bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Basis of Hsp90 Function
Authors: Prodromou Chrisostomos , Pearl Laurence H.
Published: October 2013

Heat shock protein 90 (Hsp90) stands at the crossroads of many signaling pathways responsible for cell proliferation, differentiation, cell homeostasis and apoptosis. Consequently, it is no surprise that Hsp90 is associated with all the six hallmarks of cancer and has become a prime anticancer target. Central to the Hsp90 mechanism is its ATPase activity, which is coupled to a conformational cycle involving a complex set of structural changes that involve all Hsp90 domains. The mechanism by which Hsp90 activates “client” protein is still poorly understood. However, there has been excellent progress on elucidating the molecular details of the complex structural changes required for Hsp90’s catalytically active state and how this activity is influenced by a variety of co-chaperones and client proteins. This review aims to bring together structural investigations that have so far contributed to our understanding of this ATPase-coupled conformational cycle and how this activity is regulated and ultimately has become the prime target for Hsp90 drugs.
Structure and Function of Hsp70 Molecular Chaperones
Authors: Clerico Eugenia M. , Gierasch Lila M.
Published: October 2013

Hsp70s comprise a group of highly conserved chaperones essential to cellular homeostasis. They take part in a wide array of processes, including their key roles in protein homeostasis in which they guard the proteome by binding partially folded proteins, thus protecting them from aggregation and allowing them to fold. Hsp70s work through binding and release of hydrophobic protein segments at the C-terminal substrate-binding domain (SBD), the affinity of which is modulated by ATP binding and hydrolysis to the N-terminal nucleotide-binding domain (NBD): When ATP binds to the NBD, the SBD has low affinity for substrate; when ATP is hydrolyzed and ADP is bound to the NBD, the SBD has high substrate affinity. This allosteric mechanism is regulated by co-chaperones: J proteins deliver substrates to Hsp70s and accelerate ATP hydrolysis; nucleotide exchange factors facilitate exchange of ADP by ATP. In humans, Hsp70 members are expressed in all cell types and many subcellular compartments. The functional diversity of Hsp70s is stunning, including shepherding of nascent chains, protein translocation across membranes, disassembly of complexes and recovery of proteins from aggregates. Some Hsp70s focus on housekeeping functions, while others are highly expressed under stress, promote cell survival and are essential for the cell to cope with adverse conditions. Consequently, Hsp70s are crucial for tumor cells to thrive and constitute a promising target for cancer treatments; in addition, Hsp70s have ameliorative effects on protein misfolding diseases. This review describes structural features and cellular functions of Hsp70s that are relevant to design of Hsp70-targeted drugs.
N-density representability and the optimal transport limit of the Hohenberg-Kohn functional
Authors: Friesecke Gero , Mendl Christian B. , Pass Brendan , Cotar Codina , Klüppelberg Claudia
Published: October 2013

We derive and analyze a hierarchy of approximations to the strongly correlated limit of the Hohenberg-Kohn functional. These “density representability approximations” are obtained by first noting that in the strongly correlated limit, N-representability of the pair density reduces to the requirement that the pair density must come from a symmetric N-point density. One then relaxes this requirement to the existence of a representing symmetric k-point density with k < N. The approximate energy can be computed by simulating a fictitious k-electron system. We investigate the approximations by deriving analytically exact results for a 2-site model problem, and by incorporating them into a self-consistent Kohn-Sham calculation for small atoms. We find that the low order representability conditions already capture the main part of the correlations.
Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. I. Theory
Authors: Maschio Lorenzo , Kirtman Bernard , Rérat Michel , Orlando Roberto , Dovesi Roberto
Published: October 2013

We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.
Imperialistic competition algorithm: Novel advanced approach to optimal sizing of hybrid power system
Authors: Moosavian Seyed Mahdi , Modiri-Delshad Mostafa , Rahim Nasrudin Abd , Selvaraj Jeyraj
Published: October 2013

Energy is vital to social and economic development. Increased energy demand and reduced fossil fuel resources led to use of renewable energy (RE) resources, whose intermittence and high investment cost spur research into optimal sizing of hybrid systems. Advancements in computer hardware and software enable solution of optimization problems through algorithms such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO), etc. The recently introduced Imperialistic Competition Algorithm (ICA) has shown excellent capability in solving various optimization problems. This paper introduces it and shows its benefits to an optimal-sizing problem of a hybrid RE system. The results will be shown and the effect of changing optimization's parameters will be discussed. To test the potential of proposed algorithm for minimum cost solution finding, a comparison between ICA and PSO algorithm will be provided. Results show the advantage of using ICA algorithm to find a better optimum solution for hybrid power system.
Simple approach to estimate residual flexural strength distribution of composite sandwich structure with impact-induced damage
Authors: Lee Jang-Ho , Kim Jae-Hoon , Choi Chang-Woong , Kang Ki-Weon
Published: October 2013

