bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial distribution of microbial communities in the cystic fibrosis lung
Authors: Willner Dana , Haynes Matthew R , Furlan Mike , Schmieder Robert , Lim Yan Wei , Rainey Paul B , Rohwer Forest , Conrad Douglas
Published: July 2011

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.
Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily
Authors: Coleman Nicholas V , Le Nga B , Ly Mai A , Ogawa Hitoha E , McCarl Victoria , Wilson Neil L , Holmes Andrew J
Published: July 2011

The copper membrane monooxygenases (CuMMOs) are an important group of enzymes in environmental science and biotechnology. Areas of relevance include the development of green chemistry for sustainable exploitation of methane (CH4) reserves, remediation of chlorinated hydrocarbon contamination and monitoring human impact in the biogeochemical cycles of CH4 and nitrogen. Challenges for all these applications are that many aspects of the ecology, physiology and structure–function relationships in the CuMMOs are inadequately understood. Here, we describe genetic and physiological characterization of a novel member of the CuMMO family that has an unusual physiological substrate range (C2–C4 alkanes) and a distinctive bacterial host (Mycobacterium). The Mycobacterial CuMMO genes (designated hmoCAB) were amenable to heterologous expression in M. smegmatis—this is the first example of recombinant expression of a complete and highly active CuMMO enzyme. The apparent specific activity of recombinant cells containing hmoCAB ranged from 2 to 3 nmol min–1 per mg protein on ethane, propane and butane as substrates, and the recombinants could also attack ethene, cis-dichloroethene and 1,2-dichloroethane. No detectable activity of recombinants or wild-type strains was seen with methane. The specific inhibitor allylthiourea strongly inhibited growth of wild-type cells on C2–C4 alkanes, and omission of copper from the medium had a similar effect, confirming the physiological role of the CuMMO for growth on alkanes. The hydrocarbon monooxygenase provides a new model for studying this important enzyme family, and the recombinant expression system will enable biochemical and molecular biological experiments (for example, site-directed mutagenesis) that were previously not possible.
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide
Authors: He Zhili , Piceno Yvette , Deng Ye , Xu Meiying , Lu Zhenmei , DeSantis Todd , Andersen Gary , Hobbie Sarah E , Reich Peter B , Zhou Jizhong
Published: July 2011

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO2, and such significant effects of eCO2 on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO2. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO2. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO2 and environmental factors shaping the microbial community structure.
Variability In The Ecoraces Of Tropical Tasar Sillkworm Antheraea Mylitta Drury
Authors: Sinha Ajit Kumar
Published: July 2011

Tropical tasar silkworm, Antheraea mylitta Drury is exploited in countries for commercial silk production and improved varieties of these silkworms can be evolved by employing various breeding techniques. As the insect has established itself in various forms of ecological populations (Commonly called as ecoraces) in different geographical niches of the country depending on food plants and micro-environmental conditions available to them, the species exists in the form of nearly 44 ecoraces (Singh and Srivastava,1997, Srivastava,2002 and Srivastava et at. 2007) distributed over different states. However, due to free interbreeding in nature for centuries, the fauna is highly heterogeneous.Tasar culture is a forest based industry being practiced as tradition, since time immemorial by the tribes of Central India, extending from West Bengal in the East to Karnataka in South. The species A. mylitta D. is polyphagous in nature. The present study comprises the ecoraces of tropical tasar silkworm of A. mylitta D. These ecoraces are mainly restricted in the tropical moist deciduous forest area where the average rainfall varies between 1200-2000 mm and the deciduous zone of the dry tropical forest area where the average rainfall has been observed to be about 1000 mm. The Primary food plants of the insects are Terminalia tomentosa, Terminalia arjuna and Shorea robusta and secondary food plants are Terminalia chebula, T. bellerica, T. peniculata, Zizyphus jujuba etc. The phenotypic and genotypic variability is very much prominent. The present review paper comprises the extent and degree of natural variation in tropical tasar silkworm A. mylitta D.
On- and off-axis second harmonic generation from an array of gold metallic nanocylinders
Authors: Awada Ch. , Kessi F. , Jonin Ch. , Adam P. M. , Kostcheev S. , Bachelot R. , Royer P. , Russier-Antoine I. , Benichou E. , Bachelier G. , Brevet P. F.
Published: July 2011

The optical second harmonic (SH) response from gold metallic nanocylinders with diameters of 80 and 120 nm arranged in hexagonal arrays has been determined as a function of the input fundamental polarization angle for the on- and off-axis transmission geometries and crossed output polarization configurations. For the on-axis transmission geometry, the nonlinear response of the nanocylinders is shown to be mainly incoherent, of pure electric dipole nature and arising from the breaking of the centrosymmetric shape of the body of the cylinders in a plane parallel to the substrate surface. Small angle off-axis experiments however show that the coherent contribution to the nonlinear response is size dependent suggesting that, besides the out-of-plane nonlinearity, retardation effects may also play a nonnegligible role.
Electric breakdown of longitudinally shocked Pb(Zr0.52Ti0.48)O3 ceramics
Authors: Shkuratov Sergey I. , Talantsev Evgueni F. , Baird Jason
Published: July 2011

