bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictors of Accurate Maternal Perception of Their Preschool Child's Weight Status Among Hispanic WIC Participants
Authors: Chaparro M. Pia , Langellier Brent A. , Kim Loan P. , Whaley Shannon E.
Published: May 2011

Childhood obesity is a growing problem in the United States. Parental perception of their children's weight status is a key factor that needs to be considered when developing prevention programs for preschool children. Using a randomly selected sample of participants of Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in Los Angeles County, we assessed accuracy of maternal perceptions of their children's weight status by comparing children's weight classification to the mothers' response to the question “Do you consider your child to be overweight, underweight or about right weight for (his) (her) height?” Additionally, we identified possible predictors of accurate maternal perception of their children's weight status by conducting a logistic regression model with child's gender, child's birth weight, maternal age, maternal BMI, maternal education, maternal acculturation level, and maternal language preference as potential predictors. Almost all mothers in the study classified their overweight or obese child as being about the right weight (93.6% and 77.5% of mothers, respectively). Maternal BMI and child's birth weight were the only predictors of maternal perception of their child's weight. Both were negatively associated with accuracy, with higher maternal BMI and higher infant birthweight associated with less accurate maternal perception of child weight. Parents need to be educated on the importance of childhood obesity and how to identify if their children are overweight or obese. If parents fail to recognize that their overweight child is overweight, then it is unlikely that they will recognize that interventions targeting obesity are relevant to their families.
Neural Responses to Visual Food Stimuli After a Normal vs. Higher Protein Breakfast in Breakfast‐Skipping Teens: A Pilot fMRI Study
Authors: Leidy Heather J. , Lepping Rebecca J. , Savage Cary R. , Harris Corey T.
Published: May 2011

This functional magnetic resonance imaging (fMRI) pilot study identified whether breakfast consumption would alter the neural activity in brain regions associated with food motivation and reward in overweight “breakfast skipping” (BS) adolescent girls and examined whether increased protein at breakfast would lead to additional alterations. Ten girls (Age: 15 ± 1 years; BMI percentile 93 ± 1%; BS 5 ± 1×/week) completed 3 testing days. Following the BS day, the participants were provided with, in randomized order, normal protein (NP; 18 ± 1 g protein) or higher protein (HP; 50 ± 1 g protein) breakfast meals to consume at home for 6 days. On day 7 of each pattern, the participants came to the laboratory to consume their respective breakfast followed by appetite questionnaires and an fMRI brain scan to identify brain activation responses to viewing food vs. nonfood images prior to lunch. Breakfast consumption led to enduring (i.e., 3‐h post breakfast) reductions in neural activation in the hippocampus, amygdala, cingulate, and parahippocampus vs. BS. HP led to enduring reductions in insula and middle prefrontal cortex activation vs. NP. Hippocampal, amygdala, cingulate, and insular activations were correlated with appetite and inversely correlated with satiety. In summary, the addition of breakfast led to alterations in brain activation in regions previously associated with food motivation and reward with additional alterations following the higher‐protein breakfast. These data suggest that increased dietary protein at breakfast might be a beneficial strategy to reduce reward‐driven eating behavior in overweight teen girls. Due to the small sample size, caution is warranted when interpreting these preliminary findings.
Initial cone-in-shell fast-ignition experiments on OMEGA
Authors: Theobald W. , Solodov A. A. , Stoeckl C. , Anderson K. S. , Betti R. , Boehly T. R. , Craxton R. S. , Delettrez J. A. , Dorrer C. , Frenje J. A. , Glebov V. Yu. , Habara H. , Tanaka K. A. , Knauer J. P. , Lauck R. , Marshall F. J. , Marshall K. L. , Meyerhofer D. D. , Nilson P. M. , Patel P. K. , Chen H. , Sangster T. C. , Seka W. , Sinenian N. , Ma T. , Beg F. N. , Giraldez E. , Stephens R. B.
Published: May 2011

Fast ignition is a two-step inertial confinement fusion concept where megaelectron volt electrons ignite the compressed core of an imploded fuel capsule driven by a relatively low-implosion velocity. Initial surrogate cone-in-shell, fast-ignitor experiments using a highly shaped driver pulse to assemble a dense core in front of the cone tip were performed on the OMEGA/OMEGA EP Laser [T. R. Boehly et al., Opt. Commun. 133, 495 (1997); L. J. Waxer et al., Opt. Photonics News 16, 30 (2005)]. With optimal timing, the OMEGA EP pulse produced up to ∼1.4 × 107 additional neutrons which is a factor of ∼4 more neutrons than without short-pulse heating. Shock-breakout measurements performed with the same targets and drive conditions demonstrate an intact cone tip at the time when the additional neutrons are produced. Velocity interferometer system for any reflector measurements show that x-rays from the shell’s coronal plasma preheat the inner cone wall of thin-walled Au cones, while the thick-walled cones that are used in the integrated experiments are not affected by preheat.
Expansion dynamics of laser produced plasma
Authors: Doggett B. , Lunney J. G.
Published: May 2011

