bluuebunny/crossref_metadata_2025 huggingface dataset:
QSAR and Docking Studies of Gallic Acid Derivatives for Anticancer and Immunomodulatory Activity
Authors: Yadav Dharmendra Kumar , Khan Feroz , Negi Arvind Singh
Published: November 2011

Immuno-modulation is the process of alteration in immune response due to foreign intrusion of molecules inside the body. In the present communication QSAR and molecular docking studies for immuno-modulatory activity of derivatives of gallic acid were performed. Molecular docking studies showed higher binding affinity with INFα-2, IL-6, and IL-4 receptors. Binding site residues indicate hydrogen bonds formation with gallic acid derivative compounds G-3, G-4, G-5, G-6, G-7 and G-10. Further screening through quantitative structure activity relationship model establishes the immuno-modulatory activity of the compounds G-4, G-7, G-9, G-10, G-12 and G-13. Activity was predicted through a robust statistical model, developed by forward feed multiple linear regression method with leave-one-out approach. Relationship correlating measure (r2) and prediction accuracy (rCV2) of QSAR model were 0.99 and 0.96, respectively. QSAR studies indicate that dipole moment, steric energy, amide group count, λ max (UV-visible) and molar refractivity correlate well with their activities, while decrease in dipole moment, steric energy and molar refractivity have negative correlation. Moreover, on the basis of bioavailability, in-silico ADME and toxicity risk assessment screening, we concluded that compounds G-4, G-7, G-9, G-10, G-12 and G-13 have marked immuno-modulatory activity comparable to standard drugs.
The effect of chemical residues on the physical and electrical properties of chemical vapor deposited graphene transferred to SiO2
Authors: Pirkle A. , Chan J. , Venugopal A. , Hinojos D. , Magnuson C. W. , McDonnell S. , Colombo L. , Vogel E. M. , Ruoff R. S. , Wallace R. M.
Published: November 2011

The effects of residues introduced during the transfer of chemical vapor deposited graphene from a Cu substrate to an insulating (SiO2) substrate on the physical and electrical of the transferred graphene are studied. X-ray photoelectron spectroscopy and atomic force microscopy show that this residue can be substantially reduced by annealing in vacuum. The impact of the removal of poly(methyl methacrylate) residue on the electrical properties of graphene field effect devices is demonstrated, including a nearly 2 × increase in average mobility from 1400 to 2700 cm2/Vs. The electrical results are compared with graphene doping measurements by Raman spectroscopy.
Nanoparticles in SiH4-Ar plasma: Modelling and comparison with experimental data
Authors: Gordiets B. F. , Inestrosa-Izurieta M. J. , Navarro A. , Bertran E.
Published: November 2011

Experimental and theoretical investigations for growth of silicon nanoparticles (4 to 14 nm) in radio frequency discharge were carried out. Growth processes were performed with gas mixtures of SiH4 and Ar in a plasma chemical reactor at low pressure. A distinctive feature of presented kinetic model of generation and growth of nanoparticles (compared to our earlier model) is its ability to investigate small “critical” dimensions of clusters, determining the rate of particle production and taking into account the influence of SiH2 and Si2Hm dimer radicals. The experiments in the present study were extended to high pressure (≥20 Pa) and discharge power (≥40 W). Model calculations were compared to experimental measurements, investigating the dimension of silicon nanoparticles as a function of time, discharge power, gas mixture, total pressure, and gas flow.
Fabrication, charge carrier transport, and application of printable nanocomposites based on indium tin oxide nanoparticles and conducting polymer 3,4-ethylenedioxythiophene/polystyrene sulfonic acid
Authors: Maksimenko Ilja , Kilian Daniel , Mehringer Christian , Voigt Michael , Peukert Wolfgang , Wellmann Peter J.
Published: November 2011

Printable transparent hybrid composites consisting of indium tin oxide (In2O3:Sn; ITO) nanoparticles and conducting polymer 3,4-polyethylenedioxythiophene (PEDOT) as matrix material were developed. The basic idea is to fill up the pores of the highly porous nanoparticulate ITO network to improve the interparticle contact and hence the conductivity of printed ITO thin films. Ready-to-use and stable aqueous dispersions were fabricated starting from ITO nanoparticles and aqueous formulation of conducting PEDOT and polystyrene sulfonic acid (PSS). This report presents and discusses key factors to obtain stable ITO-PEDOT dispersions with different mixing ratios and their application for printable devices as transparent electrode material. It was found that the ζ-potential value is crucial for preparation of stable dispersions. Electrical and optical properties of the hybrid ITO-PEDOT coatings were analyzed. Temperature dependent resistivity measurements reveal that conduction occurs by fluctuation induced tunneling. Transparent and conducting nanocomposite layers with a conductivity as high as 132 Ω−1cm−1 were fabricated by a low-temperature (T = 130 °C) and entirely vacuum-free process. An all-printed electroluminescent lamp on a flexible substrate was realized as a demonstrator showing the applicability of such coatings for voltage-driven optoelectronic devices.
Evaluation of magnetic terms in Cu4O4 cubane-like systems from selected configuration interaction calculations: A case study of polynuclear transition-metal systems
Authors: Calzado Carmen J. , Maynau Daniel
Published: November 2011

