bluuebunny/crossref_metadata_2025 huggingface dataset:
Micromagnetics of paleomagnetically significant mineral grains with complex morphology
Authors: Williams W. , Evans M. E. , Krása D.
Published: February 2010

Micromagnetic calculations relevant to paleomagnetism have generally focused on ideal shapes such as spheres and cubes. However, oxide grains that occur naturally in rocks often have irregular morphologies, highly skeletal dendritic forms being particularly common. To investigate the potential effects of complex grain morphology on magnetic stability, we have carried out two parallel sets of calculations. The first is based on randomly distorted 30–120 nm magnetite spheres. We use a three‐dimensional finite element/boundary integral micromagnetic model able to generate suitable morphologies unrestricted by the regular cell structure required by finite difference models. The second model consists of a 300 nm magnetite octahedron from which most of the material has been removed to leave a small octahedral crystallite at each of the six apices connected by an orthogonal framework of thin rods. The results obtained imply that micromagnetic models currently provide no unambiguous evidence that morphological complexities endow magnetite nanoparticles with enhanced coercivity.
Solubility of water in pyrope‐rich garnet at high pressures and temperature
Authors: Mookherjee Mainak , Karato Shun‐ichiro
Published: February 2010

The water solubility in pyrope‐rich garnet was determined between pressures of 5–9 GPa and temperatures of 1373–1473 K under silica activity and oxygen fugacity similar to those expected in the Earth's upper mantle. We found that pyrope‐rich garnet has substantial water solubility up to ∼0.1 wt% under these conditions. In addition, the water content in garnet varied as a function of chemical conditions. In particular, the variation in water fugacity (and Mg#) caused a variation in water partitioning with olivine The substantial water solubility in pyrope‐rich garnet under deep upper mantle conditions might have significant influence on physical and transport properties.
Distribution of normalized water‐leaving radiances at UV and visible wave bands in relation with chlorophyll a and colored detrital matter content in the southeast Pacific
Authors: Tedetti Marc , Charrière Bruno , Bricaud Annick , Para Julien , Raimbault Patrick , Sempéré Richard
Published: February 2010

In‐water radiometric measurements were performed in the southeast Pacific (8°S–35°S, 141°W–72°W) from October to December 2004 during the Biogeochemistry and Optics South Pacific Experiment cruise. Normalized water‐leaving radiances (nLw(λ)) were determined at eight wave bands within the ultraviolet (UV) (305, 325, 340, and 380 nm) and visible (412, 443, 490, and 565 nm) spectral domains. The highest nLw(λ) (μW cm−2 sr−1) were recorded in the hyperoligotrophic waters of the South Pacific Gyre, with values increasing with wavelength from 305 (nLw = 0.64) to 380 nm (nLw = 3.18) in the UV range and decreasing from 412 (nLw = 4.46) to 565 nm (nLw = 0.23) in the visible region. The intense nLw(λ) observed in the violet‐blue domains were attributed to very low absorptions of colored detrital matter (CDM), likely related to a strong photobleaching of colored dissolved organic matter in the surface waters. We evaluated the relationships between the UV, violet, or blue/green wave band ratios of nLw(λ) and surface total chlorophyll a (TChl a) concentration and CDM absorption (aCDM(λ)). For TChl a, the best correlation was found with the blue/green ratio at 443 nm: TChl a (mg m−3) = 2.37[nLw(443)/nLw(565)]−1.51 (r2 = 0.86 and RMS error (RMSE) = 23%). By contrast, for aCDM(λ), the best correlation was observed when using the UV/green ratio at 325 nm: aCDM(325) (m−1) = 0.16[nLw(325)/nLw(565)]−0.69 (r2 = 0.82 and RMSE = 16%). These results show the potential role of nLw(λ) at UV wave bands for the assessment, through empirical algorithms, of colored detrital matter in the surface oceanic waters.
Influence of parameterized ice habit on simulated mixed phase Arctic clouds
Authors: Avramov Alexander , Harrington Jerry Y.
Published: February 2010

The phase partitioning of cloud mass between liquid and ice in mixed phase clouds and its dependence on ambient ice nuclei (IN) concentrations and ice habit parameterizations is explored in this paper. Single‐layered and multilayered cloud systems observed during the Mixed‐Phase Arctic Cloud Experiment were simulated with a cloud‐resolving model. The model used a two‐moment (mass and number concentration) microphysical scheme with ice crystal habit parameterized by mass and fall speed relationships and IN prediction scheme that accounts for depletion of IN through nucleation scavenging. The mixed phase cloud simulations show a strong sensitivity to the ambient deposition/condensation freezing IN concentrations, which is similar to some prior studies. This sensitivity depends on the mass, fall speed, and capacitance relationships used to parameterize crystal habit and vapor growth: Mass and fall speed relationships associated with compact, high‐density crystals produce clouds with a weaker sensitivity to ambient IN concentrations, whereas more extreme crystal shapes (e.g., dendrites) produce clouds with strong IN concentration sensitivity. This sensitivity also affects the number of liquid layers (from 1 to 5) predicted for the multilayer case. The strength of the vapor growth rates and the crystal fall speeds appear to be of roughly equal importance for determining the strength of mixed phase cloud sensitivity to ice concentrations.
Tissue‐Specificity and Ethnic Diversity in Obesity‐Related Risk of Cancer May Be Explained by Variability in Insulin Response and Insulin Signaling Pathways
Authors: Speakman John R. , Goran Michael I.
Published: February 2010

