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  • 1
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    WormBase 2016: expanding to enable helminth genomic research (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: WormBase ( www.wormbase.org ) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite ( parasite.wormbase.org ) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Real-time generation of atmospheric turbulence phase screen with non-uniform fast Fourier transform (2015)
    Oxford University Press
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    Publication Date: 2015-04-16
    Description: High-fidelity Monte Carlo simulation of atmospheric turbulence phase screens is important for performance testing of astronomical adaptive optics systems. With a sparse spectrum model and an optimal sampling method, it is possible to generate an atmospheric turbulence phase screen with high fidelity. However, the phase screen generation speed is limited by the algorithm structure of this technique. A non-uniform fast Fourier transform technique is proposed in this paper to accelerate phase screen generation speed. This method is able to generate huge atmospheric turbulence phase screens with high fidelity and an acceptable time-cost enabling practical adaptive optics simulations of forthcoming Extremely Large Telescopes.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Simulation of atmospheric turbulence phase screen for large telescope and optical interferometer (2015)
    Oxford University Press
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    Publication Date: 2015-01-24
    Description: As the pupil size of ground-based telescopes increases, adaptive optics systems become more and more important for almost all astronomical observations. To test the performance of adaptive optics systems through simulation and with test bench experiments, we need to model the atmospheric turbulence with high fidelity. To fulfil this goal, a new method based on optimal sampling with a sparse spectrum model is discussed. This method can effectively simulate the atmospheric phase screen of any power spectrum with a controllable error budget.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Alteration in immune responses toward N-deacetylation of hyaluronic acid (2014)
    Oxford University Press
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    Publication Date: 2014-10-29
    Description: Hyaluronic acid (HA) is an ubiquitous nonsulfated glycosaminoglycan of the extracellular matrix in all mammalian connective tissues. Along with the age growth, HA will lose its N -acetyl groups in vivo; however, the significance of this physiological process remains largely unknown. Herein, three highly N -deacetylated HAs (dHAs), dHA-5 kDa (Mw: 5 kDa, DD: 100%), dHA-16 kDa (Mw: 16 kDa, DD: 94%) and dHA-110 kDa (Mw: 110 kDa, DD: 72%), were generated after hydrazinolysis. Their capability in the activation of antigen-presenting cells (APCs) was compared with that of their respective HAs. Our results demonstrated that both HAs and dHAs could activate the nuclear factor-kappa B (NF-B) transcription factor in APCs and induced cytokine production through the Toll-like receptor (TLR)/MyD88 pathway. Notably, the capacity of dHAs in cytokine induction was much lower than that of HAs. In addition, the TLR-2 pathway was much involved following the appearance of zwitterionic motifs in dHAs. Thus, our findings highlight that N-deacetylation renders HA divergences in immune response, which might be implicated in age-induced functional change in endogenous glycosaminoglycans due to the structural modification in vivo.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    A comprehensive analysis of GATA-1-regulated miRNAs reveals miR-23a to be a positive modulator of erythropoiesis (2013)
    Oxford University Press
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    Publication Date: 2013-04-14
    Description: miRNAs play important roles in many biological processes, including erythropoiesis. Although several miRNAs regulate erythroid differentiation, how the key erythroid regulator, GATA-1, directly orchestrates differentiation through miRNA pathways remains unclear. In this study, we identified miR-23a as a key regulator of erythropoiesis, which was upregulated both during erythroid differentiation and in GATA-1 gain-of-function experiments, as determined by miRNA expression profile analysis. In primary human CD34+ hematopoietic progenitor cells, miR-23a increased in a GATA-1-dependent manner during erythroid differentiation. Gain- or loss-of-function analysis of miR-23a in mice or zebrafish demonstrated that it was essential for normal morphology in terminally differentiated erythroid cells. Furthermore, a protein tyrosine phosphatase, SHP2, was identified as a downstream target of miR-23a that mediated its regulation of erythropoiesis. Taken together, our data identify a key GATA-1–miRNA axis in erythroid differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    WormBase 2014: new views of curated biology (2013)
    Oxford University Press
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    Publication Date: 2013-12-29
    Description: WormBase ( http://www.wormbase.org/ ) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans . With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Electrical resistivity of coal-bearing rocks under high temperature and the detection of coal fires using electrical resistance tomography (2016)
    Oxford University Press
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    Publication Date: 2016-01-02
