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  • 2010-2014  (2,006)
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  • 11
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    Three-dimensional curved grid finite-difference modelling for non-planar rupture dynamics (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-07
    Description: In this study, we present a new method for simulating the 3-D dynamic rupture process occurring on a non-planar fault. The method is based on the curved-grid finite-difference method (CG-FDM) proposed by Zhang & Chen and Zhang et al. to simulate the propagation of seismic waves in media with arbitrary irregular surface topography. While keeping the advantages of conventional FDM, that is computational efficiency and easy implementation, the CG-FDM also is flexible in modelling the complex fault model by using general curvilinear grids, and thus is able to model the rupture dynamics of a fault with complex geometry, such as oblique dipping fault, non-planar fault, fault with step-over, fault branching, even if irregular topography exists. The accuracy and robustness of this new method have been validated by comparing with the previous results of Day et al. , and benchmarks for rupture dynamics simulations. Finally, two simulations of rupture dynamics with complex fault geometry, that is a non-planar fault and a fault rupturing a free surface with topography, are presented. A very interesting phenomenon was observed that topography can weaken the tendency for supershear transition to occur when rupture breaks out at a free surface. Undoubtedly, this new method provides an effective, at least an alternative, tool to simulate the rupture dynamics of a complex non-planar fault, and can be applied to model the rupture dynamics of a real earthquake with complex geometry.
    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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  • 12
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    Tumor-targeted in vivo gene silencing via systemic delivery of cRGD-conjugated siRNA (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: RNAi technology is taking strong position among the key therapeutic modalities, with dozens of siRNA-based programs entering and successfully progressing through clinical stages of drug development. To further explore potentials of RNAi technology as therapeutics, we engineered and tested VEGFR2 siRNA molecules specifically targeted to tumors through covalently conjugated cyclo(Arg-Gly-Asp- d -Phe-Lys[PEG-MAL]) (cRGD) peptide, known to bind αvβ3 integrin receptors. cRGD-siRNAs were demonstrated to specifically enter and silence targeted genes in cultured αvβ3 positive human cells (HUVEC). Microinjection of zebrafish blastocysts with VEGFR2 cRGD-siRNA resulted in specific inhibition of blood vessel growth. In tumor-bearing mice, intravenously injected cRGD-siRNA molecules generated no innate immune response and bio-distributed to tumor tissues. Continuous systemic delivery of two different VEGFR2 cRGD-siRNAs resulted in down-regulation of corresponding mRNA (55 and 45%) and protein (65 and 45%) in tumors, as well as in overall reduction of tumor volume (90 and 70%). These findings demonstrate strong potential of cRGD-siRNA molecules as anti-tumor therapy.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 13
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    High-speed microscopic imaging of flagella motility and swimming in Giardia lamblia trophozoites [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-08-24
    Description: We report, in this paper, several findings about the swimming and attachment mechanisms of Giardia lamblia trophozoites. These data were collected using a combination of a high-contrast CytoViva imaging system and a particle image velocimetry camera, which can capture images at speeds greater than 800 frames/s. Using this system, we discovered that, during rapid swimming of Giardia trophozoites, undulations of the caudal region contributed to forward propulsion combined with the beating of the flagella pairs. It was also discovered, in contrast to previous studies with 10 times slower image sampling technique, that the anterior and posterolateral flagella beat with a clearly defined power stroke and not symmetrical undulations. During the transition from free swimming to attachment, trophozoites modified their swimming behavior from a rapid rotating motion to a more stable planar swimming. While using this planar swimming motion, the trophozoites used the flagella for propulsion and directional control. In addition to examination of the posterolateral and anterior flagella, a model to describe the motion of the ventral flagella was derived, indicating that the ventral flagella beat in an expanding sine wave. In addition, the structure of the ventrocaudal groove creates boundary conditions that determine the form of beating of the ventral flagella. The results from this study indicate that Giardia is able to simultaneously generate both ciliary beating and typical eukaryotic flagellar beating using different pairs of flagella.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 14
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    Complex frequency-shifted multi-axial perfectly matched layer for elastic wave modelling on curvilinear grids (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-21
    Description: Perfectly matched layer (PML) is an efficient absorbing technique for numerical wave simulations. Since it appeared, various improvements have been made. The complex frequency-shifted PML (CFS-PML) improves the absorbing performance for near-grazing incident waves and evanescent waves. The auxiliary differential equation (ADE) formulation of the PML provides a convenient unsplit-field PML implementation that can be directly used with high order time marching schemes. The multi-axial PML (MPML) stabilizes the PML on anisotropic media. However, these improvements were generally developed for Cartesian grids. In this paper, we extend the ADE CFS-PML to general curvilinear (non-orthogonal) grids for elastic wave modelling. Unlike the common implementations to absorb the waves in the computational space, we apply the damping along the perpendicular direction of the PML layer in the local Cartesian coordinates. Further, we relate the perpendicular and parallel components of the gradient operator in the local Cartesian coordinates to the derivatives in the curvilinear coordinates, to avoid mapping the wavefield to the local Cartesian coordinates. It is thus easy to be incorporated with numerical schemes on curvilinear grids. We derive the PML equations for the interior region and for the free surface separately because the free surface boundary condition modifies the elastic wave equations. We show that the elastic wave modelling on curvilinear grids exhibits anisotropic effects in the computational space, which may lead to unstable simulations. To stabilize the simulation, we adapt the MPML strategy to also absorb the wavefield along the two parallel directions of the PML. We illustrate the stability of this ADE CFS-MPML for finite-difference elastic wave simulations on curvilinear grids by two numerical experiments.
