bluuebunny/crossref_metadata_2025 huggingface dataset:
High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of nickel carbide (NiC) and its cation (NiC+)
Authors: Lau Kai-Chung , Chang Yih Chung , Shi Xiaoyu , Ng C. Y.
Published: September 2010

The ionization energy (IE) of NiC and the 0 K bond dissociation energies (D0) and heats of formation at 0 K (ΔHof0) and 298 K (ΔHof298) for NiC and NiC+ are predicted by the wavefunction based CCSDTQ(Full)/CBS approach and the multireference configuration interaction (MRCI) method with Davidson correction (MRCI+Q). The CCSDTQ(Full)/CBS calculations presented here involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation, core-valence electronic (CV), spin-orbit coupling (SO), and scalar relativistic effect (SR) corrections. The present calculations provide the correct symmetry predictions for the ground states of NiC and NiC+ to be ∑1+ and ∑2+, respectively. The CCSDTQ(Full)/CBS IE(NiC)=8.356 eV is found to compare favorably with the experimental IE value of 8.372 05±0.000 06 eV. The predicted IE(NiC) value at the MRCI+Q/cc-pwCV5Z level, including the ZPVE, SO, and SR effects is 8.00 eV, which is 0.37 eV lower than the experimental value. This work together with the previous experimental and theoretical investigations supports the conclusion that the CCSDTQ(Full)/CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC and NiC. Furthermore, the CCSDTQ(Full)/CBS calculations give the prediction of D0(NiC)−D0(Ni+C)=0.688 eV, which is also consistent with the experimental determination of 0.732 21±0.000 06 eV, whereas the MRCI+Q calculations (with relativistic and CV effects) predict a significantly lower value of 0.39 eV for D0(NiC)−D0(Ni+C). The analysis of the correction terms shows that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of NiC/NiC+. For the experimental D0 and ΔHof0 values of NiC/NiC+, which are not known experimentally, we recommend the CCSDTQ(Full)/CBS predictions [D0(NiC)=4.048 eV, D0(Ni+C)=3.360 eV, ΔHof0(NiC)=749.0 kJ/mol, and ΔHof0(NiC+)=1555.1 kJ/mol].
Serial tempering without exchange
Authors: Nymeyer Hugh
Published: September 2010

Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a small one-dimensional system and a small solvated peptide. The suggestion is then made to replace the serial tempering protocol with the equivalent umbrella sampling calculation. This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods.
Reaction of C2(a Π3u) with methanol: Temperature dependence and deuterium isotope effect
Authors: Hu Renzhi , Zhang Qun , Chen Yang
Published: September 2010

Bimolecular rate constants for the gas-phase reactions of C2(a Π3u) with a variety of methanol isotopomers including CH3OH (k1), CH3OD (k2), CD3OH (k3), and CD3OD (k4) have been measured over the temperature range of 293–673 K by means of pulsed laser photolysis/laser-induced fluorescence technique. The rate constants, in units of cm3 molecule−1 s−1, can be fitted by the normal Arrhenius expressions: k1(T)=(1.32±0.02)×10−11 exp[−(366.80±4.44)/T], k2(T)=(1.34±0.02)×10−11 exp[−(376.86±5.09)/T], k3(T)=(1.09±0.02)×10−11 exp[−(640.00±7.23)/T], and k4(T)=(1.12±0.01)×10−11 exp[−(666.37±4.63)/T], where all error estimates are ±2σ and represent the precision of the fit. The observed deuterium kinetic isotope effects, k1/k2 and k1/k3, along with the positive temperature dependences of k(T), allow us to reach a conclusion that the reaction of C2(a Π3u) with methanol in 293–673 K proceeds via a site-specific hydrogen abstraction mechanism, that is, H-atom abstraction from the methyl site rather than from the hydroxyl site dominating reactivity.
Spherically symmetric simulation of plasma liner driven magnetoinertial fusion
Authors: Samulyak Roman , Parks Paul , Wu Lingling
Published: September 2010

Spherically symmetric simulations of the implosion of plasma liners and compression of plasma targets in the concept of the plasma jet driven magnetoinertial fusion have been performed using the method of front tracking. The cases of single deuterium and xenon liners and double layer deuterium-xenon liners compressing various deuterium-tritium targets have been investigated, optimized for maximum fusion energy gains, and compared with theoretical predictions and scaling laws of [P. Parks, Phys. Plasmas 15, 062506 (2008)]. In agreement with the theory, the fusion gain was significantly below unity for deuterium-tritium targets compressed by Mach 60 deuterium liners. The most optimal setup for a given chamber size contained a target with the initial radius of 20 cm compressed by a 10 cm thick, Mach 60 xenon liner, achieving a fusion energy gain of 10 with 10 GJ fusion yield. Simulations also showed that composite deuterium-xenon liners reduce the energy gain due to lower target compression rates. The effect of heating of targets by alpha particles on the fusion energy gain has also been investigated.
Distinctive features of ion-acoustic solitons in electron-positron-ion superdense magnetoplasmas with degenerate electrons and positrons
Authors: Akbari-Moghanjoughi M.
Published: September 2010

