• Genomics & Informatics
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• 제21권3호
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• pp.38.1-38.8
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• 2023

Non-small cell lung cancer (NSCLC) is an important cause of cancer-associated deaths worldwide. Therefore, the exact molecular mechanisms of NSCLC are unidentified. The present investigation aims to identify the miRNAs with predictive value in NSCLC. The two datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEmiRNA) and mRNAs (DEmRNA) were selected from the normalized data. Next, miRNA-mRNA interactions were determined. Then, co-expression network analysis was completed using the WGCNA package in R software. The co-expression network between DEmiRNAs and DEmRNAs was calculated to prioritize the miRNAs. Next, the enrichment analysis was performed for DEmiRNA and DEmRNA. Finally, the drug-gene interaction network was constructed by importing the gene list to dgidb database. A total of 3,033 differentially expressed genes and 58 DEmiRNA were recognized from two datasets. The co-expression network analysis was utilized to build a gene co- expression network. Next, four modules were selected based on the Z_summary score. In the next step, a bipartite miRNA-gene network was constructed and hub miRNAs (let-7a-2-3p, let-7d-5p, let-7b-5p, let-7a-5p, and let-7b-3p) were selected. Finally, a drug-gene network was constructed while SUNITINIB, MEDROXYPROGESTERONE ACETATE, DOFETILIDE, HALOPERIDOL, and CALCITRIOL drugs were recognized as a beneficial drug in NSCLC. The hub miRNAs and repurposed drugs may act a vital role in NSCLC progression and treatment, respectively; however, these results must validate in further clinical and experimental assessments.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제18권1호
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• pp.126-146
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• 2024

Caladium bicolor is one of the most popular plants in Thailand. The original species of Caladium bicolor was found a hundred years ago. Until now, there are more than 500 species through multiplication. The classification of Caladium bicolor can be done by using its color and shape. This study aims to develop a model to classify Caladium bicolor using a transfer learning technique. This work also presents a proof of concept, GUI design, and web application deployment using the user-design-center method. We also evaluated the performance of the following pre-trained models in this work, and the results are as follow: 87.29% for AlexNet, 90.68% for GoogleNet, 93.59% for XceptionNet, 93.22% for MobileNetV2, 89.83% for RestNet18, 88.98% for RestNet50, 97.46% for RestNet101, and 94.92% for InceptionResNetV2. This work was implemented using MATLAB R2023a.

• 제어로봇시스템학회:학술대회논문집
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• 제어로봇시스템학회 2004년도 ICCAS
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• pp.138-142
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• 2004

In this paper, we present a new method for monitoring of ECU's sensor signals of vehicle. In order to measure the ECU's sensor signals, the interfaced circuit is designed to communicate ECU and the Embedded Linux is used to monitor communication result through Web the Embedded Linux system and this system is said "ECU Interface Part". In ECU Interface Part the interface circuit is designed to match voltage level between ECU and SA-1110 micro controller and interface circuit to communicate ECU according to the ISO, SAE communication protocol standard. Because Embedded Linux does not allow to access hardware directly in application level, anyone who wants to modify any low level hardware must develop device driver. To monitor ECU's sensor signals the most important thing is to match serial level between ECU and ECU Interface Part. It means to communicate correctly between two hardware we need to match voltage and signal level, and need to match baudrate. The voltage of SA-1110 is 0 ${\sim}$ +3.3V and ECU is 0 ${\sim}$ +12V and, ECU's communication Line K does multiple operation so, the interface circuit is used to match voltage and signal level. In Addition to ECU's baudrate is 10400bps, it's not standard baudrate in computer environment. So, we need to develop a device driver to control the interface circuit, and change baudrate. To monitor ECU's sensor signals through web there's a network socket program is working in Embedded Linux. It works as server program and manages user's connections and commands. Anyone who wants to monitor ECU's sensor signals he just only connect to Embedded Linux system with web browser then, Embedded Linux webserver will return the ActiveX webbased measurement software. It works in web browser and inits ECU, as a result it returns sensor signals through web. All the programs are developed with GCC(GNU C Compiler) and, webbased measurement software is developed with Borland C++ Builder.

