• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1111-1113
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• 2012

The ER-/PR+ breast tumor may be the result of a false ER negative result. The aim of this study was to investigate whether there is a difference in patient and tumor characteristics of the ER-/PR+ phenotype in an Asian setting. A total of 2629 breast cancer patients were categorized on the basis of their age, ethnicity, tumor hormonal receptor phenotype, grade and histological type. There were 1230 (46.8%) ER+/PR+, 306 (11.6%) ER+/PR-, 122 (4.6%) ER-/PR+ and 972 (37%) ER-/PR-. ER-/PR+ tumors were 2.5 times more likely to be younger than 50 years at diagnosis (OR: 2.52; 95% CI: 1.72-3.67). Compared to ER+/PR+ tumors, the ER-/PR+ phenotype was twice more likely to be associated with grade 3 tumors (OR:2.02; 95%CI: 1.00-4.10). In contrast, compared to ER-/PR- tumors, the ER-/PR+ phenotype was 90% less likely to be associated with a grade 3 tumor (OR: 0.12; 95%CI:0.05-0.26), and more likely to have invasive lobular than invasive ductal histology (OR: 3.66; 95%CI: 1.47-9.11). These results show that the ER-/PR+ phenotype occurs in a younger age group and is associated with intermediate histopathological characteristics compared to ER+/PR+ and ER-/PR- tumors. This may imply that it is a distinct entity and not a technical artifact.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.559-565
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• 2015

The rind phenotype of watermelon fruits is an important agronomic characteristic in the watermelon market. Inheritance and linkage analyses were performed for three rind-related traits that together determine the rind phenotype: foreground stripe pattern, rind background color, and depth of rind color. The inheritance of the foreground stripe pattern was analyzed using three different $F_2$ populations, showing that the striped pattern is dominant over the non-striped pattern. The inheritance analysis of the rind background color was performed using $F_2$ populations of the '10909' and '109905', and the depth of rind color was analyzed using $F_2$ populations of the '90509' and '109905'. Yellow color was found to be dominant over green color, and a deep color was dominant over the standard color. Linkage analysis of the three traits was conducted using three $F_2$ populations in which two traits were segregating. Each pair of traits was inherited independently, which demonstrated that the three traits are not linked. Therefore, we propose a three-locus model for the determination of rind phenotype, providing novel insight that rind phenotype is determined by the combination of three genetically independent loci.

• Journal of Ginseng Research
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• v.34 no.1
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• pp.8-16
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• 2010

Attention deficit hyperactivity disorder (ADHD) affects 4-12% of chool-age children worldwide and is characterized by three core symptoms: hyperactivity, inattention, and impulsivity. Although standard pharmacological treatments, such as methylphenidate and atomoxetine, are available, concerns about drug-induced psychological and cardiovascular problems, as well as growth retardation and sleep disturbances, highlight the continuing need for new therapeutic interventions. Using a neonatal hypoxia-induced hyperactivity model in rats, the potential positive role that oral administration of red ginseng extract may have in relation to the hyperactive phenotype was investigated. Hypoxia was induced in 2-day-old male Sprague-Dawley (SD) rat pups by placing them in a nitrogen chamber for 15 min. The neonatal hypoxia-induced rats showed a significant increase in hyperactivity phenotype, such as increased movement duration, movement distance, and rearing frequency, which was determined by monitoring their spontaneous locomotor activity using the Ethovision video tracking system. One week of oral treatment with red ginseng extract decreased the hyperactivity phenotype of the neonatal hypoxia-induced rats and increased the locomotor activity of the control rats. In the neonatal hypoxia-induced rats, expression of the norepinephrine transporter in the forebrain was increased, and red ginseng treatment partially prevented its up-regulation, while increasing its level in the control rats. Taken together, these results suggest that red ginseng extract decreased the neonatal hypoxia-induced hyperactivity phenotype, although it increased locomotor activity in normal animals.

• Journal of Korea Society of Industrial Information Systems
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• v.25 no.5
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• pp.83-90
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• 2020

In this paper, a web-based seed phenotype visualization support system is proposed to extract and visualize data such as the surface color, length, area, perimeter and compactness of seed, which is phenotype information from the image of soybean/rice seeds. This system systematically stores data extracted from seeds in databases, and provides a web-based user interface that facilitates the analysis of data by researchers using data tables and charts. Conventional seed characteristic studies have been manually measured by humans, but the system developed in this paper allows researchers to simply upload seed images for analysis and obtain seed's numerical data after image processing. It is expected that the proposed system will be able to obtain time efficiency and remove spatial restriction, if it is used in seed characterization research, and it will be easy to analyze through systematic management of research results and visualization of the phenotype characteristics.

