198 results on '"Yumi Yamaguchi"'
Search Results
52. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals
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Masao Nagasaki, Kazuki Kumada, Kengo Kinoshita, Yoichi Suzuki, Kaname Kojima, Akira Uruno, Hiroshi Kawame, Osamu Tanabe, Masayuki Yamamoto, Seizo Koshiba, Nobuo Fuse, Kazuro Shimokawa, Nobuo Yaegashi, Jun Yasuda, Fumiki Katsuoka, Shu Tadaka, Yumi Yamaguchi-Kabata, Shigeo Kure, and Gen Tamiya
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Male ,Heterozygote ,Genomic data ,Population ,Biology ,Genome ,Infant, Newborn, Diseases ,Cohort Studies ,03 medical and health sciences ,symbols.namesake ,Hyperphenylalaninemia ,Neonatal Screening ,Asian People ,Gene Frequency ,Japan ,Genetics ,medicine ,Humans ,education ,Gene ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,Newborn screening ,education.field_of_study ,Incidence ,030305 genetics & heredity ,Genetic Diseases, Inborn ,Infant, Newborn ,Reference Standards ,medicine.disease ,Penetrance ,Mendelian inheritance ,symbols ,Female ,Genome-Wide Association Study - Abstract
Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.
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- 2019
53. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare
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Yuichi Aoki, Seizo Koshiba, Fuji Nagami, Hideyasu Kiyomoto, Yoichi Sutoh, Masao Nagasaki, Shu Tadaka, Matsuyuki Shirota, Tadashi Ishii, Hiroshi Tanaka, Takahiro Mimori, Kaname Kojima, Nobuo Fuse, Jun Yasuda, Kichiya Suzuki, Yumi Yamaguchi-Kabata, Masayuki Yamamoto, Atsushi Shimizu, Junichi Sugawara, Tsuyoshi Hachiya, Soichi Ogishima, Junko Kawashima, Yoko Kuroki, Jin Inoue, Fumiki Katsuoka, Miho Kuriki, Hiroshi Kawame, Ritsuko Shimizu, Yoichi Suzuki, Atsushi Hozawa, Kazuki Kumada, Daisuke Saigusa, Osamu Tanabe, Akihito Otsuki, Naoko Minegishi, Kengo Kinoshita, Shigeo Kure, Inaho Danjoh, Ikuko N. Motoike, Mika Sakurai-Yageta, Kenjiro Kosaki, Takako Takai-Igarashi, Sakae Saito, Akito Tsuboi, Satoshi Makino, Shinichi Kuriyama, Gen Tamiya, Yasuyuki Taki, Hiroaki Tomita, Makoto Sasaki, and Nobuo Yaegashi
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Male ,medicine.medical_specialty ,Genetics, Medical ,Population ,Genomics ,Biochemistry ,Polymorphism, Single Nucleotide ,Cohort Studies ,03 medical and health sciences ,Asian People ,Japan ,Medicine ,Humans ,Precision Medicine ,education ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,business.industry ,Genome, Human ,030302 biochemistry & molecular biology ,General Medicine ,Middle Aged ,Reference Standards ,Human genetics ,Family medicine ,Cohort ,Medical genetics ,Female ,Personalized medicine ,business ,Reference genome ,Cohort study - Abstract
Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.
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- 2018
54. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project
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Yosuke Kawai, Jun Yasuda, Kaname Kojima, Masao Nagasaki, Gen Tamiya, Atsushi Shimizu, Nobufumi Yasuda, Inaho Danjoh, Sakae Saito, Kengo Kinoshita, Koichiro Higasa, Ikuko N. Motoike, Makoto Sasaki, Motoki Iwasaki, Shu Tadaka, Nobuo Fuse, Fumiki Katsuoka, Osamu Tanabe, Mika Sakurai-Yageta, Kazuki Kumada, Masayuki Yamamoto, Fumihiko Matsuda, and Yumi Yamaguchi-Kabata
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0301 basic medicine ,lcsh:QH426-470 ,Genotype ,Population genetics ,lcsh:Biotechnology ,Population ,030105 genetics & heredity ,Biology ,Genome reference panel ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Japan ,Asian People ,lcsh:TP248.13-248.65 ,Genetics ,Humans ,1000 Genomes Project ,education ,Genetic association ,education.field_of_study ,Genotype imputation ,Genome, Human ,Haplotype ,Minor allele frequency ,lcsh:Genetics ,030104 developmental biology ,Evolutionary biology ,Human genome ,Imputation (genetics) ,Biotechnology ,Research Article - Abstract
Background Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. Results We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%. Conclusions 1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population’s genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago. Electronic supplementary material The online version of this article (10.1186/s12864-018-4942-0) contains supplementary material, which is available to authorized users.
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- 2018
55. Experiences of Teasing and Bullying in Children Who Stutter
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Yoshikazu, Kikuchi, primary, Toshiro, Umezaki, additional, Motohiro, Sawatsubashi, additional, Masahiko, Taura, additional, Yumi, Yamaguchi, additional, Daisuke, Murakami, additional, and Takashi, Nakagawa, additional
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- 2019
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56. A case of acute right-to-left shunt through a pre-existing atrial septal defect in inferior myocardial infarction
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Yumi Yamaguchi, Kuniyuki Shirasawa, Haruyuki Taguchi, and Yasushi Kono
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medicine.medical_specialty ,business.industry ,Right-to-left shunt ,Inferior Myocardial Infarction ,030204 cardiovascular system & hematology ,03 medical and health sciences ,0302 clinical medicine ,medicine.artery ,Internal medicine ,Cardiology ,Medicine ,Radiology, Nuclear Medicine and imaging ,030212 general & internal medicine ,business - Published
- 2016
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57. Evaluation of Vocal Fold Motion During Blocks in Adults Who Stutter
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Yoshikazu, Kikuchi, primary, Toshiro, Umezaki, additional, Kazuo, Adachi, additional, Motohiro, Sawatsubashi, additional, Yumi, Yamaguchi, additional, Daisuke, Murakami, additional, and Takashi, Nakagawa, additional
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- 2018
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58. Differential Diagnosis between Stuttering and Voice Disorders Using a Questionnaire
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Yoshikazu Kikuchi, Nobuhiro Sato, Toshiro Umezaki, Yumi Yamaguchi, Kazuo Adachi, and Shizuo Komune
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Speech and Hearing ,medicine.medical_specialty ,Stuttering ,business.industry ,medicine ,Differential diagnosis ,medicine.symptom ,Audiology ,LPN and LVN ,business - Published
- 2014
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59. [Breast Cancer Patient with Bone Metastases Who Was Able to Return Home without Using Opioids after Administration of Strontium-89 Chloride]
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Yumi, Yamaguchi, Chihiro, Uejima, Yoichiro, Tada, Seigo, Takaya, Yutaka, Yamashiro, Shunsuke, Shibata, Minoru, Ishiguro, Hideaki, Nishidoi, and Masami, Kobayashi
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Fatal Outcome ,Strontium ,Quality of Life ,Humans ,Pain ,Pain Management ,Bone Neoplasms ,Breast Neoplasms ,Female ,Middle Aged - Abstract
A 46-year-old woman underwent mastectomy for right inflammatory breast cancer.Three years later, she was diagnosed with multiple bone metastases and was treated with systemic chemotherapy and zoledronic acid.Six years after the mastectomy, she complained of severe sacral pain, and 40 Gy external radiotherapy was applied to the sacral metastases.Oxycodone was also administered, but dose escalation was difficult because of severe nausea and fatigue.A bone scan showed increased uptake of Tc99m in an area consistent with the painful regions, and an injection of 89SrCl2 was administered.Five weeks after the injection, her severe pain was relieved and she was able to discontinue the use of opioids completely.She successfully lived at home for 100 days without using opioids.In this case, radionuclide therapy with 89SrCl2 led to remarkable pain relief with an improvement in the quality of life of the patient.
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- 2016
60. The structural origin of metabolic quantitative diversity
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Jun Yasuda, Shigeo Kure, Hideyasu Kiyomoto, Seizo Koshiba, Nobuo Fuse, Tomo Saito, Matsuyuki Shirota, Daisuke Saigusa, Inaho Danjoh, Soichi Ogishima, Takako Takai-Igarashi, Yoichi Suzuki, Takanori Hasegawa, Sachiko Hirano, Kaname Kojima, Naoko Minegishi, Junichi Nakata, Shinichi Kuriyama, Kengo Kinoshita, Hozumi Motohashi, Yumi Yamaguchi-Kabata, Masao Nagasaki, Masayuki Yamamoto, Atsushi Hozawa, Miyuki Sakurai, Osamu Tanabe, Fumiki Katsuoka, Junichi Sugawara, Nobuo Yaegashi, Ikuko N. Motoike, and Yosuke Kawai
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0301 basic medicine ,Genetics ,Whole genome sequencing ,chemistry.chemical_classification ,education.field_of_study ,Multidisciplinary ,030102 biochemistry & molecular biology ,Metabolite ,Population ,Quantitative trait locus ,Biology ,Phenotype ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Metabolomics ,Enzyme ,chemistry ,education ,Gene - Abstract
Relationship between structural variants of enzymes and metabolic phenotypes in human population was investigated based on the association study of metabolite quantitative traits with whole genome sequence data for 512 individuals from a population cohort. We identified five significant associations between metabolites and non-synonymous variants. Four of these non-synonymous variants are located in enzymes involved in metabolic disorders, and structural analyses of these moderate non-synonymous variants demonstrate that they are located in peripheral regions of the catalytic sites or related regulatory domains. In contrast, two individuals with larger changes of metabolite levels were also identified, and these individuals retained rare variants, which caused non-synonymous variants located near the catalytic site. These results are the first demonstrations that variant frequency, structural location, and effect for phenotype correlate with each other in human population, and imply that metabolic individuality and susceptibility for diseases may be elicited from the moderate variants and much more deleterious but rare variants.
