bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates
Authors: Skerker Jeffrey M , Leon Dacia , Price Morgan N , Mar Jordan S , Tarjan Daniel R , Wetmore Kelly M , Deutschbauer Adam M , Baumohl Jason K , Bauer Stefan , Ibáñez Ana B , Mitchell Valerie D , Wu Cindy H , Hu Ping , Hazen Terry , Arkin Adam P
Published: June 2013

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA‐barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4‐fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate‐derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.
Sample Preparation and Profiling: Probing the Kinome for Biomarkers and Therapeutic Targets: Peptide Arrays for Global Phosphorylation-Mediated Signal Transduction
Authors: Kindrachuk Jason , Napper* Scott
Published: June 2013

There is a growing appreciation of the intimate relationship between protein kinase activities and human health. Cellular kinases, individually or as a collective unit (the kinome), perform indispensable roles in regulating complex biology, underlie many disease states, and represent high-priority drug targets. Recent trends of drug development, where kinase inhibitors are becoming increasingly common, highlight the potential therapeutic opportunities made available through kinase investigations. There is also considerable evidence that understanding cellular responses at the level of kinase activity has the potential to reveal complex biology as well as identify biomarkers and therapeutic targets. With these appreciations, there is growing interest in the development of technologies that enable high-throughput characterization of kinome activity. Of these emerging technologies peptide arrays are proving a robust and adaptable tool for kinome characterizations.
Cobicistat and Ritonavir as Pharmacoenhancers for Antiviral Drugs
Authors: Xu Lianhong , Desai Manoj C.
Published: June 2013

Adherence to an active antiviral regimen, driven a by a low pill burden, convenient dosing schedule, and favorable tolerability and safety profiles, plays a critical role in the successful treatment of chronic viral infection and the prevention of resistance development. Cytochrome P450 3A (CYP3A) inhibitors ritonavir and cobicistat significantly improve the pharmacokinetic profiles of therapeutic drugs, such as the HIV protease inhibitor atazanavir and integrase inhibitor elvitegravir that are metabolized by the CYP3A, resulting in reduced pill burn, decreased dosing frequency and an improved safety profile. Both ritonavir and cobicistat have contributed to the simplification of dosing regimens and improved adherence, ensuring the successful long‐term management of HIV infection.
Clinical Benefits of Single‐tablet Regimens
Authors: Porter Danielle P. , Guyer Bill
Published: June 2013

Since the advent of highly active antiretroviral therapy, considerable progress has been made in the treatment of HIV infection. Single-tablet regimens (STRs) represent substantial improvements in the treatment of HIV infection by providing all of the components of a safe and effective antiretroviral therapy regimen in a single pill that is dosed once daily, thereby allowing for simpler and more convenient treatment. Of the three FDA-approved STRs currently available in the USA, two consist of combinations of two nucleoside reverse transcriptase inhibitors (NRTIs) and one non-nucleoside reverse transcriptase inhibitor (NNRTI), efavirenz/emtricitabine/tenofovir disoproxil fumarate (EFV/FTC/TDF) and emtricitabine/rilpivirine/tenofovir disoproxil fumarate (FTC/RPV/TDF), while the third and newest STR consists of two NRTIs plus an integrase strand transfer inhibitor (INSTI), elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate (EVG/COBI/FTC/TDF). Large clinical trials and retrospective analyses have demonstrated the advantages of these STRs over other treatment regimens, including greater adherence and persistence, better health outcomes, improved patient preference and quality of life and reduced healthcare resource utilization. Because of the demonstrated advantages of STR therapies in the management of HIV and successes in other disease areas using coformulated medications, it may be beneficial to develop future STRs for the treatment of other chronic diseases.
Multivariate Regression using Artificial Neural Networks and Support Vector Machines
Authors: Manuel Andrade‐Garda José , Gestal‐Pose Marcos , Abel Cedrón‐Santaeufemia Francisco , Dorado‐de‐la‐Calle Julián , Paz Gómez‐Carracedo María
Published: June 2013

The huge efforts made currently by atomic spectroscopists to resolve interferences and optimise instrumental measuring devices to increase accuracy and precision have led to a point where many of the difficulties that need to be solved nowadays cannot be described by simple classical linear regression methods and not even by other advanced linear regression methods. Typical situations where these can fail involve spectral non‐linearities.

This chapter introduces two relatively recent regression methodologies which, in contrast to classical programming, work with rules rather than with well‐defined and fixed algorithms: artificial neural networks (ANNs), a fairly established technique nowadays, and the support vector machine (SVM), which is emerging as a powerful method to perform both classification and regression tasks.
Robust approach to repetitive controller design for uncertain feedback control systems
Authors: Doh Tae‐Yong , Ryoo Jung Rae
Published: June 2013