    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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  • 15
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    Magnetic structure and Magnetic transport Properties of Graphene Nanoribbons With Sawtooth Zigzag Edges (2014)
    Springer Nature
    Details
    Publication Date: 2014-12-24
    Description: The magnetic structure and magnetic transport properties of hydrogen-passivated sawtooth zigzag-edge graphene nanoribbons (STGNRs) are investigated theoretically. It is found that all-sized ground-state STGNRs are ferromagnetic and always feature magnetic semiconductor properties, whose spin splitting energy gap Eg changes periodically with the width of STGNRs. More importantly, for the STGNR based device, the dual spin-filtering effect with the perfect (100%) spin polarization and high-performance dual spin diode effect with a rectification ratio about 1010 can be predicted. Particularly, a highly effective spin-valve device is likely to be realized, which displays a giant magnetoresistace (MR) approaching 1010%, which is three orders magnitude higher than the value predicted based on the zigzag graphene nanoribbons and six orders magnitude higher than previously reported experimental values for the MgO tunnel junction. Our findings suggest that STGNRs might hold a significant promise for developing spintronic devices. Scientific Reports 4 doi: 10.1038/srep07587
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 16
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    Different temperature scaling of strain-induced magneto-crystalline anisotropy and Gilbert damping in Co2FeAl film epitaxied on GaAs (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-08-22
    Description: The temperature dependence of the Gilbert damping and magnetic anisotropy are investigated in L 2 1 Co 2 FeAl films epitaxially grown on GaAs (001) substrate by the time resolved magneto-optical Kerr effect. We found that the in-plane biaxial anisotropy increases by more than 90% with the temperature decreasing from 300 K to 80 K, which is mainly due to the strong variation of the magneto-elastic coefficients. In contrast, the intrinsic Gilbert damping rises only about 10%, which is mainly attributed to the reduction of the electron phonon scattering rate, independent of the strain-induced spin-orbit coupling energy.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 17
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    Characteristics, Geometry, and Segmentation of the Surface Rupture Associated with the 14 April 2010 Yushu Earthquake, Eastern Tibet, China (2012)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2012-08-01
    Description: On the morning of 14 April 2010, the M s  7.1 Yushu earthquake struck the eastern Tibet Plateau and an M s  6.3 aftershock followed west-southwest of the mainshock epicenter one and a half hours later. The Yushu earthquake occurred on the northwestern continuation of the Ganzi–Xianshuihe fault zone and reactivated two segments of the fault. Ruptures associated with Yushu earthquake span a zone 70 km long, extending from south of Jielong in the west to south of Gyêgu (Yushu) in the east. Detailed mapping of the surface rupture zone shows that it consists of two strike-slip segments, the western and eastern segments, separated by the Longbao Lake step-over (pull apart) basin. Our analysis suggests that the 18-km-long western segment of the surface rupture south of the Longbao Lake basin may have been associated with the M s  6.3 aftershock. The eastern rupture segment, which is inferred to be associated with the mainshock, is 32 km long. The main surface rupture can also be divided into two sections, with a 2-km-long gap between them. The surface rupture exhibits left-lateral slip and is localized in a zone about 50 m wide along the present-day trace of the Yushu fault. A single break, without splays or branching traces, characterizes most of the surface rupture zone. The observed magnitudes of surface displacement are typically 0.5–1 m with a maximum slip of 2 m. Both field observations and seismic inversion results suggest, rupture of M s  7.1 Yushu earthquake nucleated near the Longbao Lake step-over basin in the west, propagated unilaterally eastward, and terminated within the east segment margin of the Yushu fault.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 18
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    LncRNA loc285194 is a p53-regulated tumor suppressor (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-04
