• Asian-Australasian Journal of Animal Sciences
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• v.28 no.1
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• pp.25-36
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• 2015

The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.2027-2033
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• 2014

Background: We aimed to assess RET proto-oncogene polymorphisms in three different Iranian families with medullary thyroid cancer (MTC), and performed molecular dynamics simulations and free energy stability analysis of these mutations. Materials and Methods: This study consisted of 48 patients and their first-degree relatives with MTC confirmed by pathologic diagnosis and surgery. We performed molecular dynamics simulations and free energy stability analysis of mutations, and docking evaluation of known RET proto-oncogene inhibitors, including ZD-6474 and ponatinib, with wild-type and mutant forms. Results: The first family consisted of 27 people from four generations, in which nine had the C.G2901A (P.C634Y) mutation; the second family consisted of six people, of whom three had the C.G2901T (P.C634F) mutation, and the third family, who included 12 individuals from three generations, three having the C.G2251A (P.G691S) mutation. The automated 3D structure of RET protein was predicted using I-TASSER, and validated by various protein model verification programs that showed more than 96.3% of the residues in favored and allowed regions. The predicted instability indices of the mutated structures were greater than 40, which reveals that mutated RET protein is less thermo-stable compared to the wild-type form (35.4). Conclusions: Simultaneous study of the cancer mutations using both in silico and medical genetic procedures, as well as onco-protein inhibitor binding considering mutation-induced drug resistance, may help in better overcoming chemotherapy resistance and designing innovative drugs.

• School Mathematics
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• v.11 no.3
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• pp.431-462
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• 2009

Introduction of logarithm in mathematics textbook in the 7th national curriculum of mathematics is the inverse of exponent. This introduction is happened that students don't know the necessity for learning logarithm and the meaning of logarithm. Students also have solved many problems of logarithm by rote. Therefore, we try to present teaching unit for the logarithm according to the historico-genetic principle. We developed the learning-teaching module of unit for the logarithm according to historico-genetic principle, especially reinvention for real contexts based RME. Loaming-teaching module is carried out as the performance assessment. As a results, We find out that this module helps students understand concepts of logarithm meaningfully Also, mathematical errors of logarithm is revised after the application of learning-teaching module.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.4
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• pp.334-340
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• 2001

Two different types of molecular markers, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), were used to measure genetic diversity among five Korean, eight Thai, and three wild soybeans. For SSR analysis, a total of 20 markers were surveyed to detect polymorphisms. For SNP analysis, four primers were designed from consensus sequence regions on disease resistance protein homolog genes, and used to amplify the genomic region. The PCR products were sequenced. A number of polymorphic SSR and SNP bands were scored on all genotypes and their genetic similarity was measured. Clustering analysis was performed independently on both types of markers. Clustering based on SSR markers separated the genotypes into three main groups originated from Korea, Thailand, and wild soybeans. On the other hand, two main groups were classified using SNP analysis. It seemed that SSR was more informative than SNP in this study. This may be due to the fact that SNP was surveyed on the smaller genomic region than SSR. Grouping based on the combined data of both markers revealed similar results to that of SNP rather than that of SSR. This might be due to the fact that more loci from SNP were considered to measure genetic relatedness than those from the SSR.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.108-120
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• 2017

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene ${\beta}$ - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.17 no.4
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• pp.389-403
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• 2004

This study presents the structural model modification based on the modal data such as natural frequencies and mode shapes. Preliminary structural model can be obtained using design drawings and field measurement, and therefore the deteriorated stiffness of a structure and the effect of the boundary conditions are difficult to be evaluated in preliminary analysis model, and the preliminary model can be modified using structural response data including static and/or dynamic characteristics. In this study, the structural model is modified based on the structural modal data using genetic algorithm. Modal testing were carried out for Imjin River Bridge and Hangjoo Bridge, the modal properties were estimated using modal identification techniques, and finally the structural models were updated using genetic algorithm. The modified structural model could give us more reliable structural analysis results and therefore those can be used for structural performance evaluation such as load carrying capacity and seismic capacity.

