bluuebunny/crossref_metadata_2025 huggingface dataset:
Using a Web Page Design Activity to Promote Active Learning of Course Content in an Undergraduate Anatomy and Physiology Course
Authors: Walden Patrick R.
Published: October 2009

The purpose of this study was to evaluate student perceptions of a Web page design activity as a learning activity in an undergraduate anatomy and physiology course. One class of undergraduate majors in Speech-Language Pathology and Audiology who took part in CSD 1720: Anatomy and Physiology of the Speech Mechanism at St. John’s University’s Staten Island Campus was solicited to voluntarily and anonymously complete an online survey regarding their perceptions of the utility of building a Web page to learn course content. Nine (34.6%) of the possible 26 students enrolled in the course completed the survey. Most respondents were freshmen or sophomores. No respondent indicated that he or she was technologically incompetent. Complete survey results were communicated in tabular format. Overall, student respondents to the survey indicated positive perceptions regarding the utility of building a Web page to enhance recall and understanding of course concepts in an undergraduate anatomy and physiology course. Recommendations for future research include the continued survey of future students to make a better-informed judgment regarding the use of this activity to improve student learning of course content.
Developing Professionalism in Our Student Clinicians
Authors: Breen Phyllis , Murphy Kathy
Published: October 2009

The teaching of professionalism has become a prominent topic among academic and clinical faculty members who teach future speech-language pathologists and audiologists. This article grew from a series of conferences and discussions generated by the Midwest Clinic Directors Group and a collaborative teaching initiative conducted by the authors. Results included an interdisciplinary program and methods to measure professional development among students in Communication Sciences and Disorders (CSD) programs. This article describes the process that led to both of these outcomes and poses questions for clinical and academic faculty members in CSD programs to focus on teaching professionalism throughout the curriculum.
Professional Performance Review Process: Your Best PR Tool
Authors: Schraeder Patricia (Trici)
Published: October 2009

The Professional Performance Review Process (PPRP) was designed specifically for the school-based speech-language pathologist and enhances the four major purposes of professional performance review that have been identified in educational literature. The PPRP combines a formative self-reflection tool (including workload analysis) with a summative evaluation process.
Text Comprehension: Graphic Organizers to the Rescue
Authors: Proly Janet L. , Rivers Jessica , Schwartz Jamie
Published: October 2009

Graphic organizers are a research based strategy used for facilitating the reading comprehension of expository text. This strategy will be defined and the evolution and supporting evidence for the use of graphic organizers will be discussed. Various types of graphic organizers and resources for SLPs and other educators will also be discussed.
Assembly of viruses and the pseudo-law of mass action
Authors: Morozov Alexander Yu. , Bruinsma Robijn F. , Rudnick Joseph
Published: October 2009

The self-assembly of the protein shell (“capsid”) of a virus appears to obey the law of mass action (LMA) despite the fact that viral assembly is a nonequilibrium process. In this paper we examine a model for capsid assembly, the “assembly line model,” that can be analyzed analytically. We show that, in this model, efficient viral assembly from a supersaturated solution is characterized by a shock front propagating in the assembly configuration space from small to large aggregate sizes. If this shock front can reach the size of assembled capsids, then capsid assembly follows either the LMA or a “pseudo” LMA that describes partitioning of capsid proteins between assembled capsids and a metastable, supersaturated solution of free proteins that decays logarithmically slowly. We show that the applicability of the LMA and the pseudo-LMA is governed by two dimensionless parameters: the dimensionless nucleation rate and the dimensionless line energy of incomplete capsids.
Simultaneous in-plane and out-of-plane exchange bias using a single antiferromagnetic layer resolved by x-ray magnetic circular dichroism
Authors: Nogués J. , Stepanow S. , Bollero A. , Sort J. , Dieny B. , Nolting F. , Gambardella P.
Published: October 2009

We present a study of exchange bias in ferromagnet/antiferromagnet/ferromagnet (FM/AFM/FM) trilayers, with in-plane and out-plane easy axes. Using element-specific x-ray magnetic circular dichroism, we demonstrate that simultaneous in-plane and out-of-plane exchange bias can be induced using a single antiferromagnet and zero field cooling, whereas field cooling only induces exchange bias to the layer with easy axis parallel to the cooling field. Our results further evidence the presence of pinned uncompensated moments in both the FM and AFM layers, implying that the AFM layer is capable of supporting uncompensated spins in two orthogonal directions at the same time.
Nature of interfacial defects and their roles in strain relaxation at highly lattice mismatched 3C-SiC/Si (001) interface
Authors: Wen C. , Wang Y. M. , Wan W. , Li F. H. , Liang J. W. , Zou J.
Published: October 2009

