bluuebunny/crossref_metadata_2025 huggingface dataset:
High sensitivity optochemical and electrochemical metal ion sensor
Authors: Serry Mohamed , Gamal Asmaa , Shaban Mohamed , Sharaf AbdelHameed
Published: November 2013

A novel sensor that deploys opto‐ and electrochemical techniques for the rapid and highly sensitive separation and detection of metal ions in aqueous media is reported. The sensor comprises a porous membrane coated with an ultra‐thin porous layer of highly ordered, hexagonally packed arrays of metal (Au and Pt) nanoparticles with ≤ 25 nm sub‐gaps. This platform enables an integrated detection method that relies on in‐situ surface enhanced Raman scattering. An additional scheme is utilised based on electrochemical impedance spectroscopy to increase both the selectivity and the sensitivity of the sensor. Electrochemical separation bolsters the effectiveness of the optical method through ion separation and pre‐concentration. The latter are induced by forcing the liquid electrolyte through the membrane's nanopores through a new proposed method based on surface tension mismatch. The sensor demonstrates high selectivity for six different heavy metal ions (Hg2+, Cd2+, Pb2+, Cu2+, Co2+, Ni2+) at concentrations that range from 1 to 20 ppb (1 × 10−3 –20 × 10−3 μg/ml). The novelty of this sensor consists of the fact that the separation, pre‐concentration and detection of the targeted ions are all performed in a single stage, eliminating the need for time‐consuming and complex sample preparation steps.
Timoshenko beam effects in lateral‐mode microcantilever‐based sensors in liquids
Authors: Schultz Joshua A. , Heinrich Stephen M. , Josse Fabien , Nigro Nicholas J. , Dufour Isabelle , Beardslee Luke A. , Brand Oliver
Published: November 2013

Recent experimental and analytical research has shown that higher in‐fluid quality factors (Q) are achieved by actuating microcantilevers in the lateral flexural mode, especially for microcantilevers having larger width‐to‐length ratios. However, experimental results show that for these geometries the resonant characteristics predicted by the existing analytical models differ from the measurements. A recently developed analytical model to more accurately predict the resonant behaviour of these devices in viscous fluids is described. The model incorporates viscous fluid effects via a Stokes‐type fluid resistance assumption and ‘Timoshenko beam’ effects (shear deformation and rotatory inertia). Unlike predictions based on Euler‐Bernoulli beam theory, the new theoretical results for both resonant frequency and Q exhibit the same trends as seen in the experimental data for in‐water measurements as the beam slenderness decreases. An analytical formula for Q is also presented to explicitly illustrate how Q depends on beam geometry and on beam and fluid properties. Beam thickness effects are also examined and indicate that the analytical results yields good numerical estimates of Q for the thinner (5 μm) specimens tested, but overestimate Q for the thicker (20 μm) specimens, thus suggesting that a more accurate fluid resistance model should be introduced in the future for the latter case.
Occupancy measurement in building: A litterature review, application on an energy efficiency research demonstrated building
Authors: Caucheteux A. , Es Sabar A. , Boucher V.
Published: November 2013

Measuring the energy efficiency of buildings and its confrontation with the current Building Energy Simulations now faces knowledge of what is commonly called “occupancy”. This work has been made in order to implement a monitoring system on a research demonstrator building at DLRCA in Angers (France). The goals were first to know the occupancy as input data of models but also to build occupancy models. Occupancy can be defined as all the action of occupants that affect building energy efficiency. The chosen monitoring deals with its presence, lightning, windows opening and internal gains. It seems that the use of an Infra- red detector allows a accuracy of 5 min in the detection of presence. The use of dry contact sensors allows the detection of five different rates of slide windows opening that can affect temperature decrease. Light sensors seem to be efficient to detect artificial lighting states when correctly configured.
Acoustic metrology – an overview of calibration methods and their uncertainties
Authors: Frederiksen E.
Published: November 2013

The paper gives a brief description of the principles and the uncertainty of the acoustic calibration methods that today are applied by National Metrology Institutes and calibration service centers. Even if some of the calibration principles have been applied over more than half a century, the methods and the instrumentation are still being refined in order to minimize their uncertainty, to extend their frequency ranges, to include extra parameters and to speed up slow processes. In addition to the traditional methods for microphone sensitivity and frequency response calibration, new development areas, like for example wind power, has created needs for low-frequency and infra-sound calibration, down to 0.1 Hz. Other high-tech areas have lead to the development of methods for phase response comparison calibration of microphones for large arrays, for sound intensity measurement and for verification of dynamic linearity of microphones at very high sound pressure levels, up to about 174 dB that corresponds to 10 kPa.
Line scale measurement using image registration
Authors: Costa P.B. , Marques A. , Baldner F.O. , Leta F.R.
Published: November 2013

