bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerated increases observed for hydrochlorofluorocarbons since 2004 in the global atmosphere
Authors: Montzka S. A. , Hall B. D. , Elkins J. W.
Published: February 2009

Tropospheric accumulation rates of the three most abundant hydrochlorofluorocarbons (HCFCs) were up to two times faster during 2007 than measured in 2003–2004. Tropospheric chlorine from HCFCs increased at 10 pptCl/yr during 2006–2007, up from 6 pptCl/yr in 2003–2004, and offset declines in chlorine from other anthropogenic ozone‐depleting substances in 2007 by approximately one‐third. Derived global emissions for HCFCs increased by up to 60% since 2004, and, for HCFC‐142b, emissions during 2007 were two times larger than projected recently. Measured tropospheric distributions suggest a shift in HCFC emissions to lower latitudes of the Northern Hemisphere. These changes coincide with exponential increases in developing country production and consumption and decreases in other countries. When weighted by direct, 100‐yr global warming potentials, HCFC emissions in 2007 amounted to 0.78 GtCO2‐equivalents, or 30% larger than the average during 2000–2004, and were approximately 2.6% of fossil‐fuel and cement related CO2 emissions.
Why doesn't the ring current injection rate saturate?
Authors: Lopez R. E. , Lyon J. G. , Mitchell E. , Bruntz R. , Merkin V. G. , Brogl S. , Toffoletto F. , Wiltberger M.
Published: February 2009

For low values of the solar wind electric field, the response of the polar cap potential is essentially linear, but at high values of VBs, the polar cap potential saturates and does not increase further with increasing VBs. On the other hand, the ring current injection rate does increase linearly with VBs and shows no evidence of saturating. If enhanced convection is the origin of the ring current, this poses a paradox. How can the polar cap potential, and thus convection, saturate when the ring current does not? We examine a possible explanation based on the reexamination of the Burton equation by Vasyliunas (2006). We show that this explanation is not a viable solution to the paradox since it would require a changing polar cap flux, and we demonstrate that the polar cap flux saturates (at around 1 GWb) as the polar cap potential saturates. Instead, we argue that during storms a quasi‐steady reconnection region forms in the tail near the Earth. This reconnection region moves closer to the Earth for higher values of solar wind Bs, although the polar cap potential, the dayside merging and nightside reconnection rates, and the amount of open flux do not change much as a function of Bs once the polar cap potential has become saturated. As the neutral line moves closer, the volume per unit magnetic flux in the closed field line region is less. Flux tubes leaving the reconnection region in general have lower PVγ as Bs increases, and lower PVγ flux tubes can penetrate deeper into the inner magnetosphere, leading to a corresponding greater injection of particles into the inner magnetosphere. Thus a reconnection region that is closer to Earth is more effective in creating a strong ring current. This leads to a continued dependence of the ring current injection rate on VBs, although the polar cap potential has saturated.
Effects of the quasi‐biennial oscillation on low‐latitude transport in the stratosphere derived from trajectory calculations
Authors: Punge H. J. , Konopka P. , Giorgetta M. A. , Müller R.
Published: February 2009

The quasi‐biennial oscillation (QBO) of stratospheric zonal winds induces a secondary meridional circulation (SMC) consisting of QBO variations in meridional and vertical winds. In this work, we investigate how these instantaneous meridional circulation anomalies add over time to variations of stratospheric transport. To that end, we compute backward parcel trajectories on the basis of the output of a chemistry‐climate model (CCM). At the equator, the trajectories show the strongest vertical parcel displacement over a seasonal timescale when the QBO progresses toward easterly phase in the middle stratosphere. During the solstitial seasons a large number of parcels come from the summer hemisphere, causing in addition a QBO variation in the spread of the total ascent among equatorial parcels. A QBO effect on meridional transport is diagnosed from PV gradients during summer in the easterly phase of the QBO, which suggests a variation of the tropical‐subtropical barrier strength. Analyses of the parcel trajectories and CCM trace gas distributions confirm this finding. We suggest that this variation is due to the combined effects of QBO and annual variation in meridional advection and in wave‐induced eddy transport.
Rainfall trends analysis of Iran in the last half of the twentieth century
Authors: Modarres Reza , Sarhadi Ali
Published: February 2009

The present study performs the spatial and temporal trend analysis of the annual and 24‐hr maximum rainfall of a set of 145 precipitation gauging stations of Iran. The study shows that the annual rainfall is decreasing at 67% of the stations while the 24‐hr maximum rainfall is increasing at 50% of the stations. The negative trends of annual rainfall are mostly observed in northern and northwestern regions, whereas positive trends of 24‐hr maximum rainfall are mostly located in arid and semiarid regions of Iran. However, the Kolmogorov‐Smirnov test for Mann‐Kendall (MK) statistics show that the regional trend of annual rainfall is significant, but it is not significant for 24‐hr maximum rainfall. On the other hand, the sequential MK test reveals that the trends of annual rainfall and 24‐hr maximum rainfall began since 1970s for most of the stations. The negative trend of the rainfall for most of the country may show the initial stages of climate change in Iran, but further information and analysis is required for future studies.
Dam effects on droughts magnitude and duration in a transboundary basin: The Lower River Tagus, Spain and Portugal
Authors: López‐Moreno J. I. , Vicente‐Serrano S. M. , Beguería S. , García‐Ruiz J. M. , Portela M. M. , Almeida A. B.
Published: February 2009

