• Molecules and Cells
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• v.42 no.2
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.1
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• pp.19-29
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• 2013

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

• Genomics & Informatics
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• v.21 no.4
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• pp.45.1-45.11
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• 2023

Nonalcoholic fatty liver disease (NAFLD) is a common type of chronic liver disease, with severity levels ranging from nonalcoholic fatty liver to nonalcoholic steatohepatitis (NASH). The extent of liver fibrosis indicates the severity of NASH and the risk of liver cancer. However, the mechanism underlying NASH development, which is important for early screening and intervention, remains unclear. Weighted gene co-expression network analysis (WGCNA) is a useful method for identifying hub genes and screening specific targets for diseases. In this study, we utilized an mRNA dataset of the liver tissues of patients with NASH and conducted WGCNA for various stages of liver fibrosis. Subsequently, we employed two additional mRNA datasets for validation purposes. Gene set enrichment analysis (GSEA) was conducted to analyze gene function enrichment. Through WGCNA and subsequent analyses, complemented by validation using two additional datasets, we identified five genes (BICC1, C7, EFEMP1, LUM, and STMN2) as hub genes. GSEA analysis indicated that gene sets associated with liver metabolism and cholesterol homeostasis were uniformly downregulated. BICC1, C7, EFEMP1, LUM, and STMN2 were identified as hub genes of NASH, and were all related to liver metabolism, NAFLD, NASH, and related diseases. These hub genes might serve as potential targets for the early screening and treatment of NASH.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.185-192
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• 2013

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

• Animal Bioscience
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• v.35 no.6
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• pp.814-825
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• 2022

Objective: This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland. Methods: According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of genome wide association study (GWAS) signals, functional annotation and weighted gene co-expression network analysis (WGCNA). Results: We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from day -2 to day +1. Further, the GWAS signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted WGCNA, we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day -14, day -2, and day +1, in which, 35 lncRNAs and 319 mRNAs were involved. Conclusion: This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

• Convergence Security Journal
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• v.13 no.3
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• pp.39-46
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• 2013

Recently, the problem of global warming has become a globally important issues. and To solve these problems, has been receiving increasing attention for the Green IT. In these situation, IT techniques are evolving with variety services and hacking techniques. so, it is inevitable to the use of a many and diverse secure system. As a result, Carbon Dioxide emissions are expected to increase. Therefore, in this paper is analyzed the factors of security system's $CO_2$ emissions through Experiments and A case study. and is proved that is reducing $CO_2$ emissions by improving the functional restructuring of the security system. In a future, this paper is expected to serve as a valuable Information for security network design and performance improvements and to reduce Carbon Emissions in the Field of IT.

• Journal of Korea Society of Industrial Information Systems
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• v.22 no.4
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• pp.29-43
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• 2017

Innovation Cosystems are Conceptualized as Organizational Networks of Economic Actors, Technologies and Social Contexts that Interact for Knowledge Production, use, and Adaptation. This Paper Proposed a Conceptual Framework to Describe Value Co-creation of Organizational Networks Engaged in Technology Innovation. We Adopted Theory-Based Approach by Integrating the Perspective of Service-Dominant (S-D) Logic Into the Evolutionary Model of the Triple Helix. The Framework Gives a Plausible Explanation on how Actors Collaborate to Create Value in Dynamic Contexts of an Innovation Ecosystem. The Innovation Ecosystem can be Considered as a Composite of Sub-Ecosystems, Including Knowledge, Sectoral, and Business Ecosystems. When these Sub-Ecosystems are Recursively Transformed by Coordination of Functional Mechanisms that Serve Value Co-creation in the Innovation Process, the Innovation Ecosystem will be Re-Organized and Evolve. The case of the Digital Living Network Alliance (DLNA) was Examined to Demonstrate the Fundamental Mechanisms for Value Co-creation that was Described in the Framework. The case Study Indicates Features of Value Co-creation when Implementing Innovation in Organizational Networks.

• Journal of KIISE:Computing Practices and Letters
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• v.15 no.4
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• pp.284-288
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• 2009

With explosively growing PPI databases, the computational approach for a prediction and configuration of PPI network has been a big stream in the bioinformatics area. Recent researches gradually consider physicochemical properties of proteins and support high resolution results with integration of experimental results. With regard to current research trend, it is very close future to complete a PPI network configuration of each organism. However, direct applying the PPI network to real field is complicated problem because PPI network is only a set of co-expressive proteins or gene products, and its network link means simple physical binding rather than in-depth knowledge of biological process. In this paper, we suggest a protein functional flow model which is a directed network based on a protein functions' relation of signaling transduction pathway. The vertex of the suggested model is a molecular function annotated by gene ontology, and the relations among the vertex are considered as edges. Thus, it is easy to trace a specific function's transition, and it can be a constraint to extract a meaningful sub-path from whole PPI network. To evaluate the model, 11 functional flow models of Homo sapiens were built from KEGG, and Cronbach's alpha values were measured (alpha=0.67). Among 1023 functional flows, 765 functional flows showed 0.6 or higher alpha values.

• Macromolecular Research
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• v.11 no.3
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• pp.163-171
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• 2003

For the pervaporation of water-ethanol mixtures, new composite membranes having poly(acrylic acid)-poly (butyl methacrylate-co-methyl methacrylate) interpenetrati ng polymer network [PAA-P(BMA-co-MMA) IPN] skin layer supported on porous and crosslinked poly(BMA-co-MMA) were prepared. The morphology of the sub-layer of the composite membrane prepared in the presence of 60 wt% solvent showed cellular structure, on the other hand that of sublayer prepared in the presence of 70 wt% solvent presented very porous interconnected pore structure with macrovoids. Permeation rates of the composite membranes were largely influenced by the morphology of the sublayer. Separation factors increased with the increase of the degree of crosslinking of the PAA network. It was found that permeation rates could be increased by introducing anionic charges on carboxyl groups of the PAA. The permeation rate changes of the PAA-P(BMA-co-MMA) IPN composite membranes according to the feed compositions showed quite similar pattern with the swelling behavior in water-ethanol mixtures.

• Composites Research
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• v.28 no.6
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• pp.333-339
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• 2015

Electromagnetic interference shielding composite with low density ($1.18g/cm^3$) was fabricated using electroless plated FeCo magnetic metal hollow fibers and ethylene propylene diene monomer (EPDM) polymer. Aspect ratio of the fibers were controlled and their hollow structure was obtained by heat treatment process. The FeCo hollow fibers were then mixed with EPDM to manufacture the composite. The higher aspect ratio of the magnetic metal hollow fibers resulted in high electromagnetic interference shielding effectiveness (30 dB) of the composite due to its low sheet resistance (30 ohm/sq). The enhanced electromagnetic interference shielding effectiveness was mainly attributed to the formation of conducting network over the percolation threshold by high aspect ratio of fibers as well as an increase of the reflection loss by impedance mismatch owing to low sheet resistance, absorption loss, and multiple internal reflections loss.