Currently, most advances in dimensional metrology might be seen by the evolution of non-contact measurement (optical measurements), in order to provide traceability for different areas that needs to calibrate microscopes or optical measure machines. In a similar way, the use of image processing techniques for the measuring of objects has been the subject of recent studies in computer vision and image metrology. In the attempt to meet the requirements and demands for high accuracy dimensional metrology with image processing techniques, this work will present the application of the image registration technique for the measurement of line scales. In the conventional calibration, the scales are measured in pre-established points, generally in intervals of 10% of the total scale length. With this application, it becomes possible to provide results for all the scale marks quickly and automatically, whereas in the conventional method it would require more time and, thus, a higher cost for the fulfillment of this measurement.
Phononic crystals of spherical particles: A tight binding approach
Authors: Mattarelli M. , Secchi M. , Montagna M.
Published: November 2013

The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.
The pure rotational spectrum of ruthenium monocarbide, RuC, and relativistic ab initio predictions
Authors: Wang Fang , Steimle Timothy C. , Adam Allan G. , Cheng Lan , Stanton John F.
Published: November 2013

The J = 1 ← J = 0 and J = 2 ← J = 1 rotational transitions of ruthenium monocarbide, RuC, have been recorded using the separated field pump/probe microwave optical double resonance technique and analyzed to determine the fine and hyperfine parameters for the X1Σ+ state. The 101Ru(I = 5/2) electric quadrupole parameter, eq0Q, and nuclear spin-rotation interaction parameter, $C_I^{\it eff}$CIeff, were determined to be 433.19(8) MHz and −0.049(6) MHz, respectively. The equilibrium bond distance, re, was determined to be 1.605485(2) Å. Hartree-Fock and coupled-cluster calculations were carried out for the properties of the X1Σ+ state. Electron-correlation effects are pronounced for all properties studied. It is shown that (a) the moderate scalar-relativistic contribution to eq0Q is entirely due to the coupling between scalar-relativistic and electron-correlation effects, (b) the spin-free exact two-component theory in its one-electron variant offers a reliable and efficient treatment of scalar-relativistic effects, and (c) non-relativistic theory performs quite well for the prediction of $C_I^{elec}$CIelec, provided that electron correlation is treated accurately.
Monte Carlo simulation of gamma-ray response of BaF2 and CaF2
Authors: Gao F. , Xie Y. L. , Wang Z. G. , Kerisit S. , Wu D. X. , Campbell L. W. , Van Ginhoven R. M. , Prange M.
Published: November 2013

We have employed a Monte Carlo (MC) method to study intrinsic properties of two alkaline-earth halides, namely, BaF2 and CaF2, relevant to their use as radiation detector materials. The MC method follows the fate of individual electron-hole (e-h) pairs and thus allows for a detailed description of the microscopic structure of ionization tracks created by incident γ-ray radiation. The properties of interest include the mean energy required to create an e-h pair, W, Fano factor, F, the maximum theoretical light yield, and the spatial distribution of e-h pairs resulting from γ-ray excitation. Although W and F vary with incident photon energy at low energies, they tend to constant values at energies higher than 1 keV. W is determined to be 18.9 and 19.8 eV for BaF2 and CaF2, respectively, in agreement with published data. The e-h pair spatial distributions exhibit a linear distribution along the fast electron tracks with high e-h pair densities at the end of the tracks. Most e-h pairs are created by interband transition and plasmon excitation in both scintillators, but the e-h pairs along fast electron tracks in BaF2 are slightly clustered, forming nanoscale domains and resulting in the higher e-h pair densities than in CaF2. Combining the maximum theoretical light yields calculated for BaF2 and CaF2 with those obtained for CsI and NaI shows that the theoretical light yield decreases linearly with increasing band gap energy.
Benchmark tests and spin adaptation for the particle-particle random phase approximation
Authors: Yang Yang , van Aggelen Helen , Steinmann Stephan N. , Peng Degao , Yang Weitao
Published: November 2013

The particle-particle random phase approximation (pp-RPA) provides an approximation to the correlation energy in density functional theory via the adiabatic connection [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)]. It has virtually no delocalization error nor static correlation error for single-bond systems. However, with its formal O(N6) scaling, the pp-RPA is computationally expensive. In this paper, we implement a spin-separated and spin-adapted pp-RPA algorithm, which reduces the computational cost by a substantial factor. We then perform benchmark tests on the G2/97 enthalpies of formation database, DBH24 reaction barrier database, and four test sets for non-bonded interactions (HB6/04, CT7/04, DI6/04, and WI9/04). For the G2/97 database, the pp-RPA gives a significantly smaller mean absolute error (8.3 kcal/mol) than the direct particle-hole RPA (ph-RPA) (22.7 kcal/mol). Furthermore, the error in the pp-RPA is nearly constant with the number of atoms in a molecule, while the error in the ph-RPA increases. For chemical reactions involving typical organic closed-shell molecules, pp- and ph-RPA both give accurate reaction energies. Similarly, both RPAs perform well for reaction barriers and nonbonded interactions. These results suggest that the pp-RPA gives reliable energies in chemical applications. The adiabatic connection formalism based on pairing matrix fluctuation is therefore expected to lead to widely applicable and accurate density functionals.
Optimum high temperature strength of two-dimensional nanocomposites
Authors: Monclús M. A. , Zheng S. J. , Mayeur J. R. , Beyerlein I. J. , Mara N. A. , Polcar T. , Llorca J. , Molina-Aldareguía J. M.
Published: November 2013