We present the evaluation of magnetic terms in a Cu4O4 cubane-like system from truncated CI calculations, as a case study of polynuclear transition-metal complexes. We employ a new excitation selected configuration interaction (EXSCI) method based on the use of local orbitals. Taking advantage of the locality and then of the fact that the interactions vanish when the distance is large, the dimension of the CI is largely reduced. To the best of our knowledge these CI calculations are the largest one performed for polynuclear transition metal systems so far. The results show the presence of two leading ferromagnetic interactions between bridged Cu ions. Also the interactions between the unbridged Cu ions are ferromagnetic, but very weak, in contrast to the experimental data. The nature and amplitude of all the computed interactions are consistent with the relative orientation of the magnetic orbitals in the molecule, and correctly reproduce the susceptibility versus temperature curve. Our results indicate that it is possible to obtain similar fittings with sets of parameters representing different physical effects and put in evidence the drawbacks of the fitting based on oversimplified magnetic models. In this context, the presented computational strategy can be considered as a useful tool to help in the interpretation of the magnetic data and the validation of the magnetic interaction model in the polynuclear magnetic systems.
Potential-functional embedding theory for molecules and materials
Authors: Huang Chen , Carter Emily A.
Published: November 2011

We introduce a potential-functional embedding theory by reformulating a recently proposed density-based embedding theory in terms of functionals of the embedding potential. This potential-functional based theory completes the dual problem in the context of embedding theory for which density-functional embedding theory has existed for two decades. With this potential-functional formalism, it is straightforward to solve for the unique embedding potential shared by all subsystems. We consider charge transfer between subsystems and discuss how to treat fractional numbers of electrons in subsystems. We show that one is able to employ different energy functionals for different subsystems in order to treat different regions with theories of different levels of accuracy, if desired. The embedding potential is solved for by directly minimizing the total energy functional, and we discuss how to efficiently calculate the gradient of the total energy functional with respect to the embedding potential. Forces are also derived, thereby making it possible to optimize structures and account for nuclear dynamics. We also extend the theory to spin-polarized cases. Numerical examples of the theory are given for some homo- and hetero-nuclear diatomic molecules and a more complicated test of a six-hydrogen-atom chain. We also test our theory in a periodic bulk environment with calculations of basic properties of bulk NaCl, by treating each atom as a subsystem. Finally, we demonstrate the theory for water adsorption on the MgO(001)surface.
Secondary breakup of coal water slurry drops
Authors: Zhao Hui , Liu Hai-Feng , Xu Jian-Liang , Li Wei-Feng
Published: November 2011

To investigate secondary atomization of coal water slurry (CWS), deformation and breakup of eight kinds of CWS drops are presented using high speed digital camera. Based on morphology, deformation and breakup regimes of CWS drops can be termed some different modes: deformation, multimode breakup (including two sub-modes: hole breakup and tensile breakup), and shear breakup. Correlations on the ranges of breakup modes are also obtained. The conventional Weber number and Ohnesorge number are found to be insufficient to classify all breakup modes of CWS drops, so two other non-dimensional numbers based on rheology of CWS are suggested to use in the deformation and breakup regime map. Finally, total breakup time is studied and correlated, which increases with Ohnesorge number.
Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins
Authors: Zuev Dmitry , Bravaya Ksenia B. , Makarova Maria V. , Krylov Anna I.
Published: November 2011

Electronic structure calculations of microhydrated model chromophores (in their deprotonated anionic forms) of the photoactive yellow and green fluorescent proteins (PYP and GFP) are reported. Electron-detachment and excitation energies as well as binding energies of mono- and dihydrated isomers are computed and analyzed. Microhydration has different effects on the excited and ionized states. In lower-energy planar isomers, the interaction with one water molecule blueshifts the excitation energies by 0.1–0.2 eV, whereas the detachment energies increase by 0.4–0.8 eV. The important consequence is that microhydration by just one water molecule converts the resonance (autoionizing) excited states of the bare chromophores into bound states. In the lower-energy microhydrated clusters, interactions with water have negligible effect on the chromophore geometry; however, we also identified higher-energy dihydrated clusters of PYP in which two water molecules form hydrogen-bonding network connecting the carboxylate and phenolate moieties and the chromophore is strongly distorted resulting in a significant shift of excitation energies (up to 0.6 eV).
Insights into mechanistic photodissociation of chloroacetone from a combination of electronic structure calculation and molecular dynamics simulation
Authors: Shen Lin , Liu Lihong , Cao Jun , Fang Wei-Hai
Published: November 2011

The stationary and intersection structures on the S0 and S1 potential energy surfaces of CH3COCH2Cl have been determined by the CAS(10,8)/cc-pVDZ optimizations and their relative energies are refined by the CASPT2//CAS(10,8)/cc-pVDZ single-point calculations. Non-adiabatic molecular dynamics simulations were performed on the basis of the state-averaged CAS(10,8)/cc-pVDZ calculated energies, energy gradients, and Hessian matrix for the S0 and S1 states. It is found that the features of the S1 potential energy surface and non-adiabatic effect control the selectivity of the two α-C–C bond fissions, which provides a reasonable explanation why one α-C–C bond was observed as a primary channel and the other is ruled out even if CH3COCH2Cl is excited at 193 nm. The β-C–Cl fission is determined to be a dominant channel once the CH3COCH2Cl molecule is excited to the S1 state and the β-C–Cl:α-C–C branching ratio is estimated by the RRKM rate theory to be 15:1 at 193 nm, which is overestimated in comparison with the value of ∼11:1 inferred experimentally. The present calculation reveals that the α-C–C fission might take place in the ground electronic state as a result of the S1 → S0 internal conversion upon photolysis at 308 nm. However, the measured kinetic energy distributions of the α-C–C fission products suggest that the fission does not involve internal conversion to the ground state. To solve this issue, we need to perform non-adiabatic quantum dynamics simulation on accurate S0, S1, and S2 potential energy surfaces, which is still a challenging task currently.
Femto-second electron transit time characterization in GaN/AlGaN quantum cascade detector at 1.5 micron
Authors: Vardi A. , Sakr S. , Mangeney J. , Kandaswamy P. K. , Monroy E. , Tchernycheva M. , Schacham S. E. , Julien F. H. , Bahir G.
Published: November 2011

