• Genomics & Informatics
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• v.19 no.1
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• pp.5.1-5.11
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• 2021

Head and neck squamous cell carcinoma (HNSCC) is the most frequent type of head and neck cancer that usually arises from the mucosal surfaces of several organs including nasal cavity, paranasal sinuses, oral cavity, tongue, pharynx, and larynx. The Wnt signaling pathway is a crucial mechanism for cellular maintenance and development. It regulates cell cycle progression, apoptosis, proliferation, migration, and differentiation. Dysregulation of this pathway correlates with oncogenesis in various tissues including breast, colon, pancreatic as well as head and neck cancers. The present study aims to assess the gene alterations in the Wnt family of genes so as to derive an association with HNSCC. Computational approaches have been utilized for the identification of gene alterations in the Wnt family of genes. Several databases such as cBioportal, STRING, and UALCAN were used for the purpose. The frequency of alteration was high in case of Wnt family member 11 (5%). Gene amplification, deep deletions, missense and truncating mutations were observed in HNSCC patients. There was a marked difference in the gene expression profile of WNT11 between grades as well as normal samples. The survival probability measured using the Kaplan-Meier curve also presented with a significant difference among male and female subjects experiencing a low/medium level expression. The female patients showed less survival probability when compared to the male subjects. This provides the prognostic significance of the WNT11 gene in HNSCC. Taken together, the present study provides clues on the possible association of WNT11 gene alterations with HNSCC, which has to be further validated using experimental approaches.

• Herbal Formula Science
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• v.29 no.1
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• pp.19-31
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• 2021

Objectives : The root of Salvia miltiorrhiza, known as 'Dansam (DS, 丹參)', is used for and treating cardiovascular diseases based on its efficacy of promoting blood circulation and breaking through a blood stasis. In this study, we would like to see if DS could be effectively used for stroke from the perspective of network pharmacology. Methods : The analysis was conducted using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database to derive the main active compounds of DS and identify the mechanism of each compound acting on the human body. The networks between compounds, target protein and disease were expressed through Cytoscape. Protein-protein interaction (PPI) analysis was performed using STRING database. Results : Fifty two active compounds of DS were identified by screening the ingredients of DS through TCMSP. Based on the networks of these compounds with target protein and disease, it can be said that DS might be effective for preventing and treating stroke. PPI result showed that adrenergic receptor has many interactions among proteins, indicating its significance in stroke pathway. Conclusion : In this study, we derived target proteins and target diseases of DS that could be used in study of stroke. However, since it is uncertain if these targets can be controlled by DS extracts or not, we would like to confirm the results with further animal experiments.

• KIPS Transactions on Software and Data Engineering
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• v.11 no.1
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• pp.11-18
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• 2022

De novo drug design is the process of developing new drugs that can interact with biological targets such as protein receptors. Traditional process of de novo drug design consists of drug candidate discovery and drug development, but it requires a long time of more than 10 years to develop a new drug. Deep learning-based methods are being studied to shorten this period and efficiently find chemical compounds for new drug candidates. Many existing deep learning-based drug design models utilize recurrent neural networks to generate a chemical entity represented by SMILES strings, but due to the disadvantages of the recurrent networks, such as slow training speed and poor understanding of complex molecular formula rules, there is room for improvement. To overcome these shortcomings, we propose a deep learning model for SMILES string generation using variational autoencoders with self-attention mechanism. Our proposed model decreased the training time by 1/26 compared to the latest drug design model, as well as generated valid SMILES more effectively.

• The Journal of Korean Medical History
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• v.25 no.2
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• pp.63-96
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• 2012

The PingMaiFa chapter, which is the second chapter of SongBon ShangHanLun, is the scholarly description(專論) of the pulse and pathological mechanism but has not been studied and published yet. This study is about article 1-13 which is the first part of The PingMaiFa chapter. We compared the original texts within the editions, comparing and analyzing the annotations of successive dynastic medical group. The articles of The SongBon ShangHanLun PingMaiFa chapter 1-13 is consisted as is shown: article 1 states about the general features of normal pulse (平脈) and its physiological mechanism and the morbid pulses (病脈) caused by wind, cold, retained fluid, pain and heat vexation, article 1,10 state about the normal pulses of Five viscera (lung, heart, spleen, liver and kidney) and their manipulations in pulse taking, article 2 states about the differentiations of deficiency and excess syndrome according to pulse conditions, article 3, 4 state about the estimation of good prognoses and a factitious disorder by the combination of pulses and symptoms, article 6 states about Latent qi (伏氣) and its diagnostic features, article 5 states about inspection and listening examination as co-diagnostic methods of the pulse diagnosis, article 7, 8, 9 state that the emotions, such as fear and shame, and the dietary are important factors to consider for making diagnosis, article 11 states about the overwhelming pulse (相乘脈) which indicates the abnormal correlations between five phases and appears in four patterns as the dissolute(縱), the unrighteous(橫), the unfavorable(逆) and the favorable(順), article 12 states about 6 harmful pulses(殘賊脈), which are string-like pulse(弦脈), tight pulse(緊脈), floating pulse(浮脈), slippery pulse(滑脈), sunken pulse(沈脈), rough pulse(澁脈), article 13 states about "JaeGoe"(災怪) which is an unexpected response after treatment and it comes because of the formulas that had before. Throughout all these articles, The PingMaiFa chapter not only offers great value for Pulse-taking diagnosis, but also leads to a better understanding of clinical applications.

