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Search Results: 1 - 10 of 479791 matches for " Kyung A Kim "
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Effective Procedure for Development of EST-SSR Markers Using cDNA Library  [PDF]
Kyung A Kim, Hee-Cheon Park, Jae-Keun Sohn, Kyung-Min Kim
American Journal of Plant Sciences (AJPS) , 2012, DOI: 10.4236/ajps.2012.39159
Abstract: The present study was conducted to develop EST-SSR markers using the cDNA library from rice plant. Total RNA extracted from the leaves of brown plant hopper resistance gene originated from a rice cultivar “Cheongcheong” and sensitive rice cultivar “Nakdong” were used to synthesize a cDNA library. As a result of analyzing the cDNA library, the 17 EST-SSR primer sets were developed. This study enables to provide effective marker assisted selection (MAS) methods on the selection of white-backed planthopper resistance gene originated from a rice plant more simply, quickly and precisely. Furthermore, using this marker’s advantage of deriving from cDNA, it is possible to identify the white-backed planthopper resistance gene. In addition, this study introduces a technique for construction of a cDNA library safely without using radioactivity.
Effects of dependence in high-dimensional multiple testing problems
Kyung In Kim, Mark A van de Wiel
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-114
Abstract: We study the robustness against dependence of several FDR procedures that are popular in microarray studies, such as Benjamin-Hochberg FDR, Storey's q-value, SAM and resampling based FDR procedures. False Non-discovery Rates and estimates of the number of null hypotheses are computed from those methods and compared. Our simulation study shows that methods such as SAM and the q-value do not adequately control the FDR to the level claimed under dependence conditions. On the other hand, the adaptive Benjamini-Hochberg procedure seems to be most robust while remaining conservative. Finally, the estimates of the number of true null hypotheses under various dependence conditions are variable.We discuss a new method for efficient guided simulation of dependent data, which satisfy imposed network constraints as conditional independence structures. Our simulation set-up allows for a structural study of the effect of dependencies on multiple testing criterions and is useful for testing a potentially new method on π0 or FDR estimation in a dependency context.Scientists regularly face multiple testing of a large number of hypotheses nowadays. Typically in microarray data, one performs hypothesis testing for each gene and the number of genes is usually more than thousands. In this situation, direct application of single hypothesis testing thousands times produces a large number of false discoveries. Hence, alternative testing criterions for controlling errors of false discoveries have been introduced.It is widely recognized that dependencies are omnipresent in many high-throughput studies. Such dependencies may be regulatory or functional as in gene pathways, but also spatial such as in SNP or DNA copy number arrays because of the genomic order. Although attempts to infer such interactions from data have been made, it is a notoriously difficult problem. Usually solutions focus on some modules with relatively few elements and many samples, in particular for model organisms (see e
A generalization of Alternating Sign Matrices
Richard A. Brualdi,Hwa Kyung Kim
Mathematics , 2013,
Abstract: In alternating sign matrices the first and last nonzero entry in each row and column is specified to be +1. Such matrices always exist. We investigate a generalization by specifying independently the sign of the first and last nonzero entry in each row and column to be either a +1 or a -1. We determine necessary and sufficient conditions for such matrices to exist.
On a multi-point Schwarz-Pick lemma
Kyung Hyun Cho,Seong-A Kim,Toshiyuki Sugawa
Mathematics , 2011,
Abstract: We consider the multi-point Schwarz-Pick lemma and its associate functions due to Beardon-Minda and Baribeau-Rivard-Wegert. Basic properties of the associate functions are summarized. Then we observe that special cases of the multi-point Schwarz-Pick lemma give Schur's continued fraction algorithm and several inequalities for bounded analytic functions on the unit disk.
