bluuebunny/crossref_metadata_2025 huggingface dataset:
Lengthening the G1 Phase of Neural Progenitor Cells is Concurrent with An Increase of Symmetric Neuron Generating Division after Stroke
Authors: Zhang Rui L , Zhang Zheng G , Roberts Cynthia , LeTourneau Yvonne , Lu Mei , Zhang Li , Wang Ying , Chopp Michael
Published: October 2007

The proportion of neural progenitors that remain in ( P fraction) and exit from ( Q fraction) the cell cycle determines the degree of neurogenesis. Using S-phase labeling with 5-bromo-2′-deoxyuridine and a double nucleoside analog-labeling scheme, we measured the cell-cycle kinetics of neural progenitors and estimated the proportion of P and Q fractions in the subventricular zone (SVZ) of adult rats subjected to stroke. Stroke increased SVZ cell proliferation, starting 2 days, reaching a maximum 4 and 7 days after stroke. The cell-cycle length ( TC) of SVZ cells changed dynamically over a period of 2 to 14 days after stroke, with the shortest length of 11 h at 2 days after stroke. The reduction of the TC resulted from a decrease of the G1 phase because the G2, M, and S phases were unchanged. In addition, during this period, reduction of the G1 phase was concomitant with an increase in the P fraction, whereas an augmentation of the Q fraction was associated with lengthening of the G1 phase. Furthermore, approximately 90% of cells that exited the cell cycle were neurons and the population of a pair of dividing daughter cells with a neuronal marker increased from 9% at 2 days to 26% at 14 days after stroke. These data suggest that stroke triggers early expansion of the progenitor pool via shortening the cell-cycle length and retaining daughter cells within the cell cycle, and the lengthening of G1 leads to daughter cells exiting the cell cycle and differentiating into neurons.
GADD34 Gene Restores Virulence in Viral Vector Used in Experimental Stroke Study
Authors: McCabe Christopher , White Fiona , Brown S Moira , Macrae I Mhairi
Published: October 2007

GADD34 is expressed in the ischaemic brain and reverses protein synthesis shutdown. Consequently, GADD34 could have neuroprotective potential in stroke. BHK medium, a replication-deficient HSV viral vector (HSV1716) with no insert or containing full-length GADD34, the N terminal or a conserved portion of the gene, was injected into mouse brain before stroke. Infarct size was 1.0±0.26, 1.19±0.36, 1.5±0.36, 1.3±0.36, and 1.1±0.28 mm3, respectively. The increase in infarct size with full-length GADD34 was statistically significant ( P<0.05). Immunohistochemistry confirmed viral protein expression. Tissue culture studies revealed GADD34 gene restored virulence in HSV1716, suggesting that HSV virulence, rather than increased GADD34, exacerbated ischaemic damage.
Interaction of atomic and molecular deuterium with a nonporous amorphous water ice surface between 8 and 30K
Authors: Amiaud L. , Dulieu F. , Fillion J.-H. , Momeni A. , Lemaire J. L.
Published: October 2007

Molecular and atomic interactions of hydrogen on dust grains covered with ice at low temperatures are key mechanisms for star formation and chemistry in dark interstellar clouds. We have experimentally studied the interaction of atomic and molecular deuterium on nonporous amorphous water ice surfaces between 8 and 30K, in conditions compatible with an extrapolation to an astrophysical context. The adsorption energy of D2 presents a wide distribution, as already observed on porous water ice surfaces. At low coverage, the sticking coefficient of D2 increases linearly with the number of deuterium molecules already adsorbed on the surface. Recombination of atomic D occurs via a prompt reaction that releases molecules into the gas phase. Part of the newly formed molecules are in vibrationally excited states (v=1–7). The atomic recombination efficiency increases with the presence of D2 molecules already adsorbed on the water ice, probably because these increase the sticking coefficient of the atoms, as in the case of incident D2. We have measured the atomic recombination efficiency in the presence of already absorbed D2, as it is expected to occur in the interstellar medium. The recombination efficiency decreases rapidly with increasing temperature and is zero at 13K. This allows us to estimate an upper limit to the value of the atom adsorption energy Ea∼29meV, in agreement with previous calculations.
Formation of silver nanoparticles under anodic surface of tellurite glass via thermal poling-assisted ion implantation across solid-solid interface
Authors: Murai Shunsuke , Fujita Koji , Kawase Sonoko , Ukon Sakiko , Tanaka Katsuhisa
Published: October 2007

We have developed a technique by which poling and ion implantation in solid state are simultaneously accomplished. The technique has been applied to 2Ag2O⋅3Na2O⋅25ZnO⋅70TeO2 (in mol %) glass. The glass is sandwiched by two cover glasses containing Na+ and then the thermal poling is carried out. We have accidentally found that Ag nanoparticles are selectively precipitated in the vicinity of the anode-side glass surface. X-ray photoelectron spectroscopy reveals that the glass composition of the anode-side glass surface becomes rich in Na+ after the thermal poling, which is caused by the Na+ implantation from the cover glass at the anode side.
Manifestation of nonequilibrium initial conditions in molecular rotation: The generalized J-diffusion model
Authors: Gelin M. F. , Kosov D. S.
Published: October 2007

