On the Supply of Superior Order-1 Building Blocks for a Class of Periodical Fitness Functions

Mo, Hongqiang,Li, Zhong,Park, JinBae,Joo, YoungHoon Informa UK (Taylor Francis) 2009 International journal of computational intelligenc Vol.2 No.1

Discovery of C2 Swan Band and CN emission in Spark Discharge Experiment

In-Ok Song,Younghoon Mo,Jein Ryu,Hoyon Chang,Ki-Wook Hwang,Man-Seog Chun,Jinho Oh,Sangjoon Hahn 한국천문학회 2021 天文學會報 Vol.46 No.2

LSTM 기반 딥러닝 기법을 이용한 섬진강 구례교 지점의 홍수위 예측

정재원(Jung, Jaewon),모혜림(Mo, Hyelim),이준형(Lee, Junhyeong),유영훈(Yoo, Younghoon),김형수(Kim, Hung Soo) 한국방재학회 2021 한국방재학회논문집 Vol.21 No.3

기후변화와 기후변동으로 인한 극한 호우의 발생으로 홍수 피해는 증가하는 추세에 있다. 특히, 인명 손실을 포함한 하천홍수 피해 저감을 위해 비구조적 방법인 홍수예경보시스템은 매우 중요하게 인식되고 있으며, 홍수예경보는 물리적 모형인 강우-유출 모형에 의한 홍수량 및 홍수위 예측을 통해 이루어져 왔다. 그러나 최근에는 기존 물리적 기반의 홍수위 예측 모형의 단점을 보완한 머신러닝 기반의 홍수위 예측 모형을 적용한 연구들이 진행되고 있으나 다양한 사례에 대한 적용 연구가 지속적으로 필요한 실정이다. 따라서 본 연구에서는 Long Short-Term Memory (LSTM) 기반의 딥러닝 기법을 적용하여 섬진강 수계 구례 지점의 하천 수위를 1, 3, 6시간 선행 예측하고, 선행 예측 시간에 따른 예측 정확도를 비교 분석하고자 한다. 또한 기존의 서포트벡터머신(SVM) 모형, 다층퍼셉트론(MLP) 모형을 적용한 결과와의 비교 분석을 통해 LSTM 모형의 적용성을 평가하고자 하였다. 평가 결과, LSTM 모형이 다른 모형 보다 우수한 예측 성능을 보이고 있음을 알 수 있었으며, 향후 홍수 예측을 위해 LSTM 모형의 적용성을 보다 심층적으로 연구할 필요가 있다. Instances of flood damage caused by extreme storm rainfall due to climate change and variability have been showing an increasing trend. Particularly, a flood forecasting and warning system has been recognized as an important nonstructural measure for flood damage reduction, including loss of life. Flood forecasting and warning have been performed by the forecasts of flood discharge and flood stage using the physically based rainfall-runoff models. However, recently, studies involving the application of a machine learning-based flood forecasting models, which addresses the limitations of extant physically based flood stage forecasting models, have been performed. We may require various case studies to determine more accurate methods. Therefore, this study performed the real-time forecasting of the river water level or stage at the Gurye station of the Sumjin river with lead times of 1, 3, and 6 h by applying a long short-term memory (LSTM)-based deep learning model. In addition, the applicability of the LSTM model was evaluated by comparing the results with those from widely used models based on support vector machine and multilayer perceptron. Consequently, we noted that the LSTM model exhibited a relatively better forecasting performance. Therefore, the applicability of the LSTM model should be extensively studied for flood forecasting applications.

Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process

Wen, Xianyu,Jeong, Seorin,Kim, Younghoon,Bae, Jeong Mo,Cho, Nam Yun,Kim, Jung Ho,Kang, Gyeong Hoon BioMed Central 2017 CLINICAL EPIGENETICS Vol.9 No.-

<P><B>Background</B></P><P>Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation. To identify whether formalin fixation might impact the measured values of methylation in LINE-1 repetitive elements and whether prolonged heat-induced denaturation of DNA might reduce the artificial increases in measured values caused by formalin fixation, we analyzed paired fresh-frozen (FF) and FFPE xenograft tissue samples for their methylation levels in LINE-1 using a pyrosequencing assay. To further confirm the effect of a heating step in the measurement of LINE-1 or single gene methylation levels, we analyzed FFPE tissue samples of gastric cancer and colorectal cancer for their methylation status in LINE-1 and eight single genes, respectively.</P><P><B>Results</B></P><P>Formalin fixation led to an increase in the measured values of LINE-1 methylation regardless of the duration of fixation. Prolonged heating of the DNA at 95 °C for 30 min before bisulfite conversion was found (1) to decrease the discrepancy in the measured values between the paired FF and FFPE tissue samples, (2) to decrease the standard deviation of the measured value of LINE-1 methylation levels in FFPE tissue samples of gastric cancer, and (3) to improve the performance in the measurement of single gene methylation levels in FFPE tissue samples of colorectal cancer.</P><P><B>Conclusions</B></P><P>Formalin fixation leads to artificial increases in the measured values of LINE-1 methylation, and the application of prolonged heating of DNA samples decreases the discrepancy in the measured values of LINE-1 methylation between paired FF and FFPE tissue samples. The application of prolonged heating of DNA samples improves bisulfite conversion-based measurement of LINE-1 or single gene methylation levels in FFPE tissue samples.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s13148-016-0308-0) contains supplementary material, which is available to authorized users.</P>