• Journal of Korean Society of Industrial and Systems Engineering
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• v.40 no.4
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• pp.211-220
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• 2017

The application of the theoretical model to real assembly lines has been one of the biggest challenges for researchers and industrial engineers. There should be some realistic approach to achieve the conflicting objectives on real systems. Therefore, in this paper, a model is developed to synchronize a real system (A discrete event simulation model) with a theoretical model (An optimization model). This synchronization will enable the realistic optimization of systems. A job assignment model of the assembly line is formulated for the evaluation of proposed realistic optimization to achieve multiple conflicting objectives. The objectives, fluctuation in cycle time, throughput, labor cost, energy cost, teamwork and deviation in the skill level of operators have been modeled mathematically. To solve the formulated mathematical model, a multi-objective simulation integrated hybrid genetic algorithm (MO-SHGA) is proposed. In MO-SHGA each individual in each population acts as an input scenario of simulation. Also, it is very difficult to assign weights to the objective function in the traditional multi-objective GA because of pareto fronts. Therefore, we have proposed a probabilistic based linearization and multi-objective to single objective conversion method at population evolution phase. The performance of MO-SHGA is evaluated with the standard multi-objective genetic algorithm (MO-GA) with both deterministic and stochastic data settings. A case study of the goalkeeping gloves assembly line is also presented as a numerical example which is solved using MO-SHGA and MO-GA. The proposed research is useful for the development of synchronized human based assembly lines for real time monitoring, optimization, and control.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.680-686
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• 2014

Acanthopanacis Cortex has been used for oriental medicinal purposes in Asian countries especially in Korea and China. In the Korean Pharmacopeia, the cortexes of the dried roots, stems and branches of all species in Eleutherococcus and Eleutherococcus sessiliflorus are known as 'Ogapi'. Mostly the cortexes of E. gracilistylus roots and E.senticosus roots were used as 'Ogapi' in China and Japan, respectively. Therefore, the purpose of this study was to determine and compare the molecular authentication of Korean 'Ogapi' by using the ribosomal internal transcribed spacer (ITS) region. The ITS region has the highest possibility of effective and successful identification for the widest variety of molecular authentication. The ITS region was targeted for molecular analysis with Single nucleotide polymorphisms (SNPs) specific for morphologically similar to E. gracilistylus, E. senticosus, E. sessiliflorus from their adulterant, moreover, E. sieboldianus were detected within sequence data. Thus, based on these SNP sites, specific primers were designed and multiplex PCR analysis were conducted for molecular authentication of four plants (E. gracilistylus, E. senticosus, E. sessiliflorus, and E. sieboldianus). The findings of results indicated that ITS region might be established multiplex-PCR analysis systems and hence were proved to be an effective tools for molecular evaluation and comparison of 'Ogapi' with other plants.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.48 no.5
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• pp.413-418
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• 2003

Genetic diversity and soybean sprout-related traits were evaluated in a total of 72 soybean accessions (60 Glycine max, 7 Glycine soja, and 5 Glycine gracilis). 100-seed weight (SW) was greatly varied and ranged from 3.2g to 32.3g in 72 soybean accessions. Positive correlation was observed between GR and hypocotyl length (HL), whereas negative correlation was observed between SW and hypocotyl diameter (HD). Re-evaluation by discarding two soybean genotypes characterized with low GR indicated that much higher correlation of sprout yield (SY) with HD and SW. Based on the principal component analysis (PCA) for sprout-related traits, 57 accessions were classified. Soybean genotypes with better traits for sprout, such as small size of seeds and high SY, were characterized with high PCA 1 and PCA 2 values. The seed size in second is small but showed low GR and SY, whereas the third has large seed, high GR and more than 400% SY. In genetic similarity analysis using 60 SSR marker genotyping, 72 accessions were classified into three major and several minor groups. Nine of twelve accessions that were identified as the representatives of soybean for sprout based on PCA were in a group by the SSR marker analysis, indicating the SSR marker selection of parental genotypes for soybean sprout improvement program.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.