• ETRI Journal
• /
• v.38 no.3
• /
• pp.518-528
• /
• 2016

The searching of an extensive document database for documents that are locally similar to a given query document, and the subsequent detection of similar regions between such documents, is considered as an essential task in the fields of information retrieval and data management. In this paper, we present a framework for such a task. The proposed framework employs the method of short-read mapping, which is used in bioinformatics to reveal similarities between genomic sequences. In this paper, documents are considered biological objects; consequently, edit operations between locally similar documents are viewed as an evolutionary process. Accordingly, we are able to apply the method of evolution tracing in the detection of similar regions between documents. In addition, we propose heuristic methods to address issues associated with the different stages of the proposed framework, for example, a frequency-based fragment ordering method and a locality-aware interval aggregation method. Extensive experiments covering various scenarios related to the search of an extensive document database for documents that are locally similar to a given query document are considered, and the results indicate that the proposed framework outperforms existing methods.

• BMB Reports
• /
• v.49 no.12
• /
• pp.653-654
• /
• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Progress in Medical Physics
• /
• v.19 no.4
• /
• pp.269-275
• /
• 2008

Although MR imaging is generally applicable to depict knee joint deterioration it, is sometimes occurred to mis-read and mis-diagnose the common knee joint diseases. In this study, we employed magnetization transfer ratio (MTR) method to improve the diagnosis of the various knee joint diseases. Spin-echo (SE) T2-weighted images (TR/TE 3,400-3,500/90-100 ms) were obtained in seven cases of knee joint deterioration, FSE T2-weighted images (TR/TE 4,500-5,000/100-108 ms) were obtained in seven cases of knee joint deterioration, gradient-echo (GRE) T2-weighted images (TR/TE 9/4.56/$50^{\circ}$ flip angle, NEX 1) were obtained in 3 cases of knee joint deterioration, In six cases of knee joint deterioration, fat suppression was performed using a T2-weighted short T1/tau inverse recovery (STIR) sequence (TR/TE =2,894-3,215 ms/70 ms, NEX 3, ETL 9). Calculation of MTR for individual pixels was performed on registration of unsaturated and saturated images. After processing to make MTR images, the images were displayed in gray color. For improving diagnosis, three-dimensional isotropic volume images, the MR tristimulus color mapping and the MTR map was employed. MTR images showed diagnostic images quality to assess the patients' pathologies. The intensity difference between MTR images and conventional MRI was seen on the color bar. The profile graph on MTR imaging effect showed a quantitative measure of the relative decrease in signal intensity due to the MT pulse. To diagnose the pathologies of the knee joint, the profile graph data was shown on the image as a small cross. The present study indicated that MTR images in the knee joint were feasible. Investigation of physical change on MTR imaging enables to provide us more insight in the physical and technical basis of MTR imaging. MTR images could be useful for rapid assessment of diseases that we examine unambiguous contrast in MT images of knee disorder patients.