8 no.1
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• pp.47-52
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• 2001

It is known that the personality is the crucial factor in the treatment outcome of depression. The authors tried to identify the results of such studies and various components which determine the treatment outcome of depression. Nearly 60 papers published between the year 1990 and 2000 about the treatment of depression and personality were reviewed. Among them about 30 papers were selected to compare the research methods, results and discussions. The arguments and critics of the papers were discussed. In the many debates, the authors admitted the fact that premorbid personality trait influences the treatment outcome of depression negatively regardless of treatment method. Subtyping of depression is feasible along the presence of good or bad predictors of treatment outcome for depression. Differentiation of depression and personality seems to have no problem, however test of personality state before the development of psychiatric disorder such as depression is not amenable. For example, cluster A personality trait is often misunderstood as depression in clinical setting. In some cases cognitive behavioral therapy is effective in the treatment of depression accompanying personality disorder. The authors insist that the analysis of personality in the dimensional aspect rather than in the categorical aspect gives more information in the research of personality influencing the treatment outcome of depression. In addition, the reason why we understand the relationship between depression and personality were discussed.

• Korean Journal of Veterinary Service
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• v.32 no.3
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• pp.257-264
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• 2009

Subtyping of Brucella abortus isolates is epidemiologically important for monitoring of bovine brucellosis outbreaks. Pulsed-field gel electrophoresis (PFGE) is considered as a gold standard of molecular typing methods to study the DNA polymorphisms of bacteria. In this study, we analyzed using PFGE the DNA fragment profiles of B. abortus isolated in Gyeongbuk province from 1998 to 2006. The genomic DNA was digested with the restriction endonuclease Xba I, Xho I and Smi I followed gel electrophoresis. No distinguishable patterns of the genomic DNA digested with Xba I and Xho I were observed among the field isolates of B. abortus tested in this study. But Smi I restriction enzyme resulted in two PFGE patterns consisting of 13-15 bands that ranged in size from 33 to 668bp by standard marker. The cluster analysis by DNA fingerprinting software showed 93.75% similarity between two PFGE patterns. No different PFGE patterns were recognized among the isolates originated from various years, regions and cow breeds.

• Journal of Microbiology
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• v.39 no.3
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• pp.219-225
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• 2001

Phage typing is currently used for typing of Staphylococcus aureus strains beyond the species level in epidemiological studies. A total of 168 Staphylococcus aureus isolates from chicken meat and chicken by-products were phage-typed using the international bacteriophage set for typing Staphylococcus aureus of human origin. One hundred and forty-eight (88.79%) strains were phage-typeable (at least one phage produced 20 or more plaques of lysis). Lysis by phages of group Ⅲ was the mast frequent with 99 (58.93%) sensitive strains. This fact coincides with results of other authors. Twenty-nine different phage patterns were observed and three (95, 75/84 and 6/1030/W57) were most common. One hundred and thirty-two (89.19% of typeable strains) skewed these or indistinguishable (only one phage reaction difference) patterns. Twenty-six out of seventy chicken samples (37.14%) harboured more than one phage type of Staphylococcus aureus. This fact emphasizes the convenience of subtyping several Staphylococcus aureus isolates from the same sample in epidemiological studies. 80% of sausages and hamburgers contained the same Staphylococcus aureus phage types, which wore not found in any of the other food types. This fact suggests a cross contamination during the processing of these foods. Phages 6, 75, 84, 1030 and W57 skewed the greatest activity. None of the Staphylococcus aureus strains were sensitive to phages 47, 81 and 94.

• Food Science and Biotechnology
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• v.15 no.2
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• pp.324-327
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• 2006

The food-borne pathogen Listeria monocytogenes is commonly associated with meats and unpasteurized dairy products. To identify this pathogen in meats more efficiently than has been done in the past, we purchased meats from Korean markets and performed sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and serotyping analysis on Listeria organisms isolated from meat samples. Each Listeria species showed specific protein band patterns on SDS-PAGE. Whole-cell protein SDS-PAGE profiles indicated that the organisms isolated from meats sold in local Korean markets were L. monocytogenes with the serotypes 1/2a, 1/2b, 1/2c, and 4b. We suggest that it is possible to carry out molecular subtyping of L. monocytogenes using SDS-PAGE.

• Genomics & Informatics
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• v.6 no.1
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• pp.54-58
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• 2008

Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.

• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1470-1474
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• 2009

This paper describes the development a of direct multiplex reverse transcription-nested polymerase chain reaction (PCR) method, devised for simultaneous detection and typing of influenza viruses. This method combines the direct reverse transcription reaction without RNA purification with the enhancement of sensitivity and specificity of nested PCR. The method successfully detected three major human influenza viruses: influenza virus A subtype 1 (H1N1) and subtype 3 (H3N2), and influenza B virus (B). The minimum number of virus particles (pfu/ml) necessary for detection in spiked saliva samples was 200 (H1N1), 140 (H3N2), and 4.5 (B). The method's sensitivity and simplicity will be convenient for use in clinical laboratories for the detection and subtyping of influenza and possibly other RNA viruses.

• Korean Journal of Veterinary Research
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• v.45 no.3
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• pp.359-367
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• 2005

This study was carried out to understand the contamination patterns of Listeria in pork processing plants. A total of 402 samples were collected from carcass, pork during processing, surfaces of equipment and environment, and 238 isolates of Listeria species were identified. L. innocua was found in 64.7% of the isolates, L. monocytogenes in 33.2%, and L. welshimeri in 2.1%. Random amplified polymorphic DNA (RAPD) analysis performed to investigate the origin and routes of Listeria contamination, showed 21 composite types of L. monocytogenes and 26 composite types of L. innocua. It was confirmed that Listeria contamination begins with contaminated incoming carcass and ever-present contaminants in the processing environments. The persistence and dissemination of the same strain of L. monocytogenes and L. innocua throughout the processing line revealed that the sanitation standard operating procedure should be implemented to minimize the risk of colonization in the workplace. Molecular subtyping of L. innocua allowed us to tracing the possibility of cross-contamination during processing.

• Communications for Statistical Applications and Methods
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• v.27 no.2
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• pp.225-239
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• 2020

Analysis approaches for single compositional data are well established; however, effective analysis strategies for paired compositional data remain to be investigated. The current project was motivated by studies of age-related hearing loss (presbyacusis), where subjects are classified into four audiometric phenotypes that need to be ranked within these phenotypes based on their paired compositional data. We address this challenge by formulating this problem as a classification problem and integrating a penalized multinomial logistic regression model with compositional data analysis approaches. We utilize Elastic Net for a penalty function, while considering average, absolute difference, and perturbation operators for compositional data. We applied the proposed approach to the presbyacusis study of 532 subjects with probabilities that each ear of a subject belongs to each of four presbyacusis subtypes. We further investigated the ranking of presbyacusis subjects using the proposed approach based on previous literature. The data analysis results indicate that the proposed approach is effective for ranking subjects based on paired compositional data.