Effects of Genetically Engineered Stem Cells Expressing Cytosine Deaminase and Interferon-Beta or Carboxyl Esterase on the Growth of LNCaP Prostate Cancer Cells
Bo-Rim Yi,Kyung-A. Hwang,Yun-Bae Kim,Seung U. Kim,Kyung-Chul Choi
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms131012519
Abstract: The risk of prostate cancer has been increasing in men by degrees. To develop a new prostate cancer therapy, we used a stem cell-derived gene directed prodrug enzyme system using human neural stem cells (hNSCs) that have a tumor-tropic effect. These hNSCs were transduced with the therapeutic genes for bacterial cytosine deaminase (CD), alone or in combination with the one encoding human interferon-beta (IFN-β) or rabbit carboxyl esterase (CE) to generate HB1.F3.CD, HB1.F3.CD.IFN-β, and HB1.F3.CE cells, respectively. CD enzyme can convert the prodrug 5-fluorocytosine (5-FC) into the activated form 5-fluorouracil (5-FU). In addition, CE enzyme can convert the prodrug CPT-11 into a toxic agent, SN-38. In our study, the human stem cells were found to migrate toward LNCaP human prostate cancer cells rather than primary cells. This phenomenon may be due to interactions between chemoattractant ligands and receptors, such as VEGF/VEGFR2 and SCF/c-Kit, expressed as cancer and stem cells, respectively. The HB1.F3.CE, HB.F3.CD, or HB1.F3.CD.IFN-β cells significantly reduced the LNCaP cell viability in the presence of the prodrugs 5-FC or CPT-11. These results indicate that stem cells expressing therapeutic genes can be used to develop a new strategy for selectively treating human prostate cancer.
Analysis of Low Amylose and Processability Fractured Endosperms Derived from Somatic Variation  [PDF]
Gihwan Yi, Kyung Min Kim
Food and Nutrition Sciences (FNS) , 2013, DOI: 10.4236/fns.2013.46A003
Abstract: Recently, improving eating quality and processing properties has become one of the most important objectives in japonica rice breeding programs in Korea. This study was carried out to determine the agronomy and physicochemical characteristics of the opaque endosperm rice \"S-21-3-8\" regenerated from seed-derived callus culture of a rice cultivar, \"Ilpum\". S3 generation of opaque endosperm mutants selected from pedigree breeding was used for analysis of agronomic and physicochemical traits. Genetic segregation was observed at the highest frequency among opaque endosperm mutants, being present in 85.7% (12/14 lines) of the entire opaque lines. However, the major agricultural characteristics and grain traits of \"S-21-3-8\" were similar to those of a donor cultivar, \"Ilpum\". \"S-21-3-8\" showed significantly lower (10.6%) amylose than those (17.7%) of \"Ilpum\" in brown rice, while the protein levels were similar to those of the donor plant. The grain hardness of \"S-21-3-8\" (1.67 kgf/mm2) was lower than that of \"Ilpum\" (1.97 kgf/mm2), resulting in a high flour-milling percentage. The loosely packed starch granules of \"S-21-3-8\" in the opaque endosperm were demonstrated by SEM analysis of cross-sectioned rice grains. The opaque endosperm mutants that were of somaclonal variations in the tissue culture will lead to improved eating quality and processing properties of rice.
Factors Affecting Verbal Agitation in Dementia Patients Living in Nursing Homes, South Korea  [PDF]
Eun Kyung Kim, Heeok Park
Open Journal of Nursing (OJN) , 2018, DOI: 10.4236/ojn.2018.86028
Abstract:
The purpose of this study using secondary data analysis was to identify factors affecting verbal agitation in patients with dementia staying at nursing home. This study is a secondary analysis of an existing original quantitative data set (n = 193). A total of 166 subjects’ data were included in this current study after 27 subjects’ data were excluded from the original data because they did not appear verbal agitation. Multiple regression analyses identified hallucination (β = 0.27), total number of physiologic discomforts (β = 0.19) and pain (β = 0.17) as significant predictors of verbal agitation and these factors explained 27.8% of the variance in the model. The findings of this study showed that hallucination, total number of physiologic discomforts and pain with dementia need to be considered when intervention programs to control verbal agitation in patients with dementia were developed.