A new approach was developed to predict the statistical distribution of residual flexural strength of composite structures subjected to low velocity impact. Based on the assumption that the flexural strength of unimpacted structures follows the two-parameter Weibull distribution, the model was formulated as a function of the Weibull parameters for strength of unimpacted structures and residual strength of impacted structures. The model was verified by using an experiment for honeycomb core sandwich structure. The experiments included impact and flexural tests to generate the residual strength of structure. Theoretical predictions on the statistical distribution were in conformance with the experiments. The effect of impact energy on the distribution of residual flexural strength was also examined.
Plasma spectroscopy of metal ions for hyper-electron cyclotron resonance ion source
Authors: Muto Hideshi , Ohshiro Yukimitsu , Yamaka Shoichi , Watanabe Shin-ichi , Oyaizu Michihiro , Kubono Shigeru , Yamaguchi Hidetoshi , Kase Masayuki , Hattori Toshiyuki , Shimoura Susumu
Published: October 2013

In this research, the optical line spectra of metal ions from ECR plasma were observed using a grating monochromator with a photomultiplier. The light intensity of line spectrum from the ECR plasma had a strong correlation with ion beam intensity measured by a magnetic mass analyzer. This correlation is a significant information for the beam tuning process, because it allows to conduct the extraction of the desired metal ion species from the ECR plasma. Separation of ion species of the same charge to mass ratio with an electromagnetic mass analyzer is known to be an exceptionally complex process, but this research provides a new approach for its simplification. In this paper the grating monochromator method for metal ion beam tuning such as 40Ca12+, 56Fe15+, and 85Rb20+ of hyper-ECR ion source as an injector for RIKEN Azimuthal Varying Field cyclotron is described.
Self-Consistent Ornstein-Zernike Approximation (SCOZA) and exact second virial coefficients and their relationship with critical temperature for colloidal or protein suspensions with short-ranged attractive interactions
Authors: Gazzillo Domenico , Pini Davide
Published: October 2013

We focus on the second virial coefficient B2 of fluids with molecules interacting through hard-sphere potentials plus very short-ranged attractions, namely, with a range of attraction smaller than half hard-sphere diameter. This kind of interactions is found in colloidal or protein suspensions, while the interest in B2 stems from the relation between this quantity and some other properties of these fluid systems. Since the SCOZA (Self-Consistent Ornstein-Zernike Approximation) integral equation is known to yield accurate thermodynamic and structural predictions even near phase transitions and in the critical region, we investigate \documentclass[12pt]{minimal}\begin{document}$B_{2}^{ \mathrm{SCOZA}}$\end{document}B2 SCOZA and compare it with \documentclass[12pt]{minimal}\begin{document}$B_{2}^{\mathrm{exact}}$\end{document}B2 exact , for some typical potential models. The aim of the paper is however twofold. First, by expanding in powers of density the condition of thermodynamic consistency included in the SCOZA integral equation, a general analytic expression for \documentclass[12pt]{minimal}\begin{document}$B_{2}^{ \mathrm{SCOZA}}$\end{document}B2 SCOZA is derived. For a given potential model, a comparison between \documentclass[12pt]{minimal}\begin{document}$B_{2}^{\mathrm{SCOZA}}$\end{document}B2 SCOZA and \documentclass[12pt]{minimal}\begin{document}$B_{2}^{\mathrm{exact}}$\end{document}B2 exact may help to estimate the regimes where the SCOZA closure is reliable. Second, following the Vliegenthart-Lekkerkerker (VL) and Noro-Frenkel suggestions, the relationship between the critical B2 and the critical temperature Tc is discussed in detail for two prototype models: the square-well (SW) potential and the hard-sphere attractive Yukawa (HSY) one. The known simulation data for the SW model are revisited, while for the HSY model new SCOZA results have been generated. Although \documentclass[12pt]{minimal}\begin{document}$B_{2}^{\mathrm{HSY}}$\end{document}B2 HSY at the critical temperature is found to be a slowly varying function of the range of Yukawa attraction ΔY over a wide interval of ΔY, it turns out to diverge as ΔY vanishes. For fluids with very short-ranged attractions, such a behavior contrasts with the VL assumption that B2 at the critical temperature should be nearly independent of the range of attraction. A very simple analytic representation is found for the available Monte Carlo data for \documentclass[12pt]{minimal}\begin{document}$T_{\mathrm{c}}^{\mathrm{HSY}}$\end{document}Tc HSY and \documentclass[12pt]{minimal}\begin{document}$B_{2}^{\mathrm{HSY}}$\end{document}B2 HSY as functions of the range of attraction, for ΔY smaller than half hard-sphere diameter.
Reynolds number scaling of coherent vortex simulation and stochastic coherent adaptive large eddy simulation
Authors: Nejadmalayeri Alireza , Vezolainen Alexei , Vasilyev Oleg V.
Published: October 2013

