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Search Results: 1 - 10 of 402 matches for " Takanori Washio "
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GC-compositional strand bias around transcription start sites in plants and fungi
Shigeo Fujimori, Takanori Washio, Masaru Tomita
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-26
Abstract: Our study confirmed a significant GC-skew (C > G) in the TSS of Oryza sativa (rice) genes. The full-length cDNAs and genomic sequences from Arabidopsis and rice were compared using statistical analyses. Despite marked differences in the G+C content around the TSS in the two plants, the degrees of bias were almost identical. Although slight GC-skew peaks, including opposite skews (C < G), were detected around the TSS of genes in human and Drosophila, they were qualitatively and quantitatively different from those identified in plants. However, plant-like GC-skew in regions upstream of the translation initiation sites (TIS) in some fungi was identified following analyses of the expressed sequence tags and/or genomic sequences from other species. On the basis of our dataset, we estimated that >70 and 68% of Arabidopsis and rice genes, respectively, had a strong GC-skew (>0.33) in a 100-bp window (that is, the number of C residues was more than double the number of G residues in a +/-100-bp window around the TSS). The mean GC-skew value in the TSS of highly-expressed genes in Arabidopsis was significantly greater than that of genes with low expression levels. Many of the GC-skew peaks were preferentially located near the TSS, so we examined the potential value of GC-skew as an index for TSS identification. Our results confirm that the GC-skew can be used to assist the TSS prediction in plant genomes.The GC-skew (C > G) around the TSS is strictly conserved between monocot and eudicot plants (ie. angiosperms in general), and a similar skew has been observed in some fungi. Highly-expressed Arabidopsis genes had overall a more marked GC-skew in the TSS compared to genes with low expression levels. We therefore propose that the GC-skew around the TSS in some plants and fungi is related to transcription. It might be caused by mutations during transcription initiation or the frequent use of transcription factor-biding sites having a strand preference. In addition, GC-skew is a
Current Status and Future Development of Cell Transplantation Therapy for Periodontal Tissue Regeneration
Toshiyuki Yoshida,Kaoru Washio,Takanori Iwata,Teruo Okano,Isao Ishikawa
International Journal of Dentistry , 2012, DOI: 10.1155/2012/307024
Abstract: It has been shown that stem cell transplantation can regenerate periodontal tissue, and several clinical trials involving transplantation of stem cells into human patients have already begun or are in preparation. However, stem cell transplantation therapy is a new technology, and the events following transplantation are poorly understood. Several studies have reported side effects and potential risks associated with stem cell transplantation therapy. To protect patients from such risks, governments have placed regulations on stem cell transplantation therapies. It is important for the clinicians to understand the relevant risks and governmental regulations. This paper describes the ongoing clinical studies, basic research, risks, and governmental controls related to stem cell transplantation therapy. Then, one clinical study is introduced as an example of a government-approved periodontal cell transplantation therapy.
Identifiability of an Integer Modular Acyclic Additive Noise Model and its Causal Structure Discovery
Joe Suzuki,Takanori Inazumi,Takashi Washio,Shohei Shimizu
Statistics , 2014,
Abstract: The notion of causality is used in many situations dealing with uncertainty. We consider the problem whether causality can be identified given data set generated by discrete random variables rather than continuous ones. In particular, for non-binary data, thus far it was only known that causality can be identified except rare cases. In this paper, we present necessary and sufficient condition for an integer modular acyclic additive noise (IMAN) of two variables. In addition, we relate bivariate and multivariate causal identifiability in a more explicit manner, and develop a practical algorithm to find the order of variables and their parent sets. We demonstrate its performance in applications to artificial data and real world body motion data with comparisons to conventional methods.
Characteristics and clustering of human ribosomal protein genes
Kyota Ishii, Takanori Washio, Tamayo Uechi, Maki Yoshihama, Naoya Kenmochi, Masaru Tomita
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-37
Abstract: We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG.Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.The ribosome, which plays an important role in the translational mechanism, is universal to all organisms. Mammalian ribosomes consist of four RNA species and 79 ribosomal proteins (RPs) [1]. More than 2000 pseudogenes of RP genes are present in the human genome [2], and this has made it difficult to gain an overview of this gene family. However, we have already constructed a ribosomal protein gene database (RPG) [3,4] that contains the genomic DNA and full-length cDNA sequences. RPG also includes information on the transcription start sites, amino acid sequences encoded, and intron/exon structures
Discovering causal structures in binary exclusive-or skew acyclic models
Takanori Inazumi,Takashi Washio,Shohei Shimizu,Joe Suzuki,Akihiro Yamamoto,Yoshinobu Kawahara
Computer Science , 2012,
Abstract: Discovering causal relations among observed variables in a given data set is a main topic in studies of statistics and artificial intelligence. Recently, some techniques to discover an identifiable causal structure have been explored based on non-Gaussianity of the observed data distribution. However, most of these are limited to continuous data. In this paper, we present a novel causal model for binary data and propose a new approach to derive an identifiable causal structure governing the data based on skew Bernoulli distributions of external noise. Experimental evaluation shows excellent performance for both artificial and real world data sets.