We consider the applicability of the isentropic, adiabatic gas dynamical model of plume expansion for laser ablation in vacuum. We show that the model can be applied to ionized plumes and estimate the upper electron temperature limit on the applicability of the isentropic approximation. The model predictions are compared with Langmuir ion probe measurements and deposition profiles obtained for excimer laser ablation of silver.
Symmetry tuning for ignition capsules via the symcap technique
Authors: Kyrala G. A. , Kline J. L. , Dixit S. , Glenzer S. , Kalantar D. , Bradley D. , Izumi N. , Meezan N. , Landen O. , Callahan D. , Weber S. V. , Holder J. P. , Glenn S. , Edwards M. J. , Koch J. , Suter L. J. , Haan S. W. , Town R. P. J. , Michel P. , Jones O. , Langer S. , Moody J. D. , Dewald E. L. , Ma T. , Ralph J. , Hamza A. , Dzenitis E. , Kilkenny J.
Published: May 2011

Symmetry of an implosion is crucial to get ignition successfully. Several methods of control and measurement of symmetry have been applied on many laser systems with mm size hohlraums and ns pulses. On the National Ignition Facility [Moses et al., Phys. Plasmas 16, 041006 (2009)] we have large hohlraums of cm scale, long drive pulses of 10 s of ns, and a large number of beams with the option to tune their wavelengths. Here we discuss how we used the x-ray self-emission from imploding surrogates to ignition capsules (symcaps) to measure the symmetry of the implosion. We show that symcaps are good surrogates for low order symmetry, though having lower sensitivity to distortions than ignition capsules. We demonstrate the ability to transfer energy between laser beams in a gas-filled hohlraum using wavelength tuning, successfully tuning the lowest order symmetry of the symcaps in different size hohlraums at different laser energies within the specification established by calculations for successful ignition.
Integrated active mixing and biosensing using low frequency vibrating mixer and Love-wave sensor for real time detection of antibody binding event
Authors: Kardous F. , El Fissi L. , Friedt J-M , Bastien F. , Boireau W. , Yahiaoui R. , Manceau J.-F. , Ballandras S.
Published: May 2011

The development of lab-on-chip devices is expected to dramatically change biochemical analyses, allowing for a notable increase of processing quality and throughput, provided the induced chemical reactions are well controlled. In this work, we investigate the impact of local acoustic mixing to promote or accelerate such biochemical reactions, such as antibody grafting on activated surfaces. During microarray building, the spotting mode leads to low efficiency in the ligand grafting and heterogeneities which limits its performances. To improve the transfer rate, we induce a hydrodynamic flow in the spotted droplet to disrupt the steady state during antibody grafting. To prove that acoustic mixing increases the antibody transfer rate to the biochip surface, we have used a Love-wave sensor allowing for real-time monitoring of the biological reaction for different operating conditions (with or without mixing). An analysis of the impact of the proposed mixing on grafting kinetics is proposed and finally checked in the case of antibody-antigen combination.
Varying the concentration of single walled carbon nanotubes in thin film polymer composites, and its effect on thermoelectric power
Authors: Hewitt C. A. , Kaiser A. B. , Roth S. , Craps M. , Czerw R. , Carroll D. L.
Published: May 2011

Resistivity and thermoelectric power (TEP) measurements were conducted on single walled carbon nanotube (SWNT), polyvinylidene fluoride composite thin films of varying SWNT concentrations. This heterogeneous material was used in order to utilize the good electrical conductance of the nanotubes and the poor thermal conductance of the polymer to increase the figure of merit (ZT). As the nanotube weight percent decreased from 100% to 5%, the beneficial effects of the TEP increase and thermal conductivity decrease outweighed the negative effect of decreased electrical conductivity, resulting in an increase in ZT by a factor of 100.
Deconvolution of Thomson scattering temperature profiles
Authors: Scannell R. , Beurskens M. , Carolan P. G. , Kirk A. , Walsh M. , O’Gorman T. , Osborne T. H.
Published: May 2011

Deconvolution of Thomson scattering (TS) profiles is required when the gradient length of the electron temperature (Te) or density (ne) are comparable to the instrument function length (ΔR). The most correct method for deconvolution to obtain underlying Te and ne profiles is by consideration of scattered signals. However, deconvolution at the scattered signal level is complex since it requires knowledge of all spectral and absolute calibration data. In this paper a simple technique is presented where only knowledge of the instrument function I(r) and the measured profiles, Te, observed(r) and ne, observed(r), are required to obtain underlying Te(r) and ne(r). This method is appropriate for most TS systems and is particularly important where high spatial sampling is obtained relative to ΔR.
Quantum stochastic processes for maps on Hilbert C*-modules
Authors: Heo Jaeseong , Ji Un Cig
Published: May 2011

We discuss pairs (ϕ, Φ) of maps, where ϕ is a map between C*-algebras and Φ is a ϕ-module map between Hilbert C*-modules, which are generalization of representations of Hilbert C*-modules. A covariant version of Stinespring's theorem for such a pair (ϕ, Φ) is established, and quantum stochastic processes constructed from pairs ({ϕt}, {Φt}) of families of such maps are studied. We prove that the quantum stochastic process J = {Jt} constructed from a ϕ-quantum dynamical semigroup Φ = {Φt} is a j-map for the quantum stochastic process j = {jt} constructed from the given quantum dynamical semigroup ϕ = {ϕt}, and that J is covariant if the ϕ-quantum dynamical semigroup Φ is covariant.
Anisotropic structural and optical properties of a-plane (112¯) AlInN nearly-lattice-matched to GaN
Authors: Laskar Masihhur R. , Ganguli Tapas , Rahman A. A. , Arora Ashish , Hatui Nirupam , Gokhale M. R. , Ghosh Sandip , Bhattacharya Arnab
Published: May 2011