High-temperature nanoindentation was used to reveal nano-layer size effects on the hardness of two-dimensional metallic nanocomposites. We report the existence of a critical layer thickness at which strength achieves optimal thermal stability. Transmission electron microscopy and theoretical bicrystal calculations show that this optimum arises due to a transition from thermally activated glide within the layers to dislocation transmission across the layers. We demonstrate experimentally that the atomic-scale properties of the interfaces profoundly affect this critical transition. The strong implications are that interfaces can be tuned to achieve an optimum in high temperature strength in layered nanocomposite structures.
Dynamics of carbon-hydrogen and carbon-methyl exchanges in the collision of 3P atomic carbon with propene
Authors: Lee Shih-Huang , Chen Wei-Kan , Chin Chih-Hao , Huang Wen-Jian
Published: November 2013

We investigated the dynamics of the reaction of 3P atomic carbon with propene (C3H6) at reactant collision energy 3.8 kcal mol−1 in a crossed molecular-beam apparatus using synchrotron vacuum-ultraviolet ionization. Products C4H5, C4H4, C3H3, and CH3 were observed and attributed to exit channels C4H5 + H, C4H4 + 2H, and C3H3 + CH3; their translational-energy distributions and angular distributions were derived from the measurements of product time-of-flight spectra. Following the addition of a 3P carbon atom to the C=C bond of propene, cyclic complex c-H2C(C)CHCH3 undergoes two separate stereoisomerization mechanisms to form intermediates E- and Z-H2CCCHCH3. Both the isomers of H2CCCHCH3 in turns decompose to C4H5 + H and C3H3 + CH3. A portion of C4H5 that has enough internal energy further decomposes to C4H4 + H. The three exit channels C4H5 + H, C4H4 + 2H, and C3H3 + CH3 have average translational energy releases 13.5, 3.2, and 15.2 kcal mol−1, respectively, corresponding to fractions 0.26, 0.41, and 0.26 of available energy deposited to the translational degrees of freedom. The H-loss and 2H-loss channels have nearly isotropic angular distributions with a slight preference at the forward direction particularly for the 2H-loss channel. In contrast, the CH3-loss channel has a forward and backward peaked angular distribution with an enhancement at the forward direction. Comparisons with reactions of 3P carbon atoms with ethene, vinyl fluoride, and vinyl chloride are stated.
Nonuniqueness of two-temperature Guldberg-Waage and Saha equations: Influence on thermophysical properties of SF6 plasmas
Authors: Wang Weizong , Rong Mingzhe , Spencer Joseph W.
Published: November 2013

This paper focuses to study how the choice of Guldberg-Waage and Saha equations affects the thermodynamic properties and transport coefficients of SF6 plasmas under both thermal equilibrium and non-equilibrium conditions. The species composition is numerically determined using two typical forms of two-temperature Saha equations and Guldberg-Waage equations that have appeared in the literature. The great influence of the choice of the excitation temperature on the plasma composition and hence the thermodynamic properties and transport coefficients is discussed as well. Transport coefficients are calculated with most recent collision interaction potentials by adopting Devoto's electron and heavy particle decoupling approach but expanded to the third-order approximation (second-order for viscosity) within the framework of Chapman-Enskog method. Furthermore, an analysis of the effect of different definitions of Debye length on the properties values was performed as well. The results are computed for various values of pressures from 0.10 atm to 10 atm and non-equilibrium parameter, i.e., ratio of the electron temperature to the heavy particle temperature from 1 to 5 with electron temperature range from 300 to 40 000 K. Both forms of Guldberg-Waage and Saha equations used here can give completely the same value when the two-temperature model reaches the special case of local thermodynamic equilibrium. It has been observed that all above mentioned factors can significantly modify the plasma species composition and consequently affect the thermodynamic and transport properties.
Effects of loading mode and orientation on deformation mechanism of graphene nano-ribbons
Authors: Sun Y. J. , Ma F. , Huang Y. H. , Hu T. W. , Xu K. W. , Chu Paul K.
Published: November 2013