This study examines the effects of a large dam on hydrological droughts in the transboundary Tagus River, central Spain and Portugal. The magnitude and duration of droughts are analyzed by comparing a monthly drought index calculated for the flow series upstream and downstream of the Alcántara reservoir. The dam was built in 1969, and the reservoir is the second largest in Europe (3,162 hm3). Water management in the area is complex because of large seasonal and interannual variability in the flow regime, which is characteristic of Mediterranean environments. This paper demonstrates that, as a result of exploitation of the Alcántara reservoir, (1) during periods of water scarcity, the releases in winter and spring are reduced dramatically and the magnitude and duration of summer low flow show a slight increase and (2) the nature of droughts along the Tagus river basin downstream of the dam has shown severe changes since construction of the dam. In fact, during the predam period (1943–1969), droughts were longer and more intense in the Spanish part of the basin than that in the Portuguese part. Since the construction of the Alcántara dam, however, the Portuguese part of the basin has experienced more severe droughts than did the upstream part in terms of both magnitude and duration.
In vivo Evidence for Cerebral Depletion in High-Energy Phosphates in Progressive Supranuclear Palsy
Authors: Stamelou Maria , Pilatus Ulrich , Reuss Alexander , Magerkurth Jörg , Eggert Karla M , Knake Susanne , Ruberg Merle , Schade-Brittinger Carmen , Oertel Wolfgang H , Höglinger Günter U
Published: February 2009

Indirect evidence from laboratory studies suggests that mitochondrial energy metabolism is impaired in progressive supranuclear palsy (PSP), but brain energy metabolism has not yet been studied directly in vivo in a comprehensive manner in patients. We have used combined phosphorus and proton magnetic resonance spectroscopy to measure adenosine-triphosphate (ATP), adenosine-diphosphate (ADP), phosphorylated creatine, unphosphorylated creatine, inorganic phosphate and lactate in the basal ganglia and the frontal and occipital lobes of clinically probable patients ( N= 21; PSP stages II to III) and healthy controls ( N= 9). In the basal ganglia, which are severely affected creatine in PSP patients, the concentrations of high-energy phosphates (= ATP + phosphorylated creatine) and inorganic phosphate, but not low-energy phosphates (=ADP+ unphosphorylated creatine), were decreased. The decrease probably does not reflect neuronal death, as the neuronal marker N-acetylaspartate was not yet significantly reduced in the early-stage patients examined. The frontal lobe, also prone to neurodegeneration in PSP, showed similar alterations, whereas the occipital lobe, typically unaffected, showed less pronounced alterations. The levels of lactate, a product of anaerobic glycolysis, were elevated in 35% of the patients. The observed changes in the levels of cerebral energy metabolites in PSP are consistent with a functionally relevant impairment of oxidative phosphorylation.
Inhibition of Poly(ADP-Ribose) Polymerase Suppresses Inflammation and Promotes Recovery after Ischemic Injury
Authors: Kauppinen Tiina M , Suh Sang Won , Berman Ari E , Hamby Aaron M , Swanson Raymond A
Published: February 2009

The brain inflammatory response induced by stroke contributes to cell death and impairs neurogenesis. Poly(ADP-ribose) polymerase-1 (PARP-1) is a coactivator of the transcription factor NF-κB and required for NF-κB-mediated inflammatory responses. Here we evaluated PARP inhibition as a means of suppressing post-stroke inflammation and improving outcome after stroke. Rats were subjected to bilateral carotid occlusion-reperfusion, and treatment with the PARP inhibitor N-(6-oxo-5,6-dihydrophenanthridin-2-yl)- N,N-dimethylacetamide (PJ34) was begun 48 h later. PJ34 was found to rapidly suppress the ischemia-induced microglial activation and astrogliosis. Behavioral tests performed 6 to 8 weeks after ischemia showed deficits in spatial memory and learning that were lessened by the PJ34 treatment. Immunohistochemical evaluation of hippocampus at 8 weeks after ischemia showed increased neuronal density in CA1 layer of PJ34-treated animals relative to vehicle-treated animals. Bromodeoxyuridine labeling showed formation of new neurons in hippocampal CA1 area in PJ34-treated animals, but not in vehicle-treated animals. Together, these results suggest that treatment with a PARP inhibitor for several days after ischemia enhances long-term neuronal survival and neurogenesis by reducing inflammation.
C12ORF39, a novel secreted protein with a typical amidation processing signal
Authors: Wan Bingbing , Wang Xin-Rong , Zhou Yu-Bo , Zhang Xin , Huo Keke , Han Ze-Guang
Published: February 2009

In the present study we describe a novel secreted protein, named C12ORF39 (chromosome 12 open-reading framework 39), which contains a typical amidation/proteolytic processing signal (Gly–Arg–Arg motif). Interestingly, C12ORF39 protein is not hydrolysed, but is a full-length protein without signal peptides. Western blotting indicated that c-Myc-tagged C12ORF39 is secreted into culture medium in transfected HeLa cells. Quantitative RT-PCR (reverse transcription-PCR) analysis revealed that c12orf39 is mainly expressed in placenta and brain. Immunohistochemistry on formalin-fixed paraffin-embedded human term placenta using a rabbit antibody against human C12ORF39 demonstrated that the protein was localized extracellularly, surrounding the trophoblastic cells. In addition, C12ORF39 secretion could be blocked by brefeldin A, suggesting that the secretion of C12ORF39 is dependent on the Golgi apparatus. Furthermore, laser-scanning confocal microscopy also confirmed that the C12ORF39 protein co-localized with the Golgi apparatus. Taken together, although C12ORF39 is not a secreted small peptide, it can also be secreted to play a role in the biological functions of the placenta.
Paramagnetic spin correlations and spin dynamics in doped manganites as the precursors of their magnetic ordering
Authors: Rozenberg E. , Auslender M. , Shames A. I. , Mukovskii Ya. M. , Sominski E. , Gedanken A.
Published: February 2009

