• Computers and Concrete
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• v.19 no.6
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• pp.717-724
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• 2017

In this paper, four formulas are proposed via gene expression programming (GEP)-based models and regression analysis (RA) to predict the flexural strength ($f_s$) values of mortars containing different mineral admixtures that are ground granulated blast-furnace slag (GGBFS), silica fume (SF) and fly ash (FA) at different ages. Three formulas obtained from the GEP-I, GEP-II and GEP-III models are constituted to predict the $f_s$ values from the age of specimen, water-binder ratio and compressive strength. Besides, one formula obtained from the RA is constituted to predict the $f_s$ values from the compressive strength. To achieve these formulas in the GEP and RA models, 972 data of the experimental studies presented with mortar mixtures were gathered from the literatures. 734 data of the experimental studies are divided without pre-planned for these formulas achieved from the training and testing sets of GEP and RA models. Beside, these formulas are validated with 238 data of experimental studies un-employed in training and testing sets. The $f_s$ results obtained from the training, testing and validation sets of these formulas are compared with the results obtained from the experimental studies and the formulas given in the literature for concrete. These comparisons show that the results of the formulas obtained from the GEP and RA models appear to well compatible with the experimental results and find to be very credible according to the results of other formulas.

• Journal of Medicine and Life Science
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• v.20 no.3
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• pp.107-114
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• 2023

Epidemiological control of coronavirus disease 2019 (COVID-19) is needed to estimate the infection period of confirmed cases and identify potential cases. The present study, targeting confirmed cases for which the time of COVID-19 symptom onset was disclosed, aimed to investigate the relationship between intervals (day) from symptom onset to testing the cycle threshold (CT) values of real-time reverse transcription-polymerase chain reaction. Of the COVID-19 confirmed cases, those for which the date of suspected symptom onset in the epidemiological investigation was specifically disclosed were included in this study. Interval was defined as the number of days from symptom onset (as disclosed by the patient) to specimen collection for testing. A locally weighted regression smoothing (LOWESS) curve was applied, with intervals as explanatory variables and CT values (CTR for RdRp gene and CTE for E gene) as outcome variables. After finding its non-linear relationship, a polynomial regression model was applied to estimate the 95% confidence interval values of CTR and CTE by interval. The application of LOWESS in 331 patients identified a U-shaped curve relationship between the CTR and CTE values according to the number of interval days, and both CTR and CTE satisfied the quadratic model for interval days. Active application of these results to epidemiological investigations would minimize the chance of failing to identify individuals who are in contact with COVID-19 confirmed cases, thereby reducing the potential transmission of the virus to local communities.

• Genomics & Informatics
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• v.14 no.4
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Development and Reproduction
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• v.25 no.2
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• pp.113-121
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• 2021

This article aims to introduce German discussion on the approval of the non-invasive prenatal diagnosis (NIPD), which started with the development of PrenaTest^® by LifeCodexx AG. The discussion started with the concern that the non-invasive nature of NIPD, such as PrenaTest^®, may rapidly expand the use and scope of similar tests, thus leading to a new era of eugenics. Based on this concern, the need for clear clinical guidelines on specific indications for NIPD has been suggested. Along the same line, it was discussed whether PrenaTest^® is against the Basic Law prohibiting discrimination on grounds of disability and whether the test is outside the scope of the purpose of gene testing limited by Genetic Diagnosis Act. Through such discussion, the Federal Ministry of Health of Germany established the preconditions for inclusion of NIPD in the German public health insurance system. For this, the German motherhood guideline was amended and the information for the insured persons provided to pregnant women was included in the amended guideline. Such discussion made in Germany provides insight on which points should be considered when various gene testings are accepted in Korea, in which genetic communication has not been systematized yet. In particular, German counseling system for pregnant women will provide valuable insights for Korea where the direction for regulations on abortion has not been established even after the ruling by the Constitutional Court that charges for abortion are against the constitution.

• 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.

• Journal of the Korean Data and Information Science Society
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• v.25 no.6
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• pp.1385-1395
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• 2014

Economic traits of livestock are affected by environmental factors and genetic factors. In addition, it is not affected by one gene, but is affected by interaction of genes. We used a linear regression model in order to adjust environmental factors. And, in order to identify gene-gene interaction effect, we applied data mining techniques such as neural network, logistic regression, CART and C5.0 using five-SNPs (single nucleotide polymorphism) of FASN (fatty acid synthase). We divided total data into training (60%) and testing (40%) data, and applied the model which was designed by training data to testing data. By the comparison of prediction accuracy, C5.0 was identified as the best model. It were selected superior genotype using the decision tree.

• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.971-986
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• 2014

When thousands of hypotheses are tested simultaneously, the probability of rejecting any true hypotheses increases, and large multiplicity problems are generated. To solve these problems, researchers have proposed different approaches to multiple testing methods, considering family-wise error rate (FWER), false discovery rate (FDR) or false nondiscovery rate (FNR) as a type I error and some test statistics. In this article, we discuss Bonferroni (1960), Holm (1979), Benjamini and Hochberg (1995) and Benjamini and Yekutieli (2001) procedures based on T statistics, modified T statistics or local-pooled-error (LPE) statistics. We also consider Sun and Cai (2007) procedure based on Z statistics. These procedures are compared in the simulation and applied to Arabidopsis microarray gene expression data to identify differentially expressed genes.

• Journal of Veterinary Science
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• v.22 no.6
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• pp.76.1-76.15
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• 2021

Background: The development of a vaccine for Jembrana disease is needed to prevent losses in Indonesia's Bali cattle industry. A DNA vaccine model (pEGFP-C1-tat) that requires a functional delivery system will be developed. Polylactic-co-glycolic acid (PLGA) may have potential as a delivery system for the vaccine model. Objectives: This study aims to evaluate the in vitro potential of PLGA as a delivery system for pEGFP-C1-tat. Methods: Consensus and codon optimization for the tat gene was completed using a bioinformatic method, and the product was inserted into a pEGFP-C1 vector. Cloning of the pEGFP-C1-tat was successfully performed, and polymerase chain reaction (PCR) and restriction analysis confirmed DNA isolation. PLGA-pEGFP-C1-tat solutions were prepared for encapsulated formulation testing, physicochemical characterization, stability testing with DNase I, and cytotoxicity testing. The PLGA-pEGFP-C1-tat solutions were transfected in HeLa cells, and gene expression was observed by fluorescent microscopy and real-time PCR. Results: The successful acquisition of transformant bacteria was confirmed by PCR. The PLGA:DNA:polyvinyl alcohol ratio formulation with optimal encapsulation was 4%:0.5%:2%, physicochemical characterization of PLGA revealed a polydispersity index value of 0.246, a particle size of 925 nm, and a zeta potential value of -2.31 mV. PLGA succeeded in protecting pEGFP-C1-tat from enzymatic degradation, and the percentage viability from the cytotoxicity test of PLGA-pEGFP-C1-tat was 98.03%. The PLGA-pEGFP-C1-tat demonstrated luminescence of the EGFP-tat fusion protein and mRNA transcription was detected. Conclusions: PLGA has good potential as a delivery system for pEGFP-C1-tat.

• Clinical and Experimental Pediatrics
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• v.53 no.7
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• pp.774-777
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• 2010

Pfeiffer syndrome is a rare autosomal dominant disorder characterized by coronal craniosynostosis, brachycephaly, mid-facial hypoplasia, and broad and deviated thumbs and great toes. Pfeiffer syndrome occurs in approximately 1:100,000 live births. Clinical manifestations and molecular genetic testing are important to confirm the diagnosis. Mutations of the fibroblast growth factor receptor 1 ($FGFR1$) gene or $FGFR2$ gene can cause Pfeiffer syndrome. Here, we describe a case of Pfeiffer syndrome with a novel c833_834GC>TG mutation (encoding Cys278Leu) in the $FGFR2$ gene associated with a coccygeal anomaly, which is rare in Pfeiffer syndrome.

• Journal of Genetic Medicine
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• v.17 no.2
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• pp.108-111
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• 2020

Short stature homeobox-containing gene (SHOX) is a well-known causative gene for the short stature in Turner syndrome. The clinical manifestation of SHOX gene related disorders varies from SHOX haploinsufficiency, presenting with idiopathic short stature, disproportionate short stature, or Leri-Weill dyschondrosteosis (LWD) to recessive form of extreme dwarfism and limb deformity in Langer mesomelic dysplasia. LWD is usually diagnosed upon suspicion based on short stature and skeletal abnormalities, and it is rarely accompanied with respiratory failure in the neonatal period. Here, we report the case of a newborn infant with LWD presenting with severe micrognathia that caused respiratory distress, which was diagnosed using microarray testing. Even when the manifestation of Madelung deformity is not yet apparent, LWD should be considered as one of underlying diseases related to congenital micrognathia.