In many applications, add‐on type repetitive controllers have been reported to have prominent capability of attenuating periodic disturbances and/or tracking periodic reference commands. However, the effective information such as performance weighting functions for the design of feedback controllers has not been considered sufficiently on the design of repetitive controllers. In this study, we deal with a problem of a robust repetitive controller design for an uncertain feedback control system using its explicit performance information. We first show that a robust stability condition of repetitive control systems has a similar form with the well‐known robust performance condition of general feedback control systems. The repetitive controller is designed using the performance weighting function for the design of the robust feedback controller. It is also shown that a steady‐state tracking error of the repetitive control system is described in a simple form without time‐delay term. This result yields that the repetitive control system has a much larger loop gain in the steady state than the feedback control system. Moreover, this paper provides sufficient conditions ensuring that the power of the steady‐state tracking error in the repetitive control system is less than or equal to that of the feedback control system. Based on the obtained results, we present repetitive controller design method using the design information of the feedback control system. Finally, application studies on the track‐following control system of optical disk drives are performed to show the validity of the proposed method.
Delay‐dependent stability analysis for neural networks with additive time‐varying delay components
Authors: Zhu Xun‐Lin , Yue Dong , Wang Youyi
Published: June 2013

This article studies the problem of stability analysis for neural networks (NNs) with two additive time‐varying delay components. By taking both the independence and the variation of the two delay components into consideration, a more general Lyapunov functional is defined. By estimating the upper bound of the derivative of the Lyapunov functional more tightly, a less conservative delay‐dependent stability criterion is established in terms of linear matrix inequalities. To reduce the computational complexity, a method for eliminating slack variables is provided, and then a simplified stability criterion is obtained. Some numerical examples are given to illustrate the effectiveness of the proposed method and the significant improvement over the existing results.
Applying a direct current bias to superconducting microwave resonators by using superconducting quarter wavelength band stop filters
Authors: Li Shao-Xiong , Kycia J. B.
Published: June 2013

We have designed a superconducting quarter wavelength band stop filter which provides a high attenuation at approximately 7 GHz. Such filters were used as dc bias lines applied to whole wavelength and half wavelength superconducting resonators at two different extremes: voltage node and voltage antinode. The results obtained indicate that this filter can apply dc bias to arbitrary length superconducting coplanar waveguide resonators while maintaining high quality factor, Q∼15 000−18 000.
Object detection and tracking with active camera on motion vectors of feature points and particle filter
Authors: Chen Yong , Zhang Rong-Hua , Shang Lei , Hu Eric
Published: June 2013

A method based on motion vectors of feature points and particle filter has been proposed and developed for an active/moving camera for object detection and tracking purposes. The object is detected by histogram of motion vectors first, and then, on the basis of particle filter algorithm, the weighing factors are obtained via color information. In addition, re-sampling strategy and surf feature points are used to remedy the drawback of particle degeneration. Experimental results demonstrate the practicability and accuracy of the new method and are presented in the paper.
Elucidating the mechanisms of ion conductivity enhancement in polymer nanocomposite electrolytes for lithium ion batteries
Authors: Li Qin , Wood Eric , Ardebili Haleh
Published: June 2013

Solid polymer electrolytes in lithium ion batteries offer significant advantages compared to conventional liquid electrolytes including safety, stability, and thin film manufacturability. The major disadvantage of poor ion conductivity especially at room temperature still presents a challenge. Nanoscale fillers are shown to improve ion conductivity up to 3 orders of magnitude although the specific mechanisms for enhancement are still under debate. In this study, we investigate the mechanisms of lithium ion conductivity enhancement and degradation in polymer nanocomposite electrolytes. Agreement between our model predictions and experiments confirm that our postulated mechanisms can explain the dependence of ion conductivity on nanofillers.
The real role of active-shell in enhancing the luminescence of lanthanides doped nanomaterials
Authors: Wu Fei , Liu Xiaomin , Kong Xianggui , Zhang Youlin , Tu Langping , Liu Kai , Song Shuguang , Zhang Hong
Published: June 2013

Although it is widely recognized that doping sensitizers in the shell can improve significantly the luminescence of lanthanides doped nanocrystals, lack of an unambiguous picture of relevant luminescence enhancement mechanism seriously hinders the optimization of this approach. In this work, the complete processes of excitation energy migration, from photon absorption to emission, was dissected to unravel the role of sensitizers doped in shell in every individual stage. We revealed that the essence of doping sensitizers in the shell is just to increase the absorption efficiency whereas the quantum yield is lessened simultaneously. The optimal sensitizer doping concentration is also fixed to achieve the best luminescence performance.
Relative efficacy of vibrational vs. translational excitation in promoting atom-diatom reactivity: Rigorous examination of Polanyi's rules and proposition of sudden vector projection (SVP) model
Authors: Jiang Bin , Guo Hua
Published: June 2013

To provide a systematic and rigorous re-examination of the well-known Polanyi's rules, excitation functions of several A + BC(v = 0, 1) reactions are determined using the Chebyshev real wave packet method on accurate potential energy surfaces. Reactions with early (F + H2 and F + HCl), late (Cl + H2), and central (H/D/Mu + H2, where Mu is a short-lived light isotope of H) barriers are represented. Although Polanyi's rules are in general consistent with the quantum dynamical results, their predictions are strictly valid only in certain energy ranges divided by a cross-over point. In particular, vibrational excitation of the diatomic reactant typically enhances reactivity more effectively than translational excitation at high energies, while reverse is true at low energies. This feature persists irrespective of the barrier location. A sudden vector projection model is proposed as an alternative to Polanyi's rules. It is found to give similar, but more quantitative, predictions about mode selectivity in these reactions, and has the advantage to be extendible to reactions involving polyatomic molecules.
New Products
Authors: Mandelis Andreas
Published: June 2013