In view of the ongoing longtime pursuit of numerical approaches that can capture important flow physics of high Reynolds number flows with fewest degrees of freedom, two important wavelet-based multi-resolution schemes are thoroughly examined, namely, the Coherent Vortex Simulation (CVS) and the Stochastic Coherent Adaptive Large Eddy Simulation (SCALES) with constant and spatially/temporarily variable thresholding. Reynolds number scaling of active spatial modes for CVS and SCALES of linearly forced homogeneous turbulence at high Reynolds numbers is investigated in dynamic study for the first time. This dynamic computational complexity study demonstrates that wavelet-based methods can capture flow-physics while using substantially fewer degrees of freedom than both direct numerical simulation and marginally resolved LES with the same level of fidelity or turbulence resolution, defined as ratio of subgrid scale and the total dissipations. The study provides four important observations: (1) the linear Reynolds number scaling of energy containing structures at a fixed level of kinetic energy, (2) small, close to unity, fractal dimension for constant-threshold CVS and SCALES simulations, (3) constant, close to two, fractal dimension for constant-dissipation SCALES that is insensitive to the level of fidelity, and (4) faster than quadratic decay of the compression ratio as a function of turbulence resolution. The very promising slope for Reynolds number scaling of CVS and SCALES demonstrates the potential of the wavelet-based methodologies for hierarchical multiscale space/time adaptive variable fidelity simulations of high Reynolds number turbulent flows.
High performance rotational vibration isolator
Authors: Sunderland Andrew , Blair David G. , Ju Li , Golden Howard , Torres Francis , Chen Xu , Lockwood Ray , Wolfgram Peter
Published: October 2013

We present a new rotational vibration isolator with an extremely low resonant frequency of 0.055 ± 0.002 Hz. The isolator consists of two concentric spheres separated by a layer of water and joined by very soft silicone springs. The isolator reduces rotation noise at all frequencies above its resonance which is very important for airborne mineral detection. We show that more than 40 dB of isolation is achieved in a helicopter survey for rotations at frequencies between 2 Hz and 20 Hz. Issues affecting performance such as translation to rotation coupling and temperature are discussed. The isolator contains almost no metal, making it particularly suitable for electromagnetic sensors.
Data acquisition in a high-speed rotating frame for New Mexico Institute of Mining and Technology liquid sodium αω dynamo experiment
Authors: Si Jiahe , Colgate Stirling A. , Li Hui , Martinic Joe , Westpfahl David
Published: October 2013

New Mexico Institute of Mining and Technology liquid sodium αω-dynamo experiment models the magnetic field generation in the universe as discussed in detail by Colgate, Li, and Pariev [Phys. Plasmas 8, 2425 (2001)]. To obtain a quasi-laminar flow with magnetic Reynolds number Rm ∼ 120, the dynamo experiment consists of two co-axial cylinders of 30.5 cm and 61 cm in diameter spinning up to 70 Hz and 17.5 Hz, respectively. During the experiment, the temperature of the cylinders must be maintained to 110 °C to ensure that the sodium remains fluid. This presents a challenge to implement a data acquisition (DAQ) system in such high temperature, high-speed rotating frame, in which the sensors (including 18 Hall sensors, 5 pressure sensors, and 5 temperature sensors, etc.) are under the centrifugal acceleration up to 376g. In addition, the data must be transmitted and stored in a computer 100 ft away for safety. The analog signals are digitized, converted to serial signals by an analog-to-digital converter and a field-programmable gate array. Power is provided through brush/ring sets. The serial signals are sent through ring/shoe sets capacitively, then reshaped with cross-talk noises removed. A microcontroller-based interface circuit is used to decode the serial signals and communicate with the data acquisition computer. The DAQ accommodates pressure up to 1000 psi, temperature up to more than 130 °C, and magnetic field up to 1000 G. First physics results have been analyzed and published. The next stage of the αω-dynamo experiment includes the DAQ system upgrade.
Control of Turing patterns and their usage as sensors, memory arrays, and logic gates
Authors: Muzika František , Schreiber Igor
Published: October 2013

We study a model system of three diffusively coupled reaction cells arranged in a linear array that display Turing patterns with special focus on the case of equal coupling strength for all components. As a suitable model reaction we consider a two-variable core model of glycolysis. Using numerical continuation and bifurcation techniques we analyze the dependence of the system's steady states on varying rate coefficient of the recycling step while the coupling coefficients of the inhibitor and activator are fixed and set at the ratios 100:1, 1:1, and 4:5. We show that stable Turing patterns occur at all three ratios but, as expected, spontaneous transition from the spatially uniform steady state to the spatially nonuniform Turing patterns occurs only in the first case. The other two cases possess multiple Turing patterns, which are stabilized by secondary bifurcations and coexist with stable uniform periodic oscillations. For the 1:1 ratio we examine modular spatiotemporal perturbations, which allow for controllable switching between the uniform oscillations and various Turing patterns. Such modular perturbations are then used to construct chemical computing devices utilizing the multiple Turing patterns. By classifying various responses we propose: (a) a single-input resettable sensor capable of reading certain value of concentration, (b) two-input and three-input memory arrays capable of storing logic information, (c) three-input, three-output logic gates performing combinations of logical functions OR, XOR, AND, and NAND.
First-principles study of structural phase transitions in CsSnI3
Authors: Yu Chonglong , Ren Yuhang , Chen Zhuo , Shum Kai
Published: October 2013

