bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of the electrocaloric effect in a PbMg2/3Nb1/3O3-PbTiO3 relaxor thin film
Authors: Correia T. M. , Young J. S. , Whatmore R. W. , Scott J. F. , Mathur N. D. , Zhang Q.
Published: November 2009

Permittivity measurements of a 0.93PMN-0.07PT thin film show a broad maximum near 35 °C, and an anomaly at the depolarizing temperature Td=18 °C on heating only, suggesting a dipolar glass-relaxor phase transition. No structural phase transition at 18 °C is apparent from ferroelectric hysteresis loops taken on field cooling and field heating. These loops show the thermal hysteresis expected for ferroelectric relaxors, which has not hitherto been experimentally verified in PbMg2/3Nb1/3O3-PbTiO3 thin films. Our data suggest the intriguing possibility of a giant electrocaloric effect (ΔT=9 K, ΔE=720 kV cm−1) at and near room temperature.
Do the interfacial fluidities of cationic reverse micelles enhance with an increase in the water content?
Authors: Mali K. S. , Dutt G. B.
Published: November 2009

The role of cosurfactant and water on the interfacial fluidities of reverse micelles formed with the cationic surfactant, cetyltrimethylammonium bromide (CTAB) has been examined by measuring the fluorescence anisotropies of two structurally similar ionic solutes, rhodamine 110 and fluorescein. For this purpose, reverse micellar systems with (CTAB/1-pentanol/cyclohexane/water) and without a cosurfactant (CTAB/chloroform–isooctane/water) have been chosen. In this study, the mole ratio of water to surfactant W has been varied in the region of 4–25. Experimental results indicate that the average reorientation time of the probe, which is a measure of the fluidity near the interfacial region, decreases by a factor of 1.5 and 1.4 for rhodamine 110 and fluorescein, respectively, as W goes up from 5 to 25 in CTAB/1-pentanol/cyclohexane/water reverse micellar system. In contrast, the average reorientation time, remains invariant for both the probe molecules in CTAB/chloroform–isooctane/water reverse micellar system despite an increase in W from 4 to 24. In case of CTAB/1-pentanol/cyclohexane/water reverse micellar system, the added water binds to bromide counter ions and also the hydroxyl groups of the cosurfactant, 1-pentanol, which results in an increase in the effective head group area. Such an increase in the effective head group area leads to a decrease in the packing parameter, and hence an increase in the interfacial fluidity. On the other hand, in CTAB/chloroform–isooctane/water system, the added water merely hydrates the bromide ions, thereby leaving the effective head group area unchanged. Thus, the interfacial fluidities remain invariant upon the addition of water in the absence of a cosurfactant.
Relationship between band alignment and chemical states upon annealing in HfSiON/SiON stacked films on Si substrates
Authors: Tanimura T. , Toyoda S. , Kamada H. , Kumigashira H. , Oshima M. , Liu G. L. , Liu Z. , Ikeda K.
Published: November 2009

We have investigated the relationship between band alignment and chemical states in HfSiON/SiON stacked films on Si substrates by photoemission spectroscopy and x-ray absorption spectroscopy. Valence-band maxima mainly derived from N 2p states in HfSiON films are closely related to N–Hf bonding configurations. The valence-band offset for a thick HfSiON film is smaller than that for a thin HfSiON film, due to the amount of N–Hf bonding states. Since N–Hf bonding states decrease upon annealing, thickness dependence of valence-band offset can be eliminated. On the other hand, the conduction-band offset does not depend on either the thickness or annealing.
Chaoticity of the blood cell production system
Authors: Rudnicki Ryszard
Published: November 2009

We present a structured model of stem cells given by a partial differential equation. This equation generates a semiflow acting on the set of densities. We show that this semiflow possesses an invariant exact measure positive on open sets. From this it follows that the system is chaotic, i.e., it has dense trajectories and each trajectory is unstable.
X-ray magnetic circular dichroism studies of Fe doped fullerene and highly oriented pyrolytic graphite
Authors: Kumar Amit , Thakur P. , Brookes N. B. , Avasthi D. K.
Published: November 2009

We report the x-ray magnetic circular dichroism (XMCD) studies on Fe doped fullerene thin film and bulk highly oriented pyrolytic graphite. The element-specific hysteresis curves were recorded by measuring the XMCD at the Fe L3 edge as a function of the applied field strength at different temperatures. These investigations suggest that Fe doped fullerene is ferromagnetic at room temperature, while Fe atoms are driven to a nonmagnetic/paramagnetic state with the interaction of graphite matrix.
Small-amplitude perturbations in the three-dimensional cylindrical Richtmyer–Meshkov instability
Authors: Lombardini M. , Pullin D. I.
Published: November 2009