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- 2016
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61. [A Case of Drug-Induced Lung Injury Associated with Paclitaxel plus Bevacizumab Therapy]
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Yumi, Yamaguchi, Yoichiro, Tada, Seigo, Takaya, Akemi, Iwamoto, Yutaka, Yamashiro, Shunsuke, Shibata, Minoru, Ishiguro, and Hideaki, Nishidoi
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Bevacizumab ,Paclitaxel ,Pulse Therapy, Drug ,Antineoplastic Combined Chemotherapy Protocols ,Humans ,Breast Neoplasms ,Female ,Neoplasm Invasiveness ,Steroids ,Lung Injury ,Middle Aged ,Respiration Disorders - Abstract
A 61-year old woman with recurrent breast cancer received combined treatment with paclitaxel (PTX) and bevacizumab (BV) as the third-line chemotherapy. During the administration of PTX in the 3 courses of chemotherapy, she suddenly developed respiratory failure, and both chest X-ray and CT revealed bilateral pulmonary infiltrates. Symptoms and radiographic findings responded dramatically to steroid pulse therapy. The history of onset and laboratory data showed no evidence of infection; therefore, we made a diagnosis of acute lung injury induced by the chemotherapy. It should be noted that lung injury may be induced by both PTX and BV, and is one of the important adverse events despite the low frequency of occurrence.
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- 2016
62. Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes
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Atsushi Takahashi, Tatsuhiko Tsunoda, Yusuke Nakamura, Yumi Yamaguchi-Kabata, Naoyuki Kamatani, Natsuhiko Kumasaka, Michiaki Kubo, and Naoya Hosono
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Genetics ,Genotype ,Homozygote ,Haplotype ,Chromosome Mapping ,Genetic Variation ,Population genetics ,Genome-wide association study ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Asian People ,Gene Frequency ,Haplotypes ,Population Groups ,Genetic epidemiology ,Statistical genetics ,Genetic variation ,Humans ,Allele frequency ,Genetics (clinical) ,Genome-Wide Association Study - Abstract
Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388,591 autosomal SNPs from 18,379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.
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- 2012
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63. Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies
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Yumi Yamaguchi-Kabata, Susumu Saito, Naoyuki Kamatani, Yusuke Nakamura, Kazuyuki Nakazono, Michiaki Kubo, Naoya Hosono, and Atsushi Takahashi
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Genotype ,Population ,Single-nucleotide polymorphism ,Biology ,Population stratification ,Polymorphism, Single Nucleotide ,Article ,Asian People ,Gene Frequency ,Japan ,Population Groups ,Genetic variation ,Ethnicity ,Genetics ,Humans ,Genetics(clinical) ,International HapMap Project ,education ,Allele frequency ,Genetics (clinical) ,Genetic association ,education.field_of_study ,Polymorphism, Genetic ,Haplotype ,Genetic Variation ,Genetics, Population ,Haplotypes - Abstract
Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by "Eigenanalysis," using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.
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- 2008
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64. Effect (Comparison between Elderly Person and Youth) of the Break in the Touch Typing Learning Comparison
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Yumi Yamaguchi
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business.product_category ,Applied psychology ,education ,Computer based ,humanities ,Subjective data ,lcsh:TA1-2040 ,Vocational education ,Learning methods ,Chemistry (relationship) ,Typing ,Psychology ,business ,lcsh:Engineering (General). Civil engineering (General) ,Social psychology ,Information appliance - Abstract
The technical education using the information appliance of the old worker is required. However, an elderly person is negative about the utilization of the information appliance. I experimented on, this study about an appropriate break to suppress fatigue of the elderly person, and to learn a touch typing technology effectively and made it clear. The experiment performed two kinds of touch typing learning by the Computer Based Training software. I performed an experiment of elderly person and “Consecutive learning short break models” “Massed practice long break models” which changed the interval of learning and the break by the touch typing software for youths. I performed a questionnaire to a subject to collect the subjective data of fatigue and the learning burden at the same time. As a result, I knew the thing that “the elderly person controlled fatigue by a learning method to put a break in diligently for a short time in this experiment, and could learn a touch typing skill” “having a long it than a youth as for the time to be concerned with the touch typing of the elderly person.” that “the elderly person can learn a touch typing skill early by enjoying CBT learning.”
- Published
- 2016
65. Corticotropin-Releasing Hormone Receptor 2 Gene Variants in Irritable Bowel Syndrome
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Naoki Suzuki, Masashi Aoki, Yumi Yamaguchi-Kabata, Motoyori Kanazawa, Ayaka Sasaki, Naoko Sato, Hitoshi Warita, Shin Fukudo, Hazuki Komuro, Michiko Kano, and Yukari Tanaka
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Male ,Linkage disequilibrium ,Heredity ,Emotions ,Social Sciences ,lcsh:Medicine ,Anxiety ,Pathology and Laboratory Medicine ,Gastroenterology ,Irritable Bowel Syndrome ,0302 clinical medicine ,Genotype ,Medicine and Health Sciences ,Psychology ,lcsh:Science ,Irritable bowel syndrome ,Multidisciplinary ,Depression ,Genetic Mapping ,030211 gastroenterology & hepatology ,Female ,Research Article ,Adult ,medicine.medical_specialty ,Psychological Stress ,Single-nucleotide polymorphism ,Variant Genotypes ,Biology ,Polymorphism, Single Nucleotide ,Receptors, Corticotropin-Releasing Hormone ,03 medical and health sciences ,Young Adult ,Signs and Symptoms ,Internal medicine ,Mental Health and Psychiatry ,medicine ,Genetics ,Humans ,Allele ,Evolutionary Biology ,Population Biology ,Mood Disorders ,Haplotype ,lcsh:R ,Case-control study ,Biology and Life Sciences ,medicine.disease ,Genotype frequency ,Haplotypes ,Case-Control Studies ,Genetic Polymorphism ,lcsh:Q ,030217 neurology & neurosurgery ,Population Genetics - Abstract
Background Corticotropin-releasing hormone (CRH) plays an important role in the pathophysiology of irritable bowel syndrome (IBS) and regulates the stress response through two CRH receptors (R1 and R2). Previously, we reported that a CRHR1 gene polymorphism (rs110402, rs242924, and rs7209436) and haplotypes were associated with IBS. However, the association between the CRHR2 gene and IBS was not investigated. We tested the hypothesis that genetic polymorphisms and haplotypes of CRHR2 are associated with IBS pathophysiology and negative emotion in IBS patients. Methods A total of 142 IBS patients and 142 healthy controls participated in this study. Seven single nucleotide polymorphisms (SNPs) of the CRHR2 gene (rs4722999, rs3779250, rs2240403, rs2267710, rs2190242, rs2284217, and rs2284220) were genotyped. Subjects' psychological states were evaluated using the Perceived-Stress Scale, the State-Trait Anxiety Inventory, and the Self-Rating Depression Scale. Results We found that rs4722999 and rs3779250, located in intronic region, were associated with IBS in terms of genotype frequency (rs4722999: P = 0.037; rs3779250: P = 0.017) and that the distribution of the major allele was significantly different between patients and controls. There was a significant group effect (controls vs. IBS), and a CRHR2 genotype effect was observed for three psychological scores, but the interaction was not significant. We found a haplotype of four SNPs (rs4722999, rs3779250, rs2240403, and rs2267710) and two SNPs (rs2284217 and rs2284220) in strong linkage disequilibrium (D′ > 0.90). We also found that haplotypes of the CRHR2 gene were significantly different between IBS patients and controls and that they were associated with negative emotion. Conclusion Our findings support the hypothesis that genetic polymorphisms and haplotypes of CRHR2 are related to IBS. In addition, we found associations between CRHR2 genotypes and haplotypes and negative emotion in IBS patients and controls. Further studies on IBS and the CRH system are warranted.
