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Search Results: 1 - 10 of 20246 matches for " Yun Sang Cho "
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Prediction of novel synthetic pathways for the production of desired chemicals
Ayoun Cho, Hongseok Yun, Jin Park, Sang Lee, Sunwon Park
BMC Systems Biology , 2010, DOI: 10.1186/1752-0509-4-35
Abstract: In the present study, we propose a system framework employing a retrosynthesis model with a prioritization scoring algorithm. This new strategy allows deducing the novel promising pathways for the synthesis of a desired chemical together with information on enzymes involved based on structural changes and reaction mechanisms present in the system database. The prioritization scoring algorithm employing Tanimoto coefficient and group contribution method allows examination of structurally qualified pathways to recognize which pathway is more appropriate. In addition, new concepts of binding site covalence, estimation of pathway distance and organism specificity were taken into account to identify the best synthetic pathway. Parameters of these factors can be evolutionarily optimized when a newly proven synthetic pathway is registered. As the proofs of concept, the novel synthetic pathways for the production of isobutanol, 3-hydroxypropionate, and butyryl-CoA were predicted. The prediction shows a high reliability, in which experimentally verified synthetic pathways were listed within the top 0.089% of the identified pathway candidates.It is expected that the system framework developed in this study would be useful for the in silico design of novel metabolic pathways to be employed for the efficient production of chemicals, fuels and materials.In the past few decades, various systematic methods have been developed for the prediction of synthetic metabolic pathways for the production of chemicals by employing microorganisms [1-15]. These methods can be classified by whether the approach is based on chemical structural changes, enzymatic information, and/or reaction mechanisms. The method based on chemical structural changes is applied to reconstruct the network which represents the relationship among the biochemical compounds using the structure-based homology analysis [1-4]. This method generates a variety of novel pathways, but prediction to specify the enzymes is dif
Multi-Purpose HILS Design and Implementation for Optimal Operation Of Distributed Energy Resources with EMS
Chul-Sang Hwang, Yun-Su Kim, Jin-Hong Jeon, Changhee Cho, Minwon Park, In-Keun Yu
International Journal of Scientific Engineering and Technology , 2017, DOI: 10.5958/2277-1581.2017.00015.8
Abstract: Multi-purpose hardware in-the loop simulation (HILS) design and implementation for optimal operation of distributed energy resources (DERs) with energy management system (EMS) were performed, and the operational performance of DERs is analyzed. The DERs which includes a photovoltaic power system, an energy storage system, load and utility grid is modeled and analyzed in real time digital simulator (RTDS). An optimal operation algorithm is implemented in connection with EMS, which is connected to the RTDS through interface cards. The results demonstrated the effectiveness of the HILS and the EMS. The proposed multi-purpose HILS method can be effectively utilized to validate and test operational schemes of DERs with EMS under the practical environment without a real system.
Gene Expression Signature Analysis Identifies Vorinostat as a Candidate Therapy for Gastric Cancer
Sofie Claerhout, Jae Yun Lim, Woonyoung Choi, Yun-Yong Park, KyoungHyun Kim, Sang-Bae Kim, Ju-Seog Lee, Gordon B. Mills, Jae Yong Cho
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024662
Abstract: Background Gastric cancer continues to be one of the deadliest cancers in the world and therefore identification of new drugs targeting this type of cancer is thus of significant importance. The purpose of this study was to identify and validate a therapeutic agent which might improve the outcomes for gastric cancer patients in the future. Methodology/Principal Findings Using microarray technology, we generated a gene expression profile of human gastric cancer–specific genes from human gastric cancer tissue samples. We used this profile in the Broad Institute's Connectivity Map analysis to identify candidate therapeutic compounds for gastric cancer. We found the histone deacetylase inhibitor vorinostat as the lead compound and thus a potential therapeutic drug for gastric cancer. Vorinostat induced both apoptosis and autophagy in gastric cancer cell lines. Pharmacological and genetic inhibition of autophagy however, increased the therapeutic efficacy of vorinostat, indicating that a combination of vorinostat with autophagy inhibitors may therapeutically be more beneficial. Moreover, gene expression analysis of gastric cancer identified a collection of genes (ITGB5, TYMS, MYB, APOC1, CBX5, PLA2G2A, and KIF20A) whose expression was elevated in gastric tumor tissue and downregulated more than 2-fold by vorinostat treatment in gastric cancer cell lines. In contrast, SCGB2A1, TCN1, CFD, APLP1, and NQO1 manifested a reversed pattern. Conclusions/Significance We showed that analysis of gene expression signature may represent an emerging approach to discover therapeutic agents for gastric cancer, such as vorinostat. The observation of altered gene expression after vorinostat treatment may provide the clue to identify the molecular mechanism of vorinostat and those patients likely to benefit from vorinostat treatment.