In order to adequately describe molecular rotation far from equilibrium, we have generalized the J-diffusion model by allowing the rotational relaxation rate to be angular momentum dependent. The calculated nonequilibrium rotational correlation functions (CFs) are shown to decay much slower than their equilibrium counterparts, and orientational CFs of hot molecules exhibit coherent behavior, which persists for several rotational periods. As distinct from the results of standard theories, rotational and orientational CFs are found to dependent strongly on the nonequilibrium preparation of the molecular ensemble. We predict the Arrhenius energy dependence of rotational relaxation times and violation of the Hubbard relations for orientational relaxation times. The standard and generalized J-diffusion models are shown to be almost indistinguishable under equilibrium conditions. Far from equilibrium, their predictions may differ dramatically.
Evaluation of the impact parameter in droplet-droplet collision experiments by the aliasing method
Authors: Gotaas Cecilie , Havelka Pavel , Jakobsen Hugo A. , Svendsen Hallvard F.
Published: October 2007

A new method has been developed whereby the borders between the various collision outcome regimes for droplet/droplet impact can be determined. This method, called the aliasing method, is based on a small frequency shift between the droplet generating nozzles. The droplet collision outcomes, for a fixed Weber number, can then be visually followed continuously for the whole range of impact parameters during one collision experiment. The impact parameter can be evaluated numerically using the frequency shift between the droplet trains without using geometric image evaluations of the video recordings. This frequency shift and temporal aliasing method makes it possible to determine the impact parameter significantly more accurately and efficiently, compared to previous methods. The aliasing evaluation method for determining the impact parameter can also be used together with the modulation technique in order to extend the range of We numbers investigated. The new method has been validated with experiments using the water/air system.
Effect of viscosity on droplet-droplet collision outcome: Experimental study and numerical comparison
Authors: Gotaas Cecilie , Havelka Pavel , Jakobsen Hugo A. , Svendsen Hallvard F. , Hase Matthias , Roth Norbert , Weigand Bernhard
Published: October 2007

The influence of viscosity on droplet-droplet collision behavior at ambient conditions was studied experimentally and numerically. N-decane, monoethyleneglycol (MEG), diethyleneglycol (DEG), and triethyleneglycol were used as liquid phase providing viscosities in the range from 0.9to48mPas. Collision Weber numbers ranged approximately from 10 to 420. A direct numerical simulation code, based on the volume-of-fluid concept, was used for the simulations. Experimentally, observations of two droplet streams using a modified stroboscopic technique (aliasing method) were used to investigate the whole range of impact parameters during one experimental run. The experimental method has previously been verified for the water/air system [C. Gotaas et al., Phys. Fluids 19, 102105 (2007)]. In the present work, it was tested and validated for the n-decane/air system. Measured data agree well with those published in the literature. Well-defined regions of stretching separation and coalescence were identified, while reflexive separation regions were not found by using a single sinusoidal disturbance. However, the onset of reflexive separation was identified for MEG and DEG using an amplitude modulation technique. The results show that the criteria for onset of reflexive separation for viscous fluids provided by Y. I. Jiang et al. [J. Fluid Mech. 234, 177 (1992)] are not valid. This is consistent with the results given by K. D. Willis and M. Orme [Exp. Fluids 34, 28 (2003)]. A new empirical correlation for the onset of reflexive separation for high viscosity fluids is presented. The borders between coalescing and stretching separation were shifted toward higher Weber numbers with increasing viscosity. The lack of occurrence of reflexive separation for the single sinusoidal disturbance (small droplets), as well as the stretching separation boundary shift, can be explained by dissipation of collision kinetic energy in viscous flows inside the merged droplet after collision. Results from numerical simulations for MEG, DEG, and TEG correlated well with experimental data for the same fluids.
Three-dimensional microphotonic crystals of ZrO2 toughened Al2O3 for terahertz wave applications
Authors: Chen Weiwu , Kirihara Soshu , Miyamoto Yoshinari
Published: October 2007

This letter reports an approach, based on microstereolithography, to create three-dimensional photonic crystals of microscale structure made of ceramic-resin composite (before sintering) and dense ceramics (after sintering). For ZrO2 toughened Al2O3 ceramic-resin photonic crystals (with a lattice constant of 500μm), the forming resolution was around 10μm and the measured band gap appeared between 350 and 400GHz in the Γ-X ⟨100⟩ direction, 350 and 400GHz in the Γ-K ⟨110⟩ direction, and 270 and 360GHz in the Γ-L ⟨111⟩ direction. After sintering, the lattice constant shrunk to 380μm and the band gap was between 320 and 420GHz in the Γ-X ⟨100⟩ direction, 330 and 400GHz in the Γ-K ⟨110⟩ direction, and 260 and 355GHz in the Γ-L ⟨111⟩ direction.
Spin resolved electron number distribution functions: How spins couple in real space
Authors: Martín Pendás A. , Francisco E. , Blanco M. A.
Published: October 2007

The probabilities of finding arbitrary partitions of the Nαms=1∕2 and Nβms=−1∕2 electrons of a molecule into m arbitrary regions that exhaust the physical space are developed and computed, both for atomic and electron localization function basins, in a number of test systems. These spin resolved electron number distribution functions provide access to the coarse-grained distribution of spins in space even for singlet states, a nontrivial result. It is found that atoms within molecules partially retain their in vacuo preferences for certain spin configurations. This may lead to long range spin coupling among basins. An aufbaulike rule favoring spin coupling, particularly for Hartree-Fock wave functions, has also been found.
Effect of second ion temperature on modulation stability of dust-acoustic solitary waves with dust charge variation
Authors: El-Labany S. K. , El-Bedwehy N. A. , Abd El-Razek H. N.
Published: October 2007