• 인터넷정보학회논문지
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• 제5권5호
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• pp.1-15
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• 2004

본 논문에서는 효율적인 유전자 서열 데이터의 관리와 분석을 위한 웹 기반의 통합 시스템인 GWB(Gene WorkBench)의 설계와 구현에 대해 설명한다. 유전자 서열을 다루는 기존의 시스템들은 서열 데이터의 관리 기능과 분석 기능을 동시에 지원하는 경우가 드물고, 또한 분석 기능 역시 일부 혹은 단일 분석 기능만을 제공하는 단위 프로그램들이 대부분이다. 또 이러한 분석 프로그램들마저 서로 분산되어 있고 다른 수행환경을 필요로 한다. 따라서 이러한 프로그램들을 함께 이용하기 위해서는 많은 수작업과 변환작업을 필요로 하는 등 유전자 서열 데이터를 다루는 많은 생명과학 연구자들이 불편을 겪어왔다. 본 논문에서는 기존 시스템들의 단점을 보완하고 유전자 서열 연구에 효과적으로 도움을 줄 수 있는 보다 편리한 시스템을 구현하고자, 서열 데이터베이스 관리 기능과 다양한 분석 기능들을 하나의 시스템인 GWB로 동합하였다. GWB 시스템 설계의 가상 중요한 이슈는 서로 상이한 분석 프로그램들을 어떻게 하나의 시스템으로 통합할 것이며, 또 이들 프로그램들이 요구하는 서로 다른 서열 데이터 및 서열 데이터베이스 형태를 어떻게 제공할 수 있느냐는 것이다. GWB는 이 문제들을 해결하기 위해 공통의 입출력 인터페이스인 포장기를 이용하여 서로 다른 분석 프로그램들을 시스템에 통합시켰고, 공통 서열 데이터 형식인 KSF를 제안하였으며, 로컬 서열 데이터베이스를 관계형 데이터베이스부분과 색인 순차파일부분으로 나누어 구성하였고, 서로 상이한 서열 데이터 형식간의 변환 기능과 XML 파일로의 변환 기능을 제공하도록 하였다.유의하게 높았다 (P<0.01). 고형물질별 피복지수는 red clover는 V나 V+T(1 ： 1)로 피복한 종자에서 높았으며 tall fescue는 T, V, V + T(1 : 1로 피복한 종자)에서 가장 높게 나타났다(P<0.01). 종자피복에 있어서 red clover와 tall fescue 공히 접착제는 CF나 PVA로 하고 고형물질은 V나 V+T(1:1)로 피복함으로서 가장 좋은 피복효과를 얻을 수 있었다.. 쟁점 및 과제들이 제시되었다. cells of these species contained considerable to large amount of neutral mucin, and small to considerable amount of acid mucin, Most of the medium sized and small mucous cells contained neutral mucin and sialomucin, but a few mucous cells contained neutral mucin and strongly sulfomucin or neutral combined with strongly sulfomucin and sialomucin. Most of the esophageal mucous cells pf Bryzoichthys lysimus contained small amount of neutral mucin, while on the other hand a feww mucous cells contained small amount of neutral mucin and minimal

• Asian-Australasian Journal of Animal Sciences
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• 제27권11호
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• pp.1540-1547
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• 2014

