bluuebunny/crossref_metadata_2025 huggingface dataset:
Methane emission from Yangtze estuarine wetland, China
Authors: Wang Dongqi , Chen Zhenlou , Xu Shiyuan
Published: May 2009

Yangtze estuary, lying in the subtropical monsoon region of China, is characterized by a unique environmental setting and endemic wetland plant species (Scirpus mariqueter). Methane (CH4) emission fluxes were measured at the Yangtze estuarine wetland, Chongming Dongtan (CD), by a static closed chamber technique from May 2004 to April 2005. The results showed that CD is the source of atmospheric CH4, and emission fluxes had significant diurnal and seasonal variation. The annual average CH4 emission flux was 2.06 mg m−2 h−1 at the CD marsh site and 0.04 mg m−2 h−1 at the CD bare tidal flat (nonvegetated). Wetland plant species (S. mariqueter) and temperature were the primary factors controlling the CH4 emission. The results of the light and dark chamber comparison and plant shoot clipping experiment suggest that molecular diffusion and convective gas flow methods were the two main mechanisms of CH4 transported via S. mariqueter plants in July. However, molecular diffusion was believed to be the primary transport mechanism from August to October, with leaf resistance as one of the factors regulating CH4 diffusion. There was significant correlation between CH4 fluxes and temperature, especially the 10 cm depth ground temperature (R2 = 0.7784). Although sediment organic carbon content did not determine CH4 fluxes, net ecosystem production was significantly correlated with CH4 fluxes, suggesting that the photosynthates of S. mariqueter effectively provided the substrate for methanogenic bacteria.
Spatial and temporal variations in active layer thawing and their implication on runoff generation in peat‐covered permafrost terrain
Authors: Wright Nicole , Hayashi Masaki , Quinton William L.
Published: May 2009

The distribution of frost table depths on a peat‐covered permafrost slope was examined in a discontinuous permafrost region in northern Canada over 4 consecutive years at a variety of spatial scales, to elucidate the role of active layer development on runoff generation. Frost table depths were highly variable over relatively short distances (0.25–1 m), and the spatial variability was strongly correlated to soil moisture distribution, which was partly influenced by lateral flow converging to frost table depressions. On an interannual basis, thaw rates were temporally correlated to air temperature and the amount of precipitation input. Simple simulations show that lateral subsurface flow is governed by the frost table topography having spatially variable storage that has to be filled before water can spill over to generate flow downslope, in a similar manner that bedrock topography controls subsurface flow. However, unlike the bedrock surface, the frost table is variable with time and strongly influenced by the heat transfer involving water. Therefore, it is important to understand the feedback between thawing and subsurface water flow and to properly represent the feedback in hydrological models of permafrost regions.
Stratospheric ozone during the Last Glacial Maximum
Authors: Rind D. , Lerner J. , McLinden C. , Perlwitz J.
Published: May 2009

Stratospheric ozone during the Last Glacial Maximum (LGM) is investigated in on‐line simulations with the GISS Global Climate/Middle Atmosphere Model 3. LGM boundary conditions and atmospheric concentrations are employed in three simulations: without interactive ozone, with ozone photochemistry appropriate for that time period and with the LGM climate but current atmospheric composition for chemistry. Results show stratospheric ozone increased during the LGM due to reduced NOy and chlorine, while warmer stratospheric temperatures (from reduced stratospheric CO2) decrease ozone with current photochemistry. The stratospheric residual circulation intensified in the lowermost stratosphere, increasing stratosphere/troposphere exchange at higher latitudes, although for most of the middle atmosphere the circulation decreased; the age of air in the Middle Atmosphere increased by up to one year. Compared with the vastly different LGM conditions, increase in stratospheric ozone of 2% by mass had little effect on atmospheric dynamics, and increased the global radiation balance by <0.1 Wm−2.
Prevalence of extended reconnection X‐lines in the solar wind at 1 AU
Authors: Phan T. D. , Gosling J. T. , Davis M. S.
Published: May 2009

A survey of Wind and ACE data has been performed to address the generality of previous reports of extremely extended reconnection X‐lines in the solar wind. We have studied 51 events in which both Wind and ACE detected the same solar wind current sheets and one of the spacecraft observed a reconnection exhaust. In 50 of the 51 events, the other spacecraft also observed essentially the same reconnection signatures, and all but one of the jets pointed in the same direction at both spacecraft. In 7 of these cases, the X‐line extended more than 100 Earth radii (or 104 ion skin depths). Our findings strongly indicate that reconnection X‐lines in large‐scale current sheets (with magnetic shear >∼70°) are fundamentally extended, and not patchy and randomly distributed in space. Finally, the extended reconnecting current sheets are typically highly planar, indicating no significant current sheet warping associated with the reconnection process.
Seismic signals of snow‐slurry lahars in motion: 25 September 2007, Mt Ruapehu, New Zealand
Authors: Cole S. E. , Cronin S. J. , Sherburn S. , Manville V.
Published: May 2009