- Published
- 2016
66. IL-17B and IL-17C Are Associated with TNF-α Production and Contribute to the Exacerbation of Inflammatory Arthritis
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Keishi Fujio, Akiko Okamoto, Hirofumi Shoda, Kazuhiko Yamamoto, Koki Takahashi, Nelson H. Tsuno, and Yumi Yamaguchi
- Subjects
CD4-Positive T-Lymphocytes ,Adoptive cell transfer ,Inflammatory arthritis ,T cell ,Immunology ,Arthritis ,Cell Line ,Proinflammatory cytokine ,Mice ,Transduction, Genetic ,Animals ,Humans ,Immunology and Allergy ,Medicine ,Bone Resorption ,Interleukin 6 ,Bone Marrow Transplantation ,Transplantation Chimera ,Receptors, Interleukin-17 ,biology ,Interleukin-6 ,Tumor Necrosis Factor-alpha ,business.industry ,Interleukin-17 ,medicine.disease ,Adoptive Transfer ,Arthritis, Experimental ,IL 17 family ,medicine.anatomical_structure ,biology.protein ,Interleukin 17 ,business - Abstract
IL-17A is a T cell-derived proinflammatory cytokine that contributes to the pathogenesis of rheumatoid arthritis. Recently, six related molecules have been identified to form the IL-17 family, as follows: IL-17A, IL-17B, IL-17C, IL-17D, IL-17E, and IL-17F. Whereas IL-17A and IL-17F up-regulate IL-6 in synovial fibroblasts, IL-17B and IL-17C are reported to stimulate the release of TNF-α and IL-1β from the monocytic cell line, THP-1 cell. However, their detailed function remains to be elucidated. We report in this study the effects of IL-17 family on the collagen-induced arthritis (CIA) progression by T cell gene transfer and bone marrow chimeric mice. The mRNA expressions of IL-17 family (IL-17A, IL-17B, IL-17C, and IL-17F) and their receptor (IL-17R and IL-17Rh1) genes in the arthritic paws of CIA mice were elevated compared with controls. Although IL-17A and IL-17F were expressed in CD4+ T cells, IL-17B and IL-17C were expressed in the cartilage and in various cell populations in the CIA arthritic paws, respectively. In vitro, IL-17A, IL-17B, IL-17C, and IL-17F induced TNF-α production in mouse peritoneal exudate cells. In vivo, adoptive transfer of IL-17B- and IL-17C-transduced CD4+ T cells evidently exacerbated arthritis. Bone marrow chimeric mice of IL-17B and IL-17C exhibited elevated serum TNF-α concentration and the high arthritis score upon CIA induction. Moreover, neutralization of IL-17B significantly suppressed the progression of arthritis and bone destruction in CIA mice. Therefore, not only IL-17A, but also IL-17B and IL-17C play an important role in the pathogenesis of inflammatory arthritis.
- Published
- 2007
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67. Selection pressure on human STR loci and its relevance in repeat expansion disease
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Ranajit Chakraborty, Tadashi Imanishi, Makoto K. Shimada, Chisato Yamasaki, Yoshiyuki Suzuki, Yumi Yamaguchi-Kabata, Takashi Gojobori, and Ryoko Sanbonmatsu
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0301 basic medicine ,Neurogenesis ,Population ,Single-nucleotide polymorphism ,Biology ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Tandem repeat ,Sequence Analysis, Protein ,Genetics ,Humans ,Disease ,Selection, Genetic ,education ,Molecular Biology ,Gene ,education.field_of_study ,Genome, Human ,General Medicine ,Sequence Analysis, DNA ,Human genetics ,030104 developmental biology ,Microsatellite ,Human genome ,Trinucleotide repeat expansion ,030217 neurology & neurosurgery ,Microsatellite Repeats - Abstract
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.
- Published
- 2015
68. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
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Rumiko Saito, Kaname Kojima, Kaoru Tsuda, Atsushi Hozawa, Yukuto Sato, Nobuo Fuse, Yosuke Kawai, Shin Ito, Shigeo Kure, Junji Yokozawa, Inaho Danjoh, Masao Nagasaki, Hideyasu Kiyomoto, Yoko Kuroki, Takahiro Mimori, Yumi Yamaguchi-Kabata, Xiaoqing Pan, Fumiki Katsuoka, Kengo Kinoshita, Naoki Nariai, Shinichi Kuriyama, Sakae Saito, Osamu Tanabe, Jun Yasuda, Masayuki Yamamoto, Naoko Minegishi, James Douglas Engel, Satoshi Nishikawa, and Nobuo Yaegashi
- Subjects
Genetics ,Whole genome sequencing ,Multidisciplinary ,Genome, Human ,Haplotype ,General Physics and Astronomy ,Genetic Variation ,General Chemistry ,Biology ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,3. Good health ,Minor allele frequency ,Asian People ,Haplotypes ,Genotype ,Genetic variation ,Humans ,Human genome ,Genetic association - Abstract
The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of, The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.
- Published
- 2015
69. Adenovirus-mediated transfection of caspase-8 sensitizes hepatocellular carcinoma to TRAIL- and chemotherapeutic agent-induced cell death
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Hiroyuki Fuke, Tomoko Inoue, Katsuya Shiraki, Yumi Yamaguchi, Kazumi Miyashita, Yutaka Yamanaka, and Takeshi Nakano
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Programmed cell death ,Carcinoma, Hepatocellular ,viruses ,Genetic Vectors ,CASP8 and FADD-Like Apoptosis Regulating Protein ,Gene Expression ,Antineoplastic Agents ,Apoptosis ,Biology ,Transfection ,Caspase 8 ,Adenoviridae ,TNF-Related Apoptosis-Inducing Ligand ,Cell Line, Tumor ,Survivin ,Humans ,Molecular Biology ,Membrane Glycoproteins ,Tumor Necrosis Factor-alpha ,Cytochrome c ,Liver Neoplasms ,Intracellular Signaling Peptides and Proteins ,Cell Biology ,Molecular biology ,XIAP ,Caspases ,Cancer cell ,biology.protein ,Apoptosis Regulatory Proteins - Abstract
Caspase-8 belongs to the cysteine protease family and is known to be activated at the initial step in the cascade of TRAIL-induced apoptosis. The activation of procaspase-8 can be blocked by a relatively large amount of c-FLIP, which renders resistance to death receptor-mediated apoptosis in many types of cancer cells. To ask if extrinsic over-expression of caspase-8 contributes to the induction of apoptosis, we introduced the caspase-8 gene into HCC cells using an adenoviral (Adv) vector (Adv-Casp8). We demonstrated that Adv-Casp8 increased expression of active forms of caspase-8 in MOI-dependent manner. A large amount of Adv-Casp8 (MOI of 50) induced apoptosis significantly in HCC cells and resulted in downregulation of c-FLIP (in SK-Hep1, HLE, and HepG2 cells), XIAP, survivin, and Bcl-xL (in HLE cells) and dynamic release of cytochrome c and Smac from the mitochondria into the cytosol. On the other hand, a small amount of Adv-Casp8 (MOI of 10) causes a slight but detectable increase in the level of apoptosis with only a small effect on anti-apoptotic proteins and mitochondrial activation. However, small amounts of Adv-Casp8 augmented TRAIL- or chemotherapeutic agent-induced cell death (with an MOI of 10 or 20, respectively). These results suggest both that exogenous over-expression of caspase-8 by Adv-Casp8 may be essential for induction of HCC cell death and that the combination of Adv-Casp8 and TRAIL or chemotherapeutic agents could provide a useful strategy for treatment of HCC.
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- 2006
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70. Proteasome inhibition sensitizes hepatocellular carcinoma cells to TRAIL by suppressing caspase inhibitors and AKT pathway
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Hiroyuki Fuke, Tomoko Inoue, Yumi Yamaguchi, Katsuya Shiraki, Yutaka Yamanaka, Kazushi Sugimoto, Takeshi Nakano, Keiichi Ito, Kazumi Miyashita, and Norihiko Yamamoto
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Proteasome Endopeptidase Complex ,Cancer Research ,Carcinoma, Hepatocellular ,Leupeptins ,Down-Regulation ,Antineoplastic Agents ,Apoptosis ,macromolecular substances ,Inhibitor of apoptosis ,Receptors, Tumor Necrosis Factor ,TNF-Related Apoptosis-Inducing Ligand ,Mice ,chemistry.chemical_compound ,Survivin ,MG132 ,medicine ,Animals ,Humans ,Protease Inhibitors ,Pharmacology (medical) ,Phosphorylation ,Protein kinase B ,PI3K/AKT/mTOR pathway ,Pharmacology ,Chemistry ,Drug Synergism ,Caspase Inhibitors ,XIAP ,Cell biology ,Oncogene Protein v-akt ,Receptors, TNF-Related Apoptosis-Inducing Ligand ,Oncology ,Proteasome ,Caspases ,Proteasome inhibitor ,Cancer research ,Proteasome Inhibitors ,Proto-Oncogene Proteins c-akt ,medicine.drug - Abstract
The ubiquitin-proteasome pathway is responsible for regulating cell cycle proteins, tumor-suppressor molecules, oncogenes, transcription factors, and pro- and anti-apoptotic proteins. The aim of this study is to evaluate the effects of proteasome inhibitors on human hepatocellular carcinoma (HCC) cells. HCC cells SK-Hep1, HLE and HepG2 were treated with the proteasome inhibitors MG132 and MG115. Our data showed that both inhibitors induce apoptosis in the three cell types tested in a dose-dependent manner. Moreover, subtoxic levels of MG132 and MG115 sensitized HCC cells to TRAIL-induced apoptosis. To investigate the mechanism of increased TRAIL sensitivity in HCC cells, we first examined surface expression of TRAIL and its receptors. MG132 upregulated TRAIL and its receptors (TRAIL-R1 and -R2) in SK-Hep1 and HLE, whereas MG115 upregulated them in SK-Hep1. MG132 downregulated expression of X-linked inhibitor of apoptosis protein (XIAP) in SK-Hep1 and HLE, and of survivin in all three cell-types. MG115 downregulated expression of XIAP in SK-Hep1, and survivin in SK-Hep1 and HepG2. Furthermore, MG132 downregulated phospho-AKT and its downstream target phospho-BAD, indicating that MG132 activated the mitochondrial apoptosis pathway by inhibiting phosphorylation of AKT and BAD. In conclusion, proteasome inhibitors induced apoptosis and augmented TRAIL sensitivity via both the IAP family and AKT pathways. Thus, combining proteasome inhibitors with a TRAIL agonist may provide a new therapeutic strategy for HCC.
