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Exploring the hepatitis C virus genome using single molecule realtime sequencing

World Journal of Gastroenterology 2019年第32期25卷 4661-4672页

作者： Haruhiko Takeda taiki yamashita Yoshihide Ueda Akihiro Sekine Department of Omics-based Medicine Center for Preventive Medical ScienceChiba UniversityChiba 260-0856Japan Department of Gastroenterology and Hepatology Graduate School of MedicineKyoto UniversityKyoto 606-8507Japan

Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence *** conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real *** addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high *** advantages of long read sequencing enable accurate determination of the haplotypes of individual viral *** sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral ***,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT *** this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome *** also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.

关键词： Third generation sequencing PacBio RSII Single molecule real-time sequencing Hepatitis C virus Resistance-associated substitution Nanopore sequencer

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Automated measurement of three-dimensional cerebral cortical thickness in Alzheimer’s patients using localized gradient vector trajectory in fuzzy membership maps

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Journal of Biomedical Science and Engineering 2013年第3期6卷 327-336页

作者： Chiaki Tokunaga Hidetaka Arimura Takashi Yoshiura Tomoyuki Ohara Yasuo yamashita Kouji Kobayashi taiki Magome Yasuhiko Nakamura Hiroshi Honda Hideki Hirata Masafumi Ohki Fukai Toyofuku Department of Clinical Radiology Graduate School of Medical Sciences Kyushu University Fukuoka Japan Department of Health Sciences Faculty of Medical Sciences Kyushu University Fukuoka Japan Department of Health Sciences Graduate School of Medical Sciences Kyushu University Fukuoka Japan Department of Neuropsychiatry Graduate School of Medical Sciences Kyushu University Fukuoka Japan Division of Radiology Department of Medical Technology Kyushu University Hospital Fukuoka Japan

Our purpose in this study was to develop an automated method for measuring three-dimensional (3D) cerebral cortical thicknesses in patients with Alzheimer’s disease (AD) using magnetic resonance (MR) images. Our proposed method consists of mainly three steps. First, a brain parenchymal region was segmented based on brain model matching. Second, a 3D fuzzy membership map for a cerebral cortical region was created by applying a fuzzy c-means (FCM) clustering algorithm to T1-weighted MR images. Third, cerebral cortical thickness was three- dimensionally measured on each cortical surface voxel by using a localized gradient vector trajectory in a fuzzy membership map. Spherical models with 3 mm artificial cortical regions, which were produced using three noise levels of 2%, 5%, and 10%, were employed to evaluate the proposed method. We also applied the proposed method to T1-weighted images obtained from 20 cases, i.e., 10 clinically diagnosed AD cases and 10 clinically normal (CN) subjects. The thicknesses of the 3 mm artificial cortical regions for spherical models with noise levels of 2%, 5%, and 10% were measured by the proposed method as 2.953 ± 0.342, 2.953 ± 0.342 and 2.952 ± 0.343 mm, respectively. Thus the mean thicknesses for the entire cerebral lobar region were 3.1 ± 0.4 mm for AD patients and 3.3 ± 0.4 mm for CN subjects, respectively (p < 0.05). The proposed method could be feasible for measuring the 3D cerebral cortical thickness on individual cortical surface voxels as an atrophy feature in AD.

关键词： Alzheimer’s Disease (AD) Fuzzy C-Means Clustering (FCM) Three-Dimensional Cerebral Cortical Thickness Localized Gradient Vector

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