bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Breakfast Skipping With Visceral Fat and Insulin Indices in Overweight Latino Youth
Authors: Alexander Katharine E. , Ventura Emily E. , Spruijt‐Metz Donna , Weigensberg Marc J. , Goran Michael I. , Davis Jaimie N.
Published: May 2009

Few studies have investigated the relationship between breakfast consumption and specific adiposity or insulin dynamics measures in children. The goal of this study is to determine whether breakfast consumption is associated with adiposity, specifically intra‐abdominal adipose tissue (IAAT), and insulin dynamics in overweight Latino youth. Participants were a cross‐sectional sample of 93 overweight (≥85th percentile BMI) Latino youth (10–17 years) with a positive family history of type 2 diabetes. Dietary intake was assessed by two 24‐h recalls, IAAT, and subcutaneous abdominal adipose tissue (SAAT) by magnetic resonance imaging, body composition by dual energy X‐ray absorptiometry, and insulin dynamics by a frequently sampled intravenous glucose tolerance test and minimal modeling. Participants were divided into three breakfast consumption categories: those who reported not eating breakfast on either day (breakfast skippers; n = 20), those who reported eating breakfast on one of two days (occasional breakfast eaters; n = 39) and those who ate breakfast on both days (breakfast eaters; n = 34). Using analyses of covariance, breakfast omission was associated with increased IAAT (P = 0.003) independent of age, Tanner, sex, total body fat, total body lean tissue mass, and daily energy intake. There were no significant differences in any other adiposity measure or in insulin dynamics between breakfast categories. Eating breakfast is associated with lower visceral adiposity in overweight Latino youth. Interventions focused on increasing breakfast consumption are warranted.
Pifithrin‐α decreases the radioprotective efficacy of a Podophyllum hexandrum (Himalayan mayapple) fraction (REC‐2006) in HepG2 cells
Authors: Singh Pankaj Kumar , Kumar Raj , Sharma Ashok , Arora Rajesh , Jain Swatantra Kumar , Sharma Rakesh Kumar
Published: May 2009

Inhibition of the tumour suppressor p53 by PFT (pifithrin‐α) promotes p53‐mediated apoptosis and protects against doxorubicin‐induced apoptosis. The present study was carried out to evaluate the effect of PFT on the radioprotective potential of Podophyllum hexandrum fraction (REC‐2006) in HepG2 (p53++) cell line. REC‐2006 (10−5 μg/ml) treatment at 2 h before irradiation (10 Gy) rendered 80±3% protection in HepG2 cells, whereas PFT debilitated the radioprotective potential of REC‐2006. REC‐2006 increased the expression of Hsp70 (heat‐shock protein 70), HSF1 (heat‐shock factor 1) and Bcl‐2 in irradiated HepG2 cells, whereas PFT when treated with REC‐2006 decreased the expression of Hsp70, HSF1 and Bcl‐2 in HepG2 cells. REC‐2006 facilitated post‐irradiation DNA repair by pausing cell‐cycle progression at G1‐ and G2‐phase, whereas no such cell‐cycle arrest was observed in irradiated HepG2 cells pretreated with PFT in irradiated HepG2 cells. No change was observed in Mdm2 (murine double minute 2) and Ras‐GAP (Ras‐GTPase‐activating protein) expression with or without PFT treatment. Decrease in the expression of caspase 3 and Bax was observed in HepG2 cells when REC‐2006 treatment was given 2 h before irradiation; however, PFT treatment increased the expression of Bax leading to apoptosis. It can be concluded that p53 expression plays a major role in the REC‐2006‐mediated protection against acute irradiation in HepG2 cells. PFT treatment reduced the radioprotective efficacy of REC‐2006 by inhibiting the expression of HSF1 and Hsp70 and thereby the expression of Bcl‐2, by up‐regulating the cell‐cycle‐regulatory proteins and therefore reducing the span of time for DNA repair and also by inducing Bax‐mediated apoptosis. PFT did not, however, show any effect on p53 regulating protein (Mdm2) and pro‐survival protein (Ras‐GAP).
Cell cycle analysis of fetal germ cells during sex differentiation in mice
Authors: Spiller Cassy , Wilhelm Dagmar , Koopman Peter
Published: May 2009

Background information. Primordial germ cells in developing male and female gonads are responsive to somatic cell cues that direct their sex‐specific differentiation into functional gametes. The first divergence of the male and female pathways is a change in cell cycle state observed from 12.5 dpc (days post coitum) in mice. At this time XY and XX germ cells cease mitotic division and enter G1/G0 arrest and meiosis prophase I respectively. Aberrant cell cycle regulation at this time can lead to disrupted ovarian development, germ cell apoptosis, reduced fertility and/or the formation of germ cell tumours.

Results. In order to unravel the mechanisms utilized by germ cells to achieve and maintain the correct cell cycle states, we analysed the expression of a large number of cell cycle genes in purified germ cells across the crucial time of sex differentiation. Our results revealed common signalling for both XX and XY germ cell survival involving calcium signalling. A robust mechanism for apoptosis and checkpoint control was observed in XY germ cells, characterized by p53 and Atm (ataxia telangiectasia mutated) expression. Additionally, a member of the retinoblastoma family and p21 were identified, linking these factors to XY germ cell G1/G0 arrest. Lastly, in XX germ cells we observed a down‐regulation of genes involved in both G1‐ and G2‐phases of the cell cycle consistent with their entry into meiosis.

