bluuebunny/crossref_metadata_2025 huggingface dataset:
Specific Subtypes of Cortical GABA Interneurons Contribute to the Neurovascular Coupling Response to Basal Forebrain Stimulation
Authors: Kocharyan Ara , Fernandes Priscilla , Tong Xin-Kang , Vaucher Elvire , Hamel Edith
Published: September 2007

Neurovascular coupling, or the tight coupling between neuronal activity and regional cerebral blood flow (CBF), seems largely driven by the local processing of incoming afferent signals within the activated area. To test if cortical γ-aminobutyric acid (GABA) interneurons—the local integrators of cortical activity—are involved in this coupling, we stimulated the basalocortical pathway in vivo, monitored cortical CBF, and identified the activated interneurons (c-Fos-immunopositive) and the neuromediators involved in this response. Basal forebrain (BF) stimulation induced ipsilateral increases in CBF and selective activation of layers II to VI somatostatin- and/or neuropeptide Y-containing, as well as layer I GABA interneurons. Nitric oxide synthase interneurons displayed weak bilateral activation, whereas vasoactive intestinal polypeptide- or acetylcholine (ACh)-containing GABA interneurons were not activated. Selective cholinergic deafferentation indicated that ACh released from stimulated BF afferents triggered the CBF response, but the latter was mediated, in part, by the local release of GABA from cholinoceptive cortical interneurons, and through GABA-A receptor-mediated transmission. These data show that activation of specific subsets of GABA interneurons and their GABA-A-mediated effects on neuronal, vascular, and/or astroglial targets are necessary for the full expression of the hemodynamic response to BF stimulation. Further, these findings highlight the importance of understanding the cellular networks and circuitry that underlie hemodynamic signals, as only specific subsets of neurons may be activated by a given stimulus, depending on the afferent inputs they receive and integrate.
Velocity-scalar filtered mass density function for large eddy simulation of turbulent reacting flows
Authors: Sheikhi M. R. H. , Givi P. , Pope S. B.
Published: September 2007

A methodology termed the “velocity-scalar filtered mass density function” (VSFMDF) is developed and implemented for large eddy simulation (LES) of variable-density turbulent reacting flows. This methodology is based on the extension of the previously developed “velocity-scalar filtered density function” method for constant-density flows. In the VSFMDF, the effects of the unresolved subgrid scales (SGS) are taken into account by considering the joint probability density function of the velocity and scalar fields. An exact transport equation is derived for the VSFMDF in which the effects of SGS convection and chemical reaction are in closed forms. The unclosed terms in this equation are modeled in a fashion similar to that in Reynolds-averaged simulation procedures. A set of stochastic differential equations (SDEs) are considered which yield statistically equivalent results to the modeled VSFMDF transport equation. The SDEs are solved numerically by a Lagrangian Monte Carlo procedure in which the Itô-Gikhman character of the SDEs is preserved. The consistency of the proposed SDEs and the convergence of the Monte Carlo solution are assessed. In nonreacting flows, it is shown that the VSFMDF results agree well with those obtained by a “conventional” finite-difference LES procedure in which the transport equations corresponding to the filtered quantities are solved directly. The VSFMDF results are also compared with those obtained by the Smagorinsky closure, and all the results are assessed via comparison with data obtained by direct numerical simulation of a temporally developing mixing layer involving transport of a passive scalar. It is shown that all of the first two moments including the scalar fluxes are predicted well by the VSFMDF. Moreover, the VSFMDF methodology is shown to be able to represent the variable density effects very well. The predictive capabilities of the VSFMDF in reacting flows are further demonstrated by LES of a reacting shear flow. The predictions show favorable agreement with laboratory data, and demonstrate several of the features as observed experimentally.
Structure and properties of the low-lying electronic states of CeC2 and CeC2+
Authors: Wielgus Pawel , Majumdar D. , Roszak Szczepan , Leszczynski Jerzy
Published: September 2007

Theoretical studies on the electronic and thermodynamic properties of several electronic states of CeC2 and CeC2+ have been carried out employing state-of-the-art single- and multireference techniques. The ground and the low-lying electronic states of these two species have been found to possess C2v triangular structures. A B23 state has been found to be the ground state of CeC2 while for CeC2+ A22 is the ground state. The computed electron ionization energy is in excellent agreement with experiment. The experimentally observed thermodynamic properties (dissociation and atomization energies) of reactions involving CeC2 dissociation are corrected using the computed gas-phase properties of the molecule and the partition functions. The bent triplet and singlet state of CeC2 exhibit large dipole moments (7.0–10.5D) and it is consistent with the ionic character (through dative charge transfer) of the cluster in ground and excited states.
Fourth-order nonlinear evolution equations for a capillary-gravity wave packet in the presence of another wave packet in deep water
Authors: Debsarma Suma , Das K. P.
Published: September 2007

Starting from the Zakharov integral equation, two coupled fourth-order nonlinear equations have been derived for the evolution of the amplitudes of two capillary-gravity wave packets propagating in the same direction. The two evolution equations are used to investigate the stability of a uniform capillary-gravity wave train in the presence of another having the same group velocity. The relative changes in phase velocity of each uniform wave train due to the presence of the other one have been shown in figures for different wave numbers. The condition of instability of a wave of greater wavelength in the presence of a wave of shorter wavelength is obtained. It is observed that the instability region for a surface gravity wave train in the presence of a capillary-gravity wave train expands with the increase of wave steepness of the capillary-gravity wave train. It is found that the presence of a uniform capillary-gravity wave train causes an increase in the growth rate of instability of a uniform surface gravity wave train.
Understanding fragility in supercooled Lennard-Jones mixtures. I. Locally preferred structures
Authors: Coslovich D. , Pastore G.
Published: September 2007