We report epitaxial growth of a-plane (112¯0) AlInN layers nearly-lattice-matched to GaN. Unlike for c-plane oriented epilayers, a-plane Al1−xInxN cannot be simultaneously lattice-matched to GaN in both in-plane directions. We study the influence of temperature on indium incorporation and obtain nearly-lattice-matched Al0.81In0.19N at a growth temperature of 760 °C. We outline a procedure to check in-plane lattice mismatch using high-resolution x-ray diffraction, and evaluate the strain and critical thickness. Polarization-resolved optical transmission measurements of the Al0.81In0.19N epilayer reveal a difference in band gap of ∼140 meV between (electric field) E∥c[0001]-axis and E⊥c conditions with room-temperature photoluminescence peaked at 3.38eV strongly polarized with E∥c, in good agreement with strain-dependent band-structure calculations.
Lithium fiber growth on the anode in a nanowire lithium ion battery during charging
Authors: Liu Xiao Hua , Zhong Li , Zhang Li Qiang , Kushima Akihiro , Mao Scott X. , Li Ju , Ye Zhi Zhen , Sullivan John P. , Huang Jian Yu
Published: May 2011

Lithium (Li) dendrite formation has been recognized as one of the major safety concerns for Li metal batteries but not for conventional Li ion batteries (LIBs) where Li metal is not used. With the advanced in situ transmission electron microscopy enabling direct observation of battery operation, we found that Li fibers with length up to 35 μm grew on nanowire tip after charging. The Li fibers growth were highly directional, i.e., nucleating from the nanowire tip, and extending along the nanowire axis, which was attributed to the strong electric field enhancement effect induced by the sharp nanowire tip. This study reveals a potential safety concern of short-circuit failure for LIBs using nanowire anodes.
Thermoelectric figure of merit calculations for semiconducting nanowires
Authors: Cornett Jane E. , Rabin Oded
Published: May 2011

A model for the thermoelectric properties of nanowires was used to demonstrate the contrasting influences of quantization and degeneracy on the thermoelectric power factor. The prevailing notion that quantum confinement benefits the thermoelectric power factor is supported by the model when a single-subband dominates transport. When transport involves multiple subbands, the thermoelectric power factor in fact decreases (to ∼62% of the bulk value) as the wire radius is initially reduced. This work correctly models the power factor for wire sizes ranging from the nanoscale to bulk and settles the discrepancies between theoretical and measured thermoelectric power factors in nanowires and other nanoscale systems.
Highly sensitive linear spin valve realized by tuning 90° coupling in a NiFe/thin IrMn/biased NiFe structure through nonmagnetic spacer insertion
Authors: Liu T. , Zhu T. , Cai J. W. , Sun L.
Published: May 2011

90° magnetic coupling between a free NiFe layer and an exchange biased NiFe layer has been realized using a thin IrMn intermediate film. This 90° coupling remains after the addition of a nonmagnetic spacer (Cu, Pt, Ru, or Ta) at the free NiFe/IrMn interface. Effective anisotropy strength of the free layer can be readily adjusted through nonmagnetic layer thickness control. Spacer layer thickness increase results in significant reduction of free layer coercivity and field offset, much faster than the 90° coupling strength drop. Linear spin valves of adjustable high field sensitivity without field offset have been demonstrated using this structure.
Recombination coefficients of GaN-based laser diodes
Authors: Scheibenzuber W. G. , Schwarz U. T. , Sulmoni L. , Dorsaz J. , Carlin J.-F. , Grandjean N.
Published: May 2011

We measure the charge carrier recombination coefficients of InGaN quantum wells by analyzing the dynamical properties of (Al,In)GaN laser diodes emitting in the violet spectral range. Relaxation oscillations and turn-on delays are fitted to a rate equation model including a charge carrier density dependent recombination rate. Using optical gain spectroscopy we can directly determine the injection efficiency of the devices and thereby separate the effect of charge carrier leakage from that of carrier recombination. We find a third-order recombination coefficient of (4.5±0.9)×10-31cm6s-1 which is in agreement with theoretical predictions for phonon- and alloy-disorder-assisted Auger scattering.
Terahertz emission from InAs/GaAs quantum dot based photoconductive devices
Authors: Daghestani N. S. , Cataluna M. A. , Berry G. , Ross G. , Rose M. J.
Published: May 2011

We report terahertz (THz) generation from InAs/GaAs quantum-dot based photoconductive antennae with femtosecond optical excitation at 800 nm, with an estimated infrared-to-THz conversion efficiency of ∼0.9×10−5. The quantum dots act as recombination centers for carriers generated in the GaAs layers within the structure. Photoreflective pump-probe measurements reveal a decrease in the carrier lifetime when a lateral voltage is applied. These antennae displayed resilience to Joule heating when operated at a field strength of 46 MV/m. The breakdown field of the devices was 48 MV/m, which is comparable to the breakdown field of bulk GaAs.
Effects of gas pressure on 60/13.56 MHz dual-frequency capacitively coupled plasmas
Authors: Yuan Q. H. , Yin G. Q. , Xin Y. , Ning Z. Y.
Published: May 2011

