• Korean Journal of Ecology and Environment
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• v.42 no.2
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• pp.221-231
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• 2009

This study was carried out to comparatively identify characteristics of turbid water influence in Imha Reservoir, Soyang Reservoir, and Daecheong Reservoir in Korea. We used 3 years dataset from 2002 to 2004 and analyzed seasonal water quality characteristics, particular parameters in association with turbidity, and light transparency to figure out the trends. All parameters to be used in the study were total phosphate (TP), total nitrogen (TN), chlorophyll-${\alpha}$ (Chl), suspended solids (SS), Secchi depth (SD), conductivity, and verticallight extinction coefficienct($K_d$), euphotic zone ($Z_{eu}$), and critical depth ($Z_p$). All parameters depend on season and watershed. Suspended solids from Soyang Reservoir were usually caused by TP, mainly related to living wastes and agricultures in upper stream. Daecheong Reservoir was influenced by organic matters related to large phytoplankton biomass in summer and inorganic suspended solids by nutrients in the winter. However, in case of Imha Reservoir, turbid water, consisted in silt and clay through heavy precipitation remained in the waterbody to decrease water transparency along with TP and caused the light limitation in winter. Overall results suggest that it was necessary to establish various management programs because the reasons occurring turbidity were varied according to the reservoir circumstances.

• Journal of Biomedical Engineering Research
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• v.24 no.5
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• pp.465-471
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• 2003

The purpose of this research was to evaluate chronic stress using physiological parameters. Wistar rats were exposed to the sound stress for 14 days. Biosignals were acquired hourly. To develop a fuzzy inference system which can integrate physiological parameters. the parameters of the system were adjusted by the adaptive neuro-fuzzy inference system. Of the training dataset, input dataset was the physiological parameters from the biosignals and output dataset was the target values from the cortisol production. Physiological parameters were integrated using the fuzzy inference system. then 24-hour results were analyzed by the Cosinor method. Chronic stress was evaluated from the degree of circadian rhythm disturbance. Suppose that the degree of stress for initial rest period is 1. Then. the degree of stress after 14-day sound stress increased to 1.37, and increased to 1.47 after the 7-day recovery period. That is, the rat was exposed to 37%-increased amount of stress by the 14-day sound and did not recover after the 7-day recovery period.

• Journal of Biomedical Engineering Research
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• v.43 no.4
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• pp.290-297
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• 2022

During surgery, Surgical instruments are often left behind due to accidents. Most of these are surgical gauze, so radioactive non-permeable gauze (X-ray gauze) is used for preventing of accidents which gauze is left in the body. This gauze is divided into wire and pad type. If it is confirmed that the gauze remains in the body, gauze must be detected by radiologist's reading by imaging using a mobile X-ray device. But most of operating rooms are not equipped with a mobile X-ray device, but equipped C-Arm equipment, which is of poorer quality than mobile X-ray equipment and furthermore it takes time to read them. In this study, Use C-Arm equipment to acquire gauze image for detection and Build dataset using artificial intelligence and select a detection model to Assist with the relatively low image quality and the reading of radiology specialists. mAP@50 and detection time are used as indicators for performance evaluation. The result is that two-class gauze detection dataset is more accurate and YOLOv5 model mAP@50 is 93.4% and detection time is 11.7 ms.

• Genomics & Informatics
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• v.21 no.3
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• pp.40.1-40.11
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• 2023

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

• Genomics & Informatics
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• v.16 no.4
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• pp.34.1-34.9
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• 2018

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves, and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.

• Korean Journal of Ecology and Environment
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• v.42 no.2
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• pp.242-252
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• 2009

The purpose of this study was to develop a Multi-metric Water Quality Assessment (MWQA) model and apply it to dataset sampled from Paldang and Daechung reservoir in 2008. The various water dataset used to this study included 5 year data sets (2003${\sim}$2007) in Korean reservoirs which were obtained from the Ministry of Environment, Korea. In this study, suggested MWQA model has 4 metrics that were composed of 4 parameters such as chemical, physical, biological, and hydrological variables. And, each of the variables attributed total phosphorus (TP) concentration in water, secchi depth (SD) measure in water, chlorophyll-${\alpha}$(Chl-${\alpha}$) concentration in water and the ratio of inflow of water into lakes and efflux of water from lakes, input/output (I/O). First, we established the criteria for trophic boundaries. The boundary between oligotrophic and mesotrophic categories was defined by the lower third of the cumulative distribution of the values. The mesotrophic-eutrophic boundary was defined by the upper third of the distribution. Second, each metric was given by a point-oligo=1, meso=3, eu=5. And then, obtained total score from each metric was divided 5 grade-Excellent, Good, Fair, Poor, and Very poor. As the results of applying the proposed MWQA model, the Paldang reservoir obtained "Fair" or "Poor" grade and Daechung reservoir obtained "Excellent" or "Good" grade. The suggested MWQA model through these procedures will enable to manage efficiently the reservoir. And, more studies such as metric numbers and attributes should be done for the accurate application of the new model.