Conclusion. The present study has provided a detailed analysis of cell cycle gene expression during fetal germ cell development and identified candidate factors warranting further investigation in order to understand cases of aberrant cell cycle control in these specialized cells.
A cotton kinesin GhKCH2 interacts with both microtubules and microfilaments
Authors: Xu Tao , Qu Zhe , Yang Xueyong , Qin Xinghua , Xiong Jiyuan , Wang Youqun , Ren Dongtao , Liu Guoqin
Published: May 2009

Many biological processes require the co-operative involvement of both microtubules and microfilaments; however, only a few proteins mediating the interaction between microtubules and microfilaments have been identified from plants. In the present study, a cotton kinesin GhKCH2, which contains a CH (calponin homology) domain at the N-terminus, was analysed in vitro and in vivo in order to understand its interaction with the two cytoskeletal elements. A specific antibody against GhKCH2 was prepared and used for immunolabelling experiments. Some GhKCH2 spots appeared along a few microtubules and microfilaments in developing cotton fibres. The His-tagged N-terminus of GhKCH2 (termed GhKCH2-N) could co-precipitate with microfilaments and strongly bind to actin filaments at a ratio of monomeric actin/GhKCH2-N of 1:0.6. The full-length GhKCH2 recombinant protein was shown to bind to and cross-link microtubules and microfilaments in vitro. A GFP-fusion protein GFP–GhKCH2 transiently overexpressed in Arabidopsis protoplasts decorated both microtubules and microfilaments, confirming the binding ability and specificities of GhKCH2 on microtubules and microfilaments in living plant cells. The results of the present study demonstrate that GhKCH2, a plant-specific microtubule-dependent motor protein, not only interacts with microtubules, but also strongly binds to microfilaments. The cytoskeletal dual-binding and cross-linking ability of GhKCH2 may be involved in the interaction between microtubules and microfilaments and the biological processes they co-ordinate together in cotton cells.
Characterization of SENP7, a SUMO-2/3-specific isopeptidase
Authors: Shen Lin Nan , Geoffroy Marie-Claude , Jaffray Ellis G. , Hay Ronald T.
Published: May 2009

The modification of proteins by SUMO (small ubiquitin-related modifier) plays important roles in regulating the activity, stability and cellular localization of target proteins. Similar to ubiquitination, SUMO modification is a dynamic process that can be reversed by SENPs [SUMO-1/sentrin/SMT3 (suppressor of mif two 3 homologue 1)-specific peptidases]. To date, six SENPs have been discovered in humans, although knowledge of their regulation, specificity and biological functions is limited. In the present study, we report that SENP7 has a restricted substrate specificity, being unable to process SUMO precursors and displaying paralogue-specific isopeptidase activity. The C-terminal catalytic domain of SENP7 efficiently depolymerized poly-SUMO-2 chains but had undetectable activity against poly-SUMO-1 chains. SENP7 also displayed isopeptidase activity against di-SUMO-2- and SUMO-2-modified RanGAP1 (Ran GTPase-activating protein 1) but had limited activity against SUMO-1-modified RanGAP1. in vivo, full-length SENP7 was localized to the nucleoplasm and preferentially reduced the accumulation of high-molecular-mass conjugates of SUMO-2 and SUMO-3 compared with SUMO-1. Small interfering RNA-mediated ablation of SENP7 expression led to the accumulation of high-molecular-mass SUMO-2 species and to the accumulation of promyelocytic leukaemia protein in subnuclear bodies. These findings suggest that SENP7 acts as a SUMO-2/3-specific protease that is likely to regulate the metabolism of poly-SUMO-2/3 rather than SUMO-1 conjugation in vivo.
Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4
Authors: Lakowski Ted M. , Frankel Adam
Published: May 2009

Protein arginine N-methyltransferases (PRMTs) methylate arginine residues within proteins using S-adenosyl-L-methionine (AdoMet) to form S-adenosyl-L-homocysteine and methylarginine residues. All PRMTs produce ω-NG-monomethylarginine (MMA) residues and either asymmetric ω-NG,NG-dimethylarginine (aDMA) or symmetric ω-NG,N′G-dimethylarginine (sDMA) residues, referred to as Type I or Type II activity respectively. Here we report methylation activity from PRMT2 and compare it with PRMT1 activity using UPLC-MS/MS (ultra-performance liquid chromatography–tandem MS), gel electrophoresis, and thin-layer chromatography. We show that PRMT2 is a Type I enzyme and that the ratio of aDMA to MMA produced by PRMTs 1 and 2 is dependent on the substrate, regardless of rate or Km, suggesting that the reactions for both enzymes are distributive rather than processive. Using UPLC-MS/MS we find that, for PRMT2, the dissociation constant (KAs) and Km of AdoMet and the Km of histone H4 are similar to values for PRMT1, whereas the PRMT2 kcat is 800-fold less than the PRMT1 kcat. Although PRMT2 activity is substantially lower than PRMT1 in vitro, the fact that both enzymes selectively methylate histone H4 suggest that PRMT2, like PRMT1, may act as a transcription co-activator through this modification.
Dynamic aspects of ascorbic acid metabolism in the circulation: analysis by ascorbate oxidase with a prolonged in vivo half-life
Authors: Kasahara Emiko , Kashiba Misato , Jikumaru Mika , Kuratsune Daisuke , Orita Kumi , Yamate Yurika , Hara Kenjiro , Sekiyama Atsuo , Sato Eisuke F. , Inoue Masayasu
Published: May 2009