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- 2006
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71. An Improvement of Nested-Rectangle-Based Hierarchical Data Visualization Technique
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Takayuki Itoh, Yumi Yamaguchi, and Koji Koyamada
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business.industry ,Computer science ,Pattern recognition ,Artificial intelligence ,Rectangle ,business ,Hierarchical database model ,Visualization - Abstract
階層型データの視覚化は, さまざまな分野の大規模データの理解, 分析, 検索, 監視などの目的で有用である. 筆者らは, 葉ノードをアイコンで, 枝ノードを入れ子状の長方形で表現する新しい階層型データ視覚化手法に着目している. この視覚化手法において重要な技術は, 枝ノードを表現する長方形群を有効に画面配置する技術である. 本論文は, 階層型データの視覚化を目的とした長方形群の画面配置に関する改良手法を提案する. 提案手法では, すでに画面配置されている長方形の辺を延長する線分を用いて画面空間を格子状に分割したデータを生成する. そして, その格子分割データを参照しながら, 残りの長方形の候補位置を高速に算出し, その中から最適な位置に長方形を配置する. 本論文では, 提案手法による長方形の画面配置結果を数値評価し, 従来の階層型データ視覚化手法に対する優位性を実証する.
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- 2006
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72. Involvement of tumor necrosis factor–related apoptosis-inducing ligand and tumor necrosis factor–related apoptosis-inducing ligand receptors in viral hepatic diseases
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Yukiko Saitou, Tomoko Inoue, Yumi Yamaguchi, Katsuya Shiraki, Keiichi Ito, Yutaka Yamanaka, Takeshi Nakano, Kazushi Sugimoto, Norihik Yamamoto, Kazumi Miyashita, and Hiroyuki Fuke
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Liver Cirrhosis ,Programmed cell death ,Carcinoma, Hepatocellular ,Indoles ,Cell Survival ,Adenoviridae Infections ,Cell ,Apoptosis ,Biology ,Ligands ,Receptors, Tumor Necrosis Factor ,Pathology and Forensic Medicine ,Flow cytometry ,TNF-Related Apoptosis-Inducing Ligand ,Cell Line, Tumor ,medicine ,Humans ,Receptor ,Fluorescent Dyes ,Membrane Glycoproteins ,medicine.diagnostic_test ,Tumor Necrosis Factor-alpha ,Liver Neoplasms ,Hepatitis C, Chronic ,Flow Cytometry ,Immunohistochemistry ,Recombinant Proteins ,Receptors, TNF-Related Apoptosis-Inducing Ligand ,medicine.anatomical_structure ,Immunology ,Hepatocytes ,Cancer research ,Hepatic stellate cell ,Tumor necrosis factor alpha ,Apoptosis Regulatory Proteins ,Transforming growth factor - Abstract
Summary Tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) induces apoptosis in tumor cells, but not in most normal cells. The role of TRAIL in hepatic cell death and hepatic diseases is not well understood. The present study investigated the expression of TRAIL and TRAIL receptors (TRAIL-Rs) in patients with hepatitis C virus infection using immunohistochemistry and examined physiological roles under viral infection in the HepG2 cell line. Staining of TRAIL or TRAIL-Rs was prominent in the cytoplasm and membrane of hepatocytes in the periportal area. Some liver-infiltrating lymphocytes also displayed positive staining for TRAIL. Staining intensity was significantly increased with disease progression, particularly in the periportal area. AdCMVLacZ (Q-BIOgene, Carisbad, Calif) infection was also found to induce apoptosis in HepG2 cells and significantly augment TRAIL-induced apoptosis. Anti-TRAIL antibody significantly inhibited apoptosis induced by AdCMVLacZ infection. Flow cytometry analysis revealed that both TRAIL-R2 and TRAIL were up-regulated on the cell surface of HepG2 cells with AdCMVLacZ infection. Transforming growth factor– β 1 also enhanced TRAIL expression in HepG2 cells. These results indicate that TRAIL/TRAIL-R apoptotic pathways play important roles in the hepatic cell death during viral infection.
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- 2005
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73. Functional expression of TWEAK in human hepatocellular carcinoma: possible implication in cell proliferation and tumor angiogenesis
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Kazushi Sugimoto, Norihiko Yamamoto, Hiroshi Okano, Katsuya Shiraki, Takeshi Nakano, Yutaka Yamanaka, Tomoyuki Kawakita, Kazumoto Murata, Yumi Yamaguchi, Naoyuki Enokimura, and Yukiko Saitou
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medicine.medical_specialty ,Carcinoma, Hepatocellular ,Transcription, Genetic ,Cell Survival ,Angiogenesis ,Biophysics ,Apoptosis ,Enzyme-Linked Immunosorbent Assay ,Biology ,Transfection ,Biochemistry ,Cell Line, Tumor ,Internal medicine ,medicine ,Humans ,Autocrine signalling ,Molecular Biology ,Cells, Cultured ,Cytokine TWEAK ,Tube formation ,Neovascularization, Pathologic ,Cell growth ,Liver Neoplasms ,NF-kappa B ,Cell Biology ,Immunohistochemistry ,Recombinant Proteins ,digestive system diseases ,Endothelial stem cell ,Endocrinology ,Cell culture ,Tumor Necrosis Factors ,Cancer research ,Human umbilical vein endothelial cell ,Endothelium, Vascular ,Apoptosis Regulatory Proteins ,Carrier Proteins ,Cell Division - Abstract
TNF-like weak inducer of apoptosis (TWEAK) is a member of the TNF family whose transcripts are expressed in various human tissues. Since TWEAK has a variety of biological activities, we investigated TWEAK sensitivity, expression, and physiological role in human hepatocellular carcinomas (HCCs). Tweak receptor was detected in four kinds of HCC cells. TWEAK significantly promoted cell proliferation and induced nuclear factor-kappaB activation in all HCC cells. Surprisingly, we found that HCC cells constitutively express TWEAK. In addition, soluble TWEAK was detected in culture medium. We found that TWEAK also promotes cell proliferation and induces the secretion of IL-8 and MCP-1 in human umbilical vein endothelial cell. Finally, culture medium from Sh-Hep1 cells incubated with anti-TWEAK antibody significantly inhibited endothelial cell tube formation. In conclusion, these results indicate that TWEAK might play a critical role in HCC cellular proliferation using both autocrine and paracrine mechanisms, and modulate tumor-related angiogenesis.
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- 2004
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74. Linkage of Amino Acid Variation and Evolution of Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein (Subtype B) with Usage of the Second Receptor
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Tomoyuki Miura, Sadayuki Ohkura, Masanori Hayami, Masahiro Yamashita, and Yumi Yamaguchi-Kabata
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Receptors, CXCR4 ,Receptors, CCR5 ,Molecular Sequence Data ,HIV Envelope Protein gp120 ,V3 loop ,Biology ,CXCR4 ,Chemokine receptor ,Genetics ,Nucleotide ,Amino Acid Sequence ,Amino Acids ,Codon ,Receptor ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Tropism ,chemistry.chemical_classification ,Likelihood Functions ,Models, Genetic ,Genetic Variation ,Amino acid ,chemistry ,Biochemistry ,HIV-1 ,Databases, Nucleic Acid ,Glycoprotein ,Sequence Alignment - Abstract
To clarify the relationship between the amino acid variations of the gp120 of human immunodeficiency virus type 1 (HIV-1) and the chemokine receptors that are used as the second receptor for HIV, we evaluated amino acid site variation of gp120 between the X4 strains (use CXCR4) and the R5 strains (use CCR5) from 21 sequences of subtype B. Our analysis showed that residues 306 and 322 in the V3 loop and residue 440 in the C4 region were associated with usage of the second receptor. The polymorphism at residue 440 is clearly associated with the usage of the second receptor: The amino acid at position 440 was a basic amino acid in the R5 strains, and a nonbasic and smaller amino acid in the X4 strains, while the V3 loop of the X4 strains was more basic than that of the R5 strains. This suggests that residue 440 in the C4 region, which is close to the V3 loop in the three-dimensional structure, is critical in determining which second receptor is used. Analysis of codon frequency suggests that, in almost all cases, the difference at residue 440 between basic amino acids in the R5 strains and nonbasic amino acids in the X4 strains could be due to a single nucleotide change. These findings predict that the evolutionary changes in amino acid residue 440 may be correlated with evolutionary changes in the V3 loop. One possibility is that a change in electric charge at residue 440 compensates for a change in electric charge in the V3 loop. The amino acid polymorphism at position 440 can be useful to predict the cell tropism of a strain of HIV-1 subtype B.