Electric breakdown of longitudinally-shock-compressed Pb(Zr0.52Ti0.48)O3 (PZT 52/48) ferroelectric ceramics was experimentally investigated. It was found that a dependence of breakdown field strength, Eg, of shocked ferroelectrics on the thickness of the element, d, ranging from 0.65 to 6.5 mm is described by the Eg(d)=γ·d-w law that describes the breakdown of dielectrics at ambient conditions. It follows from the experimental results that the tunnel effect is a dominant mechanism of injection of prime electrons in the shocked ferroelectric elements. It was demonstrated that electric breakdown causes significant energy losses in miniature autonomous generators based on shock depolarization of poled ferroelectric elements.
In-situ magnetic nano-patterning of Fe films grown on Cu(100)
Authors: Zaman Sameena Shah , Dvořák Petr , Ritter Robert , Buchsbaum Andreas , Stickler Daniel , Oepen Hans Peter , Schmid Michael , Varga Peter
Published: July 2011

Metastable paramagnetic face-centered cubic (fcc) Fe films grown on a Cu(100) single crystal at room temperature can be transformed to the ferromagnetic body-centered cubic (bcc) structure by ion irradiation. We have employed this technique to write small ferromagnetic patches by Ar+ irradiation through a gold coated SiN mask with regularly arranged 80-nm diameter holes, which was placed on top of the as-prepared fcc Fe films. Nanopatterning was performed on both 8-monolayer (ML) Fe films grown in ultrahigh vacuum as well as 22-ML films stabilized by dosing carbon monoxide during growth. The structural transformation of these nano-patterned films was investigated using scanning tunneling microscopy. In both 8 and 22-ML fcc Fe films, the bcc needles are found to protrude laterally out of the irradiated part of the sample, limiting the resolution of the technique to a few 10 nm. The magnetic transformation was confirmed by magnetic force microscopy.
One-dimensional radiation-hydrodynamic scaling studies of imploding spherical plasma liners
Authors: Awe T. J. , Adams C. S. , Davis J. S. , Hanna D. S. , Hsu S. C. , Cassibry J. T.
Published: July 2011

One-dimensional radiation-hydrodynamic simulations are performed to develop insight into the scaling of stagnation pressure with initial conditions of an imploding spherical plasma shell or “liner.” Simulations reveal the evolution of high-Mach-number (M), annular, spherical plasma flows during convergence, stagnation, shock formation, and disassembly, and indicate that cm- and μs-scale plasmas with peak pressures near 1 Mbar can be generated by liners with initial kinetic energy of several hundred kilo-joules. It is shown that radiation transport and thermal conduction must be included to avoid non-physical plasma temperatures at the origin which artificially limit liner convergence and, thus, the peak stagnation pressure. Scalings of the stagnated plasma lifetime (τstag) and average stagnation pressure (Pstag, the pressure at the origin, averaged over τstag) are determined by evaluating a wide range of liner initial conditions. For high-M flows, τstag ∼ ΔR/v0, where ΔR and v0 are the initial liner thickness and velocity, respectively. Furthermore, for argon liners, Pstag scales approximately as v015/4 over a wide range of initial densities (n0) and as n01/2 over a wide range of v0. The approximate scaling Pstag ∼ M3/2 is also found for a wide range of liner-plasma initial conditions.
Actuation of a robotic fish caudal fin for low reaction torque
Authors: Yun Dongwon , Kim Kyung-Soo , Kim Soohyun , Kyung Jinho , Lee Sunghee
Published: July 2011

In this paper, a novel caudal fin for actuating a robotic fish is presented. The proposed caudal fin waves in a vertical direction with a specific spatial shape, which is determined by a so-called shape factor. For a specific shape factor, a traveling wave with a vertical phase difference is formed on a caudal fin during fin motion. It will be shown by the analysis that the maximum reaction torque at the joint of a caudal fin varies depending on the shape factors. Compared with a conventional plate type caudal fin, the proposed fin with a shape factor of 2π can eliminate the reaction torque perfectly, while keeping the propulsion force unchanged. The benefits of the proposed fin will be demonstrated by experiments.
Two-bit quantum random number generator based on photon-number-resolving detection
Authors: Jian Yi , Ren Min , Wu E , Wu Guang , Zeng Heping
Published: July 2011

Here we present a new fast two-bit quantum random number generator based on the intrinsic randomness of the quantum physical phenomenon of photon statistics of coherent light source. Two-bit random numbers were generated according to the number of detected photons in each light pulse by a photon-number-resolving detector. Poissonian photon statistics of the coherent light source guaranteed the complete randomness of the bit sequences. Multi-bit true random numbers were generated for the first time based on the multi-photon events from a coherent light source.
Towards gigawatt terahertz emission by few-cycle laser pulses
Authors: Wang Wei-Min , Kawata Shigeo , Sheng Zheng-Ming , Li Yu-Tong , Zhang Jie
Published: July 2011

