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Search Results: 1 - 10 of 4368 matches for " Etsuko Miyamoto-Sato "
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Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-350
Abstract: Here, we introduce a combinatorial approach for prediction of protein complexes focusing not only on determining member proteins in complexes but also on the DDI/PPI organization of the complexes. Our method analyzes complex candidates predicted by the existing methods. It searches for optimal combinations of domain-domain interactions in the candidates based on an assumption that the proteins in a candidate can form a true protein complex if each of the domains is used by a single protein interaction. This optimization problem was mathematically formulated and solved using binary integer linear programming. By using publicly available sets of yeast protein-protein interactions and domain-domain interactions, we succeeded in extracting protein complex candidates with an accuracy that is twice the average accuracy of the existing methods, MCL, MCODE, or clustering coefficient. Although the configuring parameters for each algorithm resulted in slightly improved precisions, our method always showed better precision for most values of the parameters.Our combinatorial approach can provide better accuracy for prediction of protein complexes and also enables to identify both direct PPIs and DDIs that mediate them in complexes.Recently developed high-throughput methods such as yeast two-hybrid or mass spectrometry to obtain protein-protein interactions (PPIs) have provided a global view of the interaction network [1-5]. As a PPI network grows, it becomes increasingly important to detect functional modules for understanding cellular organization and its dynamics [6]. Protein complexes are clusters of multiple proteins, and they often play a crucial part in basal cellular mechanism. Therefore, computational methods to predict protein complexes are becoming important.There are four steps in characterizing a protein complex [7]. The first step is to identify its member proteins. The second step is to determine its topology by identifying pairs of proteins which have direct inte
A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks
Etsuko Miyamoto-Sato,Shigeo Fujimori,Masamichi Ishizaka,Naoya Hirai,Kazuyo Masuoka,Rintaro Saito,Yosuke Ozawa,Katsuya Hino,Takanori Washio,Masaru Tomita,Tatsuhiro Yamashita,Tomohiro Oshikubo,Hidetoshi Akasaka,Jun Sugiyama,Yasuo Matsumoto,Hiroshi Yanagawa
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009289
Abstract: Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.
Mitochondria–Nucleus Shuttling FK506-Binding Protein 51 Interacts with TRAF Proteins and Facilitates the RIG-I-Like Receptor-Mediated Expression of Type I IFN
Taishin Akiyama, Takuma Shiraishi, Junwen Qin, Hiroyasu Konno, Nobuko Akiyama, Miho Shinzawa, Maki Miyauchi, Nobukazu Takizawa, Hiromi Yanai, Hiroyuki Ohashi, Etsuko Miyamoto-Sato, Hiroshi Yanagawa, Weidong Yong, Weinian Shou, Jun-ichiro Inoue
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0095992
Abstract: Virus-derived double-stranded RNAs (dsRNAs) are sensed in the cytosol by retinoic acid-inducible gene (RIG)-I-like receptors (RLRs). These induce the expression of type I IFN and proinflammatory cytokines through signaling pathways mediated by the mitochondrial antiviral signaling (MAVS) protein. TNF receptor-associated factor (TRAF) family proteins are reported to facilitate the RLR-dependent expression of type I IFN by interacting with MAVS. However, the precise regulatory mechanisms remain unclear. Here, we show the role of FK506-binding protein 51 (FKBP51) in regulating the dsRNA-dependent expression of type I IFN. The binding of FKBP51 to TRAF6 was first identified by “in vitro virus” selection and was subsequently confirmed with a coimmunoprecipitation assay in HEK293T cells. The TRAF-C domain of TRAF6 is required for its interaction, although FKBP51 does not contain the consensus motif for interaction with the TRAF-C domain. Besides TRAF6, we found that FKBP51 also interacts with TRAF3. The depletion of FKBP51 reduced the expression of type I IFN induced by dsRNA transfection or Newcastle disease virus infection in murine fibroblasts. Consistent with this, the FKBP51 depletion attenuated dsRNA-mediated phosphorylations of IRF3 and JNK and nuclear translocation of RelA. Interestingly, dsRNA stimulation promoted the accumulation of FKBP51 in the mitochondria. Moreover, the overexpression of FKBP51 inhibited RLR-dependent transcriptional activation, suggesting a scaffolding function for FKBP51 in the MAVS-mediated signaling pathway. Overall, we have demonstrated that FKBP51 interacts with TRAF proteins and facilitates the expression of type I IFN induced by cytosolic dsRNA. These findings suggest a novel role for FKBP51 in the innate immune response to viral infection.