Because AA (L-ascorbic acid) scavenges various types of free radicals to form MDAA (monodehydroascorbic acid) and DAA (dehydroascorbic acid), its regeneration from the oxidized metabolites is critically important for humans and other animals that lack the ability to synthesize this antioxidant. To study the dynamic aspects of AA metabolism in the circulation, a long acting AOase (ascorbate oxidase) derivative was synthesized by covalently linking PEG [poly(ethylene glycol)] to the enzyme. Fairly low concentrations of the modified enzyme (PEG–AOase) rapidly decreased AA levels in isolated fresh plasma and blood samples with a concomitant increase in their levels of MDAA and DAA. In contrast, relatively high doses of PEG–AOase were required to decrease the circulating plasma AA levels of both normal rats and ODS (osteogenic disorder Shionogi) rats that lack the ability to synthesize AA. Administration of 50 units of PEG–AOase/kg of body weight rapidly decreased AA levels in plasma and the kidney without affecting the levels in other tissues, such as the liver, brain, lung, adrenal grand and skeletal muscles. PEG–AOase slightly, but significantly, decreased glutathione (GSH) levels in the liver without affecting those in other tissues. Suppression of hepatic synthesis of GSH by administration of BSO [L-buthionin-(S,R)-sulfoximine] enhanced the PEG–AOase-induced decrease in plasma AA levels. These and other results suggest that the circulating AA is reductively regenerated from MDAA extremely rapidly and that hepatic GSH plays important roles in the regeneration of this antioxidant.
Ku-0063794 is a specific inhibitor of the mammalian target of rapamycin (mTOR)
Authors: García-Martínez Juan M. , Moran Jennifer , Clarke Rosemary G. , Gray Alex , Cosulich Sabina C. , Chresta Christine M. , Alessi Dario R.
Published: May 2009

mTOR (mammalian target of rapamycin) stimulates cell growth by phosphorylating and promoting activation of AGC (protein kinase A/protein kinase G/protein kinase C) family kinases such as Akt (protein kinase B), S6K (p70 ribosomal S6 kinase) and SGK (serum and glucocorticoid protein kinase). mTORC1 (mTOR complex-1) phosphorylates the hydrophobic motif of S6K, whereas mTORC2 phosphorylates the hydrophobic motif of Akt and SGK. In the present paper we describe the small molecule Ku-0063794, which inhibits both mTORC1 and mTORC2 with an IC50 of ∼10 nM, but does not suppress the activity of 76 other protein kinases or seven lipid kinases, including Class 1 PI3Ks (phosphoinositide 3-kinases) at 1000-fold higher concentrations. Ku-0063794 is cell permeant, suppresses activation and hydrophobic motif phosphorylation of Akt, S6K and SGK, but not RSK (ribosomal S6 kinase), an AGC kinase not regulated by mTOR. Ku-0063794 also inhibited phosphorylation of the T-loop Thr308 residue of Akt phosphorylated by PDK1 (3-phosphoinositide-dependent protein kinase-1). We interpret this as implying phosphorylation of Ser473 promotes phosphorylation of Thr308 and/or induces a conformational change that protects Thr308 from dephosphorylation. In contrast, Ku-0063794 does not affect Thr308 phosphorylation in fibroblasts lacking essential mTORC2 subunits, suggesting that signalling processes have adapted to enable Thr308 phosphorylation to occur in the absence of Ser473 phosphorylation. We found that Ku-0063794 induced a much greater dephosphorylation of the mTORC1 substrate 4E-BP1 (eukaryotic initiation factor 4E-binding protein 1) than rapamycin, even in mTORC2-deficient cells, suggesting a form of mTOR distinct from mTORC1, or mTORC2 phosphorylates 4E-BP1. Ku-0063794 also suppressed cell growth and induced a G1-cell-cycle arrest. Our results indicate that Ku-0063794 will be useful in delineating the physiological roles of mTOR and may have utility in treatment of cancers in which this pathway is inappropriately activated.
Morphological transitions in polymer monolayers under compression
Authors: Srivastava S. , Basu J. K. , Sprung M. , Wang J.
Published: May 2009

We present a systematic investigation of morphological transitions in poly vinylacetate Langmuir monolayers. On compression, the polymer monolayer is converted to a continuous membrane with a thickness of ∼2–3 nm. Above a certain surface concentration the monolayer, on water, undergoes a morphological transition-buckling, leading to formation of striped patterns of period of λb∼160 nm, as determined from in situ grazing incidence small angle x-ray scattering measurements. The obtained value is much smaller than what has been typically observed for Langmuir monolayers on water or thin films on soft substrates. Using existing theories for buckling of fluidlike films on fluid substrates, we obtain very low values of bending rigidity and Young’s modulus of the polymer monolayer compared to that observed earlier for lipid or polymeric monolayers. Since buckling in these monolayers occurs only above a certain surface concentration, we have looked at the possibility that the buckling in these films occurs due to changes in their mechanical properties under compression. Using the model of Huang and Suo of buckling of solidlike films on viscoelastic substrates, we find values of the mechanical properties, which are much closer to the bulk values but still significantly lower. Although the reduction could be along the lines of what has been observed earlier for ultrathin polymer film or surface layers of polymers, the possibility of micromechanical effects also determining the buckling in such polymer monolayers cannot be ruled out. We have provided possible explanation of the buckling of the poly vinylacetate monolayers in terms of the change in isothermal compression modulus with surface concentration.
Time-resolved lasing action from single and coupled photonic crystal nanocavity array lasers emitting in the telecom band
Authors: Englund Dirk , Altug Hatice , Vučković Jelena
Published: May 2009