To confront the magnetic ordering in bulk and nanometer-sized La1−xCaxMnO3 manganites with the Ca doping level x=0.1 and 0.6, the fitting of the temperature dependences of electron paramagnetic resonance linewidth and intensity to the theoretical models was combined with the magnetic measurements. In the x=0.1 case, the magnetic ordering in nanosamples changes as compared to bulk due to transition from the confined state of charge carriers in chemically disordered bulk to a mobile one in an impuritylike band in homogeneous nanocrystals. While both bulk and nano-x=0.6 samples demonstrate stable antiferromagnetic ordering in spite of strong ferromagnetic correlations in the paramagnetic state. This may be associated with the localization of doped electrons, which (together with the elastic interaction between Jahn-Teller) ions may be a prerequisite for electron-hole doping asymmetry in the phase diagram of La1−xCaxMnO3.
Design and analysis of interior-magnet outer-rotor concentric magnetic gears
Authors: Liu Xinhua , Chau K. T. , Jiang J. Z. , Yu Chuang
Published: February 2009

In this paper, a new topology of concentric magnetic gears is proposed and implemented. The key of the new topology is to bury permanent magnets (PMs) of the outer rotor into the iron core in a new way so that the mechanical integrity can be improved, and the PM material can be saved while the torque density is maintained. The proposed gear is designed with the speed reduction ratio of 7.33 and optimized by using the three-dimensional finite element method (3D-FEM). The key of the 3D-FEM is to employ scalar magnetic potential to reduce the required memory and time for data manipulation and computation. After prototyping, the measured maximum static torque well agrees with the calculated one, hence verifying the proposed design and analysis.
High temperature coercive field behavior of Fe–Zr powder
Authors: Mishra Debabrata , Perumal A. , Srinivasan A.
Published: February 2009

We report the investigation of high temperature coercive field behavior of Fe80Zr20 nanocrystalline alloy powder having two-phase microstructure prepared by mechanical alloying process. Thermomagnetization measurement shows the presence of two different magnetic phase transitions corresponding to the amorphous matrix and nonequilibrium Fe(Zr) solid solution. Temperature dependent coercivity exhibits a sharp increase in its value close to the Curie temperature of the amorphous matrix. This feature is attributed to the loss of intergranular ferromagnetic exchange coupling between the nanocrystallites due to the paramagnetic nature of the amorphous matrix. The temperature dependent coercive field behavior is ascribed to the variations in both the effective anisotropy and the exchange stiffness constant with temperature.
Effects of strain on magnetic and transport properties of Co films on plastic substrates
Authors: Chen Y. F. , McCord J. , Freudenberger J. , Kaltofen R. , Schmidt O. G.
Published: February 2009

Co films were deposited on flexible polyester substrates by dc magnetron sputtering and plastically strained in tension up to 3.7%. The magnetic measurements show that the plastic strain changes the coercivity and effective uniaxial magnetic anisotropy, as well as the magnetic domain structure of the Co films. Furthermore, the transport results show that the plastic strain strongly alters the resistance and magnetoresistance of the Co films.
Local magnetic properties of Y12Co5Bi and Gd12Co5Bi studied by muon spin relaxation
Authors: Egilmez M. , Chow K. H. , MacFarlane W. A. , Mar A. , Fan I. , Mansour A. , Schick-Martin D. , Jung J. , Tkachuk A. V. , Hitti B. , Arseneau D.
Published: February 2009

The recently discovered (RE)12Co5Bi (where RE is a rare earth element) system has rich magnetic phase diagrams. We applied muon spin relaxation to study the local magnetism in polycrystalline samples of Y12Co5Bi and Gd12Co5Bi. Our results indicate a magnetic transition at around 100K for Gd12Co5Bi. By contrast, Y12Co5Bi does not show a magnetic transition as expected since Y3+ does not contain any f electrons. These results are consistent with the dc susceptibility measurements. We also estimate and discuss the fluctuation rates in the high temperature paramagnetic regime for Gd12Co5Bi.
Representation independent algorithms for molecular response calculations in time-dependent self-consistent field theories
Authors: Tretiak Sergei , Isborn Christine M. , Niklasson Anders M. N. , Challacombe Matt
Published: February 2009

Four different numerical algorithms suitable for a linear scaling implementation of time-dependent Hartree–Fock and Kohn–Sham self-consistent field theories are examined. We compare the performance of modified Lanczos, Arooldi, Davidson, and Rayleigh quotient iterative procedures to solve the random-phase approximation (RPA) (non-Hermitian) and Tamm–Dancoff approximation (TDA) (Hermitian) eigenvalue equations in the molecular orbital-free framework. Semiempirical Hamiltonian models are used to numerically benchmark algorithms for the computation of excited states of realistic molecular systems (conjugated polymers and carbon nanotubes). Convergence behavior and stability are tested with respect to a numerical noise imposed to simulate linear scaling conditions. The results single out the most suitable procedures for linear scaling large-scale time-dependent perturbation theory calculations of electronic excitations.
Quasiclassical trajectory calculations analyzing the role of vibrational and translational energy in the F+CH2D2 reaction
Authors: Espinosa-García Joaquín
Published: February 2009