Detection of ground shaking forms the basis of many lahar‐warning systems. Seismic records of two lahar types at Ruapehu, New Zealand, in 2007 are used to examine their nature and internal dynamics. Upstream detection of a flow depends upon flow type and coupling with the ground. 3‐D characteristics of seismic signals can be used to distinguish the dominant rheology and gross physical composition. Water‐rich hyperconcentrated flows are turbulent; common inter‐particle and particle‐substrate collisions engender higher energy in cross‐channel vibrations relative to channel‐parallel. Plug‐like snow‐slurry lahars show greater energy in channel‐parallel signals, due to lateral deposition insulating channel margins, and low turbulence. Direct comparison of flow size must account for flow rheology; a water‐rich lahar will generate signals of greater amplitude than a similar‐sized snow‐slurry flow.
Vascular Graph Model to Simulate the Cerebral Blood Flow in Realistic Vascular Networks
Authors: Reichold Johannes , Stampanoni Marco , Keller Anna Lena , Buck Alfred , Jenny Patrick , Weber Bruno
Published: May 2009

At its most fundamental level, cerebral blood flow (CBF) may be modeled as fluid flow driven through a network of resistors by pressure gradients. The composition of the blood as well as the cross-sectional area and length of a vessel are the major determinants of its resistance to flow. Here, we introduce a vascular graph modeling framework based on these principles that can compute blood pressure, flow and scalar transport in realistic vascular networks. By embedding the network in a computational grid representative of brain tissue, the interaction between the two compartments can be captured in a truly three-dimensional manner and may be applied, among others, to simulate oxygen extraction from the vessels. Moreover, we have devised an upscaling algorithm that significantly reduces the computational expense and eliminates the need for detailed knowledge on the topology of the capillary bed. The vascular graph framework has been applied to investigate the effect of local vascular dilation and occlusion on the flow in the surrounding network.
H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts
Authors: Yamasaki Chisato , Murakami Katsuhiko , Takeda Jun-ichi , Sato Yoshiharu , Noda Akiko , Sakate Ryuichi , Habara Takuya , Nakaoka Hajime , Todokoro Fusano , Matsuya Akihiro , Imanishi Tadashi , Gojobori Takashi
Published: May 2009

H-Invitational Database (H-InvDB; "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene clusters based on human FLcDNAs and mRNAs.H-InvDB consists of two main views, the Transcript view and the Locus view, and six auxiliary databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view. We also provides several data mining tools such as “Navi search”: consists of 16 search contents each of which includes items for the search condition ("http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp":http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp), “PANDA”: Priority ANalysis for Disease Association (PANDA) system ("http://www.h-invitational.jp/panda/app":http://www.h-invitational.jp/panda/app), H-InvDB now provides web service APIs of SOAP and REST to use H-InvDB data in programs. ("http://www.h-invitational.jp/hinv/hws/doc/":http://www.h-invitational.jp/hinv/hws/doc/)
Ethnic‐specific Correlations of Visfatin With Circulating Markers of Endothelial Inflammation and Function
Authors: Reimann Manja , Ziemssen Tjalf , Huisman Hugo W. , Schutte Rudolph , Malan Leoné , Van Rooyen Johannes M. , Böger Rainer H. , Malan Nicolaas T. , Schutte Aletta E.
Published: May 2009

Sub‐Saharan Africa is afflicted by high hypertension prevalence that is expected to rise even further along with increasing obesity rates. The present study aimed to investigate the role of visfatin in obesity and to explore associations of visfatin with markers of endothelial function and hemodynamics in African women compared to a well‐matched white sample. The present study involved urban African (n = 102) and white (n = 115) women from South Africa, individually matched for age and BMI. We measured blood pressure, cardiac output, and arterial compliance noninvasively, and analyzed visfatin as well as circulating markers of vascular function and inflammation in serum. Serum visfatin concentration did not differ between African and white women. Visfatin was unrelated to obesity in African women but positive associations for total and abdominal obesity were found in white women. Age‐ and obesity‐adjusted univariate and multivariate analyses revealed significant positive associations of visfatin with endothelin‐1 and fibrinogen in African women. Identical analyses in white women indicated a positive association of visfatin with C‐reactive protein and von Willebrand factor. Our findings suggest a possible role of visfatin in the cardiovascular system that seems to be independent of obesity in the African women.
NEMO oligomerization and its ubiquitin-binding properties
Authors: Ivins Frank J. , Montgomery Mark G. , Smith Susan J. M. , Morris-Davies Aylin C. , Taylor Ian A. , Rittinger Katrin
Published: May 2009