Application and evaluation of the MLVA typing assay for the Brucella abortus strains isolated in Korea
Moon Her, Sung-Il Kang, Dong-Hee Cho, Yun-Sang Cho, In-Yeong Hwang, Young-Ran Heo, Suk-Chan Jung, Han-Sang Yoo
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-230
Abstract: A total of 177 isolates originating from 105 cattle farms for the period 1996 to 2008 were selected as representatives for the nine provinces of South Korea. A dendrogram of strain relatedness was constructed in accordance with the number of tandem repeat units for 17 loci so that it was possible to trace back in the restricted areas. Even in a farm contaminated by one source, however, the Brucella isolates showed an increase or decrease in one TRs copy number at some loci with high DI values. Moreover, those 17 loci was confirmed in stability via in-vitro and in-vivo passage, and found to be sufficiently stable markers that can readily identify the inoculated strain even if minor changes were detected. In the parsimony analysis with foreign Brucella isolates, domestic isolates were clustered distinctively, and located near the Central and Southern American isolates.The MLVA assay has enough discrimination power in the Brucella species level and can be utilized as a tool for the epidemiological trace-back of the B. abortus isolates. But it is important to consider that Brucella isolates may be capable of undergoing minor changes at some loci in the course of infection or in accordance with the changes of the host.Brucellosis is an important disease that is causing economic losses in the cattle industry as well as health problems in humans. Bovine brucellosis in Korea was first detected from cattle in 1955 [1]. Since then, the disease had been occurred sporadically until 1983, and the most outbreaks had been reported in dairy cattle. In spite of the eradication program, the prevalence was continuously increased [2]. For the control and prevention of brucellosis, a new intensive national Brucella eradication program was established and has been executed from July, 2004 in Korea, employing the test-and-slaughter and/or stamp-out approach. All cattle raised in the farms in Korea are regularly tested for brucellosis and a test certificate is required before they could be
Quantitative Proteomic Analysis of Human Embryonic Stem Cell Differentiation by 8-Plex iTRAQ Labelling
Mahdieh Jadaliha, Hyoung-Joo Lee, Mohammad Pakzad, Ali Fathi, Seul-Ki Jeong, Sang-Yun Cho, Hossein Baharvand, Young-Ki Paik, Ghasem Hosseini Salekdeh
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038532
Abstract: Analysis of gene expression to define molecular mechanisms and pathways involved in human embryonic stem cells (hESCs) proliferation and differentiations has allowed for further deciphering of the self-renewal and pluripotency characteristics of hESC. Proteins associated with hESCs were discovered through isobaric tags for relative and absolute quantification (iTRAQ). Undifferentiated hESCs and hESCs in different stages of spontaneous differentiation by embryoid body (EB) formation were analyzed. Using the iTRAQ approach, we identified 156 differentially expressed proteins involved in cell proliferation, apoptosis, transcription, translation, mRNA processing, and protein synthesis. Proteins involved in nucleic acid binding, protein synthesis, and integrin signaling were downregulated during differentiation, whereas cytoskeleton proteins were upregulated. The present findings added insight to our understanding of the mechanisms involved in hESC proliferation and differentiation.