An exhaustive state-to-state dynamics study was performed to analyze the effects of vibrational excitation and translational energy on the dynamics of the F+CH2D2 gas-phase reaction, which are connected to such issues as bond selectivity, mode selectivity, and Polanyi’s rules. This reaction can evolve along two channels: D-abstraction, DF(v′)+CH2D(v′), and H-abstraction, HF(v′)+CHD2(v′). Quasiclassical trajectory calculations were performed on an analytical potential energy surface previously developed by our group. Vibrational excitation of the C–D or C–H mode of CH2D2 favors slightly the D-abstraction over the H-abstraction, indicating that this reaction does not exhibit bond selectivity and suggesting a breakdown of the spectator model. For D-abstraction, the vibrational excitation of the nonreactive C–H stretch mode is partially retained in the products, and for H-abstraction, the excitation of the nonreactive C–D stretch mode is also partially retained in the products, indicating that this reaction exhibits mode selectivity only partially. Moreover, the independent excitation of the C–H symmetric or asymmetric stretch modes leads to reactions with similar (practically identical) reaction cross sections and product scattering distributions, discarding bond selectivity and mode selectivity for this reaction. Finally, for this “early transition state” reaction, vibrational energy is more effective in driving the reaction than an equivalent amount of energy in translation, indicating that the application of the Polanyi rules that are well established in atom-diatom reactions is neither straightforward nor always valid in polyatomic reactions. All these results were interpreted on the basis of strong coupling between modes along the reaction path, a behavior which seems to be more of the general tendency than the exception in polyatomic reactions.
On the relationship between finger width, velocity, and fluxes in thermohaline convection
Authors: Sreenivas K. R. , Singh O. P. , Srinivasan J.
Published: February 2009

Double-diffusive finger convection occurs in many natural processes. The theories for double-diffusive phenomena that exist at present consider systems with linear stratification in temperature and salinity. The double-diffusive systems with step change in salinity and temperature are, however, not amenable to simple stability analysis. Hence factors that control the width of the finger, velocity, and fluxes in systems that have step change in temperature and salinity have not been understood so far. In this paper we provide new physical insight regarding factors that influence finger convection in two-layer double-diffusive system through two-dimensional numerical simulations. Simulations have been carried out for density stability ratios (Rρ) from 1.5 to 10. For each density stability ratio, the thermal Rayleigh number (RaT) has been systematically varied from 7×103 to 7×108. Results from these simulations show how finger width, velocity, and flux ratios in finger convection are interrelated and the influence of governing parameters such as density stability ratio and the thermal Rayleigh number. The width of the incipient fingers at the time of onset of instability has been shown to vary as RaT−1∕3. Velocity in the finger varies as RaT1∕3∕Rρ. Results from simulation agree with the scale analysis presented in the paper. Our results demonstrate that wide fingers have lower velocities and flux ratios compared to those in narrow fingers. This result contradicts present notions about the relation between finger width and flux ratio. A counterflow heat-exchanger analogy is used in understanding the dependence of flux ratio on finger width and velocity.
Reaction hysteresis of the CO+O→CO2 reaction on palladium(111)
Authors: Karpitschka Stefan , Wehner Stefan , Küppers Jürgen
Published: February 2009

Rate measurements of the reaction CO+O→CO2 on palladium(111) single crystal surfaces have been performed by means of mass spectroscopy under ultrahigh vacuum conditions. The total flux Φ of the impinging reactants CO and O2 was held constant at 1MLs−1, whereas its CO fraction Y was varied between 0 (pure O2) and 1 (pure CO). The measurements have been performed for surface temperatures between 370 and 510K and with a wide range of sampling times, evaluating the system parameter range for bistable behavior. Long-time measurements lasting several days proved the bistable behavior to result from two stable states rather than from slow processes not visible on usual experimental time scales. Pulselike modulations of the feed gas composition revealed the mechanisms confining the experimentally observed bistable range: the high CO fraction border of the bistability is given by the equistability condition of both states, whereas the other border is found to be associated with a saddle-node bifurcation in the corresponding system of reaction diffusion equations.
Modeling the effect of upstream temperature fluctuations on shock/homogeneous turbulence interaction
Authors: Veera Vijay K. , Sinha Krishnendu
Published: February 2009

Reynolds-averaged Navier–Stokes (RANS) equations can yield significant error when applied to the interaction of turbulence with shock waves. This is often due to the fact that RANS turbulence models do not account for the underlying physical phenomena correctly. For example, in the presence of appreciable temperature fluctuations in the upstream flow, turbulence amplification across a shock is significantly affected by the magnitude of the temperature fluctuations and the sign of the upstream velocity-temperature correlation [Mahesh et al., J. Fluid Mech. 334, 353 (1997)]. Standard two-equation models with compressibility correction do not reproduce this effect. We use the interaction of homogeneous isotropic turbulence with a normal shock to suggest improvements to the k-ϵ model. The approach is similar to that presented in an earlier work [Sinha et al., Phys. Fluids 15, 2290 (2003)]. Linear inviscid analysis is used to study the effect of upstream temperature fluctuations on the evolution of turbulent kinetic energy k across the shock. The dominant mechanisms contributing to the k amplification are identified and then modeled in a physically consistent way. The dissipation rate equation is also altered based on linear analysis results. The modifications yield significant improvement over existing two-equation models and the new model predictions are found to match linear theory and direct numerical simulation data well.
Effect of tip curvature on ionic emissions from Taylor cones of ionic liquids from externally wetted tungsten tips
Authors: Castro S. , Fernández de la Mora J.
Published: February 2009