The derivative expansion perturbation method is applied to a cold plasma system consisting of dust grains with varying dust charge, electrons, and two species of ions with different temperatures. The basic system of equations is reduced to a nonlinear Schrödinger-type equation. The effect of the temperature of low temperature ions on the system parameters, e.g., angular frequency, group velocity, dispersion coefficient, and nonlinear coefficient, is investigated. It is found that the presence of low-temperature ions enhances the stability of the system. The small wave number limits of the coefficients of the nonlinear Schrödinger-type equation are found to agree exactly with the coefficients of the nonlinear Schrödinger-type equation obtained from the oscillatory solution of the Korteweg-de Vries equation of the system.
Ion beam capture and charge breeding in electron cyclotron resonance ion source plasmas
Authors: Kim Jin-Soo , Zhao L. , Cluggish B. P. , Pardo Richard
Published: October 2007

Beam capture of injected ions and charge breeding in electron cyclotron resonance (ECR) charge breeder ion source plasmas has been investigated utilizing an ECR plasma modeling code, the generalized ECR ion source model, and a Monte Carlo beam capture code. Beam capturing dynamics, charge breeding in the plasma, and the extracted charged ion states are described. Optimization of ion beam energy is performed for (1) high beam capture efficiency and (2) high charge state ion beam extractions. A sample case study for ANL-ECR has been performed. Ions entering ECR ion source plasma are slowed down mostly by the background ions. Assuming Maxwellian plasma ions, maximum beam energy loss occurs when the beam velocity is around the background thermal velocity in magnitude. It is also found that beam capture location affects charge state distribution. For instance, with a majority of beam ions captured near the middle of the device higher currents for higher charge states are obtained. The beam ions captured near the entry have a higher probability of backstreaming after they are captured. For this reason, the optimum beam energy of the injected Ar+ beam ions for charge breeding is generally higher than the optimum input beam energy for maximum beam energy loss.
Plasma irradiation damages to magnetic tunneling junction devices
Authors: Mukai Tomonori , Jinnai Butsurin , Fukumoto Yoshiyuki , Ohshima Norikazu , Hada Hiromitsu , Samukawa Seiji
Published: October 2007

We exposed magnetic tunneling junction (MTJ) devices—fabricated using Ar-ion milling—to the reactive plasma commonly used in etching to determine the mechanism of the damage caused by the exposure. Exposing MTJ devices to the conventional continuous-wave (CW) plasma widely used in plasma etching significantly degrades their magnetic characteristics. However, exposure to a pulse-time-modulated (TM) plasma does not degrade the MTJ devices’ magnetic characteristics. Analysis of transmission electron microscopy cross sections of the MTJ device structures revealed that the structure of the CoFe pinned layer was damaged in the MTJ devices exposed to a conventional CW plasma. This structural damage degraded the MTJ devices’ magnetic characteristics. No damage to the structure of the MTJ devices was seen in those exposed to a TM plasma. Therefore, using the TM plasma offers an effective, damage-free method of etching MTJ devices as part of their manufacturing process.
Variation of plasma parameters on boundary conditions in an inductively coupled plasma source for hyperthermal neutral beam generation
Authors: Joung M. , Cho M. H. , Namkung W. , Lho T. , Kim D. Ch. , Kim J. S. , Yoo S. J. , Lee B. J. , Kim G. H.
Published: October 2007

The variations of plasma parameters on the boundary conditions, especially potential, of plasmas were measured in an inductively coupled plasma source developed to generate a hyperthermal neutral beam. Hyperthermal neutrals can be produced by Auger neutralization when ions with low energy are neutralized by impinging on a metal surface called a reflector. However, the reflector is a significant source of ion drain when it is biased to a negative potential. The plasma potential can be negative with respect to the grounded chamber potential while the reflector is negatively biased, but other plasma parameters, namely density and temperature, are not sensitive to the reflector bias. If the electron loss current into the chamber wall is governed by the space charge limited current law, sustainment of the plasma with a negative potential can be explained in terms of the charge balance equations for quasineutrality.
Comparison of structural and electrical properties of praseodymium oxide and praseodymium titanium oxide charge trapping layer memories
Authors: Pan Tung-Ming , Yu Te-Yi , Hsieh Yu-Yi
Published: October 2007

The structural properties and electrical characteristics of metal-oxide-nitride-oxide-silicon memory structure by using praseodymium oxide (Pr2O3) or praseodymium titanium oxide (PrTixOy) to replace silicon nitride as the charge storage layer [resulting structure is termed metal–oxide–high-k material–oxide–silicon (MOHOS) devices] were investigated. The structural and morphological features of these high-k films were analyzed using x-ray diffraction, scanning electron microscopy, atomic force microscopy, and x-ray photoelectron spectroscopy. It was found that MOHOS memory prepared under the PrTixOy film and annealed at 800°C exhibited a large flatband voltage shift of 5.6V and low charge loss of ∼6% at room temperature. We attribute this behavior to the titanium content in the Pr2O3 film, suppressing interfacial SiO2 and silicate from forming at the PrTixOy/oxide interface and enhancing nanocrystal formation.
Embedding effects on charge-transport parameters in molecular organic materials
Authors: Lipparini Filippo , Mennucci Benedetta
Published: October 2007

