• Title/Summary/Keyword: Detection Sequence

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Complete Sequence Analysis of a Korean Isolate of Chinese Yam Necrotic Mosaic Virus and Generation of the Virus Specific Primers for Molecular Detection

  • Kwon, Sun-Jung;Cho, In-Sook;Choi, Seung-Kook;Yoon, Ju-Yeon;Choi, Gug-Seoun
    • Research in Plant Disease
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    • v.22 no.3
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    • pp.194-197
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    • 2016
  • Chinese yam necrotic mosaic virus (CYNMV) is one of the most widespread viruses in Chinese yam (Dioscorea opposita Thunb.) and causes serious yield losses. Currently, genetic information of CYNMV is very restricted and complete genome sequences of only two isolates (one from Japan and another from China) have been reported. In this study, we determined complete genome sequence of the CYNMV isolate AD collected from Andong, Korea. Genetic analysis of the polyprotein amino acid sequence revealed that the Korean isolate AD has high similarity with the Japanese isolate PES3 (97%) but relatively low similarity with the Chinese isolate FX1 (78%). Phylogenetic analysis using the CYNMV 3' proximal nucleotide sequences harboring the coat protein and 3' untranslated region further supported genetic relationship among the CYNMV isolates. Based on comparative analysis of the CYNMV genome sequences determined in this study and other previous studies, we generated molecular detection primers that are highly specific and efficient for CYNMV diagnosis.

Development and evaluation of semi-nested PCR for detection of the variable lipoprotein haemagglutinin (vlhA) gene of Mycoplasma Synoviae in chicken

  • Pohuang, Tawatchai;Phuektes, Patchara;Junnu, Sucheeva
    • Korean Journal of Veterinary Research
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    • v.60 no.3
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    • pp.109-116
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    • 2020
  • This study aimed to develop a semi-nested polymerase chain reaction assay for the direct detection of Mycoplasma synoviae (M. synoviae) from clinical samples using three newly designed oligonucleotide primers specific to the variable lipoprotein haemagglutinin (vlhA) gene and differentiate M. synoviae field strains based on a nucleotide deletion or the insertion of the proline-rich repeat (PRR) region of the vlhA gene. The developed semi-nested polymerase chain reaction (PCR) assay revealed positive results in 12 out of 100 clinical samples collected from chickens showing lameness and joint swelling. Six positive samples were selected randomly for sequencing, and sequence analysis revealed 96.3-100% nucleotide identities compared to the reference sequences. Phylogenetic analysis showed that sequences of the strains in this study were closely related to WVU1853 (Spain), CK.MS.UDL.PK.2014.2 (Pakistan), and F10-2AS (USA) strains, but they were distinct from the M. synoviae-H vaccine strain sequence. M. synoviae obtained from these samples were identified as types A and C with a length of 38 and 32 amino acids, respectively. These results indicated that the specific and sensitive semi-nested PCR could be a useful diagnostic tool for the direct identification of clinical samples, and the sequence analysis of the partial vlhA gene can be useful for typing M. Synoviae.

Thai Classical Music Matching Using t-Distribution on Instantaneous Robust Algorithm for Pitch Tracking Framework

  • Boonmatham, Pheerasut;Pongpinigpinyo, Sunee;Soonklang, Tasanawan
    • Journal of Information Processing Systems
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    • v.13 no.5
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    • pp.1213-1228
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    • 2017
  • The pitch tracking of music has been researched for several decades. Several possible improvements are available for creating a good t-distribution, using the instantaneous robust algorithm for pitch tracking framework to perfectly detect pitch. This article shows how to detect the pitch of music utilizing an improved detection method which applies a statistical method; this approach uses a pitch track, or a sequence of frequency bin numbers. This sequence is used to create an index that offers useful features for comparing similar songs. The pitch frequency spectrum is extracted using a modified instantaneous robust algorithm for pitch tracking (IRAPT) as a base combined with the statistical method. The pitch detection algorithm was implemented, and the percentage of performance matching in Thai classical music was assessed in order to test the accuracy of the algorithm. We used the longest common subsequence to compare the similarities in pitch sequence alignments in the music. The experimental results of this research show that the accuracy of retrieval of Thai classical music using the t-distribution of instantaneous robust algorithm for pitch tracking (t-IRAPT) is 99.01%, and is in the top five ranking, with the shortest query sample being five seconds long.