We measure the lasing dynamics of single and coupled photonic crystal nanocavity array lasers fabricated in the indium gallium arsenide phosphide material system. Under short optical excitation, single cavity lasers produce pulses as fast as 11ps (full width at half maximum), while coupled cavity lasers show significantly longer lasing duration which is not explained by a simple rate equation model. A finite difference time domain simulation including carrier gain and diffusion suggests that asynchronous lasing across the nanocavity array extends the laser’s pulse duration.
Temperature-induced chaos during nanorod growth by physical vapor deposition
Authors: Mukherjee S. , Zhou C. M. , Gall D.
Published: May 2009

Atomic shadowing during kinetically limited physical vapor deposition causes a chaotic instability in the layer morphology that leads to nanorod growth. Glancing angle deposition (GLAD) experiments indicate that the rod morphology, in turn, exhibits a chaotic instability with increasing surface diffusion. The measured rod width versus growth temperature converges onto a single curve for all metals when normalized by the melting point Tm. A model based on mean field nucleation theory reveals a transition from a two- to three-dimensional growth regime at (0.20±0.03)×Tm and an activation energy for diffusion on curved surfaces of (2.46±0.02)×kTm. The consistency in the GLAD data suggests that the effective mass transport on a curved surface is described by a single normalized activation energy that is applicable to all elemental metals.
Infrared absorption spectroscopy on OH–Ni complex in hydrothermally grown ZnO
Authors: Li Y. J. , Zhang B. , Lu W.
Published: May 2009

The microstructure and combination behavior of transitional metal Ni and hydrogen (H) in hydrothermally grown ZnO were investigated by infrared absorption spectroscopy. An infrared absorption peak at 2782.9 cm−1 was observed in ZnO crystal hydrogenated in H2 gas at 725 °C for 30 min. Isotope substitution experiments and polarized infrared absorption spectra revealed that this peak results from the stretch local vibrational mode of a single interstitial hydrogen bound to oxygen, with OH bond oriented at an angle of 108° to the c axis of ZnO. Different from the mode at 3577.3 cm−1 induced by the OH–Li complex in the same sample, the mode at 2782.9 cm−1 is ascribed to the OH–Ni complex related to a bond-centered hydrogen, which is sitting in the basal plane of the hexagonal lattice between the substitutional Ni at a Zn site and O. Moreover, this OH–Ni complex is thermally stable up to 500 °C.
Stress influences on magnetization and magnetostriction in magnetically annealed Tb0.36Dy0.64(Fe0.85Co0.15)2 polycrystals
Authors: Ma Tianyu , Yan Mi , Zhang Changsheng , Pei Yongmao , Jiang Chengbao
Published: May 2009

Magnetic annealing can reorient the domain moments, improving dramatically the magnetostriction of Tb–Dy–Fe oriented polycrystals without applying any prestress. In this paper, totally different stress dependences of magnetization and magnetostriction were observed in ⟨110⟩ oriented Tb0.36Dy0.64(Fe0.85Co0.15)2 polycrystals after perpendicular magnetic annealing. Under compressive prestress, no obvious increase in magnetostriction occurred but the linear magnetostriction performance was improved. The magnetization initially decreased and approached to saturation at relatively higher magnetic fields with increasing the stress magnitude. Such variation can be contributed mainly by the redistribution of initial magnetic moments and enlargement of 71° wall energy.
Moment approach to the bootstrap current in nonaxisymmetric toroidal plasmas using δf Monte Carlo methods
Authors: Matsuyama A. , Isaev M. Yu. , Watanabe K. Y. , Hanatani K. , Suzuki Y. , Nakajima N. , Cooper W. A. , Tran T. M.
Published: May 2009

To evaluate the bootstrap current in nonaxisymmetric toroidal plasmas quantitatively, a δf Monte Carlo method is incorporated into the moment approach. From the drift-kinetic equation with the pitch-angle scattering collision operator, the bootstrap current and neoclassical conductivity coefficients are calculated. The neoclassical viscosity is evaluated from these two monoenergetic transport coefficients. Numerical results obtained by the δf Monte Carlo method for a model heliotron are in reasonable agreement with asymptotic formulae and with the results obtained by the variational principle.
Hydrogen storage enhanced in Li-doped carbon replica of zeolites: A possible route to achieve fuel cell demand
Authors: Roussel Thomas , Bichara Christophe , Gubbins Keith E. , Pellenq Roland J.-M.
Published: May 2009

We first report the atomistic grand canonical Monte Carlo simulations of the synthesis of two realistic ordered microporous carbon replica in two siliceous forms of faujasite zeolite (cubic Y-FAU and hexagonal EMT). Atomistic simulations of hydrogen adsorption isotherms in these two carbon structures and their Li-doped composites were carried out to determine their storage capacities at 77 and 298 K. We found that these new forms of carbon solids and their Li-doped versions show very attractive hydrogen storage capacities at 77 and 298 K, respectively. However, for a filling pressure of 300 bars and at room temperature, bare carbons do not show advantageous performances compared to a classical gas cylinder despite of their crystalline micropore network. In comparison, Li-doped nanostructures provide reversible gravimetric and volumetric hydrogen storage capacities twice larger (3.75 wt % and 33.7 kg/m3). The extreme lattice stiffness of their skeleton will prevent them from collapsing under large external applied pressure, an interesting skill compared to bundle of carbon nanotubes, and metal organic frameworks (MOFs). These new ordered composites are thus very promising materials for hydrogen storage issues by contrast with MOFs.
Model Hamiltonian for the interaction of NO with the Au(111) surface
Authors: Roy Sharani , Shenvi Neil A. , Tully John C.
Published: May 2009