The existence of systematic variations of isobaric fragility in different supercooled Lennard-Jones binary mixtures is revealed by molecular dynamics simulations. The connection between fragility and local structures in the bulk is analyzed by means of a Voronoi construction. It is found that clusters of particles belonging to locally preferred structures form slow, long-lived domains, whose spatial extension increases with decreasing temperature. As a general rule, a more rapid growth, upon supercooling, of such domains is associated with a more pronounced super-Arrhenius behavior, and hence to a larger fragility.
Design of ferromagnetic shape memory alloy composite made of Fe and TiNi particles
Authors: Gururaja S. , Taya M. , Kang Y. S.
Published: September 2007

Ferromagnetic shape memory alloy (FSMA) particulate composites have been processed by spark plasma sintering with varying weight fractions of NiTi (51at.% Ni) and Fe powders. An assortment of experimental processing conditions such as temperature, pressure, duration of sintering, and heating rate has been chosen to characterize the relative density and superelasticity behavior of the said FSMA composite. The effective magnetic properties of these processed composites have also been experimentally estimated using vibrating sample magnetometry. An attempt at predicting the effective magnetic properties of the FSMA composite based on Eshelby’s inhomogeneous inclusion method in conjunction with Mori-Tanaka’s mean-field theory for larger concentrations of the ferromagnetic phase has also been presented in this study. The analytical model results thus obtained are compared with experimental data resulting in reasonably good agreement.
Ring current instabilities excited by the energetic oxygen ions
Authors: Kakad A. P. , Singh S. V. , Lakhina G. S.
Published: September 2007

The ring current instabilities driven by the energetic oxygen ions are investigated during the magnetic storm. The electrons and protons are considered to have Maxwellian distributions, while energetic oxygen ions are having loss-cone distribution. Dispersion relation for the quasielectrostatic modes with frequencies ω>ωcp (proton cyclotron frequency) and propagating obliquely to the magnetic field is obtained. Dispersion relation is studied numerically for the storm time ring current parameters and it is found that these instabilities are most prominent during intense storms when the oxygen ions become the dominant constituents of the ring current plasma. For some typical storm-time ring current parameters, these modes can produce quasielectrostatic noise in the range of 17–220Hz, thus providing a possible explanation of the electrostatic noise observed at the inner boundary of the ring current during magnetic storms. Further, these modes can attain saturation electric fields of the order of 100–500μV∕m, and therefore, are expected to scatter O+ ions into the loss-cone giving rise to their precipitation into the atmosphere, thus contributing to the ring current decay.
Modified Morse potential for unification of the pair interactions
Authors: Cheng Longjiu , Yang Jinlong
Published: September 2007

We designed a novel model potential that unifies the pair interactions including the well known Morse and Lennard-Jones potentials. Using two parameters, the interactions at the minimum, short range, and long range of the new model potential can be controlled separately, so the potential is very flexible to fit various systems. It is found that for potentials with similar range with the Lennard-Jones potential at the minimum, due to the difference at the short and long ranges, the favorite structures can be very different, and some previously unknown magic numbers are located.
Flow caused by a square force pulse applied to a sphere immersed in a viscous incompressible fluid
Authors: Felderhof B. U.
Published: September 2007

An analytic solution of the linearized Navier-Stokes equations is presented for the flow of an incompressible viscous fluid around a sphere subjected to a square force pulse. Mixed slip-stick boundary conditions are assumed to hold at the surface of the sphere. The transient flow pattern is expressed in terms of a Stokes stream function. This facilitates visualization of the flow.
Peculiar mean velocity profiles within a porous bed of an open channel
Authors: Pokrajac D. , Manes C. , McEwan I.
Published: September 2007

We present the velocity profile measured within a porous bed below rough turbulent open channel flow. Mean streamwise velocity has a minimum in the top pore, just below the bed surface, and then increases towards a constant value in the deeper pores. We argue that the velocity minimum in the top pore is due to enhanced turbulence generated within the external flow. This produces a flow regime similar to rough turbulent pipe flow, with very efficient momentum extraction. In the deeper pores turbulence intensities are damped so that momentum extraction is less efficient, allowing higher mean velocities to develop.
Angular distribution and dose measurements of hard x-ray emission from intense laser-plasma interaction
Authors: Rao B. S. , Naik P. A. , Arora V. , Khan R. A. , Gupta P. D.
Published: September 2007

An experimental study on hard x-ray Bremsstrahlung radiation due to fast electron generation from a planar solid copper target irradiated by 150 mJ, 45 fs Ti:sapphire laser pulses at I∼1018 W∕cm2 is reported. Angular distribution of the hard x-ray dose rate (hν≥40 keV) is observed to be strongly forward peaked in the direction of target normal with a measured peak value of 40 μSv∕h, at a distance of 500 mm from the target. Two sources of this radiation, one at the laser irradiated target and the other at the chamber wall facing the target, are inferred from the measurements of angular distribution and distance dependence of the x-ray dose rate.
Room temperature gas sensing properties of SnO2/multiwall-carbon-nanotube composite nanofibers
Authors: Yang An , Tao Xiaoming , Wang Rongxing , Lee Shuncheng , Surya Charles
Published: September 2007