It is shown by analysis and simulations that an extremely powerful terahertz (THz) radiation can be produced by a few-cycle laser pulse in a tenuous plasma. The THz amplitude scales linearly with the laser amplitude as well as with the sine of the laser carrier-envelope phase, and in particular, it increases exponentially with the decrease of the laser duration. For example, the THz amplitude increases by near 2 orders of magnitude as the laser duration decreases from one and a half cycles to one cycle; a single-cycle laser of 200 TW can drive the THz radiation of 1 GW with the energy conversion efficiency higher than 10−4.
Application of electrostatic Langmuir probe to atmospheric arc plasmas producing nanostructures
Authors: Shashurin A. , Li J. , Zhuang T. , Keidar M. , Beilis I. I.
Published: July 2011

The temporal evolution of a high pressure He arc producing nanotubes was considered and the Langmuir probe technique was applied for plasma parameter measurements. Two modes of arc were observed: cathodic arc where discharge is supported by erosion of cathode material and anodic arc which is supported by ablation of the anode packed with carbon and metallic catalysts in which carbon nanotubes are synthesized. Voltage-current (V-I) characteristics of single probes were measured and unusually low ratio of saturation current on positively biased probe to that on negatively biased of about 1–4 was observed. This effect was explained by increase of measured current at the negatively biased probe above the level of ion saturation current due to secondary electron emission from the probe surface. Since utilization of standard collisionless approach to determine plasma parameters from the measured V-I characteristic is not correct, the electron saturation current was used to estimate the plasma density.
Numerical study of the formation process of ferrofluid droplets
Authors: Liu Jing , Yap Yit Fatt , Nguyen Nam-Trung
Published: July 2011

This paper numerically investigates the influence of a uniform magnetic field on the droplet formation process at a microfluidic flow focusing configuration. The mathematical model was formulated by considering the balance of forces such as interfacial tension, magnetic force, and viscous stress across the liquid/liquid interface. A linearly magnetizable fluid was assumed. The magnetic force acts as a body force where the magnetic permeability jumps across the interface. The governing equations were solved with finite volume method on a Cartesian fixed staggered grid. The evolution of the interface was captured by the particle level set method. The code was validated with the equilibrium steady state of a ferrofluid droplet exposed to a uniform magnetic field. The evolution of the droplet formation in a flow focusing configuration was discussed. The paper mainly analyzes the effects of magnetic Bond number and the susceptibility on the velocity field and the droplet size. The droplet size increased with increasing magnetic strength and susceptibility.
High-efficiency switching effect in porphyrin-ethyne-benzene conjugates
Authors: An Yi-Peng , Yang Zhongqin , Ratner Mark A.
Published: July 2011

We have explored the electronic transport properties of porphyrin-ethyne-benzene conjugates using an ab initio method. The results indicate that these ethyne-bridged phenyl porphyrin molecules can be used as candidates for molecular switching devices. The coplanar conformation of phenyl and porphyrin moieties allows a far larger current than the perpendicular conformation due to the near vanishing overlap of the frontier molecular orbitals (π channels) in the porphyrin and phenyl parts in the latter. Higher current ratios of ON/OFF states can be obtained if amino or nitro substituent is placed at the position meta to the bridge connecting the π systems of the molecule. The substituent group affects the electronic state energy of the entire molecule in coplanar conformation, while only affecting the local part in perpendicular conformation. More complex ethyne-bridged diphenyl porphyrin molecules are found to yield more complex and interesting switching effects. Our results suggest that such molecular wires composed of appropriate π-conjugated molecules, can generally display perfect switching function and the efficiency can be tuned flexibly by adding certain substituent groups to the conjugates.
Graphene on β-Si3N4: An ideal system for graphene-based electronics
Authors: Yang Ming , Zhang Chun , Wang Shijie , Feng Yuanping , Ariando
Published: July 2011

One of the most severe limits in future design of graphene-based electronic devices is that when supported on a substrate, the electron mobility of graphene is often reduced by an order of magnitude or more. In this paper, via theoretical calculations, we show that the non-polar β-Si3N4 (0001) surface may be an excellent support for both single-layer or bi-layer graphene to overcome this limit. Since the high-κ dielectric material is an indispensable component in integrated circuits, the silicon nitride supported graphene as discussed in this paper may provide an ideal platform for future graphene-based electronics.
Color Relations Increase the Capacity of Visual Short-Term Memory
Authors: Sanocki Thomas , Sulman Noah
Published: July 2011

Do color relations such as similarity or harmony influence the ease with which colored patterns can be perceived and held in mind? We tested the influence of a relation supported in research on color harmony—similarity of hue—on the capacity of visual short-term memory (VSTM) for colors in patterns. Palettes of 4 similar-hue colors were rated as more pleasant (harmonious) than dissimilar-color palettes. The palettes were used in a VSTM color task. Patterns of 9 to 15 colored squares were presented, and accuracy of color change detection was measured. Memory performance was higher overall for similar-color palettes than for dissimilar-color palettes (experiments 1 and 3). Is this due to color similarity per se, or due to the harmony between colors in similar palettes? A final experiment provided strong support for the importance of color similarity as opposed to harmony. Overall, the advantages for color similarity, in terms of number of color squares held in memory (memory capacity) were 26% to 45% over dissimilar colors. The results indicate that color relations can have a strong impact on the capacity for perceiving and retaining color patterns.
The Perception of Humanness from the Movements of Synthetic Agents
Authors: Thompson James C , Trafton J Gregory , McKnight Patrick
Published: July 2011

