• Interdisciplinary Bio Central
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• v.6 no.4
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• pp.3.1-3.10
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• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Journal of Welding and Joining
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• v.34 no.1
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• pp.54-58
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• 2016

In this research paper, suggest method of generate same bead as an actual measurement data in virtual welding conditions, exploit morphology information of the bead that acquired through robot welding. It has many multiple risk factors to Beginners welding training, by we make possible to train welding in virtual reality, we can reduce welding training risk and welding material to exploit bead visualization algorithm that we suggest so it will be expected to achieve educational, environmental and economical effect. The proposed method is acquire data to each case performing robot welding by set the voltage, current, working angle, process angle, speed and arc length of welding condition value. As Welding condition value is most important thing in decide bead form, we would selected one of baseline each item and then acquired metal followed another factors change. Welding type is FCAW, SMAW and TIG. When welding trainee perform the training, it's difficult to save all of changed information into database likewise working angle, process angle, speed and arc length. So not saving data into database are applying the method to infer the form of bead using a neural network algorithm. The way of bead's visualization is applying the spline algorithm. To accurately represent Morphological information of the bead, requires much of morphological information, so it can occur problem to save into database that is why we using the spline algorithm. By applying the spline algorithm, it can make simplified data and generate accurate bead shape. Through the research paper, the shape of bead generated by the virtual reality was able to improve the accuracy when compared using the form of bead generated by the robot welding to using the morphological information of the bead generated through the robot welding. By express the accurate shape of bead and so can reduce the difference of the actual welding training and virtual welding, it was confirmed that it can be performed safety and high effective virtual welding education.

• Journal of Biosystems Engineering
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• v.39 no.4
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• pp.267-273
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• 2014

Purpose: This study was conducted to develop a web-based business management system to ensure the efficient operation and transparent management of government-subsidized agricultural machinery rental businesses. Methods: An MS_SQL2000 database management system (DBMS) solution was utilized in the system for high system compatibility and integrated management. This system was targeted to be compatible with Internet Explorer 6.0 or later and to ensure security and seamless web operations. The system administrator is able to manage a fleet of agricultural machinery, including various inventory codes, release and return, fleet registry, and business performance. Users (farmers) may search the database of rental machinery and reserve them. Results: With respect to rental reservations, the system administrator can manage the fleet by setting the rental status to Approved, Released, or Returned. Through the web, the administrator can also create a database that includes machinery specifications, features, and rental rates. In addition, business performance data can be analyzed using a diverse array of tools to streamline the rental business. Without having to go to the rental office, users can save time and money by searching for and renting agricultural machinery through the information available on the website, including availability, specifications, and rental fees. After deploying the system, the time required to analyze monthly performance and create reports was dramatically reduced from 20 days per person to one day per person. Conclusions: Since 2014, AMRB has been installed and is operating in agricultural machinery rental businesses in 31 cities and counties in South Korea. This study recommends continued expansion and dissemination of AMRB for the systematic and efficient management of agricultural machinery rental businesses.

• Proceedings of the KSRS Conference
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• 2007.10a
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• pp.438-441
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• 2007

Recently, due to molecular biology and engineering technology, DNA microarray makes people watch thousands of genes and the state of variation from the tissue samples of living body. With DNA Microarray, it is possible to construct a genetic group that has similar expression patterns and grasp the progress and variation of gene. This paper practices Cluster Analysis which purposes the discovery of biological subgroup or class by using gene expression information. Hence, the purpose of this paper is to predict a new class which is unknown, open leukaemia data are used for the experiment, and MCL (Markov CLustering) algorithm is applied as an analysis method. The MCL algorithm is based on probability and graph flow theory. MCL simulates random walks on a graph using Markov matrices to determine the transition probabilities among nodes of the graph. If you look at closely to the method, first, MCL algorithm should be applied after getting the distance by using Euclidean distance, then inflation and diagonal factors which are tuning modulus should be tuned, and finally the threshold using the average of each column should be gotten to distinguish one class from another class. Our method has improved the accuracy through using the threshold, namely the average of each column. Our experimental result shows about 70% of accuracy in average compared to the class that is known before. Also, for the comparison evaluation to other algorithm, the proposed method compared to and analyzed SOM (Self-Organizing Map) clustering algorithm which is divided into neural network and hierarchical clustering. The method shows the better result when compared to hierarchical clustering. In further study, it should be studied whether there will be a similar result when the parameter of inflation gotten from our experiment is applied to other gene expression data. We are also trying to make a systematic method to improve the accuracy by regulating the factors mentioned above.