Several ionic liquids (ILs) of relatively high electrical conductivity (K) and surface tension (γ) are electrosprayed under vacuum from electrochemically sharpened and roughened tungsten wires with tip radii R varying from 2 to 80 μm. All our tips exhibit a purely ionic emission, confirming the versatility of these ionic liquid ion sources (ILIS) previously demonstrated by Lozano and Martínez-Sánchez using R∼20 μm. A drastic increase in ion current from 50 to 1000 nA results when increasing R from 2.5 up to 29 μm and above, offsetting the considerable disadvantage in current emission level previously observed for ILIS (∼200 nA) versus conventional internally fed capillary tube emitters (∼1000 nA). Experiments with shielding electrodes show that this increase in current is not due to a reduction in space charge effects associated to the higher onset voltages required at smaller curvatures. It results from a reduction in flow impedance at increasing R. Long-term stable Taylor cone operation was not achieved with any of the ILs tested, even when alternating the tip voltage to minimize electrochemical reactions.
Kinetic theory analysis of laser ablation of carbon: Importance of second-order calculation
Authors: Shusser Michael
Published: February 2009

Following some recent works that used first-order numerical schemes in modeling laser ablation, this paper compares the predictions of first- and second-order calculations for a one-dimensional kinetic theory model of laser ablation of carbon based on the moment solution of the Boltzmann equation for arbitrary strong evaporation. The model considers both conduction heat transfer in the target and gas dynamics of the ablated plume coupled through the interface boundary conditions. It was found that the difference between the first-order and the second-order calculations is limited to the parts of the flow with high gradients, such as the shock wave and the contact surface. Since the ablation rate is determined by the conditions at the solid surface, which is most of the time situated far from that area, the first-order calculation predicts ablation rate correctly.
Transmission electron microscopy study of hydrogen defect formation at extended defects in hydrogen plasma treated multicrystalline silicon
Authors: Nordmark Heidi , Holmestad Randi , Walmsley John C. , Ulyashin Alexander
Published: February 2009

Hydrogenation of multicrystalline silicon for solar cell applications is considered to be an effective method of increasing the lifetime by passivating defects and impurities. Hydrogen plasma treated as-cut and chemically etched multicrystalline silicon samples have been studied by electron microscopy in order to investigate hydrogen defect formation at extended bulk defects. In chemically etched samples, the texture of the surface after hydrogen plasma treatment differs between different grains depending on grain orientation. In as-cut samples, hydrogen induced defects are formed on sawing defects that extend up to ∼5 μm below the Si surface. Intragranular defects are also observed in the ∼1 μm subsurface region. The density of defects is higher in as-cut samples than in chemically etched samples and the size of the defects increases with depth. Hydrogen induced structural defects on bulk dislocations and on dislocations in twin grain boundaries and stacking faults are found several microns below the sample surface. It is concluded that (i) the passivation efficiency of multicrystalline silicon substrates after H plasma treatment can be limited by the formation of hydrogen induced structural defects and that (ii) such defects can be used to getter unwanted impurities upon high temperature processing of the Si wafers.
Crystallinity and microstructure in Si films grown by plasma-enhanced chemical vapor deposition: A simple atomic-scale model validated by experiments
Authors: Novikov P. L. , Le Donne A. , Cereda S. , Miglio Leo , Pizzini S. , Binetti S. , Rondanini M. , Cavallotti C. , Chrastina D. , Moiseev T. , von Känel H. , Isella G. , Montalenti F.
Published: February 2009

A joint theoretical and experimental analysis of the crystalline fraction in nanocrystalline films grown by low-energy plasma enhanced chemical vapor deposition is presented. The effect of key growth parameters such as temperature, silane flux, and hydrogen dilution ratio is analyzed and modeled at the atomic scale, introducing an environment-dependent crystallization probability. A very good agreement between experiments and theory is found, despite the use of a single fitting parameter.
Electronic localization and optical absorption in embedded silicon nanograins
Authors: Bagolini Luigi , Mattoni Alessandro , Colombo Luciano
Published: February 2009

We study the spatial distribution of electron states in crystalline Si nanograins embedded into amorphous silicon. We prove that it is not possible to tune the absorption gap by only controlling the size of the grain, since no quantum confinement there occurs. The absorption properties of such a two-phase system are rather controlled by the population of localized electron states generated by large angular distortions of Si–Si bonds.
Size effect of dissipative surface stress on quality factor of microbeams
Authors: Ru C. Q.
Published: February 2009

A dissipative surface stress model is suggested to study the surface dissipation of vibrating elastic microbeams. The model is an extension of the well-known Zener model from bulk materials to the surface in the presence of an initial surface tension. Explicit formulas are derived for the frequency-dependent quality factor and the maximum surface dissipation. This model predicts a size-dependent surface dissipation when the size of the cross section downs to nanometers. In particular, the model offers plausible explanation for a few experimental phenomena reported in the most recent literature.
Systems-level analysis of cell-specific
AQP2
gene expression in renal collecting duct
Authors: Yu Ming-Jiun , Miller R. Lance , Uawithya Panapat , Rinschen Markus M. , Khositseth Sookkasem , Braucht Drew W. W. , Chou Chung-Lin , Pisitkun Trairak , Nelson Raoul D. , Knepper Mark A.
Published: February 2009