In order to supplement manufacturers' information, this Department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Wall-induced orientational order in athermal semidilute solutions of semiflexible polymers: Monte Carlo simulations of a lattice model
Authors: Ivanov V. A. , Rodionova A. S. , Martemyanova J. A. , Stukan M. R. , Müller M. , Paul W. , Binder K.
Published: June 2013

An athermal solution of semiflexible macromolecules with excluded volume interactions has been studied at various concentrations (dilute, semidilute, and concentrated solutions) in a film of thickness D between two hard walls by grand canonical Monte Carlo simulations of the bond fluctuation lattice model. Analyzing profiles of orientational order parameters across the film, we find that for thick films two phase transitions occur at chemical potentials of the polymers (or polymer densities, respectively) where the bulk polymer solution still is in the disordered isotropic phase. At rather small polymer densities, polymers accumulate at the walls due to an entropic attraction and undergo a transition to two-dimensional nematic order. Due to the properties of the lattice model, this order has Ising character, and the simulation results seem to be compatible with a second-order transition. Increasing the polymer density, nematically ordered “wetting” layers form at both walls; the increase of thickness of these layers is compatible with a logarithmic divergence when the chemical potential of the isotropic–nematic transition in the bulk is approached. In a system of finite width, D, between the walls, this leads to capillary nematization, exhibiting a reduction of the transition chemical potential inversely proportional to D. This transition exists only if D exceeds some critical value Dc, while the transition from the isotropic phase to the two-dimensional nematic state is suggested to persist down to ultrathin films.
Ab initio potential energy surface and vibration-rotation energy levels of lithium monohydroxide
Authors: Koput Jacek
Published: June 2013

The accurate ground-state potential energy surface of lithium monohydroxide (LiOH) has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. Results obtained with the conventional and explicitly correlated coupled-cluster methods were compared. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The vibration-rotation energy levels of the LiOH, LiOD, Li18OH, and 6LiOH isotopologues were predicted to near “spectroscopic” accuracy.
Hierarchy of models: From qualitative to quantitative analysis of circadian rhythms in cyanobacteria
Authors: Chaves M. , Preto M.
Published: June 2013

A hierarchy of models, ranging from high to lower levels of abstraction, is proposed to construct “minimal” but predictive and explanatory models of biological systems. Three hierarchical levels will be considered: Boolean networks, piecewise affine differential (PWA) equations, and a class of continuous, ordinary, differential equations' models derived from the PWA model. This hierarchy provides different levels of approximation of the biological system and, crucially, allows the use of theoretical tools to more exactly analyze and understand the mechanisms of the system. The Kai ABC oscillator, which is at the core of the cyanobacterial circadian rhythm, is analyzed as a case study, showing how several fundamental properties—order of oscillations, synchronization when mixing oscillating samples, structural robustness, and entrainment by external cues—can be obtained from basic mechanisms.
Calcium aluminate silicate Ca2Al2SiO7 single crystal applicable to piezoelectric sensors at high temperature
Authors: Takeda Hiroaki , Hagiwara Manabu , Noguchi Hiroaki , Hoshina Takuya , Takahashi Tomoko , Kodama Nobuhiro , Tsurumi Takaaki
Published: June 2013

Ca2Al2SiO7 (CAS) bulk single crystals were grown by the Czochralski method. Material constants of the crystal were determined over the driving temperature range of a typical combustion pressure sensor. The electrical resistivity at 800 °C was found to be of the order of 108 Ωcm. We constructed a measurement system for the direct piezoelectric effect at high temperature, and characterized the crystals in a simulated engine cylinder combustion environment. Output charge signal against applied stress was detected at 700 °C. These observations suggest that CAS crystals are superior candidate materials for high temperature for stress sensing.
On applications and limitations of one-dimensional capillarity formulations for media with heterogeneous wettability
Authors: Bucher T. M. , Vahedi Tafreshi H.
Published: June 2013

Force-balance-based one-dimensional algebraic formulations that are often used in characterizing the capillarity of a multi-component system (e.g., predicting capillary height rise in porous media) are discussed. It is shown that such formulations fail to provide accurate predictions when the distribution of wetting (or non-wetting) surfaces is not homogeneous. A more general mathematical formulation is suggested and used to demonstrate that for media with heterogeneous wettability, hydrophilic (or hydrophobic) surfaces clustered in groups will have less contribution to the overall capillarity of the system.
High pressure equation of state and ideal compressive and tensile strength of MgO single crystal: Ab-initio calculations
Authors: Mukherjee D. , Joshi K. D. , Gupta Satish C.
Published: June 2013

