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Search Results: 1 - 10 of 5074 matches for " Yutaka Suzuki "
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Magnesium dititanate (MgTi2O5) with pseudobrookite structure: a review
Yoshikazu Suzuki and Yutaka Shinoda
Science and Technology of Advanced Materials , 2011,
Abstract: Magnesium dititanate (MgTi2O5, MT2) has been synthesized since the early 1930s. It has the pseudobrookite structure (general formula Me3O5), corresponding to the Mg-enriched artificial endmember of the Fe2TiO5 (pseudobrookite)–FeTi2O5 (ferropseudobrookite)–Mg0.5Fe0.5Ti2O5 (armalcolite) solid solution. Since MgTi2O5 has relativity high thermal stability among pseudobrookite-type phases, it is expected to be a well-balanced low-thermal-expansion material. Here we review both the historical and recent studies on MgTi2O5, particularly on its crystal structure, cation order–disorder, physical properties and synthesis methods.
Cholesterol Crystal Deposition in Basal Cell Carcinoma: An Investigation of 4 Cases  [PDF]
Ken Okamura, Takayuki Konno, Masakazu Kawaguchi, Yuko Abe, Yoriko Yaguchi, Sayaka Ajima, Yutaka Hozumi, Tamio Suzuki
Journal of Cosmetics, Dermatological Sciences and Applications (JCDSA) , 2015, DOI: 10.4236/jcdsa.2015.53021
Abstract: Cholesterol crystals are a primary cause of cholesterol embolism if they appear in vessels. Various papers have reported the involvement of cholesterol crystal deposition in cutaneous diseases such as xanthoma. However, no cases of cholesterol crystal involvement in cutaneous cancer have been reported. We report four cases of basal cell carcinoma with cholesterol crystal deposition, and discuss the mechanism(s) of the condition. Disease duration, anatomical site, histopathological features, and serum lipid profiles were investigated. The median disease duration was 3.5 years, and the sites of the lesions were the scrotum (one patient) and the nose (three patients). Histopathologically, there was necrotized tissue around the clefts. In addition, we detected frequent apoptotic cells around the cholesterol clefts in two of the patients by using the terminal deoxynucleotidyl transferase dUTP nick-end labeling method. Serum lipid levels were slightly elevated in two of the patients. In conclusion, cholesterol crystal deposition in basal cell carcinoma was considered to relate to a long disease duration with a tumor in a region that was subject to external irritation. Histopathologically, apoptotic cells around the cholesterol clefts indicated that lipids from the tumor cell membranes were one of the causes of cholesterol crystal deposition.
Prospective Case Study on Characterization of Colorectal Adenomas Comparing AFI with NBI
Haruhisa Suzuki,Yutaka Saito,Takahisa Matsuda,Takeshi Nakajima,Tsuyoshi Kikuchi
Diagnostic and Therapeutic Endoscopy , 2011, DOI: 10.1155/2011/963618
Abstract: Aim. Compare the characterization ability of AFI and NBI for colorectal adenomas. Methods. We prospectively enrolled 58 patients with 89 colorectal adenomas detected by white light colonoscopy. Such lesions were subsequently observed with both AFI and NBI and then treated by endoscopic resection. With respect to the 89 lesions, 3 experienced endoscopists retrospectively evaluated the visualization quality of the AFI and NBI images in a blind manner using a three-tier scale based on excellent, fair, and poor criteria. Results. There were 54, 31, and 4 lesions considered as excellent, fair, and poor visualization, respectively, using AFI in comparison to 53, 19, and 17 lesions, respectively, with NBI. The percentage of excellent and fair visualization lesions was 95.5% with AFI and 80.9% with NBI ( ). Conclusion. This study indicated that AFI may be more effective for the characterization of colorectal adenomas because of better visualization of such lesions compared to NBI. 1. Introduction Colorectal cancer is the fourth most common form of cancer and the second leading cause of cancer-related deaths in the United States [1]. Current trends suggest that colorectal cancer will soon become a major cause of morbidity and mortality in Japan as well [2] so detection and removal of colorectal adenomas by colonoscopy is becoming an increasingly important means of preventing such cancer [3]. Small or flat adenomas may be missed, however, during conventional colonoscopy examinations [4, 5]. In particular, depressed type colorectal tumors and nongranular type laterally spreading tumors (LST-NGs) have a high potential for malignancy [6, 7] even those smaller in size, but such lesions can be difficult to detect using standard white light colonoscopy (WLC). Although chromoendoscopy provides advantages over conventional colonoscopy in the detection of small lesions, the procedure is more complicated and takes longer [8]. In order to detect colorectal adenomas without the necessity of using chromoendoscopy, therefore, a need exists for the development of a new effective endoscopic method for that specific purpose. The autofluorescence imaging (AFI) [9–12] and narrow-band imaging (NBI) [13–16] videoendoscope systems are recently developed noninvasive optical-digital imaging processes. It has been reported that both systems have an advantage over standard WLC in terms of providing better visualization and, therefore, may be able to improve the endoscopic characterization of colorectal adenomas. There have been no published reports, however, that have actually compared
GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics
Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036060
Abstract: Background A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis. Methodology/Principal Findings We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU) calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4 and 15 times faster than BLAT with 1 GPU and 4 GPUs. Conclusions We developed a GPU-optimized algorithm to perform sensitive sequence homology searches and implemented the system as GHOSTM. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We developed GHOSTM, which is a cost-efficient tool, and offer this tool as a potential solution to this problem.
CT Image Segmentation Using FEM with Optimized Boundary Condition
Hiroyuki Hishida, Hiromasa Suzuki, Takashi Michikawa, Yutaka Ohtake, Satoshi Oota
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031116
Abstract: The authors propose a CT image segmentation method using structural analysis that is useful for objects with structural dynamic characteristics. Motivation of our research is from the area of genetic activity. In order to reveal the roles of genes, it is necessary to create mutant mice and measure differences among them by scanning their skeletons with an X-ray CT scanner. The CT image needs to be manually segmented into pieces of the bones. It is a very time consuming to manually segment many mutant mouse models in order to reveal the roles of genes. It is desirable to make this segmentation procedure automatic. Although numerous papers in the past have proposed segmentation techniques, no general segmentation method for skeletons of living creatures has been established. Against this background, the authors propose a segmentation method based on the concept of destruction analogy. To realize this concept, structural analysis is performed using the finite element method (FEM), as structurally weak areas can be expected to break under conditions of stress. The contribution of the method is its novelty, as no studies have so far used structural analysis for image segmentation. The method's implementation involves three steps. First, finite elements are created directly from the pixels of a CT image, and then candidates are also selected in areas where segmentation is thought to be appropriate. The second step involves destruction analogy to find a single candidate with high strain chosen as the segmentation target. The boundary conditions for FEM are also set automatically. Then, destruction analogy is implemented by replacing pixels with high strain as background ones, and this process is iterated until object is decomposed into two parts. Here, CT image segmentation is demonstrated using various types of CT imagery.
Effects of Alu elements on global nucleosome positioning in the human genome
Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, Kenta Nakai
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-309
Abstract: With Fourier analysis, we found that this is not the case: 84-bp and 167-bp periodicities are prevalent in primates. The 167-bp periodicity is intriguing because it is almost equal to the sum of the lengths of a nucleosomal unit and its linker region. After masking Alu elements, these periodicities were greatly diminished. Next, using two independent large-scale sets of nucleosome mapping data, we analyzed the distribution of nucleosomes in the vicinity of Alu elements and showed that (1) there are one or two fixed slot(s) for nucleosome positioning within the Alu element and (2) the positioning of neighboring nucleosomes seems to be in phase, more or less, with the presence of Alu elements. Furthermore, (3) these effects of Alu elements on nucleosome positioning are consistent with inactivation of promoter activity in Alu elements.Our discoveries suggest that the principle governing nucleosome positioning differs greatly across species and that the Alu family is an important factor in primate genomes.The genomic DNA of eukaryotes forms chromatin structures with several proteins. Chromatin is composed of nucleosome cores in which 146-147 base pairs (bp) of DNA are wrapped in 1.67 turns around a histone octamer containing two copies each of four core histones: H2A, H2B, H3, and H4 [1]. Another histone (linker histone) binds to about 20 bp of DNA in the linker region flanking the nucleosome core [2,3]. Nucleosomes are involved in various cellular processes, including transcription, because chromatin can limit the accessibility of regulatory sites. For example, it has been reported in several organisms that the nucleosome occupancy rate upstream from transcription start sites (TSSs) is lower than that in other regions [4-12]. Therefore, understanding the mechanism of nucleosome positioning is important for the analysis of transcriptional regulation and promoter functions.It is known that nucleosome positioning can be affected by DNA sequence. Many previous studies have
Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs
Hiroyuki Wakaguri, Yutaka Suzuki, Masahide Sasaki, Sumio Sugano, Junichi Watanabe
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-312
Abstract: In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from Plasmodium falciparum, P. vivax, P. yoelii, P. berghei, Cryptosporidium parvum, and Toxoplasma gondii. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in T. gondii, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the T. gondii gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes.Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of apicomplexa parasites.Apicomplexa is a phylum of protozoan parasites that infects both humans and animals, causing serious health problems world-wide. Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), for example, cause malaria, which kills over a million people every year [1,2]. Toxoplasma gondii (Tg) infects one third of the entire human population, causing brain and eye defects in the unborn fetuses of infected women [3]. Cryptosporidium parvum (Cp) infects humans and other warm-blooded animals, causing severe diarrhea [4]. Genom
Endoscopic submucosal dissection for large laterally spreading tumors involving the ileocecal valve and terminal ileum
Gustavo Kishimoto,Yutaka Saito,Hajime Takisawa,Haruhisa Suzuki
World Journal of Gastroenterology , 2012, DOI: 10.3748/wjg.v18.i3.291
Abstract: Endoscopic submucosal dissection is a challenging technique that enables en-bloc resection for large colorectal tumors, as laterally spreading tumors, particularly difficult, if the ileocecal valve and terminal ileum is involved. Herein, we report on one of 4 cases. The procedures, using a bipolar needle knife (B-Knife) to reduce the perforation risk and carbon dioxide instead of conventional air insufflation for patient comfort, achieved curative resections without any complications.
TbUNC119 and Its Binding Protein Complex Are Essential for Propagation, Motility, and Morphogenesis of Trypanosoma brucei Procyclic Form Cells
Shigeru Ohshima,Mitsuko Ohashi-Suzuki,Yutaka Miura,Yoshisada Yabu,Noriko Okada,Nobuo Ohta,Takashi Suzuki
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015577
Abstract: Flagellum-mediated motility of Trypanosoma brucei is considered to be essential for the parasite to complete stage development in the tsetse fly vector, while the mechanism by which flagellum-mediated motility is controlled are not fully understood. We thus compared T. brucei whole gene products (amino acid sequence) with Caenorhabditis elegans UNC (uncoordinated) proteins, in order to find uncharacterized motility-related T. brucei genes. Through in silico analysis, we found 88 gene products which were highly similar to C. elegans UNC proteins and categorized them as TbCEUN (T. brucei gene products which have high similarity to C. elegans UNC proteins). Approximately two thirds of the 88 TbCEUN gene products were kinesin-related molecules. A gene product highly similar to C. elegans UNC119 protein was designated as TbUNC119. RNAi-mediated depletion of TbUNC119 showed no apparent phenotype. However, knock-down analysis of both TbUNC119 and its binding protein (TbUNC119BP) which was found by yeast two-hybrid analysis showed characteristic phenotypes, including reduced motility, morphological change (extended cell shape), and cellular apoptosis. Based on the observed phenotypes, possible function of the TbUNC119 and TbUNC119BP is discussed.
Is the Tokyo Foreign Exchange Market Efficient from Two Perspectives of Forward Bias and Anomaly?  [PDF]
Yutaka Kurihara
Modern Economy (ME) , 2011, DOI: 10.4236/me.2011.24067
Abstract: This paper examines the efficiency of the Tokyo Foreign Exchange Market from two perspectives. One is whether or not forward bias in this market has existed and the other is the effect of interventions in the market with a focus on whether or not a day-of-the-week anomaly exists in it. Empirical results show that forward exchange rates are a biased predictor of future spot exchange rates; however, there are some anomalies in the market. The findings suggest the conclusion that this market has not been completely efficient.
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