• Translational and Clinical Pharmacology
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• v.25 no.3
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• pp.147-152
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• 2017

This study focused on the role of cytochrome P450 2D6 (CYP2D6) genotypes to predict phenotypes in the metabolism of dextromethorphan. CYP2D6 genotypes and metabolic ratios (MRs) of dextromethorphan were determined in 201 Koreans. Unsupervised clustering algorithms, hierarchical and k-means clustering analysis, and color visualizations of CYP2D6 activity were performed on a subset of 130 subjects. A total of 23 different genotypes were identified, five of which were observed in one subject. Phenotype classifications were based on the means, medians, and standard deviations of the log MR values for each genotype. Color visualization was used to display the mean and median of each genotype as different color intensities. Cutoff values were determined using receiver operating characteristic curves from the k-means analysis, and the data were validated in the remaining subset of 71 subjects. Using the two highest silhouette values, the selected numbers of clusters were three (the best) and four. The findings from the two clustering algorithms were similar to those of other studies, classifying $^*5/^*5$ as a lowest activity group and genotypes containing duplicated alleles (i.e., $CYP2D6^*1/^*2N$) as a highest activity group. The validation of the k-means clustering results with data from the 71 subjects revealed relatively high concordance rates: 92.8% and 73.9% in three and four clusters, respectively. Additionally, color visualization allowed for rapid interpretation of results. Although the clustering approach to predict CYP2D6 phenotype from CYP2D6 genotype is not fully complete, it provides general information about the genotype to phenotype relationship, including rare genotypes with only one subject.

• The Korean Journal of Physiology and Pharmacology
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• v.26 no.5
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• pp.347-355
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• 2022

Abdominal aortic aneurysm (AAA) is a life-threatening disorder worldwide. Fibroblast growth factor 21 (FGF21) was shown to display a high level in the plasma of patients with AAA; however, its detailed functions underlying AAA pathogenesis are unclear. An in vitro AAA model was established in human aortic vascular smooth muscle cells (HASMCs) by angiotensin II (Ang-II) stimulation. Cell counting kit-8, wound healing, and Transwell assays were utilized for measuring cell proliferation and migration. RT-qPCR was used for detecting mRNA expression of FGF21 and activating transcription factor 4 (ATF4). Western blotting was utilized for assessing protein levels of FGF21, ATF4, and markers for the contractile phenotype of HASMCs. ChIP and luciferase reporter assays were implemented for identifying the binding relation between AFT4 and FGF21 promoters. FGF21 and ATF4 were both upregulated in Ang-II-treated HASMCs. Knocking down FGF21 attenuated Ang-II-induced proliferation, migration, and phenotype switch of HASMCs. ATF4 activated FGF21 transcription by binding to its promoter. FGF21 overexpression reversed AFT4 silencing-mediated inhibition of cell proliferation, migration, and phenotype switch. ATF4 transcriptionally upregulates FGF21 to promote the proliferation, migration, and phenotype switch of Ang-II-treated HASMCs.

• Genomics & Informatics
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• v.18 no.2
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• pp.14.1-14.11
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• 2020

Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.

• Annals of Clinical Neurophysiology
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• v.20 no.2
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• pp.89-92
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• 2018

Ullrich congenital muscular dystrophy (UCMD) is caused by mutations in one of three genes encoding collagen VI. Although UCMD usually shows an early onset, progressive weakness, contractures and hyperlaxity of the joints, and respiratory failure, it is well known to exhibit a wide spectrum of clinical severities. The severities of the phenotypic subtypes are mainly divided according to the ambulation status. We report a patient with the early-severe phenotype of UCMD who was diagnosed by the detection of novel recessive mutations in COL6A1.

• Journal of Microbiology
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• v.39 no.3
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• pp.236-239
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• 2001

Group A Streptococcus strain ST4529 is a provisional new ems type which has been recently reported in Malaysia (Jomal, et al. 1999. Energ. Infect . Dis. 5,10-14). This strain was found to be opacity factor (OF) negative with a Tl phenotype. Usually, OF negative strains with T1 phenotypes are associated with acute rheumatic fever. However, strain ST4529 was isolated from the blood of a patient with septicemia. Comparison of the deduced amino acid sequence of the mature hypervariable N-terminus of ST4529 showed only 43% identity with that of M5, the closest matched OF negative strain with a T1 phenotype. Thus, ST4529 most probably encodes a new serospecifically unique M protein which is associated with septicemia rather than pharyngitis infections. The strains with these phenotypes are very important because their sequences should be considered for developing any anti-streptococcal vaccines.

• Korean Journal of Veterinary Research
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• v.24 no.1
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• pp.31-35
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• 1984

The hemoglobin phenotype and the gene frequencies of 44 Formosan deer(Cervus nippon) in Kyung-Gi area were examined by using cellulose acetate and starch gel electrophoresis. 1. The method of cellulose acetate electrophoresis was simplier, more clear and preserative than starch gel electrophoresis. 2. The hemoglobin phenotype was appeared 3 types as $Hb^F$ $Hb^{FS}$ and $Hb^S$. The frequencies of appearance were $Hb^F$ 47.7%, $Hb^{FS}$ 47.7% and $Hb^S$ 4.5%, respectively. 3. The genetic factors of hemoglobin were observed as $Hb^F$ and $Hb^S$ and the rates of gene frequencies were 71.6% and 28.4%, respectively.