bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthetic aperture imaging for multilayer cylindrical object using an exterior rotating transducer
Authors: Wu Shiwei , Skjelvareid Martin H. , Yang Keji , Chen Jian
Published: August 2015

The synthetic aperture focusing technique (SAFT) with significant improvements in lateral resolution has been adapted for ultrasound imaging of multilayer objects. To apply SAFT to imaging of cylindrical objects such as solid axles or pipes with small diameter, exterior cylindrical scan is much preferred. In this paper, a frequency-domain algorithm is proposed for such cylindrical scan performed with an exterior rotating transducer. The algorithm is derived from Fourier-domain solutions to the waveequation in cylindrical coordinates, and then extended to the multilayer case. A simulation model for multilayer structure is established, and the algorithm is demonstrated for both simulated and experimental data. Compared with the raw images, the reconstructed images with proposed algorithm attain better lateral resolution for multilayer objects. It is shown that the attainable angular resolution for each layer is approximately consistent with that achieved in the single-layer case, as long as the transmission factors are approximately uniform within the divergence angle of the transducer. The performance of proposed algorithm is verified with experimental C-scan image and demonstrates that it is capable of improving the lateral resolution in both scanning directions.
Crack propagation in graphene
Authors: Budarapu P. R. , Javvaji B. , Sutrakar V. K. , Roy Mahapatra D. , Zi G. , Rabczuk T.
Published: August 2015

The crack initiation and growth mechanisms in an 2D graphene lattice structure are studied based on molecular dynamics simulations. Crack growth in an initial edge crack model in the arm-chair and the zig-zag lattice configurations of graphene are considered. Influence of the time steps on the post yielding behaviour of graphene is studied. Based on the results, a time step of 0.1 fs is recommended for consistent and accurate simulation of crack propagation. Effect of temperature on the crack propagation in graphene is also studied, considering adiabatic and isothermal conditions. Total energy and stress fields are analyzed. A systematic study of the bond stretching and bond reorientation phenomena is performed, which shows that the crack propagates after significant bond elongation and rotation in graphene. Variation of the crack speed with the change in crack length is estimated.
Structure-topology-property correlations of sodium phosphosilicate glasses
Authors: Hermansen Christian , Guo Xiaoju , Youngman Randall E. , Mauro John C. , Smedskjaer Morten M. , Yue Yuanzheng
Published: August 2015

In this work, we investigate the correlations among structure, topology, and properties in a series of sodium phosphosilicate glasses with [SiO2]/[SiO2 + P2O5] ranging from 0 to 1. The network structure is characterized by 29Si and 31P magic-angle spinning nuclear magnetic resonance and Raman spectroscopy. The results show the formation of six-fold coordinated silicon species in phosphorous-rich glasses. Based on the structural data, we propose a formation mechanism of the six-fold coordinated silicon, which is used to develop a quantitative structural model for predicting the speciation of the network forming units as a function of chemical composition. The structural model is then used to establish a temperature-dependent constraint description of phosphosilicate glass topology that enables prediction of glass transition temperature, liquid fragility, and indentation hardness. The topological constraint model provides insight into structural origin of the mixed network former effect in phosphosilicate glasses.
Phase transitions and separations in a distorted liquid crystalline mixture
Authors: Kasch Nicholas , Dierking Ingo
Published: August 2015

A theoretical method is proposed for modelling phase transitions and phase ranges in a multi-component liquid crystalline mixture where the liquid crystal structure is distorted and defects are formed. This method employs the Maier-Saupe and Kobayashi-McMillan theories of liquid crystalline ordering and the Flory-Huggins theory of mixtures. It builds on previous work on mixed systems that can form smectic-A and nematic phases by incorporating “distortion factors” into the expression for the local free energy of the mixture, which account for the effects of a deviation of the liquid crystal structure from the uniform nematic and smectic-A states. The method allows a simple description of chiral defect phases such as the blue phase and the twist grain boundary phase. In a previous work, it was shown that a model of the blue phase along these lines could effectively explain the observed effect whereby an added guest compound can stabilize the phase by separating into the high energy defect regions of the structure. It is shown here that with the correct choice of guest material a similar effect could be observed for the twist grain boundary phase.
Multipactor threshold calculation of coaxial transmission lines in microwave applications with nonstationary statistical theory
Authors: Lin S. , Wang H. , Li Y. , Liu C. , Zhang N. , Cui W. , Neuber A.
Published: August 2015