Cataloging Coding Sequence Variations in Human Genome Databases
Hong-Hee Won, Hee-Jin Kim, Kyung-A Lee, Jong-Won Kim
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003575
Abstract: Background With the recent growth of information on sequence variations in the human genome, predictions regarding the functional effects and relevance to disease phenotypes of coding sequence variations are becoming increasingly important. The aims of this study were to catalog protein-coding sequence variations (CVs) occurring in genetic variation databases and to use bioinformatic programs to analyze CVs. In addition, we aim to provide insight into the functionality of the reference databases. Methodology and Findings To catalog CVs on a genome-wide scale with regard to protein function and disease, we investigated three representative databases; the Human Gene Mutation Database (HGMD), the Single Nucleotide Polymorphisms database (dbSNP), and the Haplotype Map (HapMap). Using these three databases, we analyzed CVs at the protein function level with bioinformatic programs. We proposed a combinatorial approach using the Support Vector Machine (SVM) to increase the performance of the prediction programs. By cataloging the coding sequence variations using these databases, we found that 4.36% of CVs from HGMD are concurrently registered in dbSNP (8.11% of CVs from dbSNP are concurrent in HGMD). The pattern of substitutions and functional consequences predicted by three bioinformatic programs was significantly different among concurrent CVs, and CVs occurring solely in HGMD or in dbSNP. The experimental results showed that the proposed SVM combination noticeably outperformed the individual prediction programs. Conclusions This is the first study to compare human sequence variations in HGMD, dbSNP and HapMap at the genome-wide level. We found that a significant proportion of CVs in HGMD and dbSNP overlap, and we emphasize the need to use caution when interpreting the phenotypic relevance of these concurrent CVs. Combining bioinformatic programs can be helpful in predicting the functional consequences of CVs because it improved the performance of functional predictions.
Spectrum of EGFR Gene Copy Number Changes and KRAS Gene Mutation Status in Korean Triple Negative Breast Cancer Patients
Yoonjung Kim, Juwon Kim, Hy-De Lee, Joon Jeong, Woochang Lee, Kyung-A Lee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079014
Abstract: Anti-epidermal growth factor receptor (EGFR) therapy has been tried in triple negative breast cancer (TNBC) patients without evaluation of molecular and clinical predictors in several randomized clinical studies. Only fewer than 20% of metastatic TNBCs showed response to anti-EGFR therapy. In order to increase the overall response rate, first step would be to classify TNBC into good or poor responders according to oncogenic mutation profiles. This study provides the molecular characteristics of TNBCs including EGFR gene copy number changes and mutation status of EGFR and KRAS gene in Korean TNBC patients. Mutation analysis for EGFR, KRAS, BRAF and TP53 from a total of 105 TNBC tissue samples was performed by direct sequencing, peptide nucleic acid-mediated PCR clamping method and real-time PCR. Copy number changes of EGFR gene were evaluated using multiplex ligation-dependent probe amplification. Out of all 105 TNBCs, 15.2% (16/105) showed EGFR copy number changes. Among them, increased or decreased EGFR copy number was detected in 13 (5 single copy gain, 2 amplification and 4 high-copy number amplification) and 3 cases (3 hemizygous deletion), respectively. The mutation frequencies of KRAS, EGFR and TP53 gene were 1.9% (G12V and G12D), 1.0% (exon 19 del) and 31.4%, respectively. There was no BRAF V600E mutation found. Future studies are needed to evaluate the clinical outcomes of TNBC patients who undergo anti-EGFR therapy according to the genetic status of EGFR.
Trapa japonica Flerov Extract Attenuates Lipid Accumulation through Downregulation of Adipogenic Transcription Factors in 3T3-L1 Cells  [PDF]
Mi Jin Kim, Kyung Ran Im, Kyung-Sup Yoon
American Journal of Molecular Biology (AJMB) , 2015, DOI: 10.4236/ajmb.2015.52004
Abstract: Obesity is a major human health problem associated with various diseases, including cardiac injury and type 2 diabetes. Trapa japonica Flerov (TJF) has been used in traditional oriental medicine to treat diabetes. In this study, we evaluated the inhibitory effect of and the mechanism underlying the effect of TJF extract on adipogenesis in 3T3-L1 cells. The effects of TJF extract on cell viability were analyzed using a 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay, and the anti-adipogenic effect was measured by oil red O staining. The expression of peroxisomal proliferator activated receptor (PPAR)γ, CCAAT/enhancer-binding protein-α (C/EBP)α, adenosine monophosphate-activated protein kinase (AMPK), acetyl-CoA carboxylase (ACC), adiponectin, and fatty acid binding protein (FABP)4 involved in adipogenesis was determined by western blot analysis. TJF extract effectively inhibited lipid accumulation and the expression of PPARγ and C/EBPα in 3T3-L1 cells. TJF also increased the phosphorylation of AMPK and ACC, and decreased the expression of adiponectin and FABP4. These results indicate that TJF extract exerts its anti-obesity effect through the downregulation of adipogenic transcription factors and adipogenic marker genes.
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