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- 2004
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75. Incidence of Vibrio parahaemolyticus Sporadic Diarrhea, Isolation of V. parahaemolyticus from Sea Water and Sea Mud, and Molecular Epidemiological Analysis of the V. parahaemolyticus Isolated from Human and Sea Mud in Tohoku District
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Seizaburo Harata, Kunihiro Shinagawa, Masahide Suto, Takashi Hatakeyama, Koichi Saito, Hiroyuki Shiraishi, Jun Yatsuyanagi, Shioko Saito, Manabu Kumagai, Tomoko Takahashi, Yoshio Kobayashi, Katsumi Ootani, Yoshimitsu Otomo, Takashi Sato, Noriyuki Suzuki, Susumu Kumagai, Yoshimichi Miyajima, Nobuhiro Sugawara, Noriyuki Saito, Syouko Hirose, and Yumi Yamaguchi
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Diarrhea ,Vibrio parahaemolyticus ,Incidence (epidemiology) ,medicine ,Seawater ,medicine.symptom ,Biology ,Isolation (microbiology) ,biology.organism_classification ,Microbiology - Published
- 2004
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76. A CASE OF CECAL CANCER PRESENTED WITH APPENDICITIS AND DIAGNOSED PREOPERATIVELY
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Hideaki Nishidoi, Yumi Yamaguchi, Shunsuke Shibata, Minoru Ishiguro, and Eiichi Yurugi
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medicine.medical_specialty ,business.industry ,General surgery ,medicine ,medicine.disease ,business ,Appendicitis ,Cecal Cancer ,Surgery - Published
- 2004
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77. A CASE OF GASTRIC CANCER OCCURRED 25 YEARS AFTER SELECTIVE VAGOTOMY
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Yumi Yamaguchi, Shunsuke Shibata, Mitsuyuki Ikeda, Hirofumi Kudo, Naruo Tokuyasu, and Hideaki Nishidoi
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medicine.medical_specialty ,Selective vagotomy ,business.industry ,Internal medicine ,medicine ,Cancer ,medicine.disease ,business ,Gastroenterology - Abstract
症例は58歳,男性. 33歳時(25年前)に胃潰瘍にて幽門形成術(Finny法)を伴う選択的迷走神経切離術を受けた.その後, 25年経過し,健診で貧血を指摘され,精査の結果,胃癌と診断され当科紹介となった.前庭部小彎側に3'型の進行癌が発見され,幽門側胃切除術が行われた.切除標本では癌腫は幽門輪および幽門形成部には及ばず,病理組織学的検索では低分化型腺癌,深達度se, ly(o), v(o), stage IIであった.迷切術後の胃癌の報告は少なく本邦で自験例を含めて32例にすぎない.しかし,かつて迷切術は良性潰瘍に対して盛んに行われた術式であり,本術式の晩期合併症として無視できないものである.迷切術後の胃癌は残胃癌,胃空腸吻合術後の胃癌と類似した発生機転も推察され,本邦報告例を集計し,若干の文献的考察を加えて報告する.
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- 2004
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78. A CASE OF GENERALIZED JUVENILE GASTROINTESTINAL POLYPOSIS WITH PROTEIN LOSING GASTROPATHY
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Satoshi Murakami, Hideaki Nishidoi, Eiichi Yurugi, Yumi Yamaguchi, Minoru Ishiguro, and Shunsuke Shibata
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medicine.medical_specialty ,business.industry ,Internal medicine ,medicine ,Juvenile gastrointestinal polyposis ,Protein losing gastropathy ,business ,Gastroenterology - Abstract
患者は48歳,男性.全身倦怠感,浮腫を主訴に来院し,血液検査で貧血,低蛋白血症を指摘された.胃内視鏡検査で小ポリープが密生して巨大皺襞を形成している所見を認め,組織検査でHpの感染を伴う若年性ポリポーシスと診断した.自験例は蛋白漏出を伴う肥厚性胃炎であるメネトリエ病の範疇であると判断し,除菌療法や内科的治療を試みたが,内視鏡所見で進行性の経過をとり,症状の改善がなく胃全摘術を施行した.薬物治療に抵抗し,進行性の経過をとる若年性胃ポリポーシスにおいては,外科的治療も考慮すべきと考えられた.
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- 2004
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79. 15-Deoxy-Δ-12-14-PGJ2 Regulates Apoptosis Induction and Nuclear Factor-κB Activation Via a Peroxisome Proliferator-Activated Receptor-γ–Independent Mechanism in Hepatocellular Carcinoma
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Naoyuki Enokimura, Takeshi Nakano, Norihiko Yamamoto, Yumi Yamaguchi, Yukiko Saitou, Katsuya Shiraki, Yutaka Yamanaka, Tomoyuki Kawakita, Kazumoto Murata, Hidekazu Inoue, Hiroshi Okano, and Kazushi Sugimoto
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medicine.medical_specialty ,Carcinoma, Hepatocellular ,Cell cycle checkpoint ,Cell Survival ,Blotting, Western ,Down-Regulation ,Receptors, Cytoplasmic and Nuclear ,Apoptosis ,Caspase 3 ,Biology ,Transfection ,Inhibitor of apoptosis ,Pathology and Forensic Medicine ,TNF-Related Apoptosis-Inducing Ligand ,Internal medicine ,Tumor Cells, Cultured ,medicine ,Humans ,Receptor ,Molecular Biology ,Membrane Glycoproteins ,Dose-Response Relationship, Drug ,Prostaglandin D2 ,Tumor Necrosis Factor-alpha ,Liver Neoplasms ,NF-kappa B ,Cell Biology ,XIAP ,Endocrinology ,Cell culture ,Caspases ,Cancer research ,lipids (amino acids, peptides, and proteins) ,Apoptosis Regulatory Proteins ,Transcription Factors - Abstract
The peroxisome proliferator-activated receptor-gamma (PPARgamma) high-affinity ligand, 15-deoxy-Delta-12,14-PGJ(2) (15d-PGJ(2)), is toxic to malignant cells through cell cycle arrest and apoptosis induction. In this study, we investigated the effects of 15d-PGJ(2) on apoptosis induction and expression of apoptosis-related proteins in hepatocellular carcinoma (HCC) cells. 15d-PGJ(2) induced apoptosis in SK-Hep1 and HepG2 cells at a 50 micro M concentration. Pretreatment with the pan-caspase inhibitor, benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethyl ketone (2-VAD-fmk), only partially blocked apoptosis induced by 40 micro M 15d-PGJ(2). This indicated that 15d-PGJ(2) induction of apoptosis was associated with a caspase-3-independent pathway. 15d-PGJ(2) also induced down-regulation of the X chromosome-linked inhibitor of apoptosis (XIAP), Bclx, and apoptotic protease-activating factor-1 in SK-Hep1 cells but not in HepG2 cells. However, 15d-PGJ(2) sensitized both HCC cell lines to TNF-related apoptosis-induced ligand-induced apoptosis. In SK-Hep1 cells, cell toxicity, nuclear factor-kappaB (NF-kappaB) suppression, and XIAP down-regulation were induced by 15d-PGJ(2) treatment under conditions in which PPARgamma was down-regulated. These results suggest that the effect of 15d-PGJ(2) was through a PPARgamma-independent mechanism. Although cell toxicity was induced when PPARgamma was down-regulated in HepG2 cells, NF-kappaB suppression and XIAP down-regulation were not induced. In conclusion, 15d-PGJ(2) induces apoptosis of HCC cell lines via caspase-dependent and -independent pathways. In SK-Hep1 cells, the ability of 15d-PGJ(2) to induce cell toxicity, NF-kappaB suppression, or XIAP down-regulation seemed to occur via a PPARgamma-independent mechanism, but in HepG2 cells, NF-kappaB suppression by 15d-PGJ(2) was dependent on PPARgamma.
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- 2003
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80. A Case of Metastatic Carcinoma of the Rectum from Gastric Carcinoma Mimicking Primary Rectal Carcinoma
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Shunsuke Shibata, Yumi Yamaguchi, Minoru Ishiguro, Takuji Naka, Kenjirou Taniguchi, and Hideaki Nishidoi
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Oncology ,medicine.medical_specialty ,medicine.anatomical_structure ,business.industry ,Internal medicine ,Rectal carcinoma ,medicine ,Rectum ,Gastric carcinoma ,business ,Gastroenterology ,Metastatic carcinoma - Abstract
原発性直腸癌様所見を呈した胃癌術後直腸転移の1例を経験したので報告する.症例は58歳,女性. 1999年5月,胃癌の診断にて胃全摘術を施行した.病理組織学的所見はpor, se, INFγ, ly1, v0, n2 (+), stage IIIB,根治度Bであった.術後外来にてfollow中, 2001年12月,便秘症状がしだいにひどくなったため精査を施行した.注腸造影では直腸Raに比較的境界明瞭な約5cm大の全周性の狭窄を,また腹部CTでは直腸に全周性の壁肥厚を認め,直腸癌の診断にて低位前方切除術を施行した.病理組織学的には,胃癌と同等な低分化型腺癌が粘膜下層を中心に増殖しており,胃癌の直腸転移と診断した.胃癌の大腸転移は稀な疾患であり切除可能な症例は極めて少ない.中には原発性大腸癌との鑑別が困難な症例も散見される.注腸X線検査の詳細な検討による診断と治療方針の決定が必要とされる.
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- 2003
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81. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data
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Yukuto Sato, Naoki Nariai, Yumi Yamaguchi-Kabata, Kaname Kojima, Masao Nagasaki, Yosuke Kawai, Takahiro Mimori, Jun Yasuda, and Sakae Saito
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Genotype ,Human leukocyte antigen ,Biology ,Data sequences ,Gene Frequency ,HLA Antigens ,Genetics ,Humans ,Allele ,Allele frequency ,Gene ,Alleles ,Whole genome sequencing ,Internet ,Polymorphism, Genetic ,Genome, Human ,Histocompatibility Testing ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Bayes Theorem ,Proceedings ,Primer (molecular biology) ,DNA microarray ,Algorithms ,Biotechnology - Abstract
Background Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. Results We have developed a computational tool, HLA-VBSeq, to estimate the most probable HLA alleles at full (8-digit) resolution from whole-genome sequence data. HLA-VBSeq simultaneously optimizes read alignments to HLA allele sequences and abundance of reads on HLA alleles by variational Bayesian inference. We show the effectiveness of the proposed method over other methods through the analysis of predicting HLA types for HLA class I (HLA-A, -B and -C) and class II (HLA-DQA1,-DQB1 and -DRB1) loci from the simulation data of various depth of coverage, and real sequencing data of human trio samples. Conclusions HLA-VBSeq is an efficient and accurate HLA typing method using high-throughput sequencing data without the need of primer design for HLA loci. Moreover, it does not assume any prior knowledge about HLA allele frequencies, and hence HLA-VBSeq is broadly applicable to human samples obtained from a genetically diverse population.