• Journal of Welding and Joining
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• v.31 no.5
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• pp.35-40
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• 2013

In this paper, we propose the Tangible Virtual Reality Representation Method to using haptic device and feature to morphology of created bead from Flux Cored Arc Welding. The virtual reality was started to rising for reduce to consumable materials and welding training risk. And, we will expected maximize virtual reality from virtual welding training. In this paper proposed method is get the database to changing the input factor such as work angle, travelling angle, speed, CTWD. And, it is visualization to bead from extract to optimal morphological feature information to using the Neural Network algorithm. The database was building without error to extract data from automatic robot welder. Also, the Neural Network algorithm was set a dataset of the highest accuracy from verification process in many times. The bead was created in virtual reality from extract to morphological feature information. We were implementation to final shape of bead and overlapped in process by time to using bead generation algorithm and calibration algorithm for generate to same bead shape to real database in process of generating bead. The best advantage of virtual welding training, it can be get the many data to training evaluation. In this paper, we were representation bead to similar shape from generated bead to Flux Cored Arc Welding. Therefore, we were reduce the gap to virtual welding training and real welding training. In addition, we were confirmed be able to maximize the performance of education from more effective evaluation system.

• Environmental Analysis Health and Toxicology
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• v.26
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• pp.10.1-10.7
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• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• Herbal Formula Science
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• v.31 no.4
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• pp.295-313
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• 2023

Objectives : While treatments for cancer are advancing, the development of effective treatments for cancer metastasis, the main cause of cancer patient death, remains insufficient. Recent studies on Dichroae Radix have revealed that its active ingredients have the potential to inhibit cancer metastasis. This study aimed to investigate the cancer metastasis inhibitory effect of Dichroae Radix using network pharmacological analysis. Methods : The active compounds of Dichroae Radix have been identified using Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The UniProt database was used to collect each of information of all target proteins associated with the active compounds. To find the bio-metabolic processes associated with each target, the DAVID6.8 Gene Functional classifier tool was used. Compound-Target and Target-Pathway networks were analyzed via Cytoscape 3.40. Results : In total, 25 active compounds and their 62 non-redundant targets were selected through the TCMSP database and analysis platform. The target genes underwent gene ontology and pathway enrichment analysis. The gene list applied to the gene ontology analysis revealed associations with various biological processes, including signal transduction, chemical synaptic transmission, G-protein-coupled receptor signaling pathways, response to xenobiotic stimulus, and response to drugs, among others. A total of eleven genes, including HSP90AB1, CALM1, F2, AR, PAKACA, PTGS2, NOS2, RXRA, ESR1, ESR2, and NCOA1, were found to be associated with biological pathways related to cancer metastasis. Furthermore, nineteen of the active compounds from Dichroae Radix were confirmed to interact with these genes. Conclusions : The results provide valuable insights into the mechanism of action and molecular targets of Dichroae Radix. Notably, Berberine, the main active ingredient of Dichroae Radix, plays a significant role in degrading AR proteins in advanced prostate cancer. Further studies and validations can provide crucial data to advance cancer metastasis prevention and treatment strategies.