We have constructed a model Hamiltonian to describe the interaction of a nitric oxide (NO) molecule with a Au(111) surface. The diagonal elements of the 2×2 Hamiltonian matrix represent the diabatic potential energy surfaces corresponding to the neutral and negative-ion states of the molecule. A position-dependent off-diagonal element controls the extent of mixing of the two diabatic states. The parameters of the Hamiltonian matrix were determined from ground-state density functional theory calculations, both in the absence and presence of a small applied electric field to perturb the extent of charge transfer to the molecule. The resulting model Hamiltonian satisfactorily reproduces the ab initio results, and scattering simulations of the incident translational energy dependence of trapping probability and final rotational energy of NO agree quite well with experiment. The explicit incorporation of neutral and ionic configurations should serve as a realistic and practical platform for elucidating the importance of charge transfer and nonadiabatic effects at metal surfaces, as well as provide a useful testing ground for the development of theories of nonadiabatic dynamics.
Voltage-tunable lateral shifts of ballistic electrons in semiconductor quantum slabs
Authors: Chen Xi , Ban Yue , Li Chun-Fang
Published: May 2009

It is investigated that the lateral shifts of the ballistic electrons transmitted through semiconductor quantum slabs can be negative as well as positive, which are analogous to the anomalous lateral shifts of the transmitted light beam through a dielectric slab. The necessary condition for the shift to be negative is advanced. It is shown that the lateral shifts depend not only on the structure parameters of semiconductor quantum slab but also on the incidence angle and the incident energy. Numerical calculations further indicate that the lateral shifts can be tuned from negative to positive by the external applied electric field. The voltage-tunable lateral shifts may lead to potential applications in quantum electronic devices.
Antiferromagnetic bipolar semiconductor LaMnPO with ZrCuSiAs-type structure
Authors: Yanagi Hiroshi , Watanabe Takumi , Kodama Katsuaki , Iikubo Satoshi , Shamoto Shin-ichi , Kamiya Toshio , Hirano Masahiro , Hosono Hideo
Published: May 2009

Electronic and magnetic properties of a layered compound LaMnPO are examined in relation to a newly discovered iso-structural superconductor LaFeAs(P)O. Neutron diffraction measurements, together with temperature dependent magnetic susceptibility, clarify that LaMnPO is an antiferromagnet at least up to 375 K. The spin moment of a Mn ion is determined to be 2.26 μB at room temperature, and the spin configuration is antiparallel in the Mn–P plane and parallel between the Mn–P planes, which is rather different from that of LaFeAsO. Optical absorption spectra, photoemission spectra, and temperature dependent electrical conductivity indicate that LaMnPO is a semiconductor. Furthermore, nominally undoped LaMnPO exhibits n-type conduction while the conduction type is changed by doping of Cu or Ca to the La sites, indicating that LaMnPO is a bipolar conductor. Density functional calculation using the GGA+U approximation supports the above conclusions; the electronic band structure has an open band gap and the antiferromagnetic spin configuration is more stable than the ferromagnetic one.
The existence of nontopological vortices in a two-particle Chern–Simons system
Authors: Yang Sze-Guang
Published: May 2009

In this article, a planar relativistic self-dual Chern–Simons model with two Higgs particles and two gauge fields is considered. The main purpose is to show the existence of the nontopological multivortex solutions to the system from a mathematical perspective. Specifically, a certain type of nontopological solutions can be constructed by means of an approach of perturbation from the radially symmetric solutions of a Liouville system. These radial Liouville solutions are well depicted in terms of their asymptotic behavior prescribed at infinity. Accordingly, the values of charges and energy in response to the resulting nontopological solutions accumulate in the way that the Liouville solutions are characterized.
Local structure of reaction intermediates probed by time-resolved x-ray absorption near edge structure spectroscopy
Authors: Smolentsev G. , Guilera G. , Tromp M. , Pascarelli S. , Soldatov A. V.
Published: May 2009

A method for the analysis of time-resolved x-ray absorption near edge structure (XANES) spectra is proposed. It combines principal component analysis of the series of experimental spectra, multidimensional interpolation of theoretical XANES as a function of structural parameters, and ab initio XANES calculations. It allows to determine the values of structural parameters for intermediates of chemical reactions and the concentrations of different states as a function of time. This approach is tested using numerically generated data and its possibilities and limitations are discussed. The application of this method to a reaction with methylrhenium trioxide catalyst in solution, for which experimental data were measured using stopped-flow energy-dispersive x-ray absorption spectroscopy technique, is demonstrated. Possibilities and limitations of this experimental technique are also discussed.
Quantum mechanical study of vibrational energy transfer in Ar–O3 collisions: Influence of symmetry
Authors: Ivanov M. V. , Grebenshchikov S. Yu. , Schinke R.
Published: May 2009

The vibrational energy transfer in Ar–O3 collisions is investigated within the breathing sphere approximation. Ozone wave functions are calculated with a simplified potential energy surface and used in the close coupling scattering equations. Inelastic transition probabilities are determined for all bound states of O3. Energy transfer is studied in one asymmetric, O16O16O18, and two symmetric isotopomers, O16O16O16 and O16O18O16. Two measures of the energy transfer are considered: Microcanonical deactivation for a fixed collision energy and thermal vibrational relaxation described by the master equation at a fixed temperature. In either case, the energy transfer is symmetry independent near the dissociation threshold and the sensitivity to symmetry grows as the ozone energy decreases.
Electrical transport through ordered self-assembled protein monolayer measured by constant force conductive atomic force microscopy
Authors: Kivioja Jani M. , Kurppa Katri , Kainlauri Markku , Linder Markus B. , Ahopelto Jouni
Published: May 2009