Misfit defects in a 3C-SiC/Si (001) interface were investigated using a 200 kV high-resolution electron microscope with a point resolution of 0.194 nm. The [110] high-resolution electron microscopic images that do not directly reflect the crystal structure were transformed into the structure map through image deconvolution. Based on this analysis, four types of misfit dislocations at the 3C-SiC/Si (001) interface were determined. In turn, the strain relaxation mechanism was clarified through the generation of grow-in perfect misfit dislocations (including 90° Lomer dislocations and 60° shuffle dislocations) and 90° partial dislocations associated with stacking faults.
Forming-free colossal resistive switching effect in rare-earth-oxide Gd2O3 films for memristor applications
Authors: Cao Xun , Li Xiaomin , Gao Xiangdong , Yu Weidong , Liu Xinjun , Zhang Yiwen , Chen Lidong , Cheng Xinhong
Published: October 2009

The reproducible forming-free resistive switching (RS) behavior in rare-earth-oxide Gd2O3 polycrystalline thin film was demonstrated. The characteristic of this forming-free RS was similar to that of other forming-necessary binary RS materials except that its initial resistance starts from not the high resistance state (HRS) but the low resistance state (LRS). An ultrahigh resistance switching ratio from HRS to LRS of about six to seven orders of magnitude was achieved at a bias voltage of 0.6 V. Mechanism analysis indicated that the existence of metallic Gd in the Gd2O3 films plays an important role in the forming-free RS performance. Our work provides a novel material with interesting RS behavior, which is beneficial to deepen our understanding of the origin of RS phenomenon.
Transmission of cluster ions through a tandem accelerator of several stripper gases
Authors: Saitoh Yuichi , Chiba Atsuya , Narumi Kazumasa
Published: October 2009

The transmissions of carbon cluster ion beams through a tandem accelerator using several stripper gases (He, N2, CO2, and SF6) with a terminal voltage of 2.5 MV were measured as a function of the gas pressure in investigating the most suitable gas for cluster ion acceleration. This resulted in it being demonstrated that the highest transmission could be obtained using the smaller size gas, i.e., helium displayed the best performance of the four gases used. In addition, the ratio of transmissions of Cn with helium and nitrogen increased with increases in the n, thus revealing that helium gas should prove the most effective in larger cluster ion acceleration using the same energy.
Measurements of current-voltage-induced heating in the Al/SrTiO3−xNy/Al memristor during electroformation and resistance switching
Authors: Shkabko A. , Aguirre M. H. , Marozau I. , Lippert T. , Weidenkaff A.
Published: October 2009

Heating of the Al/SrTiO3−xNy/Al memristor is characterized during electroformation and switching of the resistances. The electrode with the higher voltage potential is heated to higher temperatures than the electrode with the lower potential, suggesting a reversible (nonstable) displacement of the anions in a low voltage region (|V|<±3 V). Application of a threshold voltage appropriate for resistance switching (|V|≥±3 V) facilitates migration of anions to the anode interface and increases the local anode temperature to a maximum of 285 °C. The hysteretic I-V curves are discussed taking into account tunnel barrier formation/break and inhomogeneous Schottky barrier modification at the anode interface.
Magnetic-electric behaviors in BiFeO3 films grown on LaNiO3-buffered Si substrate
Authors: Wang Yao , Li Zheng , Lin Yuanhua , Nan C. W.
Published: October 2009

BiFeO 3 films with different thicknesses and crystallographic orientations were grown on LaNiO3-buffered Si substrates via a modified chemical route. Remarkable size effect in ferroelectric behavior was observed with thicker films exhibiting a larger polarization value, due to combined depolarization effect and microstructure of the BiFeO3 films. High resolution transmission electron micrograph revealed a complex strain state in the BiFeO3 films, and the net magnetic moment induced by the canting of the antiparallel spins was arranged in disorder in thicker films, presenting a spin-glass state; while in the thinner BiFeO3 films, the disorder spins turned to be orderly arranged to induce a ferromagnetic behavior. Thus there exists a competition between ferroelectric and magnetic behaviors as film thickness changes. Furthermore, magnetoelectric coupling was observed in the BiFeO3 films with a magnetic-field-induced electrical voltage of around 3.5 μV/Oe.
Si nanocrystal p-i-n diodes fabricated on quartz substrates for third generation solar cell applications
Authors: Perez-Wurfl Ivan , Hao Xiaojing , Gentle Angus , Kim Dong-Ho , Conibeer Gavin , Green Martin. A.
Published: October 2009

We fabricated p-i-n diodes by sputtering alternating layers of silicon dioxide and silicon rich oxide with a nominal atomic ratio O/Si=0.7 onto quartz substrates with in situ boron for p-type and phosphorus for n-type doping. After crystallization, dark and illuminated I-V characteristics show a diode behavior with an open circuit voltage of 373 mV. Due to the thinness of the layers and their corresponding high resistivity, lateral current flow results in severe current crowding. This effect is taken into account when extracting the electronic bandgap based on temperature dependent diode I-V measurements.
Continuous wavelet transform based time-scale and multifractal analysis of the nonlinear oscillations in a hollow cathode glow discharge plasma
Authors: Nurujjaman Md. , Narayanan Ramesh , Iyengar A. N. Sekar
Published: October 2009

