bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain induced changes in the gate leakage current of n-channel metal-oxide-semiconductor field-effect transistors
Authors: Yang Xiaodong , Choi Younsung , Lim Jisong , Nishida Toshikazu , Thompson Scott
Published: July 2011

Changes in the gate direct tunneling current in the accumulation layer and in the inversion layer are measured for tensile strained n-channel metal-oxide-semiconductor-field-effect-transistors (MOSFETs) with a polysilicon gate and a TaN gate on (100) silicon wafers. The observed decrease of the polysilicon gate tunneling current in the inversion layer and the accumulation layer for uniaxial tensile stress primarily results from electron repopulation into the Δ2 valley with a larger out-of-plane effective conductivity mass. However, due to weak confinement and the Fermi energy approaching the conduction band edge in the accumulation layer, the normalized leakage current change is higher in the accumulation layer than in the inversion layer. In contrast with polysilicon gate MOSFETs, the direct tunneling current in metal gate MOSFETs increases with uniaxial tensile stress in the accumulation layer, which may be understood from the C-V measurement of the strain-induced TaN work function shift. A self-consistent solution to Poisson’s and Schrödinger’s equations, considering the strain Hamiltonian combined with the transfer matrix method, is used for modeling the electron tunneling process.
Phase transformation of Ho2O3 at high pressure
Authors: Jiang Sheng , Liu Jing , Li Xiaodong , Bai Ligang , Xiao Wansheng , Zhang Yufeng , Lin Chuanlong , Li Yanchun , Tang Lingyun
Published: July 2011

The structural stability of cubic Ho2O3 under high pressure has been investigated by angle-dispersive x-ray diffraction (ADXD) in a diamond anvil cell up to 63.0 GPa at room temperature. The diffraction data reveal two structural transformations on compression. The structural transformation from a cubic to a monoclinic structure starts at 8.9 GPa and is complete at 16.3 GPa with a ∼8.1% volume collapse. A hexagonal phase begins to appear at ∼14.8 GPa and becomes dominant at 26.4 GPa. This high-pressure hexagonal phase with a small amount of retained monoclinic phase is stable up to the highest pressure of 63.0 GPa in this study. After release of pressure, the hexagonal phase transforms to a monoclinic structure. A third-order Birch-Murnaghan fit yields zero pressure bulk moduli (B0) of 206(3), 200(7) and 204(19) GPa and their pressure derivatives (B0’) of 4.8(4), 2.1(4), 3.8(5) for the cubic, monoclinic and hexagonal phases, respectively. Comparing with other rare-earth sesquioxides, it is suggested that the transition pressure from cubic to monoclinic phase, as well as the bulk modulus of the cubic phase, increases with the decreasing of the cation radius of rare-earth sesquioxides.
The evolution of vacancy-type defects in silicon-on-insulator structures studied by positron annihilation spectroscopy
Authors: Coleman P. G. , Nash D. , Edwardson C. J. , Knights A. P. , Gwilliam R. M.
Published: July 2011

Variable-energy positron annihilation spectroscopy (VEPAS) has been applied to the study of the formation and evolution of vacancy-type defect structures in silicon (Si) and the 1.5 μm thick Si top layer of silicon-on-insulator (SOI) samples. The samples were implanted with 2 MeV Si ions at fluences between 1013 and 1015 cm−2, and probed in the as-implanted state and after annealing for 30 min at temperatures between 350 and 800 °C. In the case of SOI the ions were implanted such that their profile was predominantly in the insulating buried oxide layer, and thus their ability to combine with vacancies in the top Si layer, and that of other interstitials beyond the buried oxide, was effectively negated. No measurable differences in the positron response to the evolution of small clusters of n vacancies (Vn, n ∼ 3) in the top Si layer of the Si and SOI samples were observed after annealing up to 500 °C; at higher temperatures, however, this response persisted in the SOI samples as that in Si decreased toward zero. At 700 and 800 °C the damage in Si was below detectable levels, but the VEPAS response in the top Si layer in the SOI was consistent with the development of nanovoids.
Observation of electron behavior in ambipolar polymer-based light-emitting transistor by optical second harmonic generation
Authors: Ohshima Yuki , Lim Eunju , Manaka Takaaki , Iwamoto Mitsumasa , Sirringhaus Henning
Published: July 2011

By using the optical second harmonic generation (SHG) measurement, we directly visualized the carrier behavior leading to carrier recombination and electroluminescence (EL) in ambipolar polymer-based organic light-emitting transistor (OLET) with an active layer of poly 9,9-di-n-octylfluorene-alt-benzothiadiszole (F8BT). Eliminating photoluminescence generated at 560 nm by a two-photon absorption process, the dynamical carrier motion in the F8BT-OLET was visualized by the electric field induced SHG induced at 420 nm. Diffusion-like electron transport that starts from the drain electrode was directly caught as the transits of the SHG images. Accordingly, EL was obtained at the edge of the source electrode. The electron mobility was estimated from the visualized carrier motion as 9.2×10-4cm2/Vs, which was larger than that obtained from the transfer curve of the OLET.
Physical nature of anomalous peaks observed in extraordinary Hall effect measurement of exchange biased spin-valves with perpendicular anisotropy
Authors: Thiyagarajah Naganivetha , Wan Joo Ho , Lin Lin , Bae Seongtae
Published: July 2011