We present a generalized version of the tight-binding approach to determine the electronic coupling parameter in charge (hole) transport phenomena in organic materials. The main novelty of this approach is that the “embedding effects” of the environment (either a solvent or a crystal packing) can be explicitly included in the calculation by considering an embedded dimer. One of the main features shown by the application of the method to both model systems and oligoacene crystals is that the routinely used “energy splitting in a dimer” approximation gives reasonable results even if the transfer units are not equivalent by symmetry but the embedding effects are properly taken into account.
On rapid plasma rotation
Authors: Helander P.
Published: October 2007

The conditions under which rapid plasma rotation may occur in a general three-dimensional magnetic field with flux surfaces, such as that of a stellarator, are investigated. Rotation velocities comparable to the ion thermal speed are found to be attainable only in magnetic fields whose strength B depends on the arc length l along the field in approximately the same way for all field lines on each flux surface ψ, i.e., B≃f(ψ,l). Moreover, it is shown that the rotation must be in the direction of the vector ∇ψ×∇B.
Primary instability of a Taylor-Couette flow with a radial stratification and radial buoyancy
Authors: Jenny Mathieu , Nsom Blaise
Published: October 2007

We consider the primary instability onset of a Taylor-Couette flow with a radial stratification and radial volumic force. Our system corresponds to a simplified geophysical model that takes into account the effect of the buoyancy opposed to the centrifugal force. Three parameters of the physical problem, which correspond to the buoyancy, the diffusivity, and the rotational velocity, are considered to describe the onset of the primary instability. Using an efficient numerical method, we compute the threshold value of the Taylor number, which depends on the Froude and Schmidt numbers, and describe the most unstable mode provided by the linear analysis.
Photon-induced formation of CdS nanocrystals in selected areas of polymer matrices
Authors: Athanassiou Athanassia , Cingolani Roberto , Tsiranidou Elsa , Fotakis Costas , Laera Anna Maria , Piscopiello Emanuela , Tapfer Leander
Published: October 2007

We demonstrate light-induced formation of semiconductor quantum dots in TOPAS® polymer matrix with very high control of their size and their spatial localization. Irradiation with UV laser pulses of polymer films embedding Cd thiolate precursors results in the formation of cadmium sulfide nanocrystals well confined in the irradiation area, through a macroscopically nondestructive procedure for the host matrix. With increasing number of laser pulses, we accomplish the formation of nanoparticles with gradually increasing dimensions, resulting in the dynamic change of the spectra emitted by the formed nanocomposite areas. The findings are supported by x-ray diffraction and transmission electron microscopy measurements.
Basis set limits of the second order Møller-Plesset correlation energies of water, methane, acetylene, ethylene, and benzene
Authors: Yamaki Daisuke , Koch Henrik , Ten-no Seiichiro
Published: October 2007

We report second order Møller-Plesset (MP2) and MP2-F12 total energies on He, Ne, Ar, H2O, CH4, C2H2, C2H4, and C6H6, using the correlation consistent basis sets, aug-cc-pVXZ (X=D−7). Basis set extrapolation techniques are applied to the MP2 and MP2-F12/B methods. The performance of the methods is tested in the calculations of the atoms, He, Ne, and Ar. It is indicated that the two-point extrapolation of MP2-F12/B with the basis sets (X=5,6) is the most reliable. Similar accuracy is obtained using two-point extrapolated conventional MP2 with the basis sets (X=6,7). For the molecules investigated the valence MP2 correlation energy is estimated within 1mEh.
Loading effect on swelling of nematic elastomers
Authors: Urayama Kenji , Mashita Ryo , Kobayashi Ichiro , Takigawa Toshikazu
Published: October 2007

Externally imposed loading has substantially different effects on the swelling of nematic elastomers in the high-temperature isotropic and low-temperature nematic states. In the isotropic state, the stretching drives a considerably large degree of further swelling, whereas the stretching-induced volume change in the nematic state is significantly suppressed. In the isotropic phase that favors the less anisotropic state, the further swelling occurs to reduce the shape anisotropy caused by the imposed elongation. In the nematic phase, no significant swelling is induced because further swelling decreases the nematic order enhanced by the applied stretching. These different loading effects in the isotropic and nematic states observed in the experiments are qualitatively described by a mean field theory.
Effects of cytoskeletal disruption on transport, structure, and rheology within mammalian cells
Authors: Weihs Daphne , Mason Thomas G. , Teitell Michael A.
Published: October 2007

Quantification of cellular responses to stimuli is challenging. Cells respond to changing external conditions through internal structural and compositional and functional modifications, thereby altering their transport and mechanical properties. By properly interpreting particle-tracking microrheology, we evaluate the response of live cells to cytoskeletal disruption mediated by the drug nocodazole. Prior to administering the drug, the particles exhibit an apparently diffusive behavior that is actually a combination of temporally heterogeneous ballistic and caged motion. Selectively depolymerizing microtubules with the drug causes actively crawling cells to halt, providing a means for assessing drug efficacy, and making the caged motion of the probes readily apparent.
A new derivation of the randomness parameter
Authors: Wang Hongyun
Published: October 2007