CsSnI3 has been recently identified as a potential perovskite semiconductor compound for optoelectronic device applications. It is clearly of great importance to understand synthetic pathways starting from material precursors through studying its structural phase transitions. By constraining the regularity of SnI6 octahedra during the phase transitions, the landscape of ground state energy is being mapped out. The coordinate parameters for the undistorted α and distorted β and γ structures at zero temperature are identified and compared with available experimental data. It is predicted that the α structure is instable at any temperature and acts merely as an intermediate state while the β and γ structures are stable ones, and they can be transformed reversibly. The role of Cs atoms played for phase transitions is also investigated.
Modeling an antenna-coupled graphene field-effect terahertz detector
Authors: Tan Ren-Bing , Qin Hua , Sun Jian-Dong , Zhang Xiao-Yu , Zhang Bao-Shun
Published: October 2013

The effect of ambipolar carriers on terahertz self-mixing is theoretically investigated in an antenna-coupled graphene field-effect terahertz (GFET) detector by taking into account the spatial distributions of the charge carriers and the terahertz field. The model predicts that the charge and field distributions can be tuned by the gate voltage so that they match up with each other and enhance the photocurrent. Such a cooperative self-mixing does not occur in unipolar FET detectors. A GFET detector with a moderate carrier mobility could offer current responsivity of a few A/W and noise-equivalent power below 50 pW/Hz at room temperature.
Hollow micro/nanomaterials as nanoreactors for photocatalysis
Authors: Li Xiaobo , Liu Jian , Masters Anthony F. , Pareek Vishnu K. , Maschmeyer Thomas
Published: October 2013

Learning from nature, one of the most prominent goals of photocatalysis is to assemble multifunctional photocatalytic units in an integrated, high performance device that is capable of using solar energy to produce “solar hydrogen” from aqueous media. By analogy with natural systems it is clear that scaffolds with multi-scale structural architectures are necessary. In this perspective, recent progress related to the use of hollow micro/nanomaterials as nanoreactors for photocatalysis is discussed. Organised, multi-scale assemblies of photocatalytic units on hollow scaffolds is an emerging area that shows much promise for the synthesis of high performance photocatalysts. Not only do improved transport and diffusion characteristics play an import role, but increased electron/hole separation lifetimes as well as improved light harvesting characteristics by the hollow structures also do so and are touched upon in this short perspective.
Time-delayed beam splitting with energy separation of x-ray channels
Authors: Stetsko Yuri P. , Shvyd'ko Yuri V. , Brian Stephenson G.
Published: October 2013

We introduce a time-delayed beam splitting method based on the energy separation of x-ray photon beams. It is implemented and theoretically substantiated on an example of an x-ray optical scheme similar to that of the classical Michelson interferometer. The splitter/mixer uses Bragg-case diffraction from a thin diamond crystal. Another two diamond crystals are used as back-reflectors. Because of energy separation and a minimal number (three) of optical elements, the split-delay line has high efficiency and is simple to operate. Due to the high transparency of diamond crystal, the split-delay line can be used in a beam sharing mode at x-ray free-electron laser facilities.
Indication of liquid-liquid phase transition in CuZr-based melts
Authors: Zhou Chao , Hu Lina , Sun Qijing , Qin Jingyu , Bian Xiufang , Yue Yuanzheng
Published: October 2013

We study the dynamic behavior of CuZr-based melts well above the liquidus temperature. The results show a discontinuous change in viscosity during cooling, which is attributed to an underlying liquid-liquid phase transition (LLPT) in these melts. The LLPT is further verified by thermodynamic response in the same temperature region. We find that the LLPT in the Cu46Zr46Al8 melt is reversible above 1350 K upon repeated heating and cooling. Based on the concept of fluid cluster in metallic melts, the reversible LLPT is attributed to the structural transition from the strongly ordered high-density liquids to the weak-local low-density liquids upon cooling.
Cone-shaped forest of aligned carbon nanotubes: An alternative probe for scanning microscopy
Authors: Xiao Zhiming , Saquib Sarwar Mirza , Dahmardeh Masoud , Vahdani Moghaddam Mehran , Nojeh Alireza , Takahata Kenichi
Published: October 2013

