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  • Articles  (32)
  • Applied Physics Letters  (4)
  • Bioinformatics  (3)
  • Human Molecular Genetics  (3)
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    The tunable negative permittivity and negative permeability of percolative Fe/Al2O3 composites in radio frequency range (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-04-29
    Description: The electromagnetic properties including ac conductivity, permittivity, and permeability of percolative Fe/Al 2 O 3 composites, which were prepared by in-situ synthesis process, are investigated in the radio frequency range. There is an obvious percolation transition with the increase of iron contents. When iron content is beyond but near the percolation threshold, the negative permittivity and permeability are simultaneously obtained from 631 MHz to 1 GHz in sample FA30. Further increasing iron content, the Fano-like resonances are observed, and the resonance frequency where the permittivity changes from negative to positive shifts to lower frequency. In addition, the frequency region of negative permittivity and negative permeability are not overlapped any more. Hopefully, the percolative Fe/Al 2 O 3 composites with tunable negative permittivity and negative permeability can be used as electromagnetic wave absorber.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition (2016)
    Oxford University Press
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    Publication Date: 2016-02-02
    Description: : The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors. Availability and implementation: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/ . Contact: shuaicli@cityu.edu.hk , dbu@ict.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Multiple alignment-free sequence comparison (2013)
    Oxford University Press
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    Publication Date: 2013-10-19
    Description: Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k -tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k -tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis -regulatory module data where the task is to identify cis -regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/~fsun/Programs/multiAlignFree/multiAlignFreemain.html . Contact: reinert@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    High-quality II-VI films grown on amorphous substrates using tunable tetradymite templates (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-04
    Description: We demonstrate the growth of highly oriented CdSe and ZnTe films at ∼300 °C on amorphous substrates such as glass and flexible polyimide using ultrathin tetradymite buffer layers composed of Sb x Bi 2-x Te 3 alloys lattice-matched to the film overgrowth. This leads to significant improvement of the crystallinity, roughness, grain size, and pit density of the II-VI overlayer along with enhancement of the optoelectronic properties. For example, photoluminescence emission is observed at ∼1.74 eV for optimized CdSe films, the same as in a single crystal reference. An in-plane carrier diffusion length of ∼500 nm is inferred from transient optical data. The use of tetradymite buffer layers to control II-VI compound deposition on non-crystalline substrates is a promising route for large area optoelectronic applications such as photovoltaic, light-emission, or infrared detector devices.
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    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Genetic factors affecting gene transcription and catalytic activity of UDP-glucuronosyltransferases in human liver (2014)
    Oxford University Press
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    Publication Date: 2014-09-20
    Description: The aim of this study was to discover cis - and trans -acting factors significantly affecting mRNA expression and catalytic activity of human hepatic UDP-glucuronosyltransferases (UGTs). Transcription levels of five major hepatic UGT1A ( UGT1A1, UGT1A3, UGT1A4, UGT1A6 and UGT1A9 ) and five UGT2B ( UGT2B4, UGT2B7, UGT2B10, UGT2B15 and UGT2B17 ) genes were quantified in human liver tissue samples ( n = 125) using real-time PCR. Glucuronidation activities of 14 substrates were measured in 47 livers. We genotyped 167 tagSNPs (single-nucleotide polymorphisms) in UGT1A ( n = 43) and UGT2B ( n = 124), as well as the known functional UGT1A1*28 and UGT2B17 CNV (copy number variation) polymorphisms. Transcription levels of 15 transcription factors (TFs) known to regulate these UGTs were quantified. We found that UGT expression and activity were highly variable among the livers (median and range of coefficient of variations: 135%, 74–217% and 52%, 39–105%, respectively). CAR, PXR and ESR1 were found to be the most important trans -regulators of UGT transcription (median and range of correlation coefficients: 46%, 6–58%; 47%, 9–58%; and 52%, 24–75%, respectively). Hepatic UGT activities were mainly determined by UGT gene transcription levels. Twenty-one polymorphisms were significantly (FDR-adjusted P 〈 0.05) associated with mRNA expression and/or activities of UGT1A1 , UGT1A3 and UGT2B17 . We found novel SNPs in the UGT2B17 CNV region accounting for variability in UGT2B17 gene transcription and testosterone glucuronidation rate, in addition to that attributable to the UGT2B17 CNV. Our study discovered novel pharmacogenetic markers and provided detailed insight into the genetic network regulating hepatic UGTs.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Dual percolation behaviors of electrical and thermal conductivity in metal-ceramic composites (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-02-10
    Description: The thermal and electrical properties including the permittivity spectra in radio frequency region were investigated for copper/yttrium iron garnet (Cu/YIG) composites. Interestingly, the percolation behaviors in electrical and thermal conductivity were obtained due to the formation of copper particles' networks. Beyond the electrical percolation threshold, negative permittivity was observed and plasmon frequency was reduced by several orders of magnitude. With the increase in copper content, the thermal conductivity was gradually increased; meanwhile, the phonon scattering effect and thermal resistance get enhanced, so the rate of increase in thermal conductivity gradually slows down. Hopefully, Cu/YIG composites with tunable electrical and thermal properties have great potentials for electromagnetic interference shielding and electromagnetic wave attenuation.