Ab-initio total energy calculations have been carried out on MgO single crystal as a function of hydrostatic compression to determine the 0 K isotherm, which is then utilized to derive the 300 K isotherm, isentrope, and Hugoniot of MgO. The theoretical isotherm, isentrope, and Hugoniot compare well with the experimental data. The shock parameters C0 and s obtained from theoretical Hugoniot are 6.74 km/s and 1.23 as compared to the experimental values of 6.87 km/s and 1.24, respectively. Having theoretically reproduced the various experimentally measured physical quantities at ambient conditions, the calculations have been extended to determine the ideal compressive and tensile strength of MgO single crystal subjected to uniaxial compressive and tensile loading along [001] direction under two deformation conditions, namely, “uniaxial strain condition” and “uniaxial stress condition.” Examination of elastic stability conditions suggests that for [001] compressive loading, the MgO single crystal will fail mechanically due to shear instability, whereas for expansion it will fail due to vanishing of tensile modulus. The ideal compressive strength under “uniaxial strain condition” and “uniaxial stress condition” is determined to be −283 GPa and −115 GPa, respectively. However, ideal tensile strength is evaluated to be 20 GPa and 11 GPa, respectively, for two loading conditions. Our results suggest that MgO single crystal will offer higher resistance against failure for compression as well as expansion along [001] direction under “uniaxial strain condition” than that for the “uniaxial stress condition.”
Magnetic interaction and conical self-reorganization of aligned tin oxide nanowire array under field emission conditions
Authors: Bazargan Samad , Thomas Joseph P. , Leung K. T.
Published: June 2013

Magnetic interactions are induced between non-magnetic, vertically aligned tin dioxide nanowires under field-emission conditions. Vertically aligned nanowires of tin dioxide are synthesized along the [100] direction by pulsed laser deposition of an epitaxial (200) seed layer on c-cut sapphire substrates followed by vapor-liquid-solid growth using catalyst-assisted pulsed laser deposition method. Due to the dense arrangement of the vertically aligned ultra-long nanowires deposited in this study, magnetic interactions between the nanowires carrying parallel currents become significant within 1 μm radius and lead to their self-reorganization into conical tipi structures under field emission conditions. Optimization of the aerial density of the emission tips and reduction in the field screening effects upon self-reorganization of the nanowire array can account for the large field enhancement factor of 2.6 × 104 at low turn-on field of 3 V/μm.
Contact resistivity reduction through interfacial layer doping in metal-interfacial layer-semiconductor contacts
Authors: Gupta Shashank , Paramahans Manik Prashanth , Kesh Mishra Ravi , Nainani Aneesh , Abraham Mathew C. , Lodha Saurabh
Published: June 2013

Metal-induced-gap-states model for Fermi-level pinning in metal-semiconductor contacts has been extended to metal-interfacial layer (IL)-semiconductor (MIS) contacts using a physics-based approach. Contact resistivity simulations evaluating various ILs on n-Ge indicate the possibility of forming low resistance contacts using TiO2, ZnO, and Sn-doped In2O3 (ITO) layers. Doping of the IL is proposed as an additional knob for lowering MIS contact resistance. This is demonstrated through simulations and experimentally verified with circular-transfer length method and diode measurements on Ti/n+-ZnO/n-Ge and Ti/ITO/n-Ge MIS contacts.
Statistical properties of the electrically induced contact resistance between two stainless steel balls
Authors: Kim Sang-Kuk , Sung Lee Jae , Kwak Han , Kang Sung-Oong , Lee Jongjin , Yu In-Suk
Published: June 2013

The electrical contact resistance between two stainless steel balls was measured to study the electrical conduction of a metallic contact separated by a thin oxide layer. Through a statistical approach, the contact resistance was found to have a bimodal log-normal distribution. This result reflects conduction by tunneling and electrically induced metal bridge, which was explained by the simulation of a random circuit breaker model, inside the insulating layer. Based on the results of this study, we suggest an effective conduction model to explain macroscopic electrical contact systems with a nano- or microscopic filamentary conduction mechanism.
Single-grain Si thin-film transistors on flexible polyimide substrate fabricated from doctor-blade coated liquid-Si
Authors: Zhang J. , Trifunovic M. , van der Zwan M. , Takagishi H. , Kawajiri R. , Shimoda T. , Beenakker C. I. M. , Ishihara R.
Published: June 2013

Solution process of silicon will provide high-speed transistor fabrication with low-cost by, for example, roll-to-roll process. In this paper, a low-temperature process (350 °C) is reported for fabrication of high-quality Si devices on a polyimide substrate from doctor-blade coated liquid-Si. With this method, different semiconductor devices have been fabricated, reporting a carrier mobility of 460 cm2/V s and 121 cm2/V s for electrons and holes, respectively. The devices were peeled off and transferred onto a polyethylene naphthalate foil to achieve flexible devices. CMOS inverters were also fabricated and show full output swing.
Empirical relationship between x-ray photoemission spectra and electrical conductivity in a colossal magnetoresistive manganite La1−xSrxMnO3
Authors: Hishida T. , Ohbayashi K. , Kobata M. , Ikenaga E. , Sugiyama T. , Kobayashi K. , Okawa M. , Saitoh T.
Published: June 2013