Obesity is a predisposing risk factor for several chronic diseases. The link between obesity and cancer appears to be particularly complex. Notably only the risk for development of specific cancers appear to be affected. Moreover, the obesity‐related risk of cancer is very different across ethnic groups. African‐Americans appear particularly prone, whereas Hispanics appear to be relatively protected. Obesity is associated with increased levels of circulating insulin. These levels of elevated insulin may serve to promote proliferation of fat cells to accommodate the elevated nutrient flux. However, elevated levels of insulin may be a major mediating factor influencing cancer risk. This hypothesis alone cannot explain the complexity of the phenomenon. We suggest here that the different insulin responses to obesity of different ethnic groups may explain their different risk profiles. Moreover, we speculate that tissue‐specific variations in the insulin signaling pathways may underlie their differential susceptibility to tumorigenesis in the face of elevated obesity. Elevated cancer risk may be an unwanted side effect of insulin responding to elevated nutrient flux in the obese which it serves to proliferate fat cells that provide a location for storage of ingested fat, which consequently prevents ectopic fat storage. Hence, while Hispanics may be protected from cancer risk in obesity because of their lower insulin response, they have an elevated risk of fatty liver disease. Reduction of insulin levels in obesity as a strategy to reduce cancer risk may pose additional problems unless it is combined also with interventions that aim to limit nutrient influx.
A new aspect of nickel-catalyzed Grignard cross-coupling reactions: selective synthesis, structure, and catalytic behavior of a T-shape three-coordinate nickel(i) chloride bearing a bulky NHC ligand
Authors: Miyazaki Satoshi , Koga Yuji , Matsumoto Taisuke , Matsubara Kouki
Published: February 2010

A novel NHC-nickel(i) chloride was isolated by the reactions of Ni(IPr)2 with chloroarenes. High catalyst activity of the Ni(i) complex was first demonstrated in Grignard cross-coupling reactions of aryl halides.
Luminescence in CeIV polyoxometalate [Ce(W5O18)2]8−: a combined experimental and theoretical study
Authors: Roy Lindsay E. , Ortiz-Acosta Denisse , Batista Enrique R. , Scott Brian L. , Blair Michael W. , May Iain , Del Sesto Rico E. , Martin Richard L.
Published: February 2010

Herein we describe the unique luminescent behavior observed in [CeIV(W5O18)2]8− clusters and examine the photophysical properties using density functional theory.
Co-segregation of AMPA receptors with GM1 ganglioside in synaptosomal membrane subfractions
Authors: Cole Andy A. , Dosemeci Ayse , Reese Thomas S.
Published: February 2010

Biochemical studies have suggested that certain synaptic proteins associate with lipid rafts to perform key functions within the synapse. However, variability in biochemical preparations raises questions as to which synaptic proteins actually associate with lipid rafts. In the present study, we use both electron microscopy and biochemistry to investigate AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid) receptor localization in synaptic membrane subfractions prepared in two different ways, by Triton X-100 detergent treatment or without detergent by sonication at high pH. Immunogold electron microscopy shows that a detergent-resistant synaptosomal membrane subfraction consists of empty vesicles 0.1–1.0 μm in diameter. A subpopulation of these vesicles labelled for glycosphingolipid GM1 ganglioside, a marker of lipid rafts, and 46% of the labelled vesicles also labelled for the AMPA receptor subunit GluR2. This co-segregation into specific vesicles does not depend on effects of detergent because a similar distribution of label was found in vesicles isolated without the use of detergent. Our results suggest that AMPA receptors localize within specific regions of synaptic membranes rich in GM1 ganglioside.
Language and Social Factors in the Use of Cell Phone Technology by Adolescents With and Without Specific Language Impairment (SLI)
Authors: Conti-Ramsden Gina , Durkin Kevin , Simkin Zoë
Published: February 2010

Purpose

This study aimed to compare cell phone use (both oral and text-based) by adolescents with and without specific language impairment (SLI) and examine the extent to which language and social factors affect frequency of use.

Method

Both interview and diary methods were used to compare oral and text-based communication using cell phones by 17-year-olds: 52 adolescents with SLI and 52 typically developing (TD) peers.

Results

Overall, adolescents with SLI are motivated users of mobile technology, and they engage with both oral uses (phoning) and text-based uses (text messaging). However, adolescents with SLI do not exchange text messages as often as their TD peers. Social rather than language factors are associated with frequency of cell phone use in adolescence.

Conclusions

These findings indicate that social difficulties restrict text-based uses of cell phones by adolescents with SLI, which can in turn reduce the opportunities that these adolescents have to develop social networks and make arrangements to engage in peer social interaction.
Fabrication of size-selected Pd nanoclusters using a magnetron plasma sputtering source
Authors: Ayesh A. I. , Qamhieh N. , Ghamlouche H. , Thaker S. , El-Shaer M.
Published: February 2010

