bluuebunny/crossref_metadata_2025 huggingface dataset:
Recombinant expression, reconstitution and structure of human anaphase-promoting complex (APC/C)
Authors: Zhang Ziguo , Yang Jing , Kong Eric H. , Chao William C. H. , Morris Edward P. , da Fonseca Paula C. A. , Barford David
Published: October 2012

Mechanistic and structural studies of large multi-subunit assemblies are greatly facilitated by their reconstitution in heterologous recombinant systems. In the present paper, we describe the generation of recombinant human APC/C (anaphase-promoting complex/cyclosome), an E3 ubiquitin ligase that regulates cell-cycle progression. Human APC/C is composed of 14 distinct proteins that assemble into a complex of at least 19 subunits with a combined molecular mass of ~1.2 MDa. We show that recombinant human APC/C is correctly assembled, as judged by its capacity to ubiquitinate the budding yeast APC/C substrate Hsl1 (histone synthetic lethal 1) dependent on the APC/C co-activator Cdh1 [Cdc (cell division cycle) 20 homologue 1], and its three-dimensional reconstruction by electron microscopy and single-particle analysis. Successful reconstitution validates the subunit composition of human APC/C. The structure of human APC/C is compatible with the Saccharomyces cerevisiae APC/C homology model, and in contrast with endogenous human APC/C, no evidence for conformational flexibility of the TPR (tetratricopeptide repeat) lobe is observed. Additional density present in the human APC/C structure, proximal to Apc3/Cdc27 of the TPR lobe, is assigned to the TPR subunit Apc7, a subunit specific to vertebrate APC/C.
Radiomorphometric Quantitative Analysis of Vasculature Utilizing Micro–Computed Tomography and Vessel Perfusion in the Murine Mandible
Authors: Jing Xi Lin , Farberg Aaron S. , Monson Laura A. , Donneys Alexis , Tchanque-Fossuo Catherine N. , Buchman Steven R.
Published: October 2012

Purpose

Biomechanical, densitometric, and histological analyses have been the mainstay for reproducible outcome measures for investigation of new bone formation and osseous healing. Here we report the addition of radiomorphometric vascular analysis as a quantitative measure of vascularity in the murine mandible. To our knowledge this is the first description of using micro–computed tomography (micro-CT) to evaluate the temporal and spatial pattern of angiogenesis in the craniofacial skeleton.

Methods

The vessel perfusion technique was performed on 10 Sprague-Dawley rats using Microfil (MV-122, Flow Tech; Carver, MA). After decalcification, hemimandibles were imaged using high-resolution micro-CT. Six separate radiomorphometric vascular metrics were calculated.

Results

Radiomorphometric values were analyzed using three different thresholds on micro-CT. Experimentally, 1000 Hounsfield units was found to be the optimal threshold for analysis to capture the maximal vascular content of the bone. Data from seven hemimandibles were analyzed. Minimal statistical variance in each of the quantitative measures of vascularity resulted in reproducible metrics for each of the radiomorphometric parameters.

Conclusions

We have demonstrated that micro-CT vascular imaging provides a robust methodology for evaluation of vascular networks in the craniofacial skeleton. This technique provides 3D quantitative data analysis that differs significantly from laser Doppler and microsphere methods, which simply measure flow. This technique is advantageous over labor-intensive 2D conventional analyses using histology and X-ray microangiography. Our data establish the appropriate thresholding for optimal vascular analyses and provide baseline measurements that can be used to analyze the role of angiogenesis in bone regeneration and repair in the craniofacial skeleton.
Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences
Authors: Mou Yun , Tsai Tim W. T. , Chan Jerry C. C.
Published: October 2012

Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T2 effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C′ chemical shift tensor and the Cα–Hα dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-13C, 15N]-L-alanine and N-acetyl-[U-13C, 15N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.
Varying the charge of small cations in liquid water: Structural, transport, and thermodynamical properties
Authors: Martelli Fausto , Vuilleumier Rodolphe , Simonin Jean-Pierre , Spezia Riccardo
Published: October 2012

In this work, we show how increasing the charge of small cations affects the structural, thermodynamical, and dynamical properties of these ions in liquid water. We have studied the case of lanthanoid and actinoid ions, for which we have recently developed accurate polarizable force fields, and the ionic radius is in the 0.995–1.250 Å range, and explored the valency range from 0 to 4+. We found that the ion charge strongly structures the neighboring water molecules and that, in this range of charges, the hydration enthalpies exhibit a quadratic dependence with respect to the charge, in line with the Born model. The diffusion process follows two main regimes: a hydrodynamical regime for neutral or low charges, and a dielectric friction regime for high charges in which the contraction of the ionic radius along the series of elements causes a decrease of the diffusion coefficient. This latter behavior can be qualitatively described by theoretical models, such as the Zwanzig and the solvated ion models. However, these models need be modified in order to obtain agreement with the observed behavior in the full charge range. We have thus modified the solvated ion model by introducing a dependence of the bare ion radius as a function of the ionic charge. Besides agreement between theory and simulation this modification allows one to obtain an empirical unified model. Thus, by analyzing the contributions to the drag coefficient from the viscous and the dielectric terms, we are able to explain the transition from a regime in which the effect of viscosity dominates to one in which dielectric friction governs the motion of ions with radii of ca. 1 Å.
Computational methodology for analysis of the Soret effect in crystals: Application to hydrogen in palladium
Authors: Schelling Patrick K. , Le Timothy
Published: October 2012

