• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1496-1511
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• 2015

The study aimed to compare the necrotic enteritis (NE)-induced transcriptome differences between the spleens of Marek's disease resistant chicken line 6.3 and susceptible line 7.2 co-infected with Eimeria maxima/Clostridium perfringens using RNA-Seq. Total RNA from the spleens of two chicken lines were used to make libraries, generating 42,736,296 and 42,617,720 usable reads, which were assembled into groups of 29,897 and 29,833 mRNA genes, respectively. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change ${\geq}2$, p<0.01). The transcription levels of 14 genes identified were further examined using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using gene ontology terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change ${\geq}2$, p<0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens.

• The Korean Journal of Physiology and Pharmacology
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• v.19 no.2
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• pp.141-149
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• 2015

"G protein-coupled receptor 40" (GPR40), a receptor for long-chain fatty acids, mediates the stimulation of glucose-induced insulin secretion. We examined the profiles of differential gene expression in GPR40-activated cells treated with linoleic acid, and finally predicted the integral pathways of the cellular mechanism of GPR40-mediated insulinotropic effects. After constructing a GPR40-overexpressing stable cell line (RIN-40) from the rat pancreatic ${\beta}$-cell line RIN-5f, we determined the gene expression profiles of RIN-5f and RIN-40. In total, 1004 genes, the expression of which was altered at least twofold, were selected in RIN-5f versus RIN-40. Moreover, the differential genetic profiles were investigated in RIN-40 cells treated with $30{\mu}M$ linoleic acid, which resulted in selection of 93 genes in RIN-40 versus RIN-40 treated with linoleic acid. Based on the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG, http://www.genome.jp/kegg/), sets of genes induced differentially by treatment with linoleic acid in RIN-40 cells were found to be related to mitogen-activated protein (MAP) kinase- and neuroactive ligand-receptor interaction pathways. A gene ontology (GO) study revealed that more than 30% of the genes were associated with signal transduction and cell proliferation. Thus, this study elucidated a gene expression pattern relevant to the signal pathways that are regulated by GPR40 activation during the acute period. Together, these findings increase our mechanistic understanding of endogenous molecules associated with GPR40 function, and provide information useful for identification of a target for the management of type 2 diabetes mellitus.

• Journal of KIISE
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• v.44 no.4
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• pp.383-391
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• 2017

As we enter a new era of Big Data, the amount of semantic data has rapidly increased. In order to derive meaningful information from this large semantic data, studies that utilize the SWRL(Semantic Web Rule Language) are being actively conducted. SWRL rules are based on data extracted from a user's empirical knowledge. However, conventional reasoning systems developed on single machines cannot process large scale data. Similarly, multi-node based reasoning systems have performance degradation problems due to network shuffling. Therefore, this paper overcomes the limitations of existing systems and proposes more efficient distributed inference methods. It also introduces data partitioning strategies to minimize network shuffling. In addition, it describes a method for optimizing the incremental reasoning process through data selection and determining the rule order. In order to evaluate the proposed methods, the experiments were conducted using WiseKB consisting of 200 million triples with 83 user defined rules and the overall reasoning task was completed in 32.7 minutes. Also, the experiment results using LUBM bench datasets showed that our approach could perform reasoning twice as fast as MapReduce based reasoning systems.

• Journal of KIISE:Software and Applications
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• v.34 no.5
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• pp.465-475
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• 2007

With the spread of Internet, web users express their daily life by articles, pictures and cartons to recollect personal memory or to share their experience. For the easier recollection and sharing process, this paper proposes diverse cartoon generation methods using the landmark lists which represent the behavior and emotional status of the user. From the priority and causality of each landmark, critical landmark is selected for composing the cartoon scenario, which is revised by story ontology. Using similarity between cartoon images and each landmark in the revised scenario, suitable cartoon cut for each landmark is composed. To make cartoon story more diverse, weather, nightscape, supporting character, exaggeration and animation effects are additionally applied. Through example scenarios and usability tests, the diversity of the generated cartoon is verified.