We experimentally and theoretically demonstrate that the abrupt change in magnetostatic energy during the free and pinned [Co/Pd] layer reversal by an external magnetic field and the magnetic field dependent extraordinary Hall effect (EHE) coefficient are the main physical reasons for the anomalous peaks observed in EHE measurement of exchange biased [Pd/Co]/Cu/Co/[Pd/Co]/FeMn giant magnetoresistance spin-valves with perpendicular anisotropy (EBPA-SVs). The correlation of the anomalous EHE peaks to the extrinsic magnetic properties of EBPA-SVs paves a way to indirectly evaluate these properties.
Measurement of electron density in complex plasmas of the PK-3 plus apparatus on the International Space Station
Authors: Takahashi Kazuo , Hayashi Yasuaki , Adachi Satoshi
Published: July 2011

Dust particles in discharge are often levitated in a sheath region rather than in bulk plasma under gravitational conditions (on Earth). Gravity compresses dust clouds, and the gravitational force restricts the motion of the dust particles. Microgravity gives the plasmas, including dust particles, so-called complex (dusty) plasmas, where dust particles are embedded in a completely charge-neutral region of the bulk plasma. The dust cloud, as an uncompressed strongly-coupled Coulomb system, corresponds to an atomic model with physical phenomena, e.g., crystallization, phase transition, and so on. Since the phenomena are tightly connected to plasma states expressed by plasma parameters, it is significant to estimate the plasma parameters, such as electron density and temperature. The present work shows the electron density measured by the frequency shift probe in the apparatus for microgravity experiments currently boarding on the International Space Station (PK-3 plus). The frequency shift probe measurement gave electron density in the order of 108 cm−3 as a typical value in the apparatus, and demonstrated the detection of electrons in plasmas with dust particles. The spatial distribution profile of the electron density obtained in this measurement presents an aspect for the void formation of dust clouds under microgravity.
The relationship between microstructure and electrical breakdown in cathodic arc deposited hafnium oxide films
Authors: Field M. R. , Partridge J. G. , Mayes E. H. , Latham K. , McCulloch D. G.
Published: July 2011

Hafnium oxide films were deposited with a range of substrate temperatures using a filtered cathodic vacuum arc deposition system. The microstructure, electronic structure, and electrical breakdown of the films were characterized. In films deposited at temperatures above 200 °C, the microstructure became more ordered and x-ray diffraction indicated that the dominant phase was monoclinic hafnium oxide. Evidence for the presence of the tetragonal phase was also found in the films deposited at temperatures above 400 °C. The near edge structure of the oxygen K-edge measured using x-ray absorption spectroscopy, provided further evidence that films prepared at high temperatures contained a combination of the monoclinic and tetragonal phases. Films deposited at room temperature were disordered and exhibited the best electrical breakdown characteristics. The electrical breakdown of the films deteriorated as the crystallinity increased with increasing deposition temperature. These results support the proposition that electrical breakdown paths may occur along grain boundaries in polycrystalline hafnium oxide films and therefore a disordered microstructure is preferable.
Analysis of leakage current mechanisms in Pt/Au Schottky contact on Ga-polarity GaN by Frenkel-Poole emission and deep level studies
Authors: Rao Peta Koteswara , Park Byungguon , Lee Sang-Tae , Noh Young-Kyun , Kim Moon-Deock , Oh Jae-Eung
Published: July 2011

We report the Frenkel-Poole emission in Pt/Au Schottky contact on Ga-polarity GaN grown by molecular beam epitaxy using current-voltage-temperature (I-V-T) characteristics in the temperature ranging from 200 K to 375 K. Using thermionic emission model, the estimated Schottky barrier height is 0.49 eV at 200 K and 0.83 eV at 375 K, respectively, and it is observed that the barrier height increases with increase in temperature. The extracted emission barrier height (ϕt) for Ga-polarity GaN Schottky diode by Frenkel-Poole theory is about 0.15 eV. Deep level transient spectroscopy study shows a deep level with activation energy of 0.44 eV, having capture cross-section 6.09 × 10−14 cm2, which is located between the metal and semiconductor interface, and trap nature is most probably associated with dislocations in Ga-polarity GaN. The analysis of I-V-T characteristics represents that the leakage current is due to effects of electrical field and temperature on the emission of electron from a trap state near the metal-semiconductor interface into continuum states associated with conductive dislocations in Ga-polarity GaN Schottky diode.
Complete optimisation of multi-configuration Jastrow wave functions by variational transcorrelated method
Authors: Luo Hongjun
Published: July 2011

We investigate the performance of the newly developed variational transcorrelated (VTC) method (H. Luo, J. Chem. Phys. 133, 154109 (2010)10.1063/1.3505037) on the overall optimisation of the multi-configuration Jastrow wave function. Similar to the standard multi-configuration self consistent field methods, optimisations of orbitals are realized by iterative unitary transformations, where the skew-symmetric matrix elements are determined by using Newton-Raphson scheme. Third order density matrices are introduced to deal with the three-body VTC potential. Test calculations are performed for the C2 molecule on several small complete active spaces, and the results are compared with those of variational quantum Monte Carlo calculations. The results demonstrate that with the VTC method one can practically recover the results of highly non-linear variational calculations.
Spectroscopy of diatomic ZrF and ZrCl: 760 – 555 nm
Authors: Martinez Alonzo , Morse Michael D.
Published: July 2011