Using the extended Poincaré–Lighthill–Kuo reductive perturbation method to study the small-amplitude ion acoustic solitary wave dynamics (propagation and interaction), it is shown that in the Thomas–Fermi magnetoplasma consisting of inertial-less degenerate electrons and positrons and isothermal ions, distinctive features emerge when the ultrarelativistic degeneracy pressure applies to electrons and positrons. Calculations show that ion-acoustic solitary waves may interact differently in such plasmas under ultrarelativistic degeneracy pressure.
Probing model tumor interfacial properties using piezoelectric cantilevers
Authors: Yegingil Hakki , Shih Wan Y. , Shih Wei-Heng
Published: September 2010

Invasive malignant breast cancers are typically branchy and benign breast tumors are typically smooth. It is of interest to characterize tumor branchiness (roughness) to differentiate invasive malignant breast cancer from noninvasive ones. In this study, we examined the shear modulus (G) to elastic modulus (E) ratio, G/E, as a quantity to describe model tumor interfacial roughness using a piezoelectric cantilever capable of measuring both tissue elastic modulus and tissue shear modulus. The piezoelectric cantilever used had two lead zirconate titanate layers to facilitate all-electrical elastic (shear) modulus measurements using one single device. We constructed model tissues with tumors by embedding one-dimensional (1D) corrugated inclusions and three-dimensional (3D) spiky-ball inclusions made of modeling clay in gelatin. We showed that for smooth inclusions, G/E was 0.3 regardless of the shear direction. In contrast, for a 1D corrugated rough inclusion G/E was 0.3 only when the shear was parallel to corrugation and G/E increased with an increasing angle between the shear direction and the corrugation. When the shear was perpendicular to corrugation, G/E became >0.7. For 3D isotropic spiky-ball inclusions we showed that the G/E depended on the degree of the roughness. Using the ratio s/r of the spike length (s) to the overall inclusion radius (r) as a roughness parameter, we showed that for inclusions with s/r larger than or equal to 0.28, the G/E ratio over the inclusions was larger than 0.7 whereas for inclusions with s/r less than 0.28, the G/E decreased with decreasing s/r to around 0.3 at s/r=0. In addition, we showed that the depth limit of the G/E measurement is twice the width of the probe area of the piezoelectric cantilever.
Stability of a general mixed additive-cubic functional equation in non-Archimedean fuzzy normed spaces
Authors: Xu Tian Zhou , Rassias John Michael , Xu Wan Xin
Published: September 2010

We establish some stability results concerning the general mixed additive-cubic functional equation in non-Archimedean fuzzy normed spaces. In addition, we establish some results of approximately general mixed additive-cubic mappings in non-Archimedean fuzzy normed spaces. The results improve and extend some recent results.
Propagation of high power electromagnetic beam in relativistic magnetoplasma: Higher order paraxial ray theory
Authors: Gill Tarsem Singh , Kaur Ravinder , Mahajan Ranju
Published: September 2010

This paper presents an analysis of self-consistent, steady-state, theoretical model, which explains the ring formation in a Gaussian electromagnetic beam propagating in a magnetoplasma, characterized by relativistic nonlinearity. Higher order terms (up to r4) in the expansion of the dielectric function and the eikonal have been taken into account. The condition for the formation of a dark and bright ring derived earlier by Misra and Mishra [J. Plasma Phys. 75, 769 (2009)] has been used to study focusing/defocusing of the beam. It is seen that inclusion of higher order terms does significantly affect the dependence of the beam width on the distance of propagation. Further, the effect of the magnetic field and the nature of nonlinearity on the ring formation and self-focusing of the beam have been explored.
Effects of correlated Gaussian noise on the mean firing rate and correlations of an electrically coupled neuronal network
Authors: Sun Xiaojuan , Perc Matjaž , Lu Qishao , Kurths Jürgen
Published: September 2010

In this paper, we examine the effects of correlated Gaussian noise on a two-dimensional neuronal network that is locally modeled by the Rulkov map. More precisely, we study the effects of the noise correlation on the variations of the mean firing rate and the correlations among neurons versus the noise intensity. Via numerical simulations, we show that the mean firing rate can always be optimized at an intermediate noise intensity, irrespective of the noise correlation. On the other hand, variations of the population coherence with respect to the noise intensity are strongly influenced by the ratio between local and global Gaussian noisy inputs. Biological implications of our findings are also discussed.
Design and adaptation of a novel supercritical extraction facility for operation in a glove box for recovery of radioactive elements
Authors: Kumar V. Suresh , Kumar R. , Sivaraman N. , Ravisankar G. , Vasudeva Rao P. R.
Published: September 2010

The design and development of a novel supercritical extraction experimental facility adapted for safe operation in a glove box for the recovery of radioactive elements from waste is described. The apparatus incorporates a high pressure extraction vessel, reciprocating pumps for delivering supercritical fluid and reagent, a back pressure regulator, and a collection chamber. All these components of the system have been specially designed for glove box adaptation and made modular to facilitate their replacement. Confinement of these materials must be ensured in a glove box to protect the operator and prevent contamination to the work area. Since handling of radioactive materials under high pressure (30 MPa) and temperature (up to 333 K) is involved in this process, the apparatus needs elaborate safety features in the design of the equipment, as well as modification of a standard glove box to accommodate the system. As a special safety feature to contain accidental leakage of carbon dioxide from the extraction vessel, a safety vessel has been specially designed and placed inside the glove box. The extraction vessel was enclosed in the safety vessel. The safety vessel was also incorporated with pressure sensing and controlling device.
Gold nanoparticle-doped biocompatible silk films as a path to implantable thermo-electrically wireless powering devices
Authors: Tao Hu , Siebert Sean M. , Brenckle Mark A. , Averitt Richard D. , Cronin-Golomb Mark , Kaplan David L. , Omenetto Fiorenzo G.
Published: September 2010