This paper addresses some of the challenges met in electrical characterization of biomolecules, namely, the control of the orientation of molecules and the control of the force exerted on these soft molecules. We investigate the transport properties of small proteins called hydrophobins using conductive atomic force microscopy. The proteins have a property that they form a well ordered monolayer in which the orientation of the molecules is known. We introduce an active compensation for the electrostatic force induced by the bias voltage, which often hamper the measurements. Results suggest that the electrical transport through the hydrophobins protein monolayer occurs mainly via tunneling.
Mean free paths and elastic and related transport cross sections for neutrals and singly charged ions of Li, Be, and B in hydrogen plasmas
Authors: Krstić P. S. , Schultz D. R.
Published: May 2009

The mean free paths are computed from the momentum transfer cross sections associated with collisions of protons with Li, Be, and B and for Li, Li+, Be+, and B+ colliding with atomic hydrogen, for center of mass energies between 0.0001 and 10 000 eV. The elastic and viscosity cross sections are also calculated for these collision systems. A fully quantum mechanical approach has been used up to 100 eV along with a more approximate, quasiclassical method between ∼0.1 and 10 000 eV.
Finite orbit width effect in ion collisional transport in TJ-II
Authors: Velasco J. L. , Castejón F. , Tarancón A.
Published: May 2009

The validity of the traditional local diffusive approach and of the use of monoenergetic calculations has been studied for the stellarator TJ-II [Alejaldre et al., Fusion Technol. 17, 131 (1990)]: it is shown to be doubtful, under some circumstances, even in a purely collisional description of transport. The diffusion in physical space starting from Dirac-delta-like initial conditions has been studied using the code Integrator of Stochastic Differential Equations for Plasmas by Castejón et al. [Plasma Phys. Controlled Fusion 49, 753 (2007)]. Particles may experience large radial excursions from their original magnetic surfaces in a single collisional time. The contribution of these particles to the flux may make it nondiffusive; non-Gaussian density distributions, characterized by long tails, are observed. In the velocity space, there are important variations in the average particle kinetic energy after one collision time. We discuss the effect of this fact over the calculation of monoenergetic transport coefficients and their convolution. A simple analysis based on Hurst exponents has shown nevertheless that the description of transport by means of a pinch term and an effective transport coefficient is more correct than expected.
Effects of photointensity gradient on directional crystal growth in blends of crystalline polymer and photoreactive monomer undergoing photopolymerization-induced phase transformation
Authors: Rathi Pankaj , Park Soo Jeoung , Kyu Thein
Published: May 2009

Effects of light intensity gradient on development of intricate hierarchical morphology of semicrystalline polyethylene oxide (PEO) and photoreactive diacrylate (DA) blends undergoing photopolymerization-induced crystallization have been demonstrated experimentally and theoretically. The melting temperature of PEO was found to decline upon addition of DA monomer. A solid-liquid phase diagram has been established by self-consistently solving the combined phase field free energy of crystal solidification and Flory–Huggins (FH) free energy of liquid-liquid demixing. Dynamic calculations were performed using time-dependent Ginzburg–Landau (model C) equations by incorporating the combined phase field and FH free energy densities coupled with the photopolymerization kinetics. The spatiotemporal development of gradient morphology was computed under various intensity gradient profiles including linear, cylindrical, and Gaussian profiles. The observed seaweed or dense lamellar branching morphology of the PEO/DA blend is strikingly similar to the directionally grown interface structures observed in metals driven by external thermal gradients.
A combining rule calculation of the ground state van der Waals potentials of the mercury rare-gas complexes
Authors: Sheng X. W. , Li P. , Tang K. T.
Published: May 2009

The ground state van der Waals potentials of the Hg–RG (RG=He,Ne,Ar,Kr,Xe) systems are generated by the Tang–Toennies potential model. The parameters of the model are calculated from the potentials of the homonuclear mercury and rare-gas dimers with combining rules. The predicted spectroscopic parameters for these mercury rare-gas complexes are in good agreement with available experimental values, except for Hg–He. In the repulsive and potential well regions, the predicted potential energy curves agree with the available experimental hybrid potentials, but they differ in the long range part of the potential. On the other hand, the present potentials are in agreement with the ab initio CCSD(T) calculations in the long range part of the potential, but there are some differences in the short repulsive regions. According to the present theory, the reduced potential curves of these five systems, including Hg–He, are almost identical to each other. This reduced potential curve can also describe, within a few percent, the five reduced potentials obtained from the ab initio CCSD(T) calculations. These reduced potentials have a potential bowl that is wider than that of the rare-gas dimers, but narrower than the mercury dimer.
Quasidiabatic states described by coupled-cluster theory
Authors: Ichino Takatoshi , Gauss Jürgen , Stanton John F.
Published: May 2009

In an attempt to expand the utility of the model Hamiltonian technique developed by Köppel, Domcke, and Cederbaum (KDC) [Adv. Chem. Phys. 57, 59 (1984)], an ansatz for quasidiabatic wave functions is introduced in the framework of equation-of-motion coupled-cluster (EOM-CC) theory. Based on the ansatz, the theory for the analytic first derivative of the off-diagonal element of the quasidiabatic potential matrix is developed by extending the theory for the analytic gradient of the EOM-CC energy. This analytic derivative is implemented for EOM-CCSD (singles and doubles approximation) calculations of radicals subject to pseudo-Jahn–Teller and Jahn–Teller interactions. Its applicability in construction of the KDC quasidiabatic model potential is discussed.
Microwave analog to light scattering measurements on a fully characterized complex aggregate
Authors: Merchiers Olivier , Geffrin Jean-Michel , Vaillon Rodolphe , Sabouroux Pierre , Lacroix Bernard
Published: May 2009