• Journal of Animal Science and Technology
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• v.62 no.2
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• pp.141-158
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• 2020

Skin is a major thermoregulatory organ in the body controlling homeothermy, a critical function for climate adaptation. We compared genes expressed between tropical- and temperate-adapted cattle to better understand genes involved in climate adaptation and hence thermoregulation. We profiled the skin of representative tropical and temperate cattle using RNA-seq. A total of 214,754,759 reads were generated and assembled into 72,993,478 reads and were mapped to unique regions in the bovine genome. Gene coverage of unique regions of the reference genome showed that of 24,616 genes, only 13,130 genes (53.34%) displayed more than one count per million reads for at least two libraries and were considered suitable for downstream analyses. Our results revealed that of 255 genes expressed differentially, 98 genes were upregulated in tropically-adapted White Fulani (WF; Bos indicus) and 157 genes were down regulated in WF compared to Angus, AG (Bos taurus). Fifteen pathways were identified from the differential gene sets through gene ontology and pathway analyses. These include the significantly enriched melanin metabolic process, proteinaceous extracellular matrix, inflammatory response, defense response, calcium ion binding and response to wounding. Quantitative PCR was used to validate six representative genes which are associated with skin thermoregulation and epithelia dysfunction (mean correlation 0.92; p < 0.001). Our results contribute to identifying genes and understanding molecular mechanisms of skin thermoregulation that may influence strategic genomic selection in cattle to withstand climate adaptation, microbial invasion and mechanical damage.

• Animal Bioscience
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• v.34 no.5
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• pp.922-930
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• 2021

Objective: Tibetan pigs, predominantly originating from the Tibetan Plateau, have been subjected to long-term natural selection in an extreme environment. To characterize the metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression patterns in the livers of Tibetan and Yorkshire pigs were compared. Methods: RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology and Kyoto encyclopedia of genes and genomes functional enrichment analyses. Results: In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and 257 differentially expressed genes and proteins were identified. Evidence from functional enrichment analysis showed that many genes were involved in metabolic processes. The combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, metabolic processes, and organic hydroxyl compound metabolic processes were the major processes operating differently in the two breeds. The important genes include retinol dehydrogenase 16, adenine phosphoribosyltransferase, prenylcysteine oxidase 1, sorbin and SH3 domain containing 2, ENSSSCG00000036224, perilipin 2, ladinin 1, kynurenine aminotransferase 1, and dimethylarginine dimethylaminohydrolase 1. Conclusion: The findings of this study provide novel insight into the high-altitude metabolic adaptation of Tibetan pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.8
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• pp.1084-1094
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• 2019

Objective: The aim of this study was to select the candidate genes affecting meat quality and preliminarily explore the related molecular mechanisms in the Mashen pig. Methods: The present study explored genetic factors affecting meat quality in the Mashen pig using RNA sequencing (RNA-Seq). We sequenced the transcriptomes of 180-day-old Mashen and Large White pigs using longissimus dorsi to select differentially expressed genes (DEGs). Results: The results indicated that a total of 425 genes were differentially expressed between Mashen and Large White pigs. A gene ontology enrichment analysis revealed that DEGs were mainly enriched for biological processes associated with metabolism and muscle development, while a Kyoto encyclopedia of genes and genomes analysis showed that DEGs mainly participated in signaling pathways associated with amino acid metabolism, fatty acid metabolism, and skeletal muscle differentiation. A MCODE analysis of the protein-protein interaction network indicated that the four identified subsets of genes were mainly associated with translational initiation, skeletal muscle differentiation, amino acid metabolism, and oxidative phosphorylation pathways. Conclusion: Based on the analysis results, we selected glutamic-oxaloacetic transaminase 1, malate dehydrogenase 1, pyruvate dehydrogenase 1, pyruvate dehydrogenase kinase 4, and activator protein-1 as candidate genes affecting meat quality in pigs. A discussion of the related molecular mechanisms is provided to offer a theoretical basis for future studies on the improvement of meat quality in pigs.