As technology develops, social robots and synthetic avatars might begin to play more of a role in our lives. An influential theory of the perception of synthetic agents states that as they begin to look and move in a more human-like way, they elicit profound discomfort in the observer—an effect known as the Uncanny Valley. Previous attempts to examine the existence of the Uncanny Valley have not adequately manipulated movement parameters that contribute to perceptions of the humanness or eeriness. Here we parametrically manipulated three different kinematic features of two walking avatars and found that, contrary to the Uncanny Valley hypothesis, ratings of the humanness, familiarity, and eeriness of these avatars changed monotonically. Our results indicate that, when a full gradient of motion parameter changes is examined, ratings of synthetic agents by human observers do not show an Uncanny Valley.
Effects of irrigating forage turnips, Brassica rapa var. rapa cv. Barkant, during different periods of vegetative growth. 2. Nutritive characteristics of leaves and roots
Authors: Rowe B. A. , Neilsen J. E.
Published: July 2011

The effects of irrigating spring-sown forage turnips, Brassica rapa var. rapa cv. Barkant, during four discrete but consecutive periods of vegetative growth on the nutritive value of both leaves and roots of turnip was measured three times in 4 weeks in two field experiments conducted in north-west Tasmania during the 1999–2000 and 2000–01 spring and summer seasons. The harvests commenced ~10 weeks after sowing and near the maximum growth rate of the turnip. The harvests coincided with times when turnip would normally be grazed by dairy cows in mid lactation. The aim was to quantify both the effects of applying irrigation during four discrete but consecutive periods of vegetative growth and advancing maturity on metabolisable energy, neutral detergent fibre, crude protein and non-structural carbohydrate in both the leaves and roots. Irrigation applied during the four periods of vegetative growth produced relatively small and sometimes inconsistent effects on the nutritive characteristics of turnip leaf and root as the crop matured. However, their cumulative effect was to reduce both crude protein and the crude protein : non-structural carbohydrate ratio despite increasing total nitrogen uptake, and to increase leaf water-soluble carbohydrate and starch above rainfed turnip. These cumulative effects became more pronounced as the crop maturity increased from 27 to 75 days after the onset of root expansion. The cumulative effects on metabolisable energy and neutral detergent fibre were small and of no agricultural importance. Nutritive values were sufficient to meet the requirement of lactating dairy cows in mid lactation except for fibre and root crude protein.
Seasonal allocation of photosynthetically fixed carbon to the soybean-grown Mollisols in Northeast China
Authors: Jin J. , Wang G. H. , Liu J. D. , Liu X. B. , Liu J. J. , Yu Z. H. , Herbert S. J.
Published: July 2011

The knowledge of the contribution of carbon (C) released by growing roots to soil is essential to better understand the terrestrial C cycling and optimally manage soil organic matter in ecosystems. However, little information has been gained on quantifying the distribution of photosynthetically fixed C in the plant–soil system and its contribution to soil C over a growing season in soybean-grown Mollisols, the main soil type in Northeast China. In a pulse-chase labelling experiment, soybean plants grown in Mollisols were labelled with 13CO2 at various growth stages. More than 3/4 of fixed 13C was observed in shoots at Day 0 after labelling, and then the fixed 13C was continually exported from shoots, showing that 7.5% of 13C fixed at V4 (fourth node) and 71.1% at R6 (full seed stage) remained in shoots by the end of the growing season. The 13C recovery in roots decreased over the same period, while soil 13C was significantly increased. The allocation of 13C fixed at different growth stages to underground (roots and soil) varied at the end of the growing season, showing that 13C retained in roots and soil was 6.0 and 12.4% of the net assimilation at V4, compared with 1.4 and 2.1% of that at R6, respectively. Nodules, however, had the highest demand for C at R4 (full pod stage). The contribution of shoot C assimilation to the soil C pool was similar at the growth stages up to R5 before a sharp decrease at R6, and the cumulative contribution reached 93% at R5. Over the whole growing season, it was estimated that ~210 kg of photosynthetically fixed C per ha was accumulated in soil. This indicates that the C flow from soybean plants to soil during growth is a non-negligible source of C pool in Mollisols, and the majority of the C efflux occurs during V4–R5.
Coordinated protein and DNA remodeling by human HLTF on stalled replication fork
Authors: Achar Yathish Jagadheesh , Balogh David , Haracska Lajos
Published: July 2011