We present experimental measurements of three-dimensional electromagnetic wave scattering in the microwave frequency range, by a complex aggregate consisting of 74 primary spheres with fully known optical and geometrical properties. We measured the complete amplitude scattering matrix (or Jones matrix), from which the electric fields (amplitude and phase) with arbitrary polarization can be obtained. These results offer the opportunity to test approximate computational methods against experiments.
Kinetic nucleation model for free expanding water condensation plume simulations
Authors: Li Zheng , Zhong Jiaqiang , Levin Deborah A. , Garrison Barbara J.
Published: May 2009

Recent direct simulation Monte Carlo (DSMC) simulations of homogeneous condensation in free expansion water plumes [Z. Li, J. Zhong, D. A. Levin, and B. Garrison, AIAA J. 47, 1241 (2009)] show that the nucleation rate is a key factor for accurately modeling condensation phenomenon. In this work, we use molecular dynamics (MD) simulations of a free expansion to explore the microscopic mechanisms of water dimer formation and develop collision models required by DSMC. Bimolecular and termolecular dimer cluster formation mechanisms are considered and the former is found to be the main mechanism in expanding flows to vacuum. MD simulations between two water molecules using the simple point charge intermolecular potential were performed to predict the bimolecular dimer formation probability and the probability was found to decrease with collision energy. The formation probabilities and postcollisional velocity and energy distributions were then integrated into DSMC simulations of a free expansion of an orifice condensation plume with different chamber stagnation temperatures and pressures. The dimer mole fraction was found to increase with distance from the orifice and become constant after a distance of about two orifice diameters. Similar to experiment, the terminal dimer mole fraction was found to decrease with chamber stagnation temperatures and increase linearly with chamber stagnation pressures which is consistent with a bimolecular nucleation mechanism.
Photolysis of n-butyl nitrite and isoamyl nitrite at 355 nm: A time-resolved Fourier transform infrared emission spectroscopy and ab initio study
Authors: Ji Min , Zhen Junfeng , Zhang Qun , Chen Yang
Published: May 2009

We report on the photodissociation dynamics study of n-butyl nitrite and isoamyl nitrite by means of time-resolved Fourier transform infrared (TR-FTIR) emission spectroscopy. The obtained TR-FTIR emission spectra of the nascent NO fragments produced in the 355 nm laser photolysis of the two alkyl nitrite species showed an almost identical rotational temperature and vibrational distributions of NO. In addition, a close resemblance between the two species was also found in the measured temporal profiles of the IR emission of NO and the recorded UV absorption spectra. The experimental results are consistent with our ab initio calculations using the time-dependent density functional theory at the B3LYP/6-311G(d,p) level, which indicate that the substitution of one of the two γ-H atoms in n-C4H9ONO with a methyl group to form (CH3)2C3H5ONO has only a minor effect on the photodissociation dynamics of the two molecules.
Alignment dependence of one-dimensional electronic hopping transport observed in films of highly aligned, ultralong single-walled carbon nanotubes
Authors: Pint Cary L. , Xu Ya-Qiong , Morosan Emilia , Hauge Robert H.
Published: May 2009

The temperature dependent electrical conductivity of highly aligned, as-grown, pristine films of ultralong single-walled carbon nanotubes (SWNTs) is investigated in the framework of conduction based on phonon-assisted electron hopping. A change in transport mechanism occurs between conduction normal to and parallel to the SWNT alignment that results in evolution from bulk three-dimensional (3D) hopping conduction to a one-dimensional (1D) hopping conduction mechanism intrinsic to the electronic structure of SWNT. Vacuum annealing is observed to change the magnitude of the film conductivity but does not alter the observed 1D or 3D hopping mechanism.
Electromagnetic instability in an electron beam–ion channel system
Authors: Su D. , Tang C. J.
Published: May 2009

The transverse electromagnetic instability in the electron beam–ion channel system is investigated using kinetic theory. The equilibrium distribution function of a relativistic electron beam, which takes into account a strong ion channel effect, is obtained. The linearized Vlasov equation is solved and the dispersion relation of the system is derived by perturbing the equilibrium with a high frequency electromagnetic wave (EMW). Analysis of the dispersion relation shows that the coupling of the electron beam with the transverse high frequency EMW is achieved through the deflection of the beam electrons due to the synergistic effects of the transverse high frequency EMW and transverse betatron oscillation. The numerical calculation finds that a branch of slow wave instability (SWI) with a wide frequency band is excited. The attenuation index of the SWI increases and its frequency band broadens as the normalized beam radii increases. Besides, the SWI will be suppressed as the longitudinal velocity of the electron beam increases to a certain value; meanwhile, a bunch of fast wave instability (FWI) is excited, which is equal to the increase of the relativistic factor. Also both the SWI and the FWI reach maximum when the EMW frequency meets a resonance condition.
Self-excited surface plasmon-polaritons at the interface of counterstreaming plasmas
Authors: Lazar M. , Moslem W. M. , Smolyakov A. , Shukla P. K.
Published: May 2009

