• Clinical and Experimental Reproductive Medicine
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• v.45 no.4
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• pp.170-176
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• 2018

Objective: To assess whether the "testicular pool" could be used for histological analysis and whether it gave more accurate information than the standard testicular biopsy. Methods: Between January 2017 and March 2018, this single-center prospective study included 60 azoospermic men undergoing conventional bilateral testicular sperm extraction. Six samples were excised from each testicle and transferred to an embryologist. One additional biopsy was randomly taken from each testis for a histological analysis. After processing, the testicular pool was also sent for a histological analysis, which showed normal spermatogenesis (NS), hypospermatogenesis (HYPO), maturation arrest (MA), Sertoli cell-only syndrome (SCOS), and tubular atrophy (TA). Results: Twenty of the 60 patients (33.3%) had obstructive azoospermia (OA), while the remaining 40 (66.6%) had nonobstructive azoospermia. Their mean age was 40.5 years. All patients with OA had previously undergone unsuccessful testicular fine-needle aspiration. Successful sperm retrieval (SSR) occurred in 93.3% of patients. Histological analysis of the testicular biopsy revealed NS in 12 patients (20%), HYPO and TA in 28 patients (46.6%), MA in eight patients (13.3%), and SCOS in 12 patients (20%). The testicular pool analysis showed NS in 12 patients (20%), HYPO and TA in 44 patients (73.3%), MA in four patients (6.6%), and SCOS in no patients. In four patients with MA (6.6% of the total sample) and 12 patients with SCOS (20% of the total sample) according to the standard testicular biopsy, the embryologist found SSR with cryopreservation. Overall, in 44 patients (73.3%), the testicular pool analysis confirmed the histological findings of the standard testicular biopsy. In the 16 cases (26.6%) with a discrepancy between the single-biopsy histological findings and SSR, the testicular pool analysis confirmed the embryological data on SSR. Conclusion: The testicular pool proved to be easily analyzable, practical, manageable, and more accurate for predicting sperm retrieval than standard testicular biopsy.

• Nutrition Research and Practice
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• v.15 no.5
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• pp.604-612
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• 2021

BACKGROUND/OBJECTIVES: We aimed to investigate the association of waist circumference (WC) with body composition among individuals with a normal body mass index (BMI) to distinguish muscle and fat mass, as both affect health differently. SUBJECTS/METHODS: We analyzed dual-energy X-ray absorptiometry data (derived from the Korean National Health and Nutrition Survey, which includes information on fat and lean mass) of 7,493 adults with a normal BMI. Subjects were categorized into four groups of increasing WC. The fourth group was defined as being centrally obese. Each number of subjects are as follows: 1,870, 695, 231, and 39 among men and 3,054, 1,100, 406, and 98 among women. We conducted a sex-stratified linear regression analysis of body composition according to WC group after adjustments for covariates. RESULTS: We observed a positive association of body fat with increasing WC in both men and women (all P for trend: < 0.001). The adjusted mean values for percent body fat with 95% confidence intervals (CIs) according to the four WC groups in ascending order were 17.8 (17.5-18.3), 21.0 (20.6-21.5), 22.1 (21.5-22.8), and 25.1 (24.2-26.1) in men and 29.7 (29.4-30.0), 32.0 (31.6-32.3), 32.9 (32.4-33.4), and 34.7 (33.2-36.1) in women. However, there was an inverted J-shaped association between muscle mass and WC. The fourth group had a higher percent body fat and lower muscle mass than other groups. The adjusted mean values for appendicular skeletal muscle mass index (kg/m²) with 95% CIs according to the four WC groups in ascending order were 7.55 (7.51-7.59), 7.62 (7.56-7.68), 7.65 (7.56-7.74), and 7.22 (7.04-7.41) in men and 5.83 (5.80-5.85), 5.96 (5.92-6.00), 6.03 (5.96-6.10), and 5.88 (5.73-6.03). CONCLUSIONS: There was a positive association between body fat and WC among individuals with normal BMI; conversely there was an inverted J-shaped association between lean body mass and WC. Our findings support the WC measurement should be included in obesity evaluations for adults with a normal BMI.

• Journal of radiological science and technology
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• v.44 no.2
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• pp.91-100
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• 2021

High-Resolution thoracic CT (HRCT) is a scanning protocol in which thin slice thickness and sharpness algorithm are utilized to enhance image resolution for diagnosis and assessment of interstitial lung disease (ILD). This examination is sometimes performed in both supine and prone position to improve sensitivity to early changes of these conditions. Anatomical structures (the size of lung field and heart and descending aorta) of 150 patients who underwent HRCT were retrospectively compared. HRCT had been conducted in two positions (supine and prone). Data were divided into five groups according to patient body weights (from 40 to more than 80kg, 10kg intervals, 60 patients/each group). Quantitative analysis was utilized in Image J program. In the supine position defined as the control group, the average values of lung fields and heart size and aorta were compared with the prone position defined as the experimental group. The size of the lungs was found to be higher in the supine position, and it was confirmed that there was a statistically significant difference in patients over 70 kg (p<0.05). In addition, both sizes of the heart and descending aorta were larger in prone position, but in the case of the heart, there was no correlation with the presence or absence of ILD disease (p>0.05). Also, the area of prone in the descending aorta was higher than supine position, but there was no statistically significant difference between supine and prone position (p>0.05). In conclusion, when the severity of ILD disease was severe, there was no statistically significant difference in the area difference between supine and prone position, so it is considered that it will be helpful in diagnostic decision.