Different computational methodologies to compute thermodiffusion of hydrogen in palladium are explored. It is found that diffusion occurs rapidly enough to directly observe thermodiffusion in the presence of an applied temperature gradient. This provides an unequivocal result that hydrogen moves from low to high temperatures, corresponding to a negative value for the reduced heat of transport Q*′≈−0.3 eV, which can be used to validate other methods. Further simulations using the Green-Kubo formulae and a recently developed constrained-dynamics approach are found to be in agreement with direct simulation results. In particular, in each of the three methods used, the value of Q*′ is found to be in the range between −0.3 and −0.2 eV. We show how to correctly define and compute the partial-enthalpy term for hydrogen which is key to obtaining accurate results. The results provide important foundational and numerical validation for the constrained-dynamics approach. The advantage of the constrained-dynamics method is that it can be applied to thermodiffusion in materials where diffusion does not occur on a molecular-dynamics time scale. Finally, we show that the empirical potential predicts behavior that is not in agreement with experiment. In particular, experiments are reported to show hydrogen diffusing from high to low temperatures corresponding to a positive value for Q*′.
Plane-wave pseudopotential implementation of explicit integrators for time-dependent Kohn-Sham equations in large-scale simulations
Authors: Schleife André , Draeger Erik W. , Kanai Yosuke , Correa Alfredo A.
Published: October 2012

Explicit integrators for real-time propagation of time-dependent Kohn-Sham equations are compared regarding their suitability for performing large-scale simulations. Four algorithms are implemented and assessed for both stability and accuracy within a plane-wave pseudopotential framework, employing the adiabatic approximation to the exchange-correlation functional. Simulation results for a single sodium atom and a sodium atom embedded in bulk magnesium oxide are discussed. While the first-order Euler scheme and the second-order finite-difference scheme are unstable, the fourth-order Runge-Kutta scheme is found to be conditionally stable and accurate within this framework. Excellent parallel scalability of the algorithm up to more than a thousand processors is demonstrated for a system containing hundreds of electrons, evidencing the suitability for large-scale simulations based on real-time propagation of time-dependent Kohn-Sham equations.
Photonic non-volatile memories using phase change materials
Authors: Pernice Wolfram H. P. , Bhaskaran Harish
Published: October 2012

We propose an all-photonic, non-volatile memory, and processing element based on phase-change thin-films deposited onto nanophotonic waveguides. Using photonic microring resonators partially covered with Ge2Sb2Te5 (GST) multi-level memory operation in integrated photonic circuits can be achieved. GST provides a dramatic change in refractive index upon transition from the amorphous to crystalline state, which is exploited to reversibly control both the extinction ratio and resonance wavelength of the microcavity with an additional gating port in analogy to optical transistors. Our analysis shows excellent sensitivity to the degree of crystallization inside the GST, thus providing the basis for non-von Neumann neuromorphic computing.
Nonlocal electron-phonon coupling in the pentacene crystal: Beyond the Γ-point approximation
Authors: Yi Yuanping , Coropceanu Veaceslav , Brédas Jean-Luc
Published: October 2012

There is currently increasing interest in understanding the impact of the nonlocal (Peierls-type) electron-phonon mechanism on charge transport in organic molecular semiconductors. Most estimates of the non-local coupling constants reported in the literature are based on the Γ-point phonon modes. Here, the influence of phonon modes spanning the entire Brillouin zone (phonon dispersion) on the nonlocal electron-phonon couplings is investigated for the pentacene crystal. The phonon modes are obtained by using a supercell approach. The results underline that the overall nonlocal couplings are substantially underestimated by calculations taking sole account of the phonons at the Γ point of the unit cell. The variance of the transfer integrals based on Γ-point normal-mode calculations at room temperature is underestimated in some cases by 40% for herringbone-type dimers and by over 80% for cofacial dimers. Our calculations show that the overall coupling is somewhat larger for holes than for electrons. The results also suggest that the interactions of charge carriers (both electrons and holes) with acoustic and optical phonons are comparable. Therefore, an adequate description of the charge-transport properties in pentacene and similar systems requires that these two electron-phonon coupling mechanisms be treated on the same footing.
The origins of pressure-induced phase transformations during the surface texturing of silicon using femtosecond laser irradiation
Authors: Smith Matthew J. , Sher Meng-Ju , Franta Benjamin , Lin Yu-Ting , Mazur Eric , Gradečak Silvija
Published: October 2012