Human helicase-like transcription factor (HLTF) exhibits ubiquitin ligase activity for proliferating cell nuclear antigen (PCNA) polyubiquitylation as well as double-stranded DNA translocase activity for remodeling stalled replication fork by fork reversal, which can support damage bypass by template switching. However, a stalled replication fork is surrounded by various DNA-binding proteins which can inhibit the access of damage bypass players, and it is unknown how these proteins become displaced. Here we reveal that HLTF has an ATP hydrolysis-dependent protein remodeling activity, by which it can remove proteins bound to the replication fork. Moreover, we demonstrate that HLTF can displace a broad spectrum of proteins such as replication protein A (RPA), PCNA, and replication factor C (RFC), thereby providing the first example for a protein clearing activity at the stalled replication fork. Our findings clarify how remodeling of a stalled replication fork can occur if it is engaged in interactions with masses of proteins.
Plasticity of local GABAergic interneurons drives olfactory habituation
Authors: Das Sudeshna , Sadanandappa Madhumala K. , Dervan Adrian , Larkin Aoife , Lee John Anthony , Sudhakaran Indulekha P. , Priya Rashi , Heidari Raheleh , Holohan Eimear E. , Pimentel Angel , Gandhi Avni , Ito Kei , Sanyal Subhabrata , Wang Jing W. , Rodrigues Veronica , Ramaswami Mani
Published: July 2011

Despite its ubiquity and significance, behavioral habituation is poorly understood in terms of the underlying neural circuit mechanisms. Here, we present evidence that habituation arises from potentiation of inhibitory transmission within a circuit motif commonly repeated in the nervous system. In
Drosophila
, prior odorant exposure results in a selective reduction of response to this odorant. Both short-term (STH) and long-term (LTH) forms of olfactory habituation require function of the
rutabaga
-encoded adenylate cyclase in multiglomerular local interneurons (LNs) that mediate GABAergic inhibition in the antennal lobe; LTH additionally requires function of the cAMP response element-binding protein (CREB2) transcription factor in LNs. The odorant selectivity of STH and LTH is mirrored by requirement for NMDA receptors and GABA
A
receptors in odorant-selective, glomerulus-specific projection neurons(PNs). The need for the vesicular glutamate transporter in LNs indicates that a subset of these GABAergic neurons also releases glutamate. LTH is associated with a reduction of odorant-evoked calcium fluxes in PNs as well as growth of the respective odorant-responsive glomeruli. These cellular changes use similar mechanisms to those required for behavioral habituation. Taken together with the observation that enhancement of GABAergic transmission is sufficient to attenuate olfactory behavior, these data indicate that habituation arises from glomerulus-selective potentiation of inhibitory synapses in the antennal lobe. We suggest that similar circuit mechanisms may operate in other species and sensory systems.
Inferring the structure and dynamics of interactions in schooling fish
Authors: Katz Yael , Tunstrøm Kolbjørn , Ioannou Christos C. , Huepe Cristián , Couzin Iain D.
Published: July 2011

Determining individual-level interactions that govern highly coordinated motion in animal groups or cellular aggregates has been a long-standing challenge, central to understanding the mechanisms and evolution of collective behavior. Numerous models have been proposed, many of which display realistic-looking dynamics, but nonetheless rely on untested assumptions about how individuals integrate information to guide movement. Here we infer behavioral rules directly from experimental data. We begin by analyzing trajectories of golden shiners (
Notemigonus crysoleucas
) swimming in two-fish and three-fish shoals to map the mean effective forces as a function of fish positions and velocities. Speeding and turning responses are dynamically modulated and clearly delineated. Speed regulation is a dominant component of how fish interact, and changes in speed are transmitted to those both behind and ahead. Alignment emerges from attraction and repulsion, and fish tend to copy directional changes made by those ahead. We find no evidence for explicit matching of body orientation. By comparing data from two-fish and three-fish shoals, we challenge the standard assumption, ubiquitous in physics-inspired models of collective behavior, that individual motion results from averaging responses to each neighbor considered separately; three-body interactions make a substantial contribution to fish dynamics. However, pairwise interactions qualitatively capture the correct spatial interaction structure in small groups, and this structure persists in larger groups of 10 and 30 fish. The interactions revealed here may help account for the rapid changes in speed and direction that enable real animal groups to stay cohesive and amplify important social information.
Influence of interface roughness scattering on output characteristics of GaAs/AlGaAs quantum cascade laser in a magnetic field
Authors: Žeželj M , Milanović V , Radovanović J , Stanković I
Published: July 2011

We present a detailed theoretical analysis of LO-phonon and interface roughness scattering influence on the operation of GaAs/AlGaAs quantum cascade laser in the presence of an intense external magnetic field. The lifetime of the upper state, population inversion and optical gain show strong oscillations as a function of the magnetic field. These oscillations and their magnitude are found to be a result of the combined action of the two studied mechanisms and strongly influenced by temperature. At elevated temperatures, electrons in the relevant laser states absorb/emit more LO-phonons which results in reduction in the optical gain. We show that the decrease in the optical gain is moderated by the occurrence of interface roughness scattering, which remains unchanged with increasing temperature. Incorporation of the interface roughness scattering mechanism into the model did not create new resonant peaks of the optical gain. However, it resulted in shifting the existing peaks positions and overall reduction in the optical gain.
Conduction band structure and electron mobility in uniaxially strained Si via externally applied strain in nanomembranes
Authors: Chen Feng , Euaruksakul Chanan , Liu Zheng , Himpsel F J , Liu Feng , Lagally Max G
Published: July 2011