The ultra fast carrier dynamic in GaN/AlGaN quantum cascade detector was investigated using a time-resolved bias-lead monitoring technique. It is demonstrated that the intrinsic speed limitation, governed by the carrier transit time, is smaller than 1 ps, corresponding to a frequency cut off above 200 GHz.
Large magnetoelectric coupling coefficient in poly(vinylidene fluoride-hexafluoropropylene)/Metglas laminates
Authors: Lu S. G. , Jin J. Z. , Zhou X. , Fang Z. , Wang Q. , Zhang Q. M.
Published: November 2011

Poly(vinylidene fluoride-hexafluoropropylene) [P(VDF-HFP)] 90/10 wt% copolymers were fabricated by extrusion-blown and hot press-quench methods. The electric field induced phase transition was observed starting from 79 MV/m, and completing at 216 MV/m, in these copolymers. The transition was manifested by a change from a double hysteresis loop to a single hysteresis loop and supported by the x-ray diffraction measurement. Linear relationships between the magnetoelectric coupling coefficient and the in situ poling electric field, the remanent polarization and the field, were observed at electric fields less than 300 MV/m. A magnetoelectric coupling coefficient as large as 12 V/cm·Oe was obtained.
Effect of electron shallow trap on breakdown performance of transformer oil-based nanofluids
Authors: Du Yuefan , Lv Yuzhen , Li Chengrong , Chen Mutian , Zhou Jianquan , Li Xiaoxin , Zhou You , Tu Youping
Published: November 2011

Transformer oil-based nanofluids with TiO2 semiconductive nanoparticles exhibit substantially higher AC and positive impulse breakdown voltage levels than that of pure transformer oils. Thermally stimulated current method (TSC) and pulse electroacoustic technique (PEA) have been used to measure charge trap and transportation characteristics of pure oils and nanofluids. It is found that electron shallow trap density and charge decay rate are greatly increased in nanofluids, i.e., fast electrons may be converted to slow electrons by electron trapping and de-trapping in shallow traps of nanofluids, resulting in improved breakdown performance compared to that of pure oil.
Effect of the capping on the local Mn oxidation state in buried (001) and (110) SrTiO3/La2/3Ca1/3MnO3 interfaces
Authors: Estradé S. , Rebled J. M. , Walls M. G. , de la Peña F. , Colliex C. , Córdoba R. , Infante I. C. , Herranz G. , Sánchez F. , Fontcuberta J. , Peiró F.
Published: November 2011

The electronic stability of (001) and (110) surfaces of La2/3Ca1/3MnO3 (LCMO) capped with nanometric SrTiO3 (STO) layers in epitaxial heterostructures is addressed by (S)TEM electron energy loss spectroscopy. It is found that growth of STO on (001)LCMO promotes a significant electron doping of LCMO that extends a few nanometers deep into the film. In contrast, (110)LCMO appears to be electronically more robust and no electronic reordering has been observed. These results are in clear correlation with the distinct magnetic properties observed in those interfaces and illustrate that complex chemical phenomena take place at interfaces among multivalent oxides.
Atomic scale electron vortices for nanoresearch
Authors: Verbeeck J. , Schattschneider P. , Lazar S. , Stöger-Pollach M. , Löffler S. , Steiger-Thirsfeld A. , Van Tendeloo G.
Published: November 2011

Electron vortex beams were only recently discovered and their potential as a probe for magnetism in materials was shown. Here we demonstrate a method to produce electron vortex beams with a diameter of less than 1.2 Å. This unique way to prepare free electrons to a state resembling atomic orbitals is fascinating from a fundamental physics point of view and opens the road for magnetic mapping with atomic resolution in an electron microscope.
Al-doped ZnO nanocrystals: Electronic states through scanning tunneling spectroscopy
Authors: Ghosh Batu , Pal Amlan J.
Published: November 2011

We form a monolayer of undoped and Al-doped ZnO nanocrystals and measure tunneling current with a scanning tunneling microscope tip. From the density of states, we determine the location of conduction and valence band edges with respect to the Fermi energy. We show that with n-doping, Fermi energy of ZnO nanoparticles shifts toward the conduction band edge. The difference between the electronic states, that is, the bandgap of the nanocrystals does not change upon doping. This is in agreement with the optical absorption spectra of the nanomaterials. We also find that inhomogeneity of doping in nanoparticles is reflected in density of states. With an increase in doping concentration, the distribution of dopants among particles becomes broader. We characterize the monolayers also with Hg electrodes to comment on electrical conductivity versus doping concentration behavior.
Laser-induced charging of microfabricated ion traps
Authors: Wang Shannon X. , Hao Low Guang , Lachenmyer Nathan S. , Ge Yufei , Herskind Peter F. , Chuang Isaac L.
Published: November 2011