For a stochastic stepper that can only step forward, there are two randomnesses: (1) the randomness in the cycle time and (2) the randomness in the number of steps (cycles) over long time. The equivalence between these two randomnesses was previously established using the approach of Laplace transform [M. J. Schnitzer and S. M. Block, “Statistical kinetics of processive enzymes,” Cold Spring Harbor Symp. Quant. Biol. 60, 793 (1995)]. In this study, we first discuss the problems of this approach when the cycle time distribution has a discrete component, and then present a new derivation based on the framework of semi-Markov processes with age structure. We also show that the equivalence between the two randomnesses depends on the existence of the first moment of the waiting time for completing the first cycle, which is strongly affected by the initial age distribution. Therefore, any derivation that concludes the equivalence categorically regardless of the initial age distribution is mathematically questionable.
Gigahertz frequency flexible carbon nanotube transistors
Authors: Chimot N. , Derycke V. , Goffman M. F. , Bourgoin J. P. , Happy H. , Dambrine G.
Published: October 2007

We investigate the high frequency performances of flexible field-effect transistors based on carbon nanotubes. A large density of mostly aligned carbon nanotubes deposited on a flexible substrate by dielectrophoresis serves as the channel. The transistors display a constant transconductance up to at least 6GHz and a current gain cutoff frequency (fT) as high as 1GHz at VDS=−700mV. Bending tests show that the devices can withstand a high degree of flexion characterized by a constant transconductance for radius of curvature as small as 3.3mm.
Electrical properties in vanadyl-phthalocyanine-based metal-insulator-semiconductor devices
Authors: Wang Lijuan , Liu Guojun , Wang Haibo , Song De , Yu Bo , Yan Donghang
Published: October 2007

We investigated electrical properties of vanadyl phthalocyanine (VOPc) metal-insulator-semiconductor (MIS) devices by the measurement of capacitance and conductance, which were fabricated on ordered para-sexiphenyl (p-6P) layer by weak epitaxy growth method. The VOPc∕p-6P MIS diodes showed a negligible hysteresis effect at a gate voltage of ±20V and small hysteresis effect at a gate voltage of ±40V due to the low interface trap state density of about 1×1010eV−1cm−2. Furthermore, a high transition frequency of about 10kHz was also observed under their accumulation mode. The results indicated that VOPc was a promising material and was suitable to be applied in active matrix liquid crystal displays and organic logic circuits.
Things are Looking up: Differential Decline in Face Recognition following Pitch and Yaw Rotation
Authors: Favelle Simone K , Palmisano Stephen , Maloney Ryan T
Published: October 2007

Previous research into the effects of viewpoint change on face recognition has typically dealt with rotations around the head's vertical axis (yaw). Another common, although less studied, source of viewpoint variation in faces is rotation around the head's horizontal pitch axis (pitch). In the current study we used both a sequential matching task and an old/new recognition task to examine the effect of viewpoint change following rotation about both pitch and yaw axes on human face recognition. The results of both tasks showed that recognition performance was better for faces rotated about yaw compared to pitch. Further, recognition performance for faces rotated upwards on the pitch axis was better than for faces rotated downwards. Thus, equivalent angular rotations about pitch and yaw do not produce equivalent viewpoint-dependent declines in recognition performance.
Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z
Authors: Venkatasubrahmanyam Shivkumar , Hwang William W. , Meneghini Marc D. , Tong Amy Hin Yan , Madhani Hiten D.
Published: October 2007

In
Saccharomyces cerevisiae
, several nonessential mechanisms including histone variant H2A.Z deposition and transcription-associated histone H3 methylation antagonize the local spread of Sir-dependent silent chromatin into adjacent euchromatic regions. However, it is unclear how and where these factors cooperate. To probe this question, we performed systematic genetic array screens for gene deletions that cause a synthetic growth defect in an
htz1
Δ mutant but not in an
htz1
Δ
sir3
Δ double mutant. Of the four genes identified, three,
SET1
,
SWD1
, and
SWD3
, encode components of the Set1 complex, which catalyzes the methylation of histone H3 on lysine 4 (H3-K4), a highly conserved modification that occurs in the coding sequences of transcribed genes. Using microarray-based transcriptional profiling, we find that H2A.Z and Set1 cooperate to prevent Sir-dependent repression of a large number of genes located across the genome, rather than the local effects reported previously for the individual mechanisms. This global, redundant function appears to be direct: using a DamID chromatin profiling method, we demonstrate ectopic association of Sir3 and Sir4 in
htz1
Δ
set1
Δ mutants at loci distant from silent chromatin domains. Antisilencing mechanisms may therefore cooperate to play a considerably broader role in regulating genome-wide transcription than previously thought.
Complement factor H deficiency in aged mice causes retinal abnormalities and visual dysfunction
Authors: Coffey Peter J. , Gias Carlos , McDermott Caroline J. , Lundh Peter , Pickering Matthew C. , Sethi Charanjit , Bird Alan , Fitzke Fred W. , Maass Annelie , Chen Li Li , Holder Graham E. , Luthert Philip J. , Salt Thomas E. , Moss Stephen E. , Greenwood John
Published: October 2007