A scanning microscopy probe based on three-dimensionally shaped carbon nanotube (CNT) forests and its application to atomic-force microscopy (AFM) are reported. Micro-scale CNT forests directly grown on silicon cantilevers are patterned into cone shapes with the tips of a few individual nanotubes. The CNT-forest-based probes provide significantly higher mechanical stability/robustness than the common single-CNT probes. AFM imaging using the fabricated probes reveals their imaging ability comparable to that of commercial probes. The patterning process also improves the uniformity of the CNT forests grown on each cantilever. The results suggest a promising future for CNT scanning probes and their production approach.
Epoxy composites filled with high surface area-carbon fillers: Optimization of electromagnetic shielding, electrical, mechanical, and thermal properties
Authors: Kuzhir P. , Paddubskaya A. , Plyushch A. , Volynets N. , Maksimenko S. , Macutkevic J. , Kranauskaite I. , Banys J. , Ivanov E. , Kotsilkova R. , Celzard A. , Fierro V. , Zicans J. , Ivanova T. , Merijs Meri R. , Bochkov I. , Cataldo A. , Micciulla F. , Bellucci S. , Lambin Ph.
Published: October 2013

A comprehensive analysis of electrical, electromagnetic (EM), mechanical, and thermal properties of epoxy resin composites filled with 0.25–2.0 wt. % of carbon additives characterized by high surface area, both nano-sized, like carbon nanotubes (CNTs) and carbon black (CBH), and micro-sized exfoliated graphite (EG), was performed. We found that the physical properties of both CNTs- and CBH-based epoxy resin composites increased all together with filler content and even more clearly for CBH than for CNTs. In the case of EG-based composites, good correlation between properties and filler amount was observed for concentrations below 1.5 wt. %. We conclude that CBH and, to a lower extent, EG could replace expensive CNTs for producing effective EM materials in microwave and low-frequency ranges, which are, in addition, mechanically and thermally stable.
Carrier type dependence on spatial asymmetry of unipolar resistive switching of metal oxides
Authors: Nagashima Kazuki , Yanagida Takeshi , Kanai Masaki , Celano Umberto , Rahong Sakon , Meng Gang , Zhuge Fuwei , He Yong , Ho Park Bae , Kawai Tomoji
Published: October 2013

We report a carrier type dependence on the spatial asymmetry of unipolar resistive switching for various metal oxides, including NiOx, CoOx, TiO2−x, YSZ, and SnO2−x. n-type oxides show a unipolar resistive switching at the anode side whereas p-type oxides switch at the cathode side. During the forming process, the electrical conduction path of p-type oxides extends from the anode to cathode while that of n-type oxides forms from the cathode to anode. The carrier type of switching oxide layer critically determines the spatial inhomogeneity of unipolar resistive switching during the forming process possibly triggered via the oxygen ion drift.
Experimental demonstration of small-angle bending in an active direct-coupled chain of spherical microcavities
Authors: Kumar Tiwari Anjani , Uppu Ravitej , Mujumdar Sushil
Published: October 2013

We experimentally demonstrate collective amplified modes along bent chains of directly coupled, amplifying spherical microdroplet resonators. The chains, comprising ∼40 non-contacting resonators, were bent through angles up to ∼25°. The modal probability of the system shows a sharp drop upon bending through small angles (∼10°), and thereafter changes minimally under further bending. The frequency response is significantly maintained under bending. We numerically study the transmittance of a chain of non-contacting amplifying resonators using finite-difference-time-domain calculations, and observe that nanojet filamentation influences coupling at the bend. A self-correcting mechanism of propagation is observed, originating from the lensing effect of the spherical resonator.
Attosecond Thomson-scattering x-ray source driven by laser-based electron acceleration
Authors: Luo W. , Zhuo H. B. , Ma Y. Y. , Song Y. M. , Zhu Z. C. , Yu T. P. , Yu M. Y.
Published: October 2013

The possibility of producing attosecond x-rays through Thomson scattering of laser light off laser-driven relativistic electron beams is investigated. For a ≤200-as, tens-MeV electron bunch produced with laser ponderomotive-force acceleration in a plasma wire, exceeding 106 photons/s in the form of ∼160 as pulses in the range of 3–300 keV are predicted, with a peak brightness of ≥5 × 1020 photons/(s mm2 mrad2 0.1% bandwidth). Our study suggests that the physical scheme discussed in this work can be used for an ultrafast (attosecond) x-ray source, which is the most beneficial for time-resolved atomic physics, dubbed “attosecond physics.”
Spectral and spatial contributions to white light generation from InGaN/GaN dot-in-a-wire nanostructures
Authors: Kamali Yousef , Walsh Brenna R. , Mooney Jonathan , Nguyen Hieu , Brosseau Colin , Leonelli Richard , Mi Zetian , Kambhampati Patanjali
Published: October 2013

We analyze epitaxially grown InGaN/GaN dot-in-a-wire heterostructures to relate growth and design properties to trends seen in photoluminescence (PL) and resonance Raman spectra. Temperature-dependent PL measurement of these dot-in-a-wire heterostructures illustrate an expected decrease in integrated PL emission and an unusual narrowing of peak width with increasing temperature. Information extracted from Resonance Raman spectra was utilized in a time-dependent model to analyze and to simulate PL spectra. These spectra were found to be in good agreement with the experimental PL data and provided insight into the broadening mechanisms affecting the samples. PL measurements were taken as a function of position on the sample and radial variation of peak energies was observed. This variation was attributed to the radial temperature gradient present during nanowire growth. These additional characteristics of the nanowire heterostructures will allow for increased understanding of these systems potentials for applications in white light emitting diodes.
A comparative study on shock compression of nanocrystalline Al and Cu: Shock profiles and microscopic views of plasticity
Authors: Ma Wen , Zhu Wenjun , Hou Yong
Published: October 2013