Pure SnO2 and SnO2 polycrystalline nanofibers doped with multiwall carbon nanotubes (MWCNTs) are synthesized by electrospinning followed by calcination in air at 500°C. The measurement results by sensors fabricated from these fiber mats at steady state show that the n-type SnO2/MWCNT nanofibers are able to detect carbon monoxide at 50ppm at room temperature, while the pure SnO2 nanofibers are insensitive up to 500ppm. The MWCNT doped SnO2 nanofibers have demonstrated their potentials for wearable room temperature gas sensors with low cost and power consumption.
Surface chemical composition and optical properties of nitrogen-doped Ba0.6Sr0.4TiO3 thin films
Authors: Gao Y. H. , Shen H. , Ma J. H. , Xue J. Q. , Sun J. L. , Meng X. J. , Chu J. H. , Wang P. N.
Published: September 2007

The effect of nitrogen (N) doping on surface chemical composition and optical properties of Ba0.6Sr0.4TiO3 (BST) thin films have been investigated using x-ray photoemission spectroscopy (XPS) and transmittance measurement. It was found that the nitrogen doping induced Ti3+∕4+ states and formed Ti–N bonds in BST films. With lower implantation energy, the oxygen vacancies can be effectively eliminated because of N dopants substitution. Unfortunately, the oxygen vacancies possibly increased when enhance implantation energy. In addition, the N-doped BST films indicated larger amount of perovskite phase and lower content additional phase at surface. The chemical shifts in XPS confirmed the forming of Ba–N and Sr–N bonds in N-doped BST films. The optical properties for as-grown and N-doped BST films were considered at wavelength range from 190to1100nm. The optical constants, including refractive index n and extinction coefficient k, were calculated by fitting transmittance spectra with single Tauc-Lorenz and Lorenz models. The refractive index decreased largely with nitrogen implantation. Oppositely, the extinction coefficient increased with N dopants. The dispersion of refractive index in transparent region agreed well with a single electronic oscillator for all samples. The band gaps of N-doped BST films were much smaller than that of as-grown BST films because of localized N 2p states above the valence band edge.
A heated vapor cell unit for dichroic atomic vapor laser lock in atomic rubidium
Authors: McCarron Daniel J. , Hughes Ifan G. , Tierney Patrick , Cornish Simon L.
Published: September 2007

The design and performance of a compact heated vapor cell unit for realizing a dichroic atomic vapor laser lock (DAVLL) for the D2 transitions in atomic rubidium is described. A 5 cm long vapor cell is placed in a double-solenoid arrangement to produce the required magnetic field; the heat from the solenoid is used to increase the vapor pressure and correspondingly the DAVLL signal. We have characterized experimentally the dependence of important features of the DAVLL signal on magnetic field and cell temperature. For the weaker transitions both the amplitude and gradient of the signal are increased by an order of magnitude.
Inspection of refractive x-ray lenses using high-resolution differential phase contrast imaging with a microfocus x-ray source
Authors: Engelhardt Martin , Baumann Joachim , Schuster Manfred , Kottler Christian , Pfeiffer Franz , Bunk Oliver , David Christian
Published: September 2007

A refractive x-ray lens was characterized using a magnifying cone beam setup for differential phase contrast imaging in combination with a microfocus x-ray tube. Thereby, the differential and the total phase shift of x rays transmitted through the lens were determined. Lens aberrations have been characterized based on these refractive properties.
Strategies for employing surface plasmons in a near field transmission optical readout system
Authors: Gan Choon How , Gbur Greg
Published: September 2007

Strategies to manipulate the surface plasmon-enhanced transmission in a near field optical readout system to achieve super-resolution are investigated. Our numerical simulations demonstrate that modulation and confinement of the plasmon-assisted effects in the readout system can be accomplished through appropriately placed “plasmon pits.” It is found from the simulation results that using short metallic strips embedded in a thin dielectric film instead of a thin metal film for the data structure can aid in localizing the plasmonic effects, thereby improving the resolution of the readout system. In the simulated geometries considered, resolution up to ∼λ∕5 is achievable.
Low temperature deposited L1 FePt–C (001) films with high coercivity and small grain size
Authors: Chen J. S. , Lim B. C. , Hu J. F. , Liu B. , Chow G. M. , Ju G.
Published: September 2007

FePt–C films with high coercivity, (001) texture, and small grain size were deposited on MgO∕CrRu/glass substrate by cosputtering FePt and carbon at 350°C. The out-of-plane coercivity measured at room temperature increased from 9.6to15.1kOe when C concentrations increased from 0% to 15%. Further increasing the C contents to 20% and 25% caused the decrease of coercivity to 13.6 and 11.8kOe, respectively. With C doping, a two-layer structure of FePt–C films was formed and fcc-phase FePt particles were found. By optimizing the sputtering process, FePt–C (001) film with coercivity higher than 14.4kOe and columnar FePt grains of 7.5nm in diameter was obtained, which are suitable for ultrahigh density perpendicular recording.
Tuning ab initio data to scattering length: The aΣ+3 state of KRb
Authors: Soldán Pavel , Špirko Vladimír
Published: September 2007