In this paper, we report on gold nanoparticle (GNP) doped silk films as an implantable and degradable heating element activated by light, which can be potentially used for wireless powering of implanted microdevices. Proof-of-concept experiments have been conducted by casting a GNP doped silk film on a miniature thermal-power chip, which generates ∼20 mW when illuminated by a green laser with an output power of 450 mW/mm2 at 532 nm.
Influence of uniaxial anisotropy on the domain pinning fields of ferromagnetic Ga1−xMnxAs films
Authors: Lee Sangyeop , Lee Hakjoon , Yoo Taehee , Lee Sanghoon , Liu X. , Furdyna J. K.
Published: September 2010

The domain pinning fields of ferromagnetic Ga1−xMnxAs films were investigated using the planar Hall effect (PHE). Two in-plane components of GaMnAs films’ anisotropy fields (H4∥ and HU∥), which determine the direction of magnetic easy axes in the (001) plane, were obtained from the PHE’s angular dependence fitted with magnetic free energy within the scheme of the Stoner–Wohlfarth model. The domain pinning fields were obtained both with and without consideration of the deviation angle, δ, of magnetic easy axes from the ⟨100⟩ crystallographic direction of each sample. The values of domain pinning fields are clearly different between the two methods of analysis and the discrepancy increases with δ. This indicates that the correct direction of the magnetic easy axis (i.e., the influence of uniaxial anisotropy) must be considered to obtain precise values of pinning fields in GaMnAs films.
Homobuffer thickness effect on the background electron carrier concentration of epitaxial ZnO thin films
Authors: Yang Z. , Zhou H. M. , Chen W. V. , Li L. , Zhao J. Z. , Yu P. K. L. , Liu J. L.
Published: September 2010

Epitaxial ZnO thin films were grown on r-plane sapphire substrates using plasma-assisted molecular-beam epitaxy. ZnO homobuffer layers grown at a lower temperature were introduced to improve the crystallinity of the top ZnO thin films. Thicker homobuffer layers lead to better crystallinity of the subsequent epitaxial ZnO thin films due to the strain relaxation effect. Residual background electron carrier concentration in these undoped ZnO thin films first decreases, then increases as the buffer layer thickness increases from ∼1 to 30 nm, with a minimum electron concentration of ∼1×1017 cm−3 occurring in ZnO homobuffer of ∼5 nm. These results demonstrate that the optimized ZnO homobuffer thickness to achieve both good ZnO crystallinity and low residual electron concentration is determined by the relative electron carrier concentration ratios and mobility ratios between the buffer and epi-ZnO layers.
Synthesis of nanoparticles in laser ablation of aluminum in liquid
Authors: Kumar Bhupesh , Thareja Raj K.
Published: September 2010

We report the synthesis of aluminum nanoparticles using pulsed laser ablation in water confined plasma. Nanoparticles have spherical shape and size distribution depends on laser fluence. Strong blue photoluminescence peaks at 405 nm (3.06 eV) and 430 nm (2.89 eV) due to oxygen deficient defects (F, F+, and F++ centers) is reported with different UV excitations. A comparative study of plasma in deionized water and air ambient reveals enhanced line broadening and higher electron density in water confined plasma compared to that in air, in agreement with radiative recombination model. The temporal dependence of spectral radiant energy density of plasma is also discussed.
Broadband electromagnetic wave absorbers prepared by grading magnetic powder density
Authors: Itoh Masahiro , Terada Masao , Shogano Fumiyoshi , Machida Ken-ichi
Published: September 2010

Resin compacts including iron-based magnetic powders were prepared using a centrifugal molding technique. Energy dispersive x-ray analyses demonstrated the formation of a concentration gradient of the magnetic powder in the resin compacts. The resultant concentration-graded resin compacts exhibited better broadband electromagnetic wave absorption than the homogeneous resin compacts prepared as a reference. This absorption ability was further enhanced by attaching a urethane foam plate to the absorber surface.
Dielectric confinement in quantum dots of arbitrary shape within the local spin density approximation: Diluted regimes in elongated quantum dots
Authors: Movilla J. L. , Pi M. , Planelles J.
Published: September 2010

We propose a simplified and computationally feasible model accounting for the dielectric confinement in arbitrarily shaped many-electron quantum dots, within the local spin density approximation. The model yields quite a good agreement with full configuration interaction calculations including exact dielectric confinement. The model is used to study the influence of the dielectric confinement on the electronic charge distribution of elongated quantum dots in the low density regime.
Existence and singularities of solutions to an integrable equation governing short-waves in a long-wave model
Authors: Fu Yuxia , Yin Zhaoyang
Published: September 2010

