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  • 1
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    ROCK inhibition enhances microRNA function by promoting deadenylation of targeted mRNAs via increasing PAIP2 expression (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: The reduced expression levels and functional impairment of global miRNAs are related to various human diseases, including cancers. However, relatively little is known about how global miRNA function may be upregulated. Here, we report that global miRNA function can be enhanced by Rho-associated, coiled-coil-containing protein kinase (ROCK) inhibitors. The regulation of miRNA function by ROCK inhibitors is mediated, at least in part, by poly(A)-binding protein-interacting protein 2 (PAIP2), which enhances poly(A)-shortening of miRNA-targeted mRNAs and leads to global upregulation of miRNA function. In the presence of a ROCK inhibitor, PAIP2 expression is enhanced by the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) through increased ROCK1 nuclear localization and enhanced ROCK1 association with HNF4A. Our data reveal an unexpected role of ROCK1 as a cofactor of HNF4A in enhancing PAIP2 transcription. ROCK inhibitors may be useful for the various pathologies associated with the impairment of global miRNA function.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    VLT spectroscopy of the black hole candidate Swift J1357.2-0933 in quiescence (2015)
    Oxford University Press
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    Publication Date: 2015-05-23
    Description: We present time-resolved optical spectroscopy of the counterpart to the high-inclination black hole low-mass X-ray binary Swift J1357.2–0933 in quiescence. Absorption features from the mass donor star were not detected. Instead the spectra display prominent broad double-peaked H α emission and weaker He i emission lines. From the H α peak-to-peak separation, we constrain the radial velocity semi-amplitude of the donor star to K 2  〉 789 km s –1 . Further analysis through radial velocity and equivalent width measurements indicates that the H α line is free of variability due to S-wave components or disc eclipses. From our data and previous observations during outburst, we conclude that long-term radial velocity changes ascribed to a precessing disc were of low amplitude or not present. This implies that the centroid position of the line should closely represent the systemic radial velocity, . Using the derived  = –150 km s –1 and the best available limits on the source distance, we infer that the black hole is moving towards the plane in its current Galactic orbit unless the proper motion is substantial. Finally, the depth of the central absorption in the double-peaked profiles adds support for Swift J1357.2–0933 as a high-inclination system. On the other hand, we argue that the low hydrogen column density inferred from X-ray fitting suggests that the system is not seen edge-on.
    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 evolution of municipal structure (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: In most US states, urban expansions are governed by ‘popular determination’, under which residents make annexation decisions through referendum. Yet little research analyzes how urban spatial structure evolves under this system. We develop a model to examine how urban residents’ collective decisions on annexations and property taxes and their interactions with agricultural landowners affect municipal structure under popular determination. We find that the evolution process of an urban area can be divided into four stages similar to human life stages (infancy, juvenile, adulthood and maturity), characterized by the pace of development. The key parameters that determine urban spatial structure include agricultural rents, construction costs, interest rate, and the rate and uncertainty of income growth. Cities tend to be more spread-out and consist of a large number of smaller municipalities, in regions with lower agricultural land rents, lower construction costs, and lower rate and uncertainty of income growth.
    Keywords: H73 - Interjurisdictional Differentials and Their Effects, Q24 - Land, R14 - Land Use Patterns
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
    Published by Oxford University Press
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  • 4
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    Brunnian subgroups of mapping class groups and braid groups (2013)
    Oxford University Press
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    Publication Date: 2013-09-26
    Description: This is the second of a pair of papers on the Delta-group structure on the braid and mapping class groups of a surface. We obtain a description of the homotopy groups of these Delta-groups and generalize to an arbitrary surface the Berrick–Cohen–Wong–Wu exact sequence relating the Brunnian braid groups of the 2-sphere to its homotopy groups. We prove a similar result for Brunnian mapping class groups.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
    Published by Oxford University Press
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  • 5
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    Modification of the RpoS network with a synthetic small RNA (2013)
    Oxford University Press
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    Publication Date: 2013-09-26
    Description: Translation of the sigma factor RpoS is activated by DsrA, RprA and ArcA, three small non-coding sRNAs (sRNA) that expose the ribosome-binding site (RBS) by opening up an inhibitory loop. In the RpoS network, no sRNAs have been found to pair with the RBS, a most common sRNA target site in bacteria. Here, we generate Ribo-0, an artificial sRNA, which represses rpoS translation by pairing with the RBS. Ribo-0 bypasses the RNA chaperon Hfq but requires the RBS to be loosely blocked. Ribo-0 interacts with DsrA and reshapes the RpoS network. Specifically, in the intact RpoS network, DsrA activates rpoS translation by freeing up the RBS. In the modified RpoS network where Ribo-0 is introduced, the DsrA-caused RBS exposure facilitates Ribo-0 binding, thereby strengthening Ribo-0 inhibition. In other words, Ribo-0 changes DsrA from an activator to an accomplice for repressing rpoS translation. This work presents an artificial mechanism of rpoS regulation, reveals mutual effects of native and synthetic players and demonstrates genetic context-dependency of their functions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    MBST: Detecting Packet-Level Traffic Anomalies by Feature Stability (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: In this paper, we present a statistical