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  • 1
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    An autonomous observation and control system based on EPICS and RTS2 for Antarctic telescopes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-19
    Description: For unattended telescopes in Antarctic, the remote operation, autonomous observation and control are essential. An EPICS-(Experimental Physics and Industrial Control System) and RTS2-(Remote Telescope System, 2nd Version) based autonomous observation and control system with remoted operation is introduced in this paper. EPICS is a set of open source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments while RTS2 is an open source environment for control of a fully autonomous observatory. Using the advantage of EPICS and RTS2, respectively, a combined integrated software framework for autonomous observation and control is established that use RTS2 to fulfil the function of astronomical observation and use EPICS to fulfil the device control of telescope. A command and status interface for EPICS and RTS2 is designed to make the EPICS IOC (Input/Output Controller) components integrate to RTS2 directly. For the specification and requirement of control system of telescope in Antarctic, core components named Executor and Auto-focus for autonomous observation is designed and implemented with remote operation user interface based on browser-server mode. The whole system including the telescope is tested in Lijiang Observatory in Yunnan Province for practical observation to complete the autonomous observation and control, including telescope control, camera control, dome control, weather information acquisition with the local and remote operation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Statistics of dark matter substructure - II. Comparison of model with simulation results (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-31
    Description: We compare subhalo mass and velocity functions obtained from different simulations with different subhalo finders among each other, and with predictions from the new semi-analytical model presented in Paper I . We find that subhalo mass functions (SHMFs) obtained using different subhalo finders agree with each other at the level of ~20 per cent, but only at the low-mass end. At the massive end, subhalo finders that identify subhaloes based purely on density in configuration space dramatically underpredict the subhalo abundances by more than an order of magnitude. These problems are much less severe for subhalo velocity functions (SHVFs), indicating that they arise from issues related to assigning masses to the subhaloes, rather than from detecting them. Overall the predictions from the semi-analytical model are in excellent agreement with simulation results obtained using the more advanced subhalo finders that use information in six-dimensional phase-space. In particular, the model accurately reproduces the slope and host-mass-dependent normalization of both the subhalo mass and velocity functions. We find that the SHMFs and SHVFs have power-law slopes of 0.86 and 2.77, respectively, significantly shallower than what has been claimed in several studies in the literature.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    The endosomal sorting complex required for transport (ESCRT) is required for the sensitivity of yeast cells to nickel ions in Saccharomyces cerevisiae (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-07
    Description: Nickel is one of the toxic environment metal pollutants and is linked to various human diseases. In this study, through a functional genomics approach we have identified 16 nickel-sensitive and 22 nickel-tolerant diploid deletion mutants of budding yeast genes, many of which are novel players in the regulation of nickel homeostasis. The 16 nickel-sensitive mutants are of genes mainly involved in the protein folding, modification and destination and the cellular transport processes, while the 22 nickel-tolerant mutants are of genes encoding components of ESCRT complexes as well as protein factors involved in both the cell wall integrity maintenance and the vacuolar protein sorting process. In consistence with their phenotypes, most of these nickel-sensitive mutants show reduced intracellular nickel contents, while the majority of these nickel-tolerant mutants show elevated intracellular nickel contents, as compared to the wild type in response to nickel stress. Our data provides a basis for our understanding the regulation of nickel homeostasis and molecular mechanisms of nickel-induced human pathogenesis.
    Print ISSN: 1567-1356
    Electronic ISSN: 1567-1364
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis (2015)
    Oxford University Press
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    Publication Date: 2015-05-27
    Description: : Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. A dynamic slicing method was proposed for non-parametric dependence testing, which has been demonstrated to have higher powers compared with traditional methods such as Kolmogorov–Smirnov test. We introduce an R package dslice to facilitate the use of dynamic slicing method in bioinformatic applications such as quantitative trait loci study and gene set enrichment analysis. Availability and implementation : dslice is implemented in Rcpp and available in the Comprehensive R Archive Network. The package is distributed under the GNU General Public License (version 2 or later). Contact : zhangxg@tsinghua.edu.cn or jliu@stat.harvard.edu .