The optical spectrum of diatomic ZrF has been investigated, with transitions recorded in the range from 14 700 to 18 000 cm−1. Many bands have been observed, several of which can be grouped into three band systems. Rotationally resolved investigations are hampered by perturbations that are rampant among the excited states, but three unperturbed bands have revealed that the ground state of ZrF has Ω″ = 3/2, with a bond length of re′′ = 1.854(1) Å. Hot bands originating from v″ = 1 provide the ground state vibrational interval, ΔG1/2′′ = 691.45(2) cm−1 for 90Zr19F. Based on comparisons to ZrCl and ligand-field considerations, the ZrF ground state is assigned as a 2Δ3/2 level deriving from the 3σ2 1δ1 configuration, in agreement with a previous study. In addition to the measurements on ZrF, vibronically resolved spectra of ZrCl have been recorded over the 13 000 to 18 000 cm−1 range, and four band systems have been identified.
Ultrathin multiband gigahertz metamaterial absorbers
Authors: Li Hui , Yuan Li Hua , Zhou Bin , Shen Xiao Peng , Cheng Qiang , Cui Tie Jun
Published: July 2011

We propose ultrathin multiband metamaterial absorbers in the microwave frequencies in which the design, analysis, fabrication, and measurement of the absorbers working in multiple bands are presented. The metamaterial absorbers consist of a periodic arrangement of different scales of electric-field-coupled-LC (ELC) resonators and a metallic background plane, separated by only 1 mm dielectric spacer. By tuning the scale factor of the ELC unit cells, we achieve independently multiple absorptions at different customized frequencies. Experiments demonstrate excellent absorption rates in the designed frequency bands over wide angles of incident waves for both transverse electric and magnetic polarizations. The explanation to the physical mechanism of the multiband metamaterial absorber is presented and verified.
Comment on “Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds” [J. Chem. Phys. 132, 164101 (2010)]
Authors: Wesołowski Tomasz A.
Published: July 2011

Several assertions which are incorrect or might be misleadingly interpreted as well as omissions of issues concerning the non-additive kinetic energy potential made by Fux et al. are analyzed. They concern issues of great importance for any computational method based on the orbital-free embedding theory: evaluation of the total energy, approximating the non-additive kinetic potential, exact properties of non-additive kinetic energy potential. In a nutshell, the authors do not distinguish between two different quantities: the functional, i.e., the correspondence assigning the non-additive kinetic potential to a pair of electron densities and the function (the potential itself).
Site-selected luminescence of atomic europium in the solid rare gases
Authors: Byrne Owen , McCaffrey John G.
Published: July 2011

Site-selective excitation has been used to simplify complex emission recorded in the visible spectral region for atomic europium isolated in the solid rare gases. In addition to y8P resonance fluorescence, excitation of the y8P state produces emission from the z6P state and the metastable a10D state. Very weak emission at 690 nm is tentatively assigned to the J = 9/2 level of the z10P state. Eu atoms isolated in the red and blue sites exhibit very different temperature dependence both spectrally and temporally. For the y8P state emission the red site atoms exhibit small Stokes shifts and yield radiative lifetimes while the emission from the blue site loses intensity and the temporal profiles shorten dramatically between 10 and 16 K indicating very efficient non-radiative relaxation in this site. An analysis of the Stokes shifts exhibited for the y8P state in each site supports the attributions made in a previous publication [O. Byrne and J.G. McCaffrey, J. Chem. Phys. 134, 124501 (2011)]10.1063/1.3564947 that the smaller blue tetravacancy site has a greater repulsive interaction with the guest. With the exception of the y8P state resonance fluorescence, the recorded decay profiles of all the other emissions exhibit multiple components. This behaviour has been attributed to the existence of multiple crystal field levels arising from the splitting of the distinct spin-orbit levels from which emission occurs.
Thermodynamic and structural properties of the high density Gaussian core model
Authors: Ikeda Atsushi , Miyazaki Kunimasa
Published: July 2011

We numerically study thermodynamic and structural properties of the one-component Gaussian core model at very high densities. The solid-fluid phase boundary is carefully determined. We find that the density dependence of both the freezing and melting temperatures obey the asymptotic relation, log Tf, log Tm∝ − ρ2/3, where ρ is the number density, which is consistent with Stillinger's conjecture. Thermodynamic quantities such as the energy and pressure and the structural functions such as the static structure factor are also investigated in the fluid phase for a wide range of temperature above the phase boundary. We compare the numerical results with the prediction of the liquid theory with the random phase approximation (RPA). At high temperatures, the results are in almost perfect agreement with RPA for a wide range of density, as it has already been shown in the previous studies. In the low temperature regime close to the phase boundary line, although RPA fails to describe the structure factors and the radial distribution functions at the length scales of the interparticle distance, it successfully predicts their behaviors at longer length scales. RPA also predicts thermodynamic quantities such as the energy, pressure, and the temperature at which the thermal expansion coefficient becomes negative, almost perfectly. Striking ability of RPA to predict thermodynamic quantities even at high densities and low temperatures is understood in terms of the decoupling of the length scales which dictate thermodynamic quantities from the interparticle distance which dominates the peak structures of the static structure factor due to the softness of the Gaussian core potential.
Efficient thermoelectric van der Pauw measurements
Authors: de Boor Johannes , Schmidt Volker
Published: July 2011