This paper is concerned with the Cauchy problem of a new periodic integrable equation governing short-waves in a long-wave model. We first establish the local well-posedness for its derivative equation, which correspondingly implies the local existence and multivaluedness of solutions to the model. Then, we obtain a blow up scenario for these solutions. Finally, we show that the equation has strong solutions that develop singularities in finite time.
Mechanically generated surface chirality: Control of chiral strength
Authors: Ferjani Sameh , Pendery Joel , Rosenblatt Charles
Published: September 2010

A substrate coated with an achiral polyimide alignment layer was scribed with the stylus of an atomic force microscope having a line-to-line force profile FAFBFCFAFBFC…. The strength of the resulting chiral surface was examined using the nematic liquid crystal electroclinic effect induced by the surface. The magnitude of the electroclinic effect was found to increase with increasing scribing force, which suggests a method for controlling the chiral strength. Additionally, the electroclinic magnitude divided by the rms surface roughness was approximately constant with scribing force, suggesting that the azimuthal anchoring strength coefficient is nearly independent of the scribing force.
Biexponential theory of Drude dissipation via hierarchical quantum master equation
Authors: Tian Bao-Ling , Ding Jin-Jin , Xu Rui-Xue , Yan YiJing
Published: September 2010

A nonperturbative quantum dissipation theory is developed based on an optimal construction of biexponential Drude bath correlation function for its influence on the system dynamics. It is an advanced hierarchical quantum master equation approach, aiming at a numerically efficient non-Markovian quantum dissipation propagator, with the support of a convenient criterion to estimate in advance its accuracy for general systems. Compared to its low level, single-exponential counterpart [R. X. Xu et al., J. Chem. Phys. 131, 214111 (2009)], the present theory remarkably improves the applicability range over all-parameter space, as tested critically with electron transfer and frequency-dispersed transient absorption of exciton dimer model systems.
Prediction for room-temperature half-metallic ferromagnetism in the half-fluorinated single layers of BN and ZnO
Authors: Kan E. J. , Xiang H. J. , Wu F. , Tian C. , Lee C. , Yang J. L. , Whangbo M.-H.
Published: September 2010

On the basis of density functional calculations we explored the possibility that BN and ZnO single layers can become ferromagnetic at room temperature and half-metallic upon fluorine adsorption. Fluorine atoms form stable bonds only with the B and Zn atoms on the graphenelike BN and ZnO single layers, respectively, and the resulting fluorinated BN and ZnO single layers are expected to become ferromagnetic half metals with Curie temperatures around room temperature. The fluorination of semiconductor single layers can lead to interesting spintronics and functional applications.
First-principles study of fluorine-doped zinc oxide
Authors: Liu Bo , Gu Mu , Liu Xiaolin , Huang Shiming , Ni Chen
Published: September 2010

We present first-principles calculations for fluorine-doped zinc oxide (ZnO:F) by using density-functional theory. Under O-poor condition, fluorine substitution for oxygen (FO) is energetically favorable in ZnO. FO can effectively diminish oxygen vacancies. With high fluorine concentration, fluorine interstitial (Fi) may appear. The high transition energies of FO and Fi suggest that FO and Fi could act as deep donor and acceptor which cannot provide free carriers in ZnO at room temperature. The increase of carriers and mobility in ZnO:F could not contribute from deep donor FO, but may be due to the surface passivation effect of fluorine.
Pattern formation in drying droplets of polyelectrolyte and salt
Authors: Kaya D. , Belyi V. A. , Muthukumar M.
Published: September 2010

We have discovered spectacular patterns formed by drying aqueous drops of sodium poly(styrene sulfonate) containing fixed amounts of sodium chloride. Crystallization of salt molecules takes place at a critical concentration and several factors such as the polyelectrolyte concentration and humidity affect the final patterns formed. The observed patterns include concentric rings, needle-like structures, chains of triangular-shaped crystallites, etc. We describe the observed phenomenology accompanied by a theoretical model for the occurrence of concentric rings.
Effects of past, present, and future ocean carbon dioxide concentrations on the growth and survival of larval shellfish
Authors: Talmage Stephanie C. , Gobler Christopher J.
Published: September 2010

The combustion of fossil fuels has enriched levels of CO2in the world’s oceans and decreased ocean pH. Although the continuation of these processes may alter the growth, survival, and diversity of marine organisms that synthesize CaCO3shells, the effects of ocean acidification since the dawn of the industrial revolution are not clear. Here we present experiments that examined the effects of the ocean’s past, present, and future (21st and 22nd centuries) CO2concentrations on the growth, survival, and condition of larvae of two species of commercially and ecologically valuable bivalve shellfish (Mercenaria mercenariaandArgopecten irradians). Larvae grown under near preindustrial CO2concentrations (250 ppm) displayed significantly faster growth and metamorphosis as well as higher survival and lipid accumulation rates compared with individuals reared under modern day CO2levels. Bivalves grown under near preindustrial CO2levels displayed thicker, more robust shells than individuals grown at present CO2concentrations, whereas bivalves exposed to CO2levels expected later this century had shells that were malformed and eroded. These results suggest that the ocean acidification that has occurred during the past two centuries may be inhibiting the development and survival of larval shellfish and contributing to global declines of some bivalve populations.
Early understandings of the link between agents and order
Authors: Newman George E. , Keil Frank C. , Kuhlmeier Valerie A. , Wynn Karen
Published: September 2010