Molecular dynamics simulation is performed to analyze the deformation mechanism of graphene nanoribbons. When the load is applied along the zigzag orientation, tensile stress yields brittle fracture and compressive stress results in lattice shearing and hexagonal-to-orthorhombic phase transformation. Along the armchair direction, tensile stress produces lattice shearing and phase transformation, but compressive stress leads to a large bonding force. The phase transformation induced by lattice shearing is reversible for 17% and 30% strain in compressive loading along the zigzag direction and tensile loading along the armchair direction. The energy dissipation is less than 10% and resulting pseudo-elasticity enhances the ductility.
Generation of nitric oxide gradients in microfluidic devices for cell culture using spatially controlled chemical reactions
Authors: Chen Ying-Hua , Peng Chien-Chung , Cheng Yung-Ju , Wu Jin-Gen , Tung Yi-Chung
Published: November 2013

In this paper, we develop a microfluidic device capable of generating nitric oxide (NO) gradients for cell culture using spatially controlled chemical reactions. NO plays an essential role in various biological activities, including nervous, immune, and cardiovascular systems. The device developed in this paper can control NO gradients without utilizing expensive and hazardous high purity NO gas sources or direct addition of NO donors. Consequently, the device provides an efficient, cost-effective, robust, and stable platform to generate NO gradients for cell culture studies. In the experiments, NO gradients are first characterized using a NO-sensitive fluorescence dye, and cell experiments using aortic smooth muscle cells are conducted. The results demonstrate that the device can alter the intracellular NO concentrations and further affect the Ca2+ concentration oscillation for the cells. The device developed in this paper provides a powerful platform for researchers better study the biological roles of NO and its spatial distribution using in vitro cell models with minimal instrumentation.
Properties of localization in silicon-based lattice periodicity breaking photonic crystal waveguides
Authors: Wu Yuquan , Wang Xiaofei , Wu Yuanbin , Wang Yufang , Zhang Guoquan , Fan Wande , Cao Xuewei
Published: November 2013

The light localization effects in silicon photonic crystal cavities at different disorder degrees have been studied using the finite difference time domain (FDTD) method in this paper. Numerical results showed that localization occurs and enhancement can be gained in the region of the cavity under certain conditions. The stabilities of the localization effects due to the structural perturbations have been investigated too. Detailed studies showed that when the degree of structural disorder is small(about 10%), the localization effects are stable, the maximum enhancement factor can reach 16.5 for incident wavelength of 785 nm and 23 for 850 nm in the cavity, with the degree of disorder about 8%. The equivalent diameter of the localized spot is almost constant at different disorder degrees, approximating to ${\lambda \mathord{/ {\vphantom {\lambda 7}} \kern-\nulldelimiterspace} 7}$λ/7, which turned out to be independent on the structural perturbation.
Magnetic, dielectric and magnetodielectric properties of PVDF-La0.7Sr0.3MnO3 polymer nanocomposite film
Authors: Thirmal Ch. , Nayek Chiranjib , Murugavel P. , Subramanian V.
Published: November 2013

We have investigated the structure, magnetic and dielectric properties of PVDF-La0.7Sr0.3MnO3 polymer nanocomposite thick film fabricated by dip coating technique along with the magnetodielectric effect. The structure and dielectric properties show the enhanced β phase in the composite compared to the PVDF film. The coupling between the ferroelectric and magnetic phases in the composite is revealed in the form of dielectric anomaly at the ferromagnetic Curie temperature. We observed 1.9% magnetodielectric effect at 300 K with the possibility of enhanced effect near the transition temperature. In addition, the analysis of the electric modulus indicates that the composite exhibits interfacial related relaxation and it follows Arrhenius Law. Our study suggests that the ac conductivity of the PVDF-La0.7Sr0.3MnO3 composite could be explained by correlated barrier hopping mechanism.
Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases
Authors: Wörsdörfer Bigna , Lingaraju Mahesh , Yennawar Neela H. , Boal Amie K. , Krebs Carsten , Bollinger J. Martin , Pandelia Maria-Eirini
Published: November 2013

Significance

Evolution functionally diversifies conserved protein architectures, precluding assignment of function from structure alone. The HD structural domain was first recognized in a group of phosphohydrolases and came to be associated with that activity, but characterization of the archetypal mixed-valent diiron oxygenase (MVDO),
myo
-inositol oxygenase, attributed a very different activity, O
2
-mediated C-C bond cleavage, to an HD protein. We demonstrate that the recently discovered C-P bond-cleaving enzyme, PhnZ, is another example of an HD-domain MVDO. Sequence and functional data for the dimetal HD proteins reveal that they segregate into well-defined clades, of which several are more likely to comprise MVDOs than phosphohydrolases. This study provides a basis to assign hydrolase or oxygenase activity to proteins in this largely uncharacterized enzyme superfamily.
Modulation of the Affordance Effect through Transfer of Learning
Authors: Ottoboni Giovanni , Iani Cristina , Tessari Alessia , Rubichi Sandro
Published: November 2013