Strain changes the band structure of semiconductors. We use x-ray absorption spectroscopy to study the change in the density of conduction band (CB) states when silicon is uniaxially strained along the [1 0 0] and [1 1 0] directions. High stress can be applied to silicon nanomembranes, because their thinness allows high levels of strain without fracture. Strain-induced changes in both the sixfold degenerate Δ valleys and the eightfold degenerate L valleys are determined quantitatively. The uniaxial deformation potentials of both Δ and L valleys are directly extracted using a strain tensor appropriate to the boundary conditions, i.e., confinement in the plane in the direction orthogonal to the straining direction, which correspond to those of strained CMOS in commercial applications. The experimentally determined deformation potentials match the theoretical predictions well. We predict electron mobility enhancement created by strain-induced CB modifications.
The effect of VUV radiation from Ar/O2 plasmas on low-k SiOCH films
Authors: Lee J , Graves D B
Published: July 2011

The degradation of porous low-k materials, like SiOCH, under plasma processing continues to be a problem in the next generation of integrated-circuit fabrication. Due to the exposure of the film to many species during plasma treatment, such as photons, ions, radicals, etc, it is difficult to identify the mechanisms responsible for plasma-induced damage. Using a vacuum beam apparatus with a calibrated Xe vacuum ultraviolet (VUV) lamp, we show that 147 nm VUV photons and molecular O2 alone can damage these low-k materials. Using Fourier-transform infrared (FTIR) spectroscopy, we show that VUV/O2 exposure causes a loss of methylated species, resulting in a hydrophilic, SiO
x
-like layer that is susceptible to H2O absorption, leading to an increased dielectric constant. The effect of VUV radiation on chemical modification of porous SiOCH films in the vacuum beam apparatus and in Ar and O2 plasma exposure was found to be a significant contributor to dielectric damage. Measurements of dielectric constant change using a mercury probe are consistent with chemical modification inferred from FTIR analysis. Furthermore, the extent of chemical modification appears to be limited by the penetration depth of the VUV photons, which is dependent on wavelength of radiation. The creation of a SiO
x
-like layer near the surface of the material, which grows deeper as more methyl is extracted, introduces a dynamic change of VUV absorption throughout the material over time. As a result, the rate of methyl loss is continuously changing during the exposure. We present a model that attempts to capture this dynamic behaviour and compare the model predictions to experimental data through a fitting parameter that represents the effective photo-induced methyl removal. While this model accurately simulates the methyl loss through VUV exposure by the Xe lamp and Ar plasma, the methyl loss from VUV photons in O2 plasma are only accurately depicted at longer exposure times. We conclude that other species, such as oxygen radicals or ions, may play a major role in chemical modification at short times near the surface of the material, while VUV photons contribute to the majority of the damage in the bulk.
Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages
Authors: Golebiewska Urszula , Kay Jason G. , Masters Thomas , Grinstein Sergio , Im Wonpil , Pastor Richard W. , Scarlata Suzanne , McLaughlin Stuart
Published: July 2011

To account for the many functions of phosphatidylinositol 4,5-bisphosphate (PIP2), several investigators have proposed that there are separate pools of PIP2 in the plasma membrane. Recent experiments show the surface concentration of PIP2 is indeed enhanced in regions where phagocytosis, exocytosis, and cell division occurs. Kinases that produce PIP2 are also concentrated in these regions. However, how is the PIP2 produced by these kinases prevented from diffusing rapidly away? First, proteins could act as “fences” around the perimeter of these regions. Second, some factor could markedly decrease the diffusion coefficient, D, of PIP2 within these regions. We used fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) to investigate these two possibilities in the forming phagosomes of macrophages injected with fluorescent PIP2. FCS measurements show that PIP2 diffuses rapidly (D ∼ 1 μm2/s) in both the forming phagosomes and unengaged plasma membrane. FRAP measurements show that the fluorescence from PIP2 does not recover (>100 s) after photobleaching the entire forming phagosome but recovers rapidly (∼10 s) in a comparable area of membrane outside the cup. These results (and similar data for a plasma membrane–anchored green fluorescent protein) support the hypothesis that a fence impedes the diffusion of PIP2 into and out of forming phagosomes.
Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated
Authors: Castelli Lydia M. , Lui Jennifer , Campbell Susan G. , Rowe William , Zeef Leo A. H. , Holmes Leah E. A. , Hoyle Nathaniel P. , Bone Jonathon , Selley Julian N. , Sims Paul F. G. , Ashe Mark P.
Published: July 2011