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    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Multiple pathogenic proteins implicated in neuronopathic Gaucher disease mice (2014)
    Oxford University Press
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    Publication Date: 2014-07-05
    Description: Gaucher disease, a prevalent lysosomal storage disease (LSD), is caused by insufficient activity of acid β-glucosidase (GCase) and the resultant glucosylceramide (GC)/glucosylsphingosine (GS) accumulation in visceral organs (Type 1) and the central nervous system (Types 2 and 3). Recent clinical and genetic studies implicate a pathogenic link between Gaucher and neurodegenerative diseases. The aggregation and inclusion bodies of α-synuclein with ubiquitin are present in the brains of Gaucher disease patients and mouse models. Indirect evidence of β-amyloid pathology promoting α-synuclein fibrillation supports these pathogenic proteins as a common feature in neurodegenerative diseases. Here, multiple proteins are implicated in the pathogenesis of chronic neuronopathic Gaucher disease (nGD). Immunohistochemical and biochemical analyses showed significant amounts of β-amyloid and amyloid precursor protein (APP) aggregates in the cortex, hippocampus, stratum and substantia nigra of the nGD mice. APP aggregates were in neuronal cells and colocalized with α-synuclein signals. A majority of APP co-localized with the mitochondrial markers TOM40 and Cox IV; a small portion co-localized with the autophagy proteins, P62/LC3, and the lysosomal marker, LAMP1. In cultured wild-type brain cortical neural cells, the GCase-irreversible inhibitor, conduritol B epoxide (CBE), reproduced the APP/α-synuclein aggregation and the accumulation of GC/GS. Ultrastructural studies showed numerous larger-sized and electron-dense mitochondria in nGD cerebral cortical neural cells. Significant reductions of mitochondrial adenosine triphosphate production and oxygen consumption (28–40%) were detected in nGD brains and in CBE-treated neural cells. These studies implicate defective GCase function and GC/GS accumulation as risk factors for mitochondrial dysfunction and the multi-proteinopathies (α-synuclein-, APP- and Aβ-aggregates) in nGD.
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    Topics: Biology , Medicine
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  • 8
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    High magnetic-refrigeration performance of plate-shaped La0.5Pr0.5Fe11.4Si1.6 hydrides sintered in high-pressure H2 atmosphere (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-03-03
    Description: La(Fe, Si) 13 hydride is regarded as one of the most promising room-temperature refrigerants. However, to use the alloys in an active magnetic regenerator machine, it is vital to prepare thin refrigerants. In this work, a high H 2 gas pressure of 50 MPa was employed to suppress the desorption of hydrogen atoms during the sintering process of plate-shaped La 0.5 Pr 0.5 Fe 11.4 Si 1.6 hydrides. At 330 K, a high-density sintered thin plate shows a large magnetic-entropy change Δ S m of 15.5 J/kg K (106 mJ/cm 3  K) for a field change of 2 T. The volumetric Δ S m is almost twice as large as that of bonded La(Fe,Si) 13 hydrides. Favorably, hysteresis is almost absent due to the existence of micropores with a porosity of 0.69% which has been analyzed with high-resolution X-ray microtomography.
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  • 9
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    Room-temperature ferromagnetic Co-doped ZnO nanoneedle array prepared by pulsed laser deposition (2005)
    American Institute of Physics
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    Publication Date: 2005-10-24
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  • 10
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    High current density in bulk YBa2Cu3Oxsuperconductor (1989)
    American Institute of Physics
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    Publication Date: 1989-06-05
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