Consistent evidence shows that practising with spatially incompatible stimulus–response trials modulates performance on following tasks requiring the solution of cognitive conflict such as the Simon and Stroop tasks. In the present study we assessed whether a spatially incompatible practice can modulate another effect that is thought to be due to a conflict between two response alternatives, the affordance effect. To this end, we requested participants to categorize pictures of common objects on the basis of their upright or inverted orientation. A group of participants performed the categorization task alone, while the other two groups performed the categorization task after practising with a spatial compatibility task with either a compatible or an incompatible mapping. Results showed that the spatially incompatible practice eliminated the affordance effect. These results indicate that the conflict at the basis of the affordance effect is not unavoidable but it rather permeable to modulations affecting the response selection stage. Indeed the “emit the alternative spatial response” rule acquired during the spatially incompatible task can transfer to and modulate how the subsequent affordance task is performed.
A Configural Dominant Account of Contextual Cueing: Configural Cues are Stronger than Colour Cues
Authors: Kunar Melina A. , John Rebecca , Sweetman Hollie
Published: November 2013

Previous work has shown that reaction times to find a target in displays that have been repeated are faster than those for displays that have never been seen before. This learning effect, termed “contextual cueing” (CC), has been shown using contexts such as the configuration of the distractors in the display and the background colour. However, it is not clear how these two contexts interact to facilitate search. We investigated this here by comparing the strengths of these two cues when they appeared together. In Experiment 1, participants searched for a target that was cued by both colour and distractor configural cues, compared with when the target was only predicted by configural information. The results showed that the addition of a colour cue did not increase contextual cueing. In Experiment 2, participants searched for a target that was cued by both colour and distractor configuration compared with when the target was only cued by colour. The results showed that adding a predictive configural cue led to a stronger CC benefit. Experiments 3 and 4 tested the disruptive effects of removing either a learned colour cue or a learned configural cue and whether there was cue competition when colour and configural cues were presented together. Removing the configural cue was more disruptive to CC than removing colour, and configural learning was shown to overshadow the learning of colour cues. The data support a configural dominant account of CC, where configural cues act as the stronger cue in comparison to colour when they are presented together.
Working Memory Capacity Predicts Conflict-Task Performance
Authors: Gulbinaite Rasa , Johnson Addie
Published: November 2013

The relationship between the ability to maintain task goals and working memory capacity (WMC) is firmly established, but evidence for WMC-related differences in conflict processing is mixed. We investigated whether WMC (measured using two complex-span tasks) mediates differences in adjustments of cognitive control in response to conflict. Participants performed a Simon task in which congruent and incongruent trials were equiprobable, but in which the proportion of congruency repetitions (congruent trials followed by congruent trials or incongruent trials followed by incongruent trials) and thus the need for trial-by-trial adjustments in cognitive control varied by block. The overall Simon effect did not depend on WMC capacity. However, for the low-WMC participants the Simon effect decreased as the proportion of congruency repetitions decreased, whereas for the high- and average-WMC participants it was relatively constant across conditions. Distribution analysis of the Simon effect showed more evidence for the inhibition of stimulus location in the low- than in the high-WMC participants, especially when the proportion of congruency repetitions was low. We hypothesize that low-WMC individuals exhibit more interference from task-irrelevant information due to weaker preparatory control prior to stimulus presentation and, thus, stronger reliance on reactive recruitment of cognitive control.
Proton radiography and proton computed tomography based on time-resolved dose measurements
Authors: Testa Mauro , Verburg Joost M , Rose Mark , Min Chul Hee , Tang Shikui , Bentefour El Hassane , Paganetti Harald , Lu Hsiao-Ming
Published: November 2013