The development of powerful thermoelectric materials requires fast and simple characterization techniques. We combine three measurements to obtain a complete thermoelectric characterization. The electrical conductivity is measured by the van der Pauw method, while ZT is determined directly by means of a Harman measurement. Finally, exploiting the analogy between electrical and thermal physics, a thermal van der Pauw measurement is performed and the sample Seebeck coefficient and thermal conductivity can be determined. No temperature differences need to be measured; all quantities can be deduced from voltage measurements concurrently on the same sample which allows for quick and convenient material screening.
Influence of SrTiO3 substrate miscut angle on the transport properties of LaAlO3/SrTiO3 interfaces
Authors: Fix T. , Schoofs F. , Bi Z. , Chen A. , Wang H. , MacManus-Driscoll J. L. , Blamire M. G.
Published: July 2011

A free charge layer forms at the LaAlO3/SrTiO3 interface. We show the influence of the SrTiO3 (001) substrate miscut angle on its electronic and transport properties. Highly miscut substrates lead to a substantial mobility enhancement and a carrier density decrease at low temperature consistent with a two-carrier type model.
Impact of phase lag on uniformity in pulsed capacitively coupled plasmas
Authors: Agarwal Ankur , Rauf Shahid , Collins Ken
Published: July 2011

Process uniformity of macro-scale parameters such as electron and ion densities is critical during any plasma process. Pulsed operation of multiple frequency capacitively coupled plasmas (CCPs) has been shown to improve profile characteristics of features during plasma etching. In this work, we consider pulsing of both power sources in a dual frequency CCP. The impact of phase lag between the high frequency and low frequency power pulses on plasma uniformity is examined using a two-dimensional computational plasma model. Results for Ar/CF4 gas mixture indicate that phase lag allows one to control plasma uniformity by modulating the time for which the high or low frequency source is on.
Manganese-doped indium oxide and its application in organic light-emitting diodes
Authors: Liao Yaqin , Lu Qipeng , Fan Yi , Liu Xingyuan
Published: July 2011

Thin films of manganese-doped indium oxide (IMO) deposited by electron beam evaporation have been investigated as anodes in organic light-emitting diodes (OLEDs). The IMO films have a high work function of 5.35 eV, a desirable surface morphology with an average roughness of 1.1 nm, a high average optical transmittance of 87.2% in the visible region, and a maximum optical transmittance of 92% at 460 nm. It is demonstrated that an IMO anode can effectively improve hole injection at the anode/organic interface, resulting in OLEDs with an increased electroluminescent efficiency.
Perception as Interacting Psychophysical Functions. Could the Configuring of Features Replace a Specialised Receptor?
Authors: Booth David A , Freeman Richard P J , Konle Melanie , Wainwright Clare J , Sharpe Oliver
Published: July 2011

This paper illustrates how perception is achieved through interactions among the psychophysical functions of judged features of an object. The theory is that the perceiver places processed features in a multidimensional space of discriminal processes. Each dimension is scaled in units of discrimination performance. The zero coordinate of each feature is its level in an internal standard (norm) established by previous experience of that category of object in context. Experiments are reported which show that one, two, or three concurrent single-featured objects matched the multiple features of another object in two ways. Either stimulation from the two objects had discrimination distances from norm that added, or the stimulation by one object was processed through a concept describing stimulation by the other object. It follows that, in this case, perception via a receptor for the multi-featured object can be replaced by a point of balance among receptors for each single feature. The object with its own receptor is the gustatory stimulant L-glutamic acid as its monosodium salt. The features that stimulate diverse gustatory receptors of their own are sodium chloride, citric acid, sucrose, and caffeine. A more complex approach to dimensional coding was developed earlier for photoreceptors in colour judgments. The present approach is modality independent, mathematically simple, and economical in experimental data.
Object — Position Binding in Visual Short-Term Memory for Sequentially Presented Unfamiliar Stimuli
Authors: Sapkota Raju P , Pardhan Shahina , van der Linde Ian
Published: July 2011

The effect of spatial position on visual short-term memory (VSTM) for sequentially presented objects has been investigated relatively little, despite the fact that vision in natural environments is characterised by frequent changes in object position and gaze location. We investigated the effect of reusing previously examined spatial positions on VSTM for object appearance. Observers performed a yes – no recognition task following a memory display comprising briefly presented 1/ f noise discs (ie possessing spectral properties akin to natural images) shown sequentially at random coordinates. At test, single stimuli were presented either at original spatial positions, new positions, or at a fixed central position. Results, interpreted in terms of appearance and position preview effects, indicate that, where original spatial positions were reused at test, memory performance was elevated by more than 25%, despite that spatial position was task-irrelevant (in the sense that it could not be used to facilitate a correct response per se). This study generalises object – spatial-position binding theory to a sequential display scenario in which the influences of extrafoveal processing, spatial context cues, and long-term memory support were minimised, thereby eliminating the hypothesis that object priming is the principal cause of the ‘same-position advantage’ in VSTM.
Relative Influences of Lightness and Facial Morphology on Perceived Race
Authors: Willenbockel Verena , Fiset Daniel , Tanaka James W
Published: July 2011

