Validation of CFD Codes for the Helicopter Wake in Ground Effect

When a helicopter takes off, lands, or makes hovering or taxiing flights in ground effect, its downwash interferes with the ground. Encounters with such highly turbulent helicopter wakes have been blamed for two fixed-wing aircraft crashes in the United Kingdom. Additional incidents including tents blown away are reported in Japan. Due to these accidents, the Japan Aerospace Exploration Agency (JAXA) and the University of Glasgow (UoG) are investigating the helicopter wake structure in ground effect, especially during taxiing, by means of computational fluid dynamics (CFD). In this study, CFD codes of UoG and JAXA are validated through comparing numerical results of each party and flight experiment data. As a result, it is found that the CFD codes show qualitatively the same results each other and they are also close to the experiment

Archiving next generation sequencing data

Next generation sequencing platforms are producing biological sequencing data in unprecedented amounts. The partners of the International Nucleotide Sequencing Database Collaboration, which includes the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ), have established the Sequence Read Archive (SRA) to provide the scientific community with an archival destination for next generation data sets. The SRA is now accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html from DDBJ. Users of these resources can obtain data sets deposited in any of the three SRA instances. Links and submission instructions are provided

The Sequence Read Archive

The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the SRA. The SRA was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA, detail our support for sequencing platforms and provide recommended data submission levels and formats. We also briefly outline our response to the challenge of data growth

A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes

A Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional complex data on a two-dimensional map. We modified the conventional SOM to genome informatics, making the learning process and resulting map independent of the order of data input, and developed a novel bioinformatics tool for phylogenetic classification of sequence fragments obtained from pooled genome samples of microorganisms in environmental samples allowing visualization of microbial diversity and the relative abundance of microorganisms on a map. First we constructed SOMs of tri- and tetranucleotide frequencies from a total of 3.3-Gb of sequences derived using 113 prokaryotic and 13 eukaryotic genomes, for which complete genome sequences are available. SOMs classified the 330000 10-kb sequences from these genomes mainly according to species without information on the species. Importantly, classification was possible without orthologous sequence sets and thus was useful for studies of novel sequences from poorly characterized species such as those living only under extreme conditions and which have attracted wide scientific and industrial attention. Using the SOM method, sequences that were derived from a single genome but cloned independently in a metagenome library could be reassociated in silico. The usefulness of SOMs in metagenome studies was also discussed

G-InforBIO: integrated system for microbial genomics

BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site

DDBJ working on evaluation and classification of bacterial genes in INSDC

DNA Data Bank of Japan (DDBJ) () newly collected and released 12 927 184 entries or 13 787 688 598 bases in the period from July 2005 to June 2006. The released data contain honeybee expressed sequence tags (ESTs), re-examined and re-annotated complete genome data of Escherichia coli K-12 W3110, medaka WGS and human MGA. We also systematically evaluated and classified the genes in the complete bacterial genomes submitted to the International Nucleotide Sequence Database Collaboration (INSDC, ) that is composed of DDBJ, EMBL Bank and GenBank. The examination and classification selected 557 000 genes as reliable ones among all the bacterial genes predicted by us

Sensorimotor Modulation Differs with Load Type during Constant Finger Force or Position

During submaximal isometric contraction, there are two different load types: production of a constant force against a rigid restraint (force task), and maintenance of position against a constant load (position task). Previous studies reported that the time to task failure during a fatigue task was twice as long in the force task compared with the position task. Sensory feedback processing may contribute to these differences. The purpose of the current study was to determine the influence of load types during static muscle contraction tasks on the gating effect, i.e., attenuation of somatosensory-evoked potentials (SEPs) and the cortical silent period (cSP). Ten healthy subjects contracted their right first dorsal interosseus muscle by abducting their index finger for 90 s, to produce a constant force against a rigid restraint that was 20% of the maximum voluntary contraction (force task), or to maintain a constant position with 10° abduction of the metacarpophalangeal joint against the same load (position task). Somatosensory evoked potentials (SEPs) were recorded from C3′ by stimulating either the right ulnar or median nerve at the wrist while maintaining contraction. The cortical silent period (cSP) was also elicited by transcranial magnetic stimulation. Reduction of the amplitude of the P45 component of SEPs was significantly larger during the position task than during the force task and under control rest conditions when the ulnar nerve, but not the median nerve, was stimulated. The position task had a significantly shorter cSP duration than the force task. These results suggest the need for more proprioceptive information during the position task than the force task. The shorter duration of the cSP during the position task may be attributable to larger amplitude of heteronymous short latency reflexes. Sensorimotor modulations may differ with load type during constant finger force or position tasks.This work was supported by a Grant-in-Aid for Scientific Research (C) No. 08042773 from the Japan Society for the Promotion of Science (JSPS) (http://www.jsps.go.jp/english/e-grants/index.html) and a Research Grant from Niigata University of Health and Welfare (NUHW) (http://www.nuhw.ac.jp/e/). HK received both grants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes

Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, ) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at