By using laboratory x-ray photoemission spectroscopy (XPS) and hard x-ray photoemission spectroscopy (HX-PES) at a synchrotron facility, we report an empirical semi-quantitative relationship between the valence/core-level x-ray photoemission spectral weight and electrical conductivity in La1−xSrxMnO3 as a function of x. In the Mn 2p3∕2 HX-PES spectra, we observed the shoulder structure due to the Mn3+ well-screened state. However, the intensity at x = 0.8 was too small to explain its higher electrical conductivity than x = 0.0, which confirms our recent analysis on the Mn 2p3∕2 XPS spectra. The near-Fermi level XPS spectral weight was found to be a measure of the variation of electrical conductivity with x in spite of a far lower energy resolution compared with the energy scale of the quasiparticle (coherent) peak because of the concurrent change of the coherent and incoherent spectral weight.
Investigation of concurrent energy harvesting from ambient vibrations and wind using a single piezoelectric generator
Authors: Bibo A. , Daqaq M. F.
Published: June 2013

In this letter, a single vibratory energy harvester integrated with an airfoil is proposed to concurrently harness energy from ambient vibrations and wind. In terms of its transduction capabilities and power density, the integrated device is shown to have a superior performance under the combined loading when compared to utilizing two separate devices to harvest energy independently from the two available energy sources. Even below its flutter speed, the proposed device was able to provide 2.5 times the power obtained using two separate harvesters.
Formation of non-equilibrium Fe-Au solid solutions in nanoclusters
Authors: Mukherjee P. , Zhou Lin , Kramer M. J. , Shield J. E.
Published: June 2013

Fe-Au nanoclusters ranging in composition from ∼33 to 79 at. % Fe were prepared by inert gas condensation. Resulting phases were single crystalline solid solutions for all compositions with significant defects present. The as-deposited clusters formed in a bcc structure for Fe content >65 at. % and in a fcc structure for Fe < 65 at. %. Lattice parameters were expanded beyond rule-of-mixture estimates. The lattice expansion is explained by an analytical self-interstitial model. All clusters were ferromagnetic, although the fcc structures showed low magnetization. The low magnetizations are thought to arise from antiferromagnetic cores with uncompensated ferromagnetic surface spins.
Enhancement of bias and illumination stability in thin-film transistors by doping InZnO with wide-band-gap Ta2O5
Authors: Lan Linfeng , Xiong Nana , Xiao Peng , Li Min , Xu Hua , Yao Rihui , Wen Shangsheng , Peng Junbiao
Published: June 2013

Thin-film transistor (TFT) with Ta2O5-doped InZnO (TIZO) channel layer was demonstrated. The TIZO-TFT exhibited smaller subthreshold swing and higher capability of carrier controlling when bearing nitrogen pre-annealing than the InZnO-TFT. Detailed studies showed that Ta had an effect of suppressing oxygen out-diffusing during thermal annealing, resulting in improving of the stability under positive gate bias stress. Furthermore, the TIZO-TFT displayed better stability under light illumination than InZnO-TFT, owing to its wider band gap and lower absorption after doped with wider-band-gap Ta2O5.
A modification to Hardy's thermomechanical theory that conserves fundamental properties more accurately
Authors: Fu Yao , To Albert C.
Published: June 2013

This work proposes a modification to Hardy's atomistic-to-continuum thermomechanical theory, so that it can more accurately conserve mass, momentum, and energy for non-equilibrium thermomechanical processes. The modification proposed is a new normalization rule for the localization function employed in the theory. The improved accuracy of the modified theory is demonstrated based on several molecular dynamics (MD) simulation examples of elastic and shock wave propagation in metals. Through the simulation results, it is also found that Hardy's theory remains valid to a large extent, regardless of the width of the localization function, the interatomic potential, and crystal structure, with and without ensemble averaging. The results from this work will help inject confidence in employing the modified Hardy's theory with the proposed modifications to analyze MD simulation results for non-equilibrium thermomechanical processes and pave the way for concurrent atomistic/continuum coupled simulations.
Spall behavior of rolled aluminum 5083-H116 plate
Authors: Whelchel R. L. , Kennedy G. B. , Dwivedi S. K. , Sanders T. H. , Thadhani N. N.
Published: June 2013

The spall properties of rolled Al 5083-H116 plate are investigated using symmetric plate impact experiments over the stress range 1.5–6.2 GPa. Rear free surface velocity measurements made employing Velocity Interferometer System for Any Reflector interferometry reveal velocity profiles with clear signals of the Hugoniot elastic limit (HEL) and velocity pullback, indicative of a transition from elastic to plastic behavior and spalling. Experiments were performed on samples obtained both through the thickness and along all of the three principal axes of the rolled plate. For impact through the thickness, the average values of the HEL and spall strength are 0.43 GPa and 0.81 GPa, respectively. Decreasing the flyer plate and sample thicknesses resulted in an increased spall strength value of 0.95 GPa, while the HEL remained the same. The spall strength along the longitudinal (rolling) direction was 1.06 GPa versus 0.95 GPa for impact along either transverse direction. Spall damage for this impact direction often propagated away from the spall plane in the direction of impact and along the grain boundaries. For impact through the thickness, the fracture surface revealed a mixed mode of ductile and intergranular fracture that was not present for the fracture surface in the other two directions. This mixed fracture mode seems to correspond to a shoulder observed in the free surface velocity traces after the pullback. In all cases, cracked brittle inclusions were observed near the spall damage regions, indicating their role in nucleating voids during spall failure.
Evolution of phases and ferroelectric properties of thin Hf0.5Zr0.5O2 films according to the thickness and annealing temperature
Authors: Hyuk Park Min , Joon Kim Han , Jin Kim Yu , Lee Woongkyu , Moon Taehwan , Seong Hwang Cheol
Published: June 2013