Interaction energies for the lowest triplet state aΣ+3 of KRb are calculated using high level ab initio methods. The interaction energies are then morphed so that the resulting potential energy curve yields 32 bound states and the correct scattering length for K40Rb87. Calculated vibrational spacings are shown to be in very good agreement with the available experimental Fourier transform and photoassociation vibrational data, but a different numbering scheme has to be used for the experimental vibrational assignment.
Micromechanical resonators fabricated from lattice-matched and etch-selective GaAs∕InGaP∕GaAs heterostructures
Authors: Shim Seung Bo , Chun June Sang , Kang Seok Won , Cho Sung Wan , Cho Sung Woon , Park Yun Daniel , Mohanty Pritiraj , Kim Nam , Kim Jinhee
Published: September 2007

Utilizing lattice-matched GaAs∕InGaP∕GaAs heterostructures, clean micromechanical resonators are fabricated and characterized. The nearly perfect selectivity of GaAs∕InGaP is demonstrated by realizing paddle-shaped resonators, which require significant lateral etching of the sacrificial layer. Doubly clamped beam resonators are also created, with a Q factor as high as 17 000 at 45mK. Both linear and nonlinear behaviors are observed in GaAs micromechanical resonators. Furthermore, a direct relationship between Q factor and resonant frequency is found by controlling the electrostatic force on the paddle-shaped resonators. For beam resonators, the dissipation (Q−1) as a function of temperature obeys a power law similar to silicon resonators.
A PbS nanocrystal-C60 photovoltaic device for infrared light harvesting
Authors: Dissanayake D. M. N. M. , Hatton Ross A. , Lutz Thierry , Giusca Cristina E. , Curry Richard J. , Silva S. R. P.
Published: September 2007

PbS nanocrystal (nc-PbS)-C60 photovoltaic devices are demonstrated, in which nc-PbS function as electron donors, showing infrared photosensitivity up to 1600nm. Annealing nc-PbS is proved to remove capping oleic acid ligands, studied using x-ray photoelectron spectroscopy, significantly improving the short circuit current, open circuit voltage, and fill factor. The device performance is rationalized by quantum confinement in nc-PbS and energy level alignment at the heterojunction based on direct measurements of nc-PbS ionization potential using ultraviolet photoelectron spectroscopy.
Intersubband Raman laser from GaInAs∕AlInAs double quantum wells
Authors: Scheinert Maxi , Sigg Hans , Tsujino Soichiro , Giovannini Marcella , Faist Jérôme
Published: September 2007

We demonstrate optically pumped GaInAs∕AlInAs based intersubband lasers operating at a wavelength of ∼5.5μm applying a simple three-level design. Using a subnanosecond long pulsed excitation laser tunable over the linewidth of the transition from the first level to the third level E13, Raman shift in the lasing spectra was observed. Lasing output power of ∼14W and an internal conversion efficiency between pump and intersubband laser of ∼1.3% at 70K is observed.
Controlled production of emulsion drops using an electric field in a flow-focusing microfluidic device
Authors: Kim Haejune , Luo Dawei , Link Darren , Weitz David A. , Marquez Manuel , Cheng Zhengdong
Published: September 2007

We describe a flexible emulsification method using an electric field to generate droplets in a hydrodynamic-flow-focusing geometry in microchannels. The droplet size is controlled by the ratio of inner and outer flow rates as well as by the electric field. As the voltage increases, the droplet size decreases. A Taylor cone is formed and generates very fine droplets, less than 1μm in diameter. Small inner flow rates and high electric fields are required to form a stable Taylor cone in a dc electric field. An ac electric field produces tiny droplets periodically.
Highly confined energy propagation in a gap waveguide composed of two coupled nanorod chains
Authors: Wang F. M. , Liu H. , Li T. , Wang S. M. , Zhu S. N. , Zhu Jie , Cao Wenwu
Published: September 2007

We propose a subwavelength waveguide composed of two parallel nanorod chains. Based on the finite-difference time-domain analysis, we find that the electromagnetic energy can be highly confined in the gaps of nanorod pairs and transported in the gap waveguide through strong magnetic coupling interaction between neighboring nanorod pairs. In a structure with the rod length of 500nm and the gap size of 100nm, the energy flow cross section of the propagation mode can be restricted to the size of λ∕33×λ∕16 at the frequency of 130.0THz. The corresponding attenuation length of energy propagation reaches 7.2λ. Moreover, these propagation modes exhibit a broad continuous frequency band from zero up to a cutoff frequency ωc∼162.6THz.
Two coexisting mechanisms of dislocation reduction in an AlGaN layer grown using a thin GaN interlayer
Authors: Bai J. , Wang T. , Parbrook P. J. , Wang Q. , Lee K. B. , Cullis A. G.
Published: September 2007

A significant dislocation reduction is achieved in an AlGaN layer grown on an AlN buffer by introducing a thin GaN interlayer. The mechanisms for the dislocation reduction are explored by transmission electron microscopy, energy-dispersive x-ray spectroscopy, atomic force microscopy, and micro-Raman spectroscopy. The GaN interlayer grown on the AlN takes the form of platelets. The mechanisms of dislocation reduction in the platelet area and the area between the platelets are different. In the GaN platelets, due to the large misfit strain, the threading dislocations (TDs) in the AlN layer migrate into the interface and annihilate with each other. However, the GaN between the platelets is highly strained so that a higher density of TDs from AlN is incorporated into the upper layer. The coalescing of the platelets induced by the AlGaN growth makes the TDs in the areas between the platelets assemble and annihilate, resulting in additional dislocation reduction.
Role of oxygen migration in the kinetics of the phase separation of nonstoichiometric silicon oxide films during high-temperature annealing
Authors: Sarikov A. , Litovchenko V. , Lisovskyy I. , Maidanchuk I. , Zlobin S.
Published: September 2007