We report on the fabrication of palladium (Pd) nanoclusters using a dc magnetron sputtering source. Plasma sputtering vaporizes the target’s material forming nanoclusters by inert gas condensation. The sputtering source produces ionized nanoclusters that enable the study of the nanoclusters’ size distribution using a quadrupole mass filter. In this work, the dependence of Pd nanoclusters’ size distribution on various source parameters, such as the sputtering discharge power, inert gas flow rate, and aggregation length have been investigated. This work demonstrates the ability of tuning the palladium nanoclusters’ size by proper optimization of the source operation conditions. The experimental nanocluster sizes are compared with a theoretical model that reveals the growth of large nanoclusters from “embryos” by a two-body collision. The model is valid for a specific range of deposition parameters (low inert gas flow rates and aggregation lengths equal or below 70 mm).
Numerical study of thermoacoustic Taconis oscillations
Authors: Shimizu Dai , Sugimoto Nobumasa
Published: February 2010

This paper studies quantitatively a thermoacoustic field by the Taconis oscillations with finite amplitude in a helium-filled, quarter-wavelength tube. Numerical simulations are performed based on the one-dimensional theory in the boundary-layer approximation developed in a previous paper [N. Sugimoto and D. Shimizu, Phys. Fluids 20, 104102 (2008)] by solving initial- and boundary-value problems for a smooth step temperature distribution. It is found that the variations in the density, temperature, and entropy are so significant that the mean values deviate from the respective values in quiescent state. The mean acoustic energy flux and mean heat flux are calculated not only in the main-flow region but also in the boundary layer. The mean convective heat flux appears locally in the main-flow region due to higher-order nonlinear effects. While the total heat flux into the gas vanishes per one period, the local heat flux flows into the gas over a middle part of the tube.
Nonlinear low-frequency structures in the auroral plasma in the presence of an oxygen beam including charge separation
Authors: Moolla S. , Bharuthram R. , Singh S. V. , Lakhina G. S. , Reddy R. V.
Published: February 2010

Observations from the Fast Auroral SnapshoT (FAST) satellite indicate that the parallel and perpendicular (to the Earth’s magnetic field) electric field structures exhibit a spiky appearance. In this study, a magnetized plasma system consisting of protons, electrons, and a cold oxygen ion beam is considered. Both background electrons and protons are treated as hot species with Boltzmann density distributions. The dynamics of the oxygen ion beam is governed by the fluid equations. Effect of charge separation is studied on nonlinear fluctuations arising from a coupling of ion cyclotron and ion-acoustic waves. A scan of parameter space reveals a range of solutions for the parallel electric field from sinusoidal to sawtooth to highly spiky waveforms. The inclusion of charge separation effects tends to in most cases increase the frequency of oscillation of the nonlinear structures. In the case of a weakly magnetized plasma, the amplitude of the oscillations are found to be constant while they are modulated for a strongly magnetized plasma. The findings are compared with satellite observations.
Miscible viscous fingering involving viscosity changes of the displacing fluid by chemical reactions
Authors: Nagatsu Yuichiro , Iguchi Chika , Matsuda Kenji , Kato Yoshihito , Tada Yutaka
Published: February 2010

In our previous study, we experimentally studied the effects of changes in the viscosity of the displaced more-viscous liquid by instantaneous reactions on miscible viscous fingering pattern [Y. Nagatsu, K. Matsuda, Y. Kato, and Y. Tada, “Experimental study on miscible viscous fingering involving viscosity changes induced by variations in chemical species concentrations due to chemical reactions,” J. Fluid Mech. 571, 475 (2007)]. In the present study, experiments have been performed on the miscible viscous fingering involving changes in the viscosity of the displacing less-viscous liquid by instantaneous reactions in a radial Hele-Shaw cell. We have found that the shielding effect is suppressed and the fingers are widened when the viscosity is increased. As a result, the reaction makes the fingering pattern denser. In contrast, the shielding effect is enhanced, and the fingers are narrowed when the viscosity is decreased. As a result, the reaction makes the fingering pattern less dense. These results are essentially same as those obtained by the above-mentioned previous study. This shows that the effects of changes in the viscosity due to the instantaneous reactions are independent of whether the changes occur in the displaced liquid or in the displacing liquid. A mechanism for the independence is discussed.
The Alfvén resonance in pair plasmas
Authors: Cramer N. F.
Published: February 2010

The absorption of wave energy in a magnetized cold pair plasma at the analog of the Alfvén resonance is considered. Splitting of the parallel propagating wave modes due to imbalance of pair species densities is discussed. For oblique propagation of the waves, it is shown that, if the wave frequency is much less than the plasma frequency, there is an approximate resonance in the wave vector component perpendicular to the magnetic field, which may be identified as the analog of the Alfvén resonance in normal electron-ion plasmas. The wave differential equations for a nonuniform plasma also exhibit the resonance. The pair species charge imbalance plays a similar role in the Alfvén resonance process to the Hall term (or finite ion cyclotron frequency effect) in electron-ion plasmas. Wave absorption at the resonance can take place via mode conversion to the analog of the short wavelength inertial Alfvén wave, whose properties are discussed.
Carrier mobility of organic semiconductors based on current-voltage characteristics
Authors: Wang Z. B. , Helander M. G. , Greiner M. T. , Qiu J. , Lu Z. H.
Published: February 2010