The effects of annealing temperature (Tanneal) and film thickness (tf) on the crystal structure and ferroelectric properties of Hf0.5Zr0.5O2 films were examined. The Hf0.5Zr0.5O2 films consist of tetragonal, orthorhombic, and monoclinic phases. The orthorhombic phase content, which is responsible for the ferroelectricity in this material, is almost independent of Tanneal, but decreases with increasing tf. In contrast, increasing Tanneal and tf monotonically increases (decreases) the amount of monoclinic (tetragonal) phase, which coincides with the variations in the dielectric constant. The remanant polarization was determined by the content of orthorhombic phase as well as the spatial distribution of other phases.
Observation of optical spin injection into Ge-based structures at room temperature
Authors: Yasutake Yuhsuke , Hayashi Shuhei , Yaguchi Hiroyuki , Fukatsu Susumu
Published: June 2013

Non-zero spin polarization induced by optical orientation was clearly observed at room temperature in a Ge/Ge0.8Si0.2 quantum well grown on Ge and a Ge layer grown on Si by molecular beam epitaxy, whereas it was absent in bulk Ge. This occurred because indirect-gap photoluminescence (PL), which can obscure the spin-polarization information carried by the direct-gap PL, was quenched by unintentional growth-related defects in the epitaxial layers. Such interpretation was confirmed by applying time gating that effectively removed the indirect-gap PL characterized by a slower rise time, which allowed us to demonstrate the existence of room-temperature spin polarization in bulk Ge.
Evidence of percolation related power law behavior in the thermal conductivity of nanotube/polymer composites
Authors: Kim B.-W. , Park S.-H. , Kapadia R. S. , Bandaru P. R.
Published: June 2013

A power law relation for the thermal conductivity, indicative of percolation, is reported through measurements on carbon nanotube/polymer composites. Our results contradict earlier assertions and indicate that synthesis methodologies may be adapted to facilitate such behavior. Consistent modeling of the experimentally determined electrical and thermal conductivity anisotropy, in addition to the incorporation of interfacial resistance, was used to understand the underlying mechanisms and variations.
Interference lithography for metal nanopattern fabrication assisted by surface plasmon polaritons reflecting image
Authors: Wang Jingquan , Liang Huimin
Published: June 2013

An interference lithography technique by surface-polasmon-polaritons reflecting image is suggested for fabricating large-area metal nanopatterns in this paper. This device is designed by an attenuated total reflection mode. Enhanced interference light field is formed in the resist layer coated on any thickness metal film, which will provide a nanomask on the metal film after development. If the chemical or physical etch methods are employed, the nanomask pattern can be transferred into the metal film. Calculated and analyzed results illuminate that the incident angle, the polymer interlayer thickness, and the resist layer thickness can provide large tolerances in fabrication.
Using economic, social and ecological spatial patterns to guide policy development in the Pilbara and Southern Rangelands of Western Australia
Authors: Safstrom Rodney , Waddell Peter-Jon
Published: June 2013

The pastoral industry in the Pilbara and Southern Rangelands of Western Australia continues to face very difficult economic, social and ecological situations due to decline in terms of trade and ongoing decline in range condition. Land administration by State government for the pastoral industry has a strong focus on environmental and ecological sustainability but these goals have largely not been achieved. Regional planning and incentive-based approaches have either failed or only been partly successful at pastoral lease scale. This paper identifies four broad economic, social and ecological landscape patterns ranging from economic, social and ecological sustainability to failure across all three dimensions. Some lessees are adapting to economic decline by obtaining work off station or diversification in the limited locations where these opportunities are available, in some cases facilitating landscape restoration. Market-based incentives may be effective where economic viability is attainable but lease buy-back may be required where leaseholders are locked into a poverty cycle. Carbon-based income is problematic until governance and economic parameters are resolved. Mapping the economic, social and ecological patterns in the landscape is a basis for policy and special purpose initiatives to resolve the current very difficult economic, social and environmental situation in the Pilbara and Southern Rangelands.
Interactive effects of iron oxides and organic matter on charge properties of red soils in Thailand
Authors: Ketrot D. , Suddhiprakarn A. , Kheoruenromne I. , Singh B.
Published: June 2013

