bluuebunny/crossref_metadata_2025 huggingface dataset:
An effective method for computing the noise in biochemical networks
Authors: Zhang Jiajun , Nie Qing , He Miao , Zhou Tianshou
Published: February 2013

We present a simple yet effective method, which is based on power series expansion, for computing exact binomial moments that can be in turn used to compute steady-state probability distributions as well as the noise in linear or nonlinear biochemical reaction networks. When the method is applied to representative reaction networks such as the ON-OFF models of gene expression, gene models of promoter progression, gene auto-regulatory models, and common signaling motifs, the exact formulae for computing the intensities of noise in the species of interest or steady-state distributions are analytically given. Interestingly, we find that positive (negative) feedback does not enlarge (reduce) noise as claimed in previous works but has a counter-intuitive effect and that the multi-OFF (or ON) mechanism always attenuates the noise in contrast to the common ON-OFF mechanism and can modulate the noise to the lowest level independently of the mRNA mean. Except for its power in deriving analytical expressions for distributions and noise, our method is programmable and has apparent advantages in reducing computational cost.
Enhanced thermoelectric performance in graphitic ZnO (0001) nanofilms
Authors: Li Yan-Li , Fan Zheyong , Zheng Jin-Cheng
Published: February 2013

We investigate the thermoelectric properties of ultrathin graphitic ZnO (0001) nanofilms based on first-principles calculations and Boltzmann transport theory. Staircase-like densities of states induced by quantum confinement in the nanofilms give rise to improved Seebeck coefficients and electrical conductivities. The optimized figure of merit for the single-layer graphitic ZnO (0001) nanofilm is estimated to be 0.6 at 300 K, which is about 120 times larger than that of bulk ZnO (0.005). Our results suggest that the graphitic ZnO (0001) nanofilms can be designed for high performance thermoelectric applications.
Manipulated electromagnetic losses by integrating chemically heterogeneous components in Fe-based core/shell architecture
Authors: Huang Hao , Zhang Xue-Feng , Lv Bo , Xue Fang-Hong , Shah Asif , Su Lei , Yan Jing-Guo , Yao Man , Dong Xing-Long
Published: February 2013

Existing techniques for stabilizing and functionalizing metal nanostructures required precise control of complex procedures and probably introduce undesirable impurities. We herein report an arc-discharge chemical vapor deposition strategy for the synthesis of chemically heterogeneous core/shell metal/oxide nanocapsules Fe/TiFe2O4, Fe/MnFe2O4, and Fe/Al2O3. A universal formation mechanism based on the co-effect of oxygen potential and surface energy is further proposed, derived from fundamental thermodynamics. Such core/shell nanocapsules, integrated with tunable components, present an effective manipulability of microwave absorption at expected frequency, originating from the various dielectric behaviors of the heterogeneous oxide shells.
Modulating the secondary electron emission coefficient at the base-collector interface of the plasma bipolar junction transistor
Authors: Li B. , Houlahan T. J. , Wagner C. J. , Eden J. G.
Published: February 2013

Temporally and spatially-resolved images of the visible emission generated by the gas phase collector of an n+pn plasma bipolar junction transistor (PBJT) demonstrate the ability of the emitter-base (EB) bias to modulate the effective secondary electron emission coefficient, γSE, at the base-collector interface. Injecting charge carriers into, or withholding free electrons from, the base of a PBJT (with forward or reverse bias of the EB junction) is found to vary γSE and the collector plasma electron density by factors of 1.8–3.6 and 3.8–6.7, respectively.
Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction
Authors: Monge-Palacios M. , Rangel C. , Espinosa-Garcia J.
Published: February 2013

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200–2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.
Review of the effects of additives on biodiesel properties, performance, and emission features
Authors: Ali Obed M. , Mamat Rizalman , Faizal Che Ku M.
Published: February 2013

As a renewable, sustainable and alternative fuel for compression ignition engines, biodiesel is widely accepted as comparable fuel to diesel in compression ignition engines. This is due to several factors like decreasing the dependence on imported petroleum; providing a market for the excess production of vegetable oils and animal fats; using renewable and biodegradable fuels; reducing global warming due to its closed carbon cycle by CO2 recycling; increasing lubricity; and reducing substantially the exhaust emissions of carbon monoxide, unburned hydrocarbons, and particulate emissions from diesel engines. However, there is a major drawback in the use of biodiesel as low heating value and NOX tends to be higher. On the other hand, its relatively poor low-temperature flow properties are a characteristic of biodiesel which limits its application. Here, fuel additives become indispensable tools not only to decrease these drawbacks but also to produce specified products that meet the international and regional standards. This article is a literature review of the effect of different additives on biodiesel properties, performance, and emission characteristics. The researches published by different journals are cited preferentially. From these researches, the effect of biodiesel additives on fuel cold flow properties, engine power, fuel economy and emissions including regulated and non-regulated emissions, and the corresponding effect factors were surveyed and analyzed in detail. Varying results of improvement in cold flow properties have been obtained by using different additives. Similarly, different additives were used by different researchers to improve the performance of a compression ignition engine and its emissions. This review was taken up to identify the various additives used to improve the cold flow properties of biodiesels and improve the performance of a diesel engine and its emissions while using additive blended biodiesels. The review concludes that the additive usage in biodiesel is inseparable both for improving the cold flow properties and for better engine performance and emission control. Further research is needed to develop biodiesel specific additives.
Modeling light absorption by bound electrons in self-assembled quantum dots
Authors: Ameen Tarek A. , El-Batawy Yasser M. , Abouelsaood A. A.
Published: February 2013