Electrical charging of metal surfaces due to photoelectric generation of carriers is of concern in trapped ion quantum computation systems, due to the high sensitivity of the ions’ motional quantum states to deformation of the trapping potential. The charging induced by typical laser frequencies involved in Doppler cooling and quantum control is studied here, with microfabricated surface-electrode traps made of aluminum, copper, and gold, operated at 6 K with a single Sr+ ion trapped 100 μm above the trap surface. The lasers used are at 370, 405, 460, and 674 nm, and the typical photon flux at the trap is 1014 photons/cm2/sec. Charging is detected by monitoring the ion’s micromotion signal, which is related to the number of charges created on the trap. A wavelength and material dependence of the charging behavior is observed: Lasers at lower wavelengths cause more charging, and aluminum exhibits more charging than copper or gold. We describe the charging dynamic based on a rate-equation approach.
A method to measure fracture toughness using indentation in REBa2Cu3O7-δ superconductor single crystals
Authors: Mikowski Alexandre , Carlos Serbena Francisco , Eugênio Foerster Carlos , Roberto Jurelo Alcione , Maurício Lepienski Carlos
Published: November 2011

A method is proposed to estimate indentation fracture toughness based on the critical load for crack nucleation calculated by the derivative of the loading curve. This method is applied to REBa2Cu3O7-δ superconductor single crystals based on xenotime, where is difficult to observe well defined radial crack lengths due to its lamellar structure. The indentation fracture toughness agrees well with that obtained from the traditional method based on radial crack propagation. The proposed procedure is an alternative technique to estimate indentation fracture toughness without the necessity of measuring radial cracks lengths while keeping the advantages of the traditional method.
Indium as an efficient ohmic contact to N-face n-GaN of GaN-based vertical light-emitting diodes
Authors: Young Moon Seon , Ho Son Jun , Jin Choi Kyung , Lee Jong-Lam , Jang Ho Won
Published: November 2011

We propose indium (In), a low work function and nitride-forming element, as an efficient ohmic contact layer to N-face n-GaN. While conventional Al-based ohmic contacts show severe degradation after annealing at 300 °C, In-based ohmic contacts display considerable improvement in contact resistivity. The annealing-induced enhancement of ohmic behavior in In-based contacts is attributed to the formation of an InN interfacial layer, which is supported by x-ray photoemission spectroscopy measurements. These results suggest that In is of particular importance for application as reliable ohmic contacts to n-GaN of GaN-based vertical light-emitting diodes.
35.4 T field generated using a layer-wound superconducting coil made of (RE)Ba2Cu3O7−x (RE = rare earth) coated conductor
Authors: Trociewitz Ulf P. , Dalban-Canassy Matthieu , Hannion Muriel , Hilton David K. , Jaroszynski Jan , Noyes Patrick , Viouchkov Youri , Weijers Hubertus W. , Larbalestier David C.
Published: November 2011

To explore the limits of layer wound (RE)Ba2Cu3O7−x (REBCO, RE = rare earth) coils in a high magnetic field environment >30 T, a series of small insert coils have been built and characterized in background fields. One of the coils repeatedly reached 35.4 T using a single ∼100 m length of REBCO tape wet wound with epoxy and nested in a 31 T background magnet. The coil was quenched safely several times without degradation. Contributing to the success of this coil was the introduction of a thin polyester film that surrounded the conductor. This approach introduces a weak circumferential plane in the coil pack that prevents conductor delamination that has caused degradation of several epoxy impregnated coils previously made by this and other groups.
A novel compensation method of insertion losses for wavelet inverse-transform processors using surface acoustic wave devices
Authors: Lu Wenke , Zhu Changchun
Published: November 2011

The objective of this research was to investigate the possibility of compensating for the insertion losses of the wavelet inverse-transform processors using SAW devices. The motivation for this work was prompted by the processors which are of large insertion losses. In this paper, the insertion losses are the key problem of the wavelet inverse-transform processors using SAW devices. A novel compensation method of the insertion losses is achieved in this study. When the output ends of the wavelet inverse-transform processors are respectively connected to the amplifiers, their insertion losses can be compensated for. The bandwidths of the amplifiers and their adjustment method are also given in this paper.
Effect of dietary consumption of sheep meat on thyroid hormone levels and energy expenditure of Sprague - Dawley rats
Authors: Feng Xian-Chao , Zhuang Su , Chen Lin , Yan Zheng-Guo , Xu Xing-Lian , Zhou Guang-Hong
Published: November 2011