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- 2015
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82. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
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Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki, Kaname Kojima, Naoki Nariai, Yukuto Sato, and Takahiro Mimori
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Pipeline (computing) ,Sequence assembly ,RNA-Seq ,Computational biology ,Biology ,Bayes' theorem ,RNA Isoforms ,Complementary DNA ,Genetics ,graphical models ,Humans ,RNA, Messenger ,Sequence Analysis, RNA ,Gene Expression Profiling ,Research ,Computational Biology ,Genetic Variation ,Bayes Theorem ,Transcript isoform quantification ,Gene expression profiling ,DNA microarray ,variational Bayesian inference ,Algorithms ,Software ,Biotechnology ,HeLa Cells - Abstract
Background High-throughput RNA sequencing (RNA-Seq) enables quantification and identification of transcripts at single-base resolution. Recently, longer sequence reads become available thanks to the development of new types of sequencing technologies as well as improvements in chemical reagents for the Next Generation Sequencers. Although several computational methods have been proposed for quantifying gene expression levels from RNA-Seq data, they are not sufficiently optimized for longer reads (e.g. > 250 bp). Results We propose TIGAR2, a statistical method for quantifying transcript isoforms from fixed and variable length RNA-Seq data. Our method models substitution, deletion, and insertion errors of sequencers based on gapped-alignments of reads to the reference cDNA sequences so that sensitive read-aligners such as Bowtie2 and BWA-MEM are effectively incorporated in our pipeline. Also, a heuristic algorithm is implemented in variational Bayesian inference for faster computation. We apply TIGAR2 to both simulation data and real data of human samples and evaluate performance of transcript quantification with TIGAR2 in comparison to existing methods. Conclusions TIGAR2 is a sensitive and accurate tool for quantifying transcript isoform abundances from RNA-Seq data. Our method performs better than existing methods for the fixed-length reads (100 bp, 250 bp, 500 bp, and 1000 bp of both single-end and paired-end) and variable-length reads, especially for reads longer than 250 bp.
- Published
- 2015
83. Transfer Functions Composition for Volume Data Mining
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Yumi Yamaguchi, Yuriko Takeshima, Takayuki Itoh, Shigeo Takahashi, and Issei Fujishiro
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Computer science ,Media Technology ,Planning target volume ,Key (cryptography) ,Volume (computing) ,Context (language use) ,Data mining ,Electrical and Electronic Engineering ,Composition (combinatorics) ,computer.software_genre ,Transfer function ,computer ,Computer Science Applications - Abstract
Analytic, simulated, scanned datasets were used to evaluate two representative data-centric methods for designing transfer functions (TFs), which are a key factor determining the quality of volume rendered images. They map the physical fields of a given volume dataset to the optical properties, such as color and opacity. Designing proper TFs is difficult because they depend on both the context of the target volume dataset and the purpose of the visual exploration. A system called “Ivory” was developed to assist in the design of TFs. With it, a better TF can be composed so as to inherit different features from two original TFs.
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- 2002
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84. Visualization of Web access logs using Data Jewelry Box
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Takayuki Itoh, Yuko Ikehata, Yasumasa Kajinaga, and Yumi Yamaguchi
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World Wide Web ,Set (abstract data type) ,Bar (music) ,Bar chart ,law ,Computer science ,Web page ,Icon ,Web access ,computer ,computer.programming_language ,Visualization ,law.invention - Abstract
This paper presents a tool for visualizing Web access logs, which has two views. The left view represents Web sitemaps by a set of webpage icons. It places the icons onto display spaces by data jewelry box algorithm. The right view represents Web access statistics by a bar chart. It aggregates the accesses according to user-specified attributes, such as time, client, and status. When a user clicks a bar in the right view, the left view highlights icons that have corresponding accesses. When a user clicks an icon in the left view, the right view shows the access statistics of the clicked webpage. These combinations of the two views help users to find problems of websites, and discover trends of accesses.
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- 2002
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85. Nucleophilic allylation of N,O-acetals with allylic alcohols promoted by Pd/Et3B and Pd/Et2Zn systems
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Yumi Yamaguchi, Masanari Kimura, Katsumi Tohyama, and Mariko Hashimoto
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Carbohydrate ,Allylic rearrangement ,Allylation ,Hemiacetal ,Organic Chemistry ,Umpolung ,chemistry.chemical_element ,Biochemistry ,chemistry.chemical_compound ,chemistry ,Nucleophile ,Deoxyribose ,Drug Discovery ,Ribose ,Organic chemistry ,Palladium - Abstract
Pd/Et3B and Pd/Et2Zn systems promote the nucleophilic allylations of 2-aminotetrahydrofuran and 2-aminotetrahydropyran with allylic alcohols to provide ω-hydroxyhomoallylamines in high yields. The transformation is applicable to the allylation of non-protective carbohydrates, such as ribose and deoxyribose., Tetrahedron Letters, 52(8), pp.913-915; 2011
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- 2011
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86. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
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Yukuto Sato, Kengo Kinoshita, Xiaoqing Pan, Masayuki Yamamoto, Inaho Danjoh, Shin Ito, Mitsuyo Matsumoto, Kaoru Tsuda, Naoki Nariai, Tomo Saito, Matsuyuki Shirota, Rumiko Saito, Satoshi Nishikawa, Junji Yokozawa, Ikuko N. Motoike, Hisaaki Kudo, Masao Nagasaki, Ichiko Nishijima, Kaname Kojima, Naoko Minegishi, Osamu Tanabe, Jun Yasuda, Kazuhiko Igarashi, Nobuo Fuse, Sakae Saito, Fumiki Katsuoka, and Yumi Yamaguchi-Kabata
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Male ,Semiconductor-type sequencer ,Population genetics ,Population ,Genomics ,Biology ,Polymorphism, Single Nucleotide ,Deep sequencing ,Single nucleotide variations ,Next-generation sequencer ,Human population genetics ,Genetics ,Humans ,Exome ,education ,Exome sequencing ,Whole genome sequencing ,Whole-genome sequencing ,Base Composition ,education.field_of_study ,Genome, Human ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Sequence Analysis, DNA ,SNP genotyping ,Semiconductors ,Female ,Research Article ,Biotechnology - Abstract
Background Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. Results Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. Conclusions Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.
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- 2014
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87. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing
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Naoki Nariai, Kaname Kojima, Takahiro Mimori, Masao Nagasaki, Mamoru Takahashi, Yosuke Kawai, Yukuto Sato, and Yumi Yamaguchi-Kabata
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media_common.quotation_subject ,Population ,MiSeq ,Statistics as Topic ,Detailed data ,Computational biology ,Biology ,computer.software_genre ,Computer graphics ,Data cleaning ,User-Computer Interface ,Data sequences ,Software ,Genetics ,Computer Graphics ,Humans ,Quality (business) ,education ,Graphical user interface ,media_common ,education.field_of_study ,business.industry ,Illumina HiSeq ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Automated analysis ,Sequence Analysis, DNA ,High-Throughput DNA Sequencing ,NGS ,Data mining ,business ,computer ,Biotechnology - Abstract
Background Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. Results We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. Conclusion The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.
- Published
- 2014
88. O3‐04‐04: TRANSCRIPTOME ANALYSIS OF DISTINCT MOUSE STRAINS REVEALS KLC1 SPLICE VARIANT E AS AN ABETA ACCUMULATION MODIFIER
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Masatoshi Takeda, Kozin Kamino, Takashi S. Kodama, Toshihisa Tanaka, Tatsuhiko Tsunoda, Kanta Yanagida, Takashi Morihara, Noriyuki Hayashi, Michael A. Silverman, Yumi Yamaguchi, Masahiro Sato, Mikiko Yokokoji, and Hiroyasu Akatsu
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Transcriptome ,Genetics ,Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,Developmental Neuroscience ,Epidemiology ,Health Policy ,Alternative splicing ,Neurology (clinical) ,Geriatrics and Gerontology ,Biology - Published
- 2014
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89. Transcriptome analysis of distinct mouse strains reveals kinesin light chain-1 splicing as an amyloid-β accumulation modifier
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Taiichi Katayama, Hironori Takamura, Tatsuhiko Tsunoda, Yuhki Saito, Hiroaki Kazui, Takashi Kudo, Naohiro Itoh, Ryo Kimura, Ryota Hashimoto, Shinji Tagami, Mikiko Yokokoji, Kouzin Kamino, Nobuyuki Kimura, Toshihisa Tanaka, Masayasu Okochi, Takashi S. Kodama, Yumi Yamaguchi-Kabata, Hiroyasu Akatsu, Kouhei Nishitomi, Masahiro Sato, Takashi Morihara, Yoshio Hashizume, Masatoshi Takeda, Michael A. Silverman, Noriyuki Hayashi, Toshiharu Suzuki, and Kanta Yanagida
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Candidate gene ,Kinesins ,Biology ,Transcriptome ,Mice ,Species Specificity ,Alzheimer Disease ,Animals ,Humans ,Protein Isoforms ,education ,Gene ,Crosses, Genetic ,education.field_of_study ,Gene knockdown ,Multidisciplinary ,Amyloid beta-Peptides ,Gene Expression Profiling ,Alternative splicing ,Brain ,Biological Sciences ,Molecular biology ,Kinesin light chain 1 ,RNA splicing ,Microtubule-Associated Proteins ,Intracellular - Abstract
Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-β (Aβ). The genes that govern this process, however, have remained elusive. To this end, we combined distinct mouse strains with transcriptomics to directly identify disease-relevant genes. We show that AD model mice (APP-Tg) with DBA/2 genetic backgrounds have significantly lower levels of Aβ accumulation compared with SJL and C57BL/6 mice. We then applied brain transcriptomics to reveal the genes in DBA/2 that suppress Aβ accumulation. To avoid detecting secondarily affected genes by Aβ, we used non-Tg mice in the absence of Aβ pathology and selected candidate genes differently expressed in DBA/2 mice. Additional transcriptome analysis of APP-Tg mice with mixed genetic backgrounds revealed kinesin light chain-1 (Klc1) as an Aβ modifier, indicating a role for intracellular trafficking in Aβ accumulation. Aβ levels correlated with the expression levels of Klc1 splice variant E and the genotype of Klc1 in these APP-Tg mice. In humans, the expression levels of KLC1 variant E in brain and lymphocyte were significantly higher in AD patients compared with unaffected individuals. Finally, functional analysis using neuroblastoma cells showed that overexpression or knockdown of KLC1 variant E increases or decreases the production of Aβ, respectively. The identification of KLC1 variant E suggests that the dysfunction of intracellular trafficking is a causative factor of Aβ pathology. This unique combination of distinct mouse strains and model mice with transcriptomics is expected to be useful for the study of genetic mechanisms of other complex diseases.