A theoretical model of the absorption coefficient of quantum dot devices is presented. Both of bound to bound absorption and bound to continuum absorption are taken into consideration in this model which is based on the effective mass theory and the nonequilibrium Greens function formalism. The results of the model have been compared with a published experimental work and a good agreement is obtained. The effects of the dot dimensions and electron filling on the bound to continuum absorption coefficient are also investigated. In general, increasing the dot filling increases the absorption and decreasing the dots dimensions will increase the absorption and move the absorption peak towards longer wavelengths.
Performance of an inverted ion source
Authors: Salvadori M. C. , Teixeira F. S. , Sgubin L. G. , Araujo W. W. R. , Spirin R. E. , Oks E. M. , Brown I. G.
Published: February 2013

Whereas energetic ion beams are conventionally produced by extracting ions (say, positive ions) from a plasma that is held at high (positive) potential, with ion energy determined by the potential drop through which the ions fall in the beam formation electrode system, in the device described here the plasma and its electronics are held at ground potential and the ion beam is formed and injected energetically into a space maintained at high (negative) potential. We refer to this configuration as an “inverted ion source.” This approach allows considerable savings both technologically and economically, rendering feasible some ion beam applications, in particular small-scale ion implantation, that might otherwise not be possible for many researchers and laboratories. We have developed a device of this kind utilizing a metal vapor vacuum arc plasma source, and explored its operation and beam characteristics over a range of parameter variation. The downstream beam current has been measured as a function of extraction voltage (5–35 kV), arc current (50–230 A), metal ion species (Ti, Nb, Au), and extractor grid spacing and beamlet aperture size (3, 4, and 5 mm). The downstream ion beam current as measured by a magnetically-suppressed Faraday cup was up to as high as 600 mA, and with parametric variation quite similar to that found for the more conventional metal vapor vacuum arc ion source.
Enhancement of optical gain and amplified spontaneous emission due to waveguide geometry in the conjugated polymer poly[2-methoxy-5-(2′-ethylhexyloxy)-p-phenylene vinylene]
Authors: Lampert Zach E. , Papanikolas John M. , Lewis Reynolds C.
Published: February 2013

We report enhanced amplified spontaneous emission (ASE) and optical gain performance in a conjugated polymer (CP)-based thin film waveguide (WG) Si(100)/SiO2/poly[2-methoxy-5-(2′-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) by encapsulating the active layer with a transparent dielectric film of poly(methyl methacrylate) (PMMA). With index matched SiO2 and PMMA claddings, symmetric WGs are formed that exhibit increased mode confinement and reduced propagation loss enabling lower ASE threshold (40%) and higher optical gain (50%) compared to Si(100)/SiO2/MEH-PPV/air asymmetric WGs. An extremely large net gain coefficient of 500 cm−1 is achieved under picosecond pulse excitation, which is >4× larger than values previously reported in the literature. Fabrication of symmetric WGs requires no complex processing techniques, thus offering a simple, low-cost approach for effectively controlling the ASE behavior of CP-based WGs and related optical devices.
Synchrotron radiation based cross-sectional scanning photoelectron microscopy and spectroscopy of n-ZnO:Al/p-GaN:Mg heterojunction
Authors: Lee Kai-Hsuan , Chang Ping-Chuan , Chen Tse-Pu , Chang Sheng-Po , Shiu Hung-Wei , Chang Lo-Yueh , Chen Chia-Hao , Chang Shoou-Jinn
Published: February 2013

Al-doped ZnO (AZO) deposited by radio frequency co-sputtering is formed on epitaxial Mg-doped GaN template at room temperature to achieve n-AZO/p-GaN heterojunction. Alignment of AZO and GaN bands is investigated using synchrotron radiation based cross-sectional scanning photoelectron microscopy and spectroscopy on the nonpolar side-facet of a vertically c-axis aligned heterostructure. It shows type-II band configuration with valence band offset of 1.63 ± 0.1 eV and conduction band offset of 1.61 ± 0.1 eV, respectively. Rectification behavior is clearly observed, with a ratio of forward-to-reverse current up to six orders of magnitude when the bias is applied across the p-n junction.
Observation of the spin Seebeck effect in epitaxial Fe3O4 thin films
Authors: Ramos R. , Kikkawa T. , Uchida K. , Adachi H. , Lucas I. , Aguirre M. H. , Algarabel P. , Morellón L. , Maekawa S. , Saitoh E. , Ibarra M. R.
Published: February 2013

