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  • 1
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    Hamiltonian non-displaceability of Gauss images of isoparametric hypersurfaces (2016)
    Oxford University Press
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    Publication Date: 2016-09-20
    Description: In this article, we study the Hamiltonian non-displaceability of Gauss images of isoparametric hypersurfaces in the spheres as Lagrangian submanifolds embedded in complex hyperquadrics.
    Print ISSN: 0024-6093
    Electronic ISSN: 1469-2120
    Topics: Mathematics
    Published by Oxford University Press
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  • 2
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    Measures for the degree of overlap of gene signatures and applications to TCGA (2015)
    Oxford University Press
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    Publication Date: 2015-09-16
    Description: For cancer and many other complex diseases, a large number of gene signatures have been generated. In this study, we use cancer as an example and note that other diseases can be analyzed in a similar manner. For signatures generated in multiple independent studies on the same cancer type and outcome, and for signatures on different cancer types, it is of interest to evaluate their degree of overlap. Many of the existing studies simply count the number (or percentage) of overlapped genes shared by two signatures. Such an approach has serious limitations. In this study, as a demonstrating example, we consider cancer prognosis data under the Cox model. Lasso, which is representative of a large number of regularization methods, is adopted for generating gene signatures. We examine two families of measures for quantifying the degree of overlap. The first family is based on the Cox-Lasso estimates at the optimal tunings, and the second family is based on estimates across the whole solution paths. Within each family, multiple measures, which describe the overlap from different perspectives, are introduced. The analysis of TCGA (The Cancer Genome Atlas) data on five cancer types shows that the degree of overlap varies across measures, cancer types and types of (epi)genetic measurements. More investigations are needed to better describe and understand the overlaps among gene signatures.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 3
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    Metals and Metalloids in Precipitation Collected during CHINARE Campaign from Shanghai, China to Zhongshan Station, Antarctica: Spatial Variability and Source Identification (2015)
    Wiley
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    Publication Date: 2015-05-15
    Description: Metals and metalloids in continental precipitation have been widely observed, but the data over open oceans are still very limited. Investigation of metals and metalloids in marine precipitation is of great significance to understand global transport of these elements in the atmosphere and their input fluxes to the oceans. So, shipboard sampling of precipitation was conducted during a Chinese National Antarctic Research Expedition (CHINARE) campaign from Shanghai, China to Zhongshan Station, East Antarctica, and 22 samples (including 17 rainfall and 5 snowfall events) were collected and analyzed for concentrations of Pb, Ni, Cr, Cu, Co, Hg, As, Cd, Sb, Se, Zn, Mn and Ti. Results show that concentrations of both metals and metalloids vary considerably along the cruise, with higher concentrations at coastal sites and lower values on the south Indian Ocean. Although only soluble fractions were determined for elements, concentrations in this study are generally comparable to the reported values of marine rain. Enrichment factor analysis shows that most of metals and metalloids are enriched versus crustal sources, even in the samples collected from remote south Indian Ocean. In addition, metals and metalloids in precipitation are also very enriched above sea-salt abundance, indicating that impacts of sea salt aerosols on their concentrations are negligible. Main sources of metals and metalloids were explored with the aid of multivariate statistical analyses. The results show that human emissions have far-reaching distribution, which may exert an important influence on the solubility of elements in precipitation. This investigation provides valuable information on spatial variation and possible sources of trace elements in precipitation over the open oceans corresponding to understudied region.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination (2015)
    Oxford University Press
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    Publication Date: 2015-07-12
    Description: Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The S P preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or R P -biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Spatial gradients from irregular, multiple-point spacecraft configurations (2012)
    Wiley
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    Publication Date: 2012-11-14
    Description: We present a generalized multipoint analysis of physical quantities, such as magnetic field and plasma flow, based on spatial gradient properties, where the multipoint data may be taken by irregular (distorted) configurations of any number of spacecraft. The methodology is modified from a previous, fully 3-D gradient analysis technique, designed to apply strictly to 4-point measurements and to be stable for regular spacecraft configurations. Here, we adapt the method to be tolerant against distorted configurations and to return a partial result when fewer spacecraft measurements are available. We apply the method to a variety of important physical quantities, such as the electric current density and the vorticity of plasma flows based on Cluster and THEMIS multiple-point measurements. The method may also have valuable applications on the coming Swarm mission.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    UV-B has larger negative impacts on invasive populations of Triadica sebifera but ozone impacts do not vary (2016)
    Oxford University Press
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    Publication Date: 2016-01-29
    Description: Aims Abiotic stresses may interact with each other to determine impacts on plants so that their combined impact is less than or more than additive. Increasing UV-B radiation and surface ozone (O 3 ) are two major components of global change that may have such interactive impacts. Moreover, invasive and native populations of plants may respond differently to stresses as they can vary in primary and secondary metabolism. Methods Here, we conducted a factorial field experiment with open-top chambers assigned to an ozone treatment (ambient, 100 ppb, or 150 ppb) and UV-B treatment (ambient or increased 20%). We grew seedlings of native and invasive populations of Triadica sebifera in these chambers for one growing season. Important Findings Invasive plants grew faster than native plants in ambient UV-B but they did not differ significantly in elevated UV-B. Litter production of invasive plants was especially sensitive to UV-B in a way that increased with UV-B for native plants but decreased for invasive plants which may be important for nutrient cycling. In ambient UV-B, total mass decreased as ozone increased. Total mass was lower with elevated UV-B but there was no additional impact of increasing ozone. Leaf area did not decrease with UV-B so SLA and LAR were lowest at ambient ozone levels. These results suggest that the effects of ozone will depend on UV-B conditions perhaps due to changes in foliar traits. The traits that allow invasive populations of plants to be successful invaders may make them especially sensitive to UV-B which may reduce their success in future climatic conditions.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Interactive effects of water and nitrogen addition on soil microbial communities in a semiarid steppe (2012)
