• ETRI Journal
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• v.38 no.3
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• pp.487-493
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• 2016

Two new methods are proposed for an unsupervised adaptation of a language model (LM) with a single sentence for automatic transcription tasks. At the training phase, training documents are clustered by a method known as Latent Dirichlet allocation (LDA), and then a domain-specific LM is trained for each cluster. At the test phase, an adapted LM is presented as a linear mixture of the now trained domain-specific LMs. Unlike previous adaptation methods, the proposed methods fully utilize a trained LDA model for the estimation of weight values, which are then to be assigned to the now trained domain-specific LMs; therefore, the clustering and weight-estimation algorithms of the trained LDA model are reliable. For the continuous speech recognition benchmark tests, the proposed methods outperform other unsupervised LM adaptation methods based on latent semantic analysis, non-negative matrix factorization, and LDA with n-gram counting.

• Journal of Life Science
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• v.19 no.10
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• pp.1360-1367
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• 2009

Liver fibrosis is a process of healing and scarring in response to chronic liver injury. Following injury, an acute inflammation response takes place resulting in moderate cell necrosis and extracellular matrix damage. To develop a novel therapeutic approach in hepatic fibrogenesis, we examined the simultaneous suppression of the transcription factors NF-$\kappa$B and Sp1, which regulate acute inflammation and continuous deposition of extracellular matrix in liver fibrosis. We employed chimeric decoy oligodeoxynucleotide containing the consensus sequences of both NF-$\kappa$B and Sp1 binding sites, to suppress these transcription factors simultaneously. Treatment of chimeric decoy oligodeoxynucleotide reduced the activity of hepatic stellate cells in vitro, and decreased the expression of fibrotic and proinflammatory gene responses in a mouse model of liver fibrosis. These results suggest that chimeric decoy oligodeoxynucleotide strategy can be a potential therapeutic application to prevent liver fibrosis.

• BMB Reports
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• v.44 no.7
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• pp.490-495
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• 2011

Transcription factor AP-$2{\alpha}$ involves in the process of mammalian embryonic development and tumorigenesis. Many studies have shown that AP-$2{\alpha}$ functions in association with other interacting proteins. In a two-hybrid screening, the regulatory subunit ${\beta}$ of protein casein kinase 2 ($CK2{\beta}$) was identified as an interacting protein of AP-$2{\alpha}$; we confirmed this interaction using in-vitro GST pull-down and in-vivo co-immunoprecipitation assays; in an endogenous co-immunoprecipitation experiment, we further found the catalytic subunit ${\alpha}$ of protein casein kinase 2 ($CK2{\alpha}$) also exists in the complex. Phosphorylation analysis revealed that AP-$2{\alpha}$ was phosphorylated by CK2 kinase majorly at the site of Ser429, and such phosphorylation could be blocked by CK2 specific inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB) in a dose-dependent manner. Luciferase assays demonstrated that both $CK2{\alpha}$ and $CK2{\beta}$ enhanced the transcription activity of AP-$2{\alpha}$; moreover, $CK2{\beta}$ increased the stability of AP-$2{\alpha}$. Our data suggest a novel cellular function of CK-2 as a transcriptional co-activator of AP-$2{\alpha}$.

• The Journal of Internal Korean Medicine
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• v.22 no.3
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• pp.367-377
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• 2001

