• Genomics & Informatics
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• 제21권4호
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• pp.48.1-48.8
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• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• Asian Pacific Journal of Cancer Prevention
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• 제13권1호
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• pp.111-115
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• 2012

Variants of X-ray repair cross-complementing group 1 (XRCC1) are involved in the development of cancer, but studies investigating the association of XRCC1-77T>C polymorphism with cancer risk have reported conflicting results. To clarify the effect of the XRCC1 -77T>C polymorphism on cancer risk, we performed a meta-analysis by conducting searches of the published literature in PubMed, Embase and CBM databases. Finally, 13 studies were included into our meta-analysis, involving a total of 11, 678 individuals. Subgroup analyses were performed by ethnicity and cancer type. The results of this meta-analysis showed that there was significant association between the C variant of XRCC1-77T>C polymorphism and cancer risk in all four genetic comparison models (ORC vs. T =1.19, 95%CI 1.07-1.31, P = 0.001; OR homozygote model =1.28, 95%CI 1.07-1.52, P = 0.007; OR recessive genetic model =1.22, 95%CI 1.04-1.44, P = 0.015; OR dominant model =1.21, 95% CI 1.07-1.35, P = 0.001). In the subgroup analyses based on ethnicity, the association was still significant in the Asian population (all p values<0.001), but not in the Caucasian population (all p values > 0.05). Thus, the XRCC1 -77T>C polymorphism is associated with cancer risk, and individuals with XRCC1 -77C variant have a significantly higher cancer risk, particularly in the Asian population.

• 산업경영시스템학회지
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• 제21권46호
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• pp.33-49
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• 1998

In order to improve the performance of relational databases, one has to reduce the number of disk accesses necessary to transfer data from disk to main memory. The paper proposes to reduce the number of disk I/O accesses by vertically partitioning relation into fragments and allowing attribute replication to fragments if necessary. When zero-one integer programming model is solved by the branch-and-bound method, it requires much computing time to solve a large sized problem. Therefore, heuristic solutions using genetic algorithm(GA) are presented. GA in this paper adapts a few ideas which are different from traditional genetic algorithms, for examples, a rank-based sharing fitness function, elitism and so on. In order to improve performance of GA, a set of optimal parameter levels is determined by the experiment and makes use of it. As relations are vertically partitioned allowing attribute replications and saved in disk, an attribute replicating vertical partition method by GA can attain less access cost than non-attribute-replication one and require less computing time than the branch-and-bound method in large-sized problems. Also, it can acquire a good solution similar to the optimum solution in small-sized problem.

• 정보처리학회논문지D
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• 제16D권3호
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• pp.295-306
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• 2009

질의실행시간최소화는 분산 데이타베이스 설계에 있어 가장 중요한 목적중의 하나이다. 총시간최소화는 온라인거래처리시스템의 목적인 반면, 반응시간최소화는 의사결정지원 질의시스템의 목적이다. 본 논문에서는 질의실행시간최소화를 달성하기 위해 질의를 세분화하여 최적의 데이터베이스 사이트에 할당하는 분석모델을 개발하였으며, 문제해결방법으로 유전자알고리즘을 채택하였다. 총시간최소화 관점에서의 질의실행 계획은 반응시간최소화 관점의 질의실행계획에는 적합하지 않다는 것을 증명하였으며, 그 반대의 경우도 증명하였다. 최대 20개의 조인이 포함되는 질의를 설계하여 시뮬레이션 실험을 통해 테스트를 수행하였고, 유전자알고리즘과 완전한 전수조사와의 결과를 비교함으로써 모든 경우에 유전자알고리즘을 채택한 해결책이 최적의 결과를 도출하였음을 증명하였다.

• Nuclear Engineering and Technology
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• 제56권2호
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• pp.644-654
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• 2024

After the Tohoku earthquake and tsunami (Japan, 2011), regulatory efforts to mitigate external hazards have increased both the safety requirements and the total capital cost of nuclear power plants (NPPs). In these circumstances, identifying not only disaster robustness but also cost-effective capacity setting of NPPs has become one of the most important tasks for the nuclear power industry. A few studies have been performed to relocate the seismic capacity of NPPs, yet the effects of multiple hazards have not been accounted for in NPP capacity optimization. The major challenges in extending this problem to the multihazard dimension are (1) the high computational costs for both multihazard risk quantification and system-level optimization and (2) the lack of capital cost databases of NPPs. To resolve these issues, this paper proposes an effective method that identifies the optimal multihazard capacity of NPPs using a multi-objective genetic algorithm and the two-stage direct quantification of fault trees using Monte Carlo simulation method, called the two-stage DQFM. Also, a capacity-based indirect capital cost measure is proposed. Such a proposed method enables NPP to achieve safety and cost-effectiveness against multi-hazard simultaneously within the computationally efficient platform. The proposed multihazard capacity optimization framework is demonstrated and tested with an earthquake-tsunami example.