We first study the linear stability of an interface between two fluids following the passage of an imploding or exploding shock wave. Assuming incompressible flow between the refracted waves following shock impact, we derive an expression for the asymptotic growth rate for a three-dimensional combination of azimuthal and axial perturbations as a function of the Atwood ratio, the axial and azimuthal wave numbers, the initial radial position and perturbation amplitude of the interface, and the interface velocity gain due to the shock interaction. From the linearized theory, a unified expression for the impulsive asymptotic growth rate in plane, cylindrical, and spherical geometries is obtained which clearly delineates the effects of perturbation growth due to both geometry and baroclinic vorticity deposition. Several different limit cases are investigated, allowing recovery of Mikaelian’s purely azimuthal theory and Richtmyer’s plane model. We discuss the existence of three-dimensional perturbations with zero growth, typical of curvilinear geometries, as first observed by Mikaelian. The effect of shock proximity on the interface growth rate is studied in the case of a reflected shock. Analytical predictions of the effect of the incident shock strength and the perturbation wave numbers are then compared with results obtained from highly resolved numerical simulations of cylindrical imploding Richtmyer–Meshkov instability for ideal gases. A parallel is made with the instability growth in spherical and plane geometry. In particular, we propose a representation of the perturbation growth by considering the volume of the perturbed layer. This volume is found to grow faster in the plane case than in the imploding cylindrical geometry, among other results.
Energy recovery from sugarcane biomass residues: Challenges and opportunities of bio-oil production in the light of second generation biofuels
Authors: Alonso-Pippo W. , Luengo Carlos A. , Felfli F. Fonseca , Garzone Pietro , Cornacchia Giacinto
Published: November 2009

The lack of an alternative energy carrier to electricity with storage capability for use in off-season has to date been an unsolvable question for the sugar agroindustry. The improvement in cogeneration capacity via implementation of condensing extraction steam turbines or biomass integrated gasifier/gas turbine combined cycle and the barriers for their implementation were analyzed. The introduction of a fast pyrolysis (3 tons/h) module (FPM3) as a solution for off-season energy demand in the sugarcane agroindustry was also analyzed. The production cost of 1 ton of bio-oil for FPM3 condition was calculated at 87 USD/ton of bio-oil (0.104 USD/l of bio-oil). The economic feasibility of the FPM3 was estimated, comparing the added values for two alternatives: first alternative regarding the sugar and bioethanol simultaneous production (first generation biofuel production) and second alternative regarding the sugar and bio-oil simultaneous production (second generation biofuel production). Although the highest added value figure for a ton of sugarcane (49.30 USD) was gotten by the second alternative, the bioethanol production for cars fuel continues to be most attractive business option because of large fuel ethanol market demand.
Global mode analysis of axisymmetric bluff-body wakes: Stabilization by base bleed
Authors: Sanmiguel-Rojas E. , Sevilla A. , Martínez-Bazán C. , Chomaz J.-M.
Published: November 2009

The flow around a slender body with a blunt trailing edge is unstable in most situations of interest. Usually the flow instabilities are generated within the wake behind the bluff body, inducing fluctuating forces and introducing the possibility of resonance mechanisms with modes of the structure. Base bleed is a simple and well-known means of stabilizing the wake. In the present research, we investigate the global instability properties of the laminar-incompressible flow that develops behind a cylinder with sharp edges and axis aligned with the free stream using a spectral domain decomposition method. In particular, we describe the flow instability characteristics as a function of the Reynolds number, Re=ρW∞D/μ, and the bleed coefficient, defined as the bleed-to-free-stream velocity ratio, Cb=Wb/W∞, where D is the diameter of the body and ρ and μ the density and viscosity of the free stream, respectively. For a truncated cylinder of aspect ratio L/D=5, where L is the length of the body, our calculations reveal the presence of a first steady bifurcation in the wake at Re≃391, as well as a second oscillatory one at Re≃715 with an associated Strouhal number St≃0.0905 for the most unstable azimuthal mode |m|=1. In addition, we report the existence of two critical values of the bleed coefficient Cb1∗(Re,|m|) and Cb2∗(Re,|m|)<Cb1∗, which vary with the aspect ratio of the body, needed to stabilize both the first and second bifurcations in the range of Reynolds numbers under study, 0≤Re≤2200. Finally, the numerical results for the oscillatory mode obtained for a bulletlike body of aspect ratio L/D=2 without base bleed are compared with experiments performed in a wind tunnel using hot-wire anemometry, showing the limitations of using an axisymmetric basic flow at Reynolds numbers higher than the critical one corresponding to the first steady bifurcation in the global stability analysis.
Temperature- and magnetic-field-controlled magnetic pole reversal in a molecular magnetic compound
Authors: Yusuf S. M. , Kumar Amit , Yakhmi J. V.
Published: November 2009

A highly reversible (bipolar) switching of magnetization in a Prussian blue type molecular magnet Cu0.73Mn0.77[Fe(CN)6]⋅zH2O using low magnetic fields is demonstrated. The studied molecular compound also shows both positive and negative magnetocaloric effects below its magnetic ordering temperature. A molecular field theory calculation has also been done to explain the observed temperature dependent magnetization reversal behavior. Possible applications of the magnetic pole reversal phenomenon in magnetoelectronic and magnetocaloric devices such as magnetic memory and magnetic cooling/heating based constant temperature bath have been revealed.
Infrared carpet cloak designed with uniform silicon grating structure
Authors: Xu Xiaofei , Feng Yijun , Hao Yu , Zhao Juming , Jiang Tian
Published: November 2009

Through a particularly chosen coordinate transformation, we propose an optical carpet cloak that only requires homogeneous anisotropic dielectric material. The proposed cloak could be easily imitated and realized by alternative layers of isotropic dielectrics. To demonstrate the cloaking performance, we have designed a two-dimensional version that a uniform silicon grating structure fabricated on a silicon-on-insulator wafer could work as an infrared carpet cloak. The cloak has been validated through full wave electromagnetic simulations, and the nonresonance feature also enables a broadband cloaking for wavelengths ranging from 1372 to 2000 nm.
Nonequilibrium dynamical ferromagnetism of interacting single-molecule magnets
Authors: Liu Gui-Bin , Liu Bang-Gui
Published: November 2009