We report the experimental observation of the spin Seebeck effect in magnetite thin films. The signal observed at temperatures above the Verwey transition is a contribution from both the anomalous Nernst (ANE) and spin Seebeck (SSE) effects. The contribution from the ANE of the Fe3O4 layer to the SSE is found to be negligible due to the resistivity difference between Fe3O4 and Pt layers. Below the Verwey transition, the SSE is free from the ANE of the ferromagnetic layer and it is also found to dominate over the ANE due to magnetic proximity effect on the Pt layer.
Electronic states of thiophene/phenylene co-oligomers: Extreme-ultra violet excited photoelectron spectroscopy observations and density functional theory calculations
Authors: Kawaguchi Yoshizo , Sasaki Fumio , Mochizuki Hiroyuki , Ishitsuka Tomoaki , Tomie Toshihisa , Ootsuka Teruhisa , Watanabe Shuji , Shimoi Yukihiro , Yamao Takeshi , Hotta Shu
Published: February 2013

We have investigated electronic states in the valence electron bands for the thin films of three thiophene/phenylene co-oligomer (TPCO) compounds, 2,5-bis(4-biphenylyl)thiophene (BP1T), 1,4-bis(5-phenylthiophen-2-yl)benzene (AC5), and 1,4-bis{5-[4-(trifluoromethyl)phenyl]thiophen-2-yl}benzene (AC5-CF3), by using extreme-UV excited photoelectron spectroscopy (EUPS). By comparing both EUPS spectra and secondary electron spectra between AC5 and AC5-CF3, we confirm that CF3 substitution to AC5 deepens valence states by 2 eV, and increases the ionization energy by 3 eV. From the cut-off positions of secondary electron spectra, the work functions of AC5, AC5-CF3, and BP1T are evaluated to be 3.8 eV, 4.8 eV, and 4.0 eV, respectively. We calculate molecular orbital (MO) energy levels by the density functional theory and compare results of calculations with those of experiments. Densities of states obtained by broadening MO levels well explain the overall features of experimental EUPS spectra of three TPCOs.
High resolution transmission electron microscopy characterization of fcc → 9R transformation in nanocrystalline palladium films due to hydriding
Authors: Amin-Ahmadi Behnam , Idrissi Hosni , Delmelle Renaud , Pardoen Thomas , Proost Joris , Schryvers Dominique
Published: February 2013

Sputtered nanocrystalline palladium thin films with nanoscale growth twins have been subjected to hydriding cycles. The evolution of the twin boundaries has been investigated using high resolution transmission electron microscopy. Surprisingly, the ∑3{112} incoherent twin boundaries dissociate after hydriding into two phase boundaries bounding a 9R phase. This phase which corresponds to single stacking faults located every three {111} planes in the fcc Pd structure was not expected because of the high stacking fault energy of Pd. This observation is connected to the influence of the Hydrogen on the stacking fault energy of palladium and the high compressive stresses building up during hydriding.
Nanochemical effects in femtosecond laser ablation of metals
Authors: Vorobyev A. Y. , Guo Chunlei
Published: February 2013

We study chemical energy released from the oxidation of aluminum in multipulse femtosecond laser ablation in air and oxygen. Our study shows that the released chemical energy amounts to about 13% of the incident laser energy, and about 50% of the ablated material is oxidized. The ablated material mass per laser pulse is measured to be on the nanogram scale. Our study indicates that femtosecond laser ablation is capable of inducing nanochemical reactions since the femtosecond laser pulse can controllably produce nanoparticles, clusters, and atoms from a solid target.
Origin of the defects-induced ferromagnetism in un-doped ZnO single crystals
Authors: Zhan Peng , Xie Zheng , Li Zhengcao , Wang Weipeng , Zhang Zhengjun , Li Zhuoxin , Cheng Guodong , Zhang Peng , Wang Baoyi , Cao Xingzhong
Published: February 2013

We clarified, in this Letter, that in un-doped ZnO single crystals after thermal annealing in flowing argon, the defects-induced room-temperature ferromagnetism was originated from the surface defects and specifically, from singly occupied oxygen vacancies denoted as F+, by the optical and electrical properties measurements as well as positron annihilation analysis. In addition, a positive linear relationship was observed between the ferromagnetism and the F+ concentration, which is in support with the above clarification.
Tunneling of holes is observed by second-harmonic generation
Authors: Vanbel M. K. , Afanas'ev V. V. , Adelmann C. , Caymax M. , Valev V. K. , Verbiest T.
Published: February 2013