This paper presents a statistical theory for the initial onset of multipactor breakdown in coaxial transmission lines, taking both the nonuniform electric field and random electron emission velocity into account. A general numerical method is first developed to construct the joint probability density function based on the approximate equation of the electron trajectory. The nonstationary dynamics of the multipactor process on both surfaces of coaxial lines are modelled based on the probability of various impacts and their corresponding secondary emission. The resonant assumption of the classical theory on the independent double-sided and single-sided impacts is replaced by the consideration of their interaction. As a result, the time evolutions of the electron population for exponential growth and absorption on both inner and outer conductor, in response to the applied voltage above and below the multipactor breakdown level, are obtained to investigate the exact mechanism of multipactor discharge in coaxial lines. Furthermore, the multipactor threshold predictions of the presented model are compared with experimental results using measured secondary emission yield of the tested samples which shows reasonable agreement. Finally, the detailed impact scenario reveals that single-surface multipactor is more likely to occur with a higher outer to inner conductor radius ratio.
Influence of centrifugal effects on particle and momentum transport in National Spherical Torus Experiment
Authors: Buchholz R. , Grosshauser S. , Guttenfelder W. , Hornsby W. A. , Migliano P. , Peeters A. G. , Strintzi D.
Published: August 2015

This paper studies the effect of rotation on microinstabilities under experimentally relevant conditions in the spherical tokamak National Spherical Torus Experiment (NSTX). The focus is specifically on the centrifugal force effects on the impurity and momentum transport in the core (r/a=0.7) of an H-mode plasma. Due to relatively high beta, the linear simulations predict the presence of both microtearing mode (MTM) and hybrid ion temperature gradient-kinetic ballooning mode (ITG-KBM) electromagnetic instabilities. Rotation effects on both MTM and ITG-KBM growth rates and mode frequencies are found to be small for the experimental values. However, they do influence the quasi-linear particle and momentum fluxes predicted by ITG-KBM (MTM contributes only to electron heat flux). The gradient of the intrinsic carbon impurity in the source-free core region is predicted to be locally hollow, strengthened by centrifugal effects. This result is consistent with experimental measurements and contradicts neoclassical theory that typically provides a reasonable explanation of the impurity profiles in NSTX. The diffusive and Coriolis pinch contributions to momentum transport are found to be relatively weak. Surprisingly, the strongest contribution derives from a centrifugal effect proportional to the product of rotation and rotation shear, which predicts an inward momentum flux roughly three times bigger than the Coriolis pinch, suggesting it should be considered when interpreting previous experimental pinch measurements.
Coupling of magnetic electron drift vortex mode with longitudinal perturbations in collision-less and dissipative electron and electron-ion plasmas
Authors: Haque Q. , Saleem H.
Published: August 2015

The plasma density non-uniformity gives rise to the coupling of transverse magnetic electron drift vortex (MEDV) mode with the longitudinal perturbations in dissipative and non-dissipative electron plasmas. This coupling produces partially transverse and partially longitudinal low frequency instabilities in classical un-magnetized laser plasmas. The MEDV mode couples with the ion acoustic wave, when the ion dynamics is also included. Both the modes have frequencies of the same order of magnitude and couple to give rise to electromagnetic instabilities in un-magnetized plasmas.
Thermoelectric properties of Si/SiB3 sub-micro composite prepared by melt-spinning technique
Authors: Xie Jun , Ohishi Yuji , Miyazaki Yoshinobu , Yusufu Aikebaier , Muta Hiroaki , Kurosaki Ken , Yamanaka Shinsuke
Published: August 2015

This study presents a new self-assembly process to form a fine structure in bulk Si. We fabricated a semiconducting composite material consisting of sub-micro-sized (100–500 nm) SiB3 precipitates distributed in a Si matrix whose grain size was on the order of microns. The sub-micro-sized SiB3 particles were precipitated during the spark plasma sintering process of a metastable Si-B (Si:B = 92:8) supersaturated solid solution prepared by the melt-spinning technique. The composite was a heavily doped (5 × 1020 cm−3) p-type semiconductor. The SiB3 precipitates did not affect the Seebeck coefficient, slightly reduced the carrier mobility, and greatly reduced the lattice thermal conductivity. Specifically, the lattice thermal conductivity was reduced by 44% compared with that of p-type Si without precipitates at room temperature. The SiB3 precipitates improved the thermoelectric figure of merit ZT from 0.17 to 0.23 at 1073 K, which indicates that the formation of small precipitates effectively improves the thermoelectric performance of Si-based thermoelectric materials.
Complementary layer pairs of plasmonic ladder-like structured films: Fabrication and visible-near-infrared properties
Authors: Behera Gangadhar , Mandal P. , Ramakrishna S. Anantha
Published: August 2015

Complementary layer pairs consisting of an array of elongated gold patches on one layer with the complementary elongated holes on a second separated gold layer were fabricated by laser interference lithography using a double-exposure method. The anisotropic complementary layers, with a stretched hexagonal lattice, show polarization dependent enhanced transmittance at near-infrared wavelengths. The wavelengths of the peak transmittance through the plasmonic films are well correlated with the wavelengths of the resonant excitations of surface plasmon resonances of the system. The enhanced transmittance through such complementary layer pairs and the role played by the plasmonic resonances at the wavelengths with peak transmittance are confirmed through electromagnetic simulations. The enhanced transmittance is mediated by the plasmonic resonances of the hole arrays or cavity resonances due to the pair of complementary layers.
Rate dependent direct inverse hysteresis compensation of piezoelectric micro-actuator used in dual-stage hard disk drive head positioning system
Authors: Rahman Md. Arifur , Al Mamun Abdullah , Yao Kui
Published: August 2015