Differential Features of Microsatellite-Unstable Colorectal Carcinomas Depending on EPCAM Expression Status

Kim, Jung Ho,Bae, Jeong Mo,Kim, Kyung-Ju,Rhee, Ye-Young,Kim, Younghoon,Cho, Nam-Yun,Lee, Hye Seung,Chang, Mee Soo,Kang, Gyeong Hoon The Korean Society of Pathologists and The Korean 2014 KOREAN JOURNAL OF PATHOLOGY - Vol.48 No.4

<P><B>Background</B></P><P>Recent studies have revealed that a small subset of Lynch syndrome-associated colorectal carcinomas (CRCs) is caused by a germline <I>EPCAM</I> deletion-induced <I>MSH2</I> epimutation. Based on the finding of this genetic alteration, we investigated the implications of EPCAM expression changes in microsatellite instability-high (MSI-H) CRCs.</P><P><B>Methods</B></P><P>Expression of EPCAM and DNA mismatch repair proteins was assessed by immunohistochemistry in 168 MSI-H CRCs. Using DNA samples of these tumors, <I>MLH1</I> promoter methylation status was also determined by methylation-specific real-time polymerase chain reaction method (MethyLight).</P><P><B>Results</B></P><P>Among 168 MSI-H CRCs, complete loss (CL) and focal loss (FL) of EPCAM expression was observed in two (1.2%) and 22 (13.1%) cases, respectively. Both of the EPCAM-CL cases were found in MSH2-negative tumors without <I>MLH1</I> promoter methylation. However, only nine of the 22 EPCAM-FL tumors had MSH2 deficiency. Of the 22 EPCAM-FL tumors, 13 showed MLH1 loss, and among them, nine cases were determined to have <I>MLH1</I> methylation. EPCAM-FL was significantly associated with advanced stage (p=.043), distant metastasis (p=.003), poor differentiation (p=.001), and signet ring cell component (p=.004).</P><P><B>Conclusions</B></P><P>Loss of EPCAM expression is differentially associated with clinicopathological and molecular features, depending on the completeness of the loss, in MSI-H CRCs.</P>

Metabolic Regulation of Longevity and Immune Response in Caenorhabditis elegans by Ingestion of Lacticaseibacillus rhamnosus IDCC 3201 Using Multi-Omics Analysis

Daniel Junpyo Lee,Ju Young Eor,Min-Jin Kwak,Junbeom Lee,An Na Kang,Daye Mun,Hyejin Choi,Minho Song,Jong Nam Kim,Jun-Mo Kim,Jungwoo Yang,Hyung Wook Kim,Sangnam Oh,Younghoon Kim The Korean Society for Microbiology and Biotechnol 2024 Journal of microbiology and biotechnology Vol.34 No.5

Probiotics, specifically Lacticaseibacillus rhamnosus, have garnered attention for their potential health benefits. This study focuses on evaluating the probiotic properties of candidate probiotics L. rhamnosus IDCC 3201 (3201) using the Caenorhabditis elegans surrogate animal model, a well-established in vivo system for studying host-bacteria interactions. The adhesive ability to the host's gastrointestinal tract is a crucial criterion for selecting potential probiotic bacteria. Our findings demonstrated that 3201 exhibits significantly higher adhesive capabilities compared with Escherichia coli OP50 (OP50), a standard laboratory food source for C. elegans and is comparable with the widely recognized probiotic L. rhamnosus GG (LGG). In lifespan assay, 3201 significantly increased the longevity of C. elegans compared with OP50. In addition, preconditioning with 3201 enhanced C. elegans immune response against four different foodborne pathogenic bacteria. To uncover the molecular basis of these effects, transcriptome analysis elucidated that 3201 modulates specific gene expression related to the innate immune response in C. elegans. C-type lectin-related genes and lysozyme-related genes, crucial components of the immune system, showed significant upregulation after feeding 3201 compared with OP50. These results suggested that preconditioning with 3201 may enhance the immune response against pathogens. Metabolome analysis revealed increased levels of fumaric acid and succinic acid, metabolites of the citric acid cycle, in C. elegans fed with 3201 compared with OP50. Furthermore, there was an increase in the levels of lactic acid, a well-known antimicrobial compound. This rise in lactic acid levels may have contributed to the robust defense mechanisms against pathogens. In conclusion, this study demonstrated the probiotic properties of the candidate probiotic L. rhamnosus IDCC 3201 by using multi-omics analysis.