Twenty-Two-Year Observation on Urinary Cadmium and ß2-Microglobulin in Inhabitants after Cessation of Cadmium-Exposure in Japan  [PDF]
Reiko Sato, Teruhiko Kido, Hideaki Nakagawa, Muneko Nishijo, Ryumon Honda, Etsuko Kobayashi, Yasushi Suwazono
Open Journal of Nephrology (OJNeph) , 2013, DOI: 10.4236/ojneph.2013.34035
Abstract:

Objective: This is an epidemiological survey that was conducted for 22 years to investigate the physical effects on inhabitants who had been exposed to cadmium (Cd) from processing of remnants discharged at the time of copper refinement. It was possible to obtain findings on physical effects 27 years after Cd exposure. Materials and Methods: Of the inhabitants who were 50 years old or younger in 1981 and who were living in the most contaminated area in the Kakehashi River basin, 68 (32 males and 36 females) who underwent all of the 5 screenings during the 22-year period were extracted as subjects. Early morning urine was collected for urinalysis, and Cd and ?2-MG concentrations were determined. Results: 27 years after cessation of Cd exposure, it was shown that urinary Cd concentrations were significantly decreased and urinary ?2-MG concentrations were significantly increased. Conclusion: Once exposed to Cd, it takes about 30 years for the Cd that remains in the body to decrease by half. Once renal tubular dysfunction occurs after Cd exposure, irreversible aggravation is inevitable.

Non-Gaussian isocurvature perturbations in dark radiation
Etsuko Kawakami,Masahiro Kawasaki,Koichi Miyamoto,Kazunori Nakayama,Toyokazu Sekiguchi
Physics , 2012, DOI: 10.1088/1475-7516/2012/07/037
Abstract: We study non-Gaussian properties of the isocurvature perturbations in the dark radiation, which consists of the active neutrinos and extra light species, if exist. We first derive expressions for the bispectra of primordial perturbations which are mixtures of curvature and dark radiation isocurvature perturbations. We also discuss CMB bispectra produced in our model and forecast CMB constraints on the nonlinearity parameters based on the Fisher matrix analysis. Some concrete particle physics motivated models are presented in which large isocurvature perturbations in extra light species and/or the neutrino density isocurvature perturbations as well as their non-Gaussianities may be generated. Thus detections of non-Gaussianity in the dark radiation isocurvature perturbation will give us an opportunity to identify the origin of extra light species and lepton asymmetry.
Primary Neuroendocrine Carcinoma Combined with Squamous Cell Carcinoma of the Soft Palate: A Case Report and Review of Literature  [PDF]
Chatchaphan Udompatanakorn, Naomi Yada, Ayataka Ishikawa, Ikuya Miyamoto, Yukiko Sato, Kou Matsuo
Open Journal of Stomatology (OJST) , 2018, DOI: 10.4236/ojst.2018.83008
Abstract: Background: Neuroendocrine carcinomas (NECs) are rare neoplasms that widely occur in various organs. They are heterogeneous and vary from low to high grade malignant. NEC presenting with a squamous cell carcinoma (SCC) component is referred to as a composite tumor. Thus far, few cases of this composite tumor in the oral cavity have been reported in the literature; thus, the histogenesis remains unclear. ase Presentation: We encountered a rare case of a primary NEC combined with SCC, occurring at the soft palate in a 59-year-old man. A resected specimen of the tumor was composed of two components: NEC and SCC. The NEC area contained small round to oval atypical cells arranged in nests with a glandular-like-pattern, hyperchromatic molded nuclei, a high nuclear-to-cytoplasmic ratio, and a scant eosinophilic cytoplasm. The SCC area was composed of non-keratotic, dysplastic oval to spindle-shaped squamous cells with indistinct cell borders and large nuclei that were hyperchromatic and pleomorphic. Immunohistochemically, the tumor cells of the NEC component were positive for chromagranin A, synaptophysin, CD56, and p16, whereas those of the SCC component were positive for 34βE12, p63, and p16. Conclusion: In consideration of the morphological and immunohistochemical results, the final diagnosis was a primary NEC combined with SCC of the soft palate.