The head positioning servo system in hard disk drive is implemented nowadays using a dual-stage actuator—the primary stage consisting of a voice coil motor actuator providing long range motion and the secondary stage controlling the position of the read/write head with fine resolution. Piezoelectric micro-actuator made of lead zirconate titanate (PZT) has been a popular choice for the secondary stage. However, PZT micro-actuator exhibits hysteresis—an inherent nonlinear characteristic of piezoelectric material. The advantage expected from using the secondary micro-actuator is somewhat lost by the hysteresis of the micro-actuator that contributes to tracking error. Hysteresis nonlinearity adversely affects the performance and, if not compensated, may cause inaccuracy and oscillation in the response. Compensation of hysteresis is therefore an important aspect for designing head-positioning servo system. This paper presents a new rate dependent model of hysteresis along with rigorous analysis and identification of the model. Parameters of the model are found using particle swarm optimization. Direct inverse of the proposed rate-dependent generalized Prandtl-Ishlinskii model is used as the hysteresis compensator. Effectiveness of the overall solution is underscored through experimental results.
A lab-based ambient pressure x-ray photoelectron spectrometer with exchangeable analysis chambers
Authors: Newberg John T. , Åhlund John , Arble Chris , Goodwin Chris , Khalifa Yehia , Broderick Alicia
Published: August 2015

Ambient pressure X-ray photoelectron spectroscopy (APXPS) is a powerful spectroscopy tool that is inherently surface sensitive, elemental, and chemical specific, with the ability to probe sample surfaces under Torr level pressures. Herein, we describe the design of a new lab-based APXPS system with the ability to swap small volume analysis chambers. Ag 3d(5/2) analyses of a silver foil were carried out at room temperature to determine the optimal sample-to-aperture distance, x-ray photoelectron spectroscopy analysis spot size, relative peak intensities, and peak full width at half maximum of three different electrostatic lens modes: acceleration, transmission, and angular. Ag 3d(5/2) peak areas, differential pumping pressures, and pump performance were assessed under varying N2(g) analysis chamber pressures up to 20 Torr. The commissioning of this instrument allows for the investigation of molecular level interfacial processes under ambient vapor conditions in energy and environmental research.
A novel vacuum spectrometer for total reflection x-ray fluorescence analysis with two exchangeable low power x-ray sources for the analysis of low, medium, and high Z elements in sequence
Authors: Wobrauschek P. , Prost J. , Ingerle D. , Kregsamer P. , Misra N. L. , Streli C.
Published: August 2015

The extension of the detectable elemental range with Total Reflection X-ray Fluorescence (TXRF) analysis is a challenging task. In this paper, it is demonstrated how a TXRF spectrometer is modified to analyze elements from carbon to uranium. Based on the existing design of a vacuum TXRF spectrometer with a 12 specimen sample changer, the following components were renewed: the silicon drift detector with 20 mm2 active area and having a special ultra-thin polymer window allowing the detection of elements from carbon upwards. Two exchangeable X-ray sources guarantee the efficient excitation of both low and high Z elements. These X-ray sources were two light-weighted easily mountable 35 W air-cooled low-power tubes with Cr and Rh anodes, respectively. The air cooled tubes and the Peltier-cooled detector allowed to construct a transportable tabletop spectrometer with compact dimensions, as neither liquid nitrogen cooling for the detector nor a water cooling circuit and a bulky high voltage generator for the X-ray tubes are required. Due to the excellent background conditions as a result of the TXRF geometry, detection limits of 150 ng for C, 12 ng for F, and 3.3 ng for Na have been obtained using Cr excitation in vacuum. For Rh excitation, the detection limits of 90 pg could be achieved for Sr. Taking 10 to 20 μl of sample volume, extrapolated detection limits in the ng/g (ppb) range are resulting in terms of concentration.
Subspace formulation of time-dependent density functional theory for large-scale calculations
Authors: Zhang Xu , Lu Gang
Published: August 2015

A subspace formulation of time-dependent density functional theory (TDDFT) is proposed for large-scale calculations based on density functional perturbation theory. The formulation is implemented in conjunction with projector augmented-wave method and plane-wave basis set. A key bottleneck of conventional TDDFT method is circumvented by projecting the time-dependent Kohn-Sham eigenvalue equations from a full Hilbert space to a substantially reduced sub-Hilbert space. As a result, both excitation energies and ionic forces can be calculated accurately within the reduced subspace. The method is validated for several model systems and exhibits the similar accuracy as the conventional TDDFT method but at a computational cost of the ground state calculation. The Born-Oppenheimer molecular dynamics can be successfully performed for excited states in C60 and T12 molecules, opening doors for many applications involving excited state dynamics.
Derivative discontinuity with localized Hartree-Fock potential
Authors: Nazarov V. U. , Vignale G.
Published: August 2015