Age-related macular degeneration is the most common form of legal blindness in westernized societies, and polymorphisms in the gene encoding complement factor H (
CFH
) are associated with susceptibility to age-related macular degeneration in more than half of affected individuals. To investigate the relationship between complement factor H (CFH) and retinal disease, we performed functional and anatomical analysis in 2-year-old CFH-deficient (
cfh
−/−
) mice.
cfh
−/−
animals exhibited significantly reduced visual acuity and rod response amplitudes on electroretinography compared with age-matched controls. Retinal imaging by confocal scanning laser ophthalmoscopy revealed an increase in autofluorescent subretinal deposits in the
cfh
−/−
mice, whereas the fundus and vasculature appeared normal. Examination of tissue sections showed an accumulation of complement C3 in the neural retina of the
cfh
−/−
mice, together with a decrease in electron-dense material, thinning of Bruch's membrane, changes in the cellular distribution of retinal pigment epithelial cell organelles, and disorganization of rod photoreceptor outer segments. Collectively, these data show that, in the absence of any specific exogenous challenge to the innate immune system, CFH is critically required for the long-term functional health of the retina.
Sugar binding induces an outward facing conformation of LacY
Authors: Smirnova Irina , Kasho Vladimir , Choe Jun-Yong , Altenbach Christian , Hubbell Wayne L. , Kaback H. Ronald
Published: October 2007

According to x-ray structure, the lactose permease (LacY) is a monomer organized into N- and C-terminal six-helix bundles that form a deep internal cavity open on the cytoplasmic side with a single sugar-binding site at the apex. The periplasmic side of the molecule is closed. During sugar/H
+
symport, a cavity facing the periplasmic side is thought to open with closure of the inward-facing cytoplasmic cavity so that the sugar-binding site is alternately accessible to either face of the membrane. Double electron–electron resonance (DEER) is used here to measure interhelical distance changes induced by sugar binding to LacY. Nitroxide-labeled paired-Cys replacements were constructed at the ends of transmembrane helices on the cytoplasmic or periplasmic sides of wild-type LacY and in the conformationally restricted mutant Cys-154→Gly. Distances were then determined in the presence of galactosidic or nongalactosidic sugars. Strikingly, specific binding causes conformational rearrangement on both sides of the molecule. On the cytoplasmic side, each of six nitroxide-labeled pairs exhibits decreased interspin distances ranging from 4 to 21 Å. Conversely, on the periplasmic side, each of three spin-labeled pairs shows increased distances ranging from 4 to 14 Å. Thus, the inward-facing cytoplasmic cavity closes, and a cleft opens on the tightly packed periplasmic side. In the Cys-154→Gly mutant, sugar-induced closing is observed on the cytoplasmic face, but little or no change occurs on periplasmic side. The DEER measurements in conjunction with molecular modeling based on the x-ray structure provide strong support for the alternative access model and reveal a structure for the outward-facing conformer of LacY.
A global review of the threat of
Phytophthora ramorum
infections and the prospects for effective control strategies.
Authors: Appiah A. A.
Published: October 2007

Phytopathogenic Oomycetes continue to demonstrate their historic dominance as major plant pathogens capable of causing serious epidemics in crops and forest ecosystems. The emergence of
Phytophthora ramorum
as a devastating non-host-specific pathogen of both ornamentals and forest tree species in North America and Europe has rekindled the continuous battle between man, through his activities that have tremendous impact on the natural ecological balance, and pathogens, which are constantly evolving, causing significant damage to plants. This paper provides a global up-to-date review of the threats of
P. ramorum
and the progress made in research and management efforts. It also discusses the need for continual vigilance and for serious consideration of new reports of unknown diseases and their associated pathogens, as these become established in our constantly changing ecosystem with severe consequences to man and his way of life.
Applications of horse genomics.
Authors: Bailey E.
Published: October 2007

Completion of the entire horse DNA sequence was a watershed event for horse research. From this time onwards, scientists need not clone and sequence genes before studying gene expression and genetic variation among horses. This information has become freely available online. Applications have already been made in the form of diagnostic tests for inherited diseases and coat colour patterns. As the field of genomics matures, we will begin to see applications for nonhereditary traits. Indeed, everything we do to a horse changes the set of genes expressed in muscle, lungs, liver, immune systems, gut and elsewhere. Understanding the impact of management on gene expression will lead to new management systems and therapeutic treatments to benefit the health and welfare of horses.
Using geographic information systems to assess pesticide risks to groundwater.
Authors: Salvucci A. E. , Walter M. T.
Published: October 2007

The increasing availability and subsequent use of geographic information system (GIS) technologies has shifted groundwater risk assessment from site-specific or field-scale analyses to watershed- and regional-scale evaluations. This review recognizes two primary categories of pesticide risk assessment: namely, vulnerability-index methods and physically-based simulation models. The critical challenge to future advances of groundwater risk assessment will be improving our understanding of how critical flow parameters are spatially distributed, especially potentially transient features such as macropores.
The local Gromov-Witten theory of curves
Authors: Bryan Jim , Pandharipande Rahul
Published: October 2007