Iron (Fe) oxides and organic matter (OM) play important roles in maintaining the fertility of highly weathered soils. The main objective of this study was to investigate the interactive effects of variable surface charge minerals, particularly Fe oxide minerals, and OM on the charge properties of red soils from Thailand. We also evaluated the effect of the 5 m NaOH procedure, used to concentrate Fe oxides from soils, on the charge characteristics of Fe oxide concentrates. Fourteen clay fractions (untreated and OM-free clay fractions), and Fe oxide concentrates of these clays, were used in the study. Cation exchange capacity (CEC) and electrophoretic mobility (EM) were measured for the soil clays, artificial mixtures, and goethite adsorbed with humic acid (HA) and phosphate (P). Kaolinite and Fe oxides (predominantly a mixture of hematite and goethite) were the main minerals in the clay fraction. Results indicated that OM or metal–OM complexes may have blocked or neutralised negatively charged sites on clay minerals. After OM removal these sites became accessible, inducing an increase in CEC and shifting the EM values towards more negative values and the isoelectric point (IEP) towards lower pH for many samples. The CEC values of Fe oxide concentrates prepared by 5 m NaOH treatment were overestimated and their EM and IEP shifted towards more negative values. It is possible that the amorphous phase from clay dissolution was still present in the Fe oxide concentrates, or the adsorption of silicate ions modified the surfaces of Fe oxides concentrates. Humic acid and P adsorbed on Fe oxide surfaces caused the IEP to shift to lower values. In natural soil conditions, a variety of anions can be adsorbed on Fe oxide surfaces, which might lead to higher values of negative charge and lower IEP than observed for pure synthetic minerals.
Optimal sampling of visual information for lightness judgments
Authors: Toscani Matteo , Valsecchi Matteo , Gegenfurtner Karl R.
Published: June 2013

The variable resolution and limited processing capacity of the human visual system requires us to sample the world with eye movements and attentive processes. Here we show that where observers look can strongly modulate their reports of simple surface attributes, such as lightness. When observers matched the color of natural objects they based their judgments on the brightest parts of the objects; at the same time, they tended to fixate points with above-average luminance. When we forced participants to fixate a specific point on the object using a gaze-contingent display setup, the matched lightness was higher when observers fixated bright regions. This finding indicates a causal link between the luminance of the fixated region and the lightness match for the whole object. Simulations with rendered physical lighting show that higher values in an object’s luminance distribution are particularly informative about reflectance. This sampling strategy is an efficient and simple heuristic for the visual system to achieve accurate and invariant judgments of lightness.
Phosphorylation of the Bin, Amphiphysin, and RSV161/167 (BAR) domain of ACAP4 regulates membrane tubulation
Authors: Zhao Xuannv , Wang Dongmei , Liu Xing , Liu Lifang , Song Zhenwei , Zhu Tongge , Adams Gregory , Gao Xinjiao , Tian Ruijun , Huang Yuejia , Chen Runhua , Wang Fengsong , Liu Dong , Yu Xue , Chen Yong , Chen Zhengjun , Teng Maikun , Ding Xia , Yao Xuebiao
Published: June 2013

ArfGAP With Coiled-Coil, Ankyrin Repeat And PH Domains 4 (ACAP4) is an ADP-ribosylation factor 6 (ARF6) GTPase-activating protein essential for EGF-elicited cell migration. However, how ACAP4 regulates membrane dynamics and curvature in response to EGF stimulation is unknown. Here, we show that phosphorylation of the N-terminal region of ACAP4, named the Bin, Amphiphysin, and RSV161/167 (BAR) domain, at Tyr34 is necessary for EGF-elicited membrane remodeling. Domain structure analysis demonstrates that the BAR domain regulates membrane curvature. EGF stimulation of cells causes phosphorylation of ACAP4 at Tyr34, which subsequently promotes ACAP4 homodimer curvature. The phospho-mimicking mutant of ACAP4 demonstrates lipid-binding activity and tubulation in vitro, and ARF6 enrichment at the membrane is associated with ruffles of EGF-stimulated cells. Expression of the phospho-mimicking ACAP4 mutant promotes ARF6-dependent cell migration. Thus, the results present a previously undefined mechanism by which EGF-elicited phosphorylation of the BAR domain controls ACAP4 molecular plasticity and plasma membrane dynamics during cell migration.
Prenylome profiling reveals S-farnesylation is crucial for membrane targeting and antiviral activity of ZAP long-isoform
Authors: Charron Guillaume , Li Melody M. H. , MacDonald Margaret R. , Hang Howard C.
Published: June 2013

S-prenylation is an important lipid modification that targets proteins to membranes for cell signaling and vesicle trafficking in eukaryotes. As S-prenylated proteins are often key effectors for oncogenesis, congenital disorders, and microbial pathogenesis, robust proteomic methods are still needed to biochemically characterize these lipidated proteins in specific cell types and disease states. Here, we report that bioorthogonal proteomics of macrophages with an improved alkyne-isoprenoid chemical reporter enables large-scale profiling of prenylated proteins, as well as the discovery of unannotated lipidated proteins such as isoform-specific S-farnesylation of zinc-finger antiviral protein (ZAP). Notably, S-farnesylation was crucial for targeting the long-isoform of ZAP (ZAPL/PARP-13.1/zc3hav1) to endolysosomes and enhancing the antiviral activity of this immune effector. These studies demonstrate the utility of isoprenoid chemical reporters for proteomic analysis of prenylated proteins and reveal a role for protein prenylation in host defense against viral infections.
Revisiting the biosynthesis of dehydrophos reveals a tRNA-dependent pathway
Authors: Bougioukou Despina J. , Mukherjee Subha , van der Donk Wilfred A.
Published: June 2013

