• BMB Reports
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• 제51권1호
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• pp.1-2
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• 2018

Positive selection on a new beneficial mutation generates a characteristic pattern of DNA sequence polymorphism when it reaches an intermediate allele frequency. On genome sequences of African Drosophila melanogaster, we detected such signatures of selection at 37 candidate loci and identified "sweeping haplotypes (SHs)" that are increasing or have increased rapidly in frequency due to hitchhiking. Based on geographic distribution of SH frequencies, we could infer whether selective sweeps occurred starting from de novo beneficial mutants under simple constant selective pressure. Single SHs were identified at more than half of loci. However, at many other loci, we observed multiple independent SHs, implying soft selective sweeps due to a high beneficial mutation rate or parallel evolution across space. Interestingly, SH frequencies were intermediate across multiple populations at about a quarter of the loci despite relatively low migration rates inferred between African populations. This invokes a certain form of frequency-dependent selection such as heterozygote advantage. At one locus, we observed a complex pattern of multiple independent that was compatible with recurrent frequency-dependent positive selection on new variants. In conclusion, genomic patterns of positive selection are very diverse, with equal contributions of hard and soft sweeps and a surprisingly large proportion of frequency-dependent selection in D. melanogaster populations.

• Animal Bioscience
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• 제35권9호
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• pp.1303-1313
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• 2022

Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds. Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 ㎍ of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds. Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication. Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.

• Journal of the Korean Physical Society
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• 제80권
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• pp.247-256
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• 2022

Our objective was to investigate radiomics signatures and prediction models defined by four segmentation methods in using 2-[¹⁸F]fluoro-2-deoxy-d-glucose positron emission tomography (¹⁸F-FDG PET) imaging of lung metastases of soft-tissue sarcomas (STSs). For this purpose, three fixed threshold methods using the standardized uptake value (SUV) and gradient-based edge detection (ED) were used for tumor delineation on the PET images of STSs. The Dice coefficients (DCs) of the segmentation methods were compared. The least absolute shrinkage and selection operator (LASSO) regression and Spearman's rank, and Friedman's ANOVA test were used for selection and validation of radiomics features. The developed radiomics models were assessed using ROC (receiver operating characteristics) curve and confusion matrices. According to the results, the DC values showed the biggest difference between SUV40% and other segmentation methods (DC: 0.55 and 0.59). Grey-level run-length matrix_run-length nonuniformity (GLRLM_RLNU) was a common radiomics signature extracted by all segmentation methods. The multivariable logistic regression of ED showed the highest area under the ROC (receiver operating characteristic) curve (AUC), sensitivity, specificity, and accuracy (AUC: 0.88, sensitivity: 0.85, specificity: 0.74, accuracy: 0.81). In our research, the ED method was able to derive a significant model of radiomics. GLRLM_RLNU which was selected from all segmented methods as a meaningful feature was considered the obvious radiomics feature associated with the heterogeneity and the aggressiveness. Our results have apparently showed that radiomics signatures have the potential to uncover tumor characteristics.

• Molecules and Cells
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• 제38권5호
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• Genes and Genomics
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• 제40권11호
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• pp.1249-1258
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• 2018

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju${\times}$Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas $r^2$ values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (-0.009) than in Jeju crossbred (-0.035) and Jeju horse (-0.038). $F_{ST}$ value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

• 한국소음진동공학회논문집
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• 제24권9호
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• pp.675-681
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• 2014

This paper proposes a fault diagnosis system for an induction motor. This system uses empirical mode decomposition(EMD) to extract fault signatures and multi-layer perceptron(MLP) neural network to facilitate an accurate fault diagnosis. EMD can not only decompose a signal adaptively but also provide intrinsic mode functions(IMFs) containing natural oscillatory modes of the signal. However, every IMF does not represent fault signature, an IMF selection algorithm based on harmonics and their energy of each IMF is proposed. The selected IMFs are utilized for fault classification using MLP and this system shows approximately 98 % diagnosis accuracy for the fault vibration signal of the induction motor.

• 정보과학회 컴퓨팅의 실제 논문지
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• 제24권2호
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• pp.99-104
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• 2018

최근 랜섬웨어에 의한 피해가 전 세계적으로 급증하고 있으며, 국가 기관, 기업, 민간 등 사회전반에 막대한 피해를 입히고 있다. 랜섬웨어는 컴퓨터 시스템을 감염시켜 사용자의 접근을 제한하고 일종의 몸값을 요구하는 악성 소프트웨어이다. 컴퓨터 시스템 자체를 잠그거나 하드 디스크에 존재하는 파일들을 암호화하여 사용자가 컴퓨터를 정상적으로 이용할 수 없게 만들고, 컴퓨터의 정상 복구를 위해 사용자들은 공격자로부터 몸값(Ransom) 지불을 요구받는다. 기존의 기타 악성코드들에 비해 공격수법이 매우 악랄하고 피해규모가 막대하므로 확실한 해결책이 필요하다. 악성코드 분석 방식은 크게 정적 분석, 동적 분석 두 가지로 나뉜다. 최신 악성코드들은 정교한 패킹 기술이 도입된 경우가 많아 정적분석은 분석에 한계가 있다. 따라서 본 논문에서는 랜섬웨어의 활동 모니터링 및 보다 정밀한 분석을 위해 동적 분석 방법을 제안한다. 정상파일, 랜섬웨어, 기타 악성코드의 시그니처를 추출하는 방법과 랜섬웨어 탐지에 가장 적절한 시그니처를 선정하는 방법을 제안한다.

• BMB Reports
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• 제49권9호
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• pp.514-519
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• 2016

Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene.

• 한국정보처리학회논문지
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• 제5권11호
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• pp.2884-2896
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• 1998

온라인 서명검증을 위해서는 서명의 국부적인 형태가 중요한 판단 근거가 된다. 함수적 접근이나 매개변수적 접근과 같은 지금까지의 접근방법은 서명을 시간에 대한 함수로 나타내거나, 특징집합으로 표현함으로써, 서명의 국부적인 모양을 무시한 채로 서명검증에서 유용한 요소로 사용될 수 있는 국부적인 모양에서의 다양한 특징, 국부적인 모양의 변화, 형태의 복잡성 등을 사용하지 않았다. 이 논문에서는 서명을 구성 형태에 근거한 구조적인 표현 방법으로 나타내어 서명의 국부적인 모양의 분석과 중요한 부분에 대한 선택적인 사용이 가능한 새로운 접근방식의 서명 검증 기법을 제시하였다. 즉, 서명의 구조적 표현에 근거하여 국부적 가중치 적용방법과 진위판단을 위한 임계치의 개인별 차등화 방법을 고안하였고, 이에 대한 실험결과를 분석하였다.

• BMB Reports
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• 제43권10호
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• pp.643-648
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• 2010

Sir William Osler (1849-1919) recognized that "variability is the law of life, and as no two faces are the same, so no two bodies are alike, and no two individuals react alike and behave alike under the abnormal conditions we know as disease". Accordingly, the traditional methods of medicine are not always best for all patients. Over the last decade, the study of genomes and their derivatives (RNA, protein and metabolite) has rapidly advanced to the point that genomic research now serves as the basis for many medical decisions and public health initiatives. Genomic tools such as sequence variation, transcription and, more recently, personal genome sequencing enable the precise prediction and treatment of disease. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. In order to make personalized medicine effective, these genomic techniques must be standardized and integrated into health systems and clinical workflow. In addition, full application of personalized or genomic medicine requires dramatic changes in regulatory and reimbursement policies as well as legislative protection related to privacy. This review aims to provide a general overview of these topics in the field of personalized medicine.