Omega-3 index and smoking in patients with acute ST-elevation myocardial infarction taking statins: a case-control study in Korea
Young Kim, Dong Jeong, Jeong Lee, Han Lee, Sang Lee, Yun Kim, Yu Yi, Yong Park, Young Cho, Mi Bae, Eun Choi
Lipids in Health and Disease , 2012, DOI: 10.1186/1476-511x-11-43
Abstract: We conducted a case-control study in which omega-3 fatty acids and lifestyle factors were determined in 24 consecutive Korean patients taking statins with angiographically confirmed acute STEMI and 68 healthy controls without acute STEMI. The omega-3 index was calculated by the sum of eicosapentaenoic acid and docosahexaenoic acid in erythrocyte membranes. Multivariable adjusted regression analysis was used to assess independent associations between acute STEMI, omega-3 index, and lifestyle factors after adjusting for age, sex, and body mass index (BMI).The mean age of total subjects was 59.9 years, and 57.6% of the subjects were male. The omega-3 index was significantly lower in cases (8.83%) than controls (11.13%; P < 0.001); however, total trans-fatty acids were not different between the two groups. The omega-3 index was inversely associated with odds for being a case (OR 0.16 (95% CI 0.03-1.14); P = 0.047), while smoking was positively associated with odds for being a case (OR 6.67 (95% CI 1.77-25.23); P = 0.005) after adjusting for all confounding variables.This study shows that relative to controls, acute STEMI cases are more likely to be smokers and to have a lower omega-3 index, even though the cases were taking statins. An omega-3 index of at least 11% and abstinence from smoking are associated with cardioprotection for Koreans.Cardiovascular disease (CVD) is one of the most common causes of mortality and morbidity across the globe [1]. Studies that have focused on the prevention of coronary heart disease (CHD) have reported that lifestyle modifications such as smoking cessation, adequate alcohol consumption, exercise, stress reduction, weight control, and diet are preventable factors of CVD [2-5]. Dietary n-3 polyunsaturated fatty acids (PUFA) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are found in fish meat and fish oil, have also been shown to protect against CVD during the past three decades [6]. Since the first observatio
Outcome of laparoscopic cholecystectomy is not influenced by chronological age in the elderly
Hyung Ook Kim, Jung Won Yun, Jun Ho Shin, Sang Il Hwang, Yong Kyun Cho, Byung Ho Son, Chang Hak Yoo, Yong Lai Park, Hungdai Kim
World Journal of Gastroenterology , 2009,
Abstract: AIM: To evaluate the outcome of laparoscopic cholecystectomy (LC) in patients aged 80 years and older.METHODS: A total of 353 patients aged 65 to 79 years (group 1) and 35 patients aged 80 years and older (group 2) underwent LC. Patients were further classified into two other groups: those with uncomplicated gallbladder disease (group A) or those with complicated gallbladder disease (group B).RESULTS: There were no significant differences between the age groups (groups 1 and 2) with respect to clinical characteristics such as age, gender, comorbid disease, or disease presentation. Mean operative time, conversion rate, and the incidence of major postoperative complications were similar in groups 1 and 2. However, the percentage of high-risk patients was significantly higher in group 2 than in group 1 (20.0% vs 5.7%, P < 0.01). Group A comprised 322 patients with a mean age of 71.0 ± 5.3 years, and group B comprised 51 patients with a mean age of 69.9 ± 4.8 years. In group B, mean operative time (78.4 ± 49.3 min vs 58.3 ± 35.8 min, P < 0.01), mean postoperative hospital stay (7.9 ± 6.5 d vs 5.0 ± 3.7 d, P < 0.01), and the incidence of major postoperative complications (9.8% vs 3.1%, P < 0.05) were significantly greater than in group A. The conversion rate tended to be higher in group B, but this difference was not significant.CONCLUSION: Perioperative outcomes in elderly patients who underwent LC seem to be influenced by the severity of gallbladder disease, and not by chronologic age. In octogenarians, LC should be performed at an earlier, uncomplicated stage of the disease whenever possible to improve perioperative outcomes.
Exploring Codon Optimization and Response Surface Methodology to Express Biologically Active Transmembrane RANKL in E. coli
Sushila Maharjan, Bijay Singh, Jin-Duck Bok, Jeong-In Kim, Tao Jiang, Chong-Su Cho, Sang-Kee Kang, Yun-Jaie Choi
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0096259
Abstract: Receptor activator of nuclear factor (NF)-κB ligand (RANKL), a master cytokine that drives osteoclast differentiation, activation and survival, exists in both transmembrane and extracellular forms. To date, studies on physiological role of RANKL have been mainly carried out with extracellular RANKL probably due to difficulties in achieving high level expression of functional transmembrane RANKL (mRANKL). In the present study, we took advantage of codon optimization and response surface methodology to optimize the soluble expression of mRANKL in E. coli. We optimized the codon usage of mRANKL sequence to a preferred set of codons for E. coli changing its codon adaptation index from 0.64 to 0.76, tending to increase its expression level in E. coli. Further, we utilized central composite design to predict the optimum combination of variables (cell density before induction, lactose concentration, post-induction temperature and post-induction time) for the expression of mRANKL. Finally, we investigated the effects of various experimental parameters using response surface methodology. The best combination of response variables was 0.6 OD600, 7.5 mM lactose, 26°C post-induction temperature and 5 h post-induction time that produced 52.4 mg/L of fusion mRANKL. Prior to functional analysis of the protein, we purified mRANKL to homogeneity and confirmed the existence of trimeric form of mRANKL by native gel electrophoresis and gel filtration chromatography. Further, the biological activity of mRANKL to induce osteoclast formation on RAW264.7 cells was confirmed by tartrate resistant acid phosphatase assay and quantitative real-time polymerase chain reaction assays. Importantly, a new finding from this study was that the biological activity of mRANKL is higher than its extracellular counterpart. To the best of our knowledge, this is the first time to report heterologous expression of mRANKL in soluble form and to perform a comparative study of functional properties of both forms of RANKL.