The IKK [IκB (inhibitory κB) kinase] complex is a key regulatory component of NF-κB (nuclear factor κB) activation and is responsible for mediating the degradation of IκB, thereby allowing nuclear translocation of NF-κB and transcription of target genes. NEMO (NF-κB essential modulator), the regulatory subunit of the IKK complex, plays a pivotal role in this process by integrating upstream signals, in particular the recognition of polyubiquitin chains, and relaying these to the activation of IKKα and IKKβ, the catalytic subunits of the IKK complex. The oligomeric state of NEMO is controversial and the mechanism by which it regulates activation of the IKK complex is poorly understood. Using a combination of hydrodynamic techniques we now show that apo-NEMO is a highly elongated, dimeric protein that is in weak equilibrium with a tetrameric assembly. Interaction with peptides derived from IKKβ disrupts formation of the tetrameric NEMO complex, indicating that interaction with IKKα and IKKβ and tetramerization are mutually exclusive. Furthermore, we show that NEMO binds to linear di-ubiquitin with a stoichiometry of one molecule of di-ubiquitin per NEMO dimer. This stoichiometry is preserved in a construct comprising the second coiled-coil region and the leucine zipper and in one that essentially spans the full-length protein. However, our data show that at high di-ubiquitin concentrations a second weaker binding site becomes apparent, implying that two different NEMO–di-ubiquitin complexes are formed during the IKK activation process. We propose that the role of these two complexes is to provide a threshold for activation, thereby ensuring sufficient specificity during NF-κB signalling.
Risk for Noise-Induced Hearing Loss From Use of Portable Media Players: A Summary of Evidence Through 2008
Authors: Fligor Brian J.
Published: May 2009

A growing body of evidence suggests that a small, but significant, percent of users of portable media players (PMP) are at risk for noise-induced hearing loss (NIHL) from abusive use. This manuscript provides a brief review of damage-risk criteria and the methodological hurdles to accurately measuring sound exposure from earphones. The capacity of all generations of PMP exists to produce sound levels that would allow a user to exceed established damage-risk criteria. Whether or not a PMP user exceeds damage-risk criteria depends in part on the type of earphone used and the background noise that exists in the ambient listening environment. To date, estimates of noise dose from PMP use suggest that only a fraction of consumers are at risk for NIHL, but, given the extraordinary population of these devices, the absolute number affected may be quite large. Estimates of noise-induced permanent threshold shift from using PMP at high levels for 2 and 4 hours per day over a 10-year period are given, as well as an estimate of the number of people who may have NIHL from PMP use.
Direct confirmation of biaxiality in a bent-core mesogen through the measurement of electro-optic characteristics
Authors: Lee Gak Seok , Cho Jin Seok , Kim Jae Chang , Yoon Tae-Hoon , Shin Sung Tae
Published: May 2009

We propose a method to confirm the biaxial phase in thermotropic nematic liquid crystals from measurement of the electro-optic characteristics. The electro-optic transmittance curve shows monotonic decrease to zero in the uniaxial phase but the curve shows a U-shaped behavior (or a monotonic decrease to nonzero transmittance) in the biaxial phase. In a bent-core mesogen 4,4′(1,3,4oxadiazole2,5diyl)dipheptylbenzoate (ODBP-Ph-C7), known to be in the nematic phase at temperatures between 173 and 222 °C, it has been found that its electro-optic curve at 190 °C shows a U-shaped behavior, while the curve at 210 °C shows a monotonic decrease to zero transmittance. We believe that these experimental results confirm the biaxial nature of ODBP-Ph-C7.
Analytical solutions of gas transport problems in inorganic/organic hybrid structures for gas barrier applications
Authors: Jang Changsoo , Han Bongtae
Published: May 2009

The analytical solutions of the ideal laminate theory-based gas transport model are obtained for inorganic/organic hybrid structures used in gas barrier applications. Nondimensionalized solutions are provided for two cases that can be encountered in real applications: (1) gas diffusion-into and (2) gas transmission-through the barrier structures. The two cases represent (1) gas absorption into flexible organic electronic devices encapsulated by barrier structures and (2) the conventional gas transmission test conditions of barrier structures, respectively. The solutions are utilized to address gas transport behavior in two important practical applications.
Contrast mechanisms in cross-sectional scanning tunneling microscopy of GaSb/GaAs type-II nanostructures
Authors: Timm R. , Feenstra R. M. , Eisele H. , Lenz A. , Ivanova L. , Lenz E. , Dähne M.
Published: May 2009

Cross-sectional scanning tunneling microscopy results on GaSb quantum wells and dots in GaAs are found to exhibit a narrow, sharply defined contrast of the nanostructure at negative sample bias, but a smoothly broadened contrast at positive sample bias. This contrast is related to the specific type-II band alignment of GaSb/GaAs heterostructures in combination with tip-induced band bending. The corresponding model is quantitatively verified by numerical simulations of band bending and tunnel current profiles combined with calculations of cleavage-induced strain relaxation.
Ambient effects on fullerene/copper phthalocyanine photovoltaic interface
Authors: Ng T. W. , Lo M. F. , Zhou Y. C. , Liu Z. T. , Lee C. S. , Kwon Ohyun , Lee S. T.
Published: May 2009

Effects of ambient-air exposure on the energy levels at photovoltaic interface of fullerene (C60)/copper phthalocyanine (CuPc) were studied using ultraviolet photoemission spectroscopy. The junction prepared in ultrahigh vacuum showed flat energy levels with little vacuum level offset, while exposure to ambient air at 10−5 Torr induced p-type doping of C60 with energy levels bend up for 0.27 eV. The energy difference between HOMOCuPc−LUMOC60, describing the theoretical maximum open-circuit voltage, increased from 0.64 to 0.81 eV. The exposure moved the LUMOC60 away from the Fermi level, leading to reduction in carrier concentration and film conductivity.
Spin splitting in AlxGa1−xN/GaN quasiballistic quantum wires
Authors: Lo Ikai , Chen Y. L. , Pang W. Y. , Hsu Y. C. , Chiang Jih-Chen , Yang C. C. , Su J. Y.
Published: May 2009

