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  • Articles  (21)
  • Glycobiology  (4)
  • Physics of Plasmas  (3)
  • Physical Review B  (2)
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  • Articles  (21)
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  • 1
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    Flux tube train model for local turbulence simulation of toroidal plasmas (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-02-11
    Description: A new simulation method for local turbulence in toroidal plasmas is developed by extending the conventional idea of the flux tube model. In the new approach, a train of flux tubes is employed, where flux tube simulation boxes are serially connected at each end along a field line so as to preserve a symmetry of the local gyrokinetic equations for image modes in an axisymmetric torus. Validity of the flux tube train model is confirmed against the toroidal ion temperature gradient turbulence for a case with a long parallel correlation of fluctuations, demonstrating numerical advantages over the conventional method in the time step size and the symmetry-preserving property.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    Abrupt change in the energy gap of superconducting Ba_{1-x}K_{x}Fe_{2}As_{2} single crystals with hole doping (2012)
    American Physical Society (APS)
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    Publication Date: 2012-10-11
    Description: Author(s): W. Malaeb, T. Shimojima, Y. Ishida, K. Okazaki, Y. Ota, K. Ohgushi, K. Kihou, T. Saito, C. H. Lee, S. Ishida, M. Nakajima, S. Uchida, H. Fukazawa, Y. Kohori, A. Iyo, H. Eisaki, C.-T. Chen, S. Watanabe, H. Ikeda, and S. Shin We performed a laser angle-resolved photoemission spectroscopy (ARPES) study on a wide doping range of Ba 1- x K x Fe 2 As 2 (BaK) and precisely determined the doping evolution of the superconducting gaps in this compound. The gap size of the outer hole Fermi-surface (FS) sheet around the Brillouin zone (BZ... [Phys. Rev. B 86, 165117] Published Wed Oct 10, 2012
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Nodal gap structure of superconducting BaFe_{2}(As_{1−x}P_{x})_{2} from angle-resolved thermal conductivity in a magnetic field (2011)
    American Physical Society (APS)
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    Publication Date: 2011-08-19
    Description: Author(s): M. Yamashita, Y. Senshu, T. Shibauchi, S. Kasahara, K. Hashimoto, D. Watanabe, H. Ikeda, T. Terashima, I. Vekhter, A. B. Vorontsov, and Y. Matsuda The structure of the superconducting order parameter in the iron-pnictide superconductor BaFe 2 (As 0.67 P 0.33 ) 2 ( T c =31 K) with line nodes is studied by the angle-resolved thermal conductivity measurements in a magnetic field rotated within the basal plane. We find that the thermal conductivity displays... [Phys. Rev. B 84, 060507] Published Thu Aug 18, 2011
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    Versican/PG-M is essential for ventricular septal formation subsequent to cardiac atrioventricular cushion development (2012)
    Oxford University Press
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    Publication Date: 2012-07-28
    Description: Versican (Vcan)/proteoglycan (PG)-M is a large chondroitin sulfate proteoglycan which forms a proteoglycan/hyaluronan (HA) aggregate in the extracellular matrix (ECM). We tried to generate the Vcan knockout mice by a conventional method, which resulted in mutant mice Vcan 3/3 whose Vcan lacks the A subdomain of the G1 domain. The Vcan knockout embryos died during the early development stage due to heart defects, but some Vcan 3/3 embryos survived through to the neonatal period. The hearts in Vcan 3/3 newborn mice showed normal cardiac looping, but had ventricular septal defects. Their atrioventricular canal (AVC) cushion was much smaller than those of wild-type (WT) embryos, and the extracellular space for cardiac jelly was narrow. The Vcan deposition in the Vcan 3/3 AVC cushion had decreased, whereas the HA deposition was maintained and condensed. In the tip of ventricular septa, both Vcan and HA had decreased. The cell proliferation based on the number of Ki67-positive cells had remarkably increased in both the AVC cushion and ventricular septa, compared with that of WT embryos. Vcan 3/3 seemed to have endocardial and mesenchymal mixed characteristics. When the ex vivo explant culture of these regions was performed on the collagen gel, hardly any migration to make sufficient space for the ECM construction was apparent. Our results suggest that the proteoglycan aggregates are necessary in both the AVC cushion and ventricular septa to fuse interventricular septa, and the Vcan A subdomain plays an essential role for the interventricular septal formation by constituting the proteoglycan aggregates.