The world around us presents two fundamentally different forms of patterns: those that appear random and those that appear ordered. As adults we appreciate that these two types of patterns tend to arise from very different sorts of causal processes. Typically, we expect that, whereas agents can increase the orderliness of a system, inanimate objects can cause only increased disorder. Thus, one major division in the world of causal entities is between those that are capable of “reversing local entropy” and those that are not. In the present studies we find that sensitivity to the unique link between agents and order emerges quite early in development. Results from three experiments suggest that by 12 mo of age infants associate agents with the creation of order and inanimate objects with the creation of disorder. Such expectations appear to be robust into children's preschool years and are hypothesized to result from a more general understanding that agents causally intervene on the world in fundamentally different ways from inanimate objects.
Bihemispheric foundations for human speech comprehension
Authors: Bozic Mirjana , Tyler Lorraine K. , Ives David T. , Randall Billi , Marslen-Wilson William D.
Published: September 2010

Emerging evidence from neuroimaging and neuropsychology suggests that human speech comprehension engages two types of neurocognitive processes: a distributed bilateral system underpinning general perceptual and cognitive processing, viewed as neurobiologically primary, and a more specialized left hemisphere system supporting key grammatical language functions, likely to be specific to humans. To test these hypotheses directly we covaried increases in the nonlinguistic complexity of spoken words [presence or absence of an embedded stem, e.g.,
claim
(
clay
)] with variations in their linguistic complexity (presence of inflectional affixes, e.g.,
play+ed
). Nonlinguistic complexity, generated by the on-line competition between the full word and its onset-embedded stem, was found to activate both right and left fronto-temporal brain regions, including bilateral BA45 and -47. Linguistic complexity activated left-lateralized inferior frontal areas only, primarily in BA45. This contrast reflects a differentiation between the functional roles of a bilateral system, which supports the basic mapping from sound to lexical meaning, and a language-specific left-lateralized system that supports core decompositional and combinatorial processes invoked by linguistically complex inputs. These differences can be related to the neurobiological foundations of human language and underline the importance of bihemispheric systems in supporting the dynamic processing and interpretation of spoken inputs.
Controlled enzymatic production of astrocytic hydrogen peroxide protects neurons from oxidative stress via an Nrf2-independent pathway
Authors: Haskew-Layton Renée E. , Payappilly Jimmy B. , Smirnova Natalya A. , Ma Thong C. , Chan Kelvin K. , Murphy Timothy H. , Guo Hengchang , Langley Brett , Sultana Rukhsana , Butterfield D. Allan , Santagata Sandro , Alldred Melissa J. , Gazaryan Irina G. , Bell George W. , Ginsberg Stephen D. , Ratan Rajiv R.
Published: September 2010

Neurons rely on their metabolic coupling with astrocytes to combat oxidative stress. The transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) appears important for astrocyte-dependent neuroprotection from oxidative insults. Indeed, Nrf2 activators are effective in stroke, Parkinson disease, and Huntington disease models. However, key endogenous signals that initiate adaptive neuroprotective cascades in astrocytes, including activation of Nrf2-mediated gene expression, remain unclear. Hydrogen peroxide (H
2
O
2
) plays an important role in cell signaling and is an attractive candidate mediator of adaptive responses in astrocytes. Here we determine (
i
) the significance of H
2
O
2
in promoting astrocyte-dependent neuroprotection from oxidative stress, and (
ii
) the relevance of H
2
O
2
in inducing astrocytic Nrf2 activation. To control the duration and level of cytoplasmic H
2
O
2
production in astrocytes cocultured with neurons, we heterologously expressed the H
2
O
2
-producing enzyme
Rhodotorula gracilis
D-amino acid oxidase (rgDAAO) selectively in astrocytes. Exposure of rgDAAO-astrocytes to D-alanine lead to the concentration-dependent generation of H
2
O
2
. Seven hours of low-level H
2
O
2
production (∼3.7 nmol·min·mg protein) in astrocytes protected neurons from oxidative stress, but higher levels (∼130 nmol·min·mg protein) were neurotoxic. Neuroprotection occurred without direct neuronal exposure to astrocyte-derived H
2
O
2
, suggesting a mechanism specific to astrocytic intracellular signaling. Nrf2 activation mimicked the effect of astrocytic H
2
O
2
yet H
2
O
2
-induced protection was independent of Nrf2. Astrocytic protein tyrosine phosphatase inhibition also protected neurons from oxidative death, representing a plausible mechanism for H
2
O
2
-induced neuroprotection. These findings demonstrate the utility of rgDAAO for spatially and temporally controlling intracellular H
2
O
2
concentrations to uncover unique astrocyte-dependent neuroprotective mechanisms.
Defining the mechanism of polymerization in the serpinopathies
Authors: Ekeowa Ugo I. , Freeke Joanna , Miranda Elena , Gooptu Bibek , Bush Matthew F. , Pérez Juan , Teckman Jeff , Robinson Carol V. , Lomas David A.
Published: September 2010