Al2O3 passivated n-doped Si substrates are investigated by second-harmonic generation (SHG) upon applying an external electric field by a corona wire. The observed change in the SHG response upon applying an external electric field is attributed to charge transfer in the semiconductor. Capacitance-voltage measurements are performed to affirm this conclusion. Upon applying a large negative electric field over the structure, a clear alteration in SHG signal is observed, which corresponds to tunneling of holes from the n-doped silicon into the aluminum oxide layer.
An integrated inductor for high current with using Fe-Si metal alloy composite films
Authors: Tae Lim Sung , Kim Hee-Jun , Bum Jeong In , Kyeong Lee Tae , Hwang Hee
Published: February 2013

An integrated inductor, using 0.1 mm Fe-Si alloy composite films, has been developed with a dimension of 4.8 mm × 4.5 mm × 1.0 mm thickness. The developed inductor is structured by stacking of metal alloy composite films with μR = 19.5, which consist of mixed Fe-Si alloy powders and epoxy resin for high current application. These stacked films have an etched spiral copper trace with 9 and quarter turns for 4 layers on each film. Copper trace is patterned with a dimension of 0.07 mm thickness, 0.45 mm width, and 1 mm pitch using photolithography technology. In order to evaluate the performance of the developed inductor, inductance and DC resistance were simulated and measured. The simulated result of 1.05 μH and 83 mΩ is well coincided with measured results of 1 μH and 88 mΩ. It is also confirmed that the inductor has a high current capacity of 3 A rated and 6 A saturated values. As an application, a synchronous step down DC-DC converter using the developed inductor is fabricated with the output power of 6.6 W (3.3 V/2 A) and the switching frequency of 3 MHz. Finally, the maximum efficiency of 87% is achieved from the experiment of this DC-DC converter.
Magnetoresistance in inhomogeneous graphene/metal hybrids
Authors: Moktadir Zakaria , Mizuta Hiroshi
Published: February 2013

We investigate extraordinary magnetoresistance (EMR) of inhomogeneous graphene-metal hybrids using finite element modelling. Inhomogeneous graphene is a binary system made of electron and hole puddles. Two geometries of the embedded metallic structure were considered: circular and fishbone geometries. We found that the breaking of graphene into charge puddles weakens the magnetoresistance of the hybrid system compared to a homogeneous graphene-metal system. For a fixed value of the magnetic field, the magnetoresistance increases with decreasing area fraction occupied by electrons puddles. Fishbone geometry showed an enhanced magnetoresistance compared to circular geometry. The EMR is also investigated as a function of the contact resistance for the fishbone geometry where it was found that a minimal contact resistance is essential to obtain enhanced EMR in graphene-metal hybrid devices.
A simple method for evaluating the trapping performance of acoustic tweezers
Authors: Li Ying , Lee Changyang , Ho Lam Kwok , Kirk Shung K.
Published: February 2013

The purpose of this paper is to present a rapid and simple method to evaluate the trapping performance of high frequency focused ultrasonic transducers for acoustic tweezer applications. The method takes into consideration the friction between the particle to be trapped and the surface that it resides on. As a result it should be more reliable and accurate than the methods proposed previously. The trapping force produced by a 70-MHz press-focused transducer was measured to evaluate the performance of this approach. This method demonstrates its potential in optimizing the excitation conditions for acoustic tweezer applications and the design of acoustic tweezers.
Influence of Pt spacer thickness on the domain nucleation in ultrathin Co/Pt/Co trilayers
Authors: Shull R. D. , Iunin Y. L. , Kabanov Y. P. , Nikitenko V. I. , Skryabina O. V. , Chien C. L.
Published: February 2013

The effect of varying the interlayer coupling between two 0.6 nm thick Co layers with perpendicular anisotropy on their magnetic ground state and the domain nucleation processes during a field reversal was studied. A transition from out-of-plane to in-plane anisotropy was revealed as the Pt spacer thickness decreased below 1.6 nm. For Pt thicknesses in the range of 1.6–5.4 nm, domain nucleation occurred in both Co layers in a correlated manner, and subsequent motion of the domain walls proceeded as though bound together. A transition to uncorrelated domain nucleation and independent wall motion was observed at Pt thicknesses above 5.4 nm. Both conventional and “asymmetrical” domain nucleation centers were observed in the whole range of platinum spacer thicknesses.
Optimization of microfluidic microsphere-trap arrays
Authors: Xu Xiaoxiao , Sarder Pinaki , Li Zhenyu , Nehorai Arye
Published: February 2013