Anomaly Detection for User Action with Generative Adversarial Networks (적대적 생성 모델을 활용한 사용자 행위 이상 탐지 방법)

  • Choi, Nam woong;Kim, Wooju
    • Journal of Intelligence and Information Systems
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    • v.25 no.3
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    • pp.43-62
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    • 2019
  • At one time, the anomaly detection sector dominated the method of determining whether there was an abnormality based on the statistics derived from specific data. This methodology was possible because the dimension of the data was simple in the past, so the classical statistical method could work effectively. However, as the characteristics of data have changed complexly in the era of big data, it has become more difficult to accurately analyze and predict the data that occurs throughout the industry in the conventional way. Therefore, SVM and Decision Tree based supervised learning algorithms were used. However, there is peculiarity that supervised learning based model can only accurately predict the test data, when the number of classes is equal to the number of normal classes and most of the data generated in the industry has unbalanced data class. Therefore, the predicted results are not always valid when supervised learning model is applied. In order to overcome these drawbacks, many studies now use the unsupervised learning-based model that is not influenced by class distribution, such as autoencoder or generative adversarial networks. In this paper, we propose a method to detect anomalies using generative adversarial networks. AnoGAN, introduced in the study of Thomas et al (2017), is a classification model that performs abnormal detection of medical images. It was composed of a Convolution Neural Net and was used in the field of detection. On the other hand, sequencing data abnormality detection using generative adversarial network is a lack of research papers compared to image data. Of course, in Li et al (2018), a study by Li et al (LSTM), a type of recurrent neural network, has proposed a model to classify the abnormities of numerical sequence data, but it has not been used for categorical sequence data, as well as feature matching method applied by salans et al.(2016). So it suggests that there are a number of studies to be tried on in the ideal classification of sequence data through a generative adversarial Network. In order to learn the sequence data, the structure of the generative adversarial networks is composed of LSTM, and the 2 stacked-LSTM of the generator is composed of 32-dim hidden unit layers and 64-dim hidden unit layers. The LSTM of the discriminator consists of 64-dim hidden unit layer were used. In the process of deriving abnormal scores from existing paper of Anomaly Detection for Sequence data, entropy values of probability of actual data are used in the process of deriving abnormal scores. but in this paper, as mentioned earlier, abnormal scores have been derived by using feature matching techniques. In addition, the process of optimizing latent variables was designed with LSTM to improve model performance. The modified form of generative adversarial model was more accurate in all experiments than the autoencoder in terms of precision and was approximately 7% higher in accuracy. In terms of Robustness, Generative adversarial networks also performed better than autoencoder. Because generative adversarial networks can learn data distribution from real categorical sequence data, Unaffected by a single normal data. But autoencoder is not. Result of Robustness test showed that he accuracy of the autocoder was 92%, the accuracy of the hostile neural network was 96%, and in terms of sensitivity, the autocoder was 40% and the hostile neural network was 51%. In this paper, experiments have also been conducted to show how much performance changes due to differences in the optimization structure of potential variables. As a result, the level of 1% was improved in terms of sensitivity. These results suggest that it presented a new perspective on optimizing latent variable that were relatively insignificant.

Analysis and Detection of Coast Protein Gene of Barley Yellow Mosaic Virus and Barley Mield Mosaic Virus by RT-PCR (RP-PCR을 이용한 보리누른모자이크바이러스 (BaYMV)와 보리마일드모자이크바이러스(BaMMV)의 외피단백질 유전자 검정 및 해석)

  • 이귀재
    • Korean Journal Plant Pathology
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    • v.14 no.4
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    • pp.314-318
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    • 1998
  • Using the reverse transcription polymerase chain reaction (RT-PCR), a rapid and sensitive assay method for the detection and identification of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) was adapted. Two units of primers from each virus were selected and used for the determination of two different viruses. PCR fragments of BaYMV (ca. 0.9kb) and BaMMV (ca. 0.8kb) were obtained from the designed method for the assay of BaYMV and BaMMV coat protein. PT-PCR fragments were cloned using vector pT7 Blue and the sequences of the selected clones were analyzed. coat protein of BaYMV and that of BaMMV consisted of 297 amino acids (891 nucleotides) and 251 amino acids (753 nucleotides), respectively. The snalysis of coat protein genes from these two viruses showed that 45.6% of nucleotides sequence ad 34.9% of amino acid in BaYMV were homologous to those in BaMMV.

