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Search Results: 1 - 10 of 398 matches for " Hidenori Inaoka "
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Lower expression of genes near microRNA in C. elegans germline
Hidenori Inaoka, Yutaka Fukuoka, Isaac S Kohane
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-112
Abstract: We analyzed gene expression levels around the 84 of 113 know miRNAs for which there are nearby gene that were measured in the data in two independent C. elegans expression data sets. The expression levels are lower for genes in the vicinity of 59 of 84 (71%) miRNAs as compared to genes far from such miRNAs. Analysis of the genes with lower expression in proximity to the miRNAs reveals increased frequency matching of the 7 nucleotide "seed"s of these miRNAs.We found decreased messenger RNA (mRNA) abundance, localized within a 10 kb of chromosomal distance of some miRNAs, in C. elegans germline. The increased frequency of seed matching near miRNA can explain, in part, the localized effects.MicroRNAs (miRNAs) are short (~22 nt-long) non-protein-coding RNAs. In metazoans, miRNA initially thought to be primarily involved in post-transcriptional control [1] have now been shown to have profound and tissue-specific effects on mRNA transcript abundance across significant fractions of the transcriptome [2]. Concurrently it has been demonstrated that miRNAs have a central role in development and organogenesis [3,4]. In the context of the apparent interactions between miRNA and transcriptional control and mounting evidence for the localized component of transcriptional control [5,6], we performed a genome-wide study of C. elegans to determine a) if there were localized effects of miRNA on transcription and b) if previously identified "seed matching" between miRNA and their gene targets could explain, in part, the observed decrease in expression around some miRNAs.First, the 113 known miRNAs in C. elegans were mapped to the worm genome and genes near each miRNAs were sought. Ninety-six miRNAs were found with at least one gene within 10 kb and 31 miRNA were found within the introns of protein-coding genes. Detailed information about the miRNAs is found in supplemental data. Two experiments of genome-wide expression profiling in C. elegans were analyzed. The first dataset by Kim e
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
Yutaka Fukuoka, Hidenori Inaoka, Isaac S Kohane
BMC Genomics , 2004, DOI: 10.1186/1471-2164-5-4
Abstract: We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes.We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.As a consequence of DNA sequencing activities, whole-genome sequences for many microbial organisms as well as eukaryotic species are available in publicly accessible databases. DNA microarray technology makes it possible to simultaneously monitor expression patterns of thousand of genes. Expression profiles combined with whole-genome information, especially map information, enable us to investigate a relationship between co-expression of genes and a chromosomal distance (CD).In the pioneering work in this field, Cohen et al. (2000) and Kruglyak and Tang (2000) independently showed that in yeast (Saccharomyces cerevisiae), adjacent pairs of genes show correlated expression [1,2]. In the nematode worm (Caenorhabditis elegans), a study of the relationship between physical distance and expression similarity found many co-expressed pairs of neighboring genes within a distance range of 20 kbp [3]. Clustering of co-expressed genes has been found in humans (Homo sapiens) [4], worm [5] and
Adaptive thresholds to detect differentially expressed genes in microarray data
Yutaka Fukuoka*,Hidenori Inaoka,Makoto Noshiro
Bioinformation , 2011,
Abstract: To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method.
Can 5-mm Axial CT Images Sufficiently Depict the Hyperdense Middle Cerebral Artery Sign in Patients with Acute Brain Ischemia?  [PDF]
Tomoya Nakatsuka, Mamoru Kurotsuchi, Hideo Morita, Tsutomu Inaoka, Hitoshi Terada
Open Journal of Radiology (OJRad) , 2013, DOI: 10.4236/ojrad.2013.34031

The purpose of this study was to determine whether 5-mm axial CT images can sufficiently depict the hyperdense middle cerebral artery (MCA) sign in patients with acute brain ischemia. Materials and Methods: A retrospective review of 92 cases of ischemic brain infarction confirmed nine patients showing hyperdense MCA signs. CT images were acquired on a 64-slice helical scanner. Images were reconstructed into contiguous 5-mm axial, coronal and sagittal datasets. The first CT scan images of the patients with hyperdense MCA signs and an equal number of CT scans without hyperdense MCA signs inserted at random were analyzed in a blinded review. The presence of the hyperdense MCA sign in M1 segments was recorded. Round regions of interest (ROI) were placed over the M1 segments of the MCAs and the attenuation values in Hounsfield units (HU) were measured on the sagittal and axial images. Results: Nine patients showed a hyperdense MCA sign. They consisted of 4 male and 5 female (mean age, 74.3 years; age range, 45 - 88 years). On the blinded review, hyperdense MCA signs were detected on axial images in 7 patients. In four of the 7 patients, the hyperdense MCA sign was more conspicuous on sagittal images than that on axial images. Hyperdense MCA sign was detected on sagittal images of all 9 patients and exclusive to the sagittal images in two patients. The ROI study showed higher attenuation for the affected MCA on sagittal images (46 - 65 HU) than that on axial images (36 - 54 HU). Conclusion: In patients with acute brain ischemia, 5-mm axial CT images cannot sufficiently depict the hyperdense MCA sign. Sagittal images may be superior to axial images for identifying the sign.