In a recent study (Brooks and Gwinn, 2010 Perception 39 1142 – 1145), the lightness contrast illusion was employed to study the influences of skin tone and facial morphology on race perception. The findings were rather counterintuitive: they suggested that skin tone does not play a major role in racial categorisation. To investigate this further, we used a parametric paradigm including five lightness levels, five morphing levels, and two face orientations. In accordance with Brooks and Gwinn, we found that race categorisation of African – American and Caucasian faces by Caucasian participants relied mainly on morphological cues. However, the relative influence of lightness increased when morphological information was ambiguous and when the faces were upside down. Overall, the results point to a flexible multicue-based mechanism underlying race perception.
Contrasting hydraulic regulation in closely related forage grasses: implications for plant water use
Authors: Holloway-Phillips Meisha-Marika , Brodribb Timothy J.
Published: July 2011

Plant traits that improve crop water use efficiency are highly sought after but difficult to isolate. Here, we examine the integrated function of xylem and stomata in closely related forage grasses to determine whether quantitative differences in water transport properties could be used to predict plant performance under limited water conditions. Cultivars of two forage grass species with different drought tolerance ratings, Lolium multiflorum Lam. and Festuca arundinacea Schreb., were assessed for maximum hydraulic conductivity (Kmax), vulnerability of xylem to hydraulic dysfunction (P50) and stomatal sensitivity to leaf water potential. Species-specific differences were observed in several of these traits, and their effect on whole-plant performance was examined under well-watered and restricted watering conditions. It was shown that although P50 was comparable between species, for F. arundinacea cultivars, there was greater hydraulic risk associated with reduced stomatal sensitivity to leaf hydration. In contrast, L. multiflorum cultivars expressed a higher capacity for water transport, but more conservative stomatal regulation. Despite different susceptibilities to leaf damage observed during acute drought, under the sustained moderate drought treatment, the two strategies were balanced in terms of water conservation and hydraulic utilisation, resulting in similar dry matter production. Characterisation of water use patterns according to the key hydraulic parameters is discussed in terms of implications to yield across different environmental scenarios as well as the applicability of water transport related traits to breeding programs.
The evolution and functional significance of leaf shape in the angiosperms
Authors: Nicotra Adrienne B. , Leigh Andrea , Boyce C. Kevin , Jones Cynthia S. , Niklas Karl J. , Royer Dana L. , Tsukaya Hirokazu
Published: July 2011

Angiosperm leaves manifest a remarkable diversity of shapes that range from developmental sequences within a shoot and within crown response to microenvironment to variation among species within and between communities and among orders or families. It is generally assumed that because photosynthetic leaves are critical to plant growth and survival, variation in their shape reflects natural selection operating on function. Several non-mutually exclusive theories have been proposed to explain leaf shape diversity. These include: thermoregulation of leaves especially in arid and hot environments, hydraulic constraints, patterns of leaf expansion in deciduous species, biomechanical constraints, adaptations to avoid herbivory, adaptations to optimise light interception and even that leaf shape variation is a response to selection on flower form. However, the relative importance, or likelihood, of each of these factors is unclear. Here we review the evolutionary context of leaf shape diversification, discuss the proximal mechanisms that generate the diversity in extant systems, and consider the evidence for each the above hypotheses in the context of the functional significance of leaf shape. The synthesis of these broad ranging areas helps to identify points of conceptual convergence for ongoing discussion and integrated directions for future research.
Deep drainage and soil salt loads in the Queensland Murray - Darling Basin using soil chloride: comparison of land uses
Authors: Tolmie P. E. , Silburn D. M. , Biggs A. J. W.
Published: July 2011

Increases in deep drainage below the root-zone can lead to secondary salinity. Few data were available for drainage under dryland cropping and pastures in the Queensland Murray–Darling Basin (QMDB) before this study. Modelled estimates were available; however, without measured drainage these could not be validated. Soil chloride (Cl) mass-balance was used to provide an extensive survey of deep drainage. The method is ‘backward-looking’ and can detect low rates of drainage over longer times. Soil Cl and other soil properties were collated for a number of soils, mostly Vertosols and Sodosols, for paired native vegetation, cropped and sometimes pasture sites, from historical data and new soil sampling.
Large amounts of salt and Cl had accumulated under native vegetation (Cl mean 25 t/ha, range 6–54, in 2.4 m depth), due to low rates of drainage. Steady-state Cl balances for native vegetation gave average drainage of 1.2 mm/year at wetter, eastern sites and 0.3 mm/year for Sodosols and Grey Vertosols in drier, western areas. Chloride profiles were mostly of a shape indicating matrix/piston flow. One site (Hermitage fallow trial) appeared to be affected by diffusion of Cl to a watertable.
The Cl profiles from 14 longer term cropping sites (18–70 years), mainly used for winter cropping/summer fallow, indicate: (i) large losses of Cl since clearing (mean 50%, range 13-85% for 0–1.5 m soil); and (ii) drainage rates from transient Cl balance are a relatively low percentage of rainfall but are considerably higher than under native vegetation. Drainage averaged 8 mm/year and ranged from 2 to 18 mm/year. This variation is partly explained by rainfall (R2 = 0.63) (500–730 mm/year) and soil plant-available water capacity (R2 = 0.77) (80–300 mm). Deep drainage increases with increasing rainfall and with decreasing available water capacity. Drainage under pasture was less than under cropping but greater than under native vegetation.
The deep drainage water (leachate) was of poor quality and will increase salinity if added to good quality groundwater. Leachate at nine sites was too saline to be used (undiluted) for irrigation (>2500 mg Cl/L) and was marginal at the remainder of sites (~800 mg Cl/L). Cropping areas in the QMDB have the precursors for secondary salinity development—high salt loads and an increase in drainage after clearing. The Vertosols and Sodosols studied occur in 90% of croplands in the QMDB. Salinisation will depend on the properties of the underlying regolith and groundwater systems.
Listeria monocytogenes
engineered to activate the Nlrc4 inflammasome are severely attenuated and are poor inducers of protective immunity
Authors: Sauer John-Demian , Pereyre Sabine , Archer Kristina A. , Burke Thomas P. , Hanson Bill , Lauer Peter , Portnoy Daniel A.
Published: July 2011