Continuous wavelet transform (CWT) based time-scale and multifractal analyses have been carried out on the anode glow related nonlinear floating potential fluctuations in a hollow cathode glow discharge plasma. CWT has been used to obtain the contour and ridge plots. Scale shift (or inversely frequency shift), which is a typical nonlinear behavior, has been detected from the undulating contours. From the ridge plots, we have identified the presence of nonlinearity and degree of chaoticity. Using the wavelet transform modulus maxima technique we have obtained the multifractal spectrum for the fluctuations at different discharge voltages and the spectrum was observed to become a monofractal for periodic signals. These multifractal spectra were also used to estimate different quantities such as the correlation and fractal dimension, degree of multifractality, and complexity parameters. These estimations have been found to be consistent with the nonlinear time series analysis.
Optimization of a gas discharge plasma source for extreme ultraviolet interference lithography at a wavelength of 11 nm
Authors: Bergmann K. , Danylyuk S. V. , Juschkin L.
Published: October 2009

In this work, we report about the optimization of the spectral emission characteristic of a gas discharge plasma source for high-resolution extreme ultraviolet (EUV) interference lithography based on achromatic Talbot self-imaging. The working parameters of the source are optimized to achieve a required narrowband emission spectrum and to fulfill the necessary coherence and intensity requirements. The intense 4f-4d transitions around 11 nm in a highly ionized (Xe8+–Xe12+) xenon plasma are chosen to provide the working wavelength. This allows us to increase the available radiation intensity in comparison with an in-band EUV xenon emission at 13.5 nm and opens up the possibility to strongly suppress the influence of the 5p-4d transitions at wavelengths between 12 and 16 nm utilizing a significant difference in conditions for optical thickness between 4f-4d and 5p-4d transitions. The effect is achieved by using the admixture of argon to the pinch plasma, which allows keeping the plasma parameters approximately constant while, at the same time, reducing the density of xenon emitters. It is demonstrated that with this approach it is possible to achieve a high intensity 11 nm EUV radiation with a bandwidth of 3%–4% without the use of multilayer mirrors or other additional spectral filters in the vicinity of the working wavelength. The achieved radiation parameters are sufficient for high-performance interference lithography based on the achromatic Talbot effect.
Implementation of the incremental scheme for one-electron first-order properties in coupled-cluster theory
Authors: Friedrich Joachim , Coriani Sonia , Helgaker Trygve , Dolg Michael
Published: October 2009

A fully automated parallelized implementation of the incremental scheme for coupled-cluster singles-and-doubles (CCSD) energies has been extended to treat molecular (unrelaxed) first-order one-electron properties such as the electric dipole and quadrupole moments. The convergence and accuracy of the incremental approach for the dipole and quadrupole moments have been studied for a variety of chemically interesting systems. It is found that the electric dipole moment can be obtained to within 5% and 0.5% accuracy with respect to the exact CCSD value at the third and fourth orders of the expansion, respectively. Furthermore, we find that the incremental expansion of the quadrupole moment converges to the exact result with increasing order of the expansion: the convergence of nonaromatic compounds is fast with errors less than 16 mau and less than 1 mau at third and fourth orders, respectively (1 mau=10−3ea02); the aromatic compounds converge slowly with maximum absolute deviations of 174 and 72 mau at third and fourth orders, respectively.
Separating forward and backward pathways in nonequilibrium umbrella sampling
Authors: Dickson Alex , Warmflash Aryeh , Dinner Aaron R.
Published: October 2009

Umbrella sampling enforces uniform sampling of steady-state distributions that are functions of arbitrary numbers of order parameters. The key to applying such methods to nonequilibrium processes is the accumulation of fluxes between regions. A significant difference between microscopically reversible and irreversible systems is that, in the latter case, the transition path ensemble for a reaction can be significantly different for “forward” and “backward” trajectories. Here, we show how to separately treat forward and backward pathways in nonequilibrium umbrella sampling simulations by working in an extended space. In this extended space, the exact rate (for equilibrium or nonequilibrium processes) can be calculated “for free” as a flux in phase space. We compare the efficiency of this rate calculation with forward flux sampling for a two-dimensional potential and show that nonequilibrium umbrella sampling is more efficient when an intermediate is present. We show that this technique can also be used to describe steady-state limit cycles by examining a simulation of circadian oscillations. We obtain the path of the limit cycle in a space of 22 order parameters, as well as the oscillation period. The relation of our method to others is discussed.
Dust kinetic Alfvén and acoustic waves in a Lorentzian plasma
Authors: Rubab N. , Erkaev N. V. , Biernat H. K.
Published: October 2009

Dust kinetic Alfvén waves (DKAWs) with finite Larmor radius effects have been examined rigorously in a uniform dusty plasma in the presence of an external magnetic field. A dispersion relation of low-frequency DKAW on the dust acoustic velocity branch is obtained in a low-β Lorentzian plasma. It is found that the influence of the Lorentzian distribution function is more effective for perpendicular component of group velocity as compared with parallel one. Lorentzian-type charging currents are obtained with the aid of Vlasov theory. Damping/instability due to dust charge fluctuation is found to be insensitive with the form of distribution function for DKAW. The possible applications to dusty space plasmas are pointed out.
Micro-Hall position sensing of magnetic nanowires
Authors: Mihajlović G. , Hoffmann A. , von Molnár S.
Published: October 2009