We present a proof of principle study of proton radiography and proton computed tomography (pCT) based on time-resolved dose measurements. We used a prototype, two-dimensional, diode-array detector capable of fast dose rate measurements, to acquire proton radiographic images expressed directly in water equivalent path length (WEPL). The technique is based on the time dependence of the dose distribution delivered by a proton beam traversing a range modulator wheel in passive scattering proton therapy systems. The dose rate produced in the medium by such a system is periodic and has a unique pattern in time at each point along the beam path and thus encodes the WEPL. By measuring the time dose pattern at the point of interest, the WEPL to this point can be decoded. If one measures the time–dose patterns at points on a plane behind the patient for a beam with sufficient energy to penetrate the patient, the obtained 2D distribution of the WEPL forms an image. The technique requires only a 2D dosimeter array and it uses only the clinical beam for a fraction of second with negligible dose to patient. We first evaluated the accuracy of the technique in determining the WEPL for static phantoms aiming at beam range verification of the brain fields of medulloblastoma patients. Accurate beam ranges for these fields can significantly reduce the dose to the cranial skin of the patient and thus the risk of permanent alopecia. Second, we investigated the potential features of the technique for real-time imaging of a moving phantom. Real-time tumor tracking by proton radiography could provide more accurate validations of tumor motion models due to the more sensitive dependence of proton beam on tissue density compared to x-rays. Our radiographic technique is rapid (∼100 ms) and simultaneous over the whole field, it can image mobile tumors without the problem of interplay effect inherently challenging for methods based on pencil beams. Third, we present the reconstructed pCT images of a cylindrical phantom containing inserts of different materials. As for all conventional pCT systems, the method illustrated in this work produces tomographic images that are potentially more accurate than x-ray CT in providing maps of proton relative stopping power (RSP) in the patient without the need for converting x-ray Hounsfield units to proton RSP. All phantom tests produced reasonable results, given the currently limited spatial and time resolution of the prototype detector. The dose required to produce one radiographic image, with the current settings, is ∼0.7 cGy. Finally, we discuss a series of techniques to improve the resolution and accuracy of radiographic and tomographic images for the future development of a full-scale detector.
An efficient algorithm for second-order cone linear complementarity problems
Authors: Zhang Lei-Hong , Yang Wei Hong
Published: November 2013

Recently, the globally uniquely solvable (GUS) property of the linear transformation

M
∈

R

n
×
n

M\in \mathbb {R}^{n\times n}

in the second-order cone linear complementarity problem (SOCLCP) receives much attention and has been studied substantially. Yang and Yuan contributed a new characterization of the GUS property of the linear transformation, which is formulated by basic linear-algebra-related properties. In this paper, we consider efficient numerical algorithms to solve the SOCLCP where the linear transformation

M
M

has the GUS property. By closely relying on the new characterization of the GUS property, a globally convergent bisection method is developed in which each iteration can be implemented using only

2

n
2

2n^2

flops. Moreover, we also propose an efficient Newton method to accelerate the bisection algorithm. An attractive feature of this Newton method is that each iteration only requires

5

n
2

5n^2

flops and converges quadratically. These two approaches make good use of the special structure contained in the SOCLCP and can be effectively combined to yield a fast and efficient bisection-Newton method. Numerical testing is carried out and very encouraging computational experiments are reported.
Mutations in Fis1 disrupt orderly disposal of defective mitochondria
Authors: Shen Qinfang , Yamano Koji , Head Brian P. , Kawajiri Sumihiro , Cheung Jesmine T. M. , Wang Chunxin , Cho Jeong-Hoon , Hattori Nobutaka , Youle Richard J. , van der Bliek Alexander M.
Published: November 2013

Mitochondrial fission is mediated by the dynamin-related protein Drp1 in metazoans. Drp1 is recruited from the cytosol to mitochondria by the mitochondrial outer membrane protein Mff. A second mitochondrial outer membrane protein, named Fis1, was previously proposed as recruitment factor, but Fis1−/− cells have mild or no mitochondrial fission defects. Here we show that Fis1 is nevertheless part of the mitochondrial fission complex in metazoan cells. During the fission cycle, Drp1 first binds to Mff on the surface of mitochondria, followed by entry into a complex that includes Fis1 and endoplasmic reticulum (ER) proteins at the ER–mitochondrial interface. Mutations in Fis1 do not normally affect fission, but they can disrupt downstream degradation events when specific mitochondrial toxins are used to induce fission. The disruptions caused by mutations in Fis1 lead to an accumulation of large LC3 aggregates. We conclude that Fis1 can act in sequence with Mff at the ER–mitochondrial interface to couple stress-induced mitochondrial fission with downstream degradation processes.
Analysis of Xanthomonas oryzae pv. oryzicola Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity
Authors: Wonni I. , Cottyn B. , Detemmerman L. , Dao S. , Ouedraogo L. , Sarra S. , Tekete C. , Poussier S. , Corral R. , Triplett L. , Koita O. , Koebnik R. , Leach J. , Szurek B. , Maes M. , Verdier V.
Published: November 2013

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on ‘Kitaake’ rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.
An electrical analogy for the Pentland Firth tidal stream power resource
Authors: Draper Scott , Adcock Thomas A. A. , Borthwick Alistair G. L. , Houlsby Guy T.
Published: November 2013