Microarray devices are powerful for detecting and analyzing biological targets. However, the potential of these devices may not be fully realized due to the lack of optimization of their design and implementation. In this work, we consider a microsphere-trap array device by employing microfluidic techniques and a hydrodynamic trapping mechanism. We design a novel geometric structure of the trap array in the device, and develop a comprehensive and robust framework to optimize the values of the geometric parameters to maximize the microsphere arrays' packing density. We also simultaneously optimize multiple criteria, such as efficiently immobilizing a single microsphere in each trap, effectively eliminating fluidic errors such as channel clogging and multiple microspheres in a single trap, minimizing errors in subsequent imaging experiments, and easily recovering targets. We use finite element simulations to validate the trapping mechanism of the device, and to study the effects of the optimization geometric parameters. We further perform microsphere-trapping experiments using the optimized device and a device with randomly selected geometric parameters, which we denote as the un-optimized device. These experiments demonstrate easy control of the transportation and manipulation of the microspheres in the optimized device. They also show that the optimized device greatly outperforms the un-optimized device by increasing the packing density by a factor of two, improving the microsphere trapping efficiency from 58% to 99%, and reducing fluidic errors from 48% to a negligible level (less than 1%). The optimization framework lays the foundation for the future goal of developing a modular, reliable, efficient, and inexpensive lab-on-a-chip system.
Analysis of the influence of external biasing on Texas Helimak turbulence
Authors: Toufen D. L. , Guimarães-Filho Z. O. , Caldas I. L. , Szezech J. D. , Lopes S. , Viana R. L. , Gentle K. W.
Published: February 2013

We analyze alterations on the electrostatic turbulence in experiments with imposed bias to control the plasma radial electric field in Texas Helimak (K. W. Gentle and H. He, Plasma Sci. Technol. 10, 284 (2008)), a toroidal plasma device with a one-dimensional equilibrium, magnetic curvature, and shear. Comparing discharges from different biased potentials, we identify, in a roughly uniform gradient region, a continuous variation from low turbulence level and narrower frequency spectra, for negative bias, to high turbulence level and broadband spectra for positive bias. Overall, we distinguish two kinds of perturbed turbulence, classified according to their intensity, spectral, statistical, and recurrence properties. When the bias is positive, the turbulence shows enhanced and broadband spectra with non Gaussian probability distribution functions having noticeable long tails (extreme events) similar to the turbulence in tokamak scrape-off layer. On the other hand, negative bias reduces the turbulence level and decreases the spectrum widths. Also for negative bias, we found large frequency widths whenever the coupling between drift waves and the sheared plasma flow is fast enough to allow the enhancement of sidebands modes.
Lead incorporation mechanism in LiF crystals
Authors: D'Acapito F. , Pochet P. , Somma F. , Aloe P. , Montereali R. M. , Vincenti M. A. , Polosan S.
Published: February 2013

The doping process of LiF with Pb has been described by using structural ab initio modeling and experimental results. The values of formation energy of several complexes involving Pb ions show that the presence of charge-balancing vacancies ease the metal incorporation in the crystal. The metal successively captures the vacancies to form a final stable complex PbLi•+VLi′. Experimental data from X-ray absorption spectroscopy confirm the presence of Pb in LiF crystals in this site revealing both Pb-F bonds and collinear Pb-F-Li atomic configurations. A maximum solubility of Pb in LiF of the order of 3×1020/cm3 can be estimated from these calculations.
Fano line shapes in transmission spectra of silicon photonic crystal resonators
Authors: Mehta Karan K. , Orcutt Jason S. , Ram Rajeev J.
Published: February 2013

Transmission measurements on symmetrically waveguide-loaded one-dimensional silicon photonic crystal microresonators are observed to exhibit Fano line shapes, which we find to be due to the interference between the resonant transmission and a leaky second-order quasi-transverse-electric mode partially guided through the photonic crystal. The line shape is tunable by varying the exciting fiber position, the material index, and via the cavity nonlinearity. This two-mode interference method applied to a one-dimensional silicon photonic crystal cavity represents a compact and tunable approach to obtaining such line shapes in integrated optical devices, with implications for efficient modulation of optical signals and nonlinear all-optical switching.
GaN-based high contrast grating surface-emitting lasers
Authors: Wu Tzeng-Tsong , Wu Shu-Hsien , Lu Tien-Chang , Wang Shing-Chung
Published: February 2013

GaN-based high contrast grating surface-emitting lasers (HCG SELs) with AlN/GaN distributed Bragg reflectors were reported. The device exhibited a low threshold pumping energy density of about 0.56 mJ/cm2 and the lasing wavelength was at 393.6 nm with a high degree of polarization of 73% at room temperature. The specific lasing mode and polarization characterisitcs agreed well with the theoretical modeling. The low threshold characteristics of our GaN-based HCG SELs faciliated by the Fano resonance can serve as the best candidate in blue surface emitting laser sources.
The role of charge on the diffusion of solutes and nanoparticles (silicon nanocrystals, nTiO2, nAu) in a biofilm
Authors: Golmohamadi Mahmood , Clark Rhett J. , Veinot Jonathan G. C. , Wilkinson Kevin J.
Published: February 2013