Inflammasomes are intracellular multiprotein signaling complexes that activate Caspase-1, leading to the cleavage and secretion of IL-1β and IL-18, and ultimately host cell death. Inflammasome activation is a common cellular response to infection; however, the consequences of inflammasome activation during acute infection and in the development of long-term protective immunity is not well understood. To investigate the role of the inflammasome in vivo, we engineered a strain of
Listeria monocytogenes
that ectopically expresses
Legionella pneumophila
flagellin, a potent activator of the Nlrc4 inflammasome. Compared with wild-type
L. monocytogenes
, strains that ectopically secreted flagellin induced robust host cell death and IL-1β secretion. These strains were highly attenuated both in bone marrow-derived macrophages and in vivo compared with wild-type
L. monocytogenes
. Attenuation in vivo was dependent on Nlrc4, but independent of IL-1β/IL-18 or neutrophil activity.
L. monocytogenes
strains that activated the inflammasome generated significantly less protective immunity, a phenotype that correlated with decreased induction of antigen-specific T cells. Our data suggest that avoidance of inflammasome activation is a critical virulence strategy for intracellular pathogens, and that activation of the inflammasome leads to decreased long-term protective immunity and diminished T-cell responses.
Stereospecific gating of functional motions in Pin1
Authors: Namanja Andrew T. , Wang Xiaodong J. , Xu Bailing , Mercedes-Camacho Ana Y. , Wilson Kimberly A. , Etzkorn Felicia A. , Peng Jeffrey W.
Published: July 2011

Pin1 is a modular enzyme that accelerates the
cis
-
trans
isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival. We have used NMR to investigate the interaction of Pin1 with three related ligands that include a pS-P substrate peptide, and two pS-P substrate analogue inhibitors locked in the
cis
and
trans
conformations. Specifically, we compared the ligand binding modes and binding-induced changes in Pin1 side-chain flexibility. The
cis
and
trans
binding modes differ, and produce different mobility in Pin1. The
cis
-locked inhibitor and substrate produced a loss of side-chain flexibility along an internal conduit of conserved hydrophobic residues, connecting the domain interface with the isomerase active site. The
trans
-locked inhibitor produces a weaker conduit response. Thus, the conduit response is stereoselective. We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication. Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins.
Histone H4 lysine 16 hypoacetylation is associated with defective DNA repair and premature senescence in Zmpste24-deficient mice
Authors: Krishnan Vaidehi , Chow Maggie Zi Ying , Wang Zimei , Zhang Le , Liu Baohua , Liu Xinguang , Zhou Zhongjun
Published: July 2011

Specific point mutations in lamin A gene have been shown to accelerate aging in humans and mice. Particularly, a de novo mutation at G608G position impairs lamin A processing to produce the mutant protein progerin, which causes the Hutchinson Gilford progeria syndrome. The premature aging phenotype of Hutchinson Gilford progeria syndrome is largely recapitulated in mice deficient for the lamin A-processing enzyme, Zmpste24. We have previously reported that Zmpste24 deficiency results in genomic instability and early cellular senescence due to the delayed recruitment of repair proteins to sites of DNA damage. Here, we further investigate the molecular mechanism underlying delayed DNA damage response and identify a histone acetylation defect in

Zmpste24
−/−

mice. Specifically, histone H4 was hypoacetylated at a lysine 16 residue (H4K16), and this defect was attributed to the reduced association of a histone acetyltransferase, Mof, to the nuclear matrix. Given the reversible nature of epigenetic changes, rescue experiments performed either by Mof overexpression or by histone deacetylase inhibition promoted repair protein recruitment to DNA damage sites and substantially ameliorated aging-associated phenotypes, both in vitro and in vivo. The life span of

Zmpste24
−/−

mice was also extended with the supplementation of a histone deacetylase inhibitor, sodium butyrate, to drinking water. Consistent with recent data showing age-dependent buildup of unprocessable lamin A in physiological aging, aged wild-type mice also showed hypoacetylation of H4K16. The above results shed light on how chromatin modifications regulate the DNA damage response and suggest that the reversal of epigenetic marks could make an attractive therapeutic target against laminopathy-based progeroid pathologies.
Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids
Authors: Sanei Maryam , Pickering Richard , Kumke Katrin , Nasuda Shuhei , Houben Andreas
Published: July 2011