We propose a nonequilibrium Monte Carlo (MC) approach to explore nonequilibrium dynamical ferromagnetism of interacting single molecule magnets (SMMs). Both quantum spin tunneling and thermally activated spin reversal are implemented in the same MC simulation framework. Applied to a typical example, this simulation method satisfactorily reproduces experimental magnetization curves with experimental parameters. Our results show that both quantum and classical effects are essential to determine the hysteresis behaviors. This method is effective and reliable to gain deep insights into SMMs.
Birefringence-induced mode-dependent tuning of liquid crystal infiltrated InGaAsP photonic crystal nanocavities
Authors: Dündar M. A. , Kicken H. H. J. E. , Silov A. Yu. , Nötzel R. , Karouta F. , Salemink H. W. M. , van der Heijden R. W.
Published: November 2009

Mode-dependent shifts of resonant frequencies of cavities in liquid crystal (LC) infiltrated planar photonic crystals (PhC) are experimentally observed when the temperature is varied across the LC ordering transition. The shifts can be in opposite directions, even for two very similar nearly degenerate modes. The behavior is attributed to the different interactions of the modes with the two components of the refractive index of the LC infill and directly demonstrates that at least a substantial amount of the LC is oriented perpendicular to the PhC-hole axis.
Effect of polarization on spectral switches in the diffraction of stochastic electromagnetic beams
Authors: Pan Liuzhan , Zhao Zhiguo , Ding Chaoliang , Lü Baida
Published: November 2009

We consider the stochastic electromagnetic Gaussian Schell-model (EGSM) beam and show that the polarization of stochastic electromagnetic EGSM beams in the source plane affect spectral switches of diffracted stochastic electromagnetic EGSM beams in the far field. For two cases of fully coherent and partially coherent δxx=δyy the behavior of spectral switches are same in different degrees of polarization of the source.
A relook at the compliance constants in redundant internal coordinates and some new insights
Authors: Vijay Madhav M. , Manogaran S.
Published: November 2009

The compliance constants, the inverse of the force constant matrix elements offer the advantage that any one of them could be calculated directly without the need to calculate the full Hessian. Here we show that such a direct calculation produces accurate results. Since the diagonal G and the compliance matrix elements (Gii,Cii) give unique values that are independent of the other internal coordinates, an internal frequency (ν¯) is defined which could be effectively used to study related molecules. The conventional coordinates used for benzene and cubane give some of the compliance constants, which differ from the values obtained by the direct method by 5%–40%, indicating that the coordinate systems used are deficient. We identify the source of this discrepancy and find a way to form the correct coordinate system in the sense that the Hessian method and the direct method will lead to the same compliance constants. This procedure takes away the simplicity of local coordinates at least in highly symmetric molecules and it is advantageous to have the potential energy distribution in redundant internal coordinates. A method is proposed for this purpose. All these imply that the most satisfactory way of describing the molecular force field is in terms of redundant internal compliance constants.
Effects of surface ligands on the charge memory characteristics of CdSe/ZnS nanocrystals in TiO2 thin film
Authors: Kang Seung-Hee , Kumar Ch. Kiran , Lee Zonghoon , Radmilovic Velimir , Kim Eui-Tae
Published: November 2009

Charge memory characteristics have been systematically studied based on colloidal CdSe/ZnS nanocrystal quantum dots (QDs) embedded in ∼50 nm-thick TiO2 film. Ligand-capped QDs showed negligible electron charging effect, implying that the electron affinity of QDs was significantly decreased by surface dipole layer surrounding QDs. In contrast, the hole charging was affected by the carrier injection blocking effect of the surface ligands. Efficient electron and hole charging characteristics were realized by removing the surface ligands via H2 plasma treatment.
Ab initio study of the excited singlet states of all-trans α,ω-diphenylpolyenes with one to seven polyene double bonds: Simulation of the spectral data within Franck–Condon approximation
Authors: Mizukami Wataru , Kurashige Yuki , Ehara Masahiro , Yanai Takeshi , Itoh Takao
Published: November 2009

Computational simulations of the electronic spectra with ab initio electronic structure calculations are presented for all-trans α,ω-diphenylpolyenes with the polyene double bond number (N) from 1 to 7. A direct comparison of the fluorescence spectra of diphenylpolyenes was made between the results of highly accurate calculations and the experimental data for the systems with various chain lengths. For the realistic simulation of the emission, the total vibrational wave function was described approximately as a direct product of one-dimensional (1D) vibrational wave functions along the normal coordinates that are determined from the vibrational analysis of the ground state. The observed spectra can be reproduced in a computationally efficient way by selecting effective C–C and C=C stretching modes for the constructions of the 1D vibrational Hamiltonians. The electronic structure calculations were performed using the multireference Møller–Plesset perturbation theory with complete active space configuration interaction reference functions. Based on the vertical excitation energies computed, the lowest singlet excited state of diphenylbutadiene is shown to be the optically forbidden 2 A1g state. The simulations of fluorescence spectra involving vibronic coupling effects reveal that the observed strong single C=C band consists of two major degenerate vibrational C=C modes for the shorter diphenylpolyenes with N=3 and 5. Further, the relative intensities of the C–C stretching modes in the fluorescence spectra tend to be larger than those of the C=C stretching modes for the systems with N over 5. This indicates that the geometric differences of the energy minima between the ground (1 A1g) and 2 A1g states grow larger towards the direction of the C–C stretching mode with increasing N.
Purified Si film formation from metallurgical-grade Si by hydrogen plasma induced chemical transport
Authors: Ohmi Hiromasa , Goto Akihiro , Kamada Daiki , Hamaoka Yoshinori , Kakiuchi Hiroaki , Yasutake Kiyoshi
Published: November 2009