The electron energy probability functions (EEPFs) were measured with increasing gas pressure in 60/13.56 MHz dual-frequency capacitively coupled plasma (DF-CCP) using compensated Langmiur electrostatic probe. The transition pressure of heating mode from collisionless to collisional heating in 60/13.56 MHz DF-CCP is found to be significantly lower than that in 13.56 MHz single-frequency CCP. As the pressure increases, the EEPFs change from bi-Maxwellian to Druyvesteyn type which is similar with that in 60 MHz single-frequency CCP. The pressure dependence of electron densities, effective electron temperatures, floating potentials, and plasma potentials in 60/13.56 MHz DF-CCP were measured and were compared with that in 60 MHz single-frequency CCP. The pressure dependence of these plasma parameters in 60/13.56 MHz DF-CCP is similar with that in 60 MHz single-frequency CCP.
Thermodynamic theory of controlled formation of strained quantum dots on hole-patterned substrates
Authors: Li Xinlei , Ouyang Gang
Published: May 2011

We have established a thermodynamic model to address the strained quantum dots (QDs) formation on hole-patterned substrates. Based on the investigation on the morphologies at the initial stages of thin wetting layer growth, we found that the thickness of wetting layer inside of hole is larger than that on the terrace between holes due to the concave surface during the initial layer-by-layer growth process. The increased thickness on the inside of hole results in the different formation sites for different growth temperatures, i.e., QDs form on the inside of hole at low temperature, and QDs form on the terrace between holes at high temperature.
Measurements of the critical strain for rippling in carbon nanotubes
Authors: Jackman H. , Krakhmalev P. , Svensson K.
Published: May 2011

We report measurements of the bending stiffness in free standing carbon nanotubes, using atomic force microscopy inside a scanning electron microscope. Two regimes with different bending stiffness were observed, indicative of a rippling deformation at high curvatures. The observed critical strains for rippling were in the order of a few percent and comparable to previous modeling predictions. We have also found indications that the presence of defects can give a higher critical strain value and a concomitant reduction in Young’s modulus.
Magnetic diode exploiting giant positive magnetoresistance in ferrite/semiconductor heterostructures
Authors: Adhikari R. , Sarkar A. , Patta G. R. , Das A. K.
Published: May 2011

Fe 3 O 4 / p-Si and NiFe2O4/p-Si heterostructures were fabricated and their electrotransport and magnetotransport properties were studied. Both heterostructures showed rectifying as well as spin valve property below a critical temperature of 50 K which is independent of Curie temperature of magnetic films. Fe3O4/p-Si and NiFe2O4/p-Si heterostructures show giant positive junction magnetoresistance (JMR) of 2000% and 200% at 10 K, respectively. The JMR for Fe3O4/p-Si saturates at a much lower magnetic field compared to the other heterostructures, thus making it a better choice for magnetic diode.
2.4 W room temperature continuous wave operation of distributed feedback quantum cascade lasers
Authors: Lu Q. Y. , Bai Y. , Bandyopadhyay N. , Slivken S. , Razeghi M.
Published: May 2011

We demonstrate high power continuous-wave room-temperature operation surface-grating distributed feedback quantum cascade lasers at 4.8 μm. High power single mode operation benefits from a combination of high-reflection and antireflection coatings. Maximum single-facet continuous-wave output power of 2.4 W and peak wall plug efficiency of 10% from one facet is obtained at 298 K. Single mode operation with a side mode suppression ratio of 30 dB and single-lobed far field without beam steering is observed.
Experimental investigation of a Ka band high power millimeter wave generator operated at low guiding magnetic field
Authors: Zhu Jun , Shu Ting , Zhang Jun , Li Guolin , Zhang Zehai , Fan Yuwei
Published: May 2011

An overmoded slow wave type Ka band generator is investigated experimentally to produce high power millimeter waves in this paper. The experiments were carried out at the TORCH-01 accelerator. The produced microwave frequency was measured by dispersive line method, and the power was estimated by integrating over the radiation pattern at far field. With relatively low guiding magnetic field of 0.8 T and diode voltage and beam current of 590 kV and 5.2 kA, respectively, a 33.56 GHz millimeter wave with an output power of 320 MW was generated, and the microwave mode was quasi-TM01 mode.
Effect of sol-age on the surface and optical properties of sol-gel derived mesoporous zirconia thin films
Authors: Kumar Manish , Reddy G. B.
Published: May 2011

Mesoporous ZrO2 thin films have been deposited by a modified sol-gel dip coating technique using HCl as catalyst. Effects of sol-age on the surface and on the optical properties are studied. Transmission electron micrographs of the films reveal the pore dimensions in mesoporous regime. A strong correlation in surface topography with sol-age has been observed where increase in sol-age induces a systematic enhancement in the value of root mean square roughness of the films. Optical study shows that deposited films have high transmittance and an enhancement of 5.6 times in porosity in films prepared with sol-age of 10 days with respect to that of 1 day. Band gap estimation by Tauc's plots of films is observed to 5.74 eV, which shows invariance with the sol-age.
Identifying sources and trends for productivity growth in a sample of Queensland broad-acre beef enterprises
Authors: Gregg Daniel , Rolfe John
Published: May 2011