Quantitative Measurement of Organic Acids in Tissues from Gastric Cancer Patients Indicates Increased Glucose Metabolism in Gastric Cancer
Hoon Hur, Man Jeong Paik, Yi Xuan, Duc-Toan Nguyen, In-Hye Ham, Jisoo Yun, Yong Kwan Cho, Gwang Lee, Sang-Uk Han
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0098581
Abstract: The levels of organic acids representing metabolic pathway end products are important indicators of physiological status, and may be associated with metabolic changes in cancer. The aim of this study is to investigate the levels of organic acids in cancerous and normal tissues from gastric cancer patients and to confirm the role of metabolic alterations in gastric carcinogenesis. Organic acids in normal and cancerous tissues from forty-five patients with gastric adenocarcinoma were investigated by gas chromatography-mass spectrometry in selected ion monitoring mode as methoxime/tert-butyldimethylsilyl derivatives. We analysed the significant differences in the levels of organic acids in normal and cancer tissues and investigated the correlation of these levels in cancer tissues with clinicopathological features. The levels of Krebs cycle components, including α-ketoglutaric acid, succinic acid, fumaric acid, malic acid and oxaloacetic acid, were significantly increased in cancer tissues compared to normal tissues. In addition, the levels of glycolytic products, including pyruvic acid and lactic acid, as well as the levels of ketone bodies, including 3-hydroxybutyric acid, were also significantly increased in cancer tissues compared to normal tissues. The levels of ketone bodies in cancer tissues with differentiated histology and in intestinal-type cancer tissues were significantly increased. The organic acid profiling analysis described here may be a generally useful clinical tool for understanding the complexity of metabolic events in gastric adenocarcinoma, and organic acids may have potential as metabolic markers for the future discovery of diagnostic and therapeutic modalities.
A Case of Possible Neurosarcoidosis Presenting as Intractable Headache and Panhypopituitarism
Jin Kyung Hwang,Joo Hee Cho,So Young Park,Jung Il Son,Uk Jo,Sang Ouk Chin,Yun Jung Lee,Moon Chan Choi,Sang Youl Rhee,Eui Jong Kim,Suk Chon
Case Reports in Endocrinology , 2013, DOI: 10.1155/2013/816236
Abstract: Sarcoidosis is a chronic multisystemic inflammatory disease of unknown etiology, which is characterized by noncaseating granulomatous inflammation of the involved organs. It is known that neurosarcoidosis involving the nervous system occurs in about 5% of patients with sarcoidosis. However, neurosarcoidosis without systemic involvement is extremely rare. We present a case of suspicious neurosarcoidosis affecting the pituitary gland, which was manifested as chronic uncontrolled headache, panhypopituitarism, central diabetes insipidus, and hypercalcemia. Though the biopsy at the pituitary lesion was not performed due to the high risk of surgical complication, treatment was needed urgently and we started steroid therapy. After steroid therapy, we observed the immediate symptom relief with improved hypercalcemia. According to the follow-up examination, no recurrent symptom was seen, and resolution of the pituitary lesion with improving panhypopituitarism was noted. 1. Introduction Sarcoidosis is a noncaseating granulomatous disease that can affect any system of the body [1]. Neurosarcoidosis involves the nervous system and occurs in less than 5% of patients with systemic sarcoidosis. Isolated neurosarcoidosis without systemic involvement is extremely rare [2]. We describe a case of possible neurosarcoidosis of the pituitary gland without any other systemic involvement. The patient presented with panhypopituitarism, central diabetes insipidus, and hypercalcemia. Sellar magnetic resonance imaging (MRI) showed an infiltrating mass of the pituitary gland with invasion of stalk and cavernous sinus. Steroid therapy resulted in the resolution of the pituitary lesion on sellar MRI and all symptoms. 2. Case Presentation A 39-year-old man presented to our clinic with nausea and headache. He reported that these symptoms had waxed and waned for five years and were aggravated for three weeks before admission. His medical history revealed that he had been diagnosed with a pituitary microadenoma at the age of thirty four with symptoms of polyuria, polydipsia, and severe headache. Initial sellar MRI showed a pituitary microadenoma with stalk deviation and thickening (Figure 1(a)). An anterior pituitary function test revealed minimal elevation of prolactin (20.2?ng/mL) with no other significant abnormalities. He began to take lisuride hydrogen maleate, which decreased his serum prolactin level. Although intranasal vasopressin therapy significantly relieved the polyuria and polydipsia, his headache did not subside, and, thus, intermittent low-dose steroid therapy was
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