Purified Si film is prepared directly from metallurgical-grade Si (MG-Si) by using hydrogen plasma induced chemical transport at subatmospheric pressure. The purification mechanism is based on the different hydrogenation behaviors of the various impurity elements in MG-Si. The prepared Si films clearly had fewer typical metal impurities (Fe, Al, Ti, Cr, Mn, etc.) than those in the MG-Si. In particular, the Fe concentration was drastically reduced from 6900 mass ppm to less than 0.1 mass ppm by one time chemical transport. Furthermore, metal impurity concentrations were further reduced by repeating chemical transport deposition.
Density imbalances and free energy of lipid transfer in supported lipid bilayers
Authors: Xing Chenyue , Faller Roland
Published: November 2009

Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and at the same time have a fundamental structure approximating cell membranes. However, in computer simulations these systems have been studied only rarely up to now. An important property, which cannot be easily determined by molecular dynamics or experiments, is the unsymmetrical density profiles of bilayer leaflets (density imbalance) inflicted on the membrane by the support. This imbalance in the leaflets composition has consequences for membrane structure and phase behavior, and therefore we need to understand it in detail. The free energy can be used to determine the equilibrium structure of a given system. We employ an umbrella sampling approach to obtain the free energy of a lipid crossing the membrane (i.e., lipid flip-flop) as a function of bilayer composition and hence the equilibrium composition of the supported bilayers. In this paper, we use a variant of the coarse-grained Martini model. The results of the free energy calculation lead to a 5% higher density in the proximal leaflet. Recent data obtained by large scale modeling using a water free model suggested that the proximal leaflet had 3.2% more lipids than the distal leaflet [Hoopes et al., J. Chem. Phys. 129, 175102 (2008)]. Our findings are in line with these results. We compare results of the free energy of transport obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences, but the overall picture is consistent. We additionally characterize the intermediate states, which determine the barrier height and therefore the rate of translocation. Calculations on unsupported bilayers are used to validate the approach and to determine the barrier to flip-flop in a free membrane.
Dynamics of multidissociation paths of acetaldehyde photoexcited at 157 nm: Branching ratios, distributions of kinetic energy, and angular anisotropies of products
Authors: Lee Shih-Huang
Published: November 2009

After the photolysis of acetaldehyde (CH3CHO) at 157.6 nm in a molecular-beam apparatus using photofragment translational spectroscopy and vacuum-ultraviolet photoionization to detect products, we observed 13 photofragments associated with six primary dissociation channels and secondary dissociation of products CH3CO and HCO. We measured time-of-flight spectra and spatial angular anisotropies of products and evaluated the branching ratios of products. All photoproducts have nearly isotropic angular distributions with an average |β| value less than 0.05. Primary dissociations to CH3CO+H and CH3+HCO are two major paths; most CH3CO subsequently decomposes spontaneously to CH3+CO and CH2CO+H and most HCO decomposes to H+CO. The ternary dissociation to CH3+CO+H thus accounts for approximately half of the total branching. Dissociations to CH2CO+H2 and CH2+CH2O are observable, but the production of CH4+CO is ambiguous. The productions of C2H3+OH and C2H2+H2O indicate that isomerization from acetaldehyde to ethenol occurs before fragmentation. After photoexcitation to the n-3p state, most acetaldehyde converts into states T1 and S0 but a little isomerizes to ethenol followed by multichannel decomposition.
Spin-dependent intergranular transport in highly spin-polarized Co1−xFexS2 thin films
Authors: Manno M. , Frakie R. , Bolon B. , Leighton C.
Published: November 2009

Magnetic and magnetotransport measurements on polycrystalline thin film Co1−xFexS2, a system that exhibits tunable conduction electron spin polarization in bulk, are reported. The films exhibit a low field hysteretic magnetoresistance (MR) due to spin-dependent intergranular tunneling, thus providing a simple probe of the spin polarization. The MR increases rapidly with x, saturating as the magnetization reaches 1.0μB/Co, demonstrating that high, doping tunable, spin polarization can be readily achieved in thin films synthesized by simple methods. Quantitative estimates yield spin polarizations as high as 90%.
Microbubble-enhanced ultrasound-modulated fluorescence in a turbid medium
Authors: Yuan Baohong , Liu Yuan , Mehl Patrick M. , Vignola Joseph
Published: November 2009

