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Search Results: 1 - 10 of 1780 matches for " Ryu Ogawa "
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Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
Nobuaki Kono,Kazuharu Arakawa,Ryu Ogawa,Nobuhiro Kido,Kazuki Oshita,Keita Ikegami,Satoshi Tamaki,Masaru Tomita
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007710
Abstract: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage.
Genome Projector: zoomable genome map with multiple views
Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-31
Abstract: This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://www.g-language.org/GenomeProjector/ webcite. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site.Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.In molecular biology, it is important to look at reactions and behaviours of specific molecular components, both at the micro-level and at the macro-level, which we refer to as -omics. Biologists therefore must constantly traverse across micro-, meso-, and macro-levels of biological knowledge to gain insight into the workings of the cell. Moreover, our current understanding of cellular phenomena is also highly multi-layered, organised as assemblages of several -omic spaces such as the genome, transcriptome, proteome, metabolome, and biochemical pathways [1]. Each of these layers represents a projection of cellular anatomy containing unique sets of molecules and interactions and is often epitomised by distinct, high-throughput experimental technology for the comprehensive measurement of constituent entities. -Omic layers also provide a biological context for the visualisation and interpretation of data, and serve as a gateway to information stored in a database [2]. For example, the popular two-dimensional genome map viewer, Gbrow
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification
Tadasu Nozaki, Nozomu Yachie, Ryu Ogawa, Anton Kratz, Rintaro Saito, Masaru Tomita
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-416
Abstract: Here, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones.These results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture.Recent progress in high-throughput technologies has made it possible to collect a variety of "omics" data on transcripts and on the epigenetic behaviors of the histones that are often associated with these transcripts [1-5].Cap analysis of gene expression (CAGE) is a high-throughput method that enables large-scale identification of transcription start sites (TSSs) of eukaryotic species. This method measures gene expression levels simultaneously with TSS identification by counting the sequenced 5' ends of full-length cDNAs, termed CAGE tags [2,6]. With the development of deep sequencing methods, more high-throughput, and high resolution "tag depth" measurements have become available (DeepCAGE, nanoCAGE and CAGEscan) [1,7]. Such recent whole-cell-level pictures of quantitative transcriptomes have revealed the complex transcriptional network of mammalian species [1,2,6]. According to recent CAGE-based analyses of human TSSs, the human "promotome"
Carbon Dioxide Capture and Utilization for Gas Engine  [PDF]
Takashi Ogawa
Energy and Power Engineering (EPE) , 2013, DOI: 10.4236/epe.2013.510064
Abstract:

Sodium glycinate absorption and ethylene carbonate synthesis from a mixture gas of ethylene oxide and carbon dioxide are evaluated as carbon dioxide capture and utilization system for gas engine flue gas. The energy requirement for CO2 capture is estimated at 3.3 GJ/tonne CO2. The ethylene carbonate synthesis utilizes more than 90% of the captured CO2 and supply 2.5 GJ/tonne CO2 of thermal energy, which is 76% of the energy requirement for CO2 capture. The thermal integration of the sodium glycinate absorption and the ethylene carbonate synthesis reduces the energy requirement for CO2 capture from 3.3 GJ/tonne CO2 to 0.8 GJ/tonne CO2. The energy requirement for the CO2 capture is supplied using the steam saturated at 0.78 MPa from the gas engine without its electric power reduction.