    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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    Verification of gyrokinetic microstability codes with an LHD configuration (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-11-20
    Description: We extend previous benchmarks of the GS2 and GKV-X codes to verify their algorithms for solving the gyrokinetic Vlasov-Poisson equations for plasma microturbulence. Code benchmarks are the most complete way of verifying the correctness of implementations for the solution of mathematical models for complex physical processes such as those studied here. The linear stability calculations reported here are based on the plasma conditions of an ion-ITB plasma in the LHD configuration. The plasma parameters and the magnetic geometry differ from previous benchmarks involving these codes. We find excellent agreement between the independently written pre-processors that calculate the geometrical coefficients used in the gyrokinetic equations. Grid convergence tests are used to establish the resolution and domain size needed to obtain converged linear stability results. The agreement of the frequencies, growth rates, and eigenfunctions in the benchmarks reported here provides additional verification that the algorithms used by the GS2 and GKV-X codes are correctly finding the linear eigenvalues and eigenfunctions of the gyrokinetic Vlasov-Poisson equations.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Quasilinear carbon transport in an impurity hole plasma in LHD (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-08-06
    Description: Comprehensive electrostatic gyrokinetic linear stability calculations for ion-scale microinstabilities in an LHD plasma with an ion-internal transport barrier (ITB) and carbon “impurity hole” are used to make quasilinear estimates of particle flux to explore whether microturbulence can explain the observed outward carbon fluxes that flow “up” the impurity density gradient. The ion temperature is not stationary in the ion-ITB phase of the simulated discharge, during which the core carbon density decreases continuously. To fully sample these varying conditions, the calculations are carried out at three radial locations and four times. The plasma parameter inputs are based on experimentally measured profiles of electron and ion temperature, as well as electron and carbon density. The spectroscopic line-average ratio of hydrogen and helium densities is used to set the density of these species. Three ion species (H,He,C) and the electrons are treated kinetically, including collisions. Electron instability drive does enhance the growth rate significantly, but the most unstable modes have characteristics of ion temperature gradient modes in all cases. As the carbon density gradient is scanned between the measured value and zero, the quasilinear carbon flux is invariably inward when the carbon density profile is hollow, so turbulent transport due to the instabilities considered here does not explain the observed outward flux of impurities in impurity hole plasmas. The stiffness of the quasilinear ion heat flux is found to be 1.7–2.3, which is lower than several estimates in tokamaks.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Sequence determination of synthesized chondroitin sulfate dodecasaccharides (2016)
    Oxford University Press
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    Publication Date: 2016-04-28
    Description: Chondroitin sulfate (CS) is a linear acidic polysaccharide composed of repeating disaccharide units of glucuronic acid and N -acetyl- d -galactosamine. The polysaccharide is modified with sulfate groups at different positions by a variety of sulfotransferases. CS chains exhibit various biological and pathological functions by interacting with cytokines and growth factors and regulating their signal transduction. The fine structure of the CS chain defines its specific biological roles. However, structural analysis of CS has been restricted to disaccharide analysis, hampering the understanding of the structure–function relationship of CS chains. Here, we chemo-enzymatically synthesized CS dodecasaccharides having various sulfate modifications using a bioreactor system of bacterial chondroitin polymerase mutants and various CS sulfotransferases. We developed a sequencing method for CS chains using the CS dodecasaccharides. The method consists of (i) labeling a reducing end with 2-aminopyridine (PA), (ii) partial digestion of CS with testicular hyaluronidase, followed by separation of PA-conjugated oligosaccharides with different chain lengths, (iii) limited digestion of these oligosaccharides with chondroitin lyase AC II into disaccharides, followed by labeling with 2-aminobenzamide, (iv) CS disaccharide analysis using a dual-fluorescence HPLC system (reversed-phase ion-pair and ion-exchange chromatography), and (v) estimation of the composition by calculating individual disaccharide ratios. This CS chain sequencing allows characterization of CS-modifying enzymes and provides a useful tool toward understanding the structure–function relationship of CS chains.