The serpinopathies result from the ordered polymerization of mutants of members of the serine proteinase inhibitor (serpin) superfamily. These polymers are retained within the cell of synthesis where they cause a toxic gain of function. The serpinopathies are exemplified by inclusions that form with the common severe Z mutant of
α
1
-antitrypsin that are associated with liver cirrhosis. There is considerable controversy as to the pathway of serpin polymerization and the structure of pathogenic polymers that cause disease. We have used synthetic peptides, limited proteolysis, monoclonal antibodies, and ion mobility-mass spectrometry to characterize the polymerogenic intermediate and pathological polymers formed by Z
α
1
-antitrypsin. Our data are best explained by a model in which polymers form through a single intermediate and with a reactive center loop-β-sheet A linkage. Our data are not compatible with the recent model in which polymers are linked by a β-hairpin of the reactive center loop and strand 5A. Understanding the structure of the serpin polymer is essential for rational drug design strategies that aim to block polymerization and so treat
α
1
-antitrypsin deficiency and the serpinopathies.
IFN-γ produced by CD8 T cells induces T-bet–dependent and –independent class switching in B cells in responses to alum-precipitated protein vaccine
Authors: Mohr Elodie , Cunningham Adam F. , Toellner Kai-Michael , Bobat Saeeda , Coughlan Ruth E. , Bird Roger A. , MacLennan Ian C. M. , Serre Karine
Published: September 2010

Alum-precipitated protein (alum protein) vaccines elicit long-lasting neutralizing antibody responses that prevent bacterial exotoxins and viruses from entering cells. Typically, these vaccines induce CD4 T cells to become T helper 2 (Th2) cells that induce Ig class switching to IgG1. We now report that CD8 T cells also respond to alum proteins, proliferating extensively and producing IFN-γ, a key Th1 cytokine. These findings led us to question whether adoptive transfer of antigen-specific CD8 T cells alters the characteristic CD4 Th2 response to alum proteins and the switching pattern in responding B cells. To this end, WT mice given transgenic ovalbumin (OVA)-specific CD4 (OTII) or CD8 (OTI) T cells, or both, were immunized with alum-precipitated OVA. Cotransfer of antigen-specific CD8 T cells skewed switching patterns in responding B cells from IgG1 to IgG2a and IgG2b. Blocking with anti–IFN-γ antibody largely inhibited this altered B-cell switching pattern. The transcription factor T-bet is required in B cells for IFN-γ–dependent switching to IgG2a. By contrast, we show that this transcription factor is dispensable in B cells both for IFN-γ–induced switching to IgG2b and for inhibition of switching to IgG1. Thus, T-bet dependence identifies distinct transcriptional pathways in B cells that regulate IFN-γ–induced switching to different IgG isotypes.
Autotrophic ammonia oxidation by soil thaumarchaea
Authors: Zhang Li-Mei , Offre Pierre R. , He Ji-Zheng , Verhamme Daniel T. , Nicol Graeme W. , Prosser James I.
Published: September 2010

Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, rather than growing autotrophically. In this soil microcosm study, stable isotope probing was used to demonstrate incorporation of
13
C-enriched carbon dioxide into the genomes of thaumarchaea possessing two functional genes:
amoA
, encoding a subunit of ammonia monooxygenase that catalyses the first step in ammonia oxidation; and
hcd
, a key gene in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle, which has been found so far only in archaea. Nitrification was accompanied by increases in archaeal
amoA
gene abundance and changes in
amoA
gene diversity, but no change was observed in bacterial
amoA
genes. Archaeal, but not bacterial,
amoA
genes were also detected in
13
C-labeled DNA, demonstrating inorganic CO
2
fixation by archaeal, but not bacterial, ammonia oxidizers. Autotrophic archaeal ammonia oxidation was further supported by coordinate increases in
amoA
and
hcd
gene abundance in
13
C-labeled DNA. The results therefore provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate autotrophic growth of ammonia oxidizing archaea in soil.
Conservation, development, and function of a cement gland-like structure in the fish
Astyanax mexicanus
Authors: Pottin Karen , Hyacinthe Carole , Rétaux Sylvie
Published: September 2010

The larvae of the fish
Astyanax mexicanus
transiently develop a flat and adhesive structure on the top of their heads that we have called “the casquette” (cas, meaning “hat”). We hypothesized that the cas may be a teleostean homolog of the well-studied
Xenopus
cement gland, despite their different positions and structures. Here we show that the cas has an ectodermal origin, secretes mucus, expresses bone morphogenic protein 4 (
Bmp4
) and pituitary homeobox 1/2 (
Pitx1/2
), is innervated by the trigeminal ganglion and serotonergic raphe neurons, and has a role in the control and the development of the larval swimming behavior. These developmental, connectivity, and behavioral functional data support a level of deep homology between the frog cement gland and the
Astyanax
cas and suggest that attachment organs can develop in varied positions on the head ectoderm by recruitment of a Bmp4-dependent developmental module. We also show that the attachment organs of the cichlid
Tilapia mariae
larvae display some of these features. We discuss the possibility that these highly diversified attachment glands may be ancestral to chordates and have been lost repetitively in many vertebrate classes.
Retina is structured to process an excess of darkness in natural scenes
Authors: Ratliff Charles P. , Borghuis Bart G. , Kao Yen-Hong , Sterling Peter , Balasubramanian Vijay
Published: September 2010