The feasibility of using ultrasound to modulate fluorescence in a turbid medium is still in debate due to the difficulty of detecting the modulated signal. We have demonstrated a system that could detect the weak signals of ultrasound-modulated fluorescence (UMF) by using a broadband lock-in amplifier and microbubbles as enhancement agents. By detecting the microbubble-enhanced UMF signal, a sub-millimeter fluorescent tube submerged in a turbid medium with a depth of 2 cm has been clearly observed with an ultrasonic spatial resolution. The modulation efficiency was significantly improved by using microbubbles, and was found to linearly increase with the drive voltage applied to the ultrasound transducer and the fluorophore concentration within the range adopted in this study. Possible modulation mechanisms are discussed.
Optical properties of 1.3 μm InAs/GaAs bilayer quantum dots with high areal density
Authors: Ngo C. Y. , Yoon S. F. , Lim D. R. , Wong Vincent , Chua S. J.
Published: November 2009

InAs/GaAs bilayer quantum dots (BQDs) are interesting structures for long wavelength emission due to its ability to tune the areal density and dot size separately. However, the need for two sets of growth rate and temperature for the respective QD layers complicates the growth procedures. Furthermore, the highest areal density reported for BQDs with 1.3 μm emission is only in the low 1010 cm−2. In this letter, we investigated the effect of GaAs spacer thickness and monolayer coverage of the active QDs on the optical properties of InAs/GaAs BQDs grown with constant growth rate and temperature. Consequently, high areal density (∼1.2×1011 cm−2) and room temperature photoluminescence emission at 1304 nm with spectral width of 24 meV was obtained.
Intronic enhancers coordinate epithelial-specific looping of the active
CFTR
locus
Authors: Ott Christopher J. , Blackledge Neil P. , Kerschner Jenny L. , Leir Shih-Hsing , Crawford Gregory E. , Cotton Calvin U. , Harris Ann
Published: November 2009

The regulated expression of large human genes can depend on long-range interactions to establish appropriate three-dimensional structures across the locus. The cystic fibrosis transmembrane conductance regulator (
CFTR
) gene, which encompasses 189 kb of genomic DNA, shows a complex pattern of expression with both spatial and temporal regulation. The flanking loci,
ASZ1
and
CTTNBP2
, show very different tissue-specific expression. The mechanisms governing control of
CFTR
expression remain poorly understood, although they are known to involve intronic regulatory elements. Here, we show a complex looped structure of the
CFTR
locus in cells that express the gene, which is absent from cells in which the gene is inactive. By using chromatin conformation capture (3C) with a bait probe at the
CFTR
promoter, we demonstrate close interaction of this region with sequences in the middle of the gene about 100 kb from the promoter and with regions 3′ to the locus that are about 200 kb away. We show that these interacting regions correspond to prominent DNase I hypersensitive sites within the locus. Moreover, these sequences act cooperatively in reporter gene constructs and recruit proteins that modify chromatin structure. The model for
CFTR
gene expression that is revealed by our data provides a paradigm for other large genes with multiple regulatory elements lying within both introns and intergenic regions. We anticipate that these observations will enable original approaches to designing regulated transgenes for tissue-specific gene therapy protocols.
Ecological specialization and population size in a biodiversity hotspot: How rare species avoid extinction
Authors: Williams S. E. , Williams Y. M. , VanDerWal J. , Isaac J. L. , Shoo L. P. , Johnson C. N.
Published: November 2009

Species with narrow environmental niches typically have small geographic ranges. Small range size is, in turn, often associated with low local abundance. Together, these factors should mean that ecological specialists have very small total populations, putting them at high risk of extinction. But some specialized and geographically restricted species are ancient, and some ecological communities have high proportions of rare and specialized endemics. We studied niche characteristics and patterns of distribution and abundance of terrestrial vertebrates in the rainforests of the Australian Wet Tropics (AWT) to identify mechanisms by which rare species might resist extinction. We show that species with narrow environmental niches and small geographic ranges tend to have high and uniform local abundances. The compensation of geographic rarity by local abundance is exact, such that total population size in the rainforest vertebrates of the AWT is independent of environmental specialization. This effect would tend to help equalize extinction risk for specialists and generalists. Phylogenetic analysis suggests that environmental specialists have been gradually accumulating in this fauna, indicating that small range size/environmental specialization can be a successful trait as long as it is compensated for by demographic commonness. These results provide an explanation of how range-restricted specialists can persist for long periods, so that they now form a major component of high-diversity assemblages such as the AWT.
Niche conservatism above the species level
Authors: Hadly Elizabeth A. , Spaeth Paula A. , Li Cheng
Published: November 2009

Traits that enable species to persist in ecological environments are often maintained over time, a phenomenon known as niche conservatism. Here we argue that ecological niches function at levels above species, notably at the level of genus for mammals, and that niche conservatism is also evident above the species level. Using the proxy of geographic range size, we explore changes in the realized niche of North American mammalian genera and families across the major climatic transition represented by the last glacial–interglacial transition. We calculate the mean and variance of range size for extant mammalian genera and families, rank them by range size, and estimate the change in range size and rank during the late Pleistocene and late Holocene. We demonstrate that range size at the genus and family levels was surprisingly constant over this period despite range shifts and extinctions of species within the clades. We suggest that underlying controls on niche conservatism may be different at these higher taxonomic levels than at the species level. Niche conservatism at higher levels seems primarily controlled by intrinsic life history traits, whereas niche conservatism at the species level may reflect underlying environmental controls. These results highlight the critical importance of conserving the biodiversity of mammals at the genus level and of maintaining an adequate species pool within genera.
Oxidative challenges sensitize the capsaicin receptor by covalent cysteine modification
Authors: Chuang Huai-hu , Lin Stephanie
Published: November 2009

