• KIISE Transactions on Computing Practices
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• v.22 no.7
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• pp.315-319
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• 2016

Recurrent neural network based language models (RNN LM) have shown improved results in language model researches. The RNN LMs are limited to post processing sessions, such as the N-best rescoring step of the wFST based speech recognition. However, it has considerable vocabulary problems that require large computing powers for the LM training. In this paper, we try to find the 1st pass N-gram model using word embedding, which is the simplified deep neural network. The class based language model (LM) can be a way to approach to this issue. We have built class based vocabulary through word embedding, by combining the class LM with word N-gram LM to evaluate the performance of LMs. In addition, we propose that part-of-speech (POS) tagging based LM shows an improvement of perplexity in all types of the LM tests.

• Genomics & Informatics
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• v.10 no.2
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• pp.81-87
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• 2012

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional $F_{ST}$ measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the $F_{ST}$ estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific $F_{ST}$ and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.

• Genomics & Informatics
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• v.8 no.4
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• pp.185-193
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• 2010

Histone deacetylation and demethylation are epigenetic mechanisms implicated in cancer. Studies regarding the role of modulation of gene expression utilizing the histone deacetylase inhibitor scriptaid and the demethylating agent 5-azacytidine in HL-60 leukemia cells have been limited. We studied the possibility of recovering epigenetically silenced genes by scriptaid and 5-azacytidine in human leukemia cells by DNA microarray analysis. The first group was leukemia cells that were cultured with 5-azacytidine. The second group was cultured with scriptaid. The other group was cultured with both agents. Two hundred seventy newly developed genes were expressed after the combination of 5-azacytidine and scriptaid. Twenty-nine genes were unchanged after the combination treatment of 5-azacytidine and scriptaid. Among the 270 genes, 13 genes were differed significantly from the control. HPGD, CPA3, CEACAM6, LOC653907, ETS1, RAB37, PMP22, FST, FOXC1, and CCL2 were up-regulated, and IGLL3, IGLL1, and ASS1 were down-regulated. Eleven genes associated with oncogenesis were found among the differentially expressed genes: ETS1, ASCL2, BTG2, BTG1, SLAMF6, CDKN2D, RRAS, RET, GIPC1, MAGEB, and RGL4. We report the results of our leukemia cell microarray profiles after epigenetic combination therapy with the hope that they are the starting point of selectively targeted epigenetic therapy.

• Journal of Oriental Neuropsychiatry
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• v.22 no.2
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• pp.129-146
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• 2011

Objectives : The purpose of this study was to characterize the putative antidepressant and antianxiolytic effects of the 70% ethanol extract of Polygala japonica(EEPJ) using animal's behavioral experiment in mice. Methods : The effect of EEPJ on the anxioty and depressive disorder was investigated via mice's behavioral experiment like Elevated plus-maze, Horizontal wire test, Open field test, Forced swimming test, Tail suspension test, and it was happen via any mechanism by WAY 100635, a 5-HT1A receptor antagonist and by Flumazenil, a GABAA antagonist Results : 1. In the EPM, single treatments of the EEPJ(200 and 400mg/kg) had usefully antianxiolytic effects versus vehicle, which was medicated via the serotonergic nervous system. 2. In the HWT, single treatments of the EEPJ were no changes in the myorelaxant effects versus vehicle. 3. In the OFT, single treatments of the EEPJ were no changes in the locomotor activity versus vehicle. 4. In the FST, single treatments of the EEPJ(50mg/kg) significantly reduced the immobility time versus vehicle. 5. In the TST, single treatments of the EEPJ(50mg/kg) significantly reduced the immobility time versus vehicle. Conclusions : These results indicate that EEPJ is an effective antidepressant and antianxiolytic activity in mice, and it might be usefully applied for prevention and treatment of depressive disorder through evolutive study like development of various experimental models.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1710-1720
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• 2008

A comprehensive genome profiling study was undertaken based on automated genotyping and analysis of 20 microsatellite markers that involved 155 birds representing eight different populations. The distribution of microsatellite markers in each of these breeds helped us to decipher genetic heterogeneity, population genetic structure and evolutionary relationships of the present day chicken populations in India. All the microsatellite loci utilized for the analysis were polymorphic and reasonably informative. A total of 285 alleles were documented at 20 loci with a mean of 14.25 alleles/locus. A total of 103 alleles were found to be population/strain specific of which, only 30 per cent had a frequency of more than 10. The mean PIC values ranged from 0.39 for the locus ADL158 to 0.71 for loci MCW005 or ADL267 across the genomes and 0.55 in Dahlem Red to 0.71 in Desi (non-descript), among the populations. The overall mean expected and observed heterozygosity estimates for our populations were 0.68 and 0.64, respectively. The overall mean inbreeding coefficients (FIS) varied between -0.05 (Babcock) and 0.16 (Rhode Island Red). The pairwise FST estimates ranged from 0.06 between Aseel and Desi (non-descript) to 0.14 between Dahlem Red and Babcock. The Nei's genetic distance varied from 0.30 (WLH-IWD and WLH-IWF) to 0.80 (Dahlem Red and Babcock. Phylogenetic analysis grouped all the populations into two main clusters, representing i) the pure breeds, Dahlem Red and Rhode Island Red, and ii) the remaining six populations/strains. All the chicken populations studied were in the state of mild to moderate inbreeding except for commercial birds. A planned breeding is advised for purebreds to revive their genetic potential. High genetic diversity exists in Desi (non-descript), local birds, which can be exploited to genetically improve the birds suitable for backyard poultry.

