• Genomics & Informatics
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• v.17 no.4
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• pp.47.1-47.12
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• 2019

The achievements of genome-wide association studies have suggested ways to predict diseases, such as type 2 diabetes (T2D), using single-nucleotide polymorphisms (SNPs). Most T2D risk prediction models have used SNPs in combination with demographic variables. However, it is difficult to evaluate the pure additive contribution of genetic variants to classically used demographic models. Since prediction models include some heritable traits, such as body mass index, the contribution of SNPs using unmatched case-control samples may be underestimated. In this article, we propose a method that uses propensity score matching to avoid underestimation by matching case and control samples, thereby determining the pure additive contribution of SNPs. To illustrate the proposed propensity score matching method, we used SNP data from the Korea Association Resources project and reported SNPs from the genome-wide association study catalog. We selected various SNP sets via stepwise logistic regression (SLR), least absolute shrinkage and selection operator (LASSO), and the elastic-net (EN) algorithm. Using these SNP sets, we made predictions using SLR, LASSO, and EN as logistic regression modeling techniques. The accuracy of the predictions was compared in terms of area under the receiver operating characteristic curve (AUC). The contribution of SNPs to T2D was evaluated by the difference in the AUC between models using only demographic variables and models that included the SNPs. The largest difference among our models showed that the AUC of the model using genetic variants with demographic variables could be 0.107 higher than that of the corresponding model using only demographic variables.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.26 no.6
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• pp.805-810
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• 2002

Development of a small gas-turbine combustor for 100㎾ class APU(Auxiliary Power Unit) has been performed. This combustor is a reverse-annular type and has a tangential swiller in the liner head to improve the fuel/air mixing and flame stability. Three main and three pilot fuel injectors of the simplex pressure-swirl type are used. The performance target at the design condition includes a turbine inlet temperature of l170k, a combustion efficiency of 99%, a pattern factor of 30%, and an engine durability of 3000 hours. Under developing the combustor, we conducted the performance test of our first prototype(TS1) with some variants. As a result of the test, the performance targets of the combustor are satisfied except that the pattern factor is about 4% higher than the target value. Therefore, the second prototype(TS2) was redesigned and the performance test was conducted with the critical focus on the pattern factor and the exit mean temperature. We adopted TS2 four variants to check the improvement of the pattern factor. As a result, the pattern factors of several variants were satisfied with the performance target. Finally, the TS2A variant was chosen as a final combustor fur our APU model.

• Horticultural Science & Technology
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• v.17 no.3
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• pp.352-354
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• 1999

Randomly and specifically amplified polymorphic DNA band patterns based on polymerase chain reaction (PCR) analysis were used to assess genetic variation of somaclonal variants obtained from tissue culture of lisianthus (Eustoma grandiflorum). Five different types of variant were classified by morphological characters such as leaflet number, leaf shape, caulicle length, plant height, and leaf area. Five primers out of 20 primers (10 mer) resulted in 34 random amplified DNA fragments with polymorphisms (64.7%) in all tested plants. The dissimilarity coefficient was from 0.71 to 0.91 by UPGMA cluster analysis. Based on the presence of polymorphic bands, normal plant and five somaclonal variants were divided into two groups at the similarity coefficient value of 0.79.

• Environmental Mutagens and Carcinogens
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• v.23 no.1
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• pp.1-6
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• 2003

The purpose of this study was to evaluate whether the MTHFR variants, folate and vitamin $B_{12}$ deficiencies increase the risk of hyperhomocysteinaemia and adverse pregnancy outcome such as short gestational age or reduced birth weight. Healthy pregnant women (n=136; 24-28 gestational weeks; 20-40 years old), who visited Ewha Womans University Hospital for prenatal care, participated in this study. At the time of delivery, trained nurses recorded the pregnancy outcome from medical chart. We determined maternal MTHFR polymorphisms (C to T subsitution at nucleotide 677) and measured serum homocyteine, vitamin $B_{12}$, and folate concentrations. We compared serum homocysteine level by MTHFR genotype, serum folate and serum vitamin B12 levels using ANOVA. To evaluate the association between serum homocysteine level and pregnancy outcome, we compared the gestational age and birth weight by serum homocysteine levels using multiple regression analysis, adjusting for other potential predictors. Mean level of serum homocysteine was highest among pregnant women of the MTHFR variants with low levels of serum folate and vitamin $B_{12}$. Regarding association with birth outcome, we found the relationship between homocysteine levels and increased gestational age (p=0.03) and reduced birth outcome (p>0.05). Our data demonstrates that serum level of folate and vitamin $B_{12}$ among pregnant women affects significantly serum homocysteine levels, and the genetic polymorphism of MTHFR modulates the relationship between them. However, we did not have conclusive evidence of association between high homocysteine level and adverse pregnancy outcome such as preterm or low birth weight.