We have observed beating Shubnikov–de Haas oscillations in Al0.18Ga0.82N/GaN [112¯0]-direction quantum wires grown on (0001) sapphire. The spin-splitting energy, (2.4±0.3) meV for 200 nm wire, was suppressed to (1.2±0.3) meV for 100 nm wire and smeared by the scattering from edge states and intersubbands. The spin splitting of Rashba effect can be used to control the differential phase shift of spin-polarized electrons when a gate bias is applied to a nanometer arm of quantum ring. Based on the results of spin-splitting for the [112¯0]-direction AlxGa1−xN/GaN nanowire, the spin splitting of one-dimensional electron system in AlGaN/GaN nanowire can be applied to a low-power consuming quantum-ring interferometer.
Thermomigration and electromigration in Sn58Bi solder joints
Authors: Gu Xin , Chan Y. C.
Published: May 2009

Thermomigration (TM) in Sn58Bi solder was detected in Cu/Sn58Bi/Ni solder joints supplied with direct current. Thermal electric finite-element simulation showed that a thermal gradient of 527 °C/cm existed in a solder joint when a current density of 5×103 A/cm2 was applied to the structure at 50 °C. Depending on the direction of the current, TM was found to assist or counteract electromigration (EM) on the diffusion of Bi atoms. The atomic fluxes of Bi induced by EM and TM were estimated separately. EM-enhanced cross interaction between Cu and Ni across the solder joint was also detected, which led to the intermetallic compound (IMC) at Ni side or the Cu side of the joint that electron flow was from the Cu side to the Ni side is thinner than that of corresponding IMC in the joint stressed with current in opposite direction. For the joint as reflowed, the IMC at the Ni side was (Cu,Ni)6Sn5 instead of Ni3Sn4 and the IMC at the Cu side was Cu6Sn5 without Ni atoms contained. When Ni wire set as anode, the IMC at the Ni side was still (Cu,Ni)6Sn5 even after the joint was stressed for 384 h. However, it turned into (Ni,Cu)3Sn4 if Ni wire set as cathode. Regardless of the directions of the electric current, the IMC at the Cu side was Cu6Sn5 at all time. For the joint that Cu wire set as anode, the growth of Ni3Sn4 at the cathode side was enhanced by EM and TM, while the growth of Cu6Sn5 at the anode side was retarded.
Multilayer liquid spreading on superhydrophilic nanostructured surfaces
Authors: Xiao Rong , Chu Kuang-Han , Wang Evelyn N.
Published: May 2009

A phenomenon is presented where a propagating liquid on an array of nanopillars with scalloped features can separate into multiple layers of liquid films. The scallops were found to act as energy barriers that favor liquid separation into several layers over spreading in a uniform film. An analytical model based on surface energy was developed to explain the phenomenon. Additional tailored pillar geometries were fabricated and tested to validate the theory and model. The results provide design guidelines for geometries that promote multiple layer separation and offer opportunities to control liquid film thickness on superhydrophilic surfaces.
Dynamic transitions in a two dimensional associating lattice gas model
Authors: Szortyka Marcia M. , Henriques Vera B. , Girardi Mauricio , Barbosa Marcia C.
Published: May 2009

Using Monte Carlo simulations we investigate some new aspects of the phase diagram and the behavior of the diffusion coefficient in an associating lattice gas (ALG) model on different regions of the phase diagram. The ALG model combines a two dimensional lattice gas where particles interact through a soft core potential and orientational degrees of freedom. The competition between soft core potential and directional attractive forces results in a high density liquid phase, a low density liquid phase, and a gas phase. Besides anomalies in the behavior of the density with the temperature at constant pressure and of the diffusion coefficient with density at constant temperature are also found. The two liquid phases are separated by a coexistence line that ends in a bicritical point. The low density liquid phase is separated from the gas phase by a coexistence line that ends in tricritical point. The bicritical and tricritical points are linked by a critical λ-line. The high density liquid phase and the fluid phases are separated by a second critical τ-line. We then investigate how the diffusion coefficient behaves on different regions of the chemical potential-temperature phase diagram. We find that diffusivity undergoes two types of dynamic transitions: a fragile-to-strong transition when the critical λ-line is crossed by decreasing the temperature at a constant chemical potential; and a strong-to-strong transition when the critical τ-line is crossed by decreasing the temperature at a constant chemical potential.
Calculation of the surface tension from Monte Carlo simulations: Does the model impact on the finite-size effects?
Authors: Biscay F. , Ghoufi A. , Goujon F. , Lachet V. , Malfreyt P.
Published: May 2009