Several locations in the Pentland Firth, UK, have been earmarked for the deployment of separate farms of tidal turbines. However, recent numerical modelling suggests that these farms will be inter-dependent and that they must work together to optimize their collective performance. To explain this inter-dependence, in this paper we develop an electrical circuit analogy to describe flow through the Pentland Firth, in which parallel connections in the circuit represent different sub-channels formed by the islands of Swona, Stroma and the Pentland Skerries. The analogy is introduced in stages, beginning with turbines placed in a single channel, then turbines placed in a sub-channel connected in parallel to another sub-channel, and finally more complicated arrangements, in which turbines are installed both in parallel and in series within a multiply connected channel. The analogy leads to a general formula to predict the tidal power potential of turbines placed in a sub-channel connected in parallel to another sub-channel, and a predictive model for more complicated multiply connected channel arrangements. Power estimates made using the formula and predictive model (which may be applied using only measurements of the undisturbed natural tidal hydrodynamics) are shown to agree well with numerical model predictions for the Pentland Firth, providing useful insight into how to best develop the resource.
Pseudonocardia sediminis sp. nov., isolated from marine sediment
Authors: Zhang Dao-Feng , Jiang Zhao , Li Li , Liu Bing-Bing , Zhang Xiao-Mei , Tian Xin-Peng , Zhang Si , Li Wen-Jun
Published: November 2013

A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141T, was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1–3 % (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus

Pseudonocardia

, showing highest levels of similarity with respect to

Pseudonocardia sichuanensis

KLBMP 1115T (97.1 %),

Pseudonocardia tetrahydrofuranoxydans

K1T (97.1 %) and

Pseudonocardia kunmingensis

YIM 63158T (97.0 %). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA–DNA relatedness with

P. tetrahydrofuranoxydans

DSM 44239T was 42.8±3.5 % (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus

Pseudonocardia

, for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141T ( = DSM 45779T = JCM 18540T).
An update of ‘basic light and scanning electron microscopic methods for taxonomic studies of ciliated protozoa’
Authors: Foissner Wilhelm
Published: November 2013

This is an update of the review by Foissner (1991). Since then, I have improved some methods considerably. The following methods are described in detail: live observation, supravital staining with methyl green-pyronin, dry silver nitrate impregnation, wet silver nitrate impregnation, silver carbonate impregnation, protargol impregnation (three procedures), scanning electron microscopy, and deciliation. Familiarity with these methods (or modifications) is a prerequisite for successful taxonomic work. No staining method is equally appropriate to all kinds of ciliates. A table is provided which indicates those procedures which work best for certain groups of ciliates. A second table relates to the structures revealed by the procedures. Good descriptions usually demand at least live observation, silver nitrate and protargol or silver carbonate impregnation. Some instructions are provided for distinguishing mono- and dikinetids as well as ciliated and non-ciliated basal bodies in silvered ciliates. Furthermore, I added a section on ‘Deposition and Labeling of Preparations’. All methods work not only with ciliates but also with many other heterotrophic and autotrophic flagellated and amoeboid protists. The brilliancy of silver preparations has tempted some taxonomists to neglect live observation. However, many important species characteristics cannot be seen or are changed in silvered specimens. I thus consider all species descriptions based exclusively on silver slides as incomplete and of doubtful value for both α-taxonomists and ecologists.
In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase
Authors: İrigül-Sönmez Öykü , Köroğlu Türkan E. , Öztürk Büşra , Kovács Ákos T. , Kuipers Oscar P. , Yazgan-Karataş Ayten
Published: November 2013

ThelutRgene, encoding a product resembling a GntR-family transcriptional regulator, has previously been identified as a gene required for the production of the dipeptide antibiotic bacilysin inBacillus subtilis. To understand the broader regulatory roles of LutR inB. subtilis, we studied the genome-wide effects of alutRnull mutation by combining transcriptional profiling studies using DNA microarrays, reverse transcription quantitative PCR,lacZfusion analyses and gel mobility shift assays. We report that 65 transcriptional units corresponding to 23 mono-cistronic units and 42 operons show altered expression levels inlutRmutant cells, as compared withlutR+wild-type cells in early stationary phase. Among these, 11 single genes and 25 operons are likely to be under direct control of LutR. The products of these genes are involved in a variety of physiological processes associated with the onset of stationary phase inB. subtilis, including degradative enzyme production, antibiotic production and resistance, carbohydrate utilization and transport, nitrogen metabolism, phosphate uptake, fatty acid and phospholipid biosynthesis, protein synthesis and translocation, cell-wall metabolism, energy production, transfer of mobile genetic elements, induction of phage-related genes, sporulation, delay of sporulation and cannibalism, and biofilm formation. Furthermore, an electrophoretic mobility shift assay performed in the presence of both SinR and LutR revealed a close overlap between the LutR and SinR targets. Our data also revealed a significant overlap with the AbrB regulon. Together, these findings reveal that LutR is part of the global complex, interconnected regulatory systems governing adaptation of bacteria to the transition from exponential growth to stationary phase.
Regulation of the Bacillus subtilis mannitol utilization genes: promoter structure and transcriptional activation by the wild-type regulator (MtlR) and its mutants
Authors: Heravi Kambiz Morabbi , Altenbuchner Josef
Published: November 2013