• Asian-Australasian Journal of Animal Sciences
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• v.11 no.3
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• pp.318-322
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• 1998

Using polyacrylamide-gel isoelectric focusing followed by immunoblotting, genetic polymorphism of plasma vitamin D-binding protein (Gc) was examined in Asian sheep. The Gc polymorphism was revealed in the Khalkhas sheep of Mongolia, consisting of F, S and W variants, and the Yunnan native sheep of China, consisting of F and S variants. In particular, W was a new variant. The V variant detected in European sheep up to now was not observed in these sheep. The Bhyanglung, Baruwal, Kagi and Lampuchhre sheep of Nepal and local sheep of Bangladesh and Vietnam were monomorphic for the S variant. Family data and population genetic data supported the hypothesis that these variants were controlled by codominant alleles. In these Asian sheep, distribution of the $Gc^s$ allele was predominant (0.9571-1) and was seen as well in European sheep (Suffolk, Corriedale, Cheviot and Finnish Landrace) raised in Japan. $Gc^w$ allele was detected only in the Khalkhas sheep with the low frequency of 0.0025. The $Gc^v$ allele was detected in the Suffolk and Corriedale sheep (0.0080 and 0.0682), but not in any of the Asian sheep studied.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.3989-3995
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• 2016

Background: Childhood acute lymphoblastic leukemia (ALL) is a heterogeneous genetic disease and its etiology remains poorly understood. Recent genome wide association and replication studies have highlighted specific polymorphisms contributing to childhood ALL predispositions mostly in European populations. It is unclear if these observations generalize to other populations with a lower incidence of ALL. The current case-control study evaluated variants in ARID5B (rs7089424, rs10821936), IKZF1 (rs4132601) and CEBPE (rs2239633) genes, which appear most significantly associated with risk of developing childhood B-lineage ALL. Materials and Methods: Using TaqMan assays, genotyping was conducted for 162 de novo B-lineage ALL cases and 150 unrelated healthy controls in India. Appropriate statistical methods were applied. Results: Genotypic and allelic frequencies differed significantly between cases and controls at IKZF1-rs4132601 (p=0.039, p=0.015) and ARID5B-rs10821936 (p=0.028, p=0.026). Both rs10821936 (p=0.019; OR 0.67; 95% CI=0.47-0.94) and rs4132601 (p=0.018; OR 0.67; 95%CI 0.48-0.94) were associated with reduced disease risk. Moreover, gender-analysis revealed male-specific risk associations for rs10821936 (p=0.041 CT+CC) and rs4132601 (p=0.005 G allele). Further, ARID5B-rs7089424 and CEBPE-rs2239633 showed a trend towards decreased disease risk but without significance (p=0.073; p=0.73). Conclusions: Our findings provide the first evidence that SNPs ARID5B-rs10821936 and IKZF1-rs4132601 are associated with decreased B-lineage ALL susceptibility in Indian children. Understanding the effects of these variants in different ethnic groups is crucial as they may confer different risk of ALL within different populations.

• Journal of The Korean Association For Science Education
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• v.32 no.8
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• pp.1295-1317
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• 2012

There has been disagreement on the importance of definitions in science education. Yager (1983) believes that one crisis in science education was due to the considerable emphasis upon the learning of definitions. Hobson (2004) disagrees with physics textbooks that do not provide general definition on energy. Some textbooks explain that "there is no completely satisfactory definition of energy" or they can only "struggle to define it." In general, imprecise definitions in textbooks (Bauman, 1992) and inaccuracies in definition provided by teachers (Galili & Lehavi, 2006) may cause alternative conceptions. Besides, there are at least four challenges in defining physical concepts: precision, circularity, context and completeness in knowledge. These definitional problems that have been discussed in The Feynman Lectures, may impede the learning of physical concepts. A meta-study approach is employed to examine about five hundreds journal papers that may discuss definitions in physics, problems in defining physical concepts and how they may result in alternative conceptions. These journal papers are mainly selected from journals such as American Journal of Physics, International Journal of Science Education, Journal of Research in Science Teaching, Physics Education, The Physics Teachers, and so on. There are also comparisons of definitions with definitions from textbooks, Dictionaries of Physics, and English Dictionaries. To understand the nature of alternative conception, Lee et al. (2010) have suggested a theoretical framework to describe the learning issues by synthesizing cognitive psychology and science education approaches. Taking it a step further, this study incorporates the challenges in semantics and epistemology, proposes that there are at least four variants of alternative conceptions. We may coin the term, 'alternative definitions', to refer to the commonly available definitions, which have these four problems in defining physics concepts. Based on this study, alternative definitions may result in at least four variants of alternative conceptions. Note that these four definitional problems or challenges in definitions cannot be easily resolved. Educators should be cognizant of the four variants of alternative conceptions which can arise from alternative definitions. The concepts of alternative definitions can be useful and possibly generalized to science education and beyond.