Bioactive natural products containing a C-P bond act as mimics of phosphate esters and carboxylic acids, thereby competing with these compounds for active sites of enzymes. Dehydrophos (DHP), a broad-spectrum antibiotic, is a phosphonotripeptide produced by
Streptomyces luridus
, in which glycine and leucine are linked to an aminophosphonate analog of dehydroalanine, ΔAla(P). This unique feature, in combination with the monomethylation of the phosphonic acid, renders DHP a Trojan horse type antibiotic because peptidase-mediated hydrolysis will release methyl acetylphosphonate, a potent inhibitor of pyruvate dehydrogenase. Bioinformatic analysis of the biosynthetic gene cluster suggested that ΔAla(P) would be generated from Ser(P), the phosphonate analog of Ser, by phosphorylation and subsequent elimination, and that ΔAla(P) would be condensed with Leu-tRNA
Leu
. DhpH was anticipated to carry out this elimination/ligation cascade. DhpH is a multidomain protein, in which a pyridoxal phosphate binding domain is fused to an
N
-acetyltransferase domain related to the general control nonderepressible-5 (GCN5) family. In this work, the activity of DhpH was reconstituted in vitro. The enzyme was able to catalyze the β-elimination reaction of pSer(P) to generate ΔAla(P), but it was unable to condense ΔAla(P) with Leu. Instead, ΔAla(P) is hydrolyzed to acetyl phosphonate, which is converted to Ala(P) by a second pyridoxal phosphate-dependent enzyme, DhpD. Ala(P) is the substrate for the condensation with Leu-tRNA
Leu
catalyzed by the C-terminal domain of DhpH. DhpJ, a 2-oxoglutarate/Fe(II)-dependent enzyme, introduces the vinyl functionality into Leu-Ala(P) acting as a desaturase, and addition of Gly by DhpK in a Gly-tRNA
Gly
-dependent manner completes the in vitro biosynthesis of dehydrophos.
The antibiotic planosporicin coordinates its own production in the actinomycete
Planomonospora alba
Authors: Sherwood Emma J. , Bibb Mervyn J.
Published: June 2013

Significance

A mechanism for regulating production of the antibiotic planosporicin by
Planomonospora alba
is described. A low level of planosporicin biosynthesis, probably stimulated by nutrient limitation, functions in a feed-forward mechanism to release a key regulatory protein required for high level production. Planosporicin also functions as an extracellular signaling molecule to induce its own synchronous production, presumably ensuring ecologically effective levels of the antibiotic by coordinating biosynthesis in the multicellular colony, regions of which have reached different levels of maturity. This information was used to increase the level of planosporicin production, with important implications for strain improvement.
Fractalkine mediates inflammatory pain through activation of satellite glial cells
Authors: Souza Guilherme R. , Talbot Jhimmy , Lotufo Celina M. , Cunha Fernando Q. , Cunha Thiago M. , Ferreira Sérgio H.
Published: June 2013

The activation of the satellite glial cells (SGCs) surrounding the dorsal root ganglion (DRG) neurons appears to play a role in pathological pain. We tested the hypothesis that fractalkine, which is constitutively expressed by primary nociceptive neurons, is the link between peripheral inflammation and the activation of SGCs and is thus responsible for the genesis of the inflammatory pain. The injection of carrageenin into the rat hind paw induced a decrease in the mechanical nociceptive threshold (hypernociception), which was associated with an increase in mRNA and GFAP protein expression in the DRG. Both events were inhibited by anti-fractalkine antibody administered directly into the DRG (L5) [intraganglionar (i.gl.)]. The administration of fractalkine into the DRG (L5) produced mechanical hypernociception in a dose-, time-, and CX3C receptor-1 (CX3CR1)–dependent manner. Fractalkine’s hypernociceptive effect appears to be indirect, as it was reduced by local treatment with anti–TNF-α antibody, IL-1–receptor antagonist, or indomethacin. Accordingly, the in vitro incubation of isolated and cultured SGC with fractalkine induced the production/release of TNF-α, IL-1β, and prostaglandin E2. Finally, treatment with i.gl. fluorocitrate blocked fractalkine (i.gl.)- and carrageenin (paw)-induced hypernociception. Overall, these results suggest that, during peripheral inflammation, fractalkine is released in the DRG and contributes to the genesis of inflammatory hypernociception. Fractalkine’s effect appears to be dependent on the activation of the SGCs, leading to the production of TNFα, IL-1β, and prostanoids, which are likely responsible for the maintenance of inflammatory pain. Thus, these results indicate that the inhibition of fractalkine/CX3CR1 signaling in SGCs may serve as a target to control inflammatory pain.
Neuronal correlates of a visual “sense of number” in primate parietal and prefrontal cortices
Authors: Viswanathan Pooja , Nieder Andreas
Published: June 2013

“Sense of number” refers to the classical idea that we perceive the number of items (numerosity) intuitively. However, whether the brain signals numerosity spontaneously, in the absence of learning, remains unknown; therefore, we recorded from neurons in the ventral intraparietal sulcus and the dorsolateral prefrontal cortex of numerically naive monkeys. Neurons in both brain areas responded maximally to a given number of items, showing tuning to a preferred numerosity. Numerosity was encoded earlier in area ventral intraparietal area, suggesting that numerical information is conveyed from the parietal to the frontal lobe. Visual numerosity is thus spontaneously represented as a perceptual category in a dedicated parietofrontal network. This network may form the biological foundation of a spontaneous number sense, allowing primates to intuitively estimate the number of visual items.