Environmental context The mobility and bioavailability of both contaminants and nutrients in the environment depends, to a large extent, on their diffusion. Because the majority of microorganisms in the environment are embedded in biofilms, it is essential to quantify diffusion in biofilms in order to evaluate the risk of emerging contaminants, including nanomaterials and charged solutes. This study quantifies diffusion, in a model environmental biofilm, for a number of model contaminants of variable size and charge. Abstract The effect of solute and biofilm charge on self-diffusion (Brownian motion) in biofilms is examined. Diffusion coefficients (D) of several model (fluorescent) solutes (rhodamine B; tetramethylrhodamine, methyl ester; Oregon Green 488 carboxylic acid, succinimidyl ester and Oregon Green 488 carboxylic acid) and nanoparticles (functionalised silicon, gold and titanium) were determined using fluorescence correlation spectroscopy (FCS). Somewhat surprisingly, little effect due to charge was observed on the diffusion measurements in the biofilms. Furthermore, the ratio of the diffusion coefficient in the biofilm with respect to that in water (Db/Dw) remained virtually constant across a wide range of ionic strengths (0.1–100mM) for both negatively and positively charged probes. In contrast, the self-diffusion coefficients of nanoparticles with sizes >10nm greatly decreased in the biofilms with respect to those in water. Furthermore, much larger nanoparticles (>66nm) appeared to be completely excluded from the biofilms. The results indicated that for many oligotrophic biofilms in the environment, the diffusion of solutes and nanoparticles will be primarily controlled by obstruction rather than electrostatic interactions. The results also imply that most nanomaterials will become significantly less mobile and less bioavailable (to non-planktonic organisms) as they increase in size beyond ~10nm.
In search of potential source regions of semi-volatile organic contaminants in air in the Yukon Territory, Canada from 2007 to 2009 using hybrid receptor models
Authors: Westgate John N. , Sofowote Uwayemi M. , Roach Pat , Fellin Phil , D'Sa Ivy , Sverko Ed , Su Yushan , Hung Hayley , Wania Frank
Published: February 2013

Environmental context
Some long-lived organic contaminants, such as chlorinated organics, brominated flame retardants and polycyclic aromatic hydrocarbons, can undergo transport through the atmosphere to remote regions. A series of measurements of these compounds taken over almost 3 years in the air at a remote location was combined with meteorological data to try to reveal potential source areas. After adjusting several parameters to optimise the method’s ability to identify sources it was found that for most contaminants no definitive sources are revealed.

Abstract
A suite of brominated flame retardants, chlorinated organic pesticides and some metabolites thereof were analysed in week-long and day-long air samples collected at Little Fox Lake in Canada’s Yukon Territory from 2007 to 2009. Several trajectory-based methods for source region identification were applied to this dataset, as well as to polycyclic aromatic hydrocarbon (PAH) concentrations in those same samples reported previously. A type of concentration weighted trajectory (CWT) analysis, using a modified grid to avoid difficulties near the Earth’s poles, and removing trajectory endpoints at altitudes greater than 700m did not identify distinct source regions for most analytes. Decreasing the spatial resolution of the grid made interpretation simpler but reinforced patterns that may have stemmed from single trajectories. The potential source contribution function (PSCF) is similar to CWT but treats the concentration data categorically, rather than numerically. PSCF provides more distinct results, highlighting the Arctic Ocean as a potential source of para,para′-dichlorodiphenyldichloroethene and both northern Siberia and Canada’s Yukon and Northwest Territories as potential sources of PAHs. To simulate the uncertainty associated with individual trajectories, a set of trajectories was also generated for six points surrounding the sampling station and included in the trajectory analyses. This had the effect of smoothing the CWT and PSCF values for those analytes with no clearly definable sources, and highlighting the source regions for the two that did. For the bulk of the analytes discussed here, Little Fox Lake is well positioned to act as a background monitoring site.
Installation of impervious surface in urban areas affects microbial biomass, activity (potential C mineralisation), and functional diversity of the fine earth
Authors: Wei Zongqiang , Wu Shaohua , Zhou Shenglu , Lin Chen
Published: February 2013

Artificial soil sealing in urban areas has attracted increasing attention due to its potential hazard to urban ecosystems. It has negative impacts on soil function and the urban environment, since the impervious surface can hamper the exchange of material and energy between the soil and other environmental compartments. However, information about the effects of artificial soil sealing in urban area on soil quality and properties, especially the microbiological components, is still limited. Ten plots which differed in land use were selected from Nanjing City, China, to investigate the effects of impervious surfaces on microbiological characteristics in urban soil. Plot types were paved road, residential paved square, residential paved alley, and grassed area. Soil microbial biomass carbon (Cmic) and nitrogen (Nmic), and activities were analysed, and the microbial functional diversity of fine earth (<2 mm material) was characterised by the Biolog EcoPlate technique. Mean concentrations of soil organic carbon (SOC), Cmic, and Nmic in fine earth from the impervious areas (0–20 cm) were, respectively, 6.5 g kg–1, 55.8 mg kg–1, and 12.2 mg kg–1, which were significantly lower than concentrations from grass areas. Urban sealing also resulted in decreases in soil microbial activity and functional diversity, but the influences on soil microbial diversity varied among land uses, with road pavement having the most negative effect. Substrate use patterns showed that microorganisms in urban sealed soils had higher utilisation of polymers (P < 0.05) but lower use of carbohydrates and amines/amides (P < 0.05). These findings demonstrate that SOC in the sealed soils was more stable than in open soils, and the installation of impervious surfaces such as asphalt and concrete, which are very common in urban areas, can result in decreases in SOC content, soil microbial activity, and diversity in urban soil.
Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations
Authors: Williams Zev , Ben-Dov Iddo Z. , Elias Rony , Mihailovic Aleksandra , Brown Miguel , Rosenwaks Zev , Tuschl Thomas
Published: February 2013