Causal Discovery in a Binary Exclusive-or Skew Acyclic Model: BExSAM
Takanori Inazumi,Takashi Washio,Shohei Shimizu,Joe Suzuki,Akihiro Yamamoto,Yoshinobu Kawahara
Computer Science , 2014,
Abstract: Discovering causal relations among observed variables in a given data set is a major objective in studies of statistics and artificial intelligence. Recently, some techniques to discover a unique causal model have been explored based on non-Gaussianity of the observed data distribution. However, most of these are limited to continuous data. In this paper, we present a novel causal model for binary data and propose an efficient new approach to deriving the unique causal model governing a given binary data set under skew distributions of external binary noises. Experimental evaluation shows excellent performance for both artificial and real world data sets.
Dietary γ-Aminobutyric Acid Shortens the Life Span of Stroke-Prone Spontaneously Hypertensive Rats  [PDF]
Nakamichi Watanabe, Naomi Washio
Food and Nutrition Sciences (FNS) , 2011, DOI: 10.4236/fns.2011.24043
Abstract: Dietary γ-amino butyric acid (GABA) has been suggested to decrease systolic blood pressure. This study aimed to ex-amine the effects of dietary GABA on the life span of stroke-prone spontaneously hypertensive rats (SHRSPs). In this study, life span was determined for SHRSPs provided 1% NaCl solution or 0.01% GABA in 1% NaCl solution as drinking water. The life span of the GABA-fed group (76.3 ± 1.65 days) was significantly shorter than that of the control group (81.6 ± 0.88 days). The results of this study may not be applicable to humans. Future studies will be necessary to elucidate the mechanism underlying this phenomenon.
DirectLiNGAM: A direct method for learning a linear non-Gaussian structural equation model
Shohei Shimizu,Takanori Inazumi,Yasuhiro Sogawa,Aapo Hyvarinen,Yoshinobu Kawahara,Takashi Washio,Patrik O. Hoyer,Kenneth Bollen
Statistics , 2011,
Abstract: Structural equation models and Bayesian networks have been widely used to analyze causal relations between continuous variables. In such frameworks, linear acyclic models are typically used to model the data-generating process of variables. Recently, it was shown that use of non-Gaussianity identifies the full structure of a linear acyclic model, i.e., a causal ordering of variables and their connection strengths, without using any prior knowledge on the network structure, which is not the case with conventional methods. However, existing estimation methods are based on iterative search algorithms and may not converge to a correct solution in a finite number of steps. In this paper, we propose a new direct method to estimate a causal ordering and connection strengths based on non-Gaussianity. In contrast to the previous methods, our algorithm requires no algorithmic parameters and is guaranteed to converge to the right solution within a small fixed number of steps if the data strictly follows the model.
High-Resolution Micro-Siting Technique for Large Scale Wind Farm Outside of Japan Using LES Turbulence Model  [PDF]
Takanori Uchida
Energy and Power Engineering (EPE) , 2017, DOI: 10.4236/epe.2017.912050
Abstract: The spatial distribution of wind speed varies greatly over steep complex terrain, thus the selection of an optimal site in such terrain for wind turbine construction requires great care. We have developed a numerical model for simulating unsteady flows called RIAM-COMPACT (Research Institute for Applied Mechanics, Kyushu University, COM putational Prediction of Airflow over Complex Terrain), which is based on the LES (Large-Eddy Simulation) technique. The computational domain of RIAM-COMPACT can be varied from several meters to several kilometers, and the model is able to predict airflow over complex terrain with high accuracy. The present paper discusses the application of RIAM-COMPACT to the micro-siting of wind turbines at sites outside Japan. The results from two case studies will be presented.
High-Resolution LES of Terrain-Induced Turbulence around Wind Turbine Generators by Using Turbulent Inflow Boundary Conditions  [PDF]
Takanori Uchida
Open Journal of Fluid Dynamics (OJFD) , 2017, DOI: 10.4236/ojfd.2017.74035
Abstract:
We have developed an LES (Large-Eddy Simulation) code called RIAM-COMPACT (Research Institute for Applied Mechanics, Kyushu University, Computational Prediction of Airflow over Complex Terrain). The analysis do-main of this numerical model extends from several meters to several kilometers. The model is able to predict airflow over complex terrain with high accuracy and is also now able to estimate the annual power output of wind turbine generators with the use of field observation data. In the present study, a numerical simulation of turbulent airflow over an existing wind farm was performed using RIAM-COMPACT and high-resolution elevation data. Based on the simulation results, suitable and unsuitable locations for the operation of WTGs (Wind Turbine Generators) were identified. The latter location was subject to the influence of turbulence induced by small topographical variations just upwind of the WTG location.
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