Surface plasma modes are coupled electromagnetic/electrostatic (plasmon-polariton) excitations of free electrons near the vacuum-plasma or plasma-plasma interface. The surface plasmon-polariton propagates along the surface plane and decays on both sides of the boundary. The effect of counterstreaming on the surface plasmon-polariton excitation is examined. It is shown that the two-stream instability can excite self-consistently the surface modes at the interface of two counterstreaming plasmas. The dispersion relation is derived and the exact numerical solutions are plotted for comparison to the excitations of a nonstreaming plasma-plasma interface. Such plasma models are of interest in electronic signal transmission, as well as in astrophysical applications and in beam-plasma experiments.
Rippling instability on surfaces of stressed crystalline conductors
Authors: Tomar Vivek , Gungor M. Rauf , Maroudas Dimitrios
Published: May 2009

We report a surface morphological stability analysis for stressed, conducting crystalline solids without and with the simultaneous application of an electric field based on self-consistent dynamical simulations according to a fully nonlinear model. The analysis reveals that in addition to a cracklike surface instability, a very-long-wavelength instability may be triggered that leads to the formation of secondary ripples on the surface morphology. We demonstrate that the number of ripples formed scales linearly with the wavelength of the initial perturbation from the planar surface morphology and that a sufficiently strong electric field inhibits both the cracklike and the rippling instability.
Terahertz localized plasmonic properties of subwavelength ring and coaxial geometries
Authors: Lu Xinchao , Zhang Weili
Published: May 2009

We study terahertz properties of periodic arrays of subwavelength metallic ring and coaxial ring-disk structures. Terahertz time-domain spectroscopy and numerical simulations have revealed unique resonance behaviors at terahertz frequencies. A high-frequency antisymmetric resonance in the rings concurs simultaneously with the symmetric mode. In the coaxial structures, the strong and weak resonance interactions are characterized by the plasmon hybridization theory, while the anomalous interaction results in a degenerate resonance which has not yet been observed at visible frequencies. The frequency tunability and strong electric field enhancement in such subwavelength structures are promising in terahertz sensing, spectroscopy, and integrated components.
Christopher Charles Heyde 1939 - 2008
Authors: Seneta E. , Gani J. M.
Published: May 2009

An account of the Heyde family is followed by a description of Chris's childhood, schooling and university training at Sydney and the ANU. Chris spent most of his academic career at the ANU, CSIRO and Columbia University. He made an outstanding contribution to probability theory and its applications. His theoretical work focused mainly on the laws of large numbers, branching processes, martingale theory, estimation theory and, most recently, financial mathematics. He also had a lasting interest in the history of probability and statistics. Chris received considerable recognition, including Fellowship of the Australian Academy of Science and of the Academy of Social Sciences in Australia, as well as Membership of the Order of Australia.
Character displacement of song and morphology in African tinkerbirds
Authors: Kirschel Alexander N. G. , Blumstein Daniel T. , Smith Thomas B.
Published: May 2009

Divergence in acoustic signals between populations of animals can lead to species recognition failure, reproductive isolation, and speciation. Character displacement may facilitate coexistence of species in natural communities, yet evidence for character displacement in acoustic signals is scant. Here, we find evidence of character displacement in song as well as body size and bill size of 2 related African tinkerbirds. Playback experiments indicate that related species' songs are perceived differently in sympatry than in allopatry. We suggest character displacement occurs in phenotypic traits facilitating species recognition, which has important implications for understanding the processes that lead to speciation and diversification. Because many of the sites where the 2 species coexist are areas where pristine rainforest has been degraded, results also suggest that anthropogenic pressures resulting from deforestation may be a contributing cause of character displacement in these species.
Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans
Authors: Arnesen Thomas , Van Damme Petra , Polevoda Bogdan , Helsens Kenny , Evjenth Rune , Colaert Niklaas , Varhaug Jan Erik , Vandekerckhove Joël , Lillehaug Johan R. , Sherman Fred , Gevaert Kris
Published: May 2009

N
α
-terminal acetylation is one of the most common protein modifications in eukaryotes. The COmbined FRActional DIagonal Chromatography (COFRADIC) proteomics technology that can be specifically used to isolate N-terminal peptides was used to determine the N-terminal acetylation status of 742 human and 379 yeast protein N termini, representing the largest eukaryotic dataset of N-terminal acetylation. The major N-terminal acetyltransferase (NAT), NatA, acts on subclasses of proteins with Ser-, Ala-, Thr-, Gly-, Cys- and Val- N termini. NatA is composed of subunits encoded by y
ARD1
and y
NAT1
in yeast and h
ARD1
and h
NAT1
in humans. A yeast
ard1
-Δ
nat1
-Δ strain was phenotypically complemented by h
ARD1
h
NAT1
, suggesting that yNatA and hNatA are similar. However, heterologous combinations, h
ARD1
y
NAT1
and y
ARD1
h
NAT1
, were not functional in yeast, suggesting significant structural subunit differences between the species. Proteomics of a yeast
ard1
-Δ
nat1
-Δ strain expressing hNatA demonstrated that hNatA acts on nearly the same set of yeast proteins as yNatA, further revealing that NatA from humans and yeast have identical or nearly identical specificities. Nevertheless, all NatA substrates in yeast were only partially N-acetylated, whereas the corresponding NatA substrates in HeLa cells were mainly completely N-acetylated. Overall, we observed a higher proportion of N-terminally acetylated proteins in humans (84%) as compared with yeast (57%). N-acetylation occurred on approximately one-half of the human proteins with Met-Lys- termini, but did not occur on yeast proteins with such termini. Thus, although we revealed different N-acetylation patterns in yeast and humans, the major NAT, NatA, acetylates the same substrates in both species.