The localized Hartree-Fock potential has proven to be a computationally efficient alternative to the optimized effective potential, preserving the numerical accuracy of the latter and respecting the exact properties of being self-interaction free and having the correct −1/r asymptotics. In this paper we extend the localized Hartree-Fock potential to fractional particle numbers and observe that it yields derivative discontinuities in the energy as required by the exact theory. The discontinuities are numerically close to those of the computationally more demanding Hartree-Fock method. Our potential enjoys a “direct-energy” property, whereby the energy of the system is given by the sum of the single-particle eigenvalues multiplied by the corresponding occupation numbers. The discontinuities c↑ and c↓ of the spin-components of the potential at integer particle numbers N↑ and N↓ satisfy the condition c↑N↑ + c↓N↓ = 0. Thus, joining the family of effective potentials which support a derivative discontinuity, but being considerably easier to implement, the localized Hartree-Fock potential becomes a powerful tool in the broad area of applications in which the fundamental gap is an issue.
Computational investigation on tunable optical band gap in armchair polyacenes
Authors: Das Mousumi
Published: August 2015

Polyacenes in their armchair geometry (phenacenes) have recently been found to possess appealing electronic and optical properties with higher chemical stability and comparatively larger band gap as compared to linear polyacenes. They also behave as high-temperature superconductors upon alkali metal doping. Moreover, the optical properties of crystalline picene can be finely tuned by applying external pressure. We investigated the variation of optical gap as a function of altering the interplanar distances between parallel cofacial phenacene dimers. We employed both time-dependent density functional theory and density matrix renormalization group (DMRG) technique to investigate the lowest singlet excitations in phenacene dimer. Our study showed that the lowest singlet excitation in these systems evolved as a function of interplanar separation. The optical excitation energy gap decreases as a function of inverse interplanar separation of the phenacene dimer. The distant dependent variation of optical absorption at the dimer level may be comparable with experimental observation in picene crystal under pressure. DMRG study also demonstrates that besides picene, electronic properties of higher phenacenes can also be tunable by altering interplanar separation.
Bulk elastic waves with unidirectional backscattering-immune topological states in a time-dependent superlattice
Authors: Swinteck N. , Matsuo S. , Runge K. , Vasseur J. O. , Lucas P. , Deymier P. A.
Published: August 2015

Recent progress in electronic and electromagnetic topological insulators has led to the demonstration of one way propagation of electron and photon edge states and the possibility of immunity to backscattering by edge defects. Unfortunately, such topologically protected propagation of waves in the bulk of a material has not been observed. We show, in the case of sound/elastic waves, that bulk waves with unidirectional backscattering-immune topological states can be observed in a time-dependent elastic superlattice. The superlattice is realized via spatial and temporal modulation of the stiffness of an elastic material. Bulk elastic waves in this superlattice are supported by a manifold in momentum space with the topology of a single twist Möbius strip. Our results demonstrate the possibility of attaining one way transport and immunity to scattering of bulk elastic waves.
Improvement on output torque of dielectric elastomer minimum energy structures
Authors: Zhao Jianwen , Niu Junyang , McCoul David , Ge Yong , Pei Qibing , Liu Liwu , Leng Jinsong
Published: August 2015

The dielectric elastomer minimum energy structure (DEMES) can realize large angular deformations by a small voltage-induced strain of the dielectric elastomer (DE), so it is a suitable candidate to make a rotary joint for a soft robot. However, the payload capacity of a DEMES joint is small compared with other types of dielectric elastomer actuators. Stacking layers of pre-strained DE thin films can increase the output torque of DEMES, but greater driving power will be needed, limiting application in mobile or flying soft robots. In this paper, based on static analysis, a design of DEMES is proposed that has larger torque than the traditional design with the same number of layers of dielectric elastomer. As an experimental example, the torque of the film with the improved design is larger than 1.7 times that of the traditional design. Experiments validate the theoretical analysis and demonstrate the improvement of DEMES output torque.
The effect of processing additives for charge generation, recombination, and extraction in bulk heterojunction layers of all-polymer photovoltaics
Authors: Kim Yu Jin , Ahn Sunyong , Wang Dong Hwan , Park Chan Eon
Published: August 2015

Bulk heterojunction all-polymer solar cells, fabricated with poly{[4,8-bis-(2-ethyl-hexyl-thiophene-5-yl)-benzo[1,2-b:4,5-b′]dithiophene-2,6-diyl]-alt-[2-(2-ethyl-hexanoyl)-thieno[3,4-b′]thiophen-4,6-diyl]} (PBDTTT-CT) as a donor polymer, and a acceptor polymer, poly{[N,N′-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5′-(2,2′-bithiophene)} (P(NDI2OD-T2)), have been demonstrated and have achieved a power conversion efficiency exceeding 3.7% by using 1,8-diiodooctane (DIO) as a processing additive. Based on the analysis of charge carrier dynamics (charge generation, separation, and extraction), we found that the appropriate ratio of processing solvent additive (5 vol. % DIO) leads to enhanced device performance and favorable morphological characteristics. This research, therefore, indicates that the incorporation of a DIO additive in all-polymer blends is an effective way to form a morphologically ideal heterojunction network and thereby improve charge carrier kinetics for efficient photovoltaic devices.
Magnetically tunable microwave bandpass filter structure composed of ferrite rods and metallic slits
Authors: Bi Ke , Zeng Lingyu , Chai Kejia , Fan Zixuan , Liu Liangjingrong , Wang Qingmin , Lei Ming
Published: August 2015