The local Gromov-Witten theory of curves is solved by localization and degeneration methods. Localization is used for the exact evaluation of basic integrals in the local Gromov-Witten theory ofP1\mathbb P^1. A TQFT formalism is defined via degeneration to capture higher genus curves. Together, the results provide a complete and effective solution. The local Gromov-Witten theory of curves is equivalent to the local Donaldson-Thomas theory of curves, the quantum cohomology of the Hilbert scheme points ofC2\mathbb C^2, and the orbifold quantum cohomology of the symmetric product ofC2\mathbb C^2. The results of the paper provide the local Gromov-Witten calculations required for the proofs of these equivalences.
Schubert polynomials for the affine Grassmannian
Authors: Lam Thomas
Published: October 2007

Confirming a conjecture of Mark Shimozono, we identify polynomial representatives for the Schubert classes of the affine Grassmannian as the

k
k

-Schur functions in homology and affine Schur functions in cohomology. The results are obtained by connecting earlier combinatorial work of ours to certain subalgebras of Kostant and Kumar’s nilHecke ring and to work of Peterson on the homology of based loops on a compact group. As combinatorial corollaries, we settle a number of positivity conjectures concerning

k
k

-Schur functions, affine Stanley symmetric functions and cylindric Schur functions.
The conformally invariant measure on self-avoiding loops
Authors: Werner Wendelin
Published: October 2007

We show that there exists a unique (up to multiplication by constants) and natural measure on simple loops in the plane and on each Riemann surface, such that the measure is conformally invariant and also invariant under restriction (i.e. the measure on a Riemann surfaceS′S’that is contained in another Riemann surfaceSSis just the measure onSSrestricted to those loops that stay inS′S’). We study some of its properties and consequences concerning outer boundaries of critical percolation clusters and Brownian loops.
Formal degrees and adjoint 𝛾-factors
Authors: Hiraga Kaoru , Ichino Atsushi , Ikeda Tamotsu
Published: October 2007

We give a conjectural formula for the formal degree of a discrete series representation in terms of the adjoint

γ
\gamma

-factor. Our conjecture is supported by various examples and is compatible with the Weyl dimension formula. Using twisted endoscopy, we also verify the conjecture for a stable discrete series representation of

U
⁡
(
3
)

\operatorname {U}(3)

over a non-archimedean local field of characteristic zero.
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data
Authors: Talloen Willem , Clevert Djork-Arné , Hochreiter Sepp , Amaratunga Dhammika , Bijnens Luc , Kass Stefan , Göhlmann Hinrich W.H.
Published: October 2007

Motivation: DNA microarray technology typically generates many measurements of which only a relatively small subset is informative for the interpretation of the experiment. To avoid false positive results, it is therefore critical to select the informative genes from the large noisy data before the actual analysis. Most currently available filtering techniques are supervised and therefore suffer from a potential risk of overfitting. The unsupervised filtering techniques, on the other hand, are either not very efficient or too stringent as they may mix up signal with noise. We propose to use the multiple probes measuring the same target mRNA as repeated measures to quantify the signal-to-noise ratio of that specific probe set. A Bayesian factor analysis with specifically chosen prior settings, which models this probe level information, is providing an objective feature filtering technique, named informative/non-informative calls (I/NI calls).

Results: Based on 30 real-life data sets (including various human, rat, mice and Arabidopsis studies) and a spiked-in data set, it is shown that I/NI calls is highly effective, with exclusion rates ranging from 70% to 99%. Consequently, it offers a critical solution to the curse of high-dimensionality in the analysis of microarray data.

Availability: This filtering approach is publicly available as a function implemented in the R package FARMS (www.bioinf.jku.at/software/farms/farms.html).

Contact:  wtalloen@prdbe.jnj.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Rodent sociality and parasite diversity
Authors: Bordes Frédéric , Blumstein Daniel T , Morand Serge
Published: October 2007

The risk of parasitism is considered to be a general cost of sociality and individuals living in larger groups are typically considered to be more likely to be infected with parasites. However, contradictory results have been reported for the relationship between group size and infection by directly transmitted parasites. We used independent contrasts to examine the relationship between an index of sociality in rodents and the diversity of their macroparasites (helminths and arthropods such as fleas, ticks, suckling lice and mesostigmatid mites). We found that the species richness of directly transmitted ectoparasites, but not endoparasites, decreased significantly with the level of rodent sociality. A greater homogeneity in the biotic environment (i.e. a reduced number of cohabiting host species) of the more social species may have reduced ectoparasites' diversity by impairing ectoparasites transmission and exchange. Our finding may also result from beneficial outcomes of social living that include behavioural defences, like allogrooming, and the increased avoidance of parasites through dilution effects.
Fear, human shields and the redistribution of prey and predators in protected areas
Authors: Berger Joel
Published: October 2007

Protected areas form crucial baselines to judge ecological change, yet areas of Africa, Asia and North America that retain large carnivores are under intense economic and political pressures to accommodate massive human visitation and attendant infrastructure. An unintended consequence is the strong modulation of the three-way interaction involving people, predators and prey, a dynamic that questions the extent to which animal distributions and interactions are independent of subtle human influences. Here, I capitalize on the remarkable 9-day synchronicity in which 90% of moose neonates in the Yellowstone Ecosystem are born, to demonstrate a substantive change in how prey avoid predators; birth sites shift away from traffic-averse brown bears and towards paved roads. The decade-long modification was associated with carnivore recolonization, but neither mothers in bear-free areas nor non-parous females altered patterns of landscape use. These findings offer rigorous support that mammals use humans to shield against carnivores and raise the possibility that redistribution has occurred in other mammalian taxa due to human presence in ways we have yet to anticipate. To interpret ecologically functioning systems within parks, we must now also account for indirect anthropogenic effects on species distributions and behaviour.
Blow up and instability of solitary wave solutions to a generalized Kadomtsev–Petviashvili equation and two-dimensional Benjamin–Ono equations
Authors: Chen Jianqing , Guo Boling , Han Yongqian
Published: October 2007