The Hall voltage output of a micro-Hall magnetic sensor depends on the relative position of a magnetic nanowire with respect to its sensing area. Following this idea, we performed analytical calculations which show that, under certain conditions, these devices can track the position of a magnetic nanowire with subnanometer resolution. Our results suggest that micro-Hall sensors can be utilized to provide a direct electronic readout of the position of magnetic nanowires in their applications as biomolecular manipulators or dynamic components in micro- and nanoscale devices.
Automated calculation of anharmonic vibrational contributions to first hyperpolarizabilities: Quadratic response functions from vibrational configuration interaction wave functions
Authors: Hansen Mikkel Bo , Christiansen Ove , Hättig Christof
Published: October 2009

Quadratic response functions are derived and implemented for a vibrational configuration interaction state. Combined electronic and vibrational quadratic response functions are derived using Born–Oppenheimer vibronic product wave functions. Computational tractable expressions are derived for determining the total quadratic response contribution as a sum of contributions involving both electronic and vibrational linear and quadratic response functions. In the general frequency-dependent case this includes a new and more troublesome type of electronic linear response function. Pilot calculations for the FH, H2O, CH2O, and pyrrole molecules demonstrate the importance of vibrational contributions for accurate comparison to experiment and that the vibrational contributions in some cases can be very large. The calculation of transition properties between vibrational states is combined with sum-over-states expressions for analysis purposes. On the basis of this some simple analysis methods are suggested. Also, a preliminary study of the effect of finite lifetimes on quadratic response functions is presented.
Basic results on the equations of magnetohydrodynamics of partially ionized inviscid plasmas
Authors: Núñez Manuel
Published: October 2009

The equations of evolution of partially ionized plasmas have been far more studied in one of their many simplifications than in its original form. They present a relation between the velocity of each species, plus the magnetic and electric fields, which yield as an analog of Ohm’s law a certain elliptic equation. Therefore, the equations represent a functional evolution system, not a classical one. Nonetheless, a priori estimates and theorems of existence may be obtained in appropriate Sobolev spaces.
Excess of low frequency vibrational modes and glass transition: A molecular dynamics study for soft spheres at constant pressure
Authors: Flores-Ruiz Hugo M. , Naumis Gerardo G.
Published: October 2009

Using molecular dynamics at constant pressure, the relationship between the excess of low frequency vibrational modes (known as the boson peak) and the glass transition is investigated for a truncated Lennard-Jones potential. It is observed that the quadratic mean displacement is enhanced by such modes, as predicted using a harmonic Hamiltonian for metastable states. As a result, glasses loose mechanical stability at lower temperatures than the corresponding crystal, since the Lindemann criteria are observed, as is also deduced from density functional theory. Finally, we found that the average force and elastic constant are reduced in the glass due to such excess of modes. The ratio between average elastic constants can be approximated using the 2/3 rule between melting and glass transition temperatures.
Impact of surface charges on the solvation forces in confined colloidal solutions
Authors: Grandner Stefan , Zeng Yan , Klitzing Regine v. , Klapp Sabine H. L.
Published: October 2009

Combining computer simulations and experiments we address the impact of charged surfaces on the solvation forces of a confined, charged colloidal suspension (slit-pore geometry). Investigations based on the colloidal-probe atomic-force-microscope technique indicate that an increase in surface charges markedly enhances the oscillations of the force in terms of their amplitude. To understand this effect on a theoretical level we perform grand-canonical Monte-Carlo simulations (GCMC) of a coarse-grained model system. It turns out that various established approaches of the interaction between a charged colloid and a charged wall, such as linearized Poisson–Boltzmann (PB) theory involving the bulk screening length, do not reproduce the experimental observations. We thus introduce a modified PB potential with a space-dependent screening parameter. The latter takes into account, in an approximate way, the fact that the charged walls release additional (wall) counterions which accumulate in a thin layer at the surface(s). The resulting, still purely repulsive fluid-wall potential displays a nonmonotonic behavior as function of the surface potential with respect to the strength and range of repulsion. GCMC simulations based on this potential reproduce the experimentally observed charge-induced enhancement in the force oscillations. We also show, both by experiment and by simulations, that the asymptotic wave- and decay length of the oscillating force do not change with the wall charge, in agreement with predictions from density functional theory.
Identical phase oscillators with global sinusoidal coupling evolve by Möbius group action
Authors: Marvel Seth A. , Mirollo Renato E. , Strogatz Steven H.
Published: October 2009

Systems of N identical phase oscillators with global sinusoidal coupling are known to display low-dimensional dynamics. Although this phenomenon was first observed about 20 years ago, its underlying cause has remained a puzzle. Here we expose the structure working behind the scenes of these systems by proving that the governing equations are generated by the action of the Möbius group, a three-parameter subgroup of fractional linear transformations that map the unit disk to itself. When there are no auxiliary state variables, the group action partitions the N-dimensional state space into three-dimensional invariant manifolds (the group orbits). The N−3 constants of motion associated with this foliation are the N−3 functionally independent cross ratios of the oscillator phases. No further reduction is possible, in general; numerical experiments on models of Josephson junction arrays suggest that the invariant manifolds often contain three-dimensional regions of neutrally stable chaos.
Spin-flip processes of polarons by magnetic impurities in conjugated polymers
Authors: Zhao Hui , Chen Yu-Guang , Yao Yao , Wu Chang-Qin , Zhang Xu-Ming , An Zhong
Published: October 2009

