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  • 1
    Publication Date: 2016-01-07
    Description: The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org ) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-07-18
    Description: We present infrared (IR) galaxy luminosity functions (LFs) in the AKARI North Ecliptic Pole (NEP) deep field using recently-obtained, wider Canada–France–Hawaii Telescope (CFHT) optical/near-IR images. AKARI has obtained deep images in the mid-infrared (IR), covering 0.6 deg 2 of the NEP deep field. However, our previous work was limited to the central area of 0.25 deg 2 due to the lack of optical coverage of the full AKARI NEP survey. To rectify the situation, we recently obtained CFHT optical and near-IR images over the entire AKARI NEP deep field. These new CFHT images are used to derive accurate photometric redshifts, allowing us to fully exploit the whole AKARI NEP deep field. AKARI 's deep, continuous filter coverage in the mid-IR wavelengths (2.4, 3.2, 4.1, 7, 9, 11, 15, 18, and 24 μm) exists nowhere else, due to filter gaps of other space telescopes. It allows us to estimate rest-frame 8 and 12 μm luminosities without using a large extrapolation based on spectral energy distribution fitting, which was the largest uncertainty in previous studies. Total infrared (TIR) luminosity is also obtained more reliably due to the superior filter coverage. The resulting rest-frame 8 and 12 μm, and TIR LFs at 0.15 〈  z  〈 2.2 are consistent with previous works, but with reduced uncertainties, especially at the high-luminosity end, thanks to the wide-field coverage. In terms of cosmic infrared luminosity density ( IR ), we found that the IR evolves as (1 +  z ) 4.2 ± 0.4 .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2015-10-23
    Description: Mowat–Wilson syndrome (MOWS) is caused by de novo heterozygous mutation at ZEB2 ( SIP1, ZFHX1B ) gene, and exhibit moderate to severe intellectual disability (ID), a characteristic facial appearance, epilepsy and other congenital anomalies. Establishing a murine MOWS model is important, not only for investigating the pathogenesis of this disease, but also for identifying compounds that may improve the symptoms. However, because the heterozygous Zeb2 knockout mouse could not be maintained as a mouse line with the inbred C57BL/6 background, it was difficult to use those mice for the study of MOWS. Here, we systematically generated de novo Zeb2 ex7/+ mice by inducing the Zeb2 mutation in the germ cells using conditional recombination system. The de novo Zeb2 ex7/+ mice with C57BL/6 background developed multiple defects relevant to MOWS, including craniofacial abnormalities, defective corpus callosum formation and the decreased number of parvalbumin interneurons in the cortex. In behavioral analyses, these mice showed reduced motor activity, increased anxiety and impaired sociability. Notably, during the Barnes maze test, immobile Zeb2 mutant mice were observed over repeated trials. In contrast, neither the mouse line nor the de novo Zeb2 ex7/+ mice with the closed colony ICR background showed cranial abnormalities or reduced motor activities. These results demonstrate the advantages of using de novo Zeb2 ex7/+ mice with the C57BL/6 background as the MOWS model. To our knowledge, this is the first time an inducible de novo mutation system has been applied to murine germline cells to produce an animal model of a human congenital disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2015-03-27
    Description: Functional encryption (FE) systems provide a flexible and expressive encryption mechanism that private keys and ciphertexts are associated with attributes and predicate formulae and decryption are possible whenever keys and ciphertexts are related, i.e. . In this work, we put forward a leakage-resilient FE scheme against the amount of leakage output over a hard-to-invert function family. In our scheme, the encryption policy is specified as an arbitrary monotonic formula, and the adversary can learn the arbitrary length output of the master key and the private key from any computationally irreversible function with the input (master) keys. To improve the efficiency, we employ the set of minimal sets to describe the predicate formula or access structure, and initiate the formal model of leakage-resilient FE, which is a generic extension of identity-based encryption and attribute-based encryption in the presence of key leakage with auxiliary inputs. We provide the concrete construction in bilinear groups of composite order, and prove the adaptively leakage-resilient security in the standard model based on static assumptions. Our hard-to-invert leakage resilience employs the Goldreich–Levin theorem and its extension as a hard-core value over large fields. We also give an extensional construction in the case of obtaining the hard-to-invert randomness leakage of the encryption, which uses a strong extractor to prevent leakage of randomness and a hard-to-invert encryption to prevent the leakage of the key. Finally, we analyze and discuss the stepped-up security on master leakage and continual leakage, and the lower bound of the irreversible leakage function.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 5
    Publication Date: 2012-04-03
    Description: In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV ( http://togotv.dbcls.jp/en/ ) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 6
    Publication Date: 2014-08-25