• Biomedical Science Letters
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• v.15 no.4
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• pp.301-307
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• 2009

Whole-body insulin resistance results largely from impaired insulin-stimulated glucose disposal in skeletal muscle. Our previous studies using differential display and quantitative real-time RT-PCR have shown that a novel cDNA band (DD23) had a higher level of expression in insulin resistant skeletal muscle and it was correlated with whole-body insulin action, independent of age, sex, and percent body fat. In this study, we cloned and characterized DD23. The DD23 sequence is part of the 3'UTR region of the RNA binding motif, single stranded interacting protein (RBMS3). We have cloned the full length cDNA for RBMS3 and identified two splice variants. These variants named DD23-L and DD23-S have 15 and 14 exons respectively and differ from RBMS3 in the 3'UTR significantly. Northern blot analyses showed that an ~8.8 kb mRNA transcript of DD23 was predominantly expressed in skeletal muscle and to a lesser extent in placenta, but not in heart, brain, lung, liver, or kidney, unlike RBMS3. Elevated expression levels of these novel alternatively spliced variants of RBMS3 in skeletal muscle may play a role in whole body insulin resistance.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.12
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• pp.1716-1721
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• 2003

Steroid hormones and their receptors play an important role in reproductive process. Estrogen is intimately involved with pregnancy and its function is mediated through the estrogen receptor which has been chosen as a candidate gene to study litter size in pigs. In this study, we report that two estrogen receptor variants, designated pER-1 and pER-2 were co-expressed in the uteri of normal cycling Lan-Yu pig (Sus vittatus; a small-ear miniature in Taiwan) with the pER-1 expression level appeared to be several times higher than that of pER-2. These receptor variants were isolated using reverse transcription-PCR from the pig uteri and their sequences were determined. The pER-1 and pER-2 sequences, which are homologous to those found in other mammalian estrogen receptors, encode putative proteins consisting of 574 and 486 amino acids, respectively. A deletion in exon I was identified in both sequences, with deletion lengths of 63 bp in pER-1 and 327 bp in pER-2. The deletion in pER-1 is internal to that in pER-2 and both deletions resulted in a truncation of the B domain, which confers the transactivating activity of estrogen receptor protein. This result describes the existence of estrogen receptor variants with a deletion in exon I and implies the possibility that physiological functioning of an estrogen receptor may not require the presence of an intact B domain.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.3
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• pp.1539-1546
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• 2016

Specific patterns of the hereditary breast and ovarian cancer (HBOC) syndrome are related to mutations in the BRCA1 gene. One hundred unrelated breast cancer patients were interviewed to obtain clinical symptoms and signs, pedigree and familial history of HBOC syndrome related cancer. Subsequently, data were calculated using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk prediction model. Patients with high score of BOADICEA were offered genetic testing. Eleven patients with high score of BOADICEA, 2 patients with low score of BOADICEA, 2 patient's family members and 15 controls underwent BRCA1 genetic testing. Mutation screening using PCR-HRM was carried out in 22 exons (41 amplicons) of BRCA1 gene. Sanger sequencing was subjected in all samples with aberrant graph. This study identified 10 variants in the BRCA1 gene, consisting of 6 missense mutations (c.1480C>A, c.2612C>T, c.2566T>C, c.3113A>G, c.3548 A>G, c.4837 A>G), 3 synonymous mutations (c.2082 C>T, c.2311 T>C and c.4308T>C) and one intronic mutation (c.134+35 G>T). All variants tend to be polymorphisms and unclassified variants. However, no known pathogenic mutations were found.