The kinetics of phase separation and growth of Si precipitates during high-temperature annealing of nonstoichiometric SiOx films is theoretically studied. The mechanisms of silicon diffusion and capture by Si precipitates as well as oxygen emission and out diffusion from the Si precipitate interface toward the silicon oxide bulk are compared. The experimental kinetics of phase separation within 1s annealing SiOx films at 1000°C can be explained by the latter mechanism involving either neutral or negatively charged oxygen atoms. The maximum values of the activation energy of oxygen emission are estimated to match the simulation results to the experimental data.
Field-driven structural phase transition and sign-switching magnetocaloric effect in Ni–Mn–Sn
Authors: Pasquale M. , Sasso C. P. , Giudici L. , Lograsso T. , Schlagel D.
Published: September 2007

Depending on the starting equilibrium temperature, the application of a magnetic field on a sample of Ni–Mn–Sn produces sample heating or cooling during adiabatic experiments. The competition between endothermal and exothermal effects is observed close to the martensite-to-austenite magnetostructural phase transition. A model assuming the coexistence of two phases and a field dependence of their volume allows to compute the evolution of entropy and heat capacity during the phase transition. The correct fitting of the results suggests that the field-induced reduction of the martensite-to-austenite transition temperature is responsible for the observed sign switching of the magnetocaloric effect.
Microspectroscopic detection of local conducting areas generated by electric-pulse-induced phase transition in VO2 films
Authors: Lee J. S. , Ortolani M. , Schade U. , Chang Y. J. , Noh T. W.
Published: September 2007

Insulator-metal phase transitions were induced in VO2∕Al2O3 films by applying a voltage pulse to a micrometric junction. We investigated the mechanism involved both spatially and temporally using midinfrared microspectroscopy. At the phase transition, we found that multilevel current switching occurred, a behavior typical of numerous compounds showing electric-pulse-induced resistance switching. We were able to demonstrate that in the case of our VO2 film, the multilevel switching was directly related to the formation of local conducting paths, which originated from sample inhomogeneity.
High bias voltage effect on spin-dependent conductivity and shot noise in carbon-doped Fe(001)∕MgO(001)∕Fe(001) magnetic tunnel junctions
Authors: Guerrero R. , Herranz D. , Aliev F. G. , Greullet F. , Tiusan C. , Hehn M. , Montaigne F.
Published: September 2007

Low temperature (10K) high voltage bias dynamic conductivity (up to 2.7V) and shot noise (up to 1V) were studied in epitaxial Fe(100)∕Fe–C∕MgO(100)∕Fe(100) magnetic tunnel junctions as a function of the magnetic state. The junctions show large tunnel magnetoresistance (185% at 300K and 330% at 4K). Multiple sign inversion of the magnetoresistance is observed for bias polarity when the electrons scan the electronic structure of the bottom Fe–C interface. The shot noise shows a Poissonian character. This demonstrates a pure spin-dependent direct tunneling mechanism and validates the high structural quality of the MgO barrier.
Large seeds, extinct vectors and contemporary ecology: testing dispersal in a locally distributed cycad, Macrozamia lucida (Cycadales)
Authors: Snow E. L. , Walter G. H.
Published: September 2007

The possible reasons for the localised distribution of Macrozamia lucida Johnson in south-eastern Queensland were investigated through testing and quantifying aspects of seed dispersal, ex situ germination across local substrates and the spatial distribution of plants of different ages. Seeds of cones exposed to animals were moved significantly further (108.4 ± 13 cm, n = 10 cones) than those of cones not exposed to animals (49 ± 11 cm, n = 4). Only two mammal species interacted with seeds, common brushtail possums (Trichosurus vulpecula) and bush rats (Rattus fuscipes), but relatively infrequently. The possums were both seed dispersers and predators, whereas the rats ate only sarcotesta. Seed predation and removal occurred at a constant but low rate at cones exposed to animals, compared with no seed removal at unexposed cones. Seeds with sarcotesta intact and sarcotesta alone suffered significantly higher rates of removal by mammals. Seeds in soil had a significantly higher rate of germination (50%) than those in gravel (24.4%) or leaf litter (25.6%) and partially buried seeds germinated at a significantly higher rate (51.2%) than those on the surface (23.2%) and those buried completely (25.6%). In summary, this population appears to be localised spatially by low rates of dispersal, restricted dispersal distance and limited sites for successful germination. The results are discussed in relation to the possible extinction of the original seed dispersers of these organisms and the limitations this imposes on these plants should they be exposed to an unfavourable climatic regime.
PfEMP1-DBL1α amino acid motifs in severe disease states of
Plasmodium falciparum
malaria
Authors: Normark Johan , Nilsson Daniel , Ribacke Ulf , Winter Gerhard , Moll Kirsten , Wheelock Craig E. , Bayarugaba Justus , Kironde Fred , Egwang Thomas G. , Chen Qijun , Andersson Björn , Wahlgren Mats
Published: September 2007