Let

with
p
being the ratio of an even to an odd integer. For the generalized Kadomtsev–Petviashvili equation, coupled with Benjamin–Ono equations, in the form

it is proved that the solutions blow up in finite time even for those initial data with positive energy. As a by-product, it is proved that for all

, the solitary waves

are strongly unstable if

. This result, even in a special case

, improves a previous work by Liu (Liu 2001
Trans. AMS
353
, 191–208) where the instability of solitary waves was proved only in the case of

.
A sequential importance sampling filter with a new proposal distribution for state and parameter estimation of nonlinear dynamical systems
Authors: Ghosh Shuva J , Manohar C.S , Roy D
Published: October 2007

The problem of estimating parameters of nonlinear dynamical systems based on incomplete noisy measurements is considered within the framework of Bayesian filtering using Monte Carlo simulations. The measurement noise and unmodelled dynamics are represented through additive and/or multiplicative Gaussian white noise processes. Truncated Ito–Taylor expansions are used to discretize these equations leading to discrete maps containing a set of multiple stochastic integrals. These integrals, in general, constitute a set of non-Gaussian random variables. The system parameters to be determined are declared as additional state variables. The parameter identification problem is solved through a new sequential importance sampling filter. This involves Ito–Taylor expansions of nonlinear terms in the measurement equation and the development of an ideal proposal density function while accounting for the non-Gaussian terms appearing in the governing equations. Numerical illustrations on parameter identification of a few nonlinear oscillators and a geometrically nonlinear Euler–Bernoulli beam reveal a remarkably improved performance of the proposed methods over one of the best known algorithms, i.e. the unscented particle filter.
Apoptosis and autophagy as mechanisms of dinoflagellate symbiont release during cnidarian bleaching: every which way you lose
Authors: Dunn Simon R , Schnitzler Christine E , Weis Virginia M
Published: October 2007

Cnidarian bleaching results from the breakdown in the symbiosis between the host cnidarian and its dinoflagellate symbiont. Coral bleaching in recent years has increasingly caused degradation and mortality of coral reefs on a global scale. Although much is understood about the environmental causes of bleaching, the underlying cellular mechanisms of symbiont release that drive the process are just beginning to be described. In this study, we investigated the roles of two cellular pathways, host cell apoptosis and autophagy, in the bleaching process of the symbiotic anemone
Aiptasia pallida
. Host cell apoptosis was experimentally manipulated using gene knockdown of an anemone caspase by RNA interference, chemical inhibition of caspase using ZVAD-fmk and an apoptosis-inducer wortmannin. Autophagy was manipulated by chemical inhibition using wortmannin or induction using rapamycin. The applications of multiple single treatments resulted in some increased bleaching in anemones under control conditions but no significant drop in bleaching in individuals subjected to a hyperthermic stress. These results indicated that no single pathway is responsible for symbiont release during bleaching. However, when multiple inhibitors were applied simultaneously to block both apoptosis and autophagy, there was a significant reduction in bleaching in heat-stressed anemones. Our results allow us to formulate a model for cellular processes involved in the control of cnidarian bleaching where apoptosis and autophagy act together in a see-saw mechanism such that if one is inhibited the other is induced. Similar interconnectivity between apoptosis and autophagy has previously been shown in vertebrates including involvement in an innate immune response to pathogens and parasites. This suggests that the bleaching response could be a modified immune response that recognizes and removes dysfunctional symbionts.
Convergent setal morphology in sand-covering spiders suggests a design principle for particle capture
Authors: Duncan Rebecca P , Autumn Kellar , Binford Greta J
Published: October 2007

Sicarius
and
Homalonychus
are unrelated, desert-dwelling spiders that independently evolved the ability to cover themselves in fine sand particles, making them cryptic against their background. Observations that particles associate with these spiders' setae inspired us to investigate the role of setal microstructure in particle capture and retention. Here we report that
Sicarius
and
Homalonychus
convergently evolved numerous high aspect ratio, flexible fibres that we call ‘hairlettes’ protruding from the setal shaft. We demonstrate that particles attach more densely to regions of
Homalonychus
with hairlettes than to other regions of the same animal where hairlettes are absent, and document close contact of hairlettes to sand particles that persists after applying force. Mathematical models further suggest that adhesion of hairlettes to sand particles is a sufficient mechanism of particle capture and retention. Together, these data provide the first evidence that hairlettes facilitate sand retention through intermolecular adhesion to particles. Their independent evolutionary origins in
Sicarius
and
Homalonychus
suggest that the unique setal structure is adaptive and represents a general biomechanical mechanism for sand capture to cuticle. This discovery has implications for the design of inventions inspired by this system, from camouflage to the management of granular systems.