We used a systems biology-based approach to investigate the basis of cell-specific expression of the water channel aquaporin-2 (AQP2) in the renal collecting duct. Computational analysis of the 5′-flanking region of the
AQP2
gene (Genomatix) revealed 2 conserved clusters of putative transcriptional regulator (TR) binding elements (BEs) centered at −513 bp (corresponding to the SF1, NFAT, and FKHD TR families) and −224 bp (corresponding to the AP2, SRF, CREB, GATA, and HOX TR families). Three other conserved motifs corresponded to the ETS, EBOX, and RXR TR families. To identify TRs that potentially bind to these BEs, we carried out mRNA profiling (Affymetrix) in mouse
mpkCCDc14
collecting duct cells, revealing expression of 25 TRs that are also expressed in native inner medullary collecting duct. One showed a significant positive correlation with
AQP2
mRNA abundance among
mpkCCD
subclones (
Ets1
), and 2 showed a significant negative correlation (
Elf1
and an orphan nuclear receptor
Nr1h2
). Transcriptomic profiling in native proximal tubules (PT), medullary thick ascending limbs (MTAL), and IMCDs from kidney identified 14 TRs (including
Ets1
and
HoxD3
) expressed in the IMCD but not PT or MTAL (candidate
AQP2
enhancer roles), and 5 TRs (including
HoxA5
,
HoxA9
and
HoxA10
) expressed in PT and MTAL but not in IMCD (candidate
AQP2
repressor roles). In luciferase reporter assays, overexpression of 3 ETS family TRs transactivated the mouse proximal
AQP2
promoter. The results implicate ETS family TRs in cell-specific expression of
AQP2
and point to HOX, RXR, CREB and GATA family TRs as playing likely additional roles.
Cell Adhesion under Flow
Authors: LEY KLAUS
Published: February 2009

Cell adhesion under flow is a central function of the microcirculation during inflammation, hemostasis, and immune regulation. This special issue of Microcirculation explores the common and distinct mechanisms that myeloid cells, lymphocytes, platelets, and sickle erythrocytes use to adhere to microvascular endothelium and the underlying basement membrane structures. A common theme in these processes is the need for rapid integrin activation, often initiated by binding of ligands to their cognate G protein–coupled receptors, followed by adhesion strengthening associated with integrin redistribution and outside‐in signaling. These elements have been identified for all cells tested except sickle erythrocytes.
Infection Control Practices in Assisted Living Facilities: A Response to Hepatitis B Virus Infection Outbreaks
Authors: Patel Ami S. , White-Comstock Mary Beth , Woolard C. Diane , Perz Joseph F.
Published: February 2009

Background.

The medical needs of the approximately 1 million persons residing in assisted living facilities (ALFs) continually become more demanding. Moreover, the number of ALF residents is expected to double by 2030. ALFs are not subject to federal oversight; state regulations that govern ALF infection control are variable. In 2005, two outbreaks of acute hepatitis B virus (HBV) infection in ALFs in Virginia were associated with sharing fingerstick devices used in blood glucose monitoring.

Objective.

To characterize infection control practices, determine compliance with guidelines, and identify educational and policy needs in ALFs in Virginia.

Methods.

Following the outbreaks of HBV infection, educational packets were sent to ALFs in Virginia to inform them of infection control guidelines and recommendations regarding glucose monitoring. A follow-up survey consisting of on-site interviews was conducted in a random sample of ALFs. Differences among infection control practices, according to the size and ownership of the ALFs, were assessed.

Results.

Fifty of 155 ALFs in central Virginia were surveyed. Of the 45 ALFs that had used fingerstick devices, 7 (16%) had shared these devices (without cleaning) between residents. Sharing practices for glucose monitoring equipment did not differ by facility size or ownership. Of all 50 ALFs, 17 (34%) did not offer employees HBV vaccine. HBV vaccine was less frequently offered at ALFs that had fewer than 50 residents, compared with ALFs with at least 50 residents (P< .01), and HBV vaccine was less frequently offered at ALFs that were individually owned, compared with those that were not individually owned (P= .02).

Conclusions.

Despite outreach and long-standing recommendations, approximately 1 in 6 facilities shared fingerstick devices, and more than one-third of ALFs surveyed were considered noncompliant with federal guidelines (Occupational Safety and Health Administration Bloodborne Pathogens Standard). Public health and licensing agencies should work with ALFs to implement infection control measures and prevent disease transmission.
VANO: a volume-object image annotation system
Authors: Peng Hanchuan , Long Fuhui , Myers Eugene W.
Published: February 2009

Volume-object annotation system (VANO) is a cross-platform image annotation system that enables one to conveniently visualize and annotate 3D volume objects including nuclei and cells. An application of VANO typically starts with an initial collection of objects produced by a segmentation computation. The objects can then be labeled, categorized, deleted, added, split, merged and redefined. VANO has been used to build high-resolution digital atlases of the nuclei of Caenorhabditis elegans at the L1 stage and the nuclei of Drosophila melanogaster's ventral nerve cord at the late embryonic stage.

Availability: Platform independent executables of VANO, a sample dataset, and a detailed description of both its design and usage are available at research.janelia.org/peng/proj/vano. VANO is open-source for co-development.