An infection with
Plasmodium falciparum
may lead to severe malaria as a result of excessive binding of infected erythrocytes in the microvasculature. Vascular adhesion is mediated by
P. falciparum
erythrocyte membrane protein-1 (PfEMP1), which is encoded for by highly polymorphic members of the
var
-gene family. Here, we profile
var
gene transcription in fresh
P. falciparum
trophozoites from Ugandan children with malaria through
var
-specific DBL1α-PCR amplification and sequencing. A method for subsectioning region alignments into homology areas (MOTIFF) was developed to examine collected sequences. Specific PfEMP1-DBL1α amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to distinct regions of receptor interaction. The method is potentially applicable to other families of variant proteins and may be useful in identifying sequence-phenotype relationships. The results suggest that certain PfEMP1 sequences are predisposed to inducing severe malaria.
FOXO and insulin signaling regulate sensitivity of the circadian clock to oxidative stress
Authors: Zheng Xiangzhong , Yang Zhaohai , Yue Zhifeng , Alvarez John D. , Sehgal Amita
Published: September 2007

Circadian rhythms can be regulated by many environmental and endogenous factors. We show here a sensitivity of circadian clock function to oxidative stress that is revealed in flies lacking the
foxo
gene product. When exposed to oxidative stress, wild-type flies showed attenuated clock gene cycling in peripheral tissues, whereas
foxo
mutants also lost behavioral rhythms driven by the central clock. FOXO is expressed predominantly in the fat body, and transgenic expression in this tissue rescued the mutant behavioral phenotype, suggesting that
foxo
has non-cell-autonomous effects on central circadian clock function. Overexpression of signaling molecules that affect FOXO activity, such as the insulin receptor or
Akt
, in the fat body also increased susceptibility of the central clock to oxidative stress. Finally,
foxo
mutants showed a rapid decline in rest:activity rhythms with age, supporting the idea that the increase of oxidative stress contributes to age-associated degeneration of behavioral rhythms and indicating the importance of FOXO in mitigating this deterioration. Together these data demonstrate that metabolism affects central clock function and provide a link among insulin signaling, oxidative stress, aging, and circadian rhythms.
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution
Authors: Buck Janina , Fürtig Boris , Noeske Jonas , Wöhnert Jens , Schwalbe Harald
Published: September 2007

Structural transitions of RNA between alternate conformations with similar stabilities are associated with important aspects of cellular function. Few techniques presently exist that are capable of monitoring such transitions and thereby provide insight into RNA dynamics and function at atomic resolution. Riboswitches are found in the 5′-UTR of mRNA and control gene expression through structural transitions after ligand recognition. A time-resolved NMR strategy was established in conjunction with laser-triggered release of the ligand from a photocaged derivative
in situ
to monitor the hypoxanthine-induced folding of the guanine-sensing riboswitch aptamer domain of the
Bacillus subtilis xpt-pbuX
operon at atomic resolution. Combining selective isotope labeling of the RNA with NMR filter techniques resulted in significant spectral resolution and allowed kinetic analysis of the buildup rates for individual nucleotides in real time. Three distinct kinetic steps associated with the ligand-induced folding were delineated. After initial complex encounter the ligand-binding pocket is formed and results in subsequent stabilization of a remote long-range loop–loop interaction. Incorporation of NMR data into experimentally restrained molecular dynamics simulations provided insight into the RNA structural ensembles involved during the conformational transition.
Two Cys residues essential for von Willebrand factor multimer assembly in the Golgi
Authors: Purvis Angie R. , Gross Julia , Dang Luke T. , Huang Ren-Huai , Kapadia Milan , Townsend R. Reid , Sadler J. Evan
Published: September 2007

Von Willebrand factor (VWF) dimerizes through C-terminal CK domains, and VWF dimers assemble into multimers in the Golgi by forming intersubunit disulfide bonds between D3 domains. This unusual oxidoreductase reaction requires the VWF propeptide (domains D1D2), which acts as an endogenous pH-dependent chaperone. The cysteines involved in multimer assembly were characterized by using a VWF construct that encodes the N-terminal D1D2D′D3 domains. Modification with thiol-specific reagents demonstrated that secreted D′D3 monomer contained reduced Cys, whereas D′D3 dimer and propeptide did not. Reduced Cys in the D′D3 monomer were alkylated with
N
-ethylmaleimide and analyzed by mass spectrometry. All 52 Cys within the D′D3 region were observed, and only Cys
1099
and Cys
1142
were modified by
N
-ethylmaleimide. When introduced into the D1D2D′D3 construct, the mutation C1099A or C1142A markedly impaired the formation of D′D3 dimers, and the double mutation prevented dimerization. In full-length VWF, the mutations C1099A and C1099A/C1142A prevented multimer assembly; the mutation C1142A allowed the formation of almost exclusively dimers, with few tetramers and no multimers larger than hexamers. Therefore, Cys
1099
and Cys
1142
are essential for the oxidoreductase mechanism of VWF multimerization. Cys
1142
is reported to form a Cys
1142
–Cys
1142
intersubunit bond, suggesting that Cys
1099
also participates in a Cys
1099
–Cys
1099
disulfide bond between D3 domains. This arrangement of intersubunit disulfide bonds implies that the dimeric N-terminal D′D3 domains of VWF subunits align in a parallel orientation within VWF multimers.
Alterations in an inositol phosphate code through synergistic activation of a G protein and inositol phosphate kinases
Authors: Otto James C. , Kelly Patrick , Chiou Shean-Tai , York John D.
Published: September 2007