Surface texturing of silicon using femtosecond (fs) laser irradiation is an attractive method for enhancing light trapping, but the laser-induced damage that occurs in parallel with surface texturing can inhibit device performance. In this work, we investigate the light-material interaction during the texturing of silicon by directly correlating the formation of pressure-induced silicon polymorphs, fs-laser irradiation conditions, and the resulting morphology and microstructure using scanning electron microscopy, micro-Raman spectroscopy, and transmission electron microscopy. We show that raster scanning a pulsed laser beam with a Gaussian profile enhances the formation of crystalline pressure-induced silicon polymorphs by an order of magnitude compared with stationary pulsed fs-laser irradiation. Based on these observations, we identify resolidification-induced stresses as the mechanism responsible for driving sub-surface phase transformations during the surface texturing of silicon, the understanding of which is an important first step towards reducing laser-induced damage during the texturing of silicon with fs-laser irradiation.
Light-induced degradation in n-type Czochralski silicon by boron-doping and thermal donor compensation
Authors: Chen Peng , Yu Xuegong , Wu Yichao , Zhao Jianjiang , Yang Deren
Published: October 2012

In this paper, the behaviors of boron-oxygen complexes related to the light-induced degradation (LID) have been studied in n-type boron-doped Czochralski silicon (Cz-Si) with different levels of thermal donors (TDs) compensation. The degradation is found to have two stages, a fast- and a slow-process, similar to that in p-type boron-doped Cz-Si. In order to compare with the properties of LID in p-type Si, we systematically investigate the dependence of the saturated defect concentration (Nt*) and the defect generation rate constant (Rgen) in our TD-compensated n-type Cz-Si on the carrier concentrations, i.e., the net electron concentration (n0) and the excess hole concentration (Δp). Moreover, we determine the activation energy for the slow-process to be 0.4 eV. Based on our results, we suggest that the LID effect in boron-doped Si, either in p-type case or in n-type case by compensation, should be attributed to the same defects.
Ultrafast excited-state dynamics associated with the photoisomerization of a cyanine dye
Authors: Wang Zhenwei , Chu Saisai , Wang Shufeng , Gong Qihuang
Published: October 2012

The ultrafast excited-state dynamics of a cyanine dye, 3,3′-bis(3-sulfopropyl)-5,5′-dimethoxy-thiacyanine triethylaminium salt, was investigated by using conventional time-resolved fluorescence up-conversion technique. The fluorescence decay can be well described as tri-exponential kinetics, which indicates the excited-state population decays through the bond-twist, vibrational and radiative relaxation channels. Further analysis shows that the contributions of the three relaxation channels to the fluorescence decay demonstrate very different change with increasing the fluorescence wavelength, through which the detailed dynamics at different regions in the excited-state potential energy surface can be retrieved.
Combined effect of nanoscale grain size and porosity on lattice thermal conductivity of bismuth-telluride-based bulk alloys
Authors: Takashiri Masayuki , Tanaka Saburo , Hagino Harutoshi , Miyazaki Koji
Published: October 2012

Here, we investigate the combined effect of the nanoscale crystal grains and porosity on the lattice thermal conductivity of bismuth-telluride-based bulk alloys using both experimental studies and modeling. The fabricated bulk alloys exhibit average grain sizes of 30 < d < 60 nm and porosities of 12% < Φ < 18%. The total thermal conductivities were measured using a laser flash method at room temperature, and they were in the range 0.24 to 0.74 W/m/K. To gain insight into the phonon transport in the nanocrystalline and nanoporous bulk alloys, we estimate the lattice thermal conductivities and compare them with those obtained from a simplified phonon transport model that accounts for the grain size effect in combination with the Maxwell-Garnett model for the porosity effect. The results of this combined model are consistent with the experimental results, and it shows that the grain size effect in the nanoscale regime accounts for a significant portion of the reduction in lattice thermal conductivity.
Quantum mechanical simulation of graphene photodetectors
Authors: Gao Qun , Guo Jing
Published: October 2012

Graphene photodetectors promise ultrafast speed and wide bandwidth. Interplay of quantum transport effects, such as Klein tunneling, with electron-photon coupling can play an important role in device physics of graphene photodetectors. A quantum mechanical simulation approach, which solves quantum transport equation using the non-equilibrium Green's function formalism and treats electron-photon and electron-phonon coupling in the self-consistent Born approximation, is developed to model graphene photodetectors. A mode space approach utilizing parallel computing is implemented to achieve ultimate computational efficiency. It is found that using two metal contacts with distinctively different work function significantly improves the device performance. The photoresponse is strongest when the light spot is focused at the contact regions and is insensitive to the photon energy, which is in qualitative agreement with experiment. The effect of different device designs on the quantum efficiency and the effect of phonon scattering are examined. The simulation results also indicate wide band response of graphene photodetectors.
Electronic states and curved surface effect of silicon quantum dots
Authors: Huang Wei-Qi , Huang Zhong-Mei , Cheng Han-Qiong , Miao Xin-Jian , Shu Qin , Liu Shi-Rong , Qin Chao-Jian
Published: October 2012