The purpose of the present study was to investigate the effects of a sheep meat-based diet on the thyroid hormone concentrations and energy expenditure of Sprague–Dawley rats. The diets, a sheep meat diet (SMD) or a casein control diet (CD), each based on a standard formulation (AIN-93G), contained 18.3% protein, 7.4% fat and 60.0% carbohydrate, and were isocaloric (15.9kJ/g dry matter). Serum tri-iodothryonine (T3), thyroxine (T4), free tri-iodothyronine (FT3) and free thyroxine (FT4) concentrations, oxygen consumption rate (OCR), bodyweight, bodyweight gain and activities of liver sodium–potassium-adenosinetriphosphatase (Na,K-ATPase) and Ca2+-dependent adenosine triphosphatase (Ca-ATPase) were measured. Compared with the CD, the SMD increased the serum FT3 concentration on Day 7 (P = 0.004) and Day 14 (P < 0.001). Serum albumin concentrations, which may influence the amount of thyroid hormones bound, were significantly lower in the SMD group on Day 7 (P < 0.001) and Day 14 (P = 0.02) than those in the CD group. Both liver Na,K-ATPase and Ca-ATPase activities were significantly higher in rats consuming the SMD on Day 7 (P < 0.001, P = 0.001) and Day 14 (P < 0.001, P < 0.001) respectively. OCRs were significantly higher in rats consuming the SMD on Day 6 (P = 0.023) and Day 13 (P = 0.014). Both bodyweight and bodyweight gains were significantly lower in the SMD group. We concluded that sheep meat consumption decreased the serum albumin concentrations, which increased the serum FT3 concentrations. This lead to FT3 promoting the OCRs and the activities of Na,K-ATPase and Ca-ATPase, resulting in reduced bodyweight and bodyweight gain, presumably through greater energy expenditure. Thus, energy expenditure appears to have been enhanced in rats fed the SMD.
Fluctuations in the concentration of ergovaline and lolitrem B produced by the wild-type endophyte (Neotyphodium lolii) in perennial ryegrass (Lolium perenne) pasture
Authors: Reed K. F. M. , Nie Z. N. , Walker L. V. , Kearney G.
Published: November 2011

Mammalian toxins produced by the wild-type endophyte, Neotyphodium lolii, in perennial ryegrass (PRG) pasture cause production losses and animal health and welfare problems in livestock. Managing this risk is limited by the lack of information on fluctuations in the concentration of toxin in Australian pasture. We investigated how the toxin concentrations may be related to recent observations of weather. Swards sown from common seedlots of two cultivars of wild endophyte-infected PRG, grazed short by sheep, were sampled at 2–4 weekly intervals from spring to autumn at two sites in Victoria. The highest concentration of ergovaline and lolitrem B was observed at Hamilton, the site with the longer-growing season. The concentration of ergovaline peaked in early summer, coinciding with seed development, and declined through summer, before increasing with the commencement of autumn growth. The concentration of lolitrem B remained low in summer, then rose in autumn. Variation between the two cultivars in the concentration of toxins was small and rarely significant. The concentration of ergovaline declined as the mean daily maximum temperature over the preceding 1–5 days increased. Similarly, for lolitrem B, the concentration declined over the temperature range 12−20°C, from 1.3 to 0.3 mg/kg. At Hamilton, where solar radiation and soil temperature were recorded, both were superior to maximum temperature for predicting lolitrem B. Serial sampling of PRG from old naturalised pasture on seven farms across south-eastern Australia found two seasonal peaks for both alkaloids in most pastures. The concentration of ergovaline reached or exceeded tolerance levels for livestock in 23 of 43 samples, compared with 5 of 43 for lolitrem B. Ergovaline concentrations initially peaked (at 1.0–1.6 mg/kg) when mature reproductive material was present (coinciding with peduncle elongation and seed development). In pastures with low grazing pressure, i.e. where growth was allowed to continue through summer, ergovaline concentration was relatively low (<0.7 mg/kg) but in a hard-grazed pasture (sward height 3 cm), the ergovaline concentration was greater (up to 1.1 mg/kg). Concentration of lolitrem B also peaked in December, except on pasture where growth continued through summer. High concentrations of lolitrem B associated with neurotoxic signs in sheep (viz. 2.4–3.9 mg/kg) were observed only in mid-summer and autumn, and only if conditions favoured growth or where close grazing by sheep left the crown as the dominant source of herbage.
Source apportionment of PM2.5 at two receptor sites in Brisbane, Australia
Authors: Friend Adrian J. , Ayoko Godwin A. , Stelcer Eduard , Cohen David
Published: November 2011

Environmental contextFine particles affect air quality locally, regionally and globally. Determining the sources of fine particle is therefore critical for developing strategies to reduce their adverse effects. Advanced data analysis techniques were used to determine the sources of fine particles at two sites, providing information for future pollution reduction strategies not only at the study sites but in other areas of the world as well.
AbstractIn this study, samples of particulate matter with aerodynamic diameter less than 2.5 µm (PM2.5) collected at two sites in the south-east Queensland region, a suburban (Rocklea) and a roadside site (South Brisbane), were analysed for H, Na, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Pb and black carbon (BC). Samples were collected during 2007–10 at the Rocklea site and 2009–10 at the South Brisbane site. The receptor model Positive Matrix Factorisation was used to analyse the samples. The sources identified included secondary sulfate, motor vehicles, soil, sea salt and biomass burning. Conditional probability function analysis was used to determine the most likely directions of the sources. Future air quality control strategies may focus on the particular sources identified in the analysis.
Salinity drives host reaction in Phaseolus vulgaris (common bean) to Macrophomina phaseolina
Authors: You Ming Pei , Colmer Timothy D. , Barbetti Martin J.
Published: November 2011