We report two-phase Monte Carlo simulations of the liquid-vapor interface of the Lennard-Jones (LJ) fluids in order to study the impact of the methodology used for the energy calculation on the oscillatory behavior of the surface tension with the system sizes. The surface tension values are illustrated through the LJ parameters of methane. The first methodology uses a standard truncated LJ potential, the second one adds a long range correction (LRC) contribution to the energy into the Metropolis scheme, and the third one uses a LJ potential modified by a polynomial function in order to remove the discontinuities at the cutoff distance. The surface tension is calculated from the mechanical and thermodynamic routes and the LRCs to the surface tension are systematically calculated from appropriate expressions within these definitions. The oscillatory behavior has been studied as a function of the size of the interfacial area and of the length of the dimension perpendicular to the surface. We show that the methodology has an important effect on the oscillatory variation in the surface tension with the system size. This oscillatory variation in the surface tension with the system size is investigated through its intrinsic and LRC contributions. We complete this work by studying the dependence of the surface tension with respect to the cutoff distance when the LRC part to the energy is considered into the Metropolis scheme.
Experimental and numerical results on three-dimensional instabilities in a rotating disk–tall cylinder flow
Authors: Sørensen J. N. , Gelfgat A. Yu. , Naumov I. V. , Mikkelsen R. F.
Published: May 2009

The three-dimensional axisymmetry-breaking instability of axisymmetric flow between a rotating lid and a stationary cylinder is analyzed both numerically and experimentally for the case of tall cylinders with the height/radius aspect ratio between 3.3 and 5.5. A complete stability diagram for the primary three-dimensional instability is obtained experimentally and computed numerically. The instability sets in due to different three-dimensional disturbance modes that are characterized by different azimuthal wavenumbers. The critical Reynolds numbers and associated frequencies are identified for each mode. The onset of three-dimensional flow behavior is measured by combining the high spatial resolution of particle image velocimetry and the temporal accuracy of laser Doppler anemometry. The results are compared to the numerical stability analysis. The measured onset of three dimensionality is in a good agreement with the numerical results. Disagreements observed in supercritical regimes can be explained by secondary bifurcations that are not accounted for by linear stability analysis of the primary base flow.
Time domain measurement of phase noise in a spin torque oscillator
Authors: Keller Mark W. , Kos A. B. , Silva T. J. , Rippard W. H. , Pufall M. R.
Published: May 2009

We measure oscillator phase from the zero crossings of the voltage versus time waveform of a spin torque nanocontact oscillating in a vortex mode. The power spectrum of the phase noise varies with Fourier frequency f as 1/f2, consistent with frequency fluctuations driven by a thermal source. The linewidth implied by phase noise alone is about 70% of that measured using a spectrum analyzer. A phase-locked loop reduces the phase noise for frequencies within its 3 MHz bandwidth.
Dissipative-particle dynamics simulations of flow over a stationary sphere in compliant channels
Authors: Reddy Harinath , Abraham John
Published: May 2009

Dissipative-particle dynamics (DPD), a particle-based fluid-simulation approach, is employed to simulate isothermal pressure-driven flow across a sphere in compliant cylindrical channels. The sphere is represented by frozen DPD particles, while the surrounding fluid is modeled using simple fluid particles. The channel walls are made up of interconnected finite extensible nonlinear elastic bead-spring chains. The wall particles at the inlet and outlet ends of the channel are frozen so as to hinge the channel. The model is assessed for accuracy by computing the drag coefficient CD in shear flow past a uniform sphere in unbounded flow, and comparing the results with those from correlations in literature. The effect of the aspect ratio λ of the channel, i.e., the ratio of the sphere diameter d to the channel diameter D, on the drag force FD on the sphere is investigated, and it is found that FD decreases as λ decreases toward the values predicted by the correlations as λ approaches zero. The effect of the elasticity of the wall is also studied. It is observed that as the wall becomes more elastic, there is a decrease in FD on the sphere.
Transplanting assembly of carbon-nanotube-tipped atomic force microscope probes
Authors: Kim Soohyung , Lee Hyung Woo , Kim Sang-Gook
Published: May 2009

Carbon-nanotube (CNT)-tipped atomic force microscope (AFM) probes were assembled in a deterministic and reproducible manner by transplanting a CNT bearing polymeric carrier to a microelectromechanical systems cantilever. Single-strand CNTs were grown vertically at predefined locations where each CNT was encapsulated into a cylindrical polymer carrier block. Double-layer carriers were used for controlling the release of blocks and the exposed length of CNT tips after the assembly. Much reduced complexity in assembly was achieved by transplanting individual CNTs to AFM probes, which could scan nanotrenches and biostructures with little probe artifacts.
Transition from smoothing to roughening of ion-eroded GaSb surfaces
Authors: Keller A. , Biermanns A. , Carbone G. , Grenzer J. , Facsko S. , Plantevin O. , Gago R. , Metzger T. H.
Published: May 2009

During ion sputtering of GaSb(100) surfaces a transient behavior from initial smoothing to roughening accompanied by self-organized pattern formation has been observed using in situ x-ray reflectivity and grazing incidence small angle scattering. The induced patterns show hexagonally ordered nanodot arrays with a spatial periodicity of 30 nm. The correlation length of the pattern increases with ion fluence. In the framework of the Bradley–Harper model [R. M. Bradley and J. M. E. Harper, J. Vac. Sci. Technol. A 6, 2390 (1988)], where the dot pattern formation results from an interplay of surface roughening due to sputtering and surface smoothing due to diffusion, the initial smoothing behavior is explained by the same surface diffusion processes as the pattern formation.
A model of vegetative flush development and its potential use managing macadamia (Macadamia integrifolia) tree canopies
Authors: Wilkie J. D. , Sedgley M. , Olesen T.
Published: May 2009