    Description: Protein-coding genes account for only a small part of the human genome, whereas the vast majority of transcripts make up the non-coding RNAs including long non-coding RNAs (lncRNAs). Accumulating evidence indicates that lncRNAs could play a critical role in regulation of cellular processes such as cell growth and apoptosis as well as cancer progression and metastasis. LncRNA loc285194 was previously shown to be within a tumor suppressor unit in osteosarcoma and to suppress tumor cell growth. However, it is unknown regarding the regulation of loc285194. Moreover, the underlying mechanism by which loc285194 functions as a potential tumor suppressor is elusive. In this study, we show that loc285194 is a p53 transcription target; ectopic expression of loc285194 inhibits tumor cell growth both in vitro and in vivo . Through deletion analysis, we identify an active region responsible for tumor cell growth inhibition within exon 4, which harbors two miR-211 binding sites. Importantly, this loc285194-mediated growth inhibition is in part due to specific suppression of miR-211. We further demonstrate a reciprocal repression between loc285194 and miR-211; in contrast to loc285194, miR-211 promotes cell growth. Finally, we detect downregulation of loc285194 in colon cancer specimens by quantitative PCR arrays and in situ hybridization of tissue microarrays. Together, these results suggest that loc285194 is a p53-regulated tumor suppressor, which acts in part through repression of miR-211.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 19
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    A Novel HSF4 Gene Mutation Causes Autosomal-Dominant Cataracts in a Chinese Family (2014)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2014-05-17
    Description: Congenital cataracts are a significant cause of visual impairment or blindness in children. One-third of cases estimated to have a genetic cause. We carried out gene analysis and bioinformatics analysis to map the locus and to identify the underlying genetic defect in a 12-member, four-generation Chinese family affected with bilateral congenital cataracts. We screened individuals of the family and discovered a distinct missense mutation in HSF4 (a gene at this locus that encodes teat-shock transcription factor 4). Bioinformatics analysis was used to determine possible changes in the protein structure that could affect the phenotype. Sequencing of the candidate genes showed a heterozygous c.69 G-〉T change in the heat shock transcription factor 4 ( HSF4 ) gene, which resulted in the substitution of a lysine with an asparagine (p. K23N). This mutation cosegregated with all affected individuals and was not observed in unaffected family members. Bioinformatics analysis indicated that the p. K23N mutation was predicted to be disease causing. This is the first report of the novel missense mutation, c.69 G-〉T (p. K23N), in exon 3 of the HSF4 locus on 16q21-q22 associated with bilateral congenital cataracts in a Chinese family. This novel mutation could enable propergenetic diagnostics and counseling in affected families and could lead to a better understanding of the structure and function of HSF4 in health and disease.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 20
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    In vivo imaging of protein-protein and RNA-protein interactions using novel far-red fluorescence complementation systems (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-01
    Description: Imaging of protein–protein and RNA–protein interactions in vivo , especially in live animals, is still challenging. Here we developed far-red mNeptune-based bimolecular fluorescence complementation (BiFC) and trimolecular fluorescence complementation (TriFC) systems with excitation and emission above 600 nm in the ‘tissue optical window’ for imaging of protein–protein and RNA–protein interactions in live cells and mice. The far-red mNeptune BiFC was first built by selecting appropriate split mNeptune fragments, and then the mNeptune-TriFC system was built based on the mNeptune-BiFC system. The newly constructed mNeptune BiFC and TriFC systems were verified as useful tools for imaging protein–protein and mRNA–protein interactions, respectively, in live cells and mice. We then used the new mNeptune-TriFC system to investigate the interactions between human polypyrimidine-tract-binding protein (PTB) and HIV-1 mRNA elements as PTB may participate in HIV mRNA processing in HIV activation from latency. An interaction between PTB and the 3'long terminal repeat region of HIV-1 mRNAs was found and imaged in live cells and mice, implying a role for PTB in regulating HIV-1 mRNA processing. The study provides new tools for in vivo imaging of RNA–protein and protein–protein interactions, and adds new insight into the mechanism of HIV-1 mRNA processing.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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