Productivity of Phaseolus vulgaris L. (common bean) is often limited by diseases such as seedling blight and root and stem rot caused by the fungus Macrophomina phaseolina and by abiotic stresses such as salinity. This paper reports controlled environment studies examining the interaction of biotic (M. phaseolina) and abiotic (NaCl) stresses. Studies were conducted at 32°C. On potato dextrose agar, the growth of two isolates of M. phaseolina (M1, M2) was differentially stimulated by 40 mM NaCl with 1 mM CaSO4. M. phaseolina was applied as either soil-borne inoculum or directly injected into P. vulgaris hypocotyls. For direct hypocotyl inoculation experiments, there was no difference in disease severity resulting from the two isolates. However, when soil inoculation was undertaken, isolate M2 caused more disease than M1. Addition of 40 mM NaCl to the soil increased disease development and severity (evident 4 days after inoculation), particularly as demonstrated in the hypocotyl inoculation tests, suggesting that salinity stress predisposes plants to infection by this pathogen. Plants infested by M. phaseolina showed increased tissue concentrations of Na+ and Cl– but decreased K+ concentration. Hypocotyls generally contained higher Na+ concentrations than shoots. Inoculated plants had higher Na+ and lower K+ concentrations than uninoculated plants. Our studies indicate that M. phaseolina will be a more severe disease threat where P. vulgaris is cultivated in areas affected by soil salinity.
Temporal candidate gene expression in the sow placenta and embryo during early gestation and effect of maternal Progenos supplementation on embryonic and placental development
Authors: Novak S. , Paradis F. , Patterson J. L. , Pasternak J. A. , Oxtoby K. , Moore H. S. , Hahn M. , Dyck M. K. , Dixon W. T. , Foxcroft G. R.
Published: November 2011

The present study characterised gene expression associated with embryonic muscle development and placental vascularisation during early gestation in the pig and examined effects of Progenos supplementation in early pregnancy. Tissues were collected from commercial multiparous sows (n = 48) from Days 16 to 49 of gestation. In the placenta, qPCR revealed that vascular endothelial growth factor (VEGFA) expression did not change from Day 17 to 49 of gestation; however, KDR receptor and angiopoietin-1 and -2 expression were differentially regulated, with periods of high expression corresponding to two critical phases of angiogenesis in the pig. In the embryo, the pattern of myogenesis-related gene expression was consistent with available literature. A commercially available nutritional supplement Progenos (20 g day–1 l-arginine) added to the diet of sows from either Day 15 to 29 (P15–29; n = 33), Day 30 to 44 (n = 29) or from Day 15 to 44 (n = 76) of gestation tended to increase (P = 0.058) embryonic growth rate compared with non-supplemented controls (n = 79) and angiogenin expression was higher (P = 0.028) at Day 30 of gestation in placentae from sows on the P15–29 Progenos treatment. These results are consistent with proposed beneficial effects of l-arginine on early embryonic development and placental vascularisation.
Helping with All Your Heart: The Effect of Cardioids Cue on Compliance to a Request for Humanitarian Aid
Authors: Guéguen Nicolas , Jacob Céline , Charles-Sire Virginie
Published: November 2011

Some studies have shown that figurative cues, presented in the immediate environment of an individual, can affect his or her later behavior. This effect was applied in a fundraising context. In 12 bakeries, a pink opaque donation box was placed near the cash register with a message soliciting donations for a humanitarian project. The moneybox had a cardioids (heart-like) shape, a round shape, or a square shape. Results showed that more donations were found with the moneybox with the cardioids shape. The spreading activation theory is used to explain these results.
“Don't Just Say it Matters”: Reducing the Inequalities in Cervical Screening in New Zealand
Authors:   The National Social Marketing Centre Research Team
Published: November 2011

“Don't Just SAY It Matters” is an ongoing three-phase program that addresses ethnicity-based health inequalities in New Zealand. It aims to increase cervical screening among New Zealand's Māori (indigenous Polynesian) and Pacific women by creating an understanding of the importance of screening and enhancing the service to support uptake. Funded by the New Zealand National Screening Unit, the program was launched in September 2007 and is ongoing until 2013. Phase One aimed to start conversations about cervical screening, Phase Two aimed to motivate women to be screened, and Phase Three has built on this work with the introduction of further interventions. By April 2010, screening coverage was Pacific women — 60.90%, a relative increase of 31.25%; Māori women — 55.40%, a relative increase of 16.63%; and all women — 76.10% a relative increase of 7.94% (National Screening Unit, 2010; absolute change is defined as the difference from a previous value to a new value).
Bone mineral density and body composition in elite female golf and netball players
Authors: Chang Ruth P. Y. , Briffa Kathy N. , Edmondston Stephen J.
Published: November 2011