We examined the relationship between shoot growth and temperature and solar radiation in macadamia (Macadamia integrifolia Maiden and Betche, M. integrifolia × tetraphylla Johnson) as an aid to developing pruning strategies for this crop. Trees growing at Alstonville (28.9°S) in northern NSW, Australia, were pruned at various times to promote vegetative flushing under a range of environmental conditions.
Flush development in macadamia is cyclic: bud release and stem elongation followed by a period of dormancy, before bud release of the subsequent flush. The rate of bud release after pruning was best correlated with the product of the mean temperature and solar radiation (r2 = 0.75, P < 0.0001), whereas the rate of flush development was best correlated with the mean temperature (r2 = 0.76, P < 0.0001). The number of buds released per pruned stem was greater under higher temperatures and solar radiation (r2 = 0.37, P < 0.001), but the length of the flush after pruning decreased with increasing temperatures (r2 = 0.32, P < 0.01).
The descriptive models were combined with long-term weather data to predict the duration and characteristics of flushes following pruning at various times of the year along Australia’s eastern seaboard, from Mareeba (17.0°S) to Coffs Harbour (30.3°S). Flush duration and stem length following June pruning were predicted to be greater than following early autumn or September pruning and to vary from year to year, and with location (latitude). We discuss the implications of the model predictions for productivity and propose pruning times intended to optimise flowering and yield. Further research is required to test these proposed pruning strategies.
Brahman and Brahman crossbred cattle grown on pasture and in feedlots in subtropical and temperate Australia. 1. Carcass quality
Authors: Schutt K. M. , Burrow H. M. , Thompson J. M. , Bindon B. M.
Published: May 2009

Brahmans are known to have poorer carcass quality relative to Bos taurus breeds and crossbreds under temperate environments; however, little is known of their performance in subtropical environments. The Cooperative Research Centre for Cattle and Beef Industry (Meat Quality) initiated a crossbred progeny test experiment to compare straightbred Brahmans with Brahman crossbreds finished on pasture and grain, in subtropical and temperate environments, to carcass quality specifications of Australian domestic and export markets. Brahman, Belmont Red, Santa Gertrudis, Angus, Hereford, Shorthorn, Charolais and Limousin sires were mated to Brahman females in subtropical Queensland over 3 years to produce 1750 progeny. At a common age at slaughter, Charolais crossbreds had the highest hot carcass weight (CWT) but were not significantly heavier than Limousin or British crossbred progeny. At common carcass weights, breeds within breed type (British, Continental, tropically adapted) performed similarly. British and Santa Gertrudis crossbreds had the fattest carcasses and lowest yields. British and Belmont Red crossbreds had the highest intramuscular fat percentage (IMF). Continental crossbreds had the highest retail beef yield (RBY), kilograms of retail primals (RTPM) and percent retail primals (pcRTPM) and leanest carcasses. Brahmans had the lowest CWT, intermediate subcutaneous fat cover, high yields and low IMF. Animals finished in the subtropics on pasture were significantly older, leaner and had higher RBY, RTPM and pcRTPM than subtropical feedlot-finished contemporaries. Temperate feedlot animals had significantly more IMF, less subcutaneous fat at the P8 site and slightly lower yields than subtropical feedlot contemporaries, indicating possible effects of postweaning growth path on fat distribution. Belmont Red crossbreds demonstrated the advantages of adaptation with the highest IMF in both subtropical finishing regimes, while Angus progeny had the highest IMF in the temperate feedlot environment and highest IMF overall when analysed across finishing regimes. Significant interactions were mainly the result of scale effects rather than breed re-ranking for carcass traits across markets and finishing regimes. Therefore, breeds that performed well for certain carcass traits in subtropical environments performed consistently for those traits in temperate environments relative to other sire breeds, regardless of market endpoint or finishing nutrition.
Consequences of prenatal and preweaning growth for yield of beef primal cuts from 30-month-old Piedmontese- and Wagyu-sired cattle
Authors: Greenwood P. L. , Cafe L. M. , Hearnshaw H. , Hennessy D. W. , Morris S. G.
Published: May 2009

Cattle sired by Piedmontese or Wagyu bulls were bred and grown within pasture-based nutritional systems followed by feedlot finishing. Effects of low (mean 28.6 kg, n = 120) and high (38.8 kg, n = 120) birthweight followed by slow (mean 554 g/day, n = 119) or rapid (875 g/day, n = 121) growth to weaning on beef primal cut weights at ~30 months of age were examined. Cattle of low birthweight or grown slowly to weaning had smaller primal cuts at 30 months as a result of reduced liveweight and smaller carcasses compared with their high birthweight or rapidly grown counterparts. Hence they require additional nutritional and economic inputs to reach target market weights. At equivalent carcass weights (380 kg), cattle restricted in growth from birth to weaning yielded slightly more beef and were somewhat leaner than their rapidly grown counterparts, resulting in primal cuts being up to 4% heavier in the slowly grown compared with the rapidly grown cattle. Compositional differences due to birthweight were less apparent at the same carcass weight, although low birthweight cattle had a slightly (~2%) heavier forequarter and slightly lower (~1%) hindquarter retail yield, and less shin-shank meat (~2%) than high birthweight cattle, suggesting only minor effects on carcass tissue distribution. There were few interactions between sire genotype and birthweight or preweaning growth, and interactions between birthweight and preweaning growth were not evident for any variables. However, variability between cohorts in their long-term responses to growth early in life suggests other environmental factors during early-life and/or subsequent growth influenced carcass yield characteristics. Overall, this study shows that effects of birthweight and preweaning growth rate on carcass compositional and yield characteristics were mostly explained by variation in carcass weight and, hence, in whole body growth to 30 months of age.
Economic effects of alternate growth path, time of calving and breed type combinations across southern Australian beef cattle environments: industry-wide effects
Authors: Griffith G. R.
Published: May 2009