Shock compressions of nanocrystalline (nc) metals Al and Cu with the same grain size and texture are studied by using molecular dynamics simulations. Results have revealed that the shock front of both Al and Cu can be divided into three stages: elastic, grain-boundary-mediated, and dislocation-mediated plastic deformation. The transition planes among these three stages are proven to be non-planar by two-dimensional shock response analysis, including local stress, shear, temperature, and atom configuration. The difference between shocked Al and Cu is that the rise rate of the elastic stage of Cu is slightly higher than that of Al, and that the shock-front width of Al is wider than Cu at the same loading conditions. For the plastic stage, the dislocation density of shocked Al is lower than Cu, and the contribution of grain-boundary-mediated plasticity to shock front and strain for nc Al is more pronounced than for nc Cu. These results are explained through intrinsic material properties and atomistic analysis of the plastic process. In the case of the shocked Al sample, partial dislocations, perfect dislocations, and twins are observed, but few evidence of perfect dislocations and twins are observed in the shocked Cu.
Super-resolution fluorescence imaging of nanoimprinted polymer patterns by selective fluorophore adsorption combined with redox switching
Authors: Yabiku Yu , Kubo Shoichi , Nakagawa Masaru , Vacha Martin , Habuchi Satoshi
Published: October 2013

We applied a super-resolution fluorescence imaging based on selective adsorption and redox switching of the fluorescent dye molecules for studying polymer nanostructures. We demonstrate that nano-scale structures of polymer thin films can be visualized with the image resolution better than 80 nm. The method was applied to image 100 nm-wide polymer nanopatterns fabricated by thermal nanoimprinting. The results point to the applicability of the method for evaluating residual polymer thin films and dewetting defect of the polymer resist patterns which are important for the quality control of the fine nanoimprinted patterns.
Window to the Wandering Mind: Pupillometry of Spontaneous Thought While Reading
Authors: Franklin Michael S. , Broadway James M. , Mrazek Michael D. , Smallwood Jonathan , Schooler Jonathan W.
Published: October 2013

Mind-wandering is both pervasive and detrimental to task performance. As such, identifying covert physiological measures that are associated with this off-task state could inform theories of mind-wandering and lead to interventions that improve task focus. Although previous work suggests that pupil dilation (PD) may vary between on- and off-task states, no studies have examined whether PD systematically varies within a subject as they report becoming disengaged from a task—a key step in developing useful mind-wandering prediction algorithms. In the present study, PD was measured while participants advanced through a passage one word at a time. Spontaneous mind-wandering was assessed during reading using standard thought probe methodology. Results revealed higher PD prior to off-task than prior to on-task reading. This newly discovered relationship between momentary fluctuations of attention and PD offers promise for future innovations that use these systematic changes in PD to predict and better control mind-wandering.
ATHENA: the analysis tool for heritable and environmental network associations
Authors: Holzinger Emily R. , Dudek Scott M. , Frase Alex T. , Pendergrass Sarah A. , Ritchie Marylyn D.
Published: October 2013

Motivation: Advancements in high-throughput technology have allowed researchers to examine the genetic etiology of complex human traits in a robust fashion. Although genome-wide association studies have identified many novel variants associated with hundreds of traits, a large proportion of the estimated trait heritability remains unexplained. One hypothesis is that the commonly used statistical techniques and study designs are not robust to the complex etiology that may underlie these human traits. This etiology could include non-linear gene × gene or gene × environment interactions. Additionally, other levels of biological regulation may play a large role in trait variability.

Results: To address the need for computational tools that can explore enormous datasets to detect complex susceptibility models, we have developed a software package called the Analysis Tool for Heritable and Environmental Network Associations (ATHENA). ATHENA combines various variable filtering methods with machine learning techniques to analyze high-throughput categorical (i.e. single nucleotide polymorphisms) and quantitative (i.e. gene expression levels) predictor variables to generate multivariable models that predict either a categorical (i.e. disease status) or quantitative (i.e. cholesterol levels) outcomes. The goal of this article is to demonstrate the utility of ATHENA using simulated and biological datasets that consist of both single nucleotide polymorphisms and gene expression variables to identify complex prediction models. Importantly, this method is flexible and can be expanded to include other types of high-throughput data (i.e. RNA-seq data and biomarker measurements).

Availability: ATHENA is freely available for download. The software, user manual and tutorial can be downloaded from http://ritchielab.psu.edu/ritchielab/software.