Uniparental chromosome elimination occurs in several interspecific hybrids of plants. We studied the mechanism underlying selective elimination of the paternal chromosomes during the early development of
Hordeum vulgare
×
Hordeum bulbosum
embryos. The following conclusions regarding the role of the centromere-specific histone H3 variant (CENH3) in the process of chromosome elimination were drawn: (
i
) centromere inactivity of
H. bulbosum
chromosomes triggers the mitosis-dependent process of uniparental chromosome elimination in unstable
H. vulgare
×
H. bulbosum
hybrids; (
ii
) centromeric loss of CENH3 protein rather than uniparental silencing of
CENH3
genes causes centromere inactivity; (
iii
) in stable species combinations, cross-species incorporation of CENH3 occurs despite centromere-sequence differences, and not all CENH3 variants get incorporated into centromeres if multiple CENH3s are present in species combinations; and (
iv
) diploid barley species encode two
CENH3
variants, the proteins of which are intermingled within centromeres throughout mitosis and meiosis.
Identification of unique mechanisms for triterpene biosynthesis in
Botryococcus braunii
Authors: Niehaus Tom D. , Okada Shigeru , Devarenne Timothy P. , Watt David S. , Sviripa Vitaliy , Chappell Joe
Published: July 2011

Botryococcene biosynthesis is thought to resemble that of squalene, a metabolite essential for sterol metabolism in all eukaryotes. Squalene arises from an initial condensation of two molecules of farnesyl diphosphate (FPP) to form presqualene diphosphate (PSPP), which then undergoes a reductive rearrangement to form squalene. In principle, botryococcene could arise from an alternative rearrangement of the presqualene intermediate. Because of these proposed similarities, we predicted that a botryococcene synthase would resemble squalene synthase and hence isolated squalene synthase-like genes from
Botryococcus braunii
race B. While
B. braunii
does harbor at least one typical squalene synthase, none of the other three squalene synthase-like (SSL) genes encodes for botryococcene biosynthesis directly. SSL-1 catalyzes the biosynthesis of PSPP and SSL-2 the biosynthesis of bisfarnesyl ether, while SSL-3 does not appear able to directly utilize FPP as a substrate. However, when combinations of the synthase-like enzymes were mixed together, in vivo and in vitro, robust botryococcene (SSL-1+SSL-3) or squalene biosynthesis (SSL1+SSL-2) was observed. These findings were unexpected because squalene synthase, an ancient and likely progenitor to the other
Botryococcus
triterpene synthases, catalyzes a two-step reaction within a single enzyme unit without intermediate release, yet in
B. braunii
, these activities appear to have separated and evolved interdependently for specialized triterpene oil production greater than 500 MYA. Coexpression of the SSL-1 and SSL-3 genes in different configurations, as independent genes, as gene fusions, or targeted to intracellular membranes, also demonstrate the potential for engineering even greater efficiencies of botryococcene biosynthesis.
Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore-only proteins
Authors: Shaya David , Kreir Mohamed , Robbins Rebecca A. , Wong Stephanie , Hammon Justus , Brüggemann Andrea , Minor Daniel L.
Published: July 2011

Many voltage-gated ion channel (VGIC) superfamily members contain six-transmembrane segments in which the first four form a voltage-sensing domain (VSD) and the last two form the pore domain (PD). Studies of potassium channels from the VGIC superfamily together with identification of voltage-sensor only proteins have suggested that the VSD and the PD can fold independently. Whether such transmembrane modularity is common to other VGIC superfamily members has remained untested. Here we show, using protein dissection, that theSilicibacter pomeroyivoltage-gated sodium channel (NaVSp1) PD forms a stand-alone, ion selective pore (NaVSp1p) that is tetrameric, α-helical, and that forms functional, sodium-selective channels when reconstituted into lipid bilayers. Mutation of the NaVSp1p selectivity filter from LESWSM to LDDWSD, a change similar to that previously shown to alter ion selectivity of the bacterial sodium channel NaVBh1 (NaChBac), creates a calcium-selective pore-only channel, CaVSp1p. We further show that production of PDs can be generalized by making pore-only proteins from two other extremophile NaVs: one from the hydrocarbon degraderAlcanivorax borkumensis(NaVAb1p), and one from the arsenite oxidizerAlkalilimnicola ehrlichei(NaVAe1p). Together, our data establish a family of active pore-only ion channels that should be excellent model systems for study of the factors that govern both sodium and calcium selectivity and permeability. Further, our findings suggest that similar dissection approaches may be applicable to a wide range of VGICs and, thus, serve as a means to simplify and accelerate biophysical, structural, and drug development efforts.
Structure of FcRY, an avian immunoglobulin receptor related to mammalian mannose receptors, and its complex with IgY
Authors: He Yongning , Bjorkman Pamela J.
Published: July 2011