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Identification of the endosomal sorting complex required for transport-I (ESCRT-I) as an important modulator of anti-miR uptake by cancer cells (2015)
    Oxford University Press
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    Publication Date: 2015-01-24
    Description: Mechanisms of unassisted delivery of RNA therapeutics, including inhibitors of microRNAs, remain poorly understood. We observed that the hepatocellular carcinoma cell line SKHEP1 retains productive free uptake of a miR-21 inhibitor (anti-miR-21). Uptake of anti-miR-21, but not a mismatch (MM) control, induces expression of known miR-21 targets (DDAH1, ANKRD46) and leads to dose-dependent inhibition of cell growth. To elucidate mechanisms of SKHEP1 sensitivity to anti-miR-21, we conducted an unbiased shRNA screen that revealed tumor susceptibility gene 101 (TSG101), a component of the endosomal sorting complex required for transport (ESCRT-I), as an important determinant of anti-proliferative effects of anti-miR-21. RNA interference-mediated knockdown of TSG101 and another ESCRT-I protein, VPS28, improved uptake of anti-miR-21 in parental SKHEP1 cells and restored productive uptake to SKHEP1 clones with acquired resistance to anti-miR-21. Depletion of ESCRT-I in several additional cancer cell lines with inherently poor uptake resulted in improved activity of anti-miR-21. Finally, knockdown of TSG101 increased uptake of anti-miR-21 by cancer cells in vivo following systemic delivery. Collectively, these data support an important role for the ESCRT-I complex in the regulation of productive free uptake of anti-miRs and reveal potential avenues for improving oligonucleotide free uptake by cancer cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    The autoinhibitory CARD2-Hel2i Interface of RIG-I governs RNA selection (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-30
    Description: RIG-I (Retinoic Acid Inducible Gene-I) is a cytosolic innate immune receptor that detects atypical features in viral RNAs as foreign to initiate a Type I interferon signaling response. RIG-I is present in an autoinhibited state in the cytoplasm and activated by blunt-ended double-stranded (ds)RNAs carrying a 5' triphosphate (ppp) moiety. These features found in many pathogenic RNAs are absent in cellular RNAs due to post-transcriptional modifications of RNA ends. Although RIG-I is structurally well characterized, the mechanistic basis for RIG-I's remarkable ability to discriminate between cellular and pathogenic RNAs is not completely understood. We show that RIG-I's selectivity for blunt-ended 5'-ppp dsRNAs is 3000 times higher than non-blunt ended dsRNAs commonly found in cellular RNAs. Discrimination occurs at multiple stages and signaling RNAs have high affinity and ATPase turnover rate and thus a high k atpase / K d . We show that RIG-I uses its autoinhibitory CARD2-Hel2i (second CARD-helicase insertion domain) interface as a barrier to select against non-blunt ended dsRNAs. Accordingly, deletion of CARDs or point mutations in the CARD2-Hel2i interface decreases the selectivity from 3000 to 150 and 750, respectively. We propose that the CARD2-Hel2i interface is a ‘gate’ that prevents cellular RNAs from generating productive complexes that can signal.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    On the segregation of dark matter substructure (2015)
    Oxford University Press
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    Publication Date: 2015-11-04
    Description: We present the first comprehensive analysis of the segregation of dark matter subhaloes in their host haloes. Using three different numerical simulations, and two different segregation strength indicators, we examine the segregation of 12 different subhalo properties with respect to both orbital energy and halocentric radius (in real space as well as in projection). Subhaloes are strongly segregated by accretion redshift, which is an outcome of the inside-out assembly of their host haloes. Since subhaloes that were accreted earlier have experienced more tidal stripping, subhaloes that have lost a larger fraction of their mass at infall are on more bound orbits. Subhaloes are also strongly segregated in their masses and maximum circular velocities at accretion. We demonstrate that part of this segregation is already imprinted in the infall conditions. For massive subhaloes, it is subsequently boosted by dynamical friction, but only during their first radial orbit. The impact of these two effects is counterbalanced, though, by the fact that subhaloes with larger accretion masses are accreted later. Because of tidal stripping, subhaloes reveal little to no segregation by present-day mass or maximum circular velocity, while the corresponding torques cause subhaloes on more bound orbits to have smaller spin. There is a weak tendency for subhaloes that formed earlier to be segregated towards the centre of their host halo, which is an indirect consequence of the fact that (sub)halo formation time is correlated with other, strongly segregated properties. We discuss the implications of our results for the segregation of satellite galaxies in galaxy groups and clusters.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-10
