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

A Study on Squeeze Films Between Porous Rubber Surface and Rigid Surface: Analysis Based on the Viscoelastic Continuum Model

The squeeze-film effect between a porous rubber surface and a rigid surface has been investigated as a problem of viscoelastic hydrodynamic lubrication (VEHL

Spontaneous Remission of Solitary-Type Infantile Myofibromatosis

Infantile myofibromatosis is a rare fibrous tumor of infancy. The cutaneous solitary type has typically an excellent prognosis. However, histologically, it is important to rule out leiomyosarcoma, which has a poor prognosis. The low frequency of mitosis was definitive for a diagnosis of infantile myofibromatosis. We present a cutaneous solitary-type case of infantile myofibromatosis. Following incisional biopsy, the tumor remitted spontaneously

The capacity-building and science-enabling activities of the IUGONET for the solar-terrestrial research community

[Background]This paper presents an overview of the capacity-building activities and science-enabling services of the Inter-university Upper atmosphere Global Observation NETwork (IUGONET) project. This Japanese program, which started in 2009, is building a metadata database (MDDB) of ground-based observations and is developing an analysis software to handle the data linked to the MDDB system for use by the solar-terrestrial physics community. Because the institutional members of the IUGONET are mainly universities in Japan, we explore tools that can contribute to advanced education as well as promote research activities. [Findings]In this paper, we describe the utilities of the IUGONET for education, including our capacity-building activities in developing countries. We have regularly facilitated training seminars for Japanese students on the use of our tools (IUGONET MDDB and the software), and we have held capacity-building seminars for young scientists in developing countries. In addition to the MDDB, we have prepared various ‘gateway’ tools for users who are unfamiliar with ‘keywords’ to search for data. One of these is a geographical display tool that uses Google Earth (KML file), which is included as supplemental material to this paper. The usefulness of the IUGONET has been proven over its first 5 years of operation by the increasing number of its users, which has led to the production of approximately 500 scientific papers, including 42 thesis papers. [Conclusions]The IUGONET community collaborates with the Scientific Committee on Solar-Terrestrial Physics program, not only in its scientific activities, but also in the establishment of E-infrastructure and capacity building

Targeting diamondback moths in greenhouses by attracting specific native parasitoids with herbivory-induced plant volatiles

植物の香りで特定の天敵を誘引し、標的とした害虫の発生抑制に成功 --植物の香りを用いた新しい害虫防除法--. 京都大学プレスリリース. 2020-12-02.We investigated the recruitment of specific parasitoids using a specific blend of synthetic herbivory-induced plant volatiles (HIPVs) as a novel method of pest control in greenhouses. In the Miyama rural area in Kyoto, Japan, diamondback moth (DBM) (Plutella xylostella, Lepidoptera: Plutellidae) larvae are an important pest of cruciferous crops in greenhouses, and Cotesia vestalis (Hymenoptera: Braconidae), a larval parasitoid of DBM, is found in the surrounding areas. Dispensers of HIPVs that attracted C. vestalis and honey feeders were set inside greenhouses (treated greenhouses). The monthly incidence of DBMs in the treated greenhouses was significantly lower than that in the untreated greenhouses over a 2-year period. The monthly incidences of C. vestalis and DBMs were not significantly different in the untreated greenhouses, whereas monthly C. vestalis incidence was significantly higher than monthly DBM incidence in the treated greenhouses. Poisson regression analyses showed that, in both years, a significantly higher number of C. vestalis was recorded in the treated greenhouses than in the untreated greenhouses when the number of DBM adults increased. We concluded that DBMs were suppressed more effectively by C. vestalis in the treated greenhouses than in the untreated greenhouses

An Empirical Assessment of the Business Value Derived from Implementing Mobile Technology: A Case Study of Two Organizations

