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Search Results: 1 - 10 of 152 matches for " Akito Taneda "
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An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
Akito Taneda
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-521
Abstract: We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp) sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%). By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences.The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.The RNA worlds in both experimental and computational fields have recently grown rapidly, and non-coding RNAs (ncRNAs) have increased their importance in life sciences. One of the most important breakthrough from the experimental side is the high-throughput experiments which have unveiled the existence of many non-protein coding transcripts in various species [1,2]. While function-known ncRNAs, which often harbor family-specific conserved secondary structure, such as tRNAs and miRNAs have been intensively studied in detail, no functional annotation has been assig
MODENA: a multi-objective RNA inverse folding
Akito Taneda
Advances and Applications in Bioinformatics and Chemistry , 2011, DOI: http://dx.doi.org/10.2147/AABC.S14335
Abstract: : a multi-objective RNA inverse folding Original Research (3175) Total Article Views Authors: Akito Taneda Published Date December 2010 Volume 2011:4 Pages 1 - 12 DOI: http://dx.doi.org/10.2147/AABC.S14335 Akito Taneda Graduate School of Science and Technology, Hirosaki University, Hirosaki, Japan Abstract: Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. In the present study, we developed a multi-objective genetic algorithm, MODENA (Multi-Objective DEsign of Nucleic Acids), for RNA inverse folding. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts. MODENA and previous RNA inverse folding programs were benchmarked with 29 target structures taken from the Rfam database, and we found that MODENA can successfully design 23 RNA sequences folding into the target structures; this result is better than those of the other benchmarked RNA inverse folding programs. The multi-objective genetic algorithm gives a useful framework for a functional biomolecular design. Executable files of MODENA can be obtained at http://rna.eit.hirosaki-u.ac.jp/modena/.
MODENA: a multi-objective RNA inverse folding
Akito Taneda
Advances and Applications in Bioinformatics and Chemistry , 2010,
Abstract: Akito TanedaGraduate School of Science and Technology, Hirosaki University, Hirosaki, JapanAbstract: Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. In the present study, we developed a multi-objective genetic algorithm, MODENA (Multi-Objective DEsign of Nucleic Acids), for RNA inverse folding. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts. MODENA and previous RNA inverse folding programs were benchmarked with 29 target structures taken from the Rfam database, and we found that MODENA can successfully design 23 RNA sequences folding into the target structures; this result is better than those of the other benchmarked RNA inverse folding programs. The multi-objective genetic algorithm gives a useful framework for a functional biomolecular design. Executable files of MODENA can be obtained at http://rna.eit.hirosaki-u.ac.jp/modena/.Keywords: multi-objective genetic algorithm, secondary structure, RNA sequence design, Rfam
Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design
Akito Taneda
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00036
Abstract: RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding. In the new version of MODENA, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, IPknot and HotKnots, are used to evaluate the designed RNA sequences, allowing us to perform the inverse folding of pseudoknotted RNAs. The new version of MODENA with the new crossover operator was benchmarked with a dataset composed of natural pseudoknotted RNA secondary structures, and we found that MODENA can successfully design more pseudoknotted RNAs compared to the other pseudoknot design algorithm. In addition, a sequence constraint function newly implemented in the new version of MODENA was tested by designing RNA sequences which fold into the pseudoknotted structure of a hepatitis delta virus ribozyme; as a result, we successfully designed eight RNA sequences. The new version of MODENA is downloadable from http://rna.eit.hirosaki-u.ac.jp/modena/.
Heterostructure Solar Cells Based on Sol-Gel Deposited SnO2 and Electrochemically Deposited Cu2O  [PDF]
Akito Fukuda, Masaya Ichimura
Materials Sciences and Applications (MSA) , 2013, DOI: 10.4236/msa.2013.46A001
Abstract:

To fabricate a heterostructure solar cell using environmentally friendly materials and low cost techniques, tin oxide (SnO2) and cuprous oxide (Cu2O) were deposited by the sol-gel method and the electrochemical deposition, respectively. The SnO2 films were deposited from a SnCl2 solution containing ethanol and acetic acid. The Cu2O films were deposited using a galvanostatic method from an aqueous bath containing CuSO4 and lactic acid at a temperature of 40°C. The Cu2O/SnO2 heterostructure solar cells showed rectification and photovoltaic properties, and the best cell showed a conversion efficiency of 6.6 × 10-2 % with an open-circuit voltage of 0.29 V, a short-circuit current of 0.58 mA/cm2, and a fill factor of 0.39.