By employing an adaptive time-dependent density-matrix-renormalization-group method, the spin-flip process of polarons is investigated in a polymer chain with magnetic impurities. Being driven by an external electric field, a polaron carrying both spin 1/2 and charge ±e moves at a constant speed in the polymer chain. When the polaron passes through a specific site, which couples to a magnetic impurity via spin-exchange interaction, a spin-flip process is observed if its spin is antiparallel to the impurity spin. Our results show that the spin-flip probability is enhanced by the on-site Coulomb interaction and increases with increase in the spin-exchange integral. Additionally, some possible applications of the spin-state swap between the polaron and the impurity are discussed.
Enhancement of p-type conductivity by modifying the internal electric field in Mg- and Si-δ-codoped AlxGa1−xN/AlyGa1−yN superlattices
Authors: Li Jinchai , Yang Weihuang , Li Shuping , Chen Hangyang , Liu Dayi , Kang Junyong
Published: October 2009

The internal electric field is modified by using Mg- and Si-δ-codoped AlxGa1−xN/AlyGa1−yN superlattices (SLs). The first-principles simulation results show that the internal electric field in SL has been significantly intensified due to the charge transferring from Si-doped interface to Mg-doped interface. Accordingly, the Mg- and Si-δ-codoped p-type Al0.2Ga0.8N/GaN SLs are grown by metalorganic vapor phase epitaxy and higher hole concentration as much as twice of that in modulation-doped SL has been achieved, as determined by Hall effect measurements. Furthermore, by applying Mg- and Si-δ-codoped AlxGa1−xN/AlyGa1−yN SLs with high Al content as the p-type layers, we have fabricated deep ultraviolet light emitting diodes with superior current-voltage characteristics by lowering Mg-acceptor activation energy.
Terahertz spectroscopy of shift currents resulting from asymmetric (110)-oriented GaAs/AlGaAs quantum wells
Authors: Priyadarshi Shekhar , Leidinger Markus , Pierz Klaus , Racu Ana M. , Siegner Uwe , Bieler Mark , Dawson Philip
Published: October 2009

We report the observation and the study of an additional shift current tensor element in (110)-oriented GaAs quantum wells, which arises from an out-of-plane asymmetry of the quantum well structure. The current resulting from this tensor element is optically induced with 150 fs laser pulses and detected by measuring the simultaneously emitted terahertz radiation. This terahertz spectroscopy of shift currents is a powerful technique for symmetry investigations, which shows, for example, that our nominally symmetric (110)-oriented GaAs/AlGaAs quantum wells grown by molecular beam epitaxy are in reality asymmetric structures with different right and left interfaces.
The internal energy of CO2 produced by the catalytic oxidation of CH3OH by O2 on polycrystalline platinum
Authors: Peng T. L. , Bernasek S. L.
Published: October 2009

The dynamics of steady state catalytic methanol oxidation on a polycrystalline Pt surface over a range of surface temperatures and reactant flow conditions were investigated by monitoring the kinetics with mass spectrometry and the internal state distribution of nascent CO2 with tunable diode laser absorption spectroscopy. The results indicate that CO2 formation proceeds via three distinct reaction pathways. The first produced CO2, which is vibrationally excited relative to CO2 in thermal equilibrium with the surface and shows preferential excitation in the asymmetric stretch. This pathway proceeds via the decomposition of CH3OH and the subsequent oxidation of nascent CO adsorbed to Pt in a weakly held precursor state. CO2 production via this pathway is favored at high surface temperatures and high oxygen coverage. The second forms CO2, which is vibrationally deactivated relative to CO2 in thermal equilibrium with the surface and exhibits no preferential excitation among its three nondegenerate vibrational modes or the rotational energy. This pathway involves the decomposition of CH3OH and subsequent oxidation of nascent CO adsorbed to Pt in a more strongly held chemisorbed state. CO2 production via this pathway is favored at low surface temperatures and low oxygen coverage. The third forms CO2 with preferential excitation in the asymmetric stretch but with less overall vibrational excitation than CO2 from the first pathway and more vibrational excitation than CO2 from the second. This third pathway occurs via the complete dehydrogenation of CH3OH and subsequent oxidation of nascent CO adsorbed to Pt in a bridged state bound through both ends of the molecule. CO2 production via this pathway is favored at intermediate surface temperatures and oxygen coverage, conditions which favor overall oxidation to form CO2.
Shaping the response pulse of superconducting nanowire single photon detection with a snubber
Authors: You L. X. , Shen X. F.
Published: October 2009