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Involvement of heparan sulfate 6-O-sulfation in the regulation of energy metabolism and the alteration of thyroid hormone levels in male mice (2013)
    Oxford University Press
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    Publication Date: 2013-06-29
    Description: Here, we report that male heparan sulfate 6- O- sulfotransferase-2 ( Hs6st2 ) knockout mice showed increased body weight in an age-dependent manner even when fed with a normal diet and showed a phenotype of impaired glucose metabolism and insulin resistance. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that the expression of mitochondrial uncoupling proteins Ucp1 and Ucp3 was reduced in the interscapular brown adipose tissue (BAT) of male Hs6st2 knockout mice, suggesting reduced energy metabolism. The serum level of thyroid-stimulating hormone was significantly higher and that of thyroxine was lower in the knockout mice. When cultures of brown adipocytes from wild-type and Hs6st2 knockout mice isolated and differentiated in vitro were treated with FGF19 (fibroblast growth factor 19) or FGF21 in the presence or the absence of heparitinase I, phosphorylation of p42/p44 mitogen-activated protein (MAP) kinase was reduced. Heparan sulfate (HS) 6- O -sulfation was reduced not only in BAT but also in the thyroid tissue of the knockout mice. Thus, 6- O -sulfation in HS seems to play an important role in mediating energy metabolism by controlling thyroid hormone levels and signals from the FGF19 subfamily proteins, and the alteration of the HS composition may result in metabolic syndrome phenotypes such as altered glucose and insulin tolerance.
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    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 9
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    Chondroitinase from baculovirus Bombyx mori nucleopolyhedrovirus and chondroitin sulfate from silkworm Bombyx mori (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-05
    Description: Chondroitin sulfate (CS) is a linear polysaccharide composed of repeating disaccharide units of glucuronic acid (GlcUA) and N -acetyl- d -galactosamine (GalNAc) with sulfate groups at various positions. Baculovirus is an insect-pathogenic virus that infects Lepidoptera larvae. Recently, we found that the occlusion-derived virus envelope protein 66 (ODV-E66) from Autographa californica nucleopolyhedrovirus (AcMNPV) exhibits chondroitin (CH)-digesting activity with distinct substrate specificity. Here, we demonstrate that the ODV-E66 protein from Bombyx mori nucleopolyhedrovirus (BmNPV) exhibits 92% homology to the amino acid sequence and 83% of the CH lyase activity of ODV-E66 from AcMNPV. ODV-E66 cleaves glycosyl bonds at nonreducing sides of disaccharide units consisting of nonsulfated and 6- O -sulfated GalNAc residues. We then investigated CS in the silkworm, Bombyx mori , which is the host of BmNPV. CS was present in insect tissues such as the midgut, peritrophic membrane, silk gland and skin. The polysaccharide consisted of a nonsulfated disaccharide unit, mono-sulfated disaccharide at Position 4 of the GalNAc residue and mono-sulfated disaccharide at Position 6 of the GalNAc residue. With regard to immunohistochemical analysis, the staining patterns of the silkworm tissues were different among anti-CS antibodies. Chondroitn sulfate that is digestible by ODV-E66 exists sufficiently in the peritrophic membrane protecting the midgut epithelium from ingested pathogens. Our results suggest that ODV-E66 facilitates the primary infection of the virus by digestion of CS in the peritrophic membrane.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Metal-insulator transition inNiS2−xSexand the local impurity self-consistent approximation model (1998)
    American Physical Society
    Details
    Publication Date: 1998-08-15
    Print ISSN: 0163-1829
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society
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