The ‘Regional Combinations’ project and its biophysical outcomes, and the subsequent identification of the most profitable beef cattle production systems across different environments in southern Australia, have been described in several other papers in this special edition. In this paper, the economic calculations reported for each of the individual beef enterprises representative of the various state sites are aggregated up to the level of the Australian cattle and beef industry and then projected forward over several years into the future. To do this, an existing model of the world beef market is used. The analyses suggest that both the fast-growth-rate technology and the time-of-calving technology have the potential to generate significant economic benefits for the southern Australia cattle and beef industries. The cumulative present values of each technology are around $70 million over a 15-year time horizon at a 7% real discount rate.
Economic effects of nutritional constraints early in life of cattle
Authors: Alford A. R. , Cafe L. M. , Greenwood P. L. , Griffith G. R.
Published: May 2009

An experiment was conducted at the Grafton Agricultural Research Station on the northern coast of New South Wales whereby low and high pasture nutritional systems were imposed on a herd of Hereford cows during pregnancy and from birth to weaning in a factorial design. Offspring representing extremes of growth to birth and/or weaning were then selected for study of long-term consequences of growth early in life. Implications of the nutritional treatments of cows on subsequent weaning rates were also tested with data from previous studies. The extent to which these extreme maternal nutritional and offspring growth scenarios affected herd profitability was tested with the Beef-N-Omics decision support package. For the representative cattle enterprise modelled, gross margin per hectare ranged from $A114 to $A132. In all cases, the gross margin for those groups with fetal growth based on a higher level of nutrition exceeded that of their peers on a lower level of nutrition. It is more profitable for cows and calves to have access to a high standard of nutrition during pregnancy and up to weaning than for them to have access only to a poor standard of nutrition. Incorporating differential weaning rates following maternal nutritional treatments reduced gross margins per hectare by up to 30%. On average, a 1% reduction in weaning rate resulted in a 4.5% reduction in gross margin. Restricted cow–calf nutrition affects the future cow fertility, as well as the current calf progeny, economically.
Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling
Authors: Mannige Ranjan V. , Brooks Charles L.
Published: May 2009

Spherical capsids are shells of protein subunits that protect the genomes of many viral strains. Although nature displays a range of spherical capsid sizes (reflected by the number of subunits in the formation), specific strains display stringent requirements for forming capsids of specific sizes, a requirement that appears crucial to infectivity. Despite its importance in pathogenicity, little is known regarding the determinants of capsid size. Still less is known about exactly which capsids can undergo maturation events such as buckling transitions—postcapsid-assembly events that are crucial to some virus strains. We show that the exclusive determinant of capsid size is hexamer shape, as defined by subunit–subunit dihedral angles. This conclusion arises from considering the dihedral angle patterns within hexamers belonging to natural canonical capsids and geometric capsid models (deltahedra). From simple geometric models and an understanding of endo angle propagation discussed here, we then suggest that buckling transitions may be available only to capsids of certain size (specifically,
T
< 7 capsids are precluded from such transformations) and that
T
> 7 capsids require the help of auxiliary mechanisms for proper capsid formation. These predictions, arising from simple geometry and modeling, are backed by a body of empirical evidence, further reinforcing the extent to which the evolution of the atomistically complex virus capsid may be principled around simple geometric design/requirements.
Heterogeneous preferences, decision-making capacity, and phase transitions in a complex adaptive system
Authors: Wang Wei , Chen Yu , Huang Jiping
Published: May 2009

There has been a belief that with the directing power of the market, the efficient state of a resource-allocating system can eventually be reached even in a case where the resource is distributed in a biased way. To mimic the realistic huge system for the resource allocation, we designed and conducted a series of economic experiments. From the experiments we found that efficient allocation can be realized despite a lack of communications among the participants or any instructions to them. To explain the underlying mechanism, an extended minority game model called the market-directed resource allocation game (MDRAG) is constructed by introducing heterogeneous preferences into the strategy-building procedures. MDRAG can produce results in good agreement with the experiments. We investigated the influence of agents' decision-making capacity on the system behavior and the phase structure of the MDRAG model as well. A number of phase transitions are identified in the system. In the critical region, we found that the overall system will behave in an efficient, stable, and unpredictable mode in which the market's invisible hand can fully play its role.
Anomalous compressibility of ferropericlase throughout the iron spin cross-over
Authors: Wentzcovitch R. M. , Justo J. F. , Wu Z. , da Silva C. R. S. , Yuen D. A. , Kohlstedt D.
Published: May 2009