Magnetically tunable microwave bandpass filter structure have been designed and prepared by filling the ferrite rods into the metallic slits. The electromagnetic wave cannot propagate through the metallic slits. By filling the ferrite rods into the metallic slits, an enhanced optical transmission is obtained, which can be ascribed to the ferromagnetic resonance of the ferrite rods. Both the experimental and the simulated results show the center frequency and bandwidth of the passband can be tuned by the applied magnetic field, which exhibits a magnetically tunable behavior. This approach opens a way for designing tunable microwave bandpass filters.
Analytical solutions of the planar cyclic voltammetry process for two soluble species with equal diffusivities and fast electron transfer using the method of eigenfunction expansions
Authors: Samin Adib , Lahti Erik , Zhang Jinsuo
Published: August 2015

Cyclic voltammetry is a powerful tool that is used for characterizing electrochemical processes. Models of cyclic voltammetry take into account the mass transport of species and the kinetics at the electrode surface. Analytical solutions of these models are not well-known due to the complexity of the boundary conditions. In this study we present closed form analytical solutions of the planar voltammetry model for two soluble species with fast electron transfer and equal diffusivities using the eigenfunction expansion method. Our solution methodology does not incorporate Laplace transforms and yields good agreement with the numerical solution. This solution method can be extended to cases that are more general and may be useful for benchmarking purposes.
High electrical conductivity in out of plane direction of electrodeposited Bi2Te3 films
Authors: Rojo Miguel Muñoz , Manzano Cristina V. , Granados Daniel , Osorio M. R. , Borca-Tasciuc Theodorian , Martín-González Marisol
Published: August 2015

The out of plane electrical conductivity of highly anisotropic Bi2Te3 films grown via electro-deposition process was determined using four probe current-voltage measurements performed on 4.6 - 7.2 μm thickness Bi2Te3 mesa structures with 80 - 120 μm diameters sandwiched between metallic film electrodes. A three-dimensional finite element model was used to predict the electric field distribution in the measured structures and take into account the non-uniform distribution of the current in the electrodes in the vicinity of the probes. The finite-element modeling shows that significant errors could arise in the measured film electrical conductivity if simpler one-dimensional models are employed. A high electrical conductivity of (3.2 ± 0.4) ⋅ 105 S/m is reported along the out of plane direction for Bi2Te3 films highly oriented in the [1 1 0] direction.
Light-controlled microwave whispering-gallery-mode quasi-optical resonators at 50W LED array illumination
Authors: Yurchenko V. B. , Ciydem M. , Altintas A.
Published: August 2015

We present experimental observations of light-controlled resonance effects in microwave whispering-gallery-mode quasi-optical dielectric-semiconductor disk resonators in the frequency band of 5 GHz to 20 GHz arising due to illumination from a light emitting diode (LED) of 50W power range. We obtain huge enhancement of photo-sensitivity (growing with the resonator Q-factor) that makes light-microwave interaction observable with an ordinary light (no laser) at conventional brightness (like an office lighting) in quasi-optical microwave structures at rather long (centimeter-scale) wavelength. We also demonstrate non-conventional photo-response of Fano resonances when the light suppresses one group of resonances and enhances another group. The effects could be used for the optical control and quasi-optical switching of microwave propagation through either one or another frequency channel.
Sequential zinc and iron biofortification of bread-wheat grains: from controlled to uncontrolled environments
Authors: Lidon Fernando C. , Almeida Ana S. , Costa Ana R. , Bagulho Ana S. , Scotti-Campos Paula , Semedo José N. , Maçãs Benvindo , Coutinho José , Pinheiro Nuno , Gomes Conceição , Leitão António E. , Pais Isabel P. , Silva Maria M. , Reboredo Fernando H. , Pessoa Maria F. , Ramalho José C.
Published: August 2015