• Journal of Gastric Cancer
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• v.21 no.2
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• pp.191-202
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• 2021

Purpose: A near-infrared (NIR) fluorescence imaging is a promising tool for cancer-specific image guided surgery. Human epidermal receptor 2 (HER2) is one of the candidate markers for gastric cancer. In this study, we aimed to synthesize HER2-specific NIR fluorescence probes and evaluate their applicability in cancer-specific image-guided surgeries using an animal model. Materials and Methods: An NIR dye emitting light at 800 nm (IRDye800CW; Li-COR) was conjugated to trastuzumab and an HER2-specific affibody using a click mechanism. HER2 affinity was assessed using surface plasmon resonance. Gastric cancer cell lines (NCI-N87 and SNU-601) were subcutaneously implanted into female BALB/c nu (6-8 weeks old) mice. After intravenous injection of the probes, biodistribution and fluorescence signal intensity were measured using Lumina II (Perkin Elmer) and a laparoscopic NIR camera (InTheSmart). Results: Trastuzumab-IRDye800CW exhibited high affinity for HER2 (K_D=2.093(3) pM). Fluorescence signals in the liver and spleen were the highest at 24 hours post injection, while the signal in HER2-positive tumor cells increased until 72 hours, as assessed using the Lumina II system. The signal corresponding to the tumor was visually identified and clearly differentiated from the liver after 72 hours using a laparoscopic NIR camera. Affibody-IRDye800CW also exhibited high affinity for HER2 (K_D=4.71 nM); however, the signal was not identified in the tumor, probably owing to rapid renal clearance. Conclusions: Trastuzumab-IRDye800CW may be used as a potential NIR probe that can be injected 2-3 days before surgery to obtain high HER2-specific signal and contrast. Affibody-based NIR probes may require modifications to enhance mobilization to the tumor site.

• Journal of Life Science
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• v.31 no.6
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• pp.568-573
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• 2021

This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.

• Journal of Biomedical Engineering Research
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• v.43 no.5
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• pp.341-352
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• 2022

Medical image segmentation is the most important task in radiation therapy. Especially, when segmenting medical images, the liver is one of the most difficult organs to segment because it has various shapes and is close to other organs. Therefore, automatic segmentation of the liver in computed tomography (CT) images is a difficult task. Since tumors also have low contrast in surrounding tissues, and the shape, location, size, and number of tumors vary from patient to patient, accurate tumor segmentation takes a long time. In this study, we propose a method algorithm for automatically segmenting the liver and tumor for this purpose. As an advantage of setting the boundaries of the tumor, the liver and tumor were automatically segmented from the CT image using the 2D CoordConv DeepLab V3+ model using the CoordConv layer. For tumors, only cropped liver images were used to improve accuracy. Additionally, to increase the segmentation accuracy, augmentation, preprocess, loss function, and hyperparameter were used to find optimal values. We compared the CoordConv DeepLab v3+ model using the CoordConv layer and the DeepLab V3+ model without the CoordConv layer to determine whether they affected the segmentation accuracy. The data sets used included 131 hepatic tumor segmentation (LiTS) challenge data sets (100 train sets, 16 validation sets, and 15 test sets). Additional learned data were tested using 15 clinical data from Seoul St. Mary's Hospital. The evaluation was compared with the study results learned with a two-dimensional deep learning-based model. Dice values without the CoordConv layer achieved 0.965 ± 0.01 for liver segmentation and 0.925 ± 0.04 for tumor segmentation using the LiTS data set. Results from the clinical data set achieved 0.927 ± 0.02 for liver division and 0.903 ± 0.05 for tumor division. The dice values using the CoordConv layer achieved 0.989 ± 0.02 for liver segmentation and 0.937 ± 0.07 for tumor segmentation using the LiTS data set. Results from the clinical data set achieved 0.944 ± 0.02 for liver division and 0.916 ± 0.18 for tumor division. The use of CoordConv layers improves the segmentation accuracy. The highest of the most recently published values were 0.960 and 0.749 for liver and tumor division, respectively. However, better performance was achieved with 0.989 and 0.937 results for liver and tumor, which would have been used with the algorithm proposed in this study. The algorithm proposed in this study can play a useful role in treatment planning by improving contouring accuracy and reducing time when segmentation evaluation of liver and tumor is performed. And accurate identification of liver anatomy in medical imaging applications, such as surgical planning, as well as radiotherapy, which can leverage the findings of this study, can help clinical evaluation of the risks and benefits of liver intervention.