The calculation results show that the bonding energy and electronic states of silicon quantum dots (Si QDs) are different on various curved surfaces (CS), for example, a Si-O-Si bridge bond on curved surface provides the localized levels in band gap and its bonding energy is shallower than that on facet. Curved surface breaks symmetrical shape of silicon quantum dots on which some bonds can produce localized electronic states in band gap. The red-shifting of photoluminescence spectra on smaller silicon quantum dots can be explained by CS effect. In CS effect, surface curvature is determined by the shape of Si QDs or silicon nanostructures, which is independent of their sizes. The CS effect has the interesting fundamental physical properties in nanophysics as that of quantum confinement effect.
Temperature-dependent mechanical-resonance frequencies and damping in ensembles of gallium nitride nanowires
Authors: Montague J. R. , Bertness K. A. , Sanford N. A. , Bright V. M. , Rogers C. T.
Published: October 2012

We have measured singly clamped cantilever mechanical-resonances in ensembles of as-grown gallium nitride nanowires (GaN NWs), from 12 K to 320 K. Resonance frequencies are approximately linearly dependent on temperature near 300 K with relative shifts of 40 ± 20 ppm/K, consistent with temperature-dependent elastic moduli. Below 100 K, we find that some GaN NWs have mechanical quality factors well above 400 000, at mechanical resonance frequencies near 1 MHz. We also observe a correlation between increased amplitude of dissipation and increased temperature dependence of resonance frequencies. The microwave homodyne detection technique we use is simple, allows for the investigation of as-grown or processed NWs, and is sensitive enough to observe the thermal motion of individual NWs while providing for the simultaneous measurement of large ensembles of NW mechanical resonances.
Addition of regiorandom poly(3-hexylthiophene) to solution processed poly(3-hexylthiophene):[6,6]-phenyl-C61-butyric acid methyl ester graded bilayers to tune the vertical concentration gradient
Authors: Vohra Varun , Higashimine Koichi , Murakami Tatsuya , Murata Hideyuki
Published: October 2012

Donor-acceptor vertical concentration gradient in the active layer is of crucial importance in graded bilayer poly(3-hexylthiophene):[6,6]-phenyl-C61-butyric acid methyl ester (P3HT:PCBM) solar cells. We demonstrate that upon addition of regiorandom P3HT to graded regioregular P3HT:PCBM bilayers, we are able to tune the vertical concentration gradient. With the help of energy-dispersive x-ray spectroscopy elemental mapping of the device cross-sections, we find a strong relationship between the concentration gradient profile and the device performances. Upon addition of regiorandom P3HT, the devices exhibit power conversion efficiencies up to 3.83% (compare to 3.09% for regioregular P3HT devices).
Fermi-level depinning at the metal-germanium interface by the formation of epitaxial nickel digermanide NiGe2 using pulsed laser anneal
Authors: Shi Ya Lim Phyllis , Zhi Chi Dong , Cai Wang Xin , Yeo Yee-Chia
Published: October 2012

A reduced effective electron Schottky barrier height ΦBn,eff of 0.37 eV is obtained at the epitaxial-NiGe2/Ge(100) interface. This is substantially lower than an ΦBn,eff of 0.60 eV obtained at the NiGe/Ge(100) interface. The Fermi-level pinning effect, which is commonly observed between metals and Ge, is reduced at the NiGe2/Ge(100) interface. This is attributed to the formation of epitaxial NiGe2 on Ge(100), which is expected to have a lower density of interface states due to reduced number of dangling bonds.
Metamaterial particles for electromagnetic energy harvesting
Authors: Ramahi Omar M. , Almoneef Thamer S. , AlShareef Mohammed , Boybay Muhammed S.
Published: October 2012

Metamaterials are typically made of an ensemble of electrically small resonators such as metallic loops. The fact that such particles resonate individually to generate a bulk material behavior having enhanced constitutive parameters is essentially indicative of these particles' ability to collect energy. We show that such particles act as energy collectors when a resistive load is inserted within the particle's gap. A proof of concept is provided using a 5.8 GHz field and a split-ring resonator (SRR) as the electromagnetic energy collecting cell. Numerical simulation for a 9 × 9 SRR array shows the effectiveness of an SRR array as an energy collector plate.
Can larval snapper, Pagrus auratus, smell their new home?
Authors: Radford C. A. , Sim-Smith C. J. , Jeffs A. G.
Published: October 2012

The ability to find a suitable settlement habitat after a pelagic larval period represents a significant challenge to marine settlement-stage larvae, and the mechanisms by which they achieve this are poorly understood. There is good evidence that olfactory cues are used by some coral reef fish larvae to locate suitable settlement habitats; however, the same understanding is lacking for marine temperate fish. Here we show for the first time that the larvae of an important commercial and recreational marine temperate fish, Pagrus auratus, can use olfactory cues to orient to appropriate settlement habitat. Using pairwise choice experiments, naive hatchery reared fish were offered water collected from a range of habitats in the Kaipara Harbour, an important nursery area for P. auratus. Larvae selected to swim towards water taken from over seagrass beds, their preferred settlement habitat, than water taken from the harbour entrance, Asian date mussel habitat, artificial seawater or artificial seawater in which seagrass had been soaked. The preference by the fish for water from the seagrass habitat over artificial seawater in which seagrass had been soaked strongly suggests that chemical cues from sources other than seagrass, such as from prey or conspecifics present in the seagrass habitat, may also be involved.
The importance of affect, perceived risk and perceived benefit in understanding support for fuels management among wildland–urban interface residents
Authors: Ascher Timothy J. , Wilson Robyn S. , Toman Eric
Published: October 2012