The development of knowledge on bread wheat (Triticum aestivum L.) biofortification in zinc (Zn) and iron (Fe), related to its potential agronomical use and the nutritional and technological implications, is becoming important to strategies for improving human nutrition. In this context, we studied the accumulation of Zn and Fe in grains, considering potential uptake and translocation kinetics, photoassimilate production and deposition, and related yields, in grains of cv. Roxo produced under controlled-environment conditions and used thereafter in field trials. The metabolic plasticity of this wheat genotype grown under controlled-environment conditions allowed a 10- and 4-fold enhancement in accumulation of Zn and Fe in the grains after nutrient supplementation with a 5-fold concentrated Hoagland solution (5S), after two generations. Moreover, when these seeds were sown under field conditions and the resulting plants supplemented with or without Zn and Fe, the accumulation of these nutrients decreased within the next two generations. Such field seeds obtained without further Zn and Fe supplementation (with nitrogen only; F3(S) and F4(S)) maintained enhanced levels of Zn (~400%) and Fe (40–50%) compared with the initial seeds. If Zn and Fe supplement was given to the plants germinated from F2(5S), the subsequent F3(5S) and F4(5S) seeds maintained the Zn increase (~400%), whereas a further enhancement was observed for Fe, to 75% and 89%, respectively. Toxic limits were not reached for photosynthetic functioning. Even under the highest Zn and Fe supplement dose given to the F3(5S) plants, there was only a slight effect on photosystem II photochemical performance; in fact, enhanced net photosynthesis values were observed. In conclusion, within this experimental design, Zn and Fe biofortification can be obtained without toxicity effects on photosynthetic performance and with negligible modifications to grain texture and nutritional value (protein quality and contents as well as fatty acids).
Transformations that affect fate, form and bioavailability of inorganic nanoparticles in aquatic sediments
Authors: Cross Richard Kynaston , Tyler Charles , Galloway Tamara S
Published: August 2015

Environmental context Engineered nanomaterials are increasingly being used and their release to the aquatic environment poses potential risk. We review the research on transformations of engineered nanomaterial in the aquatic sediment environments, and consider the implications of their release. The key factors defining the fate of engineered nanomaterials in aqueous and sediment systems are identified. Abstract Inorganic nanoparticles are at risk of release into the aquatic environment owing to their function, use and methods of disposal. Aquatic sediments are predicted to be a large potential sink for such engineered nanomaterial (ENM) emissions. On entering water bodies, ENMs undergo a range of transformations dependent on the physicochemical nature of the immediate environment, as they pass from the surface waters to sediments and into sediment-dwelling organisms. This review assesses the current state of research on transformations of metal-based ENMs in the aquatic environment, and considers the implications of these transformations for the fate and persistence of ENMs and their bioavailability to organisms within the benthos. We identify the following factors of key importance in the fate pathways of ENMs in aqueous systems: (1) extracellular polymeric substances, prevalent in many aquatic systems, create the potential for temporal fluxes of ENMs to the benthos, currently unaccounted for in predictive models. (2) Weak secondary deposition onto sediment grains may dominate sediment–ENM interactions for larger aggregates >500nm, potentially granting dynamic long-term mobility of ENMs within sediments. (3) Sulfurisation, aggregation and reduction in the presence of humic acid is likely to limit the presence of dissolved ions from soluble ENMs within sediments. (4) Key benthic species are identified based on their ecosystem functionality and potential for ENM exposure. On the basis of these findings, we recommend future research areas which will support prospective risk assessment by enhancing our knowledge of the transformations ENMs undergo and the likely effects these will have.
Questions of size and numbers in environmental research on microplastics: methodological and conceptual aspects
Authors: Filella Montserrat
Published: August 2015

Environmental context Microplastics, either purposefully manufactured or formed by fragmentation of discarded ‘end-of-life’ macroplastic items, are accumulating in environmental compartments. As more and more data are collected on microplastics in the environment, discussion of two issues has become indispensable: (i) how reliable are the results in terms of the inherent capabilities and limitations of current methods used for sampling, counting and measuring microplastic particles; and (ii) how can the fate of microplastics be understood in the context of natural particles and colloids? Abstract A first important step in evaluating the impact of microplastic pollution in natural systems is assessing the reliability of the results obtained according to the inherent capabilities and limitations of the methods used for sampling, counting and measuring microplastic particles. This study, based on the critical reading of 55 studies containing quantitative microplastic data in waters and sediments, is an attempt to analyse these issues in the light of existing knowledge in the field of natural colloid studies. Existing results are highly dependent on the sampling and methodological procedure chosen and are essentially descriptive. Moreover, often they lack standardisation and adequate reporting of basic information such as the meaning of the size parameter measured. Colloid theory may provide the theoretical background needed to explain microplastic behaviour or, at least, to identify the parameters (e.g. density, surface characteristics, shape) that need to be known in order to gain a predictive knowledge of the subject. They are introduced and discussed. Finally, microplastics are not alone in environmental compartments. For this reason, when possible, published microplastic particle size distributions in natural waters have been quantitatively situated in the context of natural particles.
Clostridium perfringens extracellular toxins and enzymes: 20 and counting
Authors: Revitt-Mills Sarah A , Rood Julian I , Adams Vicki
Published: August 2015