Expression of mannitol utilization genes in Bacillus subtilis is directed by P
mtlA
, the promoter of the mtlAFD operon, and P
mtlR
, the promoter of the MtlR activator. MtlR contains phosphoenolpyruvate-dependent phosphotransferase system (PTS) regulation domains, called PRDs. The activity of PRD-containing MtlR is mainly regulated by the phosphorylation/dephosphorylation of its PRDII and EIIBGat-like domains. Replacing histidine 342 and cysteine 419 residues, which are the targets of phosphorylation in these two domains, by aspartate and alanine provided MtlR-H342D C419A, which permanently activates P
mtlA in vivo. In the mtlR-H342D C419A mutant, P
mtlA
was active, even when the mtlAFD operon was deleted from the genome. The mtlR-H342D C419A allele was expressed in an Escherichia coli strain lacking enzyme I of the PTS. Electrophoretic mobility shift assays using purified MtlR-H342D C419A showed an interaction between the MtlR double-mutant and the Cy5-labelled P
mtlA
and P
mtlR
DNA fragments. These investigations indicate that the activated MtlR functions regardless of the presence of the mannitol-specific transporter (MtlA). This is in contrast to the proposed model in which the sequestration of MtlR by the MtlA transporter is necessary for the activity of MtlR. Additionally, DNase I footprinting, construction of P
mtlA
-P
licB
hybrid promoters, as well as increasing the distance between the MtlR operator and the −35 box of P
mtlA
revealed that the activated MtlR molecules and RNA polymerase holoenzyme likely form a class II type activation complex at P
mtlA
and P
mtlR
during transcription initiation.
Essential roles of iron superoxide dismutase in photoautotrophic growth of Synechocystis sp. PCC 6803 and heterogeneous expression of marine Synechococcus sp. CC9311 copper/zinc superoxide dismutase within its sodB knockdown mutant
Authors: Ke Wen-Ting , Dai Guo-Zheng , Jiang Hai-Bo , Zhang Rui , Qiu Bao-Sheng
Published: November 2013

Synechocystissp. PCC 6803 possesses only onesodgene,sodB, encoding iron superoxide dismutase (FeSOD). It could not be knocked out completely by direct insertion of the kanamycin resistance cassette. When the promoter ofsodBin WTSynechocystiswas replaced with the copper-regulated promoter PpetE, a completely segregated PpetE–sodBstrain could be obtained. When this strain was cultured in copper-starved BG11 medium, the chlorophyllacontent was greatly reduced, growth was seriously inhibited and the strain was nearly dead during the 8 days of growth, whilst the WT strain grew well under the same growth conditions. These results indicated thatsodBwas essential for photoautotrophic growth ofSynechocystis. The reduction ofsodBgene copies in theSynechocystisgenome rendered the cells more sensitive to oxidative stress produced by methyl viologen and norflurazon.sodBstill could not be knocked out completely after active expression ofsodC(encoding Cu/ZnSOD) fromSynechococcussp. CC9311 in the neutral siteslr0168under the control of thepsbAIIpromoter, which means the function of FeSOD could not be complemented completely by Cu/ZnSOD. Heterogeneously expressedsodCincreased the oxidation and photoinhibition tolerance of theSynechocystis sodBknockdown mutant. Membrane fractionation followed by immunoblotting revealed that FeSOD was localized in the cytoplasm, and Cu/ZnSOD was localized in the soluble and thylakoid membrane fractions of the transformedSynechocystis. Cu/ZnSOD has a predicted N-terminal signal peptide, so it is probably a lumen protein. The different subcellular localization of these two SODs may have resulted in the failure of substitution ofsodCforsodB.
Role of C596 in the C-terminal extension of the haemagglutinin–neuraminidase protein in replication and pathogenicity of a highly virulent Indonesian strain of Newcastle disease virus
Authors: Kim Shin-Hee , Xiao Sa , Paldurai Anandan , Collins Peter L. , Samal Siba K.
Published: November 2013

We modified the haemagglutinin–neuraminidase (HN) glycoprotein of the virulent Newcastle disease virus (NDV) strain Banjarmasin/010/10 (Ban/010) by adding C-terminal extensions similar to those found in certain avirulent NDV strains. Extension of the 571 aa wt Ban/010 HN protein to 577 and 616 aa by removal of one or two translational stop codons moderately reduced HN function and viral pathogenicity in 1-day-old and 3-week-old chickens. Substantially greater reductions were achieved by altering the 616 aa form by introducing a R596C mutation or by replacing the C-terminal extension with that of avirulent strain Ulster, which naturally contains the amino acid 596C. These results showed that extension of the C terminus of HN reduces NDV pathogenicity, and that this effect is substantially increased by the presence of 596C. These results indicate that this attenuating mechanism in avirulent strains such as Ulster can be applied directly to a highly virulent strain recently in circulation.