Carrier mobility is one of the most critical parameters in organic electronics. There is a strong interest in measuring the mobility of thin-film organic semiconductors using simple techniques, such as from current-voltage (I-V) measurements. This paper discusses how to extract mobility from I-V characteristics, ranging from space charge limited current (SCLC) to injection limited current (ILC). It is found that the mobility extracted from SCLC may significantly deviate from the value measured by time-of-flight depending on the contacting nature at the injection interface. Therefore, the SCLC cannot in general be used to accurately measure mobility. However, the mobility extracted from ILC, which incorporates the injection barrier height measured by ultraviolet photoelectron spectroscopy, is found to be more reliable for unknown materials systems.
Influence of an electric field on the operation of terahertz intracenter silicon lasers
Authors: Pavlov S. G. , Böttger U. , Abrosimov N. V. , Irmscher K. , Riemann H. , Hübers H.-W.
Published: February 2010

We have investigated the influence of a pulsed electric field on the intracenter population inversion between phosphorus donor states in silicon. Terahertz-range electroluminescence resulted from the populated excited donor states. It grows linearly above the impurity breakdown field but saturates at excitation powers exceeding 100 W at 5 μs pulse length. An electric field applied to the optically pumped silicon laser reduces the efficiency of the 2p0→1s(T2) phosphorus transition already at voltages below the impurity breakdown. The appearance of a current through the laser sample results in a fast quenching of the laser emission that indicates a reduction in the inversed population between the laser states.
Confinement of Ar between two identical parallel semi-infinite walls
Authors: Sartarelli Salvador A. , Szybisz Leszek
Published: February 2010

The confinement of Ar in planar slits of two identical parallel semi-infinite walls of alkali metals, alkaline-earth metal Mg, and CO2 is investigated within the framework of the density functional theory. It is assumed that (1) the fluid atoms interact via a recently proposed effective attractive pair potential with strength, εff, which reproduces the experimental data of the surface tension of the liquid-vapor interface at the bulk coexistence curve, and (2) the adsorption on the walls is described by ab initio potentials characterized by a well depth, Wsf. In this way the systems were studied in the framework of a realistic approach. We found that for small coverages, the slit is always filled by forming two symmetric vapor films, one at each wall. For increasing coverage the behavior depends on the ratio Wsf/εff and the temperature T. In the case of alkali metals, we found at the triple point, Tt, of the adsorbate a regime of average density ρav∗ in which the ground state exhibits asymmetric density profiles, leading to the so-called spontaneous symmetry breaking (SSB) effect. The SSB appears at an average density ρsb1∗ and disappears at a higher average density ρsb2∗. When T is increased, the range of densities ρsb1∗≤ρav∗≤ρsb2∗ diminishes and eventually the SSB disappears at a critical temperature, Tsb, which coincides with the critical prewetting temperature Tcpw observed in the adsorption on a single wall. For T>Tcpw the slit is filled symmetrically up to the phase transition to capillary condensation. All these features are examined as a function of the strength of the substrate and the width of the slit. Furthermore, no SSB effect was found for Mg and CO2.
Features of ion acoustic waves in collisional plasmas
Authors: Vranjes J. , Poedts S.
Published: February 2010

The effects of friction on the ion acoustic (IA) wave in fully and partially ionized plasmas are studied. In a quasineutral electron-ion plasma the friction between the two species cancels out exactly and the wave propagates without any damping. If the Poisson equation is used instead of the quasineutrality, however, the IA wave is damped and the damping is dispersive. In a partially ionized plasma, the collisions with the neutrals modify the IA wave beyond recognition. For a low density of neutrals the mode is damped. Upon increasing the neutral density, the mode becomes first evanescent and then reappears for a still larger number of neutrals. A similar behavior is obtained by varying the mode wavelength. The explanation for this behavior is given. In an inhomogeneous plasma placed in an external magnetic field, and for magnetized electrons and unmagnetized ions, the IA mode propagates in any direction and in this case the collisions make it growing on the account of the energy stored in the density gradient. The growth rate is angle dependent. A comparison with the collisionless kinetic density gradient driven IA instability is also given.
Strain modulation-enhanced Mg acceptor activation efficiency of Al0.14Ga0.86N/GaN superlattices with AlN interlayer
Authors: Wang Lei , Li Rui , Li Ding , Liu Ningyang , Liu Lei , Chen Weihua , Wang Cunda , Yang Zhijian , Hu Xiaodong
Published: February 2010

AlN layer was grown as interlayer between undoped GaN and Mg doped Al0.14Ga0.86N/GaN superlattices (SLs) epilayer to modulate the strain distribution between Al0.14Ga0.86N barrier and GaN well layers in SLs sample. Strain relaxation was observed in the SLs sample with AlN interlayer by x-ray diffraction reciprocal space mapping method. The measured hole concentration of SLs sample with AlN interlayer at room temperature was over 1.6×1018 cm−3 but that was only 6.6×1016 cm−3 obtained in SLs sample without AlN interlayer. Variable temperature Hall-effect measurement showed that the acceptor activation energy decreased from 150 to 70 meV after inserting the AlN layer, which indicated that the strain modulation of SLs induced by AlN interlayer was beneficial to the Mg acceptor activation and hole concentration enhancement.
Molecular beam epitaxy growth and optical properties of AlN nanowires
Authors: Landré O. , Fellmann V. , Jaffrennou P. , Bougerol C. , Renevier H. , Cros A. , Daudin B.
Published: February 2010