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- 2014
90. Fast isosurface generation using the volume thinning algorithm
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Takayuki Itoh, Yumi Yamaguchi, and Koji Koyamada
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Theoretical computer science ,Computer science ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Computational geometry ,Computer Graphics and Computer-Aided Design ,Reduction (complexity) ,Maxima and minima ,Signal Processing ,Isosurface ,Computer Vision and Pattern Recognition ,Algorithm ,Software ,ComputingMethodologies_COMPUTERGRAPHICS ,Volume (compression) - Abstract
One of the most effective techniques for developing efficient isosurfacing algorithms is the reduction of visits to nonisosurface cells. Recent algorithms have drastically reduced the unnecessary cost of visiting nonisosurface cells. The experimental results show almost optimal performance in their isosurfacing processes. However, most of them have a bottleneck in that they require more than O(n) computation time for their preprocessing, where n denotes the total number of cells. We propose an efficient isosurfacing technique, which can be applied to unstructured as well as structured volumes and which does not require more than O(n) computation time for its preprocessing. A preprocessing step generates an extrema skeleton, which consists of cells and connects all extremum points, by the volume thinning algorithm. All disjoint parts of every isosurface intersect at least one cell in the extrema skeleton. Our implementation generates isosurfaces by searching for isosurface cells in the extrema skeleton and then recursively visiting their adjacent isosurface cells, while it skips most of the nonisosurface cells. The computation time of the preprocessing is estimated as O(n). The computation time of the isosurfacing process is estimated as O(n/sup 1/3/m+k), where k denotes the number of isosurface cells and m denotes the number of extremum points since the number of cells in an extrema skeleton is estimated as O(n/sup 1/3/m).
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- 2001
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91. The Genetic Structure of the Raleigh Natural Population of Drosophila melanogaster Revisited
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Yumi Yamaguchi, Hiroshi Baba, Shinichi Kusakabe, and Terumi Mukai
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Male ,Genetics ,education.field_of_study ,Effective size ,Homozygote ,Population ,Biology ,biology.organism_classification ,Drosophila melanogaster ,Genetics, Population ,Natural population growth ,Evolutionary biology ,Genetic structure ,Animals ,Female ,education ,Research Article - Abstract
The Raleigh natural population of Drosophila melanogaster was reanalyzed with special attention to possible dysgenic effects during the extraction of chromosomes. About 600 second chromosomes were extracted from the Raleigh natural population, half in the cytoplasm of wild-caught females (native genetic background) and half in the cytoplasm of the laboratory line, C160(In(2LR)SM1, Cy/In(2LR)bwV1) (foreign genetic background). We could not find significant differences between the two extraction schemes in the frequency of lethal second chromosomes (Q = 0.252 for the lines with the negative genetic background vs. 0.231 for the lines with the foreign genetic background) or in the homozygous detrimental (D) and lethal (L) loads (D = 0.210 vs. 0.251; L = 0.287 vs. 0.264). The effective size of the population was estimated to be ~19,000, based on the allelism rate of lethal-bearing chromosomes. The homozygous load markedly decreased in the 15 years since a previous study of the same population.
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- 2000
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92. A Topological Analysis Approach to Dynamic Volume Data Mining
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Shigeo Takahashi, Yumi Yamaguchi, Yuriko Takeshima, and Issei Fujishiro
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Scale (ratio) ,Topological skeleton ,Volume rendering ,Data mining ,Topology ,computer.software_genre ,Transfer function ,Reeb graph ,computer ,Topology (chemistry) ,Field (computer science) ,Volume (compression) ,Mathematics - Abstract
This paper takes advantage of a 3D field topology analysis for automating transfer function design aiming at volume data mining. The conventional Reeb graph-based approach to describe the topological features of 3D surfaces is extended to capture the topological skeleton of a volumetric field. Based on the analysis results, which are represented in the form of hyper Reeb graph, we propose two principles to design appropriate color/opacity transfer functions for direct volume rendering. Feasibility study of the present methodology is performed with a large scale 4D simulated dataset from atomic collision research. In analyzing the dynamic volume data, it turned out to be effective to use transfer functions designed appropriately at each time step. The basic idea of another approach with a higher order hyper Reeb graph to dynamic volume data mining is also discussed.
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- 2000
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93. A CASE OF ENDOCRINE CELL CARCINOMA OF THE RECTUM
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Minoru Ishiguro, Shunsuke Shibata, Satoshi Murakami, Hideaki Nishidoi, Keigo Ashida, and Yumi Yamaguchi
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Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,biology ,business.industry ,Rectum ,Multimodal therapy ,medicine.disease ,medicine.anatomical_structure ,Biopsy ,Carcinoma ,Synaptophysin ,biology.protein ,Medicine ,Adenocarcinoma ,business ,Chemoradiotherapy ,Barium enema - Abstract
A 78-year-old woman was seen at the hospital because of rectal bleeding. Barium enema and colonofiberscopic examination revealed a tumor with ulceration in the lower rectum. Preoperative histological diagnosis from a biopsy specimen was undifferentiated carcinoma of the rectum. Abdomino-perineal amputaion of the rectum was performed. Immunohistochemically the resected specimen were positive for NSE and synaptophysin and an electron-microscopical examination showed membrane-bound electron opaque granules in the tumor cells. Therefore the tumor was diagnosed as endocrine cell carcinoma. The patient died of rapidly progressed multiple liver and bone metastases and local recurrences on the 80th postoperative day. Endocrine cell carcinoma has the least favorable prognosis and surgical treatment alone can not offer the cure of the disease. When undifferentiated carcinoma or poorly differentiated adenocarcinoma is indicated for rectal lesions at biopsy, aggressive exploration entertaining a possible existence of the disease is essential. And effective multimodal therapy including operation and chemoradiotherapy should be established.
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- 2000
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94. Genetic diversity of HIV-1 group M from Cameroon and Republic of Congo
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Jun Takehisa, Yumi Yamaguchi-Kabata, Eiji Ido, Yosuke Harada, B. Bikandou, Masanori Hayami, M. Ikeda, Innocent Mboudjeka, P. M’pelle, H. J. Parra, Tomoyuki Miura, L. Zekeng, Yuko Taniguchi, and L. Kaptue
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Male ,viruses ,Molecular Sequence Data ,HIV Infections ,HIV Integrase ,HIV Envelope Protein gp120 ,Polymerase Chain Reaction ,Genome ,Phylogenetics ,Virology ,Genotype ,Humans ,Amino Acid Sequence ,Cameroon ,Genetic variability ,Cloning, Molecular ,Phylogeny ,Genetics ,Genetic diversity ,Base Sequence ,Molecular epidemiology ,biology ,Strain (biology) ,Genetic Variation ,virus diseases ,Sequence Analysis, DNA ,General Medicine ,Genes, pol ,Peptide Fragments ,Integrase ,Congo ,DNA, Viral ,HIV-1 ,biology.protein ,Female ,Sequence Alignment - Abstract
We analyzed 57 HIV-1 isolates from Cameroon and the Republic of Congo, with respect to the env C2V3 and/or the pol integrase regions. The results indicated that the topology of the pol tree correlated well with that of the env tree for four clusters of subtype D, F G and H, suggesting that these trees reflect the true evolution of the overall genome structures of these subtypes. However, of 22 Cameroonian isolates that were classified as subtype A based on env, 20 of them diverged in their pol sequence into two lineages that were completely different from the prototypical subtype A, tentatively designated as subtypes A1 and A2. The subtype A1 isolates (6 out of 22) were related in their env C2V3 regions with prototypical subtype A strain, but in their pol regions, they formed an independent cluster that diverged from known HIV-1 subtypes so far reported (except for subtypes I and J). The subtype A2 isolates (14 out of 22), which represent the major epidemic type of HIV-1 in Cameroon, clustered distinctly in both the env and pol trees with the recently described A/G mosaic strains from Nigeria and Djibouti. These two lineages were not spreading in the neighboring Republic of Congo.
