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  • 1
    Electronic Resource
    Electronic Resource
    Mass data acquisition systems in JT-60 data processing system : Papers from the thirteenth topical conference on high temperature plasma diagnostics (2001)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 72 (2001), S. 517-519 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: In the data processing system for the JT-60 tokamak, a unique mass data acquisition system with fast sampling, a transient mass data storage system (TMDS), has been used since 1988. It is composed of a minicomputer and 61 channels of 4/6 MB memory modules with a sampling rate up to 200 kHz and about 300 MB of data are transferred to a main computer by using a special LAN developed by Fujitsu Ltd. TMDS can handle a large amount of data, but cannot be enlarged in its capability, such as CPU power or the number of channels. To solve the problems of TMDS, a new fast VME data acquisition system (FDS), has been developed. It can acquire 6 MB of data per channel with a sampling rate of 200 kHz or 1 MHz and consists of a workstation with VMEbus memory modules. Up to now there are three FDSs with 24 channels. The minicomputer of TMDS has been replaced with a new system based on the technology of FDS. To cope with mass data transfer to a data server, they are connected with a gigabit ethernet switch. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1319866
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  • 2
    Electronic Resource
    Electronic Resource
    Systems for remote participation in JT-60 experiments : Proceedings of the 12th topical conference on high temperature plasma diagnostics (1999)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 70 (1999), S. 502-504 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: Since 1996, the remote participation in JT-60 experiments has been successfully conducted in collaboration with JAERI, Los Alamos National Laboratory and Princeton Plasma Physics Laboratory. The remote analysis system is a computer complex consisting of an analysis server and a data server for access to JT-60 data. Collaborators of the remote participation can analyze JT-60 data by using this system through the Internet. For the remote diagnostic system, an X Window control program has been customized to communicate via the overseas line using a UNIX workstation at the remote site and one in the JT-60 control room. It has a feature of real-time remote control of diagnostic equipment and remote access to CAMAC data. Both systems are used together with the ISDN-based video-conferencing system for real-time communication between the remote laboratory and the JT-60 control room. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1149270
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  • 3
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    Submm/mm galaxy counterpart identification using a characteristic density distribution (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-03
    Description: We present a new submm/mm galaxy counterpart identification technique which builds on the use of Spitzer Infrared Array Camera (IRAC) colours as discriminators between likely counterparts and the general IRAC galaxy population. Using 102 radio- and Submillimeter Array-confirmed counterparts to AzTEC sources across three fields [Great Observatories Origins Deep Survey-North, -South and Cosmic Evolution Survey (COSMOS)], we develop a non-parametric IRAC colour–colour characteristic density distribution, which, when combined with positional uncertainty information via likelihood ratios, allows us to rank all potential IRAC counterparts around submillimetre galaxies (SMGs) and calculate the significance of each ranking via the reliability factor. We report all robust and tentative radio counterparts to SMGs, the first such list available for AzTEC/COSMOS, as well as the highest ranked IRAC counterparts for all AzTEC SMGs in these fields as determined by our technique. We demonstrate that the technique is free of radio bias and thus applicable regardless of radio detections. For observations made with a moderate beam size (~18 arcsec), this technique identifies ~85 per cent of SMG counterparts. For much larger beam sizes (30 arcsec), we report identification rates of 33–49 per cent. Using simulations, we demonstrate that this technique is an improvement over using positional information alone for observations with facilities such as AzTEC on the Large Millimeter Telescope and Submillimeter Common User Bolometer Array 2 on the James Clerk Maxwell Telescope.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    X-ray detections of submillimetre galaxies: active galactic nuclei versus starburst contribution (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-03