• Journal of Microbiology and Biotechnology
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• v.21 no.10
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• pp.1088-1096
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• 2011

The purpose of this study was to evaluate whether wild ginseng (WG) administration could attenuate anxiety- and depression-like behaviors and expression of corticotrophin-releasing factor (CRF) and neuropeptide Y (NPY) following withdrawal from repeated morphine administration in rats. Male rats were administered daily doses of WG (50, 100, or 200 mg/kg, i.p.) for 5 days, 30 min before morphine injection (40 mg/kg, s.c). The anxiety- and depression-like behavioral responses were measured 72 h after the last morphine injection using an elevated plus maze (EPM) and forced swimming test (FST), respectively. Changes in hypothalamic CRF and NPY expressions were also examined by analyzing their immunoreactivities in the hypothalamus. Daily administration of WG significantly reduced anxiety- and depression-like behavior, and elicited the suppression of CRF expression and the stimulation of NPY expression in the hypothalamus. Our results demonstrated that WG extract might be effective at inhibiting the anxiety and depression responses due to morphine withdrawal by possibly modulating the hypothalamus CRF and NPY systems. Furthermore, these findings imply that WG extract can be used for developing new medication to cure or alleviate morphine withdrawal symptoms and to prevent relapses of morphine use.

• Journal of Physiology & Pathology in Korean Medicine
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• v.34 no.2
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• pp.88-96
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• 2020

Stauntonia hexaphylla (SH) and Vaccinium bracteatum (VB) are herbal extracts widely used in food and traditional herbal medicine, and have the ability to perform a wide range of biological activities. We aimed to investigate the effects of the SH and VB combination (SHVB) on mice models of chronic restraint stress (CRS) and pentobarbital-induced sleeping behaviors to elucidate its possible mechanisms of action. CRS-exposed mice treated with SHVB showed significantly decreased immobility time, increased swimming and climbing times in the forced swim test (FST), and increased locomotor activity in the open field test (OFT). SHVB decreased serum CORT levels, but enhanced brain monoamine neurotransmitters. SHVB significantly decreased the sleep latency and increased total sleep duration in pentobarbital-induced sleeping behavior in mice. SHVB showed inhibitory effect on 5-HT_2A receptor-mediated ERK1/2 phosphorylation. These results suggest that SHVB has antidepressant and hypnotic effects by regulating the 5-HT_2A receptor.

• Korean Journal of Ecology and Environment
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• v.41 no.3
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• pp.395-401
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• 2008

Genetic diversity and differentiation within or among nine populations of introduced fish, largemouth bass Micropterus salmoides were assessed by AFLP. The AFLP analysis using three primer combinations generated 299.2. AFLP bands and percentage of polymorphic bands were similar in those nine populations, ranging 14.1 to 21%. Heterozygosity and genetic diversity within or among populations were quite low for all of these populations with average values ranging from 0.054 to 0.067 and from 0.069 to 0.085, respectively. Analyses of pairwise distance and genetic similarity among nine populations of Micropterus salmoides also revealed the similar results with low genetic differentiation one another. Although pairwise Fst values were low, they were indicated a clear distinct genetic differentiation among the nine populations. These results indicate that very small population of the largemouth bass was first introduced to Paldang reservoir and they are widely spread at most of aquatic habitats in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.2
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• pp.154-161
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• 2010

The level of genetic differentiation and genetic structure in a Chinese native chicken breed, Bian chicken, and two controlled chicken populations (Jinghai chicken and Youxi chicken in China) were analysed based on 29 microsatellite markers. A total of 166 distinct alleles were observed across the 3 breeds, and 32 of these alleles (19.3%) were unique to only 1 breed. Bian chicken carried the largest number of private alleles at 15 (46.9%), followed by the Jinghai chicken with 12 private alleles (37.5%). The average polymorphism information content (0.5168) and the average expected heterozygote frequency (0.5750) of the Bian chicken were the highest, and those of the Jinghai chicken were 0.4915 and 0.5505, respectively, which were the lowest. Among 29 microsatellite loci, there were 15 highly informative loci in Bian chicken, and the other 14 were reasonably informative loci. The highly informative loci in Jinghai chicken and Youxi chicken were 17 and 14 respectively. Significant deviations from the Hardy-Weinberg equilibrium were observed at several locus-breed combinations, showing a deficit of heterozygotes in many cases. As a whole, genetic differentiation among the breeds estimated by the fixation index (Fst) were at 6.7% (p<0.001). The heterozygote deficit within population (Fis) was 22.2% (p<0.001), with the highest (0.249) in Bian chicken and lowest (0.159) in Youxi chicken. These results serve as an initial step in the plan for genetic characterization and conservation of the Chinese chicken genetic resource of Bian, as well as Jinghai and Youxi chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.316-322
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• 2013

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$) were estimated at $7.98{\times}10^{-29}$, $2.88{\times}10^{-20}$ and $1.25{\times}10^{-08}$, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.