The research reported in this paper considers the question of the possible sources of productivity change in the broad-acre beef sector in northern Australia over the last decade. Analysis is conducted over the components of total factor productivity growth for a subset of broad-acre beef production enterprises in Queensland. Specifically we consider the contributions of technological progress, scale changes (changes in the ‘size’ of an enterprise), and technical efficiency (how efficiently an enterprise combines their inputs to produce output) changes to total factor productivity growth using an index based on a decomposition of productivity change. The analysis employed a form for the production technology, which allowed for linear technological progress over time, accounted for rainfall and differences in land types and allowed for the testing of a range of sources of efficiency change. Results suggested that productivity growth within the sample was strong between 1999 and 2008 averaging 3.8% per year. The majority of this growth appeared to originate from technological progress (average growth of 2.7% per year) but there is the possibility that sample-leakage effects caused relatively low estimated contributions from technical efficiency growth (averaged 1.2% per year). Participation in a privately operated farm-business auditing program appeared to have a positive influence on enterprise technical efficiency.
Nitrogen leaching from sheep-, cattle- and deer-grazed pastures in the Lake Taupo catchment in New Zealand
Authors: Hoogendoorn C. J. , Betteridge K. , Ledgard S. F. , Costall D. A. , Park Z. A. , Theobald P. W.
Published: May 2011

A replicated grazing study measuring nitrogen (N) leaching from cattle-, sheep- and deer-grazed pastures was conducted to investigate the impact of different animal species on N leaching in the Lake Taupo catchment in New Zealand. Leaching losses of nitrate N from intensively grazed pastures on a highly porous pumice soil in the catchment averaged 37, 26 and 25 kg N/ha.year for cattle-, sheep- and deer-grazed areas, respectively, over the 3-year study and were not significantly different (P > 0.05). Leaching losses of ammonium N were much lower (3 kg N/ha.year for all three species of grazer; P > 0.05). Amounts of dissolved organic N leached were significantly higher than that of mineral N (nitrate N + ammonium N), and over the 3-year study averaged 44, 43 and 39 kg N/ha.year for cattle-, sheep- and deer-grazed areas, respectively (P > 0.05). On a stock unit equivalence basis (1 stock unit is equivalent to 550 kg DM consumed/year), cattle-grazed areas leached significantly more mineral N than sheep- or deer-grazed areas (5.5, 2.9 and 3.4 g mineral N leached/24 h grazing by 1 stock unit, for cattle, sheep and deer, respectively) (P < 0.001). Likewise, based on the amount of N apparently consumed (estimated by difference in mass of herbage N pre- and post-grazing), cattle-grazed pastures leached more mineral N than sheep- or deer-grazed pastures (123, 75 and 75 g mineral N/kg N apparently consumed for cattle, sheep and deer, respectively) (P < 0.01). This study gives valuable information on mineral N leaching in a high-rainfall environment on this free-draining pumice soil, and provides new data to assist in developing strategies to mitigate mineral N leaching losses from grazed pastures using different animal species.
Community wildfire protection planning: is the Healthy Forests Restoration Act's vagueness genius?
Authors: Jakes Pamela J. , Nelson Kristen C. , Enzler Sherry A. , Burns Sam , Cheng Antony S. , Sturtevant Victoria , Williams Daniel R. , Bujak Alexander , Brummel Rachel F. , Grayzeck-Souter Stephanie , Staychock Emily
Published: May 2011

The Healthy Forests Restoration Act of 2003 (HFRA) encourages communities to develop community wildfire protection plans (CWPPs) to reduce their wildland fire risk and promote healthier forested ecosystems. Communities who have developed CWPPs have done so using many different processes, resulting in plans with varied form and content. We analysed data from 13 case-study communities to illustrate how the characteristics of HFRA have encouraged communities to develop CWPPs that reflect their local social and ecological contexts. A framework for analysing policy implementation suggests that some elements of HFRA could have made CWPP development and implementation problematic, but these potential shortcomings in the statute have provided communities the freedom to develop CWPPs that are relevant to their conditions and allowed for the development of capacities that communities are using to move forward in several areas.
Water molecule reorganization in cytochrome
c
oxidase revealed by FTIR spectroscopy
Authors: Maréchal Amandine , Rich Peter R.
Published: May 2011

Although internal electron transfer and oxygen reduction chemistry in cytochrome
c
oxidase are fairly well understood, the associated groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. Several possible pathways have been identified from crystallographic structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle. To date, however, comparisons of atomic structures of different oxidases in different redox or ligation states have not provided a consistent answer as to which pathways are operative or the details of their dynamic changes during catalysis. In order to provide an experimental means to address this issue, FTIR spectroscopy in the 3,560–3,800 cm
-1
range has been used to detect weakly H-bonded water molecules in bovine cytochrome
c
oxidase that might change during catalysis. Full redox spectra exhibited at least four signals at 3,674(+), 3,638(+), 3,620(−), and 3,607(+) cm
-1
. A more complex set of signals was observed in spectra of photolysis of the ferrous-CO compound, a reaction that mimics the catalytic oxygen binding step, and their D
2
O and H
2
18
O sensitivities confirmed that they arose from water molecule rearrangements. Fitting with Gaussian components indicated the involvement of up to eight waters in the photolysis transition. Similar signals were also observed in photolysis spectra of the ferrous-CO compound of bacterial C
c
O from
Paracoccus denitrificans
. Such water changes are discussed in relation to roles in hydrophilic channels and proton/electron coupling mechanism.
Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins
Authors: Zhou Huan-Xiang
Published: May 2011