The aim of this study was to compare bone density and body composition measurements in women participating in elite‐level netball and golf, two sports with contrasting loading characteristics. Bone mineral density (BMD) and body composition were measured using dual‐energy X‐ray absorptiometry (DXA) in 14 state‐level netball players (20.8±3.4 years), 11 single‐digit handicap golf players (22.4±2.1 years) and a control group (n=18) not training for sport (22.6±3.6 years). Trunk extensor endurance and grip strength were also measured using the Sorensen test and hand‐grip dynamometry respectively. Netball players had significantly higher total body, lumbar spine and hip BMD than the golf players (P<0.001) and control subjects (P<0.001). The golf players had higher BMD than the control subjects only in the lumbar spine (P<0.05). The netball players were significantly taller than the golf players and control group (P<0.01) and had a higher body mass than the control group (P<0.001). After adjustment for body height and mass, the BMD values in the netball players remained significantly higher than the control subjects at all sites (P<0.01), while the golf players had significantly higher lumbar spine BMD than the controls (P<0.05). Elite‐level netball participation is associated with increased total body, hip and lumbar spine BMD, while this response was only evident in the lumbar spine in elite golf players. The contrasting loading characteristics of these sports may be reflected in the site‐specific differences in BMD when compared to non‐athletic control subjects.
Advancing Hierarchical Equations of Motion for Efficient Evaluation of Coherent Two-dimensional Spectroscopy
Authors: Xu Jian , Xu Rui-xue , Abramavicius Darius , Zhang Hou-dao , Yan Yi-jing
Published: November 2011

To advance hierarchical equations of motion as a standard theory for quantum dissipative dynamics, we put forward a mixed Heisenberg-Schrödinger scheme with block-matrix implementation on efficient evaluation of nonlinear optical response function. The new approach is also integrated with optimized hierarchical theory and numerical filtering algorithm. Different configurations of coherent two-dimensional spectroscopy of model excitonic dimer systems are investigated, with focusing on the effects of intermolecular transfer coupling and bi-exciton interaction.
Electron Affinities of the Early Lanthanide Monoxide Molecules
Authors: Chi Chao-xian , Xie Hua , Cong Ran , Tang Zi-chao , Zhou Ming-fei
Published: November 2011

The photoelectron imagings of LaO−, CeO−, PrO−, and NdO− at 1064 nm are reported. The well resolved photoelectron spectra allow the electron affinities to be determined as 0.99(1) eV for LaO, 1.00(1) eV for CeO, 1.00(1) eV for PrO, and 1.01(1) eV for NdO, respectively. Density functional calculations and natural atomic orbital analyses show that the 4f electrons tend to be localized and suffer little from the charge states of the molecules. The photodetached electron mainly originates from the 6s orbital of the metals. The ligand field theory with the δ=2 assumption is still an effective method to analyze the ground states of the neutral and anionic lanthanide monoxides.
Characterization of NE81, the first lamin-like nucleoskeleton protein in a unicellular organism
Authors: Krüger Anne , Batsios Petros , Baumann Otto , Luckert Eva , Schwarz Heinz , Stick Reimer , Meyer Irene , Gräf Ralph
Published: November 2011

Lamins build the nuclear lamina and are required for chromatin organization, gene expression, cell cycle progression, and mechanical stabilization. Despite these universal functions, lamins have so far been found only in metazoans. We have identified protein NE81 in Dictyostelium, which has properties that justify its denomination as a lamin-like protein in a lower eukaryote. This is based on its primary structure, subcellular localization, and regulation during mitosis, and its requirement of the C-terminal CaaX box as a posttranslational processing signal for proper localization. Our knockout and overexpression mutants revealed an important role for NE81 in nuclear integrity, chromatin organization, and mechanical stability of cells. All our results are in agreement with a role for NE81 in formation of a nuclear lamina. This function is corroborated by localization of Dictyostelium NE81 at the nuclear envelope in human cells. The discovery of a lamin-like protein in a unicellular organism is not only intriguing in light of evolution, it may also provide a simple experimental platform for studies of the molecular basis of laminopathies.
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences
Authors: Kalkatawi Manal , Rangkuti Farania , Schramm Michael , Jankovic Boris R. , Kamau Allan , Chowdhary Rajesh , Archer John A. C. , Bajic Vladimir B.
Published: November 2011

Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants.

Contact:  vladimir.bajic@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
Authors: Asmann Yan W. , Middha Sumit , Hossain Asif , Baheti Saurabh , Li Ying , Chai High-Seng , Sun Zhifu , Duffy Patrick H. , Hadad Ahmed A. , Nair Asha , Liu Xiaoyu , Zhang Yuji , Klee Eric W. , Kalari Krishna R. , Kocher Jean-Pierre A.
Published: November 2011

Summary: TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways.

Availability and implementation: TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization tool, or as a comprehensive workflow integrating sequencing alignment and variant calling. The executables, instructions and the Amazon Cloud Images of TREAT can be downloaded at the website: http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm

Contact:  Hossain.Asif@mayo.edu; Kocher.JeanPierre@mayo.edu

Supplementary information:  Supplementary data are provided at Bioinformatics online.
Protein subcellular localization of fluorescence imagery using spatial and transform domain features
Authors: Tahir Muhammad , Khan Asifullah , Majid Abdul
Published: November 2011

Motivation: Subcellular localization of proteins is one of the most significant characteristics of living cells. Prediction of protein subcellular locations is crucial to the understanding of various protein functions. Therefore, an accurate, computationally efficient and reliable prediction system is required.

Results: In this article, the predictions of various Support Vector Machine (SVM) models have been combined through majority voting. The proposed ensemble SVM-SubLoc has achieved the highest success rates of 99.7% using hybrid features of Haralick textures and local binary patterns (HarLBP), 99.4% using hybrid features of Haralick textures and Local Ternary Patterns (HarLTP). In addition, SVM-SubLoc has yielded 99.0% accuracy using only local ternary patterns (LTPs) based features. The dimensionality of HarLBP feature vector is 581 compared with 78 and 52 for HarLTP and LTPs, respectively. Hence, SVM-SubLoc in conjunction with LTPs is fast, sufficiently accurate and simple predictive system. The proposed SVM-SubLoc approach thus provides superior prediction performance using the reduced feature space compared with existing approaches.