The capsaicin receptor TRPV1, one of the major transduction channels in the pain pathway, integrates information from extracellular milieu to control excitability of primary nociceptive neurons. Sensitization of TRPV1 heightens pain sensation to moderately noxious or even innocuous stimuli. We report here that oxidative stress markedly sensitizes TRPV1 in multiple species' orthologs. The sensitization can be recapitulated in excised inside-out membrane patches, reversed by strong reducing agents, and blocked by pretreatment with maleimide that alkylates cysteines. We identify multiple cysteines required for full modulation of TRPV1 by oxidative challenges. Robust oxidative modulation recovers the agonist sensitivity of receptors desensitized by prolonged exposure to capsaicin. Moreover, oxidative modulation operates synergistically with kinase or proton modulations. Thus, oxidative modulation is a robust mechanism tuning TRPV1 activity via covalent modification of evolutionarily conserved cysteines and may play a role in pain sensing processes during inflammation, infection, or tissue injury.
Activation of TRPC1 by STIM1 in ER-PM microdomains involves release of the channel from its scaffold caveolin-1
Authors: Pani Biswaranjan , Ong Hwei Ling , Brazer So-ching W. , Liu Xibao , Rauser Kristina , Singh Brij B. , Ambudkar Indu S.
Published: November 2009

Store-operated Ca
2+
entry (SOCE) is activated by redistribution of STIM1 into puncta in discrete ER-plasma membrane junctional regions where it interacts with and activates store-operated channels (SOCs). The factors involved in precise targeting of the channels and their retention at these specific microdomains are not yet defined. Here we report that caveolin-1 (Cav1) is a critical plasma membrane scaffold that retains TRPC1 within the regions where STIM1 puncta are localized following store depletion. This enables the interaction of TRPC1 with STIM1 that is required for the activation of TRPC1-SOCE. Silencing Cav1 in human submandibular gland (HSG) cells decreased plasma membrane retention of TRPC1, TRPC1-STIM1 clustering, and consequently reduced TRPC1-SOCE, without altering STIM1 puncta. Importantly, activation of TRPC1-SOCE was associated with an increase in TRPC1-STIM1 and a decrease in TRPC1-Cav1 clustering. Consistent with this, overexpression of Cav1 decreased TRPC1-STIM1 clustering and SOCE, both of which were recovered when STIM1 was expressed at higher levels relative to Cav1. Silencing STIM1 or expression of ΔERM-STIM1 or STIM1(
684
EE
685
) mutant prevented dissociation of TRPC1-Cav1 and activation of TRPC1-SOCE. However expression of TRPC1-(
639
KK
640
) with STIM1(
684
EE
685
) restored function and the dissociation of TRPC1 from Cav1 in response to store depletion. Further, conditions that promoted TRPC1-STIM1 clustering and TRPC1-SOCE elicited corresponding changes in SOCE-dependent NFkB activation and cell proliferation. Together these data demonstrate that Cav1 is a critical plasma membrane scaffold for inactive TRPC1. We suggest that activation of TRPC1-SOC by STIM1 mediates release of the channel from Cav1.
Amyloid-β and tau synergistically impair the oxidative phosphorylation system in triple transgenic Alzheimer's disease mice
Authors: Rhein Virginie , Song Xiaomin , Wiesner Andreas , Ittner Lars M. , Baysang Ginette , Meier Fides , Ozmen Laurence , Bluethmann Horst , Dröse Stefan , Brandt Ulrich , Savaskan Egemen , Czech Christian , Götz Jürgen , Eckert Anne
Published: November 2009

Alzheimer's disease (AD) is characterized by amyloid-beta (Aβ)-containing plaques, neurofibrillary tangles, and neuron and synapse loss. Tangle formation has been reproduced in P301L tau transgenic pR5 mice, whereas APP
sw
PS2
N141I
double-transgenic APP152 mice develop Aβ plaques. Cross-breeding generates triple transgenic (
triple
AD) mice that combine both pathologies in one model. To determine functional consequences of the combined Aβ and tau pathologies, we performed a proteomic analysis followed by functional validation. Specifically, we obtained vesicular preparations from
triple
AD mice, the parental strains, and nontransgenic mice, followed by the quantitative mass-tag labeling proteomic technique iTRAQ and mass spectrometry. Within 1,275 quantified proteins, we found a massive deregulation of 24 proteins, of which one-third were mitochondrial proteins mainly related to complexes I and IV of the oxidative phosphorylation system (OXPHOS). Notably, deregulation of complex I was tau dependent, whereas deregulation of complex IV was Aβ dependent, both at the protein and activity levels. Synergistic effects of Aβ and tau were evident in 8-month-old
triple
AD mice as only they showed a reduction of the mitochondrial membrane potential at this early age. At the age of 12 months, the strongest defects on OXPHOS, synthesis of ATP, and reactive oxygen species were exhibited in the
triple
AD mice, again emphasizing synergistic, age-associated effects of Aβ and tau in perishing mitochondria. Our study establishes a molecular link between Aβ and tau protein in AD pathology in vivo, illustrating the potential of quantitative proteomics.
Activation of the abundant nuclear factor poly(ADP-ribose) polymerase-1 by
Helicobacter pylori
Authors: Nossa Carlos W. , Jain Prashant , Tamilselvam Batcha , Gupta Vijay R. , Chen Lin-Feng , Schreiber Valérie , Desnoyers Serge , Blanke Steven R.
Published: November 2009