Clostridium perfringens is a Gram-positive, anaerobic bacterium that is widely distributed in the environment; it is found in soil and commonly inhabits the gastrointestinal tract of humans and animals1,2. The ubiquitous nature of this bacterium has resulted in it becoming a major cause of histotoxic and enteric diseases3. The success of C. perfringens as both a pathogen and a commensal bacterium lies in its ability to produce a large number of potent toxins and extracellular enzymes4. This diverse toxin repertoire results in a broad range of diseases including gas gangrene, various enterotoxaemias, food poisoning and necrotic enteritis4–6. Since 2007, six new toxins have been identified, adding to the ever-increasing range of potential C. perfringens virulence determinants. This paper briefly reviews the plethora of toxins and extracellular enzymes produced by C. perfringens, highlighting their importance in disease and strain classification as well as introducing the latest additions to the ever increasing C. perfringens toxin family.
Coupling anaerobic bacteria and microbial fuel cells as whole-cell environmental biosensors
Authors: Bereza-Malcolm Lara T , Franks Ashley E
Published: August 2015

Microorganisms have evolved to respond to environmental factors allowing adaption to changing conditions and minimisation of potential harm. Microbes have the ability to sense a wide range of biotic and abiotic factors including nutrient levels, analytes, temperature, contaminants, community quorum, and metabolic activity. Due to this ability, the use of whole-cell microbes as biosensors is attractive as it can provide real-time in situ information on biologically relevant factors through qualitative and quantitative outputs. Interestingly, many of the environments where these biosensors will be of most of use lack oxygen; and as such the use of anaerobic microorganisms to sense environmental factors with easy to use outputs is essential. Furthermore, sensing of contaminants can be linked with bioremediation of known contaminated environments, allowing a flexible, multiplexed device.
Changes in aquaporin 5 in the non-ciliated cells of mouse oviduct according to sexual maturation and oestrous cycle
Authors: Nah Won Heum , Oh Yeong Seok , Hwang Jung Hye , Gye M. C.
Published: August 2015

Aquaporin (AQP) water channels play an important role in fluid homeostasis and the control of epithelial cell volume. To understand the oviductal fluid homeostasis, the expression of aqp5 was examined in mouse oviduct. In the oviduct of cycling females, aqp1, aqp3, aqp4, aqp5, aqp6, aqp7, aqp8, and aqp11 mRNA were detected. Of these, expression of aqp5 mRNA increased significantly from the early prepubertal period to puberty. Epithelial AQP5 immunoreactivity was markedly increased during the same period and was most notable in the infundibulum. In immature female mice (3 weeks old), gonadotropin (pregnant mare’s serum gonadotropin (5 IU/head) and human chorionic gonadotropin (5 IU/head), single intraperitoneal injection) significantly increased oviductal aqp5 mRNA and AQP5 immunoreactivity in oviduct epithelia. In adult mouse oviduct epithelia, AQP5 was primarily found in the apical membrane, subapical cytoplasm and basolateral membrane of secretory non-ciliated cells, whereas weak to negligible immunoreactivity was found in β-tubulin-positive ciliated cells. Taking into account the fact that non-ciliated cells are well developed with subapical secretory vesicles as well as endosomes, AQP5 may also participate in the secretion and endocytosis in addition to water movement through non-ciliated secretory cells. AQP5 immunoreactivity was also found in the isthmic muscle and lamina propria beneath the epithelia. In cycling females, oviductal aqp5 mRNA levels were the highest at oestrus and the lowest at di-oestrus. AQP5 immunoreactivity in non-ciliated cells was notable in the infundibulum, where AQP5 immunoreactivity was relatively high at oestrus but low at dioestrus and pro-oestrus, indicating synchrony between aqp5 gene activation and the ovarian cycle. Together, the findings of the present study indicate that aqp5 specific to non-ciliated cells is activated during sexual maturation, supporting fluid homeostasis in mouse oviduct.
Origin of colossal magnetoresistance in LaMnO
3
manganite
Authors: Baldini Maria , Muramatsu Takaki , Sherafati Mohammad , Mao Ho-kwang , Malavasi Lorenzo , Postorino Paolo , Satpathy Sashi , Struzhkin Viktor V.
Published: August 2015

Significance

Magnetoresistance is the change of resistance in the presence of an external magnetic field. In rare-earth manganite compounds, this change is orders of magnitude stronger than usual and it is promising for developing new spintronic and electronic devices. The colossal magnetoresistance (CMR) effect has been observed only in chemically doped manganite compounds. We report the realization of CMR in a compressed single-valent LaMnO
3
manganite compound. Pressure generates an inhomogeneous phase constituted by two components: a nonconductive one with a unique structural distortion and a metallic one without distortion. The CMR takes place when the competition between the two phases is at a maximum. We identify phase separation as the driving force for generating CMR in LaMnO
3
.
Understanding deliberate practice in preschool-aged children
Authors: Davis Jac T. M. , Cullen Elizabeth , Suddendorf Thomas
Published: August 2015