Investigation of Temperature Dependence of Polymer Gels for Use with Scanning Magnetic Resonance Imaging  [PDF]
Hiraku Kawamura, Kazuya Shinoda, Hiraku Fuse, Takaoki Takanashi, Yoshikazu Shimada, Yoshiyuki Ishimori, Masahiko Monma, Katsumi Miyamoto, Hitoshi Sato, Tatsuya Fujisaki, Takeji Sakae, Akira Matsumura
International Journal of Medical Physics,Clinical Engineering and Radiation Oncology (IJMPCERO) , 2018, DOI: 10.4236/ijmpcero.2018.72022
Abstract: Polymer gels are three-dimensional dosimetric tools. The purpose of the present study was to investigate the temperature dependence of polymer gels during scanning Magnetic Resonance Imaging. Prepared gels were irradiated with a 6MV X-ray beam at intensities ranging from 0 to 20 Gy in order to investigate their dose-R2 and dose-R1 responses. Irradiated gels were evaluated from 1.5-T magnetic resonance R2 and R1 images for each 5°C change in temperature from 5°C to 41°C, and then the four-field box technique irradiation plan was used to deliver a total dose of 4 Gy using the same beam weight in each direction to the prepared gels. The profile of the dose map generated from the four-field irradiated gel data at 20°C was then compared with the planned data. The dose-R2 response curve was linear up to 20 Gy at 20°C, with a slope of 1.17 Gy-1˙s-1. The slopes of the fitted curves of the dose-R2 decreased as gel temperature increased. The slopes of the dose-R1 curves were more parallel than the slopes of the dose-R2 curves between 5 and 41°C. The difference in the full width of half maximum of the gel profile data obtained using the four-field box technique at 20°C and the planned data were below 5% on average. The dose map from the irradiated gels obtained using the dose-R2 curve was the same as that from the planned data under the same temperature conditions. Measurement of difference between various temperatures is significant with dose accuracy. It is suitable to evaluate the gel dosimeter under the thermal equilibrium condition, MRI room temperature from the point of view of the stability of the irradiated gels.
Evaluation of both perfusion and atrophy in multiple system atrophy of the cerebellar type using brain SPECT alone
Hiroshi Matsuda, Etsuko Imabayashi, Ichiei Kuji, Akira Seto, Kimiteru Ito, Daisuke Kikuta, Minoru Yamada, Yasumasa Shimano, Noriko Sato
BMC Medical Imaging , 2010, DOI: 10.1186/1471-2342-10-17
Abstract: After linear spatial normalization of brain perfusion SPECT using 99mTc-ethyl cysteinate dimer (99mTc-ECD) to a Talairach space, high-dimension-warping was done using an original 99mTc-ECD template. Contraction map images calculated from Jacobian determinants and spatially normalized SPECT images using this high-dimension-warping were compared using statistical parametric mapping (SPM2) between two groups of 16 multiple system atrophy of the cerebellar type (MSA-C) patients and 73 age-matched normal controls. This comparison was also performed in conventionally warped SPECT images.SPM2 demonstrated statistically significant contraction indicating local atrophy and decreased perfusion in the whole cerebellum and pons of MSA-C patients as compared to normal controls. Higher significance for decreased perfusion in these areas was obtained in high-dimension-warping than in conventional warping, possibly due to sufficient spatial normalization to a 99mTc-ECD template in high-dimensional warping of severely atrophied cerebellum and pons. In the present high-dimension-warping, modification of tracer activity remained within 3% of the original tracer distribution.The present new technique applying TBM to brain SPECT provides information on both perfusion and atrophy at the same time thereby enhancing the role of brain perfusion SPECTBrain perfusion single photon emission computed tomography (SPECT) has been applied to various neurodegenerative diseases such as Alzheimer's disease. Particular attention must be paid to local atrophy when interpreting brain SPECT images in neurodegenerative diseases, since tracer activity determined by SPECT with limited spatial resolution is greatly influenced by partial volume effects. Local atrophy causes underestimation of tracer activity due to these effects. To precisely evaluate this local atrophy of the brain, magnetic resonance imaging (MRI) has been commonly used. If SPECT could evaluate local atrophy as well as brain perfusion, the