In mammals, many cellular stimuli evoke a response through G protein activation of phospholipase C, which results in the lipid-derived production of inositol 1,4,5-trisphosphate (IP
3
). Although it is well established that IP
3
is converted to numerous inositol phosphates (IPs) and pyrophosphates (PP-IPs) through the action of up to six classes of inositol phosphate kinases (IPKs), it is not clear that these metabolites are influenced by G protein signaling. Here we report that activation of Gα
q
leads to robust stimulation of IP
3
to IP
8
metabolism. To expose flux through these pathways, genetic perturbation was used to alter IP homeostasis. Coupled expression of a constitutively active Gα
q
QL and one or more IPK gene products synergistically generated dramatic changes in the patterns of intracellular IP messengers. Many distinct IP profiles were observed through the expression of different combinations of IPKs, including changes in previously unappreciated pools of IP
5
and IP
6
, two molecules widely viewed as stable metabolites. Our data link the activation of a trimeric G protein to a plethora of metabolites downstream of IP
3
and provide a framework for suggesting that cells possess the machinery to produce an IPK-dependent IP code. We imply, but do not prove, that agonist-induced alterations in such a code would theoretically be capable of enhancing signaling complexity and specificity. The essential roles for IPKs in organism development and cellular adaptation are consistent with our hypothesis that such an IP code may be relevant to signaling pathways.
Exhaled methyl nitrate as a noninvasive marker of hyperglycemia in type 1 diabetes
Authors: Novak B. J. , Blake D. R. , Meinardi S. , Rowland F. S. , Pontello A. , Cooper D. M. , Galassetti P. R.
Published: September 2007

Recent technical advances allow detection of several hundred volatile organic compounds (VOCs) in human exhaled air, many of which reflect unidentified endogenous pathways. Our group has previously estimated plasma glucose levels in healthy adults during a standard oral glucose tolerance test via exhaled VOC analysis. As a result of the metabolic characteristics of hyperglycemia in the diabetic (low insulin and increased free fatty acids and ketones), we hypothesized that different exhaled VOC profiles may be present in children with type 1 diabetes mellitus (T1DM) during spontaneous hyperglycemia. Exhaled methyl nitrate strongly correlated specifically with the acute, spontaneous hyperglycemia of T1DM children. Eighteen experiments were conducted among 10 T1DM children. Plasma glucose and exhaled gases were monitored during either constant euglycemia (
n
= 5) or initial hyperglycemia with gradual correction (
n
= 13); all subjects received i.v. insulin and glucose as needed. Gas analysis was performed on 1.9-liter breath samples via gas chromatography using electron capture, flame ionization, and mass selective detection. Among the ≈100 measured exhaled gases, the kinetic profile of exhaled methyl nitrate, commonly present in room air in the range of 5–10 parts per trillion, was most strongly statistically correlated with that of plasma glucose (
P
= 0.003–0.001). Indeed, the kinetic profiles of the two variables paralleled each other in 16 of 18 experiments, including repeat subjects who at different times displayed either euglycemia or hyperglycemia.
Involvement of corepressor complex subunit GPS2 in transcriptional pathways governing human bile acid biosynthesis
Authors: Sanyal Sabyasachi , Båvner Ann , Haroniti Anna , Nilsson Lisa-Mari , Lundåsen Thomas , Rehnmark Stefan , Witt Michael Robin , Einarsson Curt , Talianidis Iannis , Gustafsson Jan-åke , Treuter Eckardt
Published: September 2007

Coordinated regulation of bile acid biosynthesis, the predominant pathway for hepatic cholesterol catabolism, is mediated by few key nuclear receptors including the orphan receptors liver receptor homolog 1 (LRH-1), hepatocyte nuclear factor 4α (HNF4α), small heterodimer partner (SHP), and the bile acid receptor FXR (farnesoid X receptor). Activation of FXR initiates a feedback regulatory loop via induction of SHP, which suppresses LRH-1- and HNF4α-dependent expression of cholesterol 7α hydroxylase (CYP7A1) and sterol 12α hydroxylase (CYP8B1), the two major pathway enzymes. Here we dissect the transcriptional network governing bile acid biosynthesis in human liver by identifying GPS2, a stoichiometric subunit of a conserved corepressor complex, as a differential coregulator of CYP7A1 and CYP8B1 expression. Direct interactions of GPS2 with SHP, LRH-1, HNF4α, and FXR indicate alternative coregulator recruitment strategies to cause differential transcriptional outcomes. In addition, species-specific differences in the regulation of bile acid biosynthesis were uncovered by identifying human CYP8B1 as a direct FXR target gene, which has implications for therapeutic approaches in bile acid-related human disorders.
A model for the role of integrins in flow induced mechanotransduction in osteocytes
Authors: Wang Yilin , McNamara Laoise M. , Schaffler Mitchell B. , Weinbaum Sheldon
Published: September 2007

