• Korean Journal of Radiology
• /
• v.25 no.4
• /
• pp.351-362
• /
• 2024

Objective: To measure inter-reader agreement and identify associated factors in interpreting complete response (CR) on magnetic resonance imaging (MRI) following chemoradiotherapy (CRT) for rectal cancer. Materials and Methods: This retrospective study involved 10 readers from seven hospitals with experience of 80-10210 cases, and 149 patients who underwent surgery after CRT for rectal cancer. Using MRI-based tumor regression grading (mrTRG) and methods employed in daily practice, the readers independently assessed mrTRG, CR on T2-weighted images (T2WI) denoted as mrCR_T2W, and CR on all images including diffusion-weighted images (DWI) denoted as mrCR_overall. The readers described their interpretation patterns and how they utilized DWI. Inter-reader agreement was measured using multi-rater kappa, and associated factors were analyzed using multivariable regression. Correlation between sensitivity and specificity of each reader was analyzed using Spearman coefficient. Results: The mrCR_T2W and mrCR_overall rates varied widely among the readers, ranging 18.8%-40.3% and 18.1%-34.9%, respectively. Nine readers used DWI as a supplement sequence, which modified interpretations on T2WI in 2.7% of cases (36/1341 [149 patients × 9 readers]) and mostly (33/36) changed mrCR_T2W to non-mrCR_overall. The kappa values for mrTRG, mrCR_T2W, and mrCR_overall were 0.56 (95% confidence interval: 0.49, 0.62), 0.55 (0.52, 0.57), and 0.54 (0.51, 0.57), respectively. No use of rectal gel, larger initial tumor size, and higher initial cT stage exhibited significant association with a higher interreader agreement for assessing mrCR_overall (P ≤ 0.042). Strong negative correlations were observed between the sensitivity and specificity of individual readers (coefficient, -0.718 to -0.963; P ≤ 0.019). Conclusion: Inter-reader agreement was moderate for assessing CR on post-CRT MRI. Readers' varying standards on MRI interpretation (i.e., threshold effect), along with the use of rectal gel, initial tumor size, and initial cT stage, were significant factors associated with inter-reader agreement.

• Research in Plant Disease
• /
• v.30 no.1
• /
• pp.60-65
• /
• 2024

In July 2020, total RNA was extracted from passion fruit (Passiflora edulis) leaves showing virus symptoms such as chlorotic spots and vein banding in Haenam, South Korea. Cucumber mosaic virus (CMV)-HN2 was identified through reverse transcription polymerase chain reaction and sequencing analysis. To confirm the biological characteristics of the CMV infecting passion fruit, 10 indicator plants were inoculated with CMV-HN2, and the results showed a typical CMV symptoms. Phylogenetic analysis based on the amino acid of the coat protein (CP) of CMVs revealed that the CMV passion fruit isolates belonged to subgroup I, among which CMV-HN2 belonged to subgroup IA. Additionally, CMVs isolated from passion fruit in Korea have amino acid sequence variation between the subgroup. Among them, CMV-HN2 had four to eight amino acid differences in CP from other CMV isolates from passion fruit. These results confirm the presence of genetic diversity in the CPs of passion fruit CMV isolates.

• Journal of Korean Society of Forest Science
• /
• v.90 no.4
• /
• pp.565-572
• /
• 2001

The spatial genetic structure of Needle fir(Abies holophylla Max.) seedlings on forest gap within a Needle fir forest at Mt. Odae in Korea was analyzed on the basis of ISSR(inter-simple sequence repeats) marker analysis. The gap size was $1,500m^2(50m{\times}30m)$, and we sampled 416 one- or two-year-old seedlings by 2m intervals. Some trees at the upper crown layer except Needle firs and all trees at the middle and lower crown layers were removed, and Needle firs at the upper crown layer showed very weak growth strength or to be withering to death. The results of spatial autocorrelation using 31 polymorphic ISSR markers revealed that it was genetically homogeneous within spatial distance of 15.6m and the randomness of genetic distribution was from 15.6m to 31.2m. The genetic patch size of seedlings in forest gap might be restricted by the density of mother trees, making allow for the average height of adult Needle firs, the seed dispersal area, and the average distance between adults. For the directionality of seedling distribution, we investigated the variography using 'genetic configuration' which was the value of configuration in Multidimensional Scaling by genetic distance. In directional variogram, the increment of spatial distance from East to West direction was inversely proportional to genetic homogeneity. We presumed that this anisotrophy of seedling distribution at this forest gap resulted from the directionality of seed dispersal rather than the difference of fecundity between mother trees or the microhabitat variation, taking the evenness of forest floor condition, a vast seed production and the random distribution of seedlings at the studied site into consideration.

