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Search Results: 1 - 10 of 605 matches for " Shigeo Fujimori "
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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
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
Density Functional Theory Studies on the Addition and Abstraction Reactions of OH Radical with Benzoate Anion  [PDF]
Nobuaki Tanaka, Shigeo Itoh
Open Journal of Physical Chemistry (OJPC) , 2013, DOI: 10.4236/ojpc.2013.31002
Abstract:

The addition and abstraction reactions of OH radical with benzoate anion are investigated by density functional theory calculations that include solvent effects using UB3LYP, UCAM-B3LYP, UmPW1PW91 and UM06-2X functionals with the 6-311++G(2d,2p) basis set. Geometry optimizations of the reactants, products and transition state species are performed for the possible reaction paths. For the addition reactions, those targeting the ipso-, ortho-, meta- and para-carbons are predicted to be exoergic. The H-atom abstraction reactions from ortho, meta and para positions are also predicted to be exoergic. On the basis of the rate constants calculated by means of the transition state theory, the H-atom abstraction reaction from the ortho position is determined to be the favored path followed by the ortho OH addition reaction.

Reading Aloud Performance and Listening Ability in an L2: The Case of College-Level Japanese EFL Users  [PDF]
Shigeo Kato, Kento Tanaka
Open Journal of Modern Linguistics (OJML) , 2015, DOI: 10.4236/ojml.2015.52015
Abstract: Recent advance in neuropsychology has evidenced a facilitative role of sensorimotor activity for the development in L2 speech perception. The study attempted to examine the relationship between reading aloud (RA) performance, grammatical knowledge and listening ability with 31 college-level Japanese EFL users. The result demonstrated highly significant correlations between all the variables, and the subsequent multiple regression analysis also indicated RA significantly accounting for listening. Supplementary analyses dividing the participants by listening ability demonstrated that while significant correlation was maintained between L2 knowledge and listening with less-proficient listeners, it disappeared with proficient listeners; in contrast, significant correlation between RA and listening performance was maintained in both groups, indicating that production accuracy/fluency still played an important role in advanced L2 listening.
Agricultural policy and conservation of biodiversity in Brazil
Shigeo,Shiki;
Estudos Sociedade e Agricultura , 2010,
Abstract: this essay discusses the complex relationship between the agrarian question and biodiversity conservation, showing that the principal disagreements have emerged from the dominant productivity-oriented model of the "green revolution". it argues that the productive efficiency did not avoid the environmental and social "tragedy of the non-commons", giving political space to agrarian reform proposals, consolidating family and peasant agriculture and paving the road for agroecological reconversion. this reconversion, however, is hampered by the high transition cost and the lack of scientific support. a new and potentially favourable policy framework that could make this transition viable is that of payment for environmental services.
On the Goursat problem for a second order equation
Shigeo Tarama
Electronic Journal of Differential Equations , 2002,
Abstract: We consider the Goursat problem for second order operators and show existence and uniqueness of smooth solutions. We prove one of the results of Hasegawa (J. Math. Soc. Japan 50 (1998), no. 3, 639--662) by the energy method. The same method is applied when one of the surfaces where the Goursat data are given is a non-characteristic.
Lateral estimates for iterated elliptic operators and analyticity
Shigeo Tarama
Electronic Journal of Differential Equations , 2009,
Abstract: Analyticity of functions satisfying the lateral estimates for iterated elliptic operators is shown.
L2-well-posed Cauchy problem for fourth-order dispersive equations on the line
Shigeo Tarama
Electronic Journal of Differential Equations , 2011,
Abstract: Mizuhara [2] obtained conditions for the Cauchy problem of a fourth-order dispersive operator to be well posed in the $L^2$ sense. Two of those conditions were shown to be necessary under additional assumptions. In this article, we prove the necessity without the additional assumptions.
Energy estimate for wave equations with coefficients in some Besov type class
Shigeo Tarama
Electronic Journal of Differential Equations , 2007,
Abstract: In this paper, we obtain an energy estimate for wave equations with coefficients satisfying Besov type conditions. We give an example of a wave equation with continuous and nowhere differentiable coefficients for which the $L^2$ estimate holds.
A Putative Link Among the Triad: Inflammation, Reprogramming, and Cancer
Shigeo Masuda
Journal of Tumor , 2013, DOI: doi:10.6051/j.issn.1819-6187.2013.01.1
Abstract: Induced pluripotent stem cells (iPSCs) are generated during ex vivo artificial process, referred to as reprogramming process; on the other hand, reprogramming has been demonstrated to be also involved in human pathological process in vivo, such as metaplastic change. Moreover, a surprising link between reprogramming and inflammation has been revealed. In this Editorial at the triple crossroads, I discuss a novel link among inflammation, reprogramming, and cancer.
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