Cellular stress can globally inhibit translation initiation, and glucose removal from yeast causes one of the most dramatic effects in terms of rapidity and scale. Here we show that the same rapid inhibition occurs during yeast growth as glucose levels diminish. We characterize this novel regulation showing that it involves alterations within the 48S preinitiation complex. In particular, the interaction between eIF4A and eIF4G is destabilized, leading to a temporary stabilization of the eIF3–eIF4G interaction on the 48S complex. Under such conditions, specific mRNAs that are important for the adaptation to the new conditions must continue to be translated. We have determined which mRNAs remain translated early after glucose starvation. These experiments enable us to provide a physiological context for this translational regulation by ascribing defined functions that are translationally maintained or up-regulated. Overrepresented in this class of mRNA are those involved in carbohydrate metabolism, including several mRNAs from the pentose phosphate pathway. Our data support a hypothesis that a concerted preemptive activation of the pentose phosphate pathway, which targets both mRNA transcription and translation, is important for the transition from fermentative to respiratory growth in yeast.
Vacuolar H+-ATPase subunits Voa1 and Voa2 cooperatively regulate secretory vesicle acidification, transmitter uptake, and storage
Authors: Saw Ner Mu Nar , Kang Soo-Young Ann , Parsaud Leon , Han Gayoung Anna , Jiang Tiandan , Grzegorczyk Krzysztof , Surkont Michael , Sun-Wada Ge-Hong , Wada Yoh , Li Lijun , Sugita Shuzo
Published: July 2011

The Vo sector of the vacuolar H+-ATPase is a multisubunit complex that forms a proteolipid pore. Among the four isoforms (a1–a4) of subunit Voa, the isoform(s) critical for secretory vesicle acidification have yet to be identified. An independent function of Voa1 in exocytosis has been suggested. Here we investigate the function of Voa isoforms in secretory vesicle acidification and exocytosis by using neurosecretory PC12 cells. Fluorescence-tagged and endogenous Voa1 are primarily localized on secretory vesicles, whereas fluorescence-tagged Voa2 and Voa3 are enriched on the Golgi and early endosomes, respectively. To elucidate the functional roles of Voa1 and Voa2, we engineered PC12 cells in which Voa1, Voa2, or both are stably down-regulated. Our results reveal significant reductions in the acidification and transmitter uptake/storage of dense-core vesicles by knockdown of Voa1 and more dramatically of Voa1/Voa2 but not of Voa2. Overexpressing knockdown-resistant Voa1 suppresses the acidification defect caused by the Voa1/Voa2 knockdown. Unexpectedly, Ca2+-dependent peptide secretion is largely unaffected in Voa1 or Voa1/Voa2 knockdown cells. Our data demonstrate that Voa1 and Voa2 cooperatively regulate the acidification and transmitter uptake/storage of dense-core vesicles, whereas they might not be as critical for exocytosis as recently proposed.
EphrinA/EphA signal facilitates insulin-like growth factor-I–induced myogenic differentiation through suppression of the Ras/extracellular signal–regulated kinase 1/2 cascade in myoblast cell lines
Authors: Minami Masayoshi , Koyama Tatsuya , Wakayama Yuki , Fukuhara Shigetomo , Mochizuki Naoki
Published: July 2011

Insulin-like growth factor-I (IGF-I) activates not only the phosphatidylinositol 3-kinase (PI3K)–AKT cascade that is essential for myogenic differentiation but also the extracellular signal–regulated kinase (ERK) 1/2 cascade that inhibits myogenesis. We hypothesized that there must be a signal that inhibits ERK1/2 upon cell–cell contact required for skeletal myogenesis. Cell–cell contact–induced engagement of ephrin ligands and Eph receptors leads to downregulation of the Ras-ERK1/2 pathway through p120 Ras GTPase-activating protein (p120RasGAP). We therefore investigated the significance of the ephrin/Eph signal in IGF-I–induced myogenesis. EphrinA1-Fc suppressed IGF-I–induced activation of Ras and ERK1/2, but not that of AKT, in C2C12 myoblasts, whereas ephrinB1-Fc affected neither ERK1/2 nor AKT activated by IGF-I. IGF-I–dependent myogenic differentiation of C2C12 myoblasts was potentiated by ephrinA1-Fc. In p120RasGAP-depleted cells, ephrinA1-Fc failed to suppress the Ras-ERK1/2 cascade by IGF-I and to promote IGF-I–mediated myogenesis. EphrinA1-Fc did not promote IGF-I–dependent myogenesis when the ERK1/2 was constitutively activated. Furthermore, a dominant-negative EphA receptor blunted IGF-I–induced myogenesis in C2C12 and L6 myoblasts. However, the inhibition of IGF-I–mediated myogenesis by down-regulation of ephrinA/EphA signal was canceled by inactivation of the ERK1/2 pathway. Collectively, these findings demonstrate that the ephrinA/EphA signal facilitates IGF-I–induced myogenesis by suppressing the Ras-ERK1/2 cascade through p120RasGAP in myoblast cell lines.
GSK3β inactivation induces apoptosis of leukemia cells by repressing the function of c-Myb
Authors: Zhou Fangfang , Zhang Long , van Laar Theo , van Dam Hans , ten Dijke Peter
Published: July 2011