We develop a theory for the rapid search of specific sites on DNA, via a mechanism in which a nonspecifically-bound protein can switch between two conformations. In the “inactive” conformation, the bound protein has favorable, nonspecific interactions with the DNA, but cannot be recognized by the target site. In the “active” conformation, the protein is recognized by the target site but has a very rugged energy surface elsewhere on the DNA. The rate constant for protein binding to the specific site is calculated by an approach in which the protein, after reaching the DNA surface via 3D diffusion, searches for the target site via 1D diffusion while being allowed to escape to the bulk solution. Mindful of the pitfalls of many previous approximate treatments, we validate our approach against a rigorous solution of the problem when the protein has a fixed conformation. In the 1D diffusion toward the specific site, a conformationally switchable protein predominantly adopts the inactive conformation due to the favorable nonspecific interactions with the DNA, thus maximizing the 1D diffusion constant and minimizing the chance of escape to the bulk solution. Once at the target site, a transition to the active conformation allows the protein to be captured. This induced-switch mechanism provides robust speedup of protein-DNA binding rates, and appears to be adopted by many transcription factors and DNA-modifying enzymes.
Laboratory synthesis of an independently reproducing vertebrate species
Authors: Lutes Aracely A. , Baumann Diana P. , Neaves William B. , Baumann Peter
Published: May 2011

Speciation in animals commonly involves an extrinsic barrier to genetic exchange followed by the accumulation of sufficient genetic variation to impede subsequent productive interbreeding. All-female species of whiptail lizards, which originated by interspecific hybridization between sexual progenitors, are an exception to this rule. Here, the arising species instantaneously acquires a novel genotype combining distinctive alleles from two different species, and reproduction by parthenogenesis constitutes an effective intrinsic barrier to genetic exchange. Fertilization of diploid parthenogenetic females by males of sexual species has produced several triploid species, but these instantaneous speciation events have neither been observed in nature nor have they been reconstituted in the laboratory. Here we report the generation of four self-sustaining clonal lineages of a tetraploid species resulting from fertilization of triploid oocytes from a parthenogenetic
Aspidoscelis exsanguis
with haploid sperm from
Aspidoscelis inornata.
Molecular and cytological analysis confirmed the genetic identity of the hybrids and revealed that the females retain the capability of parthenogenetic reproduction characteristic of their triploid mothers. The tetraploid females have established self-perpetuating clonal lineages which are now in the third generation. Our results confirm the hypothesis that secondary hybridization events can lead to asexual lineages of increased ploidy when favorable combinations of parental genomes are assembled. We anticipate that these animals will be a critical tool in understanding the mechanisms underlying the origin and subsequent evolution of asexual amniotes.
Coincident mass extirpation of neotropical amphibians with the emergence of the infectious fungal pathogen
Batrachochytrium dendrobatidis
Authors: Cheng Tina L. , Rovito Sean M. , Wake David B. , Vredenburg Vance T.
Published: May 2011

Amphibians highlight the global biodiversity crisis because ∼40% of all amphibian species are currently in decline. Species have disappeared even in protected habitats (e.g., the enigmatic extinction of the golden toad,
Bufo periglenes
, from Costa Rica). The emergence of a fungal pathogen,
Batrachochytrium dendrobatidis
(Bd), has been implicated in a number of declines that have occurred in the last decade, but few studies have been able to test retroactively whether Bd emergence was linked to earlier declines and extinctions. We describe a noninvasive PCR sampling technique that detects Bd in formalin-preserved museum specimens. We detected Bd by PCR in 83–90% (
n
= 38) of samples that were identified as positive by histology. We examined specimens collected before, during, and after major amphibian decline events at established study sites in southern Mexico, Guatemala, and Costa Rica. A pattern of Bd emergence coincident with decline at these localities is revealed—the absence of Bd over multiple years at all localities followed by the concurrent emergence of Bd in various species at each locality during a period of population decline. The geographical and chronological emergence of Bd at these localities also indicates a southbound spread from southern Mexico in the early 1970s to western Guatemala in the 1980s/1990s and to Monteverde, Costa Rica by 1987. We find evidence of a historical “Bd epidemic wave” that began in Mexico and subsequently spread to Central America. We describe a technique that can be used to screen museum specimens from other amphibian decline sites around the world.
Facilitation versus Inhibition in the Masked Priming Same–Different Matching Task
Authors: Perea Manuel , Moret-Tatay Carmen , Carreiras Manuel
Published: May 2011

In the past years, growing attention has been devoted to the masked priming same–different task introduced by Norris and Kinoshita (2008, Journal of Experimental Psychology: General). However, a number of researchers have raised concerns on the nature of the cognitive processes underlying this task—in particular the suspicion that masked priming effects in this task are mostly inhibitory in nature and may be affected by probe–prime contingency. To examine the pattern of facilitative/inhibitory priming effects in this task, we conducted two experiments with an incremental priming paradigm using four stimulus–onset asynchronies (13, 27, 40, and 53 ms). Experiment 1 was conducted under a predictive-contingency scenario (probe–prime–target; i.e., “same” trials: HOUSE– house– HOUSE vs. house– water– HOUSE; “different” trials: field– house– HOUSE vs. field– water– HOUSE), while Experiment 2 employed a zero-contingency scenario (i.e., “same” trials: HOUSE– house– HOUSE vs. house– water– HOUSE; “different” trials: field– field– HOUSE vs. field– water– HOUSE). Results revealed that, for “same” responses, both facilitation and inhibition increased linearly with prime duration in the two scenarios, whereas the pattern of data varied for “different” responses, as predicted by the Bayesian Reader model.
Practical limits for detection of ferromagnetism using highly sensitive magnetometry techniques
Authors: Pereira L M C , Araújo J P , Van Bael M J , Temst K , Vantomme A
Published: May 2011