One factor that is critical to human judgments about risk, and was often overlooked in past research on public support for fuels treatment, is affect or the largely unconscious negative or positive feelings invoked by a stimulus (in this case, fuels management). This study aims to test a model for public support based on individual knowledge, exposure, affective response, perceived risk and perceived benefit associated with fuels management. Data collection occurred in residential communities throughout the Lake Tahoe Basin, located in the intermountain western region of the United States. Path analyses indicated that support for both prescribed burning and mechanical thinning is driven largely by the perceived benefits of the technique and affective responses (negative or positive reactions to the images automatically associated with a specific technique). Affect also has a significant influence on perceived risk for prescribed burning, whereas perceived risk, in turn, has a significant influence on support for prescribed burning. The results suggest that communication efforts aimed at building support should focus on the benefits to forest health and future fire risk reduction, as these were the most prevalent positive affective associations and the primary benefits of the techniques. For prescribed burning, emphasising the degree of control that managers have over the technique could also counteract negative affective associations and decrease perceived risk.
Duff mound consumption and cambium injury for centuries-old western larch from prescribed burning in western Montana
Authors: Harrington Michael G.
Published: October 2012

Western larch is one of the most fire-adapted conifers in western North America. Its historical perpetuation depended upon regular fire disturbances, which creates open stand conditions and mineral seedbeds. A stand of 200- to 500-year-old larch in western Montana with deep duff mounds resulting from an unusually long 150-year fire-free period was mechanically thinned and prescribed burned to reduce the probability of high intensity wildfire near a community and increase opportunities for larch regeneration. Little documentation is available regarding basal damage to larch from lengthy duff mound burning; therefore this study was established to assess: duff consumption from prescribed burning and resulting cambial damage and tree vitality. Ninety trees averaging 91-cm diameter at breast height were selected, half with duff mounds measured and burned in autumn and half with mounds removed. Duff depths nearest the bole averaged 20 cm and mound consumption approached 100% including large amounts of the basal bark with smouldering combustion lasting 18–24 h. Cambial mortality ranged from 0 to 36% of the basal circumference but no trees had died after 7 years. The cambium mortality was likely due to the spatially infrequent coincident of deep duff and thinner bark. Under similar site and environmental conditions removal of the potential duff consumption injury hazard appears unwarranted.
Integrating geospatial information into fire risk assessment
Authors: Chuvieco E. , Aguado I. , Jurdao S. , Pettinari M. L. , Yebra M. , Salas J. , Hantson S. , de la Riva J. , Ibarra P. , Rodrigues M. , Echeverría M. , Azqueta D. , Román M. V. , Bastarrika A. , Martínez S. , Recondo C. , Zapico E. , Martínez-Vega F. J.
Published: October 2012

Fire risk assessment should take into account the most relevant components associated to fire occurrence. To estimate when and where the fire will produce undesired effects, we need to model both (a) fire ignition and propagation potential and (b) fire vulnerability. Following these ideas, a comprehensive fire risk assessment system is proposed in this paper, which makes extensive use of geographic information technologies to offer a spatially explicit evaluation of fire risk conditions. The paper first describes the conceptual model, then the methods to generate the different input variables, the approaches to merge those variables into synthetic risk indices and finally the validation of the outputs. The model has been applied at a national level for the whole Spanish Iberian territory at 1-km2 spatial resolution. Fire danger included human factors, lightning probability, fuel moisture content of both dead and live fuels and propagation potential. Fire vulnerability was assessed by analysing values-at-risk and landscape resilience. Each input variable included a particular accuracy assessment, whereas the synthetic indices were validated using the most recent fire statistics available. Significant relations (P < 0.001) with fire occurrence were found for the main synthetic danger indices, particularly for those associated to fuel moisture content conditions.
Fire history and forest structure of an endangered subtropical ecosystem in the Florida Keys, USA
Authors: Harley Grant L. , Grissino-Mayer Henri D. , Horn Sally P.
Published: October 2012

We focussed on the influence of historical fire and varied fire management practices on the structure of globally endangered pine rockland ecosystems on two adjacent islands in the Florida Keys: Big Pine Key and No Name Key. We reconstructed fire history in two stands from fire scars on South Florida slash pines (Pinus elliottii Engelm. var. densa Little & Dor.) that were accurately dated using dendrochronology, and quantified stand structure to infer successional trajectories. Fire regimes on Big Pine Key and No Name Key over the past 150 years differed in fire return interval and spatial extent. Fire scar analysis indicated that fires burnt at intervals of 6 and 9 years (Weibull median probability interval) on Big Pine Key and No Name Key with the majority of fires occurring late in the growing season. On Big Pine Key, pine recruitment was widespread, likely due to multiple, widespread prescribed burns conducted since 2000. No Name Key experienced fewer fires than Big Pine Key, but pines recruited at the site from at least the 1890s through the 1970s. Today, pine recruitment is nearly absent on No Name Key, where fire management practices since 1957 could result in loss of pine rockland habitat.
TRAIL: not just for tumors anymore?
Authors: Benedict Chris A. , Ware Carl F.
Published: October 2012