    Description: We present a large-scale study of the X-ray properties and near-IR-to-radio spectral energy distributions (SEDs) of submillimetre galaxies (SMGs) detected at 1.1 mm with the AzTEC instrument across a ~1.2 square degree area of the sky. Combining deep 2–4 Ms Chandra data with Spitzer IRAC/MIPS and Very Large Array data within the Great Observatories Origins Deep Survey North (GOODS-N), GOODS-S and COSMOS fields, we find evidence for active galactic nucleus (AGN) activity in ~14 per cent of 271 AzTEC SMGs, ~28 per cent considering only the two GOODS fields. Through X-ray spectral modelling and multiwavelength SED fitting using Monte Carlo Markov chain techniques to Siebenmorgen et al. (AGN) and Efstathiou, Rowan-Robinson & Siebenmorgen (starburst) templates, we find that while star formation dominates the IR emission, with star formation rates (SFRs) ~100–1000 M yr –1 , the X-ray emission for most sources is almost exclusively from obscured AGNs, with column densities in excess of 10 23 cm –2 . Only for ~6 per cent of our sources do we find an X-ray-derived SFR consistent with NIR-to-radio SED derived SFRs. Inclusion of the X-ray luminosities as a prior to the NIR-to-radio SED effectively sets the AGN luminosity and SFR, preventing significant contribution from the AGN template. Our SED modelling further shows that the AGN and starburst templates typically lack the required 1.1 mm emission necessary to match observations, arguing for an extended, cool dust component. The cross-correlation function between the full samples of X-ray sources and SMGs in these fields does not indicate a strong correlation between the two populations at large scales, suggesting that SMGs and AGNs do not necessarily trace the same underlying large-scale structure. Combined with the remaining X-ray-dim SMGs, this suggests that sub-mm-bright sources may evolve along multiple tracks, with X-ray-detected SMGs representing transitionary objects between periods of high star formation and AGN activity, while X-ray-faint SMGs represent a brief starburst phase of more normal galaxies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-18
    Description: The human genome contains thousands of retrocopies, mostly as processed pseudogenes, which were recently shown to be prevalently transcribed. In particular, those specifically acquired in the human lineage are able to modulate gene expression in a manner that contributed to the evolution of human-specific traits. Therefore, knowledge of the human-specific retrocopies that are transcribed or their full-length transcript structure contributes to better understand human genome evolution. In this study, we identified 16 human-specific retrocopies that harbor 5' CpG islands by in silico analysis and showed that 12 were transcribed in normal tissues and cancer cell lines with a variety of expression patterns, including cancer-specific expression. Determination of the structure of the transcripts associated with the retrocopies revealed that none were transcribed from their 5' CpG islands, but rather, from inside the 3' UTR and the nearby 5' flanking region of the retrocopies as well as the promoter of neighboring genes. The multiple forms of the transcripts, such as chimeric and individual transcripts in both the sense and antisense orientation, might have introduced novel post-transcriptional regulation into the genome during human evolution. These results shed light on the potential role of human-specific retrocopies in the evolution of gene regulation and genomic disorders.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Timely binding of IHF and Fis to DARS2 regulates ATP-DnaA production and replication initiation (2014)
    Oxford University Press
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    Publication Date: 2014-11-28
    Description: In Escherichia coli , the ATP-bound form of DnaA (ATP–DnaA) promotes replication initiation. During replication, the bound ATP is hydrolyzed to ADP to yield the ADP-bound form (ADP–DnaA), which is inactive for initiation. The chromosomal site DARS2 facilitates the regeneration of ATP–DnaA by catalyzing nucleotide exchange between free ATP and ADP bound to DnaA. However, the regulatory mechanisms governing this exchange reaction are unclear. Here, using in vitro reconstituted experiments, we show that two nucleoid-associated proteins, IHF and Fis, bind site-specifically to DARS2 to activate coordinately the exchange reaction. The regenerated ATP–DnaA was fully active in replication initiation and underwent DnaA–ATP hydrolysis. ADP–DnaA formed heteromultimeric complexes with IHF and Fis on DARS2 , and underwent nucleotide dissociation more efficiently than ATP–DnaA. Consistently, mutant analyses demonstrated that specific binding of IHF and Fis to DARS2 stimulates the formation of ATP–DnaA production, thereby promoting timely initiation. Moreover, we show that IHF– DARS2 binding is temporally regulated during the cell cycle, whereas Fis only binds to DARS2 in exponentially growing cells. These results elucidate the regulation of ATP–DnaA and replication initiation in coordination with the cell cycle and growth phase.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    AzTEC/ASTE 1.1-mm survey of SSA22: Counterpart identification and photometric redshift survey of submillimetre galaxies (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-19
    Description: We present the results from a 1.1-mm imaging survey of the SSA22 field, known for having an overdensity of z  = 3.1 Lyman α emitting galaxies (LAEs), taken with the astronomical thermal emission camera (AzTEC) on the Atacama Submillimeter Telescope Experiment (ASTE). We imaged a 950-arcmin 2 field down to a 1 sensitivity of 0.7–1.3 mJy beam –1 to find 125 submillimetre galaxies (SMGs) with a signal-to-noise ratio ≥3.5. Counterpart identification using radio and near/mid-infrared data was performed and one or more counterpart candidates were found for 59 SMGs. Photometric redshifts based on optical to near-infrared images were evaluated for 45 of these SMGs with Spitzer /IRAC data and the median value is found to be z  = 2.4. By combining these estimations with estimates from the literature, we determined that 10 SMGs might lie within the large-scale structure at z  = 3.1. The two-point angular cross-correlation function between LAEs and SMGs indicates that the positions of the SMGs are correlated with the z  = 3.1 protocluster. These results suggest that the SMGs were formed and evolved selectively in the high dense environment of the high-redshift Universe. This picture is consistent with the predictions of the standard model of hierarchical structure formation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Effects of polyamines from Thermus thermophilus, an extreme-thermophilic eubacterium, on tRNA methylation by tRNA (Gm18) methyltransferase (TrmH) (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-28