Retinal ganglion cells that respond selectively to a dark spot on a brighter background (OFF cells) have smaller dendritic fields than their ON counterparts and are more numerous. OFF cells also branch more densely, and thus collect more synapses per visual angle. That the retina devotes more resources to processing dark contrasts predicts that natural images contain more dark information. We confirm this across a range of spatial scales and trace the origin of this phenomenon to the statistical structure of natural scenes. We show that the optimal mosaics for encoding natural images are also asymmetric, with OFF elements smaller and more numerous, matching retinal structure. Finally, the concentration of synapses within a dendritic field matches the information content, suggesting a simple principle to connect a concrete fact of neuroanatomy with the abstract concept of information: equal synapses for equal bits.
Next-generation protein-rich potato expressing the seed protein gene
AmA1
is a result of proteome rebalancing in transgenic tuber
Authors: Chakraborty Subhra , Chakraborty Niranjan , Agrawal Lalit , Ghosh Sudip , Narula Kanika , Shekhar Shubhendu , Naik Prakash S. , Pande P. C. , Chakrborti Swarup Kumar , Datta Asis
Published: September 2010

Protein deficiency is the most crucial factor that affects physical growth and development and that increases morbidity and mortality especially in developing countries. Efforts have been made to improve protein quality and quantity in crop plants but with limited success. Here, we report the development of transgenic potatoes with enhanced nutritive value by tuber-specific expression of a seed protein, AmA1 (Amaranth Albumin 1), in seven genotypic backgrounds suitable for cultivation in different agro-climatic regions. Analyses of the transgenic tubers revealed up to 60% increase in total protein content. In addition, the concentrations of several essential amino acids were increased significantly in transgenic tubers, which are otherwise limited in potato. Moreover, the transgenics also exhibited enhanced photosynthetic activity with a concomitant increase in total biomass. These results are striking because this genetic manipulation also resulted in a moderate increase in tuber yield. The comparative protein profiling suggests that the proteome rebalancing might cause increased protein content in transgenic tubers. Furthermore, the data on field performance and safety evaluation indicate that the transgenic potatoes are suitable for commercial cultivation. In vitro and in vivo studies on experimental animals demonstrate that the transgenic tubers are also safe for human consumption. Altogether, these results emphasize that the expression of AmA1 is a potential strategy for the nutritional improvement of food crops.
Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism
Authors: Herrou Julien , Bompard Coralie , Wintjens René , Dupré Elian , Willery Eve , Villeret Vincent , Locht Camille , Antoine Rudy , Jacob-Dubuisson Françoise
Published: September 2010

Two-component sensory transduction systems control important bacterial programs. In
Bordetella pertussis
, expression of the virulence regulon is controlled by the unorthodox BvgAS two-component system. BvgS is the prototype of a family of sensor-kinases that harbor periplasmic domains homologous to bacterial solute-binding proteins. Although BvgAS is active under laboratory conditions, no activating signal has been identified, only negative modulators. Here we show that the second periplasmic domain of BvgS interacts with modulators and adopts a Venus flytrap (VFT) fold. X-ray crystallography reveals that the two lobes of VFT2 delimitate a ligand-binding cavity enclosing fortuitous ligands. Most substitutions of putative ligand-binding residues in the VFT2 cavity keep BvgS active, and alteration of the cavity's electrostatic potential affects responsiveness to modulation. The crystal structure of this VFT2 variant conferring constitutive kinase activity to BvgS shows a closed cavity with another nonspecific ligand. Thus, VFT2 is closed and active without a specific agonist ligand, in contrast to typical VFTs. Modulators are antagonists of VFT2 that interrupt signaling. BvgAS is active for most of the
B. pertussis
infectious cycle, consistent with the proposed mechanism.
Sexual dimorphism of gonadal structure and gene expression in germ cell-deficient loach, a teleost fish
Authors: Fujimoto Takafumi , Nishimura Toshiya , Goto-Kazeto Rie , Kawakami Yutaka , Yamaha Etsuro , Arai Katsutoshi
Published: September 2010

Germ cell-deficient fish usually develop as phenotypic males. Thus, the presence of germ cells is generally considered to be essential for female gonadal differentiation or the maintenance of ovarian structure. However, little is known of the role of germ cells in the determination of the sexual fate of gonadal somatic cells. We have established an inducible germ cell deficiency system in the loach (
Misgurnus anguillicaudatus
, Cypriniformes: Cobitidae), a small freshwater fish, using knockdown of the
dead end
gene with a morpholino antisense oligonucleotide. Interestingly, loach lacking germ cells could develop as either phenotypic males or females, as characterized morphologically by the presence or absence of bony plates in the pectoral fins, respectively. The phenotypic males and females had testicular and ovarian structures, respectively, but lacked germ cells. Gene expression patterns in these male and female germ cell-deficient gonads were essentially the same as those in gonads of normal fish. Our observations indicate that sexually dimorphic gonads can develop in germ cell-deficient loach. In contrast to the situation in other model fish species, the gonadal somatic cells in phenotypic females autonomously differentiated into ovarian tissues and also played a role in the maintenance of gonadal structure. On the basis of our observations, we propose two possible models to explain the role of germ cells in sex determination in fish.
Direct search for a ferromagnetic phase in a heavily overdoped nonsuperconducting copper oxide
Authors: Sonier J. E. , Kaiser C. V. , Pacradouni V. , Sabok-Sayr S. A. , Cochrane C. , MacLaughlin D. E. , Komiya S. , Hussey N. E.
Published: September 2010