Since the discovery of TNF-related apoptosis-inducing ligand (TRAIL) and its network of receptors, the majority of attention has focused on the clinical potential of manipulating this pathway in cancer therapy. However, the widespread expression of TRAIL under inflammatory conditions and the ability to induce both apoptotic and prosurvival signaling pathways has suggested that TRAIL plays broader roles in regulating immune processes. Two new studies now show that expression of TRAIL by neutrophils in the lung facilitates defenses against bacterial pathogens, whereas expression of TRAIL by cells within arterioles exacerbates vascular disease. These differentiating results highlight that the context of TRAIL signaling can determine whether the outcome is beneficial or pathogenic for the host.
First Report of Tomato mosaic virus Infecting Pepino in China
Authors: Ge B.-B. , Liu G.-J. , Wang H.-Q.
Published: October 2012

Pepino (Solanum muricatum L.) is a vegetatively propagated plant that is native to South America and is commercially grown in many countries (4) including China for its juicy and fragrant fruits. An unusual disease of pepino characterized by a yield reduction of fruits and mosaic, puckering, and distortion of leaves was observed in surveys conducted during 2010 to 2011 in pepino growing regions of Gansu, Jilin, and Yunnan provinces. These symptoms were similar to a disease caused by the Tomato mosaic virus (ToMV) first reported in Spain in 1998 (3). The sap from infected pepino was mechanically inoculated to 12 plants each of Chenopodium quinoa, Lycopersicon esculentum, and Gomphrena globosa, and the resulting symptoms were similar to those incited by ToMV (1). Symptoms included yellowish local lesions on inoculated leaves of C. quinoa and systemic mosaic in L. esculentum. Necrotic or semi-necrotic local lesions developed on inoculated leaves of G. globosa followed by systemic mosaic 7 dpi. Symptomatic pepino and indicator plants were tested for the presence of ToMV using commercial double-antibody sandwich-ELISA diagnostic kits (Agdia, Elkhart, IN). The virus incidence ranged from 33.3 to 75% in pepino and the other three indicator plants. To further confirm the presence of ToMV, ELISA-positive samples were subjected to total RNA extraction using Trizol (Invitrogen) followed by reverse transcription (RT)-PCR with ToMV-specific forward (5′-ATGTCTTACTCAATCACTTC-3′) and reverse primers (5′-TTAA(G)GAT(C) GCA(T)GGTGCAG(C)AGG-3′), designed to amplify a 480-bp fragment of the coat protein. Amplicons of the expected size were obtained from all ELISA-positive samples, but not from healthy pepino plants. The amplicons were cloned into the pMD18-T (TaKaRa, Da Lian, China) vector and transformed into E. coli DH-5α competent cells. The sequences obtained (GenBank Accession Nos. JX025562, JX025563, JX025565, and JX025566) shared 99.58 to 99.79% similarity with the ToMV reference sequence (Accession No. NC002692). To our knowledge, this is the first report of ToMV infecting pepino in China. ToMV is an important pathogen that is mechanically transmitted with high efficiency as a result of agricultural practices. The disease is difficult to control once infection occurs in the field. This disease has caused serious economic loss in Spain (2), thus it is important to survey and monitor the incidence and distribution of ToMV in China.

References: (1) I. Kamenova et al. Acta Hort. 722:277, 2006. (2) L. Pérez-Benlloch et al. Euphytica. 120:247, 2001. (3) J. Prohens et al. Plant Dis. 82:1281, 1998. (4) J. Prohens et al. Acta Hort. 523:53, 2000.
First Report of Thiophanate-Methyl Resistance in Botrytis cinerea on Strawberry from South Carolina
Authors: Fernández-Ortuño D. , Schnabel G.
Published: October 2012

Botrytis cinerea Pers.:Fr. is the causal agent of gray mold disease and one of the most important plant-pathogenic fungi affecting strawberry (Fragaria× ananassa). Control of gray mold mainly depends on fungicides, including the methyl benzimidazole carbamate (MBC) thiophanate-methyl. In 2011, strawberries with gray mold symptoms were collected from commercial fields near Chesnee, Florence, Lexington, McBee, Monetta, and North Augusta, all in South Carolina. MBC fungicides were used in most of these fields for gray mold control during the last 3 years. A total of 124 single spore B. cinerea isolates were obtained, each from a different fruit. Resistance to thiophanate-methyl (Topsin M 70WP, Cerexagri-Nisso LLC, King of Prussia, PA) was determined using a conidial germination assay as described previously (1). The majority of isolates (81.4%) were resistant; the rest were sensitive. Resistant isolates were found in all locations with some populations (Chesnee, McBee, and Lexington) revealing no sensitive isolates. Genomic DNA from 35 resistant isolates (representing all locations) and 10 sensitive isolates (from Chesnee, Monetta, and North Augusta, SC) was extracted, and the molecular basis of MBC fungicide resistance was determined as described previously (2). All MBC-resistant isolates possessed the E198A mutation known to confer high levels of MBC fungicide resistance in many fungi, including B. cinerea (2,3). Disease was assessed using a detached strawberry fruit assay. Commercially grown strawberry fruit (24 in total for each isolate and fungicide treatment) were rinsed with water, dried, and sprayed 4 h prior to inoculation with either water or 2.4 g/liter of Topsin M to runoff using a hand mister. Fruit was stab-wounded with a sterile syringe and inoculated with a 30-μl droplet of a conidial suspension (106 spores/ml) of either a sensitive or resistant isolate. After inoculation, the fruit were kept at 22°C for 4 days. The sensitive isolate developed gray mold disease in untreated but not Topsin M-treated fruit. The resistant isolate developed gray mold disease of equal severity in both, the control and fungicide-treated fruit. This experiment was repeated once. The results of the study show that resistance to MBC fungicides is common and widespread in B. cinerea from strawberry in South Carolina. Prior to this study, resistance to MBCs has only been reported in B. cinerea from ornamental crops grown in greenhouses in South Carolina (4).