Use of anthropometric indicators in screening for undiagnosed vertebral fractures: A cross-sectional analysis of the Fukui Osteoporosis Cohort (FOC) study
Kiyoko Abe, Junko Tamaki, Eiko Kadowaki, Yuho Sato, Akemi Morita, Misa Komatsu, Sayaka Takeuchi, Etsuko Kajita, Masayuki Iki
BMC Musculoskeletal Disorders , 2008, DOI: 10.1186/1471-2474-9-157
Abstract: Lateral imaging of the spine by single energy X-ray absorptiometry and vertebral morphometry were conducted in 116 Japanese women (mean age: 69.9 ± 9.3 yr). Vertebral deformities were diagnosed by the McCloskey-Kanis criteria and were used as a proxy for vertebral fractures. We evaluated whether anthropometric parameters including arm span-height difference (AHD), wall-occiput distance (WOD), and rib-pelvis distance (RPD) were related to vertebral deformities. Positive findings were defined for AHD as ≥ 4.0 cm, for WOD as ≥ 5 mm, and for RPD as ≤ two fingerbreadths. Receiver operating characteristics curves analysis was performed, and cut-off values were determined to give maximum difference between sensitivity and false-positive rate. Expected probabilities for vertebral deformities were calculated using logistic regression analysis.The mean AHD for those participants with and without vertebral deformities were 7.0 ± 4.1 cm and 4.2 ± 4.2 cm (p < 0.01), respectively. Sensitivity and specificity for use of AHD-positive, WOD-positive and RPD-positive values in predicting vertebral deformities were 0.85 (95% CI: 0.69, 1.01) and 0.52 (95% CI: 0.42, 0.62); 0.70 (95% CI: 0.50, 0.90) and 0.67 (95% CI: 0.57, 0.76); and 0.67 (95% CI: 0.47, 0.87) and 0.59 (95% CI: 0.50, 0.69), respectively. The sensitivity, specificity, and likelihood ratio for a positive result (LR) for use of combined AHD-positive and WOD-positive values were 0.65 (95% CI: 0.44, 0.86), 0.81 (95% CI: 0.73, 0.89), and 3.47 (95% CI: 3.01, 3.99), respectively. The expected probability of vertebral deformities (P) was obtained by the equation; P = 1-(exp [-1.327-0.040 × body weight +1.332 × WOD-positive + 1.623 × AHD-positive])-1. The sensitivity, specificity and LR for use of a 0.306 cut-off value for probability of vertebral fractures were 0.65 (95% CI: 0.44, 0.86), 0.87 (95% CI: 0.80, 0.93), and 4.82 (95% CI: 4.00, 5.77), respectively.Both WOD and AHD effectively predicted vertebral deformities. This screenin
Seguran?a alimentar em domicílios chefiados por idosos, Brasil
Rosa, Tereza Etsuko da Costa;Mondini, Lenise;Gubert, Muriel Bauermann;Sato, Geni Satiko;Benício, Maria Helena D'Aquino;
Revista Brasileira de Geriatria e Gerontologia , 2012, DOI: 10.1590/S1809-98232012000100008
Abstract: food security in households headed by elderly people has special dimension as for health and welfare, since it is clearly important to ensure that they go on contributing to society in an active and productive way. objective: to determine the prevalence of food insecurity in households whose heads are older, according to socio-demographic characteristics. methods: it is a descriptive study with households whose heads have 60 years of age or over declared, selected from the national sample household survey - pnad 2004. we applied the brazilian food insecurity scale, ranking the households into food security and food insecurity, moderate and severe. descriptive analysis of data included the frequency distribution of households according to levels of food insecurity in the strata of socio-demographic variables, taking into account the design effect. results: the study showed that 29.8% of households were in the condition of food insecurity and that this condition was significantly associated with less affluent regions (north / northeast, rural), with the most vulnerable population segments (the poorest and least educated) and also with characteristics of gender (women) and race (indian, mulatto and black) which is known to occupy the lower levels of social hierarchy. conclusion: the distribution of food insecurity in households headed by elderly people, following a similar trend of brazilian households, confirms the higher prevalence of this condition in socioeconomic disadvantaged population or characteristics associated with poverty.
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