Modification of eukaryotic proteins is a powerful strategy used by pathogenic bacteria to modulate host cells during infection. Previously, we demonstrated that
Helicobacter pylori
modify an unidentified protein within mammalian cell lysates in a manner consistent with the action of a bacterial ADP-ribosylating toxin. Here, we identified the modified eukaryotic factor as the abundant nuclear factor poly(ADP-ribose) polymerase-1 (PARP-1), which is important in the pathologies of several disease states typically associated with chronic
H. pylori
infection. However, rather than being ADP-ribosylated by an
H. pylori
toxin, the intrinsic poly(ADP-ribosyl) polymerase activity of PARP-1 is activated by a heat- and protease-sensitive
H. pylori
factor, resulting in automodification of PARP-1 with polymers of poly(ADP-ribose) (PAR). Moreover, during infection of gastric epithelial cells,
H. pylori
induce intracellular PAR-production by a PARP-1-dependent mechanism. Activation of PARP-1 by a pathogenic bacterium represents a previously unrecognized strategy for modulating host cell signaling during infection.
Erythrocyte scaffolding protein p55/MPP1 functions as an essential regulator of neutrophil polarity
Authors: Quinn Brendan J. , Welch Emily J. , Kim Anthony C. , Lokuta Mary A. , Huttenlocher Anna , Khan Anwar A. , Kuchay Shafi M. , Chishti Athar H.
Published: November 2009

As mediators of innate immunity, neutrophils respond to chemoattractants by adopting a highly polarized morphology. Efficient chemotaxis requires the formation of one prominent pseudopod at the cell front characterized by actin polymerization, while local inhibition suppresses the formation of rear and lateral protrusions. This asymmetric control of signaling pathways is required for directional migration along a chemotactic gradient. Here, we identify the MAGUK protein p55/MPP1 as a mediator of the frontness signal required for neutrophil polarization. We developed a p55 knockout (p55
−/−
) mouse model, and demonstrate that p55
−/−
neutrophils form multiple transient pseudopods upon chemotactic stimulation, and do not migrate efficiently in vitro. Upon agonist stimulation, p55 is rapidly recruited to the leading edge of neutrophils in mice and humans. Total F-actin polymerization, along with Rac1 and RhoA activation, appear to be normal in p55
−/−
neutrophils. Importantly, phosphorylation of Akt is significantly decreased in p55
−/−
neutrophils upon chemotactic stimulation. The activity of immunoprecipitated phosphatidylinositol 3-kinase γ (PI3Kγ), responsible for chemoattractant-induced synthesis of PIP
3
and Akt phosphorylation, is unperturbed in p55
−/−
neutrophils. Although the total amount of PIP
3
is normal in p55
−/−
neutrophils, PIP
3
is diffusely localized and forms punctate aggregates in activated p55
−/−
neutrophils, as compared to its accumulation at the leading edge membrane in the wild type neutrophils. Together, these results show that p55 is required for neutrophil polarization by regulating Akt phosphorylation through a mechanism that is independent of PI3Kγ activity.
A transcription co-factor integrates cell adhesion and motility with the p53 response
Authors: Coutts Amanda S. , Weston Louise , La Thangue Nicholas B.
Published: November 2009

Despite its obvious importance in tumorigenesis, little information is available on the mechanisms that integrate cell motility and adhesion with nuclear events. JMY is a transcription co-factor that regulates the p53 response. In addition, JMY contains a series of WH2 domains that facilitate in vitro actin nucleation. We show here that the ability of JMY to influence cell motility is dependent, in part, on its control of cadherin expression as well as the WH2 domains. In DNA damage conditions JMY undergoes nuclear accumulation, which drives the p53 transcription response but reduces its influence on cell motility. Consequently, the role of JMY in actin nucleation is less in damaged cells, although the WH2 domains remain functional in the nucleus where they impact on p53 activity. Together, these findings demonstrate a pathway that links the cytoskeleton with the p53 response, and further suggest that the ability of JMY to regulate actin and cadherin is instrumental in coordinating cell motility with the p53 response.
A functional role for the ventrolateral prefrontal cortex in non-spatial auditory cognition
Authors: Cohen Y. E. , Russ B. E. , Davis S. J. , Baker A. E. , Ackelson A. L. , Nitecki R.
Published: November 2009

Spatial and non-spatial sensory information is hypothesized to be evaluated in parallel pathways. In this study, we tested the spatial and non-spatial sensitivity of auditory neurons in the ventrolateral prefrontal cortex (vPFC), a cortical area in the non-spatial pathway. Activity was tested while non-human primates reported changes in an auditory stimulus' spatial or non-spatial features. We found that vPFC neurons were reliably modulated during a non-spatial auditory task but were not modulated during a spatial auditory task. The degree of modulation during the non-spatial task correlated positively with the monkeys' behavioral performance. These results are consistent with the hypotheses that the vPFC is part of a circuit involved in non-spatial auditory processing and that the vPFC plays a functional role in non-spatial auditory cognition.
Essential role of MALT1 protease activity in activated B cell-like diffuse large B-cell lymphoma
Authors: Hailfinger Stephan , Lenz Georg , Ngo Vu , Posvitz-Fejfar Anita , Rebeaud Fabien , Guzzardi Montserrat , Penas Eva-Maria Murga , Dierlamm Judith , Chan Wing C. , Staudt Louis M. , Thome Margot
Published: November 2009