We profiled microRNAs (miRNAs) in cell-free serum and plasma samples from human volunteers using deep sequencing of barcoded small RNA cDNA libraries. By introducing calibrator synthetic oligonucleotides during library preparation, we were able to calculate the total as well as specific concentrations of circulating miRNA. Studying trios of samples from newborn babies and their parents we detected placental-specific miRNA in both maternal and newborn circulations and quantitated the relative contribution of placental miRNAs to the circulating pool of miRNAs. Furthermore, sequence variation in the placental miRNA profiles could be traced to the specific placenta of origin. These deep sequencing profiles, which may serve as a model for tumor or disease detection, allow us to define the repertoire of miRNA abundance in the circulation and potential uses as biomarkers.
Electrokinetic properties of the mammalian tectorial membrane
Authors: Ghaffari Roozbeh , Page Scott L. , Farrahi Shirin , Sellon Jonathan B. , Freeman Dennis M.
Published: February 2013

The tectorial membrane (TM) clearly plays a mechanical role in stimulating cochlear sensory receptors, but the presence of fixed charge in TM constituents suggests that electromechanical properties also may be important. Here, we measure the fixed charge density of the TM and show that this density of fixed charge is sufficient to affect mechanical properties and to generate electrokinetic motions. In particular, alternating currents applied to the middle and marginal zones of isolated TM segments evoke motions at audio frequencies (1–1,000 Hz). Electrically evoked motions are nanometer scaled (∼5–900 nm), decrease with increasing stimulus frequency, and scale linearly over a broad range of electric field amplitudes (0.05–20 kV/m). These findings show that the mammalian TM is highly charged and suggest the importance of a unique TM electrokinetic mechanism.
The brain uses adaptive internal models of scene statistics for sensorimotor estimation and planning
Authors: Kwon Oh-Sang , Knill David C.
Published: February 2013

Significance

To test the hypothesis that the brain uses adaptive models of object statistics to interpret sensory information, we measured the statistical models used by subjects to estimate object speed when asked to hit a moving object. Subjects’ behavior showed perceptual biases to the mean speed within a stimulus set that accurately adapted to changes in the variance of a stimulus set. More significantly, the results show that the way that stimuli on one trial influence following trials adapts appropriately to changes in trial-to-trial correlations in a stimulus set, although subjects’ estimates of correlations retain erroneous positive biases.
Genotype–phenotype correlations in neonatal epilepsies caused by mutations in the voltage sensor of K
v
7.2 potassium channel subunits
Authors: Miceli Francesco , Soldovieri Maria Virginia , Ambrosino Paolo , Barrese Vincenzo , Migliore Michele , Cilio Maria Roberta , Taglialatela Maurizio
Published: February 2013

Mutations in the K
V
7.2 gene encoding for voltage-dependent K
+
channel subunits cause neonatal epilepsies with wide phenotypic heterogeneity. Two mutations affecting the same positively charged residue in the S
4
domain of K
V
7.2 have been found in children affected with benign familial neonatal seizures (R213W mutation) or with neonatal epileptic encephalopathy with severe pharmacoresistant seizures and neurocognitive delay, suppression-burst pattern at EEG, and distinct neuroradiological features (R213Q mutation). To examine the molecular basis for this strikingly different phenotype, we studied the functional characteristics of mutant channels by using electrophysiological techniques, computational modeling, and homology modeling. Functional studies revealed that, in homomeric or heteromeric configuration with K
V
7.2 and/or K
V
7.3 subunits, both mutations markedly destabilized the open state, causing a dramatic decrease in channel voltage sensitivity. These functional changes were (
i
) more pronounced for channels incorporating R213Q- than R213W-carrying K
V
7.2 subunits; (
ii
) proportional to the number of mutant subunits incorporated; and (
iii
) fully restored by the neuronal K
v
7 activator retigabine. Homology modeling confirmed a critical role for the R213 residue in stabilizing the activated voltage sensor configuration. Modeling experiments in CA1 hippocampal pyramidal cells revealed that both mutations increased cell firing frequency, with the R213Q mutation prompting more dramatic functional changes compared with the R213W mutation. These results suggest that the clinical disease severity may be related to the extent of the mutation-induced functional K
+
channel impairment, and set the preclinical basis for the potential use of K
v
7 openers as a targeted anticonvulsant therapy to improve developmental outcome in neonates with K
V
7.2 encephalopathy.
Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees
Authors: Condit Richard , Engelbrecht Bettina M. J. , Pino Delicia , Pérez Rolando , Turner Benjamin L.
Published: February 2013