Unavoidable kinetic inductance of the superconducting nanowire single photon detector results in the signal pulse with a slow falling edge and a large pulse width. It has been a limit for improving the repetition rate for single photon detection. With a snubber made of a coaxial cable terminated with a resistive pot, the original signal pulse can be shaped. A sharp falling edge can be produced with suitable snubber parameters and the final output pulse has a symmetric wave. The pulse width (full width at half maximum) is reduced from 5 to 1 ns.
Corrigendum to: Piggery pond sludge as a nitrogen source for crops. 1. Mineral N supply estimated from laboratory incubations and field application of stockpiled and wet sludge
Authors: Kliese Y. J. , Dalal R. C. , Strong W. M. , Menzies N. W.
Published: October 2009

Piggery pond sludge (PPS) was applied, as-collected (Wet PPS) and following stockpiling for 12 months (Stockpiled PPS), to a sandy Sodosol and clay Vertosol at sites on the Darling Downs of Queensland. Laboratory measures of N availability were carried out on unamended and PPS-amended soils to investigate their value in estimating supplementary N needs of crops in Australia's northern grains region. Cumulative net N mineralised from the long-term (30 weeks) leached aerobic incubation was described by a first-order single exponential model. The mineralisation rate constant (0.057/week) was not significantly different between Control and PPS treatments or across soil types, when the amounts of initial mineral N applied in PPS treatments were excluded. Potentially mineralisable N (No) was significantly increased by the application of Wet PPS, and increased with increasing rate of application. Application of Wet PPS significantly increased the total amount of inorganic N leached compared with the Control treatments. Mineral N applied in Wet PPS contributed as much to the total mineral N status of the soil as did that which mineralised over time from organic N. Rates of CO2 evolution during 30 weeks of aerobic leached incubation indicated that the Stockpiled PPS was more stabilised (19.28% of applied organic C mineralised) than the Wet PPS (35.58% of applied organic C mineralised), due to higher lignin content in the former. Net nitrate-N produced following 12 weeks of aerobic non-leached incubation was highly correlated with net nitrate-N leached during 12 weeks of aerobic incubation (R2 = 0.96), although it was <60% of the latter in both sandy and clayey soils. Anaerobically mineralisable N determined by waterlogged incubation of laboratory PPS-amended soil samples increased with increasing application rate of Wet PPS. Anaerobically mineralisable N from field-moist soil was well correlated with net N mineralised during 30 weeks of aerobic leached incubation (R2 = 0.90 sandy soil; R2 = 0.93 clay soil). In the clay soil, the amount of mineral N produced from all the laboratory incubations was significantly correlated with field-measured nitrate-N in the soil profile (0.1.5 m depth) after 9 months of weed-free fallow following PPS application. In contrast, only anaerobic mineralisable N was significantly correlated with field nitrate-N in the sandy soil. Anaerobic incubation would, therefore, be suitable as a rapid practical test to estimate potentially mineralisable N following applications of different PPS materials in the field.
Water-use efficiency of dryland canola in an equi-seasonal rainfall environment
Authors: Robertson Michael J. , Kirkegaard John A.
Published: October 2009

The French and Shultz approach that relates seasonal rainfall to potential yield in wheat has yet to be applied to dryland canola. Relationships were derived between grain yield of 42 experimental crops (yield range 0.5–5.4 t/ha) free of weeds, pests, diseases, and nutrient deficiencies in southern New South Wales, and various measures of observed (rainfall, available soil water) and simulated (evapotranspiration) seasonal water supply. April to October rainfall and in-crop rainfall were the poorest predictors of yield (R2 < 0.5). By adjusting in-crop rainfall to account for stored soil water at sowing and that remaining at harvest (termed ‘seasonal water supply’), 68% of the variance in yield could be explained. Estimates derived using the APSIM-Canola simulation model or simulated totals of evapotranspiration or transpiration explained 73–82% of the variance. The slope of the regression line between yield of the 42 crops, which simulation indicated had all yielded to their water-limited potential, and seasonal water supply (termed here the water-use efficiency for grain production, WUE) was 11 kg/ha.mm above an intercept of 120 mm. WUE varied from 4 to 18 kg/ha.mm and the upper boundary for WUE in those seasons where rainfall distribution facilitated maximum efficiency was 15 kg/ha.mm. Long-term simulations, conducted at locations with mean annual rainfall of 430–660 mm, confirmed the variability of WUE due to rainfall distribution and also that WUE would be expected to decline, on average, by one-third between sowings in early April and early July. This necessitates caution in accepting a single WUE value as an indicator of agronomic constraints to yield. For the purposes of practical application by farmers and advisors, water-limited potential yield can be calculated in the region as a function of seasonal water supply minus 120 mm up to a limit of 450 mm, beyond which potential yield is not limited by water. Available soil water at sowing can be estimated from summer fallow rainfall above a threshold of 80 mm, and water remaining at harvest can be estimated from post-anthesis rainfall above a threshold of 50 mm. This improved method for estimating water-limited potential yield in canola retains the ease of use of the French and Shultz approach, so that other constraints to yield can be more accurately diagnosed in dryland environments by farmers and advisors.
Curation of wheat maps to improve map accuracy and QTL detection
Authors: Lehmensiek A. , Eckermann P. J. , Verbyla A. P. , Appels R. , Sutherland M. W. , Daggard G. E.
Published: October 2009