The thermoelastic properties of ferropericlase Mg

1−
x

Fe

x

O (
x
= 0.1875) throughout the iron high-to-low spin cross-over have been investigated by first principles at Earth's lower mantle conditions. This cross-over has important consequences for elasticity such as an anomalous bulk modulus (

K
S

) reduction. At room temperature the anomaly is somewhat sharp in pressure but broadens with increasing temperature. Along a typical geotherm it occurs across most of the lower mantle with a more significant

K
S

reduction at ≈1,400–1,600 km depth. This anomaly might also cause a reduction in the effective activation energy for diffusion creep and lead to a viscosity minimum in the mid-lower mantle, in apparent agreement with results from inversion of data related with mantle convection and postglacial rebound.
Electron transfer in the
Rhodobacter sphaeroides
reaction center assembled with zinc bacteriochlorophyll
Authors: Lin Su , Jaschke Paul R. , Wang Haiyu , Paddock Mark , Tufts Aaron , Allen James P. , Rosell Federico I. , Mauk A. Grant , Woodbury Neal W. , Beatty J. Thomas
Published: May 2009

The cofactor composition and electron-transfer kinetics of the reaction center (RC) from a magnesium chelatase (
bchD
) mutant of
Rhodobacter sphaeroides
were characterized. In this RC, the special pair (P) and accessory (B) bacteriochlorophyll (BChl) -binding sites contain Zn-BChl rather than BChl
a
. Spectroscopic measurements reveal that Zn-BChl also occupies the H sites that are normally occupied by bacteriopheophytin in wild type, and at least 1 of these Zn-BChl molecules is involved in electron transfer in intact Zn-RCs with an efficiency of >95% of the wild-type RC. The absorption spectrum of this Zn-containing RC in the near-infrared region associated with P and B is shifted from 865 to 855 nm and from 802 to 794 nm respectively, compared with wild type. The bands of P and B in the visible region are centered at 600 nm, similar to those of wild type, whereas the H-cofactors have a band at 560 nm, which is a spectral signature of monomeric Zn-BChl in organic solvent. The Zn-BChl H-cofactor spectral differences compared with the P and B positions in the visible region are proposed to be due to a difference in the 5th ligand coordinating the Zn. We suggest that this coordination is a key feature of protein–cofactor interactions, which significantly contributes to the redox midpoint potential of H and the formation of the charge-separated state, and provides a unifying explanation for the properties of the primary acceptor in photosystems I (PS1) and II (PS2).
Calix[4]arene-based conical-shaped ligands for voltage-dependent potassium channels
Authors: Martos Vera , Bell Sarah C. , Santos Eva , Isacoff Ehud Y. , Trauner Dirk , de Mendoza Javier
Published: May 2009

Potassium channels are among the core functional elements of life because they underpin essential cellular functions including excitability, homeostasis, and secretion. We present here a series of multivalent calix[4]arene ligands that bind to the surface of voltage-dependent potassium channels (K
v
1.x) in a reversible manner. Molecular modeling correctly predicts the best candidates with a conical
C
4
symmetry for optimal binding, and the effects on channel function are assessed electrophysiologically. Reversible inhibition was observed, without noticeable damage of the oocytes, for tetraacylguanidinium or tetraarginine members of the series with small lower rim
O
-substituents. Apparent binding constants were in the low micromolar range and had Hill coefficients of 1, consistent with a single site of binding. Suppression of current amplitude was accompanied by a positive shift in the voltage dependence of gating and slowing of both voltage sensor motion and channel opening. These effects are in keeping with expectations for docking in the central pore and interaction with the pore domain “turret.”
Alphaherpesvirus US3-mediated reorganization of the actin cytoskeleton is mediated by group A p21-activated kinases
Authors: Van den Broeke Céline , Radu Maria , Deruelle Matthias , Nauwynck Hans , Hofmann Clemens , Jaffer Zahara M. , Chernoff Jonathan , Favoreel Herman W.
Published: May 2009

The US3 protein is a viral serine/threonine kinase that is conserved among all members of the
Alphaherpesvirinae
. The US3 protein of different alphaherpesviruses causes dramatic alterations in the actin cytoskeleton, such as the disassembly of actin stress fibers and formation of cell projections, which have been associated with increased intercellular virus spread. Here, we find that inhibiting group A p21-activated kinases (PAKs), which are key regulators in Cdc42/Rac1 Rho GTPase signaling pathways, impairs US3-mediated actin alterations. By using PAK1
−/−
and PAK2
−/−
mouse embryo fibroblasts (MEFs), we show that US3-mediated stress fiber disassembly requires PAK2, whereas US3-mediated cell projection formation mainly is mediated by PAK1, also indicating that PAK1 and PAK2 can have different biological effects on the organization of the actin cytoskeleton. In addition, US3 was found to bind and phosphorylate group A PAKs. Lack of group A PAKs in MEFs was correlated with inefficient virus spread. Thus, US3 induces its effect on the actin cytoskeleton via group A PAKs.