• The Journal of the Petrological Society of Korea
• /
• v.17 no.2
• /
• pp.57-82
• /
• 2008

The volcanic sequence of the late Cretaceous Moonyu volcanic mass which distributed in the southwestern part of Ryeongnam massif, can be divided into felsic pyroclastic rocks, andesite and andesitic pyroclastic rocks, rhyolite in ascending order. The earliest volcanic activity might commence with intermittent eruptions of felsic magma during deposition of volcaniclastic sediments. Explosive eruptions of felsic pyroclastic rocks began with ash-falls, to progressed through pumice-falls and transmitted with dacitic to rhyolitic ash-flows. Subsequent andesite and andesitic pyroclastic rocks were erupted and finally rhyolite was intruded as lava domes along the fractures near the center of volcanic mass. Petrochemical data show that these rocks are calc-alkaline series and have close petrotectonic affinities with subduction-related continental margin arc volcanic province. Major element compositions range from medium-K to high-K. Petrochemical variation within the volcanic sequence can be largely accounted for tractional crystallization processes with subordinate mixing. The most mafic rocks are basaltic andesite, but low MgO and Ni contents indicate they are fractionated by fractional crystallization from earlier primary mafic magma, which derived from less than 20% partial melting of ultramafic rocks in upper mantle wedge. Based on the stratigraphy, the early volcanic rocks are zoned from lower felsic to upper andesitic in composition. The compositional zonation of magma chamber from upper felsic to lower andesitic, is interpreted to have resulted from fractionation within the chamber and replenishment by an influx of new mafic magma from depth. Replenishment and mixing is based on observations of disequilibrium phenocrysts in volcanic rocks. REE patterns show slight enrichment of LREE with differentiation from andesite to rhyolite. Rhyolite in the final stage can be derived from calc-alkaline andesite magma by fractional crystallization, but it might have underwent crustal contamination during the fractional crystallization.

• Korean Journal of Poultry Science
• /
• v.40 no.2
• /
• pp.139-145
• /
• 2013

There are several loci controlling the feather color of birds, of which one of the most studied is Extended black (E) encoding the melanocortin 1-receptor (MC1R). Mutations in this gene affect the relative distribution of eumelanin, phaeomelanin. The association of feather color and sequence polymorphism in the melanocortin 1-receptor (MC1R) gene was investigated using Korean native chicken H breed (H_PL) and 'Woorimatdag' commercial chickens (Woorimatdag_CC). In order to correlate gene mutation to Korean native chicken feather color, single nucleotide polymorphism (SNP) from MC1R gene sequence were investigated. A total of 307 birds from H_PL and Woorimatdag_CC were used. H_PL have black, black-brown feather color and Woorimatdag_CC have black with brown spots or brown with black spots. There are 6 SNPs in MC1R gene, locus T69C, C212T, A274G, G376A, G636A, T637C. 3 SNPs are nonsynonymous that change amino acid. But it is difficult to find correlation of feather color and polymorphisms. It will be needed to increase the population of Korean native chicken H breed and correlation analysis of genetic variation with feather colors.