    Description: Coal fires are severe hazards to environment, health and safety throughout the world. Efficient and economical extinguishing of these fires requires that the extent of the subsurface coal fires should be delineated. Electrical and electromagnetic methods have been used to detect coal fires in recent years. However, the resistivity change of coal-bearing rocks at high temperature is rarely investigated. The resistivity characteristics of coal fires at different temperatures and depths are seldomly researched as well. In this paper, we present the results of measurements of several coal-bearing rocks’ resistivity and permeability under high temperature. Two major causes for the change in resistivity with increasing temperature are recognized, there are the increase of charge carriers and thermal fracturing, of which the first one is probably the dominant cause. A set of 2-D simulations is carried out to compare the relation of resolution and efficiency of coal fires detection to temperature and depth when adopting the electrical resistance tomography. The simulation results show that the resolution and efficiency decrease with the decrease of temperature and the increase of depth. Finally, the electrical resistance tomography is used to delineate coal fires in the Anjialing Open Pit Mine. Most low-resistivity regions are verified as coal-fire areas according to the long-term monitoring of borehole temperature. The results indicate that the electrical resistance tomography can be used as a tool for the detection of coal fires.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    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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  • 8
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    Role of reactive oxygen species-mediated MAPK and NF-{kappa}B activation in polygonatum cyrtonema lectin-induced apoptosis and autophagy in human lung adenocarcinoma A549 cells (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-03
    Description: Polygonatum cyrtonema lectin (PCL), a mannose/sialic acid-binding lectin isolated from the rhizomes of Polygonatum cyrtonema Hua, has been reported to possess remarkable anti-tumour effects via inducing apoptosis and autophagy. The aim of this study was to investigate the molecular mechanisms mediating PCL-induced apoptosis and autophagy in A549 cells. Herein, we found that the treatment of A549 cells with PCL caused a remarkable generation of reactive oxygen species (ROS) and ROS scavenger N-acetyl-cysteine (NAC) inhibited PCL-induced apoptosis and autophagy. In addition, PCL treatment activated mitogen-activated protein kinase (MAPK) members extracellular signal-regulated kinase (ERK), JNK and p38, JNK inhibitor and p38 inhibitor partially reduced PCL-induced apoptosis and autophagy. Moreover, PCL administration activated NF-B survival pathway in A549 cells, NF-B inhibitor Bay11-7082 promoted PCL-induced apoptosis. Importantly, we found PCL may bind to the cell surface in a mannose-specific manner, and was then internalized and accumulated primarily onto the mitochondria. These findings may provide a new perspective of PCL as a potential anti-tumour drug targeting apoptosis and autophagy pathways for future cancer therapeutics.
    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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    Induced polarization signature of coal seam fires (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-12
    Description: Coal seam fires are a worldwide disaster of both ecological and economic importance. Their remote detection from the ground surface or using airborne techniques is required for developing efficient strategies to extinguish them. We investigate here the use of time-domain-induced polarization to localize coal seam fires. For laboratory experiments, we first introduce a modified time-domain-induced polarization methodology to quickly acquire and invert the secondary voltage distribution mapped after the shutdown of the primary current. A set of sandbox experiments is conducted in which coal is embedded into humidified sand. Raw coal alone generates significant induced polarization anomalies, above those shown by the sand. Even higher induced polarization anomalies are detected in presence of a coal seam fire. We postulate that the higher chargeability is due to the pyrolysis, which may enhance electronic polarization or the polarization associated with the cation exchange capacity (CEC) of the material. The position of the coal seam fire is well recovered inside the tank by inverting the secondary voltages in term of a source current density distribution. We also collected field data over a recognized coal seam fire in Colorado, USA. A chargeability anomaly (~800 mV V –1 ) and a resistivity anomaly (~1 Ohm m) are observed at the position of the coal seam fire. We propose a normalized burning front index (a scaled normalized chargeability) to image and localize, without ambiguity, the position of the coal seam fire in the subsurface. The 3-D reconstructed target is located below a negative self-potential anomaly (similarly to what is observed in laboratory experiments) and a temperature anomaly recorded at a depth of 30 cm.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    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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  • 10
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    Three-dimensional full waveform inversion of short-period teleseismic wavefields based upon the SEM-DSM hybrid method (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-31
    Description: We present a method for high-resolution imaging of lithospheric structures based on full waveform inversion of teleseismic waveforms. We model the propagation of seismic waves using our recently developed direct solution method/spectral-element method hybrid technique, which allows us to simulate the propagation of short-period teleseismic waves through a regional 3-D model. We implement an iterative quasi-Newton method based upon the L-BFGS algorithm, where the gradient of the misfit function is computed using the adjoint-state method. Compared to gradient or conjugate-gradient methods, the L-BFGS algorithm has a much faster convergence rate. We illustrate the potential of this method on a synthetic test case that consists of a crustal model with a crustal discontinuity at 25 km depth and a sharp Moho jump. This model contains short- and long-wavelength heterogeneities along the lateral and vertical directions. The iterative inversion starts from a smooth 1-D model derived from the IASP91 reference Earth model. We invert both radial and vertical component waveforms, starting from long-period signals filtered at 10 s and gradually decreasing the cut-off period down to 1.25 s. This multiscale algorithm quickly converges towards a model that is very close to the true model, in contrast to inversions involving short-period waveforms only, which always get trapped into a local minimum of the cost function.
    Keywords: Seismology
    Print ISSN: 0956-540X
    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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