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- 1999
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95. Human Immunodeficiency Virus Type 1 Intergroup (M/O) Recombination in Cameroon
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Lazare Kaptue, Yumi Yamaguchi-Kabata, Eiji Ido, Leopold Zekeng, Tomoyuki Miura, Innocent Mboudjeka, Yosuke Harada, Jun Takehisa, and Masanori Hayami
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Adult ,viruses ,Molecular Sequence Data ,Immunology ,HIV Infections ,Genome, Viral ,Biology ,Recombinant virus ,Polymerase Chain Reaction ,Microbiology ,Genome ,Virus ,Homology (biology) ,Phylogenetics ,Virology ,Gene duplication ,Humans ,Cameroon ,Cloning, Molecular ,Gene ,Phylogeny ,Recombination, Genetic ,Genetics ,Base Sequence ,Phylogenetic tree ,Gene Amplification ,Insect Science ,DNA, Viral ,HIV-1 ,Recombination and Evolution ,Female - Abstract
Here we describe, for the first time, recombinants between two highly divergent major groups of human immunodeficiency virus type 1 (HIV-1), M and O, within a Cameroonian woman infected with three different HIV-1 strains, a group O virus, a subtype D virus, and a recently reported IBNG (A/G)-like recombinant virus. Using nested extra-long PCR amplification, we sequenced from thepolregion to theenvregion including accessory genes of the viral genome obtained from the patient’s uncultured peripheral blood mononuclear cells and examined the phylogenetic position of each gene. Compared with sequential blood samples obtained in 1995 and 1996, there were multiple segmental exchanges between three HIV-1 strains (O, D, and IBNG) and all the recombinants appeared to be derived from a common M/O ancestor. Importantly, recombination between groups M and O occurred, even though the homology between these two groups is 69, 76, 68, and 55% in thegag,pol,vif-vpr, andenvregions, respectively. Recombination between strains with such distant lineages may contribute substantially to generating new HIV-1 variants.
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- 1999
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96. THE SIGNIFICANCE OF PREOPERATIVE CT DURING ARTERIAL PORTOGRAPHY IN SURGICAL TREATMENT OF PATIENTS WITH HEPATOCELLULAR CARCINOMA
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Yumi Yamaguchi, Yutaka Yamashiro, Takafumi Hayashi, Yasuaki Hirooka, Nobuaki Kaibara, Ichiro Konishi, Kazunori Suzuki, and Naoki Sato
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medicine.medical_specialty ,medicine.diagnostic_test ,business.industry ,Hepatocellular carcinoma ,medicine ,Computed tomography ,Imaging Procedures ,Radiology ,business ,medicine.disease ,Arterial portography ,Surgical treatment - Abstract
This study was designed to elucidate the significance of preoperative computed tomography during arterial portography (CTAP) in surgical treatment of hepatocellular carcinoma (HCC). Eighteen patients with HCC whose minute lesions had been pointed out by CTAP preoperatively (CTAP positive group) were compared with another eight patients with HCC having postoperative recurrence in a region at where no tumors had been detected by preoperative CTAP (CTAP negative group) for preoperative location of tumor and postoperative pattern of recurrence. In the CTAP positive group, 11 patients had recurrence and the remaining seven patients had not. Disease-free periods up to recurrences were 8.7 months in an average in the 11 CTAP positive patients and 16.6 months in the CTAP-negative group, showing a significantly shorter interval in the CTAP positive patients. In recurred cases from the CTAP positive group, tumors identified by imaging procedures other than CTAP were solitary in four and multiple in seven cases, while all solitary in nonrecurred cases. In the recurred CTAP positive cases, actual recurrence occurred in the same segment where a tummor had been pointed out by CTAP alone in five out of six cases of solitary recurrenc; or involved the same segment where CTAP detected tumor (s) in four out of five cases of multiple recurrence. It is indicated that the possibility of postoperative recurrence of HCC is high in cases having minute lesions visualized by CTAP alone in addition to multiple lesions visualized by imaging procedures other than CTAP. We think that periodical imaging methods including CTAP are required for HCC patients.
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- 1999
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97. A CASE OF CALCIFICATED TUMOR OF THE PANCREAS
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Nobuaki Kaibara, Yumi Yamaguchi, Tsuyoshi Ueta, Yasushi Horie, Michio Maeta, Nobuhiko Toyota, and Syunsuke Katayama
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Pathology ,medicine.medical_specialty ,medicine.anatomical_structure ,business.industry ,Medicine ,business ,Pancreas - Published
- 1999
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98. Identification of regions in which positive selection may operate in S-RNase of Rosaceae: Implication forS-allele-specific recognition sites in S-RNase
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Takeshi Ishimizu, Toshinori Endo, Shigemi Norioka, Yumi Yamaguchi-Kabata, Kazuo T. Nakamura, and Fumio Sakiyama
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Models, Molecular ,Scrophulariaceae ,RNase P ,Molecular Sequence Data ,Biophysics ,Biochemistry ,Protein Structure, Secondary ,Substrate Specificity ,Self-incompatibility ,Ribonucleases ,Structural Biology ,Non-synonymous nucleotide substitution ,Genetics ,Amino Acid Sequence ,Rosales ,Selection, Genetic ,Allele ,Molecular Biology ,Peptide sequence ,Protein secondary structure ,Alleles ,Sequence (medicine) ,Sequence Homology, Amino Acid ,biology ,Cell Biology ,biology.organism_classification ,Protein tertiary structure ,Protein Structure, Tertiary ,Positive selection ,Rosacea ,S-RNase - Abstract
A stylar S-RNase is associated with gametophytic self-incompatibility in the Rosaceae, Solanaceae, and Scrophulariaceae. This S-RNase is responsible for S-allele-specific recognition in the self-incompatible reaction, but how it functions in specific discrimination is not clear. Window analysis of the numbers of synonymous (dS) and non-synonymous (dN) substitutions in rosaceous S-RNases detected four regions with an excess of dN over dS in which positive selection may operate (PS regions). The topology of the secondary structure of the S-RNases predicted by the PHD method is very similar to that of fungal RNase Rh whose tertiary structure is known. When the sequences of S-RNases are aligned with the sequence of RNase Rh based on the predicted secondary structures, the four PS regions correspond to two surface sites on the tertiary structure of RNase Rh. These findings suggest that in S-RNases the PS regions also form two sites and are candidates for the recognition sites for S-allele-specific discrimination.
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- 1998
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99. Differences in the Evolutionary Pattern of Feline Panleukopenia Virus and Canine Parvovirus
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Morikazu Shinagawa, Motohiro Horiuchi, Yutaka Toyoda, Hideyuki Nagasawa, Takashi Gojobori, Naotaka Ishiguro, Masami Mochizuki, and Yumi Yamaguchi
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Nonsynonymous substitution ,Time Factors ,Genes, Viral ,Parvovirus, Canine ,animal diseases ,viruses ,Molecular Sequence Data ,Feline panleukopenia ,Viral Nonstructural Proteins ,Antibodies, Viral ,Polymerase Chain Reaction ,Virus ,Evolution, Molecular ,Epitopes ,Capsid ,Dogs ,Virology ,Animals ,Antigens, Viral ,Gene ,Phylogeny ,DNA Primers ,Genetics ,Base Sequence ,biology ,Phylogenetic tree ,Canine parvovirus ,Antibodies, Monoclonal ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Amino Acid Substitution ,DNA, Viral ,Mutation ,Cats ,Capsid Proteins ,Feline Panleukopenia Virus ,Synonymous substitution - Abstract
Canine parvovirus (CPV) suddenly appeared in the late 1970s after which it showed continuous antigenic changes. Virological and molecular genetic analyses mainly focused on feline panleukopenia virus (FPLV) were conducted in this study because FPLV is the suspected ancestor of CPV; the way in which FPLV evolves may help to explain the emergence of CPV. Analysis of escape mutants against FPLV-specific monoclonal antibody showed that viruses possessing CPV-like properties were not easily detected in FPLV virus stocks. Phylogenetic analysis revealed that the nonstructural protein 1 (NS1) and capsid protein 2 (VP2) genes of FPLV changed with time. A similar tendency, however, was not observed in the FPLV VP2 proteins. In contrast, the topology of the phylogenetic tree of VP2 proteins of CPV basically concurred with that of the VP2 genes. Analysis of the ratio of nonsynonymous and synonymous substitutions revealed that synonymous substitutions exceeded nonsynonymous substitutions in both the NS1 and VP2 genes of FPLV, even when the analysis focused on specific regions in the VP2 gene that are known to be located on the capsid surface. Comparison of the CPV VP2 genes revealed that nonsynonymous substitution was found to dominate over synonymous substitution in one specific region in the VP2 gene. These results suggested that FPLV has changed mainly by random genetic drift. In contrast, after the appearance of CPV, changes in the CPV VP2 gene appear to be partly selected by certain positive selection forces. CPV and FPLV are known to be closely related viruses genetically and biologically, but the evolutionary mechanisms of the two viruses appeared to be different.
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- 1998
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100. THE CLINICAL SIGNIFICANCE OF SPLENECTOMY IN PATIENTS UNDERGOING HEPATIC RESECTION FOR HEPATOCELLULAR CARCINOMA WITH LIVER CIRRHOSIS
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Naoki Satoh, Ichiro Konishi, Yasuaki Hirooka, Ryuichi Hamazoe, Takahumi Hayashi, Nobuaki Kaibara, Yutaka Yamashiro, Tetsuya Kaneko, Kiyoaki Mizusawa, and Yumi Yamaguchi
- Subjects
medicine.medical_specialty ,Cirrhosis ,Hepatic resection ,business.industry ,General surgery ,medicine.medical_treatment ,Splenectomy ,medicine.disease ,Gastroenterology ,Internal medicine ,Hepatocellular carcinoma ,Medicine ,Clinical significance ,In patient ,business - Published
- 1998
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