Comparative Study of Extracellular and Intracellular Magnetic Hyperthermia Treatments Using Magnetic Particle Imaging  [PDF]
Sayumi Kobayashi, Akiko Ohki, Minori Tanoue, Yoshimi Inaoka, Kenya Murase
Open Journal of Applied Sciences (OJAppS) , 2017, DOI: 10.4236/ojapps.2017.712047
Abstract: The purpose of this study was to evaluate the effectiveness of intracellular magnetic hyperthermia treatment (MHT) in comparison with that of extracellular MHT using magnetic particle imaging (MPI). Colon-26 cells were implanted subcutaneously into the backs of 8-week-old male BALB/c mice. When the tumor volume reached approximately 100 mm3, the mice were divided into control (n = 10), extracellular MHT (n = 8), and intracellular MHT groups (n = 7). In the control group, MHT was not performed. In the extracellular MHT and intracellular MHT groups, the tumors were injected directly with magnetic nanoparticles (MNPs) (400 mM Resovist®) and were heated for 20 min using an alternating magnetic field. During MHT, the temperatures of the tumor and rectum were measured using optical fiber thermometers. In the extracellular MHT group, MHT was performed 15 min after the injection of MNPs, whereas MHT was performed one day after the injection of MNPs in the intracellular MHT group. In both groups, MPI images were obtained using our MPI scanner immediately before, immediately after, and 7 and 14 days after MHT. After the MPI studies, we drew a region of interest (ROI) on the tumor in the MPI image and calculated the average, maximum, and total MPI values and the number of pixels within the ROI. Transmission electron microscopic (TEM) images were also obtained from resected tumors. In all groups, tumor volume was measured every day and the relative tumor volume growth (RTVG) was calculated. The TEM images showed that almost all the MNPs were aggregated in the extracellular space in the extracellular MHT group, whereas they were contained within the intracellular space in the intracellular MHT group. Although the temperature of the tumor in the intracellular MHT group was significantly lower than that in the extracellular MHT group, the RTVG value in the intracellular MHT group was significantly lower than that in the control group 2 days or more after MHT and that in the extracellular MHT group 3, 4, and 5 days after MHT. The average MPI value normalized by that immediately before MHT in the intracellular MHT group was significantly higher than that in the extracellular MHT group immediately and 7 days after MHT. The maximum and total MPI values normalized by those immediately before MHT in the intracellular MHT group were significantly higher than those in the extracellular MHT group 7 days after MHT, suggesting that the temporal change of MNPs within the tumor in the intracellular MHT group
Prevalence and Characteristics of Treatment-Resistant Hypertension among Hypertensive Japanese Outpatients  [PDF]
Keisuke Okamura, Hidenori Urata
International Journal of Clinical Medicine (IJCM) , 2015, DOI: 10.4236/ijcm.2015.69083
Abstract: Aims: To retrospectively investigate the prevalence and characteristics of treatment-resistant hypertension (R-HT) among consecutive hypertensive outpatients, since patients with R-HT are candidates for catheter-based renal sympathetic denervation (RD). Methods: Consecutive hypertensive outpatients (n = 999) were recruited in our hospital. R-HT patients who were candidates for RD had clinic systolic blood pressure > 160 mmHg despite taking three or more antihypertensive drugs including at least one diuretics at higher than standard doses. Results: Our survey indicated that only 26 patients (2.6%) were potential candidates for renal denervation. Candidates for RD showed a significantly higher age (P < 0.005), brain natriuretic peptide level (P = 0.0001), urinary albumin/creatinine excretion ratio in spot urine (P < 0.005), pulse wave velocity (P < 0.01), left ventricular end-diastolic diameter (P < 0.005), and interventricular septal thickness (P < 0.005) than the other 973 patients. Candidates for denervation had a significantly lower hemoglobin (P = 0.0001), serum albumin (P < 0.001), eGFR (P < 0.0005), plasma renin activity (P = 0.0001), and plasma aldosterone level (P < 0.005) than other patients, while their urinary sodium/creatinine ratio was higher, indicating that patients with R-HT appeared to have a high salt intake. Conclusion: Our retrospective clinical survey indicated that only 0.5% of Japanese hypertensive outpatients (5/999 patients) were candidates for RD. Therefore, establishment of hypertension cohort network will be essential to recruit R-HT patients for RD.