Growth of catalyst-free AlN nanowires has been achieved by plasma-assisted molecular beam epitaxy on SiO2/Si (100), by taking advantage of Volmer–Weber growth mode of AlN on amorphous SiO2. Using a combination of high resolution transmission electron microscopy and Raman spectroscopy, it is found that AlN nanowires are completely relaxed, which has been assigned to the compliant character of SiO2. Elastic strain relaxation of AlN nanowires has been further confirmed by photoluminescence experiments, showing in addition that spectra are dominated by near-band edge emission.
Phase coexistence and Mn-doping effect in lead-free ferroelectric (Na1/2Bi1/2)TiO3 crystals
Authors: Tu C.-S. , Huang S.-H. , Ku C.-S. , Lee H.-Y. , Chien R. R. , Schmidt V. H. , Luo H.
Published: February 2010

Phase transformations of (001)-cut (Na1/2Bi1/2)TiO3 (NBT) and 1 at. % Mn-doped NBT (Mn-NBT) crystals have been investigated by means of dielectric permittivity, conventional x-ray diffraction (XRD), and high-resolution synchrotron XRD and reciprocal space mapping. An R−R+T−T−C transition sequence was observed in NBT and Mn-NBT upon zero-field heating. R, T, and C are rhombohedral, tetragonal, and cubic phases, respectively. R+T represents that the ferroelastic T phase coexists with the ferroelectric R phase. The Mn dopant can enhance dielectric response and reduce the dielectric loss in the high-temperature region due to the increased degree of ordering.
Preference of sheep among annual legumes is more closely related to plant nutritive characteristics as plants mature
Authors: Thomas D. T. , Milton J. T. B. , Revell C. K. , Ewing M. A. , Dynes R. A. , Murray K. , Lindsay D. R.
Published: February 2010

We hypothesised that the preference of sheep among a wide range of annual legumes at successive stages of plant phenology would be related to laboratory measurements of the chemical composition of the forage. We tested this by examining the relative preferences of sheep among 20 genotypes of annual plants at three phenological stages of plant growth using the Chesson–Manly selection index. Plant material was collected for laboratory analyses at each phenological stage and samples were analysed for nitrogen, sulfur, neutral detergent fibre, acid detergent fibre, in vitro digestibility and water soluble carbohydrates. Sheep differed in relative preference among the plant genotypes within and between each of the three phenological stages. Vegetative characteristics that were correlated with relative preference also differed with plant phenology. Measured characteristics of the plant material explained an increasing proportion of the variance in relative preference with successive phenological stages (4.8, 51.1 and 60.9% at the vegetative, reproductive and senesced stages; P < 0.001). The relative preference of the sheep depended on the overall quality of the vegetation. When the quality of the vegetation was high, relative preference did not correlate well with measured nutritive characteristics. However, when the vegetation was of low quality, sheep selected plants with characteristics associated with higher nutritive value. We conclude that sheep adopt different foraging strategies in response to changing vegetation characteristics and increase their preference for plants that increase their intake of digestible dry matter as the sward matures.
Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system
Authors: Menke Matt , Berger Bonnie , Cowen Lenore
Published: February 2010

The recent explosion in newly sequenced bacterial genomes is outpacing the capacity of researchers to try to assign functional annotation to all the new proteins. Hence, computational methods that can help predict structural motifs provide increasingly important clues in helping to determine how these proteins might function. We introduce a Markov Random Field approach tailored for recognizing proteins that fold into mainly β-structural motifs, and apply it to build recognizers for the β-propeller shapes. As an application, we identify a potential class of hybrid two-component sensor proteins, that we predict contain a double-propeller domain.
Insight into the mechanism of an iron dioxygenase by resolution of steps following the Fe
IV
═O species
Authors: Grzyska Piotr K. , Appelman Evan H. , Hausinger Robert P. , Proshlyakov Denis A.
Published: February 2010

Iron oxygenases generate elusive transient oxygen species to catalyze substrate oxygenation in a wide range of metabolic processes. Here we resolve the reaction sequence and structures of such intermediates for the archetypal non-heme Fe
II
and α-ketoglutarate-dependent dioxygenase TauD. Time-resolved Raman spectra of the initial species with
16
O
18
O oxygen unequivocally establish the Fe
IV
═O structure.
1
H/
2
H substitution reveals direct interaction between the oxo group and the C1 proton of substrate taurine. Two new transient species were resolved following Fe
IV
═O; one is assigned to the
ν
FeO
mode of an Fe
III
─O(H) species, and a second is likely to arise from the vibration of a metal-coordinated oxygenated product, such as Fe
II
─O─C
1
or Fe
II
─OOCR. These results provide direct insight into the mechanism of substrate oxygenation and suggest an alternative to the hydroxyl radical rebinding paradigm.
Morphine peripheral analgesia depends on activation of the PI3Kγ/AKT/nNOS/NO/K
ATP
signaling pathway
Authors: Cunha Thiago M. , Roman-Campos Danilo , Lotufo Celina M. , Duarte Hugo L. , Souza Guilherme R. , Verri Waldiceu A. , Funez Mani I. , Dias Quintino M. , Schivo Ieda R. , Domingues Andressa C. , Sachs Daniela , Chiavegatto Silvana , Teixeira Mauro M. , Hothersall John S. , Cruz Jader S. , Cunha Fernando Q. , Ferreira Sergio H.
Published: February 2010