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.
Superiority illusion arises from resting-state brain networks modulated by dopamine
Authors: Yamada Makiko , Uddin Lucina Q. , Takahashi Hidehiko , Kimura Yasuyuki , Takahata Keisuke , Kousa Ririko , Ikoma Yoko , Eguchi Yoko , Takano Harumasa , Ito Hiroshi , Higuchi Makoto , Suhara Tetsuya
Published: February 2013

The majority of individuals evaluate themselves as superior to average. This is a cognitive bias known as the “superiority illusion.” This illusion helps us to have hope for the future and is deep-rooted in the process of human evolution. In this study, we examined the default states of neural and molecular systems that generate this illusion, using resting-state functional MRI and PET. Resting-state functional connectivity between the frontal cortex and striatum regulated by inhibitory dopaminergic neurotransmission determines individual levels of the superiority illusion. Our findings help elucidate how this key aspect of the human mind is biologically determined, and identify potential molecular and neural targets for treatment for depressive realism.
A post-Kyoto partner: Considering the stratospheric ozone regime as a tool to manage nitrous oxide
Authors: Kanter David , Mauzerall Denise L. , Ravishankara A. R. , Daniel John S. , Portmann Robert W. , Grabiel Peter M. , Moomaw William R. , Galloway James N.
Published: February 2013

Nitrous oxide (N2O) is the largest known remaining anthropogenic threat to the stratospheric ozone layer. However, it is currently only regulated under the 1997 Kyoto Protocol because of its simultaneous ability to warm the climate. The threat N2O poses to the stratospheric ozone layer, coupled with the uncertain future of the international climate regime, motivates our exploration of issues that could be relevant to the Parties to the ozone regime (the 1985 Vienna Convention and its 1987 Montreal Protocol) should they decide to take measures to manage N2O in the future. There are clear legal avenues to regulate N2O under the ozone regime as well as several ways to share authority with the existing and future international climate treaties. N2O mitigation strategies exist to address the most significant anthropogenic sources, including agriculture, where behavioral practices and new technologies could contribute significantly to reducing emissions. Existing policies managing N2O and other forms of reactive nitrogen could be harnessed and built on by the ozone regime to implement N2O controls. There are several challenges and potential cobenefits to N2O control which we discuss here: food security, equity, and implications of the nitrogen cascade. The possible inclusion of N2O in the ozone regime need not be viewed as a sign of failure of the United Nations Framework Convention on Climate Change to adequately deal with climate change. Rather, it could represent an additional valuable tool in sustainable development diplomacy.
‘My language thing … is like a big shadow always behind me’: International counselling trainees' challenges in beginning clinical practice
Authors: Georgiadou Lorena
Published: February 2013

Background: While counsellor education becomes increasingly culturally diverse, little is known about international trainees' experiences of training. Objective: The present study explores one aspect of training, namely clinical practice from the perspective of international, non‐native speaking trainees. In particular, this paper focuses on the challenges this group encounters when practicing in a second language. Methodology: Semi‐structured interviews with four non‐native English‐speaking trainees were conducted and analysed following the principles of interpretative phenomenological analysis (IPA). Results: Findings suggest that participants encounter practical difficulties related to their non‐native/foreign identity in practice, such as problems with articulate self‐expression and understanding the client's speech. These difficulties generate anxiety and impact on the trainees' confidence. Conclusions and implications for counsellor training: This study elucidates language as a fundamental aspect of culture, and identifies second language use as a significant source of difference in counselling practice. This paper highlights the need for attention to linguistic diversity and for appropriate support during counsellor education. This will improve international trainees' experiences of training, but also enhance all trainees' understanding of difference, resulting in better service provision for the community.
Does Visual Working Memory Work as a Few Fixed Slots?
Authors: Li Jie , Shao Na , Xu Haokui , Shui Rende , Shen Mowei
Published: February 2013

The present study investigated whether visual working memory (VWM) functions as a few (about 3 ∼ 4) fixed slots by examining how the distribution of VWM is adjusted. Adopting a change-detection paradigm, we required subjects to memorize four items, one of which was prioritized. If VWM functions as 3 ∼ 4 slots, allocating multiple slots to the prioritized item would leave no slot for some other items; consequently no information would be stored for them, leading to a substantial decrease in change-detection performance no matter whether small or large changes occurred. The result showed that small changes on the unfavoured items were detected less accurately, indicating that more VWM was allocated to the favoured item. Yet meanwhile large changes that occurred on those unfavoured items could still be detected as well as those on the favoured one, indicating that each of them was still stored to some extent rather than completely discarded. The results suggested that VWM may not work as 3 ∼ 4 fixed slots. Possible mechanisms were discussed based on the present results, including a modified slot model with more available slots, a continuous resource model, and a hierarchical model that assumes storage of ensemble information in addition to the information of individual items.