• Journal of Life Science
• /
• v.18 no.12
• /
• pp.1733-1738
• /
• 2008

SLC6A18, one of the neurotransmitters, was reported the possible relationship to hypertension, and it contained eight blocks of minisatellites. In this study, SLC6A18-MS5 sequence which showed the highest heterozygosity among seven minisatellites was analyzed using the Transfac software, the putative binding sites for the transcription factor Pax4 and HNF4 were discovered as a result. The HNF4 is involved in the diabetes pathway and suggested the relationship to hypertension. Thus, we investigated the putative functional significance of allelic variation in this minisatellites with respect to susceptibility for hypertension. To address this possibility, we analyzed genomic DNA from the blood of 301 hypertension-free controls and 184 cases with hypertension. A statistically significant association was not identified between the allelic distribution of SLC6A18-MS5 and occurrence of hypertension. We then examined the meiotic segregation of SLC6A18-MS5 and it was transmitted following Mendelian inheritance. Therefore, this locus could be useful markers for paternity mapping and DNA fingerprinting. Moreover, we undertook a comprehensive analysis of the genomic sequence to address the evolutionary events of these variable repeats. SLC6A18 minisatellites regions are only conserved in human and primates. This result suggestedthat intronic minisatellites analysis is powerful evolution marker for the non-coding regions in primates and can provide a great insight to the molecular evolution of repeated region in primates.

• Tuberculosis and Respiratory Diseases
• /
• v.50 no.2
• /
• pp.213-221
• /
• 2001

Background : There is a well recognized interlaboratory variation in the results using the polymerase chain reaction(PCR) to detect the IS6110 sequence. The clinical utility of a commercially developed PCR test(Amplicor) in bronchial washings for detecting pulmonary tuberculosis in smear negative patients was evaluated. The sensitivity and specificity of Amplicor was compared with that of an in-house PCR test used for detecting the IS6110 sequence of Mycobacterium tuberculosis(M.tbc) in the bronchial washing fluid. Methods : 66 patients whose sputum smear for M. tbc were negative or who could not produce any sputum were recruited from January 1999 to July 1999. They all had a bronchoscopy performed to determine if there were signs of hemoptysis, patients who could not cough up sputum, lung lesion that exclude pulmonary tuberculosis. Pulmonary tuberculosis was diagnosed on the basis of a positive culture or a response to anti-tuberculosis therapy. Results : 19 patients with tuberculosis were identified and samples from 16 patients were later confirmed by culture. Bronchial washing for Amplicor PCR revealed a sensitivity, specificity, positive and negative predictive values of 94.7%, 97.9%, 94.7%, 97.9%, respectively. Using IS6110 based PCR, the sensitivity, specificity, positive and negative predictive values were of 73.7%, 87.2%, 70%, 89.1% respectively. Conclusion : Bronchial washing for Amplicor PCR proved to be more useful than IS6110 based PCR in rapidly diagnosing smear negative pulmonary pulmoary tuberculosis in patients where tuberculosis was likely to be differential and rapid diagnosis was essential for optimal treatment.

• 한국균학회소식:학술대회논문집
• /
• 2015.05a
• /
• pp.53-53
• /
• 2015

Agrobacterium tumefaciens-mediated transformation(ATMT) of Flammulina velutipes was used to produce a diverse number of transformants to discover the functions of gene that is vital for its variation color, spore pattern and cellulolytic activity. Futhermore, the transformant pool will be used as a good genetic resource for studying gene functions. Agrobacterium-mediated transformation was conducted in order to generate intentional mutants of F. velutipes strain KACC42777. Then Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into F. velutipes. This method is use to determine the functional gene of F. velutipes. Inverse PCR was used to insert T-DNA into the tagged chromosomal DNA segments and conducting sequence analysis of the F. velutipes. But this experiment had trouble in diverse morphological mutants because of dikaryotic nature of mushroom. It needed to make monokaryotic fruiting varients which introduced genes of compatible mating types. In this study, next generation sequencing data was generated from 28 strains of Flammulina velutipes with different phenotypes using Illumina Hiseq platform. Filtered short reads were initially aligned to the reference genome (KACC42780) to construct a SNP matrix. And then we built a phylogenetic tree based on the validated SNPs. The inferred tree represented that white- and brown- fruitbody forming strains were generally separated although three brown strains, 4103, 4028, and 4195, were grouped with white ones. This topological relationship was consistently reappeared even when we used randomly selected SNPs. Group I containing 4062, 4148, and 4195 strains and group II containing 4188, 4190, and 4194 strains formed early-divergent lineages with robust nodal supports, suggesting that they are independent groups from the members in main clades. To elucidate the distinction between white-fruitbody forming strains isolated from Korea and Japan, phylogenetic analysis was performed using their SNP data with group I members as outgroup. However, no significant genetic variation was noticed in this study. A total of 28 strains of Flammulina velutipes were analyzed to identify the genomic regions responsible for producing white-fruiting body. NGS data was yielded by using Illumina Hiseq platform. Short reads were filtered by quality score and read length were mapped on the reference genome (KACC42780). Between the white- and brown fruitbody forming strains. There is a high possibility that SNPs can be detected among the white strains as homozygous because white phenotype is recessive in F. velutipes. Thus, we constructed SNP matrix within 8 white strains. SNPs discovered between mono3 and mono19, the parental monokaryotic strains of 4210 strain (white), were excluded from the candidate. If the genotypes of SNPs detected between white and brown strains were identical with those in mono3 and mono19 strains, they were included in candidate as a priority. As a result, if more than 5 candidates SNPs were localized in single gene, we regarded as they are possibly related to the white color. In F. velutipes genome, chr01, chr04, chr07,chr11 regions were identified to be associated with white fruitbody forming. White and Brown Fruitbody strains can be used as an identification marker for F. veluipes. We can develop some molecular markers to identify colored strains and discriminate national white varieties against Japanese ones.