Economic and Environmental Effects of Installing Distributed Energy Resources into a Household  [PDF]
Akito Ozawa, Yoshikuni Yoshida
Low Carbon Economy (LCE) , 2015, DOI: 10.4236/lce.2015.62006
Abstract: Improving energy efficiency in the residential sector is a pressing issue in Japan. This study examines the economic and environmental impacts of introducing the following distributed energy resources: photovoltaics (PV), a fuel cell, and a battery. We estimate electricity and hot water demand profiles of a household by using simulated living activities. Electric power from a residential PV system is also calculated from the observed solar radiation. By using mixed integer programming, we perform a cost minimization operating simulation of a residential PV, fuel cell, and battery. The result suggests that we can create a net-zero energy house by installing both a PV system and a fuel cell into one house. On the other hand, using a battery with a fuel cell increases the household energy cost, and has few effects on CO2 emission reduction.
Generalized Umemura polynomials
Anatol N. Kirillov,Makoto Taneda
Mathematics , 2000,
Abstract: We introduce and study generalized Umemura polynomials $U_{n,m}^{(k)}(z,w;a,b)$ which are a natural generalization of the Umemura polynomials $U_n(z,w;a,b)$ related to Painlev\'e $VI$ equation. We will show that if $a=b$, or $a=0$, or $b=0$ then polynomials $U_{n,m}^{(0)}(z,w;a,b)$ generate solutions to Painlev\'e $VI$. We will describe a connection between polynomials $U_{n,m}^{(0)}(z,w;a,0)$ and certain Umemura polynomials $U_k(z,w;\alpha,\beta)$.
Generalized Umemura polynomials and Hirota-Miwa equations
Anatol N. Kirillov,Makoto Taneda
Mathematics , 2001,
Abstract: We introduce and study generalized Umemura polynomials $U_{n,m}^{(k)}(z,w;a,b)$ which are the natural generalization of the Umemura polynomials $U_n(z,w;a,b)$ related to the Painleve VI equation. We show that if either a=b, or a=0, or b=0, then polynomials $U_{n,m}^{(0)}(z,w;a,b)$ generate solutions to the Painleve VI equation. We give new proof of Noumi-Okada-Okamoto-Umemura conjecture, and describe connections between polynomials $U_{n,m}^{(0)}(z,w;a,0)$ and certain Umemura polynomials $U_k(z,w;\alpha,\beta)$. Finally we show that after appropriate rescaling, Umemura's polynomials $U_k(z,w;a,b)$ satisfy the Hirota-Miwa bilinear equations.
Is sport hunting a breakthrough wildlife conservation strategy for Africa? La chasse sportive, une stratégie de préservation de la faune innovante pour l’Afrique ? Etude de cas dans le nord du Cameroun La caza deportiva: una estrategia de conservación innovadora para áfrica? Un estudio de caso en el norte de Camerún
Akito Yasuda
Field Actions Science Reports , 2012,
Abstract: Sport hunting is one of the oldest known recreational activities using wildlife. Some researchers have suggested that sport hunting can benefit the development and economy of local communities, thereby promoting the protection of wildlife resources as well as both ecological and economic sustainability. However, important debates remain regarding the social impacts of conservation and tourism on local communities near protected areas.This study using a case study from northern Cameroon aimed to 1) analyze the social impacts of sport hunting on local people and 2) discuss sustainability of sport hunting. Approximately two years of fieldwork, mainly based on interviews and observations in two villages, showed that sport hunting generated tax revenues of approximately US$1.2 million in one season as well as provided profit sharing and employment opportunities for local communities. However, the local people were affected by regulations of their rights to use natural resources. Moreover, some villages experienced forced migration for the beginning of sport hunting.Many officers and hunting operators insist that sport hunting entails ecological and economic sustainability because it is operated under strict regulations and generates enormous tax revenues. This is in contrast to hunting by local people, who do not consider the hunting regulation nor pay taxes. The question remains, however, whether the term “sustainability” should only encompass ecological and economic factors. Even if sport hunting plays an important role in community conservation, the social impacts on local communities should be considered before the activity is considered as a viable tactic for wildlife conservation. La chasse sportive est l’un des plus anciens loisirs connus axés sur la faune. D’après certains chercheurs, ce type de chasse peut être bénéfique pour le développement des communautés locales et pour leur économie, et ainsi encourager la protection des ressources naturelles ainsi que la durabilité écologique et économique.Toutefois, le débat demeure quant aux conséquences sociales de la préservation de la faune et du tourisme sur les communautés locales basées à proximité des zones protégées.Cette étude basée sur une étude de cas située dans le nord du Cameroun avait un double objectif : 1) analyser les conséquences sociales de la chasse sportive sur la population locale ; 2) aborder la durabilité de la chasse sportive. Environ deux ans de travail de terrain, consistant essentiellement en des entretiens et des observations dans deux villages, ont montré que la chasse sportive
Clustering aspects and the shell model
Akito Arima
Physics , 2004, DOI: 10.1016/j.nuclphysa.2004.04.030
Abstract: In this talk I shall discuss the clustering aspect and the shell model. I shall first discuss the $\alpha$-cluster aspects based on the shell model calculations. Then I shall discuss the spin zero ground state dominance in the presence of random interactions and a new type of cluster structure for fermions in a single-$j$ shell in the presence of only pairing interaction with the largest multiplicity.
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