Fc receptors transport maternal antibodies across epithelial cell barriers to passively immunize newborns. FcRY, the functional counterpart of mammalian FcRn (a major histocompatibility complex homolog), transfers IgY across the avian yolk sac, and represents a new class of Fc receptor related to the mammalian mannose receptor family. FcRY and FcRn bind immunoglobulins at pH ≤6.5, but not pH ≥7, allowing receptor–ligand association inside intracellular vesicles and release at the pH of blood. We obtained structures of monomeric and dimeric FcRY and an FcRY–IgY complex and explored FcRY's pH-dependent binding mechanism using electron cryomicroscopy (cryoEM) and small-angle X-ray scattering. The cryoEM structure of FcRY at pH 6 revealed a compact double-ring “head,” in which the N-terminal cysteine-rich and fibronectin II domains were folded back to contact C-type lectin-like domains 1–6, and a “tail” comprising C-type lectin-like domains 7–8. Conformational changes at pH 8 created a more elongated structure that cannot bind IgY. CryoEM reconstruction of FcRY dimers at pH 6 and small-angle X-ray scattering analysis at both pH values confirmed both structures. The cryoEM structure of the FcRY–IgY revealed symmetric binding of two FcRY heads to the dimeric FcY, each head contacting the CH4 domain of one FcY chain. FcRY shares structural properties with mannose receptor family members, including a head and tail domain organization, multimerization that may regulate ligand binding, and pH-dependent conformational changes. Our results facilitate understanding of immune recognition by the structurally related mannose receptor family and comparison of diverse methods of Ig transport across evolution.
Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth
Authors: Zhao Bo , Zou James , Wang Hongfang , Johannsen Eric , Peng Chih-wen , Quackenbush John , Mar Jessica C. , Morton Cynthia Casson , Freedman Matthew L. , Blacklow Stephen C. , Aster Jon C. , Bernstein Bradley E. , Kieff Elliott
Published: July 2011

Epstein-Barr virus nuclear antigen 2 (EBNA2) regulation of transcription through the cell transcription factor RBPJ is essential for resting B-lymphocyte (RBL) conversion to immortal lymphoblast cell lines (LCLs). ChIP-seq of EBNA2 and RBPJ sites in LCL DNA found EBNA2 at 5,151 and RBPJ at 10,529 sites. EBNA2 sites were enriched for RBPJ (78%), early B-cell factor (EBF, 39%), RUNX (43%), ETS (39%), NFκB (22%), and PU.1 (22%) motifs. These motif associations were confirmed by LCL RBPJ ChIP-seq finding 72% RBPJ occupancy and Encyclopedia Of DNA Elements LCL ChIP-seq finding EBF, NFκB RELA, and PU.1 at 54%, 31%, and 17% of EBNA2 sites. EBNA2 and RBPJ were predominantly at intergene and intron sites and only 14% at promoter sites. K-means clustering of EBNA2 site transcription factors identified RELA-ETS, EBF-RUNX, EBF, ETS, RBPJ, and repressive RUNX clusters, which ranked from highest to lowest in H3K4me1 signals and nucleosome depletion, indicative of active chromatin. Surprisingly, although quantitatively less, the same genome sites in RBLs exhibited similar high-level H3K4me1 signals and nucleosome depletion. The EBV genome also had an LMP1 promoter EBF site, which proved critical for EBNA2 activation. LCL HiC data mapped intergenic EBNA2 sites to EBNA2 up-regulated genes. FISH and chromatin conformation capture linked EBNA2/RBPJ enhancers 428 kb 5′ of
MYC
to
MYC
. These data indicate that EBNA2 evolved to target RBL H3K4me1 modified, nucleosome-depleted, nonpromoter sites to drive B-lymphocyte proliferation in primary human infection. The primed RBL program likely supports antigen-induced proliferation.
Relation of addiction genes to hypothalamic gene changes subserving genesis and gratification of a classic instinct, sodium appetite
Authors: Liedtke Wolfgang B. , McKinley Michael J. , Walker Lesley L. , Zhang Hao , Pfenning Andreas R. , Drago John , Hochendoner Sarah J. , Hilton Donald L. , Lawrence Andrew J. , Denton Derek A.
Published: July 2011

Sodium appetite is an instinct that involves avid specific intention. It is elicited by sodium deficiency, stress-evoked adrenocorticotropic hormone (ACTH), and reproduction. Genome-wide microarrays in sodium-deficient mice or after ACTH infusion showed up-regulation of hypothalamic genes, including dopamine- and cAMP-regulated neuronal phosphoprotein 32 kDa (DARPP-32), dopamine receptors-1 and -2, α-2C- adrenoceptor, and striatally enriched protein tyrosine phosphatase (STEP). Both DARPP-32 and neural plasticity regulator activity-regulated cytoskeleton associated protein (ARC) were up-regulated in lateral hypothalamic orexinergic neurons by sodium deficiency. Administration of dopamine D1 (SCH23390) and D2 receptor (raclopride) antagonists reduced gratification of sodium appetite triggered by sodium deficiency. SCH23390 was specific, having no effect on osmotic-induced water drinking, whereas raclopride also reduced water intake. D1 receptor KO mice had normal sodium appetite, indicating compensatory regulation. Appetite was insensitive to SCH23390, confirming the absence of off-target effects. Bilateral microinjection of SCH23390 (100 nM in 200 nL) into rats’ lateral hypothalamus greatly reduced sodium appetite. Gene set enrichment analysis in hypothalami of mice with sodium appetite showed significant enrichment of gene sets previously linked to addiction (opiates and cocaine). This finding of concerted gene regulation was attenuated on gratification with perplexingly rapid kinetics of only 10 min, anteceding significant absorption of salt from the gut. Salt appetite and hedonic liking of salt taste have evolved over >100 million y (e.g., being present in Metatheria). Drugs causing pleasure and addiction are comparatively recent and likely reflect usurping of evolutionary ancient systems with high survival value by the gratification of contemporary hedonic indulgences. Our findings outline a molecular logic for instinctive behavior encoded by the brain with possible important translational–medical implications.