Deliberate practice is essential for skill acquisition and expertise and may be a direct consequence of episodic foresight. However, little is known about how deliberate practice develops in children. We present two experiments testing children's ability to selectively practise a behaviour that was going to be useful in future and to reason about the role of practice in skill formation. Five-year-olds demonstrated an explicit understanding of deliberate practice both in selectively choosing to practise a future-relevant skill and in predicting skill change in others based on their practice. Four-year-olds showed some capacities, but failed to demonstrate consistent understanding of the relationship between practice and skill improvement. Children's understanding of this relationship was significantly related to their understanding of how information leads to knowledge, suggesting that both may draw on similar cognitive developmental changes.
The influence of category representations on exemplar generation
Authors: Wang Moyun , Xie Liuqing
Published: August 2015

The present study examined the influence of category representations on exemplar generation, which has been neglected in previous category research. An experiment on college students manipulated the category representation of insects in three conditions (prototypes, exemplars, and the hybrid of prototypes and exemplars). Participants were asked to generate as many exemplars as possible. The results demonstrate that category representations affect and constrain exemplar generation. The new findings are as follows. In the prototype and hybrid conditions with the prototype representation, people tend to generate more valid exemplars by using the prototype mutation mechanism, and exemplar generation conforms to the family resemblance structure. Exemplar generation in the hybrid condition is additionally constrained by known exemplars. In the exemplar condition, people tend to generate fewer valid exemplars by using miscellaneous strategies, and their exemplar generation may not conform to the family resemblance structure.
Singular semipositive metrics in non-Archimedean geometry
Authors: Boucksom Sébastien , Favre Charles , Jonsson Mattias
Published: August 2015

LetXXbe a smooth projective Berkovich space over a complete discrete valuation fieldKKof residue characteristic zero, endowed with an ample line bundleLL. We introduce a general notion of (possibly singular) semipositive (or plurisubharmonic) metrics onLLand prove the analogue of the following two basic results in the complex case: the set of semipositive metrics is compact modulo scaling, and each semipositive metric is a decreasing limit of smooth semipositive ones. In particular, for continuous metrics, our definition agrees with the one by S.-W. Zhang. The proofs use multiplier ideals and the construction of suitable models ofXXover the valuation ring ofKK, using toroidal techniques.
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
Authors: Coetzee Simon G. , Coetzee Gerhard A. , Hazelett Dennis J.
Published: August 2015

Summary: Functional annotation represents a key step toward the understanding and interpretation of germline and somatic variation as revealed by genome-wide association studies (GWAS) and The Cancer Genome Atlas (TCGA), respectively. GWAS have revealed numerous genetic risk variants residing in non-coding DNA associated with complex diseases. For sequences that lie within enhancers or promoters of transcription, it is not straightforward to assess the effects of variants on likely transcription factor binding sites. Consequently we introduce motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation is a good match, and how much information is gained or lost in one allele of the polymorphism or mutation relative to the other. MotifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from many public sources that users can choose from. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within bioconductor.

Availability and implementation:  https://github.com/Simon-Coetzee/MotifBreakR, www.bioconductor.org.

Contact:  dennis.hazelett@cshs.org
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization
Authors: Antanaviciute Agne , Watson Christopher M. , Harrison Sally M. , Lascelles Carolina , Crinnion Laura , Markham Alexander F. , Bonthron David T. , Carr Ian M.
Published: August 2015

Motivation: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task.

Results: Here we describe a new variant prioritization tool, OVA (ontology variant analysis), in which user-provided phenotypic information is exploited to infer deeper biological context. OVA combines a knowledge-based approach with a variant-filtering framework. It reduces the number of candidate variants by considering genotype and predicted effect on protein sequence, and scores the remainder on biological relevance to the query phenotype.

We take advantage of several ontologies in order to bridge knowledge across multiple biomedical domains and facilitate computational analysis of annotations pertaining to genes, diseases, phenotypes, tissues and pathways. In this way, OVA combines information regarding molecular and physical phenotypes and integrates both human and model organism data to effectively prioritize variants. By assessing performance on both known and novel disease mutations, we show that OVA performs biologically meaningful candidate variant prioritization and can be more accurate than another recently published candidate variant prioritization tool.

Availability and implementation: OVA is freely accessible at http://dna2.leeds.ac.uk:8080/OVA/index.jsp

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  umaan@leeds.ac.uk
Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
Authors: Nygaard Vegard , Rødland Einar Andreas , Hovig Eivind
Published: August 2015

Removal of, or adjustment for, batch effects or center differences is generally required when such effects are present in data. In particular, when preparing microarray gene expression data from multiple cohorts, array platforms, or batches for later analyses, batch effects can have confounding effects, inducing spurious differences between study groups. Many methods and tools exist for removing batch effects from data. However, when study groups are not evenly distributed across batches, actual group differences may induce apparent batch differences, in which case batch adjustments may bias, usually deflate, group differences. Some tools therefore have the option of preserving the difference between study groups, e.g. using a two-way ANOVA model to simultaneously estimate both group and batch effects. Unfortunately, this approach may systematically induce incorrect group differences in downstream analyses when groups are distributed between the batches in an unbalanced manner. The scientific community seems to be largely unaware of how this approach may lead to false discoveries.