The doping of charge carriers into the CuO
2
planes of copper oxide Mott insulators causes a gradual destruction of antiferromagnetism and the emergence of high-temperature superconductivity. Optimal superconductivity is achieved at a doping concentration
p
beyond which further increases in doping cause a weakening and eventual disappearance of superconductivity. A potential explanation for this demise is that ferromagnetic fluctuations compete with superconductivity in the overdoped regime. In this case, a ferromagnetic phase at very low temperatures is predicted to exist beyond the doping concentration at which superconductivity disappears. Here we report on a direct examination of this scenario in overdoped La

2-
x

Sr

x

CuO
4
using the technique of muon spin relaxation. We detect the onset of static magnetic moments of electronic origin at low temperature in the heavily overdoped nonsuperconducting region. However, the magnetism does not exist in a commensurate long-range ordered state. Instead it appears as a dilute concentration of static magnetic moments. This finding places severe restrictions on the form of ferromagnetism that may exist in the overdoped regime. Although an extrinsic impurity cannot be absolutely ruled out as the source of the magnetism that does occur, the results presented here lend support to electronic band calculations that predict the occurrence of weak localized ferromagnetism at high doping.
Tumors induce complex DNA damage in distant proliferative tissues in vivo
Authors: Redon Christophe E. , Dickey Jennifer S. , Nakamura Asako J. , Kareva Irina G. , Naf Dieter , Nowsheen Somaira , Kryston Thomas B. , Bonner William M. , Georgakilas Alexandros G. , Sedelnikova Olga A.
Published: September 2010

That tumors cause changes in surrounding tissues is well documented, but whether they also affect distant tissues is uncertain. Such knowledge may be important in understanding the relationship between cancer and overall patient health. To address this question, we examined tissues distant to sites of implanted tumors for genomic damage using cohorts of C57BL/6 and BALB/c mice with early-stage subcutaneous syngeneic grafts, specifically, B16 melanoma, MO5076 sarcoma, and COLON26 carcinoma. Here we report that levels of two serious types of DNA damage, double-strand breaks (DSBs) measured by γ-H2AX focus formation and oxidatively induced non-DSB clustered DNA lesions (OCDLs), were elevated in tissues distant from the tumor site in tumor-bearing mice compared with their age- and sex-matched controls. Most affected were crypts in the gastrointestinal tract organs and skin, both highly proliferative tissues. Further investigation revealed that, compared with controls, tumor-bearing mice contained elevated amounts of activated macrophages in the distant gastrointestinal tissues, as well as elevated serum levels of several cytokines. One of these cytokines, CCL2/MCP-1, has been linked to several inflammation-related conditions and macrophage recruitment, and strikingly, CCL2-deficient mice lacked increased levels of DSBs and OCDLs in tissues distant from implanted tumors. Thus, this study is unique in being a direct demonstration that the presence of a tumor may induce a chronic inflammatory response in vivo, leading to increased systemic levels of DNA damage. Importantly, these findings suggest that tumors may have more profound effects on their hosts than heretofore expected.
Regulation of extrafloral nectar secretion by jasmonates in lima bean is light dependent
Authors: Radhika Venkatesan , Kost Christian , Mithöfer Axel , Boland Wilhelm
Published: September 2010

To maximize fitness, plants need to perceive changes in their light environment and adjust their physiological responses accordingly. Whether and how such changes also affect the regulation of their defense responses against herbivores remains largely unclear. We addressed this issue by studying the secretion of extrafloral nectar (EFN) in lima bean (
Phaseolus lunatus
), which is known to be activated by the phytohormone jasmonic acid (JA) and functions as an indirect defense mechanism against herbivores. We found that the plant’s EFN secretion in response to JA was light dependent: In the dark, JA reduced EFN secretion, whereas under light conditions, JA induced EFN secretion relative to controls. This modulation was affected by the light’s spectral composition [i.e., ratio of red to far-red (R:FR) radiation], but not light intensity. These findings demonstrate a unique differential effect of JA on EFN secretion depending on the ambient light conditions. Interestingly, treatment with the isoleucine–JA conjugate (JA–Ile) enhanced EFN secretion under light conditions yet did not reduce EFN secretion in the dark. Moreover, inhibition of Ile biosynthesis in light-exposed plants significantly decreased the EFN secretion rate. This reduction could be recovered by additional application of JA–Ile, suggesting that JA–Ile is the active compound required to up-regulate EFN secretion. Finally, experiments with mechanically damaged plants revealed that light was required for the formation of JA–Ile, but not of JA. These results demonstrate that in lima bean, the light environment modulates the plant’s response to jasmonates as well as JA–Ile biosynthesis, which controls the subsequent EFN secretion.