References: (1) J. E. Luck and M. R. Gillings. Mycol. Res. 99:1483, 1995. (2) R. W. S. Weber and M. Hahn. J. Plant Dis. Prot. 118:17, 2011. (3) O. Yarden and T. Katan. Phytopathology 83:1478, 1993. (4) L. F. Yourman and S. Jeffers. Plant Dis. 83:569, 1999.
Iridescence: a functional perspective
Authors: Doucet Stéphanie M , Meadows Melissa G
Published: October 2012

In animals, iridescence is generated by the interaction of light with biological tissues that are nanostructured to produce thin films or diffraction gratings. Uniquely among animal visual signals, the study of iridescent coloration contributes to biological and physical sciences by enhancing our understanding of the evolution of communication strategies, and by providing insights into physical optics and inspiring biomimetic technologies useful to humans. Iridescent colours are found in a broad diversity of animal taxa ranging from diminutive marine copepods to terrestrial insects and birds. Iridescent coloration has received a surge of research interest of late, and studies have focused on both characterizing the nanostructures responsible for producing iridescence and identifying the behavioural functions of iridescent colours. In this paper, we begin with a brief description of colour production mechanisms in animals and provide a general overview of the taxonomic distribution of iridescent colours. We then highlight unique properties of iridescent signals and review the proposed functions of iridescent coloration, focusing, in particular, on the ways in which iridescent colours allow animals to communicate with conspecifics and avoid predators. We conclude with a brief overview of non-communicative functions of iridescence in animals. Despite the vast amount of recent work on animal iridescence, our review reveals that many proposed functions of iridescent coloration remain virtually unexplored, and this area is clearly ripe for future research.
Quantum demolition filtering and optimal control of unstable systems
Authors: Belavkin V. P.
Published: October 2012

A brief account of the quantum information dynamics and dynamical programming methods for optimal control of quantum unstable systems is given to both open loop and feedback control schemes corresponding respectively to deterministic and stochastic semi-Markov dynamics of stable or unstable systems. For the quantum feedback control scheme, we exploit the separation theorem of filtering and control aspects as in the usual case of quantum stable systems with non-demolition observation. This allows us to start with the Belavkin quantum filtering equation generalized to demolition observations and derive the generalized Hamilton–Jacobi–Bellman equation using standard arguments of classical control theory. This is equivalent to a Hamilton–Jacobi equation with an extra linear dissipative term if the control is restricted to Hamiltonian terms in the filtering equation. An unstable controlled qubit is considered as an example throughout the development of the formalism. Finally, we discuss optimum observation strategies to obtain a pure quantum qubit state from a mixed one.
Single photon quantum filtering using non-Markovian embeddings
Authors: Gough John E. , James Matthew R. , Nurdin Hendra I.
Published: October 2012

We determine quantum master and filter equations for continuous measurement of systems coupled to input fields in certain non-classical continuous-mode states, specifically single photon states. The quantum filters are shown to be derivable from an embedding into a larger non-Markovian system, and are given by a system of coupled stochastic differential equations.
Specification of photonic circuits using quantum hardware description language
Authors: Tezak Nikolas , Niederberger Armand , Pavlichin Dmitri S. , Sarma Gopal , Mabuchi Hideo
Published: October 2012

Following the simple observation that the interconnection of a set of quantum optical input–output devices can be specified using structural mode VHSIC hardware description language, we demonstrate a computer-aided schematic capture workflow for modelling and simulating multi-component photonic circuits. We describe an algorithm for parsing circuit descriptions to derive quantum equations of motion, illustrate our approach using simple examples based on linear and cavity-nonlinear optical components, and demonstrate a computational approach to hierarchical model reduction.
Robust stability of uncertain linear quantum systems
Authors: Petersen Ian R. , Ugrinovskii Valery , James Matthew R.
Published: October 2012

This paper considers the problem of robust stability for a class of uncertain linear quantum systems subject to unknown perturbations in the system Hamiltonian. The case of a nominal linear quantum system is considered with quadratic perturbations to the system Hamiltonian. A robust stability condition is given in terms of a strict bounded real condition.
Cationic-vacancy-induced room-temperature ferromagnetism in transparent, conducting anatase Ti