Morphine is one of the most prescribed and effective drugs used for the treatment of acute and chronic pain conditions. In addition to its central effects, morphine can also produce peripheral analgesia. However, the mechanisms underlying this peripheral action of morphine have not yet been fully elucidated. Here, we show that the peripheral antinociceptive effect of morphine is lost in neuronal nitric-oxide synthase null mice and that morphine induces the production of nitric oxide in primary nociceptive neurons. The activation of the nitric-oxide pathway by morphine was dependent on an initial stimulation of PI3Kγ/AKT protein kinase B (AKT) and culminated in increased activation of K
ATP
channels. In the latter, this intracellular signaling pathway might cause a hyperpolarization of nociceptive neurons, and it is fundamental for the direct blockade of inflammatory pain by morphine. This understanding offers new targets for analgesic drug development.
Communication via gap junctions underlies early functional and beneficial interactions between grafted neural stem cells and the host
Authors: Jäderstad Johan , Jäderstad Linda M. , Li Jianxue , Chintawar Satyan , Salto Carmen , Pandolfo Massimo , Ourednik Vaclav , Teng Yang D. , Sidman Richard L. , Arenas Ernest , Snyder Evan Y. , Herlenius Eric
Published: February 2010

How grafted neural stem cells (NSCs) and their progeny integrate into recipient brain tissue and functionally interact with host cells is as yet unanswered. We report that, in organotypic slice cultures analyzed by ratiometric time-lapse calcium imaging, current-clamp recordings, and dye-coupling methods, an early and essential way in which grafted murine or human NSCs integrate functionally into host neural circuitry and affect host cells is via gap-junctional coupling, even before electrophysiologically mature neuronal differentiation. The gap junctions, which are established rapidly, permit exogenous NSCs to influence directly host network activity, including synchronized calcium transients with host cells in fluctuating networks. The exogenous NSCs also protect host neurons from death and reduce such signs of secondary injury as reactive astrogliosis. To determine whether gap junctions between NSCs and host cells may also mediate neuroprotection in vivo, we examined NSC transplantation in two murine models characterized by degeneration of the same cell type (Purkinje neurons) from different etiologies, namely, the
nervous
and
SCA1
mutants. In both, gap junctions (containing connexin 43) formed between NSCs and host cells at risk, and were associated with rescue of neurons and behavior (when implantation was performed before overt neuron loss). Both in vitro and in vivo beneficial NSC effects were abrogated when gap junction formation or function was suppressed by pharmacologic and/or RNA-inhibition strategies, supporting the pivotal mediation by gap-junctional coupling of some modulatory, homeostatic, and protective actions on host systems as well as establishing a template for the subsequent development of electrochemical synaptic intercellular communication.
Methicillin-ResistantStaphylococcus aureusColonization or Infection in Canada: National Surveillance and Changing Epidemiology, 1995–2007
Authors: Simor Andrew E. , Gilbert Nicolas L. , Gravel Denise , Mulvey Michael R. , Bryce Elizabeth , Loeb Mark , Matlow Anne , McGeer Allison , Louie Lisa , Campbell Jennifer ,   Canadian Nosocomial Infection Surveillance Program
Published: February 2010

Objective.

To determine the incidence and describe the changing epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) colonization or infection in Canadian hospitals from 1995–2007.

Setting.

Forty-eight hospitals participating in the Canadian Nosocomial Infection Surveillance Program.

Design.

Prospective, laboratory-based surveillance for incident cases of MRSA colonization or infection among hospitalized patients.

Methods.

Clinical and epidemiologic data were obtained by review of hospital records. Standard criteria were used to determine whether MRSA colonization or infection was present and whether the MRSA strain was healthcare associated or community associated. A representative subset of isolates was characterized by use of pulsed-field gel electrophoresis and staphylococcal cassette chromosome (SCC) mec typing.

Results.

From 1995 to 2007, a total of 37,169 hospitalized patients were newly identified as either infected or colonized with MRSA, and the overall incidence of both MRSA colonization and MRSA infection increased from 0.65 to 11.04 cases per 10,000 patient-days (P< .001). Of these 37,169 patients, 11,828 (32%) had an MRSA infection, and infection rate increased from 0.36 to 3.43 cases per 10,000 patient-days. The proportion of community-associated MRSA strains increased from 6% to 23% (P< .001). The most common genotype (47% of isolates) was CMRSA-2 (USA100/800); in 2007, CMRSA-10 (USA300) was the second most common strain (27% of isolates), associated with SCCmec type IV. Patients with CMRSA-10 were predominantly from western Canada and were more likely to be children (odds ratio [OR], 10.0 [95% confidence interval {CI}, 7.4–13.4]) and to have infection (OR, 2.3 [95% CI, 1.9–2.7]), especially skin and/or soft tissue infection (OR, 5.9 [95% CI, 5.0–6.9]).

Conclusions.