• Journal of Ecology and Environment
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• v.39 no.1
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• pp.31-42
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• 2016

The object of this study was to determine long-term temporal and spatial patterns of nutrients (nitrogen and phosphorus), suspended solids, and chlorophyll (Chl) in Chungju Reservoir, based on the dataset of 1992 - 2013, and then to develop the empirical models of nutrient-Chl for predicting the eutrophication of the reservoir. Concentrations of total nitrogen (TN) and total phosphorus (TP) were largely affected by an intensity of Asian monsoon and the longitudinal structure of riverine (Rz), transition (Tz), and lacustrine zone (Lz). This system was nitrogen-rich system and phosphorus contents in the water were relatively low, implying a P-limiting system. Regression analysis for empirical model, however, showed that Chl had a weak linear relation with TP or TN, and this was mainly associated with turbid, and nutrient-rich inflows in the system. The weak relation was associated with non-algal light attenuation coefficients (Kna), which is inversely related water residence time. Thus, values of Chl had negative functional relation (R² = 0.25, p < 0.001) with nonalgal light attenuation. Thus, the low chlorophyll at a given TP indicated a light-limiting for phytoplankton growth and total suspended solids (TSS) was highly correlated (R² = 0.94, p < 0.001) with non-algal light attenuation. The relations of Trophic State Index (TSI) indicated that phosphorus limitation was weak [TSI (Chl) - TSI (TP) < 0; TSI (SD) - TSI (Chl) > 0] and the effects of zooplankton grazing were also minor [TSI (Chl) - TSI (TP) > 0; TSI (SD) - TSI (Chl) > 0].

• Genomics & Informatics
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• v.7 no.2
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• pp.122-130
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• 2009

A systems biology approach for the identification of perturbed molecular functions is required to understand the complex progressive disease such as breast cancer. In this study, we analyze the microarray data with Gene Ontology terms of molecular functions to select perturbed molecular functional modules in breast cancer tissues based on the definition of Gene ontology Functional Code. The Gene Ontology is three structured vocabularies describing genes and its products in terms of their associated biological processes, cellular components and molecular functions. The Gene Ontology is hierarchically classified as a directed acyclic graph. However, it is difficult to visualize Gene Ontology as a directed tree since a Gene Ontology term may have more than one parent by providing multiple paths from the root. Therefore, we applied the definition of Gene Ontology codes by defining one or more GO code(s) to each GO term to visualize the hierarchical classification of GO terms as a network. The selected molecular functions could be considered as perturbed molecular functional modules that putatively contributes to the progression of disease. We evaluated the method by analyzing microarray dataset of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Based on the integration approach, we selected several interesting perturbed molecular functions that are implicated in the progression of breast cancers. Moreover, these selected molecular functions include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting perturbed molecular functions that putatively play roles in the progression of diseases and provides an improved interpretability of GO terms based on the definition of Gene Ontology codes.

• Journal of Korean Biological Nursing Science
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• v.20 no.3
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• pp.169-176
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• 2018

Purpose: This study was performed to elucidate whether the obesity or body image is a barrier to breast screening compliance in Korean women. Methods: We included 54,017 women aged between 35 to 70 years from the Korea Community Health Survey (KCHS) 2014 dataset. To identify whether a mutual relationship exists between weight perceptions and breast cancer screening rates, the participants were divided into three groups according to the level of concordance between Body Mass Index (BMI) and a subjective body image. Descriptive analyses, a chi-square test, and multivariate logistic regression analyses were performed. Results: After covariate adjustment, the screening rate of the overweight group was 1.09 times higher than the normal weight group (odds ratio [OR], 1.09; confidence interval [CI], 0.00-0.16; p= .038) and the severe obesity group was 1.20 times lower (OR, 0.83; CI, -0.36-0.00; p= .047). Weight misperception also had a significant influence on breast cancer screening. Especially, The overweight distortion group was less likely to undergo breast cancer screening (OR, 0.93; CI, -0.15-0.00; p= .037). Conclusion: Obesity and weight misperceptions are associated with lower compliance with breast cancer screening guidelines.

• Molecules and Cells
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• v.21 no.1
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• pp.89-103
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• 2006

Population structure was investigated in Reticulitermes speratus populations in the Korean Peninsula and the Japanese Archipelago. All trees derived from analyses of the combined sequence dataset of two mitochondrial genes, COII and COIII, showed that R. speratus populations cluster into two major clades comprising the Korean/southern Japanese populations and the northern Japanese populations. Analysis of population genetic structure showed strong genetic partitioning between populations of the two clades. To understand historical migration routes and current distributions, the phylogeographic history of R. speratus was inferred from intra-/interspecific phylogeny and divergence times estimated between the clades of the phylogenetic tree. The estimated migration route and divergence time of ancestral R. speratus are congruent with recent paleogeographic hypotheses involving land-bridge connections between the Asian continent and the Japanese Archipelago. We suggest that ancestral R. speratus separated into northern and southern Japanese populations after its migration into the Japanese main islands from East China during the early Pleistocene via the East China Sea basin, which may have been exposed during that period. The Korean populations seem to have diverged recently from southern Japanese populations; this may explain the current distribution of R. speratus in the Japanese Arachipelago, and account for why it is restricted to northern areas of the Tokara Strait.