1−
x

Ta

x

O
2
(
x
∼0.05) thin films
Authors: Rusydi A. , Dhar S. , Barman A. Roy , Ariando  , Qi D.-C. , Motapothula M. , Yi J. B. , Santoso I. , Feng Y. P. , Yang K. , Dai Y. , Yakovlev N. L. , Ding J. , Wee A. T. S. , Neuber G. , Breese M. B. H. , Ruebhausen M. , Hilgenkamp H. , Venkatesan T.
Published: October 2012

We report room-temperature ferromagnetism (FM) in highly conducting, transparent anatase Ti

1−
x

Ta

x

O
2
 (
x
∼0.05) thin films grown by pulsed laser deposition on LaAlO
3
substrates. Rutherford backscattering spectrometry (RBS), X-ray diffraction, proton-induced X-ray emission, X-ray absorption spectroscopy (XAS) and time-of-flight secondary-ion mass spectrometry indicated negligible magnetic contaminants in the films. The presence of FM with concomitant large carrier densities was determined by a combination of superconducting quantum interference device magnetometry, electrical transport measurements, soft X-ray magnetic circular dichroism (SXMCD), XAS and optical magnetic circular dichroism, and was supported by first-principles calculations. SXMCD and XAS measurements revealed a 90 per cent contribution to FM from the Ti ions, and a 10 per cent contribution from the O ions. RBS/channelling measurements show complete Ta substitution in the Ti sites, though carrier activation was only 50 per cent at 5 per cent Ta concentration, implying compensation by cationic defects. The role of the Ti vacancy (
V
Ti
) and Ti
3+
was studied via XAS and X-ray photoemission spectroscopy, respectively. It was found that, in films with strong FM, the
V
Ti
signal was strong while the Ti
3+
signal was absent. We propose (in the absence of any obvious exchange mechanisms) that the localized magnetic moments,
V
Ti
sites, are ferromagnetically ordered by itinerant carriers. Cationic-defect-induced magnetism is an alternative route to FM in wide-band-gap semiconducting oxides without any magnetic elements.
Principles and applications of quantum control engineering
Authors: Gough John E.
Published: October 2012

This is a brief survey of quantum feedback control and specifically follows on from the two-day conference
Principles and applications of quantum control engineering,
which took place in the Kavli Royal Society International Centre at Chicheley Hall, on 12–13 December 2011. This was the eighth in a series of principles and applications of control to quantum systems workshops.
Drivers of agricultural profitability in the USA
Authors: Mishra Ashok K. , Harris J. Michael , Erickson Kenneth W. , Hallahan Charlie , Detre Joshua D.
Published: October 2012

Purpose

The aim of this study is to use a financial approach based on the Du Pont expansion to investigate the impact of demographics, specialization, tenure, vertical integration, farm type, and regional location on the three levers of performance (ROE) – namely, net profit margins, asset turnover ratio, and asset‐to‐equity ratio.

Design/methodology/approach

This research uses a system of equations in conjunction with 1996‐2009 farm‐level data from the US Department of Agriculture's Agricultural Resource Management Survey (ARMS) to evaluate the factors driving farm‐level profitability, namely, net profit margins, asset turnover ratio, and asset‐to‐equity ratio. The methodology employed in this study corrects heterogeneity and uses repeated cross‐section estimation procedure to estimate the empirical models.

Findings

The study finds that key drivers of net profit margins are operator education, farm size and typology, specialization, and level of government payments. Key factors affecting the asset turnover ratio component of the Du Pont model include asset turnover ratio is driven by operator age, contracting, specialization, and receiving government payments. Finally, key factors affecting asset‐to‐equity ratio component of the Du Pont model are farm size, farm typology, contracting, and specialization drive asset‐to‐equity ratio.

Originality/value

Existing research does not examine the factors affecting returns to equity in faring at the farm‐level. Specifically, a micro‐level analysis of American farm's future structure and financial performance that accounts for the spatial and inter‐temporal dimensions of profitability has never been conducted.
Why do credit cooperatives disappear?
Authors: Cabo Paula , Rebelo João
Published: October 2012

Purpose

The paper aims to identify “problematic” agricultural credit co‐operatives (CCAM) and to evaluate their risk of insolvency as a function of financial indicators, providing regulators and other stakeholders with a set of tools that would be predictive of future insolvency and perhaps bankruptcy.

Design/methodology/approach

Using a database of CCAM failures in the period between 1995 and 2009, statistical models of failure of CCAM, are estimated and compared, using logistic regression analysis and multiple discriminant analysis for assessing the potential failure of CCAM as a function of financial/economical indicators.

Findings

The paper identified the variables customer resources growth, transformation ratio, credit overdue, expenses ratio, structural costs, liquidity, indebtedness and financial margin as determinants of CCAM failure. It suggests that CCAM take measures geared to boosting business, to shoring up the financial margin and the deposit base, to bolstering the complementary margin and to improving the credit recovery processes. Additionally it is necessary to increase cost efficiency, rationalizing structures and procedures consistent with reducing operating costs without detriment to the quality of service provided.

Originality/value

This paper helps to understand why agricultural credit co‐operatives fail.