The accuracy of genomic estimated breeding values (GEBV) was evaluated for sixteen meat quality traits in a Berkshire population (n = 1,191) that was collected from Dasan breeding farm, Namwon, Korea. The animals were genotyped with the Illumina porcine 62 K single nucleotide polymorphism (SNP) bead chips, in which a set of 36,605 SNPs were available after quality control tests. Two methods were applied to evaluate GEBV accuracies, i.e. genome based linear unbiased prediction method (GBLUP) and Bayes B, using ASREML 3.0 and Gensel 4.0 software, respectively. The traits composed different sets of training (both genotypes and phenotypes) and testing (genotypes only) data. Under the GBLUP model, the GEBV accuracies for the training data ranged from $0.42{\pm}0.08$ for collagen to $0.75{\pm}0.02$ for water holding capacity with an average of $0.65{\pm}0.04$ across all the traits. Under the Bayes B model, the GEBV accuracy ranged from $0.10{\pm}0.14$ for National Pork Producers Council (NPCC) marbling score to $0.76{\pm}0.04$ for drip loss, with an average of $0.49{\pm}0.10$. For the testing samples, the GEBV accuracy had an average of $0.46{\pm}0.10$ under the GBLUP model, ranging from $0.20{\pm}0.18$ for protein to $0.65{\pm}0.06$ for drip loss. Under the Bayes B model, the GEBV accuracy ranged from $0.04{\pm}0.09$ for NPCC marbling score to $0.72{\pm}0.05$ for drip loss with an average of $0.38{\pm}0.13$. The GEBV accuracy increased with the size of the training data and heritability. In general, the GEBV accuracies under the Bayes B model were lower than under the GBLUP model, especially when the training sample size was small. Our results suggest that a much greater training sample size is needed to get better GEBV accuracies for the testing samples.

• 한국정보과학회논문지:소프트웨어및응용
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• 제34권12호
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• pp.1045-1055
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• 2007

잠재토픽모델(latent topic model)은 데이타에 내재된 특징적 패턴이나 데이타 정의 자질들 간의 상호 관련성을 확률적으로 모델링하고 자동 추출하는 모델로서 최근 텍스트 문서로부터의 의미 자질 자동 추출, 이미지를 비롯한 멀티미디어 데이타 분석, 생물정보학 분야 등에서 많이 응용되고 있다. 이러한 잠재토픽모델의 대규모 데이타에 대한 적용 시 그 효과 증대를 위한 중요한 이슈 중의 하나는 모델의 효율적 학습에 관한 것이다. 본 논문에서는 대표적 잠재토픽모델 중의 하나인 PLSA (probabilistic latent semantic analysis) 기법을 대상으로 점진적 EM 알고리즘을 활용한, 기본 EM 알고리즘 기반의 기존 학습에 대한 학습속도 증진 기법을 제안한다. 점진적 EM 알고리즘은 토픽 추론 시 전체 데이타에 대한 일괄적 E-step 대신에 일부 데이타에 대한 일련의 부분적 E-step을 수행하는 특징이 있으며 이전 데이터 일부에 대한 학습 결과를 바로 다음 데이타 학습에 반영함으로써 모델 학습의 가속화를 기대할 수 있다. 또한 이론적인 측면에서 지역해로의 수렴성이 보장되고 기존 알고리즘의 큰 수정 없이 구현이 용이하다는 장점이 있다. 논문에서는 해당 알고리즘의 기본적인 응용과 더불어 실제 적용과정 상에서의 가능한 데이터 분할법들을 제시하고 모델 학습 속도 개선 면에서의 성능을 실험적으로 비교 분석한다. 실세계 뉴스 문서 데이타에 대한 실험을 통해, 제안하는 기법이 기존 PLSA 학습 기법에 비해 유의미한 수준에서 학습 속도 증진을 달성할 수 있음을 보이며 추가적으로 모델의 병렬 학습 기법과의 조합을 통한 실험 결과를 간략히 제시한다.

• 한국정보과학회논문지:소프트웨어및응용
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• 제33권4호
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• pp.365-377
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• 2006