    Oxford University Press
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    Publication Date: 2012-07-10
    Description: Aims Better understanding of microbial compositional and physiological acclimation mechanisms is critical for predicting terrestrial ecosystem responses to global change. The aim is to assess variations in soil microbial communities under future scenarios of changing precipitation and N deposition in a semiarid grassland of northern China. Methods In order to explicitly estimate microbial responses, a field experiment with water and N addition was established in April 2005 and continuously conducted for 4 years. Specifically, soil microbial community composition and microbial C utilization potential were determined by phospholipid fatty acid (PLFA) and community-level physiological profiles, respectively. Important Findings Water addition had no effects on the PLFA concentrations of gram-positive (GP) and negative bacteria (GN), total bacteria and fungi. However, N addition caused significant reductions in the PLFA concentrations of GP, GN, total bacteria and fungi and thus decreased total PLFA of microbial communities. Moreover, there were interactive effects of water and N addition on GN/GP and the ratio of fungal to bacterial PLFA (F/B). In addition, synergistic effects were found between water and nitrogen in affecting microbial C utilization potentials, which implies that microbial C utilization potentials tend to be enhanced when both N and water availability are sufficient. Overall, the microbial responses to water and N addition support our hypothesis that water and N addition may be combined together to affect microbial communities in the semiarid grassland.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The Intense Substorm Incidence in Response to Interplanetary Shock Impacts and Influence on Energetic Electron Fluxes at Geosynchronous Orbit (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract The interaction between interplanetary (IP) shocks and the Earth's magnetosphere would generate/excite various types of geomagnetic phenomena. In order to analyze what kind of IP shock is more likely to trigger intense substorms (SME/AE 〉 1,000 nT) and how the energetic electrons response to intense substorms at geosynchronous orbit, we perform a systematic survey of 246 IP shock events using SuperMag and LANL observations between 2001 and 2013. The statistical analysis shows that intense substorms (SME 〉 1,000 nT) triggered by IP shocks are most likely to occur under the southward interplanetary magnetic field (IMF) and fast solar wind preconditions. Besides, intense substorms after the IP shock arrival are much more likely to occur when IMF points toward (away from) the Sun around spring (autumn) equinox, which can be ascribed to the Russell‐McPherron effect. Thus, the IMF Bs precondition of an IP shock and the Russell‐McPherron effect can be considered as precursors of an intense substorm. Furthermore, after the shock arrival associated with intense substorms, low‐energy (〈200 keV) electron fluxes increase significantly at geosynchronous orbit, and high‐energy (〉200 keV) electron fluxes decrease. The spectral index becomes softer with intense substorms and remains almost unchanged with moderate substorms no matter whether the IMF precondition is southward or northward.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    The magnetic configuration of the high-latitude cusp and dayside magnetopause under strong magnetic shears (2011)
    Wiley
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    Publication Date: 2011-09-27
    Description: This paper investigates the structure of the magnetic field near the magnetopause (MP) by analyzing the multiple-point magnetic measurements from the Cluster mission. In this paper, the spatial distribution of the curvature radius of the MP surface at the noon-midnight meridian and for situations with moderate dynamical pressure of solar wind is implied from direct measurements of magnetic field curvature for the first time. The investigation focused on conditions of strong magnetic shear and in which a clear boundary layer is present at the MP. It has been confirmed that the magnetic field lines surrounding the cusp bend sunward at the precusp region and tailward at the postcusp region, implying the existence of a cusp field indentation. The minimum curvature radius of the near-MP field at both precusp and postcusp regions is about 2 RE. As the latitude decreases, the curvature radius at the MP increases gradually, so that, as the subsolar point is approached, the curvature radius of the MP is nearly equal to the geocentric distance. These results compare well with existing MP models but reveal the limitations inherent in such statistical estimates of local MP curvature, particularly surrounding the cusp regions. The analysis of the magnetic measurements has also verified the existence of the magnetic bottles at both precusp and postcusp regions, which may play a role for the trapping of the charged particles of magnetosphere.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    Luminescent detection of DNA-binding proteins (2012)
    Oxford University Press
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    Publication Date: 2012-02-17
    Description: Transcription factors play a central role in cell development, differentiation and growth in biological systems due to their ability to regulate gene expression by binding to specific DNA sequences within the nucleus. The dysregulation of transcription factor signaling has been implicated in the pathogenesis of a number of cancers, developmental disorders, inflammation and autoimmunity. There is thus a high demand for convenient high-throughput methodologies able to detect sequence-specific DNA-binding proteins and monitor their DNA-binding activities. Traditional approaches for protein detection include gel mobility shift assays, DNA footprinting and enzyme-linked immunosorbent assays (ELISAs) which tend to be tedious, time-consuming, and may necessitate the use of radiographic labeling. By contrast, luminescence technologies offer the potential for rapid, sensitive and low-cost detection that are amenable to high-throughput and real-time analysis. The discoveries of molecular beacons and aptamers have spearheaded the development of new luminescent methodologies for the detection of proteins over the last decade. We survey here recent advances in the development of luminescent detection methods for DNA-binding proteins, including those based on molecular beacons, aptamer beacons, label-free techniques and exonuclease protection.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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