Contact:  marylyn.ritchie@psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The drivers of woody species richness and density in a Neotropical savannah
Authors: Carvalho Gustavo Henrique , Batalha Marco Antônio
Published: October 2013

Environmental filtering prevents species without certain attributes from occurring in local communities. Traits respond differently to different abiotic factors, assembling communities with varying composition along environmental gradients. Here, we measured proxies of soil fertility, disturbance by fire, response and physiological traits to assess how these variables interact to determine woody species richness and density in a Neotropical savannah. We explicitly incorporated our assumptions about how different abiotic filters influence different subsets of traits into a statistical model using structural equation modelling, yielding a more accurate representation of the assembly process. Fire had an effect on resistance traits, whereas soil fertility influenced physiological traits. Resistance traits explained both the richness and density of plots, whereas physiological traits explained only the density. Fewer fire events led to richer and denser plots. Similarly, areas with lower cation exchange capacity assembled less dense communities. Furthermore, we showed that structural equation modelling yielded a realistic representation of the bivariate interactions of distinct environmental filters with different subsets of traits.
Indian monsoons shape dispersal phenology of plants
Authors: Aravind N. A. , Ganeshaiah K. N. , Shaanker R. Uma
Published: October 2013

The Indian monsoons are a major seasonal climatic event over the Indian subcontinent, heralding the arrival of the wet season. Many features of life, biological and cultural, are intimately synchronized to this seasonality. In this paper, we show that the Indian monsoons might have played an important role in shaping the fruiting time and hence dispersal phenology of plant species in the subcontinent.
A model comparison reveals dynamic social information drives the movements of humbug damselfish (
Dascyllus aruanus
)
Authors: Mann R. P. , Herbert-Read J. E. , Ma Q. , Jordan L. A. , Sumpter D. J. T. , Ward A. J. W.
Published: October 2013

Animals make use a range of social information to inform their movement decisions. One common movement rule, found across many different species, is that the probability that an individual moves to an area increases with the number of conspecifics there. However, in many cases, it remains unclear what social cues produce this and other similar movement rules. Here, we investigate what cues are used by damselfish (
Dascyllus aruanus
) when repeatedly crossing back and forth between two coral patches in an experimental arena. We find that an individual's decision to move is best predicted by the recent movements of conspecifics either to or from that individual's current habitat. Rather than actively seeking attachment to a larger group, individuals are instead prioritizing highly local and dynamic information with very limited spatial and temporal ranges. By reanalysing data in which the same species crossed for the first time to a new coral patch, we show that the individuals use static cues in this case. This suggests that these fish alter their information usage according to the structure and familiarity of their environment by using stable information when moving to a novel area and localized dynamic information when moving between familiar areas.
Radar clutter suppression and target discrimination using twin inverted pulses
Authors: Leighton T. G. , Chua G. H. , White P. R. , Tong K. F. , Griffiths H. D. , Daniels D. J.
Published: October 2013

The proposition that the use of twin inverted pulses could enhance radar is tested. This twin inverted pulse radar (TWIPR) is applied to five targets. A representative target of interest (a dipole with a diode across its feedpoint) is typical of covert circuitry one might wish to detect (e.g. in devices associated with covert communications, espionage or explosives), and then distinguish from other metal (‘garbage’ or ‘clutter’), here represented by an aluminium plate and a rusty bench clamp. In addition, two models of mobile phones are tested to see whether TWIPR can distinguish whether each is off, on or whether it contains a valid SIM card. Given that a small, inexpensive, lightweight device requiring no batteries can produce a signal that is 50 dB above clutter in this test, the options are discussed for using such technology for animal tagging or to allow the location and identification of buried personnel who opt to carry them (rescue workers, skiers in avalanche areas, miners, etc.). The results offer the possibility that buried catastrophe victims not carrying such tags might still be located by TWIPR scattering from their mobile phones, even when the phones are turned off or the batteries have no charge remaining.
A neurotoxic pesticide changes the outcome of aggressive interactions between native and invasive ants
Authors: Barbieri Rafael F. , Lester Philip J. , Miller Alexander S. , Ryan Ken G.
Published: October 2013

Neurotoxic pesticides, such as neonicotinoids, negatively affect the cognitive capacity and fitness of non-target species, and could also modify interspecific interactions. We tested whether sublethal contamination with neonicotinoid could affect foraging, colony fitness and the outcome of behavioural interactions between a native (
Monomorium antarcticum
) and an invasive ant species (
Linepithema humile
). The foraging behaviour of both ants was not affected by neonicotinoid exposure. Colonies of the invasive species exposed to the neonicotinoid produced significantly fewer brood. In interspecific confrontations, individuals of the native species exposed to the neonicotinoid lowered their aggression towards the invasive species, although their survival probability was not affected. Exposed individuals of the invasive species interacting with non-exposed native ants displayed increased aggression and had their survival probability reduced. Non-exposed individuals of the invasive species were less aggressive but more likely to survive when interacting with exposed native ants. These results suggest that non-target exposure of invaders to neonicotinoids could either increase or decrease the probability of survival according to the exposure status of the native species. Given that, in any community, different species have different food preferences, and thus different exposure to pesticides, non-target exposure could potentially change the dynamics of communities and influence invasion success.
Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China
Authors: Briggs Brandon R. , Brodie Eoin L. , Tom Lauren M. , Dong Hailiang , Jiang Hongchen , Huang Qiuyuan , Wang Shang , Hou Weiguo , Wu Geng , Huang Liuquin , Hedlund Brian P. , Zhang Chuanlun , Dijkstra Paul , Hungate Bruce A.
Published: October 2013