Availability: A web server accompanying the proposed prediction scheme is available at http://111.68.99.218/SVM-SubLoc

Contact:  asif@pieas.edu.pk; khan.asifullah@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evidence That Thaxtomin C Is a Pathogenicity Determinant of Streptomyces ipomoeae, the Causative Agent of Streptomyces Soil Rot Disease of Sweet Potato
Authors: Guan Dongli , Grau Brenda L. , Clark Christopher A. , Taylor Carol M. , Loria Rosemary , Pettis Gregg S.
Published: November 2011

Streptomyces ipomoeae is the causal agent of Streptomyces soil rot of sweet potato, a disease marked by highly necrotic destruction of adventitious roots, including the development of necrotic lesions on the fleshy storage roots. Streptomyces potato scab pathogens produce a phytotoxin (thaxtomin A) that appears to facilitate their entrance into host plants. S. ipomoeae produces a less-modified thaxtomin derivative (thaxtomin C) whose role in pathogenicity has not been examined. Here, we cloned and sequenced the thaxtomin gene cluster (txt) of S. ipomoeae, and we then constructed targeted txt mutants that no longer produced thaxtomin C. The mutants were unable to penetrate intact adventitious roots but still caused necrosis on storage-root tissue. These results, taken in context with previous histopathological study of S. ipomoeae infection, suggest that thaxtomin C plays an essential role in inter- and intracellular penetration of adventitious sweet potato roots by S. ipomoeae. Once inside the plant host, the pathogen uses one or more yet-to-be-determined factors to necrotize root tissue, including that of any storage roots it encounters.
Use of Leaf Wetness and Temperature to Time Fungicide Applications to Control Botrytis Fruit Rot of Strawberry in Florida
Authors: MacKenzie S. J. , Peres N. A.
Published: November 2011

Botrytis fruit rot (BFR), caused by Botrytis cinerea, is a major disease of strawberry in Florida and is generally controlled by weekly fungicide applications. In this study, disease control programs using fungicides applied on a weekly basis were compared with applications based on three previously published models that correlated disease incidence with weather variables. Field trials were conducted for three seasons on two cultivars, ‘Sweet Charlie’ and ‘Strawberry Festival’. Different thresholds for predicted BFR incidence were evaluated for triggering fungicide applications for the three models. BFR incidence in nontreated control plots of Sweet Charlie and Strawberry Festival was 12.4 and 3.5%, respectively, in 2006–07, 4.2 and 0.8% in 2007–08, and 1.3 and 0.5% in 2008–09. The model of Bulger and associates, with a threshold for disease flower incidence (INFBu) of 0.50, triggered half or fewer fungicide applications compared with a calendar-standard grower program, without significantly increasing BFR incidence or reducing yield. The model of Broome and associates, at a predicted fruit disease incidence threshold (INFBr) of 0.62, performed well but required more fungicide applications than the Bulger model (INFBu ≥ 0.50). The model of Xu and associates, based on field data to predict the incidence of diseased flowers, required more fungicide applications without improving disease control. Use of higher thresholds resulted in fewer applications but increased disease incidence in some cases. The Bulger model utilizing leaf wetness and temperature during the wetness period as input variables and a threshold of INFBu of 0.50 can be used effectively in a disease-forecasting system to time fungicide treatments, and greatly reduced the number of applications without loss of disease control or yield.
Assessment of metabolic modulation in free-living versus endosymbiotic
Symbiodinium
using synchrotron radiation-based infrared microspectroscopy
Authors: Peng Shao-En , Chen Chii-Shiarng , Song Yen-Fang , Huang Huai-Ting , Jiang Pei-Luen , Chen Wan-Nan U. , Fang Lee-Shing , Lee Yao-Chang
Published: November 2011

The endosymbiotic relationship between coral hosts and dinoflagellates of the genus
Symbiodinium
is critical for the growth and productivity of coral reef ecosystems. Here, synchrotron radiation-based infrared microspectroscopy was applied to examine metabolite concentration differences between endosymbiotic (within the anemone
Aiptasia pulchella
) and free-living
Symbiodinium
over the light–dark cycle. Significant differences in levels of lipids, nitrogenous compounds, polysaccharides and putative cell wall components were documented. Compared with free-living
Symbiodinium
, total lipids, unsaturated lipids and polysaccharides were relatively enriched in endosymbiotic
Symbiodinium
during both light and dark photoperiods. Concentrations of cell wall-related metabolites did not vary temporally in endosymbiotic samples; in contrast, the concentrations of these metabolites increased dramatically during the dark photoperiod in free-living samples, possibly reflecting rhythmic cell-wall synthesis related to light-driven cell proliferation. The level of nitrogenous compounds in endosymbiotic cells did not vary greatly across the light–dark cycle and in general was significantly lower than that observed in free-living samples collected during the light. Collectively, these data suggest that nitrogen limitation is a factor that the host cell exploits to induce the biosynthesis of lipids and polysaccharides in endosymbiotic
Symbiodinium
.