    Description: Reproductive infertility affects seventh of couples, which is most attributed to the obstacle of gametogenesis. Characterizing the epigenetic modification factors involved in gametogenesis is fundamental to understand the molecular mechanisms and to develop treatments for human infertility. Although the genetic factors have been implicated in gametogenesis, no dedicated bioinformatics resource for gametogenesis is available. To elucidate the relationship of epigenetic modification and mammalian gametogenesis, we developed a new database, gametogenesis epigenetic modification database (GED), a manually curated database, which aims at providing a comprehensive resource of epigenetic modification of gametogenesis. The database integrates three kinds information of epigenetic modifications during gametogenesis (DNA methylation, histone modification and RNA regulation), and the gametogenesis has been detailed as 16 stages in seven mammal species ( Homo sapiens , Mus musculus , Rattus norvegicus , Sus scrofa , Bos taurus , Capra hircus and Ovis aries ). Besides, we have predicted the linear pathways of epigenetic modification which were composed of 211 genes/proteins and microRNAs that were involved in gametogenesis. GED is a user-friendly Web site, through which users can obtain the comprehensive epigenetic factor information and molecular pathways by visiting our database freely. GED is free available at http://gametsepi.nwsuaflmz.com .
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 9
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    Efficient Identity-Based Proxy Signature in the Standard Model (2015)
    Oxford University Press
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    Publication Date: 2015-03-27
    Description: Presently, many identity-based proxy signature (IBPS) schemes have been proposed, but most of them are constructed in the random oracle model. Also, the proposed security model for IBPS is not enough complete according to Boldyreva's work. Cao and Cao proposed an IBPS scheme in the standard model. However, their scheme is not secure because of not resisting the attack of delegator and requires more computation cost. In this paper, we present a framework for IBPS and show a detailed security model for IBPS. Under our framework, we present an efficient IBPS scheme in the standard model. Compared with other IBPS schemes, the proposed scheme has more complete security and is more efficient.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Ground-source Airborne Time-domain ElectroMagnetic (GATEM) modeling and interpretation method for a rough medium based on fractional diffusion (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The Ground-source Airborne Time-domain Electromagnetic (GATEM) method is an efficient electromagnetic prospecting technique for engineering, geological surveying and mineral exploration. The electromagnetic response and inversion are obtained via the electrical conductivity of the geological medium, which is conventionally characterized by a homogeneous half-space or a piecewise smooth spatial distribution. However, these approximations hardly reflect the conditions of real geological media because of their rough, self-similar characteristics. This paper primarily considers the GATEM response and inversion with a long grounded wire source in a rough geological medium based on the fractional diffusion. To manage the rough geological medium, the fractional Maxwell equation is solved in the Laplace domain, and then the solution is transformed to the time domain using Guptasarma¡®s digital filter method. According to the mapping relationship between the resistivity and the induced voltage theoretically calculated in a rough geological medium, the neural network method is used to invert the resistivity. The characteristics of the response in a rough medium are analysed. Then, the inversion results are verified for a layered rough geological medium model; these results are closer to those of the real model than the results of the method derived using a smooth spatial distribution. Finally, the method is applied to GATEM field data in Jincheng, Shanxi Province, China. The inversions performed using a rough geological medium result in a reliable conductivity distribution.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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