• Journal of Life Science
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• v.23 no.11
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• pp.1325-1335
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• 2013

Working dogs, such as rescue dogs, military watch dogs, guide dogs, and search dogs, are selected by in-training examination of desired traits, including concentration, possessiveness, and boldness. In recent years, genetic information has been considered to be an important factor for the outstanding abilities of working dogs. To characterize the molecular features of the canine genes related to phenotypes for working dogs, we investigated the 24 previously reported genes (AR, BDNF, DAT, DBH, DGCR2, DRD4, MAOA, MAOB, SLC6A4, TH, TPH2, IFT88, KCNA3, TBR2, TRKB, ACE, GNB1, MSTN, PLCL1, SLC25A22, WFIKKN2, APOE, GRIN2B, and PIK3CG) that were categorized to personality, olfactory sense, and athletic/learning ability. We analyzed the chromosomal location, gene-gene interactions, Gene Ontology, and expression patterns of these genes using bioinformatic tools. In addition, variable numbers of tandem repeat (VNTR) or microsatellite (MS) polymorphism in the AR, MAOA, MAOB, TH, DAT, DBH, and DRD4 genes were reviewed. Taken together, we suggest that the genetic background of the canine genes associated with various working dog behaviors and skill performance attributes could be used for proper selection of superior working dogs.

• Journal of Internet Computing and Services
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• v.17 no.1
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• pp.23-33
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• 2016

The current smart lighting is shaped to offer the lighting environment suitable for current context, after identifying user's action and location through a sensor. The sensor-based context awareness technology just considers a single user, and the studies to interpret many users' various context occurrences and conflicts lack. In existing studies, a fuzzy theory and algorithm including ReBa have been used as the methodology to solve context conflict. The fuzzy theory and algorithm including ReBa just avoid an opportunity of context conflict that may occur by providing services by each area, after the spaces where users are located are classified into many areas. Therefore, they actually cannot be regarded as customized service type that can offer personal preference-based context conflict. This paper proposes a priority-based LED lighting control system interpreting multiple context conflicts, which decides services, based on the granted priority according to context type, when service conflict is faced with, due to simultaneous occurrence of various contexts to many users. This study classifies the residential environment into such five areas as living room, 'bed room, study room, kitchen and bath room, and the contexts that may occur within each area are defined as 20 contexts such as exercising, doing makeup, reading, dining and entering, targeting several users. The proposed system defines various contexts of users using an ontology-based model and gives service of user oriented lighting environment through rule based on standard and context reasoning engine. To solve the issue of various context conflicts among users in the same space and at the same time point, the context in which user concentration is required is set in the highest priority. Also, visual comfort is offered as the best alternative priority in the case of the same priority. In this manner, they are utilized as the criteria for service selection upon conflict occurrence.

• The KIPS Transactions:PartD
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• v.14D no.2
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• pp.265-272
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• 2007

In this paper, we implement an automated composition system of web services using hybrid techniques that merge the benefit of BPEL techniques, with the advantage of OWL-S, BPEL techniques have practical capabilities that fulfil the needs of the business environment such as fault handling and transaction management. However, the main shortcoming of these techniques is the static composition approach, where the service selection and flow management are done a priori and manually. In contrast, OWL-S techniques use ontologies to provide a mechanism to describe the web services functionality in machine-understandable form, making it possible to discover, and integrate web services automatically. This allows for the dynamic integration of compatible web services, possibly discovered at run time, into the composition schema. However, the development of these approaches is still in its infancy and has been largely detached from the BPEL composition effort. In this work, we describe the design of the SemanticBPEL architecture that is a hybrid system of BPEL4WS and OWL-S, and propose algorithms for web service search and integration. In particular, the SemanticBPEL has been implemented based on the open source tools. The proposed system is compared with existing BPEL systems by functional analysis. These comparisions show that our system outperforms existing systems.