Contact:  pengh@janelia.hhmi.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Capillary Electrophoresis as a Tool for Evaluating Lactic Acid Production from Sorghum
Authors: Schober T. J. , Bean S. R. , Wang D.
Published: February 2009

Sorghum is an underutilized resource for the production of bioindustrial chemicals like lactic acid. Capillary electrophoresis (CE) was tested to monitor the fermentation process, i.e., quantify the amount of lactic acid and by‐products in the fermentation broth using phosphate buffer pH 6.25 containing the electroosmotic flow modifier cetyltrimethylammonium bromide (CTAB). High levels of calcium carbonate were required during fermentation to stabilize the pH and these caused considerably prolonged migration times in CE. A 1:10 dilution of the samples with water was the best way to reduce salt load and thus conductivity in the sample plug, and thus to eliminate the problem of prolonged migration times. Further improvements were achieved by rinsing the capillary with HCl and water after each run, rather than NaOH and water. HCl might more efficiently remove Ca2+ ions from the capillary surface. The fermentation broth studied was based on liquefied sorghum inoculated with Rhizopus oryzae. The main product was lactic acid (24.60 ± 0.56 g/L) and a significant by‐product was fumaric acid (1.07 ± 0.04 g/L).
Effect of Microbial Transglutaminase on Dough Proteins of Hard and Soft (Triticum aestivium) and Durum (Triticum durum) Wheat Cultivars
Authors: Medina‐Rodríguez Concepción L. , Torres Patricia , Martínez‐Bustos Fernando , Ramirez‐Wong Benjamin , Paredes‐López Octavio , Castaño‐Tostado Eduardo
Published: February 2009

Microbial transglutaminase (MTGase), a protein‐glutamine γ‐glutamyl transferase (E.C. 2.3.2.13), catalyzes acyl transfer reactions by introducing a covalent cross‐link between l‐lysine and l‐glutamine residues. The use of this enzyme has been proposed as an improver to increase dough strength. The objective of this study was to assess and compare the effect of MTGase on different fractions of dough proteins found in hard, soft, and durum wheat. Three different concentrations of the MTGase (0, 5, and 10U/g of gluten) were tested. Moisture, protein, and dry gluten contents were determined for each concentration in addition to rheological measurements done with the farinograph. Following each treatment, the dough proteins were extracted and analyzed by SE‐HPLC and RP‐HPLC. Soluble polymeric protein, gliadins, albumins, and globulins were quantified in addition to the gliadin subclasses and glutenin subunit types. The combustion procedure was used to determine the amount of insoluble polymeric protein. Differences were observed in susceptibility to MTGase catalysis among the dough proteins of the cultivars studied: the cultivar Cortazar (soft wheat) was the most susceptible. The proteins of this cultivar had a characteristically higher amount of ω and α+β gliadins when compared with the other cultivars. As reported earlier, solubility of high molecular weight glutenin subunits and ω‐gliadins was reduced because of the MTGase treatment. However, all gliadin subclasses, including the γ and α+β gliadins, also participated in cross‐linking. The proteins of the cultivar Altar (durum wheat) were the least susceptible to the effects of MTGase. Albumins and globulins did not show any reduction in solubility, implying that they did not participate in cross‐linking.
Ethylene Mediates Response and Tolerance to Potassium Deprivation inArabidopsis
Authors: Jung Ji-Yul , Shin Ryoung , Schachtman Daniel P.
Published: February 2009

Potassium deprivation leads to large reductions in plant growth and yields. How plants sense and transduce the stress signals initiated by potassium deprivation is poorly understood. Both ethylene production and the transcription of genes involved in ethylene biosynthesis increase when plants are deprived of potassium. To elucidate the role of ethylene in low potassium signaling pathways, we used both genetic and chemical approaches. Our results showed that ethylene is important in tolerance to low potassium and for changes in both root hair and primary root growth in Arabidopsis thaliana. We show that ethylene acts upstream of reactive oxygen species in response to potassium deprivation. The expression of High-Affinity K+ Transporter5 was used as a marker of potassium deprivation and was found to be dependent on ethylene signaling. In the ethylene insensitive2-1 (ein2-1) mutant, the ethylene-mediated low potassium responses were not completely eliminated, suggesting that some potassium deprivation–induced responses are either ethylene independent or EIN2 independent. Ethylene signaling is a component of the plant's response to low potassium that stimulates the production of reactive oxygen species and is important for changes in root morphology and whole plant tolerance to low potassium conditions.
Co‐localization of inducible nitric oxide synthase and phosphorylated Akt in the lesional skins of patients with melasma
Authors: JO Ho‐Youn , KIM Chun‐Ki , SUH In‐Bum , RYU Sook‐Won , HA Kwon‐Soo , KWON Young‐Geun , KIM Young‐Myeong
Published: February 2009

Activation of the inducible nitric oxide synthase (iNOS)/nitric oxide (NO) pathway in keratinocytes has been reported to be associated with the pathogenesis of melanogenesis. Akt activation plays an important role in the activation of the transcription factor nuclear factor (NF)‐κB and subsequent elevation of iNOS expression. In the present study, we highly detected both iNOS protein and Akt phosphorylation in keratinocytes of the basal layer of the epidermis at the junction with the dermis of melasma skin biopsy specimens, but not in normal skin tissues, from nine patients using immunohistological analysis. iNOS protein and phosphorylated Akt were co‐localized in the lesional skins, and their levels were highly correlated (R2 = 0.69). Furthermore, iNOS mRNA was also detected in an additional three skin biopsy specimens, but not in normal skin, by reverse transcription polymerase chain reaction. Our results describe that iNOS expression is elevated in human melasma lesions, probably via activation of the Akt/NF‐κB pathway, indicating that NO production plays an important role in the mechanism of hyperpigmentation in human facial melasma.
Two cases of pollen‐food allergy syndrome to soy milk diagnosed by skin prick test, specific serum immunoglobulin E and microarray analysis
Authors: YAGAMI Akiko , INABA Yasuko , KUNO Yuki , SUZUKI Kayoko , TANAKA Akira , SJOLANDER Sigrid , SAITO Hirohisa , MATSUNAGA Kayoko
Published: February 2009