Objectives: We aimed to identify. the effect of Jeongcheon-tang(定喘湯) and Cheongsangboha-tang(淸上補下湯) on the transcriptional activities of cytokine IL-4, IL-5, IL-6 and IL-10 involved in asthma model. Materials and Methods: RBL-2H3 cell lines were used. Cells were stimulated with calcium inophore($2{\mu}M$ : Sample group 1, $4{\mu}M$ : Sample group 2) for maximal gene expression. After 3rd treatment of samples and incubation(per 24hours), total cellular RNAs were collected using Trizol solution method. Then transcriptional activities of IL-4, IL-5, IL-6 and IL-10 were measured by RT-PCR with electrophoresis. Results: In IL-4 study, Jeongcheon-tang treated group showed 82.76%(Sample group 1) of transcriptional activities compared to the control group and Cheongsangboha-tang treated groups showed 85.77% (Sample group 1), 89.42% (Sample group 2) of transcriptional activities compared to the control groups. In IL-5 study, Jeongcheon-tang treated groups showed 88.24%(Sample group 1), 98.83%(Sample group 2) of transcriptional activities compared to the control groups and Cheongsangboha-tang treated group showed 73.66%(Sample group 2) of transcriptional activities compared to the control group. In IL-6 study, Jeongcheon-tang treated group showed 92.95%(Sample group 2) of transcriptional activities compared to the control group and Cheongsangboha-tang treated group showed n.40%(Sample group 2) of transcriptional activities compared to the control group. In IL-10 study, Jeongcheon-tang treated group showed 118.46% (Sample group 2) of transcriptional activities compared to the control group. Conclusions: This study shows that Jeongcheon-tang has the inhibitory effect on the transcription of IL-4, IL-5, IL-6 gene expression and the increasing effect on the transcription of IL-10 gene expression, and Cheongsangboha-tang has the inhibitory effect on the transcription of IL4, IL-5 and IL-6 gene expression in RBL-2H3 cell lines. Advanced studies are required to investigate the mechanisms of inhibition or increase by herbal medicine in asthma model.

• Molecules and Cells
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• v.39 no.1
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• pp.65-71
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• 2016

A challenge in the redox field is the elucidation of the molecular mechanisms, by which $H_2O_2$ mediates signal transduction in cells. This is relevant since redox pathways are disturbed in some pathologies. The transcription factor OxyR is the $H_2O_2$ sensor in bacteria, whereas Cys-based peroxidases are involved in the perception of this oxidant in eukaryotic cells. Three possible mechanisms may be involved in $H_2O_2$ signaling that are not mutually exclusive. In the simplest pathway, $H_2O_2$ signals through direct oxidation of the signaling protein, such as a phosphatase or a transcription factor. Although signaling proteins are frequently observed in the oxidized state in biological systems, in most cases their direct oxidation by $H_2O_2$ is too slow ($10^1M^{-1}s^{-1}$ range) to outcompete Cys-based peroxidases and glutathione. In some particular cellular compartments (such as vicinity of NADPH oxidases), it is possible that a signaling protein faces extremely high $H_2O_2$ concentrations, making the direct oxidation feasible. Alternatively, high $H_2O_2$ levels can hyperoxidize peroxiredoxins leading to local building up of $H_2O_2$ that then could oxidize a signaling protein (floodgate hypothesis). In a second model, $H_2O_2$ oxidizes Cys-based peroxidases that then through thiol-disulfide reshuffling would transmit the oxidized equivalents to the signaling protein. The third model of signaling is centered on the reducing substrate of Cys-based peroxidases that in most cases is thioredoxin. Is this model, peroxiredoxins would signal by modulating the thioredoxin redox status. More kinetic data is required to allow the identification of the complex network of thiol switches.

• Journal of Microbiology and Biotechnology
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• v.26 no.8
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• pp.1398-1403
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• 2016

The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10¹ copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10² copies/20 g fresh lettuce, 9.7 × 10³ copies/20 g frozen strawberries, and 4.1 × 10³ copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

• BMB Reports
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• v.52 no.3
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• pp.220-225
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• 2019