• Journal of Life Science
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• v.30 no.1
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• pp.45-57
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• 2020

The prenatal period in livestock animals is crucial for meat production because net increase in the number of muscle fibers is finished before birth. However, there is no study on the growth and development mechanism of muscles in Hanwoo during this period. Therefore, to find candidate genes involved in muscle growth and development during this period in Hanwoo, mRNA expression data of longissimus in Hanwoo at 6 and 9 months post-conceptional age (MPA) were analyzed. We independently identified differentially expressed genes (DEGs) using DESeq2 and edgeR which are R software packages, and considered the overlaps of the results as final-DEGs to use in downstream analysis. The DEGs were classified into several modules using WGCNA then the modules' functions were analyzed to identify modules which involved in myogenesis and adipogenesis. Finally, the hub genes which had the highest WGCNA module membership among the top 10% genes of the STRING network maximal clique centrality were identified. 913(6 MPA specific DEGs) and 233(9 MPA specific DEGs) DEGs were figured out, and these were classified into five and two modules, respectively. Two of the identified modules'(one was in 6, and another was in 9 MPA specific modules) functions was found to be related to myogenesis and adipogenesis. One of the hub genes belonging to the 6 MPA specific module was axin1 (AXIN1) which is known as an inhibitor of Wnt signaling pathway, another was succinate-CoA ligase ADP-forming beta subunit (SUCLA2) which is known as a crucial component of citrate cycle.

• Journal of Bio-Environment Control
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• v.16 no.2
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• pp.89-95
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• 2007

This study was accomplished to compare energy saving effects of several heat insulation materials in greenhouse and to develop new automatic opening and closing equipment which is suitable to the most effective heat insulation material. To find out more effective heat insulation material, the magnitude of heat transfer occurred through aluminum screen (ALS), non-woven fabric (NWF), double-layer aluminum screen with chemical cotton sheet (DAL), and multi-layer fabric screen material quilted with non-woven fabric, chemical cotton, poly foam, and polypropylene (MLF) were compared relatively. The results showed that the relative magnitude of heat transfer occurred through MLF was lower than DAL and ALS by 23.3% and 43.0% respectively. MLF screen material was the most effective compared with other heat insulation materials. But because of thickness, there was a need of new mechanism for automatic operation in greenhouse. Accordingly, new screen system using MLF-thick but profitable for keeping warm in greenhouse-was developed. Opening & closing equipment was designed to roll MLF with pipe axis during opening process and pull MLF with string during closing process with electric motors, clutches, drums, and so on. In hot pepper cultivation and energy saving test during winter time, the early stage yield of pepper under MLF screen system was higher than NWF by 27%, and gasoline consumption of MLF screen system was lower than NWF by 46%.

• Animal Bioscience
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• v.34 no.11
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• pp.1739-1748
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• 2021

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

• Food Engineering Progress
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• v.14 no.2
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• pp.85-91
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• 2010

In the food process, twist screen is widely used to divide particles on the basis of size. As screen equipped in the twist screen perfoms an important part in the particle size distribution mechanism, the contact area of screen and particles, retention time of particles on the screen, mesh and string thickness of screen and the flow pattern of particles on the screen are major points of the separation efficiency. To improve the separation efficiency, increase the retention time and control the flow pattern of particles, screen frame dam and spiral blockage are installed on the sieve of twist screen ${\emptyset}$ 1200 and ${\emptyset}$ 1500. Twist screen ${\emptyset}$ 1500 with frame dam treated similar separation capacity, 37% higher separation ratio and less non-separated particles of product output 1 than general twist screen. Twist screens with frame dam and spiral blockage showed less treatment capacity, three times higher division ratio and entire separation than general twist screen.