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high‐temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum‐level groups and 113 OTUs within 20 archaeal phylum‐level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high‐temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.
Single‐subject designs in special education: advantages and limitations
Authors: Alnahdi Ghaleb H.
Published: October 2013

Single‐subject designs provide the special education field with an alternative to group designs. The purpose of this paper is to introduce the topic of single‐subject designs by providing an overview of the relevant literature and a discussion of the major issues and applications of these designs in the field of special education. This paper is divided into four main sections: (1) characteristics of single‐subject designs; (2) types of single‐subject designs; (3) advantages of single‐subject designs; and (4) issues and concerns regarding single‐subject designs. It was concluded that a minimum of three measurements in each phase is typically required until there is a clear pattern. Flexibility and cost‐effectiveness are among the main advantages of these designs. External validity and generalisability are the main concerns. However, meta‐analytic studies can enhance the generalisability of single‐subject designs findings within similar context. Conclusions and recommendations to improve these designs are discussed.
Primary special school teachers' knowledge and beliefs about supporting learning in numeracy
Authors: Moscardini Lio
Published: October 2013

This paper presents findings from a qualitative study of a group of 12 teachers in primary special schools in Scotland for children with moderate learning difficulties. It sets out an analysis of classroom observations and interviews that explored teachers' knowledge and beliefs about teaching and learning in mathematics with children with moderate learning difficulties. The teachers were interviewed pre‐ and post‐intervention; this was a research‐based professional development programme in children's mathematical thinking (Cognitively Guided Instruction) which teachers then developed in their classrooms. The findings showed that prior to the professional development, the teachers had a limited knowledge of children's mathematical development with teaching frequently informed by intuitive beliefs and dated and sometimes discredited practices. Most teachers had low expectations of children with learning difficulties. Post‐intervention, the teachers reviewed this stance and affirmed that a deeper understanding of children's mathematical thinking provided a more secure knowledge base for instruction. They also recognised the extent to which learners were constrained by existing classroom practices. The paper argues for the commonality of this knowledge base and considers the problematic nature of viewing such knowledge as sector specific.
Psychosocial factors and mortality in women with early stage endometrial cancer
Authors: Telepak Laura C. , Jensen Sally E. , Dodd Stacy M. , Morgan Linda S. , Pereira Deidre B.
Published: October 2013

Objectives

Psychosocial factors have previously been linked with survival and mortality in cancer populations. Little evidence is available about the relationship between these factors and outcomes in gynaecologic cancer populations, particularly endometrial cancer, the fourth most common cancer among women. This study examined the relationship between several psychosocial factors prior to surgical resection and risk of all‐cause mortality in women with endometrial cancer.

Design

The study utilized a non‐experimental, longitudinal design.

Methods

Participants were 87 women (Mage = 60.69 years, SDage = 9.12 years) who were diagnosed with T1N0–T3N2 endometrial cancer and subsequently underwent surgery. Participants provided psychosocial data immediately prior to surgery. Survival statuses 4–5 years post‐diagnoses were abstracted via medical record review. Cox regression was employed for the survival analysis.

Results

Of the 87 women in this sample, 21 women died during the 4‐ to 5‐year follow‐up. Adjusting for age, presence of regional disease and medical comorbidity severity (known biomedical prognostic factors), greater use of an active coping style prior to surgery was significantly associated with a lower probability of all‐cause mortality, hazard ratio (HR) = 0.78, p = .04. Life stress, depressive symptoms, use of self‐distraction coping, receipt of emotional support and endometrial cancer quality of life prior to surgery were not significantly associated with all‐cause mortality 4–5 years following diagnosis.

Conclusions

Greater use of active coping prior to surgery for suspected endometrial cancer is associated with lower probability of all‐cause mortality 4–5 years post‐surgery. Future research should attempt to replicate these relationships in a larger and more representative sample and examine potential behavioural and neuroendocrine/immune mediators of this relationship.

Statement of contribution

What is already known on this subject? Psychosocial factors have previously been linked with clinical outcomes in a variety of cancer populations. With regards to gynecologic cancer, the majority of the research has been conducted in ovarian cancer and examines the protective role of social support in mortality outcomes.

What does this study add?

Demonstrates association between active coping during perioperative period and 5 year survival.

Demonstrates psychosocial–survival relationship exists independent of biobehavioral factors.