A fundamental paradox in bone mechanobiology is that tissue-level strains caused by human locomotion are too small to initiate intracellular signaling in osteocytes. A cellular-level strain-amplification model previously has been proposed to explain this paradox. However, the molecular mechanism for initiating signaling has eluded detection because none of the molecules in this previously proposed model are known mediators of intracellular signaling. In this paper, we explore a paradigm and quantitative model for the initiation of intracellular signaling, namely that the processes are attached directly at discrete locations along the canalicular wall by β
3
integrins at the apex of infrequent, previously unrecognized canalicular projections. Unique rapid fixation techniques have identified these projections and have shown them to be consistent with other studies suggesting that the adhesion molecules are α
v
β
3
integrins. Our theoretical model predicts that the tensile forces acting on the integrins are <15 pN and thus provide stable attachment for the range of physiological loadings. The model also predicts that axial strains caused by the sliding of actin microfilaments about the fixed integrin attachments are an order of magnitude larger than the radial strains in the previously proposed strain-amplification theory and two orders of magnitude greater than whole-tissue strains.
In vitro
experiments indicated that membrane strains of this order are large enough to open stretch-activated cation channels.
How the regulatory protein, IF
1
, inhibits F
1
-ATPase from bovine mitochondria
Authors: Gledhill Jonathan R. , Montgomery Martin G. , Leslie Andrew G. W. , Walker John E.
Published: September 2007

The structure of bovine F
1
-ATPase inhibited by a monomeric form of the inhibitor protein, IF
1
, known as I1–60His, lacking most of the dimerization region, has been determined at 2.1-Å resolution. The resolved region of the inhibitor from residues 8–50 consists of an extended structure from residues 8–13, followed by two α-helices from residues 14–18 and residues 21–50 linked by a turn. The binding site in the β
DP
-α
DP
catalytic interface is complex with contributions from five different subunits of F
1
-ATPase. The longer helix extends from the external surface of F
1
via a deep groove made from helices and loops in the C-terminal domains of subunits β
DP
, α
DP
, β
TP
, and α
TP
to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the γ-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the α
E
subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F
1
forms via the open conformation of the β
E
subunit. Then, as two ATP molecules are hydrolyzed, the β
E
-α
E
interface converts to the β
DP
-α
DP
interface via the β
TP
-α
TP
interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit β
DP
. The inhibition probably arises by IF
1
imposing the structure and properties of the β
TP
-α
TP
interface on the β
DP
-α
DP
interface, thereby preventing it from hydrolyzing the bound ATP.
Intensive training in adults refines A1 representations degraded in an early postnatal critical period
Authors: Zhou Xiaoming , Merzenich Michael M.
Published: September 2007

The spectral, temporal, and intensive selectivity of neurons in the adult primary auditory cortex (A1) is easily degraded in early postnatal life by raising rat pups in the presence of pulsed noise. The nonselective frequency tuning recorded in these rats substantially endures into adulthood. Here we demonstrate that perceptual training applied in these developmentally degraded postcritical-period rats results in the recovery of normal representational fidelity. By using a modified go/no-go training strategy, structured noise-reared rats were trained to identify target auditory stimuli of specific frequency from a set of distractors varying in frequency. Target stimuli changed daily on a random schedule. Consistent with earlier findings, structured noise exposure within the critical period resulted in disrupted tonotopicity within A1 and in degraded frequency-response selectivity for A1 neurons. Tonotopicity and frequency-response selectivity were normalized by perceptual training. Changes induced by training endured without loss for at least 2 months after training cessation. The results further demonstrate the potential utility of perceptual learning as a strategy for normalizing deteriorated auditory representations in older (postcritical-period) children and adults.
Ulcerative colitis and autoimmunity induced by loss of myeloid αv integrins
Authors: Lacy-Hulbert Adam , Smith Aileen M. , Tissire Hamid , Barry Marc , Crowley Denise , Bronson Roderick T. , Roes Jürgen T. , Savill John S. , Hynes Richard O.
Published: September 2007

The gastrointestinal tract is constantly challenged by foreign antigens and commensal bacteria but nonetheless is able to maintain a state of immunological quiescence. Recent advances have highlighted the importance of active suppression by regulatory lymphocytes and immunosuppressive cytokines in controlling mucosal immunity. Failures of these mechanisms contribute to the development of inflammatory bowel disease, but how these regulatory networks are established remains unclear. Here, we demonstrate key roles for αv integrins in regulation of mucosal immunity. We report that deletion of αv in the immune system causes severe colitis, autoimmunity, and cancer. Mice lacking immune cell αv have fewer regulatory T (Treg) cells in the colon and corresponding increases in activated T cells and T cell cytokine production, leading to colitis. Using conditional gene targeting, we demonstrate that this is specifically attributable to loss of αv from myeloid cells. Furthermore, we show that gut-associated macrophages and dendritic cells fail both to remove apoptotic cells efficiently and to induce Treg cells. Our results identify a vital role for myeloid αv integrins in generating mucosal Treg cells and emphasize the importance of antigen-presenting cells in establishing immune tolerance.
meta-PPISP: a meta web server for protein-protein interaction site prediction
Authors: Qin Sanbo , Zhou Huan-Xiang
Published: September 2007

Summary: A number of complementary methods have been developed for predicting protein-protein interaction sites. We sought to increase prediction robustness and accuracy by combining results from different predictors, and report here a meta web server, meta-PPISP, that is built on three individual web servers: cons-PPISP (http://pipe.scs.fsu.edu/ppisp.html), Promate (http://bioportal.weizmann.ac.il/promate), and PINUP (http://sparks.informatics.iupui.edu/PINUP/). A linear regression method, using the raw scores of the three servers as input, was trained on a set of 35 nonhomologous proteins. Cross validation showed that meta-PPISP outperforms all the three individual servers. At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets.

Availability: meta-PPISP can be accessed at http://pipe.scs.fsu.edu/meta-ppisp.html

Contact:  zhou@sb.fsu.edu

Supplementary information: Data sets, linear regression coefficients, and details of prediction results are shown at the site of the meta-PPISP server.