Three Australian doubled haploid populations were used to illustrate the importance of map curation in order to improve the quality of linkage maps and quantative trait locus (QTL) detection. The maps were refined and improved by re-examining the order of markers, inspection of the genetic maps in relation to a consensus map, editing the marker data for double crossovers, and determining estimated recombination fractions for all pairs of markers. The re-ordering of markers and replacing genotypes at double crossovers with missing values resulted in an overall decrease in the length of the maps. Fewer apparent genotyping errors, associated with the presence of double recombinants, were identified with restriction fragment length polymorphisms (RFLPs) than with other types of markers used in this study. The complications that translocations may cause in the ordering of markers and subsequent QTL analysis were investigated. QTL analysis using both the original and revised maps indicated that QTL peaks were more sharply located or had improved log-likelihood (LOD) scores in the revised maps. An accurate indication of the QTL peak and a significant LOD score are both essential for the identification of markers suitable for marker-assisted selection. Recommendations are provided for the improvement of the quality of linkage maps.
Comparison of small-scale and large-scale extensibility of dough produced from wheat flour
Authors: Mann Gulay , Allen Helen , Morell Matthew K. , Nath Zena , Martin Peter , Oliver John , Cullis Brian , Smith Alison
Published: October 2009

Extensibility and dough strength are key traits for varietal selection in most wheat-breeding programs. As there are several techniques for measuring these traits there is interest in examining the agreement between methods in terms of genotypic (varietal) rankings. We investigated this issue using 2 different extension methods; namely, small-scale (modified Kieffer) and large-scale (Brabender Extensograph) methods. Data were obtained from a doubled-haploid population (190 lines) from a Chara (high extensibility, excellent dough strength) × WW2449 (low extensibility, poor dough strength) cross that was grown in a field trial at the Wagga Wagga Agricultural Institute (WWAI) in 2000. Six extensional rheological traits were measured and compared according to a multivariate mixed statistical model. The estimated genetic correlation matrix for 4 of the 6 extensibility traits (R_Max, area, height, and resistance at 5 cm extension) revealed that for these dough strength related parameters, both methods were measuring equivalent traits. Comparisons of the extensibility traits length and extensibility at Rmax demonstrated that, although substantial amounts of the variance are controlled by the same glutenin loci, the traits differed in the allocation of variance across the loci, and the sources and magnitude of non-genetic variance. The data verified that small-scale testing is a robust and efficient alternative to large-scale testing for both commercial breeding and research.
RAMP based fingerprinting and assessment of relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars
Authors: Yuan H. , Yan G. , Siddique K. H. M. , Yang H.
Published: October 2009

Narrow-leafed lupin is a major winter grain legume crop in the Australian farming system and a number of commercial cultivars are currently available to growers. A significant level of polymorphism was detected in narrow-leafed lupin cultivars by the randomly amplified microsatellite polymorphism (RAMP) approach, suggesting that cultivars harbour considerable DNA variation. Seventy-seven cultivar-specific markers were found among the 23 lupin cultivars examined and a dichotomous fingerprinting key was developed for the molecular identification of lupin cultivars. Cluster analysis of pairwise distance matrix computed from RAMP profiles grouped the 23 cultivars into 4–5 clusters, which generally agreed with their pedigree relationships.
Myosin VI undergoes a 180° power stroke implying an uncoupling of the front lever arm
Authors: Reifenberger Jeff G. , Toprak Erdal , Kim HyeongJun , Safer Dan , Sweeney H. Lee , Selvin Paul R.
Published: October 2009

We simultaneously measure both the step size, via FIONA, and the 3-D orientation, via DOPI, of the light-chain domain of individual dimeric myosin VIs. This allows for the correlation of the change in orientation of the light chain domain to the stepping of the motor. Three different pairs of positions were tested using a rigid bifunctional rhodamine on the calmodulin of the IQ domain. The data for all three labeling positions support the model that the light chain domain undergoes a significant rotation of approximately 180°. Contrary to an earlier study [Sun, Y. et al. (2007)
Mol Cell
28, 954–964], our data does
not
support a model of multiple angles of the lever arm of the lead head, nor “wiggly” walking on actin. Instead, we propose that for the two heads of myosin VI to coordinate their processive movement, the lever arm of the lead head must be uncoupled from the converter until the rear head detaches. More specifically, intramolecular strain causes the myosin VI lever arm of the lead head to uncouple from the motor domain, allowing the motor domain to go through its product-release (phosphate and ADP) steps at an unstrained rate. The lever arm of the lead head rebinds to the motor and attains a rigor conformation when the rear head detaches. By coupling the orientation and position information with previously described kinetics, this allows us to explain how myosin VI coordinates its heads processively while maintaining the ability to move under load with a (semi-) rigid lever arm.
Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization
Authors: Teilum Kaare , Smith Melanie H. , Schulz Eike , Christensen Lea C. , Solomentsev Gleb , Oliveberg Mikael , Akke Mikael
Published: October 2009