Oral allergy syndrome to soy milk is classified as a phenotype of pollen‐food allergy syndrome (PFAS). As causative antigens, Gly m 4 (Bet v 1 homolog, 17 kD) and oleosin (23 kD), have been reported. In this study, we report two cases of PFAS to soy milk. Both cases showed positive reactions to soy milk in skin prick tests (SPT) and to Gly m 4 in specific serum immunoglobulin (Ig)E antibody. When we measured specific serum IgE antibody of soy‐related proteins using a new laboratory testing method, microarray analysis, both cases showed a positive reaction for Bet v 1. One case was weakly positive for a soybean protein, β‐conglycinin. Other results for reactivity to soy, peanut, cross‐reactive carbohydrate determinants and profilin were negative. Based on these results, we diagnosed the two cases as PFAS to Gly m 4. We also performed protein microarray analysis and found it useful as a screening test for immediate allergy, such as PFAS.
Laboratory appraisal of optimal gaseous conditions for growth of zoonotic Helicobacter felis ATCC 49179
Authors: Shiohara Mayumi , Kawakubo Masatomo , Matsumoto Takehisa , Kumagai Toshiko , Yamauchi Kazuyoshi , Oana Kozue , Ota Hiroyoshi , Kawakami Yoshiyuki
Published: February 2009

An attempt was made to assess the hitherto undescribed optimal gaseous conditions for growth of zoonotic Helicobacter felis, focusing on the ratio of spiral‐forms amongst the whole cells examined. The largest mean colony diameter was obtained under the gaseous condition of O2 12% and CO2 10%. In analyzing the five day old colonies, the highest percentage of spiral forms (85.5%) was observed under the condition of O2 18% and CO2 5%. In contrast, the lowest percentage of spiral forms (2.3%) was demonstrated under the condition of O2 1% and CO2 10%. The condition of O2 12% and CO2 10% was concluded to be optimal for obtaining cells with the largest colony sizes, although colonies proliferated under such conditions definitely contain many more coccoid cells than spiral forms. In culturing H. felis strains, optimal gaseous conditions should be employed according to the purposes or preferences of study designs.
Nystatin‐induced nitric oxide production in mouse macrophage‐like cell line RAW264.7
Authors: Koide Naoki , Naiki Yoshikazu , Morikawa Akiko , Tumurkhuu Gantsetseg , Dagvadorj Jargalsaikhan , Noman Abu Shadat Mohammod , Iftekar‐E‐Khuda Imtiaz , Komatsu Takayuki , Yoshida Tomoaki , Yokochi Takashi
Published: February 2009

Nystatin is known to deplete lipid rafts from mammalian cell membranes. Lipid rafts have been reported to be necessary for lipopolysaccharide signaling. In this study, it was unexpectedly found that lipopolysaccharide‐induced nitric oxide production was not inhibited, but rather increased in the presence of a non‐cytotoxic concentration of nystatin. Surprisingly, treatment with nystatin induced only NO production and iNOS expression in RAW264.7 cells. At the concentration used, no changes in the expression of GM1 ganglioside, a lipid raft marker on RAW264.7 cells, was seen. From studies using several kinds of inhibitors for signaling molecules, nystatin‐induced NO production seems to occur via the iκB/NF‐κB and the PI3 K/Akt pathway. Furthermore, because nystatin is known to activate the Na‐K pump, we examined whether the Na‐K pump inhibitor amiloride suppresses nystatin‐induced NO production. It was found that amiloride significantly inhibited nystatin‐induced NO production. The results suggest that a moderate concentration of nystatin induces NO production by Na‐pump activation through the PI3 kinase/Akt/NF‐κB pathway without affecting the condition of lipid rafts.
Hypoxia enhances stimulating effect of amyloid beta peptide (25–35) for interleukin 17 and T helper lymphocyte subtype 17 upregulation in cultured peripheral blood mononuclear cells
Authors: Yin YanHong , Wen ShiRong , Li GuoZhong , Wang DeSheng
Published: February 2009

Th17 has been demonstrated to have a key role in several autoimmune diseases. The present study was carried out to investigate changes in IL‐17 and Th17 in cultured PBMC in response to Abeta peptide (25–35) and hypoxic stimulation in vitro. PBMC were collected from adult healthy donors and cultured in normal and anaerobic conditions (hypoxia 1, 3, 6, 12, 24 hr). Each group of cells was stimulated with Abeta peptide (25–35; 3, 10 nmol/ml). ELISA was used to examine IL‐17A concentrations in the supernatants, and flow cytometry for the numbers of IL‐17A secreting CD4 positive Th17 lymphocytes. Statistically significant increases in IL‐17A and Th17 concentrations were found in groups with 10 nmol/ml Abeta (25–35) and more than three hr anaerobic culture. IL‐17A and Th17 concentrations in anaerobic groups increased gradually with time and peaked at six hr. Compared with other groups, the highest concentrations were found in those treated with 10 nmol/ml Abeta and cultured for six hr (P < 0.001). This study provides the first report that IL‐17A and Th17 lymphocytes are possibly involved in the immune pathogenesis caused by Abeta peptide (25–35). Hypoxia may enhance this response independently of time.