Trends in age distribution of participants in a self-covered and a public expense-covered health check-up programs in Japan  [PDF]
Maki Ogawa, Atsushi Imai
Health (Health) , 2012, DOI: 10.4236/health.2012.49088
Abstract: Objective: In Japan, there are unique facilities (namely Ningen Dock) of health check-up, where asymptomatic participants undergo a medical examination at their own expense. The earlier occurrence of cervical cancer and the concern on screening prompted us compare to the age distribution in the self-covered system with that of free physical check-up programs at public expense. Methods: We analyzed medical records of Japanese women, who underwent gynecological examinations at self-covered expense and at public expense between for the periods 2002-2011 and 2005-2009, respectively, restricting examinee’s age group. Results: For self-covered system, approximately 80% of the overall examinee population was occupied with three age groups 30-39, 40-49 and 50-59. The participants was extremely fewer in the over 60 years age group accounting for 10%, compared to those for the public expense-covered system, the over 60 years age group being 25%. Participant under the age of 30 years seemed to increase in chronological order in both systems. Conclusion: The level of knowledge on sexually transmitted infections may contribute to screening promotion for the younger women, while the elderly over 60 years’ attitudes toward screening may be mainly related to social-economic status and/or public expense support.
The Relationship between Privatization and Regulation on Foreign Investment Policies  [PDF]
Lihua Han, Hikaru Ogawa
Theoretical Economics Letters (TEL) , 2015, DOI: 10.4236/tel.2015.51014
Abstract: Using a simple mixed oligopoly model, this paper examines the relationship between market-openings to foreign capital and privatization of a domestic public firm. Two types of market-openings are considered. First is that, given the number of the firms, the restriction on the share of foreign capital in each corporate joint venture is relaxed. Second is that, given the share of foreign capital in each corporate joint venture, the restriction on the number of the firms is relaxed. The analysis shows that the optimal level of privatization critically depends on the types of market openings to foreign capital. The optimal level of privatization declines as the share of foreign capital in each corporate joint venture increases. By contrast, the optimal level of privatization rises with an increase in the number of the firms operating in the market. The two different strategies for market-openings result in the opposite impacts on the welfare-maximizing government’s incentive for privatization.
Mechanism of Generation and Collapse of a Longitudinal Vortex System Induced around the Leading Edge of a Delta Wing  [PDF]
Shigeru Ogawa, Jumpei Takeda
Open Journal of Fluid Dynamics (OJFD) , 2015, DOI: 10.4236/ojfd.2015.53028
Abstract: The purpose of the paper is to clarify the mechanism of generation and collapse of a longitudinal vortex system induced around the leading edge of a delta wing. CFD captured well characteristics of flow structure of the vortex system. It is found that the vortex system has a cone-shaped configuration, and both rotational velocity and vorticity have their largest values at the tip of the vortex and reduce downstream along the vortical axis. This resulted in inducing the largest negative pressure at the tip of the delta wing surface. The collapse of the vortex system was also studied. The system can still remain until the tip angle of 110 degrees. However, between 110 degrees and 120 degrees, the system becomes unstable. Over 120 degrees, the characteristics of the vortex are considered to have converted from the longitudinal vortex to the transverse one.
Heat Transfer Enhancement by Vortex Generators for Compact Heat Exchanger of Automobiles  [PDF]
Shigeru Ogawa, Soma Usui
Open Journal of Fluid Dynamics (OJFD) , 2018, DOI: 10.4236/ojfd.2018.83020
Abstract: The paper describes the effects of heat transfer enhancement and gas-flow characteristics by wing-type-vortex-generators inside a rectangular gas-flow duct of a plate-fin structure exhaust gas recirculation (EGR) cooler used in a cooled-EGR system. The analyses are conducted using computational fluid dynamics (CFD). The numerical modelling is designed as a gas-flow rectangular duct of an EGR cooler using two fluids with high temperature gas and coolant water whose flow directions are opposite. The gas-flow duct used to separate two fluids is assembled with a stainless steel material. The inlet temperature and velocity of gas flowed inside gas-flow duct are 400°C and 30 m/s, respectively. Coolant water is flowed into two ducts on both a top and a bottom surface of the gas-flow duct, and the inlet temperature and velocity is 80°C and 0.6 m/s, respectively. Wing-type-vortex-generators are designed to achieve good cooling performance and low pressure drop and positioned at the center of the gas-flow duct with angle of inclination from 30 to 150 degrees at every 15 degrees. The temperature distributions and velocity vectors gained from numerical results were compared, and discussed. As a result, it is found that the vortices guided in the proximity of heat transfer surfaces play an important role in the heat transfer enhancement and low pressure drop. The collapse of the vortices is caused by complicated flow induced in the corner constituted by two surfaces inside gas-flow duct.
Performance Improvement by Control of Wingtip Vortices for Vertical Axis Type Wind Turbine  [PDF]
Shigeru Ogawa, Yusuke Kimura
Open Journal of Fluid Dynamics (OJFD) , 2018, DOI: 10.4236/ojfd.2018.83021
Abstract: The present paper describes control of wingtip vortices generated by vertical type wind turbine. The wind turbine consists of three circular cylinders. Each cylinder rotates on its own vertical axis and moves in orbit. It is known that wingtip vortices give rise to decrease of power generation performance as well as aerodynamic noise. Therefore, the goal of the study is to control wingtip vortices and to improve power generation performance. Numerical study was conducted for 14 models to find out control factors to suppress wingtip vortices. Numerical simulation visualized wingtips by streamlines as well as pressure distribution on the circular cylinder for evaluating Magnus effect. As a result, the following findings were obtained: 1) Installation of fully covered protection plates at both ends of the circular cylinder blades is greatly effective to suppress the wingtip vortices. 2) Curved wings attached to each cylinder are more effective to enhance power generation efficiency than flat ones, due to great increase in Magnus effect caused by large pressure difference on both sides of the curved wing. The power efficiency of the optimized model was improved up to 2.8%, which means 11 times that of the original model.
Mesocosm Assessment of Stability Habitat for Halophyte  [PDF]
Sunghoon Ryu, Incheol Lee
Journal of Geoscience and Environment Protection (GEP) , 2015, DOI: 10.4236/gep.2015.36003
Abstract:

In this paper, we constructed the halophyte Mesocosm experimental group which was used as a substrate material that consisted of tidal flat and dredged sediment. Depending on whether the ingredients of vegetation and substrate material of Mesocosm, we constructed Mesocosm A (tidal flat sediment + Salicornia herbecea), Mesocosm B (only dredged sediment), Mesocosm C (dredged sediment + Salicornia herbecea). Monitoring was carried out of seawater quality factors (Chemical Oxygen Demand (COD), Total Nitrogen (T-N), Total Phosphorus (T-P), temperature, salinity), sediment factors (Chemical Oxygen Demand (COD), Total (T-N), Total Phosphorus (T-P) and growth of Salricornia herbecea) in each Mesocosm. Habitat Stability Index of vegetation was calculating by using the monitoring results. HSI of Mesocosm C was calculated from 0.87 to 0.95 as compared to the relatively high HSI Mesocosm A, it was evaluated to be able to be used in the restoration of the coastal salt marsh with dredged sediment.

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