• Journal of Wetlands Research
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• v.26 no.1
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• pp.21-31
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• 2024

Macromia daimoji Okumura, 1949 was designated as an endangered species and also categorized as Class II Endangered wildlife on the International Union for Conservation of Nature (IUCN) Red List in Korea. The spatial distribution of this species ranged within a region delimited by northern latitude from Sacheon-si(35.1°) to Yeoncheon-gun(38.0°) and eastern longitude from Yeoncheon-gun(126.8°) to Yangsan-si(128.9°). They generally prefer microhabitats such as slowly flowing littoral zones of streams, alluvial stream islands and temporarily formed puddles in the sand-based lowland streams. The objectives of this study were to analyze the similarity of benthic macroinvertebrate communities in M. daimoji habitats, to predict the current potential distribution patterns as well as the changes of distribution ranges under global climate change circumstances. Data was collected both from the Global Biodiversity Information Facility (GBIF) and by field surveys from April 2009 to September 2022. We adopted MaxEnt model to predict the current and future potential distribution for M. daimoji using downloaded 19 variables from the WorldClim database. The differences of benthic macroinvertebrate assemblages in the mainstream of Nakdonggang were smaller than those in its tributaries and the other streams, based on the surrounding environments and stream sizes. MaxEnt model presented that potential distribution displayed high inhabiting probability in Nakdonggang and its tributaries. Applying to the future scenarios by Intergovernmental Panel on Climate Change (IPCC), SSP1 scenario was predicted to expand in a wide area and SSP5 scenario in a narrow area, comparing with current potential distribution. M. daimoji is not only directly threatened by physical disturbances (e.g. river development activities) but also vulnerable to rapidly changing climate circumstances. Therefore, it is necessary to monitor the habitat environments and establish conservation strategies for preserving population of M. daimoji.

• Journal of Internet Computing and Services
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• v.17 no.2
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• pp.59-65
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• 2016

The result of analyzing the cognitive reaction due to the color environment has been applied to various filed especially in medical field. Moreover, the study about the identification of patient's condition and examination the brain activity by collecting the bio-signal based on the color environment is being actively conducted. Even though, there were a variety of experiments by convention the color environment using a light or LED color, it still has a problem that affects the psychological information. Therefore, our proposed system using a HMD (Head Mounting display) to provide a completed color environment condition. This system uses the BMS(Biomedical System) to collect the biometric information which responds to the specific color condition and the human body response information can be measured by the development the Memory and Attention test on Mobile phone. The collection of Biometric information includes electro cardiogram(ECG), respiration, oxygen saturation (Sp02), Bio-impedance, blood pressure will store in the database. In addition, we can verify the result of the human body reaction in the color environment by Memory and Attention application. By utilizing the reaction of the human body information that is collected thought the proposed system, we can analyze the correlation between the physiological information and the color environment. And we also expect that this system can apply to the medical diagnosis and treatment. For future work, we will expand the system for prediction and treatment of Alzheimer disease by analyzing the visualization data through the proposed system. We will also do evaluation on the effectiveness of the system for using in the rehabilitation program.

• Korean Journal of Medicinal Crop Science
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• v.24 no.5
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• pp.386-392
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• 2016

Background: Sorghum is a major cereal food crop used in many parts of the world. It has been grown on a subsistence level by farmers, under various conditions of environmental stresses in the semi-arid tropics of Africa and Asia. This plant has received significant attention because of its ability to reduce cholesterol in the blood, and its anti-dementia, antioxidant, and antimicrobial properties. It is possible to develop a functional and commercially viable sorghum variety by using superior cultivars of sorghum. The objective of this study was to build a database of superior sorghum accession. Methods and Results: We used 250 sorghum accessions collected from different geographical bioregions in Korea. We determined various agronomic characters including germination rate and ear length of these accessions. To determine the antioxidant capacity, we measured the 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)-diammonium salt radical scavenging activity, total phenolic contents, and total flavonoid contents. Accession 189 showed higher germination (> 80%) than the other accessions. Higher 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity was observed in 11-SB-078 ($RC_{50}$; $1.89{\pm}2.88{\mu}g/m{\ell}$), and higher 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)-diammonium salt radical scavenging activity was recorded in 11-SB-116 ($RC_{50}$; $35.48{\pm}2.42{\mu}g/m{\ell}$) than in the other accessions. The ear length ranged from 15 cm to 48 cm, the total phenolic contents ranged from $3mg{\cdot}GAE/g$ to $77mg{\cdot}GAE/g$, and total flavonoid contents ranged from $0.09mg{\cdot}QE/g$ to $1.07mg{\cdot}QE/g$. Conclusions: Among 250 sorghum accessions, we selected 10 with both superior agronomic characters and highly functional food quality.