We have identified a mechanism to diminish the proliferative capacity of cells during cell expansion using human adipose-derived stromal cells (hAD-SCs) as a model of replicative senescence. hAD-SCs of high-passage numbers exhibited a reduced proliferative capacity with accelerated cellular senescence. Levels of key bioactive sphingolipids were significantly increased in these senescent hAD-SCs. Notably, the transcription of sphingosine kinase 1 (SPHK1) was down-regulated in hAD-SCs at high-passage numbers. SPHK1 knockdown as well as inhibition of its enzymatic activity impeded the proliferation of hAD-SCs, with concomitant induction of cellular senescence and accumulation of sphingolipids, as seen in high-passage cells. SPHK1 knockdown-accelerated cellular senescence was attenuated by co-treatment with sphingosine-1-phosphate and an inhibitor of ceramide synthesis, fumonisin $B_1$, but not by treatment with either one alone. Together, these results suggest that transcriptional down-regulation of SPHK1 is a critical inducer of altered sphingolipid profiles and enhances replicative senescence during multiple rounds of cell division.

• BMB Reports
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• v.37 no.6
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• pp.648-656
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• 2004

This paper deals with the development of a predictive probabilistic model, a composite dependency-reflecting model (CDRM), which was designed to detect core promoter regions and transcription start sites (TSS) in vertebrate genomic DNA sequences, an issue of some importance for genome annotation. The model actually represents a combination of first-, second-, third- and much higher order or long-range dependencies obtained using the expanded maximal dependency decomposition (EMDD) procedure, which iteratively decomposes data sets into subsets on the basis of dependency degree and patterns inherent in the target promoter region to be modeled. In addition, decomposed subsets are modeled by using a first-order Markov model, allowing the predictive model to reflect dependency between adjacent positions explicitly. In this way, the CDRM allows for potentially complex dependencies between positions in the core promoter region. Such complex dependencies may be closely related to the biological and structural contexts since promoter elements are present in various combinations separated by various distances in the sequence. Thus, CDRM may be appropriate for recognizing core promoter regions and TSSs in vertebrate genomic contig. To demonstrate the effectiveness of our algorithm, we tested it using standardized data and real core promoters, and compared it with some current representative promoter-finding algorithms. The developed algorithm showed better accuracy in terms of specificity and sensitivity than the promoter-finding ones used in performance comparison.

• Parasites, Hosts and Diseases
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• v.39 no.2
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• pp.151-160
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• 2001

Randomly selected 435 clones from Acanthamoeba healyi cDNA library were sequenced and a total of 387 expressed sequence tags (ESTs) had been generated. Based on the results of BLAST search, 130 clones (34.4%) were identified as the genes enconding surface Proteins , enzymes for DNA, energy Production or other metabolism, kinases and phosphatases, protease, proteins for signal transduction, structural and cytoskeletal proteins, cell cycle related proteins, transcription factors, transcription and translational machineries, and transporter proteins. Most of the genes (88.5%) are newly identified in the genus Acanthamoeba. Although 15 clones matched the genes of Acanthamoeba located in the public databases, twelve clones were actin gene which was the most frequently expressed gene in this study. These ESTs of Acanthamoeba would give valuable information to study the organism as a model system for biological investigations such as cytoskeleton or cell movement, signal transduction, transcriptional and translational regulations. These results would also provide clues to elucidate factors for pathogenesis in human granulomatous amoebic encephalitis or keratitis by Acanthamoeba.

• Journal of Plant Biotechnology
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• v.42 no.2
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• pp.93-103
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• 2015

The isolation, cloning, and characterization of an R2R3-MYB transcription factor gene (MtMYB70) from the model legume Medicago truncatula is reported. MtMYB70 consists of a 768-bp coding sequence corresponding to 255 amino acids. Sequence alignment revealed that MtMYB70 cDNA contains conserved R2R3-type MYB domains with highly divergent C terminal regions. MtMYB70 was found to have relatively low sequence homology with known R2R3-MYB genes. Phylogenetic analysis placed the R2R3-MYB domain of MtMYB70 closest to PtMYB1, a known activator of lignin biosynthesis. Overexpression of MtMYB70 under the control of the 35S promoter in transgenic poplar did not cause a significant difference in total lignin content relative to the control, but glucan content was significantly increased in transgenic poplar. Therefore, MtMYB70 might have regulatory role in the biosynthesis of cell wall structural carbohydrates.