Over the last ten years, signatures of high temperature ferromagnetism have been found in thin films and nanoparticles of various materials which are non-ferromagnetic in bulk, from semiconductors to superconductors. These studies often involve state-of-the-art magnetometers working close to the limits of their sensitivity, where magnetic contaminations and measurement artefacts become non-negligible. Because such spurious effects may be involved, the reliability of magnetometry techniques for the detection of ferromagnetism in these new magnetic nanomaterials has been questioned. In this paper, we present a detailed study on magnetic contamination arising from sample processing and handling, describing how it may occur and how it can be avoided or otherwise removed. We demonstrate that, when proper procedures are followed, extrinsic magnetic signals can be reproducibly kept below 5 × 10−7 emu (5 × 10−10 A m2). We also give an overview of the expected levels of contamination when such optimum conditions cannot be guaranteed and analyse the characteristics of the resulting magnetic behaviour, discussing which features may or may not be used as criteria to distinguish it from intrinsic ferromagnetism. Although the measurements were performed using superconducting quantum interference device magnetometers, most of what we describe can also be applied when using alternating-gradient force and vibrating-sample magnetometers.
Heterogeneous ion-induced nucleation in thermal dusty plasmas
Authors: Vishnyakov V I , Kiro S A , Ennan A A
Published: May 2011

Heterogeneous ion-induced nucleation in thermal dusty plasmas such as welding fumes or combustion plasmas containing metals and metal oxide vapours is considered. The influence of nucleus charging as a result of the interphase interaction on the nucleation free energy is determined. It is shown that the environment enrichment by electrons results in the formation of nuclei at lower values of supersaturation than without electrons. The nucleus equilibrium and the critical radii dependences on the plasma temperature and dusty plasma contents are demonstrated.
Heteroepitaxial Ir layers on diamond
Authors: Martovitsky V P , Evlashin S A , Suetin N V , Khmelnitsky R A
Published: May 2011

Ir layers were deposited on single-crystal diamond using magnetron sputtering at substrate temperatures ranging from 830 to 1150 °C. The grown films have high adhesion to diamond and a low surface roughnessRq= 4–6 nm according to the AFM measurements. Crystalline perfection of Ir layers was investigated using x-ray diffraction and heteroepitaxial growth of Ir on diamond was confirmed. Because the lattice parameters of Ir and diamond are significantly different (7.65%) and because the deposition temperature of Ir is low in comparison with its melting point (2443 °C), diffraction reflections of the films are similar to analogous reflections of diamond, but wider. The films consist of elongated crystallites of length 10–100 nm. By broadening the reciprocal lattice points, we conclude that the level of microstresses in the Ir films increases as the substrate temperature during deposition of Ir films on the (0 0 1) diamond substrate increases, and that the level of microstresses decreases for the films on the (0 1 1) substrate. Simultaneously, the misorientation of Ir crystallites on the (0 1 1) substrate also decreases with increasing temperature.
Spin-polarized transport properties of Fe atomic chain adsorbed on zigzag graphene nanoribbons
Authors: Zhang Z L , Chen Y P , Xie Y E , Zhang M , Zhong J X
Published: May 2011

The spin-polarized transport properties of Fe atomic chain adsorbed on zigzag graphene nanoribbons (ZGNRs) are investigated using the density-functional theory in combination with the nonequilibrium Green's function method. We find that the Fe chain has drastic effects on spin-polarized transport properties of ZGNRs compared with a single Fe atom adsorbed on the ZGNRs. When the Fe chain is adsorbed on the centre of the ZGNR, the original semiconductor transforms into metal, showing a very wide range of spin-polarized transport. Particularly, the spin polarization around the Fermi level is up to 100%. This is because the adsorbed Fe chain not only induces many localized states but also has effects on the edge states of ZGNR, which can effectively modulate the spin-polarized transports. The spin polarization of ZGNRs is sensitive to the adsorption site of the Fe chain. When the Fe chain is adsorbed on the edge of ZGNR, the spin degeneracy of conductance is completely broken. The spin polarization is found to be more pronounced because the edge state of one edge is destroyed by the additional Fe chain. These results have direct implications for the control of the spin-dependent conductance in ZGNRs with the adsorption of Fe chains.
Folded bands in metamaterial photonic crystals
Authors: Chen P Y , Poulton C G , Asatryan A A , Steel M J , Botten L C , Martijn de Sterke C , McPhedran R C
Published: May 2011