Glycogen synthase kinase 3β (GSK3β) regulates diverse physiological processes, including metabolism, development, oncogenesis, and neuroprotection. GSK3β kinase activity has been reported to be critical for various types of cancer cells, but the mechanism has remained elusive. In this study we examine the mechanism by which GSK3β regulates the survival of leukemia cells. We demonstrate that upon GSK3β kinase inhibition different types of leukemia cells show severe proliferation defects as a result of apoptosis. The transcription factor c-Myb is found to be the main target of GSK3β inhibition in cell survival. GSK3β inactivation reduces the expression of c-Myb by promoting its ubiquitination-mediated degradation, thereby inhibiting the expression of c-Myb–dependent antiapoptotic genes Bcl2 and survivin. Coimmunoprecipitation, reporter assays, chromatin immunoprecipitation, and knockdown studies show that c-Myb needs to interact and cooperate with transcription factor LEF-1 in the activation of Bcl2 and survivin and that both transcription factors are required for cell survival. These data reveal an as-yet-unknown mechanism by which GSK3β controls cell survival.
Perioperative Single Dose Systemic Dexamethasone for Postoperative Pain
Authors: De Oliveira Gildàsio S. , Almeida Marcela D. , Benzon Honorio T. , McCarthy Robert J.
Published: July 2011

Background

Dexamethasone is frequently administered in the perioperative period to reduce postoperative nausea and vomiting. In contrast, the analgesic effects of dexamethasone are not well defined. The authors performed a meta-analysis to evaluate the dose-dependent analgesic effects of perioperative dexamethasone.

Methods

We followed the PRISMA statement guidelines. A wide search was performed to identify randomized controlled trials that evaluated the effects of a single dose systemic dexamethasone on postoperative pain and opioid consumption. Meta-analysis was performed using a random-effect model. Effects of dexamethasone dose were evaluated by pooling studies into three dosage groups: low (less than 0.1 mg/kg), intermediate (0.11-0.2 mg/kg) and high (≥ 0.21 mg/kg).

Results

Twenty-four randomized clinical trials with 2,751 subjects were included. The mean (95% CI) combined effects favored dexamethasone over placebo for pain at rest (≤ 4 h, -0.32 [0.47 to -0.18], 24 h, -0.49 [-0.67 to -0.31]) and with movement (≤ 4 h, -0.64 [-0.86 to -0.41], 24 h, -0.47 [-0.71 to -0.24]). Opioid consumption was decreased to a similar extent with moderate -0.82 (-1.30 to -0.42) and high -0.85 (-1.24 to -0.46) dexamethasone, but not decreased with low-dose dexamethasone -0.18 (-0.39-0.03). No increase in analgesic effectiveness or reduction in opioid use could be demonstrated between the high- and intermediate-dose dexamethasone. Preoperative administration of dexamethasone appears to produce a more consistent analgesic effect compared with intraoperative administration.

Conclusion

Dexamethasone at doses more than 0.1 mg/kg is an effective adjunct in multimodal strategies to reduce postoperative pain and opioid consumption after surgery. The preoperative administration of the drug produces less variation of effects on pain outcomes.
The evolutionary basis of human social learning
Authors: Morgan T. J. H. , Rendell L. E. , Ehn M. , Hoppitt W. , Laland K. N.
Published: July 2011

Humans are characterized by an extreme dependence on culturally transmitted information. Such dependence requires the complex integration of social and asocial information to generate effective learning and decision making. Recent formal theory predicts that natural selection should favour adaptive learning strategies, but relevant empirical work is scarce and rarely examines multiple strategies or tasks. We tested nine hypotheses derived from theoretical models, running a series of experiments investigating factors affecting when and how humans use social information, and whether such behaviour is adaptive, across several computer-based tasks. The number of demonstrators, consensus among demonstrators, confidence of subjects, task difficulty, number of sessions, cost of asocial learning, subject performance and demonstrator performance all influenced subjects' use of social information, and did so adaptively. Our analysis provides strong support for the hypothesis that human social learning is regulated by adaptive learning rules.
Discovery of an orthoreovirus in the aborted fetus of a Steller sea lion (Eumetopias jubatus)
Authors: Palacios Gustavo , Wellehan James F. X. , Raverty Stephen , Bussetti Ana V. , Hui Jeffrey , Savji Nazir , Nollens Hendrik H. , Lambourn Dyanna , Celone Christopher , Hutchison Stephen , Calisher Charles H. , Nielsen Ole , Lipkin W. Ian
Published: July 2011

An aborted mid-gestational male Steller sea lion fetus with an attached placenta was recovered on the floor of an open floating capture trap located off Norris Rock near Denman Island, British Columbia. Viral culture of the placenta demonstrated cytopathic effect. Although no specific signal was obtained in microarray experiments using RNA obtained from viral culture, elution and sequence analysis revealed the presence of a reovirus. Complete genome pyrosequencing led to the identification of an orthoreovirus that we have tentatively named Steller sea lion reovirus (SSRV). Phylogenetic analysis revealed similarities between SSRV and orthoreoviruses of birds, bats and other mammals that suggests potential for interspecies transmission.