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease linked to the misfolding of Cu/Zn superoxide dismutase (SOD1). ALS-related defects in SOD1 result in a gain of toxic function that coincides with aberrant oligomerization. The structural events triggering oligomerization have remained enigmatic, however, as is the case in other protein-misfolding diseases. Here, we target the critical conformational change that defines the earliest step toward aggregation. Using nuclear spin relaxation dispersion experiments, we identified a short-lived (0.4 ms) and weakly populated (0.7%) conformation of metal-depleted SOD1 that triggers aberrant oligomerization. This excited state emanates from the folded ground state and is suppressed by metal binding, but is present in both the disulfide-oxidized and disulfide-reduced forms of the protein. Our results pinpoint a perturbed region of the excited-state structure that forms intermolecular contacts in the earliest nonnative dimer/oligomer. The conformational transition that triggers oligomerization is a common feature of WT SOD1 and ALS-associated mutants that have widely different physicochemical properties. But compared with WT SOD1, the mutants have enhanced structural distortions in their excited states, and in some cases slightly higher excited-state populations and lower kinetic barriers, implying increased susceptibility to oligomerization. Our results provide a unified picture that highlights both (
i
) a common denominator among different SOD1 variants that may explain why diverse mutations cause the same disease, and (
ii
) a structural basis that may aid in understanding how different mutations affect disease propensity and progression.
Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct
Authors: Pandit Jayvardhan , Forman Michael D. , Fennell Kimberly F. , Dillman Keith S. , Menniti Frank S.
Published: October 2009

We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both catalytic and regulatory domains. PDE2A (215–900) crystallized as a dimer in which each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic domains connected by long α-helices. The subunits cross at the GAF-B/catalytic domain linker, and each side of the dimer contains in series the GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A dimer interface extends over the entire length of the molecule. The substrate binding pocket of each catalytic domain is occluded by the H-loop. We deduced from comparisons with structures of isolated, ligand-bound catalytic subunits that the H-loop swings out to allow substrate access. However, in dimeric PDE2A (215–900), the H-loops of the two catalytic subunits pack against each other at the dimer interface, necessitating movement of the catalytic subunits to allow for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215–900) with previous structures of isolated, cGMP-bound GAF domains indicates that cGMP binding induces a significant shift in the GAF-B/catalytic domain linker. We propose that cGMP binding to GAF-B causes movement, through this linker region, of the catalytic domains, such that the H-loops no longer pack at the dimer interface and are, instead, free to swing out to allow substrate access. This increase in substrate access is proposed as the basis for PDE2A activation by cGMP and may be a general mechanism for regulation of all PDEs.
A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans
Authors: Hammell Christopher M. , Karp Xantha , Ambros Victor
Published: October 2009

Animal development is remarkably robust; cell fates are specified with spatial and temporal precision despite physiological and environmental contingencies. Favorable conditions cause
Caenorhabditis elegans
to develop rapidly through four larval stages (L1–L4) to the reproductive adult. In unfavorable conditions, L2 larvae can enter the developmentally quiescent, stress-resistant dauer larva stage, enabling them to survive for prolonged periods before completing development. A specific progression of cell division and differentiation events occurs with fidelity during the larval stages, regardless of whether an animal undergoes continuous or dauer-interrupted development. The temporal patterning of developmental events is controlled by the heterochronic genes, whose products include microRNAs (miRNAs) and regulatory proteins. One of these proteins, the DAF-12 nuclear hormone receptor, modulates the transcription of certain let-7-family miRNAs, and also mediates the choice between the continuous vs. dauer-interrupted life history. Here, we report a complex feedback loop between DAF-12 and the let-7-family miRNAs involving both the repression of DAF-12 by let-7-family miRNAs and the ligand-modulated transcriptional activation and repression of the let-7-Fam miRNAs by DAF-12. We propose that this feedback loop functions to ensure robustness of cell fate decisions and to coordinate cell fate with developmental arrest.
Hitler'sRassenkampfin the East: The Forgotten Genocide of Soviet POWs
Authors: Porter Thomas Earl
Published: October 2009

The sheer enormity of Soviet losses at the hands of German forces during the Second World War staggers the mind. During the immediate post-war period, Stalin did not want the West to know just how badly the Soviet Union had been mauled or the fact that far more Soviet soldiers had died than German ones (up to three times as many); consequently, the Soviets clamed that thetotalnumber of dead was 7 million, while Western estimates were between 10 and 15 million Soviet dead. It was only during the Khrushchev era that the true scale of the disaster was revealed and the more accurate figure of 20 million dead was generally accepted. Of these, only half were soldiers. The rest were at least 10 million civilians, including 2 million who died as slave laborers in Nazi Germany. The death toll has more recently been put at 25, 27 and even 30 million, though I suspect the latter figures also take into consideration the decline in birth rates. In April 2009 Russian President Dmitrii Medvedev appointed yet another commission to give a final accounting of Soviet losses.