The overall incidence of both MRSA colonization and MRSA infection increased 17-fold in Canadian hospitals from 1995 to 2007. There has also been a dramatic increase in cases of community-associated MRSA infection due to the CMRSA-10 (USA300) clone. Continued surveillance is needed to monitor the ongoing evolution of MRSA colonization or infection in Canada and globally.
Structure and luminescence of (Ca,Sr)2SiS4 : Eu2+ phosphors
Authors: Parmentier Anthony B , Smet Philippe F , Bertram Frank , Christen Jürgen , Poelman Dirk
Published: February 2010

Sr2SiS4 : Eu2+, Ca2SiS4 : Eu2+ and the solid solution of both, europium-doped (Ca,Sr)2SiS4, were investigated as UV–VIS excitable green to red powder phosphors. Sr2SiS4 : Eu2+ shows two emission bands, peaking at 480 and 550 nm. By changing the ratio between Ca2+ and Sr2+, the photoluminescent emission spectrum can be tuned. Using x-ray diffraction, the phase composition and lattice parameters of the thiosilicate compounds were determined. The material forms a single, monoclinic Sr2SiS4-like phase up to 40% substitution of Sr2+ by Ca2+. From 50% to 90% of substitution by Ca2+, phase separation was observed, leading to more complex emission spectra. These spectra were studied in detail using photoluminescence spectroscopy, cathodoluminescence microscopy and temperature dependent optical measurements. The thermal quenching temperature decreases from 470 K in Ca2SiS4 : Eu2+ to 380 K in Sr2SiS4 : Eu2+ upon increasing substitution of Ca2+ by Sr2+. The possibilities of these materials as wavelength converters for white light emitting diodes were evaluated.
2-propanol photodegradation over molybdates: effects of chemical compositions and electronic structures
Authors: Shi Haifeng , Li Zhaosheng , Ye Jinhua , Zou Zhigang
Published: February 2010

A new kind of photocatalysts, ABi(MoO4)2 (A = Na, Ag), were prepared by a traditional solid-state reaction method. The samples were characterized by x-ray diffraction, UV–Vis diffuse reflectance spectroscopy, N2 adsorption–desorption measurement and scanning electron microscopy. The results showed that ABi(MoO4)2 (A = Na, Ag) were all crystallized in a tetragonal system with the space group I41/a. However, the substitution of A
1+ cations with different elemental compositions imposed significant effects on their electronic structures and photocatalytic performance. The photocatalytic activities were evaluated by photo-oxidation of gaseous 2-propanol. It was found that NaBi(MoO4)2 showed a higher activity than AgBi(MoO4)2. Theoretically, calculated band structures and density of states by the plane-wave density functional theory revealed that the different photophysical and photocatalytic properties of ABi(MoO4)2 (A = Na, Ag) can possibly be ascribed to their different electronic structures.
The local structure of transition metal doped semiconducting boron carbides
Authors: Liu Jing , Luo Guangfu , Mei Wai-Ning , Kizilkaya Orhan , Shepherd Eric D , Brand J I , Dowben P A
Published: February 2010

Transition metal doped boron carbides produced by plasma enhanced chemical vapour deposition of orthocarborane (closo-1,2-C2B10H12) and 3d metal metallocenes were investigated by performing K-edge extended x-ray absorption fine structure and x-ray absorption near edge structure measurements. The 3d transition metal atom occupies one of the icosahedral boron or carbon atomic sites within the icosahedral cage. Good agreement was obtained between experiment and models for Mn, Fe and Co doping, based on the model structures of two adjoined vertex sharing carborane cages, each containing a transition metal. The local spin configurations of all the 3d transition metal doped boron carbides, Ti through Cu, are compared using cluster and/or icosahedral chain calculations, where the latter have periodic boundary conditions.
Connection between Coulomb and harmonic oscillator potentials in relativistic quantum mechanics
Authors: Fu Bo , Zhang Fu-Lin , Chen Jing-Ling
Published: February 2010

The Levi-Civita transformation is applied in the two-dimensional (2D) Dirac and Klein–Gordon (KG) equations with equal external scalar and vector potentials. The Coulomb and harmonic oscillator problems are connected via the Levi-Civita transformation. These connections lead to an approach to solve the Coulomb problems using the results of the harmonic oscillator potential in the relativistic systems mentioned above.
Elastic scattering of electrons on Ne atoms at intermediate energies
Authors: L S Lino Jorge
Published: February 2010

In this work, we present a theoretical study on electron scattering by Ne in the intermediate- and high-energy range. More specifically, we report calculated differential cross sections for electron scattering by Ne in the 20–500 eV range by the Schwinger multichannel method using plane waves as a trial basis set. To include exchange plus polarization effects, we used the Born–Ochkur model and the Buckingham potential, respectively. The comparison of our calculated results with experimental data and recent theoretical studies (Jablonski et al 2004 J. Phys. Chem. Ref. Data
33 409) is encouraging.
Initial Polarized Bud Growth by Endocytic Recycling in the Absence of Actin Cable–dependent Vesicle Transport in Yeast
Authors: Yamamoto Takaharu , Mochida Junko , Kadota Jun , Takeda Miyoko , Bi Erfei , Tanaka Kazuma
Published: February 2010

The assembly of filamentous actin is essential for polarized bud growth in budding yeast. Actin cables, which are assembled by the formins Bni1p and Bnr1p, are thought to be the only actin structures that are essential for budding. However, we found that formin or tropomyosin mutants, which lack actin cables, are still able to form a small bud. Additional mutations in components for cortical actin patches, which are assembled by the Arp2/3 complex to play a pivotal role in endocytic vesicle formation, inhibited this budding. Genes involved in endocytic recycling were also required for small-bud formation in actin cable-less mutants. These results suggest that budding yeast possesses a mechanism that promotes polarized growth by local recycling of endocytic vesicles. Interestingly, the type V myosin Myo2p, which was thought to use only actin cables to track, also contributed to budding in the absence of actin cables. These results suggest that some actin network may serve as the track for Myo2p-driven vesicle transport in the absence of actin cables or that Myo2p can function independent of actin filaments. Our results also show that polarity regulators including Cdc42p were still polarized in mutants defective in both actin cables and cortical actin patches, suggesting that the actin cytoskeleton does not play a major role in cortical assembly of polarity regulators in budding yeast.
Estimating replicate time shifts using Gaussian process regression
Authors: Liu Qiang , Lin Kevin K. , Andersen Bogi , Smyth Padhraic , Ihler Alexander
Published: February 2010