• Journal of Preventive Medicine and Public Health
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• v.55 no.5
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• pp.464-474
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• 2022

Objectives: We introduced the cohort studies included in the Korean Cohort Consortium (KCC), focusing on large-scale cohort studies established in Korea with a prolonged follow-up period. Moreover, we also provided projections of the follow-up and estimates of the sample size that would be necessary for big-data analyses based on pooling established cohort studies, including population-based genomic studies. Methods: We mainly focused on the characteristics of individual cohort studies from the KCC. We developed "PROFAN", a Shiny application for projecting the follow-up period to achieve a certain number of cases when pooling established cohort studies. As examples, we projected the follow-up periods for 5000 cases of gastric cancer, 2500 cases of prostate and breast cancer, and 500 cases of non-Hodgkin lymphoma. The sample sizes for sequencing-based analyses based on a 1:1 case-control study were also calculated. Results: The KCC consisted of 8 individual cohort studies, of which 3 were community-based and 5 were health screening-based cohorts. The population-based cohort studies were mainly organized by Korean government agencies and research institutes. The projected follow-up period was at least 10 years to achieve 5000 cases based on a cohort of 0.5 million participants. The mean of the minimum to maximum sample sizes for performing sequencing analyses was 5917-72 102. Conclusions: We propose an approach to establish a large-scale consortium based on the standardization and harmonization of existing cohort studies to obtain adequate statistical power with a sufficient sample size to analyze high-risk groups or rare cancer subtypes.

• Genomics & Informatics
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• v.20 no.2
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• pp.21.1-21.14
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• 2022

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

• Wind and Structures
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• v.35 no.1
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• pp.1-20
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• 2022

This research work presents an experimental study's outcomes to reveal the impact of an O-ring on the flow control over a sphere placed in a turbulent boundary layer. The investigation is performed quantitatively and qualitatively using particle image velocimetry (PIV) and dye visualization. The sphere model having a diamater of 42.5 mm is located in a turbulent boundary layer flow over a smooth plate for gap ratios of 0≤G/D≤1.5 at Reynolds number of 5 × 10³. Flow characteristics, including patterns of instantaneous vorticity, streaklines, time-averaged streamlines, velocity vectors, velocity fluctuations, Reynolds stress correlations, and turbulence kinetic energy (), are compared and discussed for a naked sphere and spheres having O-rings. The boundary layer velocity gradient and proximity of the sphere to the flat plate profoundly influence the flow dynamics. At proximity ratios of G/D=0.1 and 0.25, a wall jet is formed between lower side of the sphere and flat plate, and velocity fluctuations increase in regions close to the wall. At G/D=0.25, the jet flow also induces local flow separations on the flat plate. At higher proximity ratios, the velocity gradient of the boundary layer causes asymmetries in the mean flow characteristics and turbulence values in the wake region. It is observed that the O-ring with various placement angles (𝜃) on the sphere has a considerable alteration in the flow structure and turbulence statistics on the wake. At lower placement angles, where the O-ring is closer to the forward stagnation point of the sphere, the flow control performance of the O-ring is limited; however, its impact on the flow separation becomes pronounced as it is moved away from the forward stagnation point. At G/D=1.50 for O-ring diameters of 4.7 (2 mm) and 7 (3 mm) percent of the sphere diameter, the -ring exhibits remarkable flow control at 𝜃=50° and 𝜃=55° before laminar flow separation occurrence on the sphere surface, respectively. This conclusion is yielded from narrowed wakes and reductions in turbulence statistics compared to the naked sphere model. The O-ring with a diameter of 3 mm and placement angle of 50° exhibits the most effective flow control. It decreases, in sequence, streamwise velocity fluctuations and length of wake recovery region by 45% and 40%, respectively, which can be evaluated as source of decrement in drag force.

• Animal Bioscience
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• v.36 no.1
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• pp.29-42
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• 2023

Objective: Pigs, an ideal biomedical model for human diseases, suffer from about 50% early embryonic and fetal death, a major cause of fertility loss worldwide. However, identifying the causal variant remains a huge challenge. This study aimed to detect single nucleotide polymorphisms (SNPs) and candidate genes for the number of mummified (NM) piglets using the imputed whole-genome sequence (WGS) and validate the potential candidate genes. Methods: The imputed WGS was introduced from genotyping-by-sequencing (GBS) using a multi-breed reference population. We performed genome-wide association studies (GWAS) for NM piglets at birth from a Landrace pig populatiGWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase on. A total of 300 Landrace pigs were genotyped by GBS. The whole-genome variants were imputed, and 4,252,858 SNPs were obtained. Various molecular experiments were conducted to determine how the genes affected NM in pigs. Results: A strong GWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase 8 (CDK8) gene, which plays a crucial role in embryonic retardation and lethality. Based on the molecular experiments, we found that Y-box binding protein 1 (YBX1) was a crucial transcription factor for CDK8, which mediated the effect of CDK8 in the proliferation of porcine ovarian granulosa cells via transforming growth factor beta/small mother against decapentaplegic signaling pathway, and, as a consequence, affected embryo quality, indicating that this pathway may be contributing to mummified fetal in pigs. Conclusion: A powerful imputation-based association study was performed to identify genes associated with NM in pigs. CDK8 was suggested as a functional gene for the proliferation of porcine ovarian granulosa cells, but further studies are required to determine causative mutations and the effect of loci on NM in pigs.