• Korean Journal of Environment and Ecology
• /
• v.31 no.4
• /
• pp.349-364
• /
• 2017

Duckweed family (Lemnaceae Martinov), including the genus Lemna L., is a typical floating aquatic perennial plant, and about five genera and 40 species in the family are in wide distribution around the world except the polar regions. The genus Lemna is the smallest and the simplest plant among the angiosperms. It has a characteristic of doubling every three days with fast vegetative propagation, which helps the organisms to increase in rapid growth. As such, the plant is ideal for environmental pollution assessment and toxicity test. Although taxonomists and scholars have used different scientific names for the species, many of them have agreed that there is only one member of species of the genus Lemna in Korea. Paying attention to the external morphological variation observed in the Korean genus Lemna, we conducted a molecular phylogenetic analysis to identify the entity of the Korean Lemna species and to investigate the possibility of two or more members of the species existing in Korea. We determined and aligned the DNA sequences of the atpF-H region of the chloroplast DNA in 37 populations of the nationally distributed Lemna species. The results showed that the sequence length of the cp DNA atpF-H region was 463-483 bp, the length of the aligned sequences was 488 bp, and the number of variation site in nucleotide sequences was 47. There were two types of aligned sequences of the cp DNA atpF-H region from 37 populations of Lemna species in Korea. The maximum parsimony analysis revealed that the Korean Lemna consists of two clades, and one of them had two subclades. The results suggest that, contrary to the general understanding, at least two taxa (L.aequinoctialis, L.minor) exist in Korea.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.61 no.3
• /
• pp.171-183
• /
• 2016

The effects of weather variations on winter hulless barley were analyzed using data obtained from winter crop situation test at Iksan from 1985 to 2015. The wintering stage in the 16 years from 2000 to 2015 has become colder and shorter than that in the previous 15 years from 1985 to 1999. This has resulted in an early sequence of regrowth date, heading date, and ripening date. Heading date of hulless barley was mostly influenced by regrowth date and period of stem elongation. Futher, the regrowth date and period of stem elongation were strongly negatively correlated with the average air temperature in February and the maximum air temperature in March, respectively. The number of spikes per $m^2$ and 1000-grain weight of Saechalssal cultivated from 2003 to 2015 showed strong positive correlations with yield. In early heading years, yield increased with extended ripening period and with increased 1000-grain weight. There was a strong negative correlation between 1000-grain weight and the average temperature during the ripening period. In the 15 years from 1985 to 1999, warm winters contributed to yield increase with increase in the number of spikes per $m^2$ and a long ripening period. In contrast, in the recent 16 years from 2000 to 2015, the large variability in air temperature during the wintering stage, the decreasing number of spikes per $m^2$ and the steadily increasing air temperature and decreasing precipitation during the ripening stage have caused high temperature stress and yield loss in late heading years.