단백질들은 서로 다른 단백질들과 상호작용 하거나 복합물을 형성함으로써 생물학적으로 중요한 기능을 한다고 알려져 있다. 때문에 대부분의 세포작용에 있어 중요한 역할을 하는 단백질 상호작용의 분석 및 예측에 대한 연구는 여러 연구그룹으로부터 풍부한 데이타가 산출되고 있는 현(現) 게놈시대에서 또 하나의 중요한 이슈가 되고 있다. 본 논문에서는 효모(Saccharomyces cerevisiae)에 대해 공개되어있는 단백질 상호작용 데이타들에서 속성들 간의 연관을 통해 유추 가능한 잠재적 단백질 상호작용들을 예측하기 위한 연관속성 마이닝 방법을 제시한다. 단백질의 속성들 중 연속값을 가지는 속성값들은 최대상호 의존성에 기반을 두어 이산화 하였으며, 정보이론기반 속성선택 알고리즘을 사용하여 단백질들 간의 상호작용 예측을 위해 고려되는 단백질의 속성(attribute) 수 증가에 따른 속성차원문제를 극복하도록 하였다. 속성들 간의 연관성 발견은 데이타마이닝 분야에서 사용되는 연관규칙 발견(association rule discovery) 방법을 사용하였다 논문에서 제안한 방법은 발견된 연관규칙을 통한 단백질 상호작용 예측문제에 있어 최대 약 96.5%의 예측 정확도를 보였으며 속성필터링을 통하여 속성필터링을 하지 않는 기존의 방법에 비해 최대 약 29.4% 연관규칙 발견속도 향상을 보였다.

• 한국방사선학회논문지
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• 제9권7호
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• pp.425-431
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• 2015

응급상황에서 중환자에게 시행되는 인공호흡 과정 중 호흡기류를 측정할 수 있도록 개발된 센서의 계측 정확도를 평가하였다. 호흡기류 센서의 압력-기류 특성식을 산출하였으며, 인공호흡시에 인가되는 호흡기류신호와 유사한 6가지 파형을 표준기류생성시스템으로 생성하여 호흡기류 센서에 가하면서 기류신호를 측정하였다. 이 기류신호로부터 일회호흡용적과 최대기류값을 산출하였으며, 이를 표준기류생성시스템에 부착되어 있고 물리적으로 오차가 없는 선형변위센서로부터 측정한 용적신호에서 산출한 표준값과 비교하였다. 일회호흡용적의 상대오차는 3% 이내이었으며, 최대기류값은 약 5% 정도로서 충분히 정확한 기류 계측이 가능함을 확인하였다. 따라서 실제 응급상황에서 호흡기류 센서로 적용하여 응급 중환자의 호흡신호와 호흡주기별 진단변수들을 실시간으로 모니터링 할 수 있는 시스템에 활용 가능할 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권8호
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• pp.1103-1109
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• 2018

Objective: This study aimed to screen and identify the target genes of miR-375 in pig Sertoli (ST) cells and to elucidate the effect of miR-375 on the proliferation of ST cells. Methods: In this study, bioinformatics software was used to predict and verify miR-375 target genes. Quantitative polymerase chain reaction (PCR) was used to detect the relationship between miR-375 and its target genes in ST cells. Enzyme-linked immunosorbent assay (ELISA) of rearranged L-myc fusion (RLF) and hypoxia-induced gene domain protein 1A (HIGD1A) was performed on porcine ST cells, which were transfected with a miR-375 mimics and inhibitor to verify the results. Dual luciferase reporter gene assays were performed to assess the interactions among miR-375, RLF, and HIGD1A. The effect of miR-375 on the proliferation of ST cells was analyzed by CellTiter 96 AQueous One Solution Cell Proliferation Assay (MTS). Results: Five possible target genes of miR-375, including RLF, HIGD1A, colorectal cancer associated 2, POU class 3 homeobox 1, and WW domain binding protein 1 like, were found. The results of quantitative PCR suggested that mRNA expression of RLF and HIGD1A had a negative correlation with miR-375, indicating that RLF and HIGD1A are likely the target genes of miR-375. The ELISA results revealed that RLF and HIGD1A were negatively correlated with the miR-375 protein level. The luminescence results for the miR-375 group cotransfected with wild-type RLF and HIGD1A vector were significantly lower than those of the miR-375 group co-transfected with the blank vector or mutant RLF and HIGD1A vectors. The present findings suggest that RLF and HIGD1A are target genes of miR-375 and that miR-375 inhibits ST cell proliferation according to MTS analysis. Conclusion: It was speculated that miR-375 affects cell proliferation through its target genes, which play an important role in the development of testicular tissue.

• Asian-Australasian Journal of Animal Sciences
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• 제32권3호
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• pp.320-333
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• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.