analysis of six traffic features based on entropy and distinct feature number at the packet level, and we find that, although these traffic features are unstable and show seasonal patterns like traffic volume in a long-time period, they are stable and consistent with Gaussian distribution in a short-time period. However, this equilibrium property will be violated by some anomalies. Based on this observation, we propose a Multi-dimensional Box plot method for Short-time scale Traffic (MBST) to classify abnormal and normal traffic. We compare our new method with the MCST method proposed in our prior work and the well-known wavelet-based and A Short-Timescale Uncorrelated-Traffic Equilibrium (ASTUTE) techniques. The detection result on synthetic anomaly traffic shows that MBST can better detect the low-rate attacks than wavelet-based and MCST methods, and detection result on real traffic demonstrates that MBST can detect more anomalies with lower false alarm rate than the two methods. Especially compared with ASTUTE, MBST performs much better for detecting anomalies involving a few large flows despite a little poor for detecting anomalies involving large number of small flows.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 7
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    Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-08
    Description: The rpoS mRNA, which encodes the master regulator S of general stress response, requires Hfq-facilitated base pairing with DsrA small RNA for efficient translation at low temperatures. It has recently been proposed that one mechanism underlying Hfq action is to bridge a transient ternary complex by simultaneously binding to rpoS and DsrA. However, no structural evidence of Hfq simultaneously bound to different RNAs has been reported. We detected simultaneous binding of Hfq to rpoS and DsrA fragments. Crystal structures of AU6A•Hfq•A7 and Hfq•A7 complexes were resolved using 1.8- and 1.9-Å resolution, respectively. Ternary complex has been further verified in solution by NMR. In vivo , activation of rpoS translation requires intact Hfq, which is capable of bridging rpoS and DsrA simultaneously into ternary complex. This ternary complex possibly corresponds to a meta-stable transition state in Hfq-facilitated small RNA–mRNA annealing process.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Tomography of X-ray Nova Muscae 1991: evidence for ongoing mass transfer and stream-disc overflow (2015)
    Oxford University Press
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    Publication Date: 2015-03-26
    Description: We present a spectroscopic analysis of the black hole binary Nova Muscae 1991 in quiescence using data obtained in 2009 with Magellan Echelette on the Magellan Clay telescope and in 2010 with IMACS on the Magellan Baade telescope at the Las Campanas Observatory. Emission from the disc is observed in Hα, Hβ and Ca  ii (8662). A prominent hotspot is observed in the Doppler maps of all three emission lines. The existence of this spot establishes ongoing mass transfer from the donor star in 2009–2010 and, given its absence in the 1993–1995 observations, demonstrates the presence of a variable hotspot in the system. We find the radial distance to the hotspot from the black hole to be consistent with the circularization radius. Our tomograms are suggestive of stream–disc overflow in the system. We also detect possible Ca  ii (8662) absorption from the donor star.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Simultaneous optical monitoring of BL Lacertae object S5 0716+714 with high temporal resolution (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: We have monitored the BL Lacertae object S5 0716+714 simultaneously in the B , R and I bands on three nights in 2014 November. The average time resolution is quite high (73, 34 and 58 s for the filters B , R and I ), which can help us trace the profile of the variation and search for the short inter-band time delay. Intra-day variability was about 0.1 mag on the first two nights and more than 0.3 mag on the third. A bluer-when-brighter colour behaviour was found. A clear loop path can be seen on the colour–magnitude diagram of the third night, revealing possible time delays between variations at high and low energies. It is the first time that the intra-day spectral hysteresis loop has been found so obviously in the optical band. We used the interpolated cross-correlation function method to further confirm the time delay and calculated the values of lag between light curves at different wavelengths on each night. On the third night, variations in the R and B bands are approximately 1.5 min lagging behind the I band. Such optical time delay is probably due to the interplay of different processes of electrons in the jet of the blazar.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Irrigation Decisions for Major West Coast Crops: Water Scarcity and Climatic Determinants (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-13
    Description: This article uses the 2007 Farm and Ranch Irrigation Survey database developed by the U.S. Department of Agriculture to assess the impact of water scarcity and climate on irrigation decisions for producers of specialty crops, wheat, and forage crops. We estimate an irrigation management model for major crops in the West Coast (California, Oregon, and Washington), which includes a farm-level equation of irrigated share and crop-specific equations of technology adoption and water application rate (orchard/vineyard, vegetable, wheat, alfalfa, hay, and pasture). We find that economic and physical water scarcity, climate, and extreme weather, such as frost, extreme heat, and drought, significantly impact producers’ irrigation decisions. Producers use sprinkler technologies or additional water applications to mitigate risk of crop damage from extreme weather. Water application rates are least responsive to surface water cost or groundwater well depth for producers of orchard/vineyard. Water supply institutions influence producers’ irrigation decisions. Producers who receive water from federal agencies use higher water application rates and are less likely to adopt water-saving irrigation technologies for some crops. Institutional arrangements, including access to distinct water sources (surface or ground) and whether surface water cost is fee based, also affect the responsiveness of water application rates to changes in surface water cost. The analysis provides valuable information about how producers in irrigated agricultural production systems would respond and adapt to water pricing policies and climate change.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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