Role Expectation of Nurse Managers in Geriatric Health Services Facilities  [PDF]
Chiharu Miyata, Hidenori Arai
Advances in Aging Research (AAR) , 2016, DOI: 10.4236/aar.2016.55012
Back ground: The characteristics of geriatric health services facilities (GHSF) in Japan include provision of care focused on the life of the residents, and there is a need for cooperation between care workers and physical therapists responsible for the care. Thus, it is expected that a nurse manager occupies specific roles suited for the above characteristics that are different from those of medical facilities. Thus, we aimed to clarify the role expected of nurse managers via a questionnaire survey administered to nurses and care workers in GHSF. Methods: We used a descriptive, cross-sectional design. The study was conducted in 56 GHSF all over Japan. The instrument used for data collection was a questionnaire. The questionnaires consisted of 35 items for determining role expectation of nurse managers, the background information of respondents. The role of nurse managers was analyzed using principal factor analysis (promax rotation). Findings: A total of 259 nurses and care workers participated in this study. We extracted 34 items by factor analysis, which were classified into three factors (promotion of home nursing, management of medical care, and environment creation for collaboration and education). Among care workers, four factors consisting of 33 items were extracted. Factors one, two, and three were similar to those of nurses; “intervention to ethical problem” was extracted as the additional fourth factor. Conclusion: The roles required for nurse managers in GHSF are the promotion of home nursing, which is the original role of the health services facilities, exhibition of the specialty as a healthcare professional, creation of a work environment that promotes mutual understanding for collaboration with other professionals, and enhancement of the education and training system.
Synovial Sarcoma Arising in the Chest Wall Following Ten Years Unexplained Chest Pain  [PDF]
Hideyasu Kudo, Tsutomu Inaoka, Wataru Tokuyama, Nobuyuki Hiruta, Akiteru Hayashi, Hitoshi Terada
Open Journal of Radiology (OJRad) , 2012, DOI: 10.4236/ojrad.2012.23016
Abstract: Synovial sarcomas are the fourth most common malignant soft-tissue tumors, and typically develop in para-articular locations of the extremities. Other less common sites include the head and neck, abdominal wall, intra-abdominal cavity, and mediastinum. However, the occurrence of these tumors in the chest wall is rare. In this article, we report the interesting case of a 31-year-old male with monophasic synovial sarcoma arising in the left anterior chest wall, who had sustained an unexplained, intermittent sharp pain in the area over a period of ten years before the development of the tumor. We discuss his clinical and radiological findings and include a brief review of the literature.
Accurate evaluation of subband structure in a carrier accumulation layer at an n-type InAs surface: LDF calculation combined with high-resolution photoelectron spectroscopy
Takeshi Inaoka,Yoshihito Sanuki,Masahiro Shoji
AIP Advances , 2012, DOI: 10.1063/1.4768671
Abstract: Adsorption on an n-type InAs surface often induces a gradual formation of a carrier-accumulation layer at the surface. By means of high-resolution photoelectron spectroscopy (PES), Betti made a systematic observation of subbands in the accumulation layer in the formation process. Incorporating a highly nonparabolic (NP) dispersion of the conduction band into the local-density-functional (LDF) formalism, we examine the subband structure in the accumulation-layer formation process. Combining the LDF calculation with the PES experiment, we make an accurate evaluation of the accumulated-carrier density, the subband-edge energies, and the subband energy dispersion at each formation stage. Our theoretical calculation can reproduce the three observed subbands quantitatively. The subband dispersion, which deviates downward from that of the projected bulk conduction band with an increase in wave number, becomes significantly weaker in the formation process. Accurate evaluation of the NP subband dispersion at each formation stage is indispensable in making a quantitative analysis of collective electronic excitations and transport properties in the subbands.
Nanofabrication of Nonfouling Surfaces for Micropatterning of Cell and Microtissue
Hidenori Otsuka
Molecules , 2010, DOI: 10.3390/molecules15085525
Abstract: Surface engineering techniques for cellular micropatterning are emerging as important tools to clarify the effects of the microenvironment on cellular behavior, as cells usually integrate and respond the microscale environment, such as chemical and mechanical properties of the surrounding fluid and extracellular matrix, soluble protein factors, small signal molecules, and contacts with neighboring cells. Furthermore, recent progress in cellular micropatterning has contributed to the development of cell-based biosensors for the functional characterization and detection of drugs, pathogens, toxicants, and odorants. In this regards, the ability to control shape and spreading of attached cells and cell-cell contacts through the form and dimension of the cell-adhesive patches with high precision is important. Commitment of stem cells to different specific lineages depends strongly on cell shape, implying that controlled microenvironments through engineered surfaces may not only be a valuable approach towards fundamental cell-biological studies, but also of great importance for the design of cell culture substrates for tissue engineering. To develop this kind of cellular microarray composed of a cell-resistant surface and cell attachment region, micropatterning a protein-repellent surface is important because cellular adhesion and proliferation are regulated by protein adsorption. The focus of this review is on the surface engineering aspects of biologically motivated micropatterning of two-dimensional surfaces with the aim to provide an introductory overview described in the literature. In particular, the importance of non-fouling surface chemistries is discussed.
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