• Genomics & Informatics
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• 제13권2호
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• pp.53-59
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• 2015

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

• 통합자연과학논문집
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• 제2권4호
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• pp.243-251
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• 2009

This paper surveys some researches to accomplish on bioinformatics. These researches wish to propose a database architecture combining a general view of bioinformatics data as a graph of data objects and data relationships, with the efficiency and robustness of data management and query provided by indexing and generic programming techniques. Here, these invert the role of the index, and make it a first-class citizen in the query language. It is possible to do this in a structured way, allowing users to mention indexes explicitly without yielding to a procedural query model, by converting functional relations into explicit functions. In the limit, the database becomes a graph, in which the edges are these indexes. Function composition can be specified either explicitly or implicitly as path queries. The net effect of the inversion is to convert the database into a hyperdatabase: a database of databases, connected by indexes or functions. The inversion approach was motivated by their work in biological databases, for which hyperdatabases are a good model. The need for a good model has slowed progress in bioinformatics.

• Genomics & Informatics
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• 제14권1호
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• pp.20-28
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• 2016

Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.

• 한국육종학회지
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• 제40권1호
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• pp.1-7
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• 2008

An attempt was made to link rice embryo proteins to DNA sequences and to understand their functions. One hundred of the 700 spots detected on the embryo 2-DE gels were microsequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were unknown in functions as previously reported (Woo et al. 2002). In addition, twenty-four protein spots with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available rice EST databases at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). The chromosomal location of some proteins were also obtained from the rice genetic map provided by Japanese Rice Genome Research Program (http://rgp.dna.affrc.go.jp). The DNA sequence databases including EST have been reported for rice (Oryza sativa L.) now provides whole or partial gene sequence, and recent advances in protein characterization allow the linking proteins to DNA sequences in the functional analysis. This work shows that proteome analysis could be a useful tool strategy to link sequence information and to functional genomics.

• Asian Pacific Journal of Cancer Prevention
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• 제15권11호
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• pp.4689-4695
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• 2014

Background: A great number of studies have shown that cytochrome P450 1A1 (CYP1A1) genetic polymorphisms, CYP1A1 Msp I and CYP1A1 Ile/Val, might be risk factors for digestive tract cancers, including esophageal cancer (EC), gastric cancer (GC), hepatic carcinoma (HC), as well as colorectal cancer (CC), but the results are controversial. In this study, a meta-analysis of this literature aimed to clarify associations of CYP1A1 genetic polymorphisms with digestive tract cancers susceptibility in Chinese populations. Materials and Methods: Eligible case-control studies published until December 2013 were retrieved by systematic literature searches from PubMed, Embase, CBM, CNKI and other Chinese databases by two investigators independently. The associated literature was acquired through deliberate search and selection based on established inclusion criteria. Fixed-effects or random-effects models were used to estimate odds ratios (ORs and 95%CIs). The meta-analysis was conducted using Review Manager 5.2 and Stata 12.0 softwares with stability evaluated by both stratified and sensitivity analyses. Moreover, sensitivity analysis and publication bias diagnostics confirmed the reliability and stability. Results: Eighteen case-control studies with 1,747 cases and 2,923 controls were selected for CYP1A1 MspI polymorphisms, and twenty case-control studies with 3, 790 cases and 4, 907 controls for the CYP1A1 Ile/Val polymorphisms. Correlation associations between CYP1A1 Ile/Val polymorphisms and digestive tract cancers susceptibility were observed in four genetic models in the meta-analysis (GG vs AA:OR= 2.03, 95%CI =1.52- 2.72; AG vs AA: OR=1.26, 95%CI =1.07-1.48; [GG+AG vs AA] :OR =1.42, 95%CI=1.20-1.68, [GG vs AA+AG]:OR=1.80, 95%CI =1.40-2.31). There was no association between CYP1A1 Msp I polymorphisms and digestive tract cancers risk. Subgroup analysis for tumor type showed a significant association of CYP1A1 Ile/Val genetic polymorphisms with EC in China. However, available data collected by the study failed to reveal remarkable associations of GC or HC with CYP1A1 Ile/Val genetic polymorphisms and EC, GC or CC with CYP1A1 MspI genetic polymorphisms. Conclusions: Our results indicated that CYP1A1 Ile/Val genetic polymorphisms, but not CYP1A1 Msp I polymorphisms, are associated with an increased digestive tract cancers risk in Chinese populations. Additional well-designed studies, with larger sample size, focusing on different ethnicities and cancer types are now warranted to validate this finding.