    Description: Thermus thermophilus is an extreme-thermophilic eubacterium, which grows at a wide range of temperatures (50–83°C). This thermophile produces various polyamines including long and branched polyamines. In tRNAs from T. thermophilus , three distinct modifications, 2’- O -methylguanosine at position 18 (Gm18), 5-methyl-2-thiouridine at position 54 and N 1 -methyladenosine at position 58, are assembled at the elbow region to stabilize the L-shaped tRNA structure. However, the structures of unmodified tRNA precursors are disrupted at high temperatures. We hypothesize that polyamine(s) might have a positive effect on the modification process of unmodified tRNA transcript. We investigated the effects of eight polyamines on Gm18 formation in the yeast tRNA Phe transcript by tRNA (Gm18) methyltransferase (TrmH). Higher concentrations of linear polyamines inhibited TrmH activity at 55°C, while optimum concentration increased TrmH activity at 45–75°C. Exceptionally, caldohexamine, a long polyamine, did not show any positive effect on the TrmH activity at 55°C. However, temperature-dependent experiments revealed that 1 mM caldohexamine increased TrmH activity at 60–80°C. Furthermore, 0.25 mM tetrakis(3-aminopropy)ammonium, a branched polyamine, increased TrmH activity at a broad range of temperatures (40–85°C). Thus, caldohexamine and tetrakis(3-aminopropy)ammonium were found to enhance the TrmH activity at high temperatures.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 9
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    Direct assessment of transcription fidelity by high-resolution RNA sequencing (2013)
    Oxford University Press
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    Publication Date: 2013-10-19
    Description: Cancerous and aging cells have long been thought to be impacted by transcription errors that cause genetic and epigenetic changes. Until now, a lack of methodology for directly assessing such errors hindered evaluation of their impact to the cells. We report a high-resolution Illumina RNA-seq method that can assess noncoded base substitutions in mRNA at 10 –4 –10 –5 per base frequencies in vitro and in vivo . Statistically reliable detection of changes in transcription fidelity through ~10 3 nt DNA sites assures that the RNA-seq can analyze the fidelity in a large number of the sites where errors occur. A combination of the RNA-seq and biochemical analyses of the positions for the errors revealed two sequence-specific mechanisms that increase transcription fidelity by Escherichia coli RNA polymerase: (i) enhanced suppression of nucleotide misincorporation that improves selectivity for the cognate substrate, and (ii) increased backtracking of the RNA polymerase that decreases a chance of error propagation to the full-length transcript after misincorporation and provides an opportunity to proofread the error. This method is adoptable to a genome-wide assessment of transcription fidelity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Trans-chromosomic mice containing a human CYP3A cluster for prediction of xenobiotic metabolism in humans (2013)
    Oxford University Press
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    Publication Date: 2013-01-12
    Description: Human CYP3A is the most abundant P450 isozyme present in the human liver and small intestine, and metabolizes around 50% of medical drugs on the market. The human CYP3A subfamily comprises four members (CYP3A4, CYP3A5, CYP3A7, CYP3A43) encoded on human chromosome 7. However, transgenic mouse lines carrying the entire human CYP3A cluster have not been constructed because of limitations in conventional cloning techniques. Here, we show that the introduction of a human artificial chromosome (HAC) containing the entire genomic human CYP3A locus recapitulates tissue- and stage-specific expression of human CYP3A genes and xenobiotic metabolism in mice. About 700 kb of the entire CYP3A genomic segment was cloned into a HAC (CYP3A-HAC), and trans-chromosomic (Tc) mice carrying a single copy of germline-transmittable CYP3A-HAC were generated via a chromosome-engineering technique. The tissue- and stage-specific expression profiles of CYP3A genes were consistent with those seen in humans. We further generated mice carrying the CYP3A-HAC in the background homozygous for targeted deletion of most endogenous Cyp3a genes. In this mouse strain with ‘fully humanized’ CYP3A genes, the kinetics of triazolam metabolism, CYP3A-mediated mechanism-based inactivation effects and formation of fetal-specific metabolites of dehydroepiandrosterone observed in humans were well reproduced. Thus, these mice are likely to be valuable in evaluating novel drugs metabolized by CYP3A enzymes and in studying the regulation of human CYP3A gene expression. Furthermore, this system can also be used for generating Tc mice carrying other human metabolic genes.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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