A key element for the development of suitable anti-cancer drugs is the identification of cancer-specific enzymatic activities that can be therapeutically targeted. Mucosa-associated lymphoid tissue transformation protein 1 (MALT1) is a proto-oncogene that contributes to tumorigenesis in diffuse large B-cell lymphoma (DLBCL) of the activated B-cell (ABC) subtype, the least curable subtype of DLBCL. Recent data suggest that MALT1 has proteolytic activity, but it is unknown whether this activity is relevant for tumor growth. Here we report that MALT1 is constitutively active in DLBCL lines of the ABC but not the GCB subtype. Inhibition of the MALT1 proteolytic activity led to reduced expression of growth factors and apoptosis inhibitors, and specifically affected the growth and survival of ABC DLBCL lines. These results demonstrate a key role for the proteolytic activity of MALT1 in DLBCL of the ABC subtype, and provide a rationale for the development of pharmacological inhibitors of MALT1 in DLBCL therapy.
Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield
Authors: Hauben Miriam , Haesendonckx Boris , Standaert Evi , Van Der Kelen Katrien , Azmi Abdelkrim , Akpo Hervé , Van Breusegem Frank , Guisez Yves , Bots Marc , Lambert Bart , Laga Benjamin , De Block Marc
Published: November 2009

Quantitative traits, such as size and weight in animals and seed yield in plants, are distributed normally, even within a population of genetically identical individuals. For example, in plants, various factors, such as local soil quality, microclimate, and sowing depth, affect growth differences among individual plants of isogenic populations. Besides these physical factors, also epigenetic components contribute to differences in growth and yield. The network that regulates crop yield is still not well understood. Although this network is expected to have epigenetic elements, it is completely unclear whether it would be possible to shape the epigenome to increase crop yield. Here we show that energy use efficiency is an important factor in determining seed yield in canola (
Brassica napus
) and that it can be selected artificially through an epigenetic feature. From an isogenic canola population of which the individual plants and their self-fertilized progenies were recursively selected for respiration intensity, populations with distinct physiological and agronomical characteristics could be generated. These populations were found to be genetically identical, but epigenetically different. Furthermore, both the DNA methylation patterns as well as the agronomical and physiological characteristics of the selected lines were heritable. Hybrids derived from parent lines selected for high energy use efficiencies had a 5% yield increase on top of heterosis. Our results demonstrate that artificial selection allows the increase of the yield potential by selecting populations with particular epigenomic states.
On the stability of the Atlantic meridional overturning circulation
Authors: Hofmann Matthias , Rahmstorf Stefan
Published: November 2009

One of the most important large-scale ocean current systems for Earth's climate is the Atlantic meridional overturning circulation (AMOC). Here we review its stability properties and present new model simulations to study the AMOC's hysteresis response to freshwater perturbations. We employ seven different versions of an Ocean General Circulation Model by using a highly accurate tracer advection scheme, which minimizes the problem of numerical diffusion. We find that a characteristic freshwater hysteresis also exists in the predominantly wind-driven, low-diffusion limit of the AMOC. However, the shape of the hysteresis changes, indicating that a convective instability rather than the advective Stommel feedback plays a dominant role. We show that model errors in the mean climate can make the hysteresis disappear, and we investigate how model innovations over the past two decades, like new parameterizations and mixing schemes, affect the AMOC stability. Finally, we discuss evidence that current climate models systematically overestimate the stability of the AMOC.
Genetic and cytological evidence that heterocyst patterning is regulated by inhibitor gradients that promote activator decay
Authors: Risser Douglas D. , Callahan Sean M.
Published: November 2009

The formation of a pattern of differentiated cells from a group of seemingly equivalent, undifferentiated cells is a central paradigm of developmental biology. Several species of filamentous cyanobacteria differentiate nitrogen-fixing heterocysts at regular intervals along unbranched filaments to form a periodic pattern of two distinct cell types. This patterning has been used to exemplify application of the activator-inhibitor model to periodic patterns in biology. The activator-inhibitor model proposes that activators and inhibitors of differentiation diffuse from source cells to form concentration gradients that in turn mediate patterning, but direct visualization of concentration gradients of activators and inhibitors has been difficult. Here we show that the periodic pattern of heterocysts produced by cyanobacteria relies on two inhibitors of heterocyst differentiation, PatS and HetN, in a manner consistent with the predictions of the activator-inhibitor model. Concentration gradients of the activator, HetR, were observed adjacent to heterocysts, the natural source of PatS and HetN, as well as adjacent to vegetative cells that were manipulated to overexpress a gene encoding either of the inhibitors. Gradients of HetR relied on posttranslational decay of HetR. Deletion of both
patS
and
hetN
genes prevented the formation of gradients of HetR, and a derivative of the inhibitors was shown to promote decay of HetR in a concentration-dependent manner. Our results provide strong support for application of the activator-inhibitor model to heterocyst patterning and, more generally, the formation of periodic patterns in biological systems.