Motivation: Time-course gene expression datasets provide important insights into dynamic aspects of biological processes, such as circadian rhythms, cell cycle and organ development. In a typical microarray time-course experiment, measurements are obtained at each time point from multiple replicate samples. Accurately recovering the gene expression patterns from experimental observations is made challenging by both measurement noise and variation among replicates' rates of development. Prior work on this topic has focused on inference of expression patterns assuming that the replicate times are synchronized. We develop a statistical approach that simultaneously infers both (i) the underlying (hidden) expression profile for each gene, as well as (ii) the biological time for each individual replicate. Our approach is based on Gaussian process regression (GPR) combined with a probabilistic model that accounts for uncertainty about the biological development time of each replicate.

Results: We apply GPR with uncertain measurement times to a microarray dataset of mRNA expression for the hair-growth cycle in mouse back skin, predicting both profile shapes and biological times for each replicate. The predicted time shifts show high consistency with independently obtained morphological estimates of relative development. We also show that the method systematically reduces prediction error on out-of-sample data, significantly reducing the mean squared error in a cross-validation study.

Availability: Matlab code for GPR with uncertain time shifts is available at http://sli.ics.uci.edu/Code/GPRTimeshift/

Contact:  ihler@ics.uci.edu
SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements
Authors: Munshaw Supriya , Kepler Thomas B.
Published: February 2010

Motivation: The inference of pre-mutation immunoglobulin (Ig) rearrangements is essential in the study of the antibody repertoires produced in response to infection, in B-cell neoplasms and in autoimmune disease. Often, there are several rearrangements that are nearly equivalent as candidates for a given Ig gene, but have different consequences in an analysis. Our aim in this article is to develop a probabilistic model of the rearrangement process and a Bayesian method for estimating posterior probabilities for the comparison of multiple plausible rearrangements.

Results: We have developed SoDA2, which is based on a Hidden Markov Model and used to compute the posterior probabilities of candidate rearrangements and to find those with the highest values among them. We validated the software on a set of simulated data, a set of clonally related sequences, and a group of randomly selected Ig heavy chains from Genbank. In most tests, SoDA2 performed better than other available software for the task. Furthermore, the output format has been redesigned, in part, to facilitate comparison of multiple solutions.

Availability: SoDA2 is available online at https://hippocrates.duhs.duke.edu/soda. Simulated sequences are available upon request.

Contact:  kepler@duke.edu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Authors: Wu Thomas D. , Nacu Serban
Published: February 2010

Motivation: Next-generation sequencing captures sequence differences in reads relative to a reference genome or transcriptome, including splicing events and complex variants involving multiple mismatches and long indels. We present computational methods for fast detection of complex variants and splicing in short reads, based on a successively constrained search process of merging and filtering position lists from a genomic index. Our methods are implemented in GSNAP (Genomic Short-read Nucleotide Alignment Program), which can align both single- and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state.

Results: In comparison testing, GSNAP has speeds comparable to existing programs, especially in reads of ≥70 nt and is fastest in detecting complex variants with four or more mismatches or insertions of 1–9 nt and deletions of 1–30 nt. Although SNP tolerance does not increase alignment yield substantially, it affects alignment results in 7–8% of transcriptional reads, typically by revealing alternate genomic mappings for a read. Simulations of bisulfite-converted DNA show a decrease in identifying genomic positions uniquely in 6% of 36 nt reads and 3% of 70 nt reads.

Availability: Source code in C and utility programs in Perl are freely available for download as part of the GMAP package at http://share.gene.com/gmap.

Contact:  twu@gene.com
Getting a Better Grip on Research: The Maze of the Most Busy Life
Authors: Maskrey Neal , Underhill Jonathan , Hutchinson Andy , Shaughnessy Allen , Slawson Dave
Published: February 2010

This is the fifth paper in a series of five describing the use of evidence to support decisions made in clinical practice. In the 21st century, health care clinicians, managers and patients expect to see the findings of research incorporated into clinical practice, taking into account the needs and wishes of individual patients. In the previous four papers in this series of five, we have examined why that happens—and often does not happen—and what clinicians and managers can do to improve the use of evidence in consultations. This, the final paper, is written as if from some point in the near future and uses a narrative approach to describe a clinician's progress on a journey to meet the real-world challenges of using evidence in practice.
Benzodiazepine Dependence in Primary Care
Authors: van Hecke Oliver
Published: February 2010

Since the first benzodiazepines were marketed in the late 1950s, their use has steadily increased, culminating in one benzodiazepine, diazepam, being one of the most widely prescribed drugs of all time. Often these drugs were prescribed long term for complaints such as anxiety, depression and ordinary life stresses. Since their potential for dependence and addiction have become readily apparent, the question of the correct use of benzodiazepines as anxiolytics and hypnotics by GPs has been hotly debated in the UK. Many doctors still feel more comfortable prescribing benzodiazepines than methadone to problem users. Strategies for discontinuation start with GPs, who are still the main prescribers.