The dispersion relation of periodic structures that include metamaterials or materials with large anomalous dispersion can give bands with infinite group velocity points. These bands do not span the entire first Brillouin zone but are instead localized ink-space. We show that these points arise when both positive and negative elements are present, with the group index rather than the refractive index being the controlling quantity. A rigorous condition and two approximations are derived, each showing that an appropriate weighted average of group index being zero leads to infinite group velocity points.
The ALPS project release 2.0: open source software for strongly correlated systems
Authors: Bauer B , Carr L D , Evertz H G , Feiguin A , Freire J , Fuchs S , Gamper L , Gukelberger J , Gull E , Guertler S , Hehn A , Igarashi R , Isakov S V , Koop D , Ma P N , Mates P , Matsuo H , Parcollet O , Pawłowski G , Picon J D , Pollet L , Santos E , Scarola V W , Schollwöck U , Silva C , Surer B , Todo S , Trebst S , Troyer M , Wall M L , Werner P , Wessel S
Published: May 2011

We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations)
project, an open source software project to develop libraries and application programs for
the simulation of strongly correlated quantum lattice models such as quantum magnets,
lattice bosons, and strongly correlated fermion systems. The code development is centered
on common XML and HDF5 data formats, libraries to simplify and speed up code
development, common evaluation and plotting tools, and simulation programs. The
programs enable non-experts to start carrying out serial or parallel numerical simulations
by providing basic implementations of the important algorithms for quantum lattice
models: classical and quantum Monte Carlo (QMC) using non-local updates,
extended ensemble simulations, exact and full diagonalization (ED), the density
matrix renormalization group (DMRG) both in a static version and a dynamic
time-evolving block decimation (TEBD) code, and quantum Monte Carlo solvers for
dynamical mean field theory (DMFT). The ALPS libraries provide a powerful
framework for programmers to develop their own applications, which, for instance,
greatly simplify the steps of porting a serial code onto a parallel, distributed
memory machine. Major changes in release 2.0 include the use of HDF5 for binary
data, evaluation tools in Python, support for the Windows operating system,
the use of CMake as build system and binary installation packages for Mac OS
X and Windows, and integration with the VisTrails workflow provenance tool.
The software is available from our web server at http://alps.comp-phys.org/.
A 𝐾-theoretic proof of the Morse index theorem in semi-Riemannian geometry
Authors: Waterstraat Nils
Published: May 2011

We give a short proof of the Morse index theorem for geodesics in semi-Riemannian manifolds by using

K
K

-theory. This makes the Morse index theorem reminiscent of the Atiyah-Singer index theorem for families of selfadjoint elliptic operators.
DREME: motif discovery in transcription factor ChIP-seq data
Authors: Bailey Timothy L.
Published: May 2011

Motivation: Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF.

Results: We present DREME, a motif discovery algorithm specifically designed to find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very large ChIP-seq datasets in minutes. Using DREME, we discover the binding motifs of the the ChIP-ed TF and many cofactors in mouse ES cell (mESC), mouse erythrocyte and human cell line ChIP-seq datasets. For example, in mESC ChIP-seq data for the TF Esrrb, we discover the binding motifs for eight cofactor TFs important in the maintenance of pluripotency. Several other commonly used algorithms find at most two cofactor motifs in this same dataset. DREME can also perform discriminative motif discovery, and we use this feature to provide evidence that Sox2 and Oct4 do not bind in mES cells as an obligate heterodimer. DREME is much faster than many commonly used algorithms, scales linearly in dataset size, finds multiple, non-redundant motifs and reports a reliable measure of statistical significance for each motif found. DREME is available as part of the MEME Suite of motif-based sequence analysis tools (http://meme.nbcr.net).

Contact:  t.bailey@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Real-time microstructure of shock-compressed single crystals from X-ray diffraction line profiles
Authors: Turneaure Stefan J. , Gupta Y. M.
Published: May 2011

Methods to obtain and analyze high-resolution real-time X-ray diffraction (XRD) measurements from shock-compressed single crystals are presented. Procedures for extracting microstructural information – the focus of this work – from XRD line profiles are described. To obtain quantitative results, careful consideration of the experimental geometry is needed, including the single-crystal nature of the sample and the removal of instrumental broadening. These issues are discussed in detail. Williamson–Hall (WH) and profile synthesis (PS) analysis procedures are presented. More accurate than WH, the PS procedure relies on a forward calculation in which a line profile is synthesized by convoluting the instrumental line profile with a line profile determined from a diffraction simulation. The diffraction simulation uses the actual experimental geometry and a model microstructure for the shocked crystal. The shocked-crystal microstructural parameters were determined by optimizing the match between the synthesized and measured line profiles. XRD measurements on an Al crystal, shocked along [100] to 7.1 GPa using plate-impact loading, are used to demonstrate the WH and PS analysis methods. In the present analysis, the microstructural line broadening arises because of a distribution of longitudinal elastic microstrains. The WH analysis resulted in FWHM longitudinal microstrain distributions of 0.22 and 0.38% for Lorentzian and Gaussian line shape assumptions, respectively. The optimal FWHM longitudinal microstrain for the PS method was 0.35% with a pseudo-Voigt distribution (40% Lorentzian–60% Gaussian). The line profile measurements and PS analysis presented in this work provide new insight into the heterogeneous distribution of elastic strains in crystals undergoing elastic–plastic deformation during shock compression. Such microstrain distribution measurements are complementary to continuum measurements, which represent averages of the heterogeneous strains or stresses. The PS analysis is a general method capable of incorporating microstructural models more complex than the microstrain distribution model used in this work. As a next step, the PS method will be applied to line profiles of multiple diffraction peaks to separate strain- and size-broadening effects in shocked crystals.