    Description: We present the first galaxy counts at 18 μm using the Japanese AKARI satellite's survey at the North Ecliptic Pole (NEP), produced from the images from the NEP-Deep and NEP-Wide surveys covering 0.6 and 5.8 deg 2 , respectively. We describe a procedure using a point source filtering algorithm to remove background structure and a minimum variance method for our source extraction and photometry that delivers the optimum signal to noise for our extracted sources, confirming this by comparison with standard photometry methods. The final source counts are complete and reliable over three orders of magnitude in flux density, resulting in sensitivities (80 per cent completeness) of 0.15 and 0.3 mJy for the NEP-Deep and NEP-Wide surveys, respectively, a factor of 1.3 deeper than previous catalogues constructed from this field. The differential source counts exhibit a characteristic upturn from Euclidean expectations at around a milliJansky and a corresponding evolutionary bump between 0.2–0.4 mJy consistent with previous mid-infrared surveys with ISO and Spitzer at 15 and 24 μm. We compare our results with galaxy evolution models confirming the striking divergence from the non-evolving scenario. The models and observations are in broad agreement implying that the source counts are consistent with a strongly evolving population of luminous infrared galaxies at redshifts higher than unity. Integrating our source counts down to the limit of the NEP survey at the 150 μJy level we calculate that AKARI has resolved approximately 55 per cent of the 18 μm cosmic infrared background relative to the predictions of contemporary source count models.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2015-01-16
    Description: The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp ) maintains and provides public archival, retrieval and analytical services for biological information. Since October 2013, DDBJ Center has operated the Japanese Genotype-phenotype Archive (JGA) in collaboration with our partner institute, the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency. DDBJ Center provides the JGA database system which securely stores genotype and phenotype data collected from individuals whose consent agreements authorize data release only for specific research use. NBDC has established guidelines and policies for sharing human-derived data and reviews data submission and usage requests from researchers. In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science. This paper describes the overview of the JGA project, updates to the DDBJ databases, and services for data retrieval, analysis and integration.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2014-11-15
    Description: We present data products from the 300 ks Chandra survey in the AKARI North Ecliptic Pole Deep Field. This field has a unique set of nine-band infrared photometry covering 2–24 μm from the AKARI Infrared Camera, including mid-infrared (MIR) bands not covered by Spitzer . The survey is one of the deepest ever achieved at ~15 μm, and is by far the widest among those with similar depths in the MIR. This makes this field unique for the MIR-selection of AGN at z ~ 1. We design a source detection procedure, which performs joint maximum likelihood PSF (point spread function) fits on all of our 15 mosaicked Chandra pointings covering an area of 0.34 deg 2 . The procedure has been highly optimized and tested by simulations. We provide a point source catalogue with photometry and Bayesian-based 90 per cent confidence upper limits in the 0.5–7, 0.5–2, 2–7, 2–4, and 4–7 keV bands. The catalogue contains 457 X-ray sources and the spurious fraction is estimated to be ~1.7 per cent. Sensitivity and 90 per cent confidence upper flux limits maps in all bands are provided as well. We search for optical–MIR counterparts in the central 0.25 deg 2 , where deep Subaru Suprime-Cam multiband images exist. Among the 377 X-ray sources detected there, ~80 per cent have optical counterparts and ~60 per cent also have AKARI MIR counterparts. We cross-match our X-ray sources with MIR-selected AGN from Hanami et al. Around 30 per cent of all AGN that have MIR SEDs purely explainable by AGN activity are strong Compton-thick AGN candidates.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2012-12-20
    Description: The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp ) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers in the sequence read archive (SRA). A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012. To cope with the ongoing genomic data deluge, in March 2012, our computer previous system was totally replaced by a commodity cluster-based system that boasts 122.5 TFlops of CPU capacity and 5 PB of storage space. During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well. As a result of the replacement process, which took more than 2 years to perform, we have achieved significant improvements in system performance.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2013-10-29
    Description: We present tentative Hα emission line detections of four submillimetre-detected galaxies at z  〉 3.5: the radio galaxies 8C1909+722 and 4C60.07 at signal-to-noise ratios (SNRs) of 3.1 and 2.5, and two submillimetre-selected galaxies (SMGs) near the first of these at SNRs of 10.0 and 2.4, made with the AKARI space telescope as part of the Follow-Up Hayai-Yasui-Umai mission programme. These are the highest redshift Hα detections in such galaxies, made possible by AKARI 's unique near-infrared spectroscopic capability. The two radio galaxies had known redshifts and surrounding structure, and we have detected broad Hα components indicating the presence of dust-shrouded quasars. We conclude that powerful active galactic nuclei (AGNs) at z  〉 3.5 occur in peaks of the star formation density fields, supporting a close connection between stellar mass build-up and black hole mass assembly at this redshift. We also show that 4C60.07 is a binary AGN. The Hα detections of the two SMGs are the first redshift determinations for these sources, confirming their physical association around their companion radio galaxy. The Hα-derived star formation rates (SFRs) for the SMGs are lower than their far-infrared derived SFRs by a factor of ~10, suggesting a level of dust obscuration similar to that found in studies at ~1 〈  z  〈 2.7.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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