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EEG WAVEFORM DETECTION BASED ON THE SEARCH OF DISTINCTIVE LINE-SEGMENTS (특징적인 직선요소들의 검색에 기초한 EEG 파형 검출)

  • Park, Seung-Hun;Chang, Tae-Kyu
    • Proceedings of the KOSOMBE Conference
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    • v.1992 no.05
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    • pp.121-122
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    • 1992
  • We present a new EEG waveform detection method, based on the search of distinctive line-segments. The method is based on the assumption that EEG waveform morphology is characterized by a sequence of its distinctive line-segments and their structural features. In this method, the distinctive line segments are first searched for, and the structural feature analysis is performed on the found line-segment sequence. Experiments of detecting epileptic spikes are performed on four different subjects.

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Moving Object Edge Extraction from Sequence Image Based on the Structured Edge Matching (구조화된 에지정합을 통한 영상 열에서의 이동물체 에지검출)

  • 안기옥;채옥삼
    • Proceedings of the IEEK Conference
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    • 2003.11a
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    • pp.425-428
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    • 2003
  • Recently, the IDS(Intrusion Detection System) using a video camera is an important part of the home security systems which start gaining popularity. However, the video intruder detection has not been widely used in the home surveillance systems due to its unreliable performance in the environment with abrupt illumination change. In this paper, we propose an effective moving edge extraction algorithm from a sequence image. The proposed algorithm extracts edge segments from current image and eliminates the background edge segments by matching them with reference edge list, which is updated at every frame, to find the moving edge segments. The test results show that it can detect the contour of moving object in the noisy environment with abrupt illumination change.

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Design and Synthesis of Metallopeptide Sensors: Tuning Selectivity with Ligand Variation

  • Kim, Joung-Min;Joshi, Bishnu Prasad;Lee, Keun-Hyeung
    • Bulletin of the Korean Chemical Society
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    • v.31 no.9
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    • pp.2537-2541
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    • 2010
  • We chose a fluorescent pentapeptide sensor (-CPGHE) containing a dansyl fluorophore as a model peptide and investigated whether the selectivity and sensitivity of the peptides for heavy and transition metal ions could be tuned by changing amino acid sequence. In this process, we developed a selective peptide sensor, Cp1-d (-HHPGE, $K_d\;=\;670\;nM$) for detection of $Zn^{2+}$ in 100% aqueous solution and a selective and sensitive peptide sensor, Cp1-e (-CCHPGE, $K_d\;=\;24\;nM$) for detection of $Cd^{2+}$ in 100% aqueous solution. Overall results indicate that the selectivity and sensitivity of the metallopeptide sensors to specific heavy and transition metal ions can be tuned by changing amino acid sequence.

Invariant Detection of Periodic Motion using Affine Model (Periodic Motion의 Invariant Detection을 위한 Affine Model 적용)

  • Choi, Woo-Jin;Chung, Chin-Hyun
    • Proceedings of the KIEE Conference
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    • 1998.07g
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    • pp.2237-2239
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    • 1998
  • A limitation is assumed that In this paper, a generalized method is proposed to extract a period of a motion of on object. To detect a periodic motion, we put restrictions on a stationary camera and on a motion of an object. We ca derive the necessary and sufficient condition that an image sequence consists of the projection of the periodic motion by the affine transformation that is a reasonally good approach to the perspective projection. The difficulty of detecting its periodic motion is to select its have period in sequence and to define its width.

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Fault Detection Relaying for Transmission line Protection using ANFIS (적응형 퍼지 시스템에 의한 송전선로보호의 고장검출 계전기법)

  • 전병준
    • Journal of the Korean Institute of Intelligent Systems
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    • v.9 no.5
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    • pp.538-544
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    • 1999
  • In this paper, we propose a new fault detection algorithm for transmission line protection using ANFIS(Adaptive Network Fuzzy Inference System). The developed system consists of two subsystems: fault type classification, and fault location estimation. We use rms value, zero sequence component and positive sequence of current, and then using learning method of neural network, premise and consequent parameters are tuned properly. To prove the performance of the proposcd system, generated data by EMTP(Electr0- Magnetic Transient Program) sin~ulationi s used. It is shown that the proposed relaying classifies fault types accurately and advances fault location estimation.

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