Mobile technologies are argued to offer unprecedented opportunities for organizations and individuals. In order for organizations to be persuaded that investment in mobile technologies is not only worthwhile, but also important to the achievement of corporate goals and objectives, then it is important to evaluate the potential of mobile technology so that the derivation of business value and the related risks involved in implementing mobile devices and services in an organization can be understood. This paper aims at understanding the organizational value that could be derived from investments in mobile technology. We present two in-depth case studies of mobile technology implementation in health care organizations. These studies show that deriving business value from the adoption and implementation of mobile devices does not seem at all certain, but is contingent upon clear business objectives and a willingness to make business changes to embrace the transformation to core business processes which are driven by the mobile technologies

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

Alveolar Bone Microstructure Surrounding Orthodontic Anchor Screws with Plasma Surface Treatment in Rats

A lateral load was applied to anchor screws that had undergone surface treatment, and the structure, cellular dynamics, and quality of the bone surrounding anchor screws were analyzed to investigate the effect of this surface treatment on the peri-implant jawbone. In addition, bone microstructural characteristics were quantitatively evaluated for each site of loading on the bone around the anchor screw. Rats were euthanized after observation on days 3, 5, or 7, and bone quality analyses were performed. Bone–implant contact rate increased more rapidly at an early stage in the treated surface group than in the untreated surface group. Bone lacuna morphometry showed that the measured values adjacent to the screw at the screw neck on the compressed side (A) and at the screw tip on the uncompressed side (D) were significantly lower than those at the screw tip on the compressed side (B) and at the screw neck on the uncompressed side (C). Collagen fiber bundle diameter showed that the measured values adjacent to regions A and D were significantly higher than those at regions B and C. Anchor screw surface activation facilitates initial bone contact of the screw, suggesting that early loading may be possible in clinical practice.Okawa K., Matsunaga S., Kasahara N., et al. Alveolar Bone Microstructure Surrounding Orthodontic Anchor Screws with Plasma Surface Treatment in Rats. Journal of Functional Biomaterials 14, 356 (2023); https://doi.org/10.3390/jfb14070356

Real-time imaging and analysis of differences in cadmium dynamics in rice cultivars (Oryza sativa) using positron-emitting107Cd tracer

<p>Abstract</p> <p>Background</p> <p>Rice is a major source of dietary intake of cadmium (Cd) for populations that consume rice as a staple food. Understanding how Cd is transported into grains through the whole plant body is necessary for reducing rice Cd concentrations to the lowest levels possible, to reduce the associated health risks. In this study, we have visualized and quantitatively analysed the real-time Cd dynamics from roots to grains in typical rice cultivars that differed in grain Cd concentrations. We used positron-emitting¹⁰⁷Cd tracer and an innovative imaging technique, the positron-emitting tracer imaging system (PETIS). In particular, a new method for direct and real-time visualization of the Cd uptake by the roots in the culture was first realized in this work.</p> <p>Results</p> <p>Imaging and quantitative analyses revealed the different patterns in time-varying curves of Cd amounts in the roots of rice cultivars tested. Three low-Cd accumulating cultivars (<it>japonica </it>type) showed rapid saturation curves, whereas three high-Cd accumulating cultivars (<it>indica </it>type) were characterized by curves with a peak within 30 min after¹⁰⁷Cd supplementation, and a subsequent steep decrease resulting in maintenance of lower Cd concentrations in their roots. This difference in Cd dynamics may be attributable to OsHMA3 transporter protein, which was recently shown to be involved in Cd storage in root vacuoles and not functional in the high-Cd accumulating cultivars. Moreover, the PETIS analyses revealed that the high-Cd accumulating cultivars were characterized by rapid and abundant Cd transfer to the shoots from the roots, a faster transport velocity of Cd to the panicles, and Cd accumulation at high levels in their panicles, passing through the nodal portions of the stems where the highest Cd intensities were observed.</p> <p>Conclusions</p> <p>This is the first successful visualization and quantification of the differences in whole-body Cd transport from the roots to the grains of intact plants within rice cultivars that differ in grain Cd concentrations, by using PETIS, a real-time imaging method.</p