bluuebunny/crossref_metadata_2025 huggingface dataset:
Clustering of eastern North Pacific tropical cyclone tracks: ENSO and MJO effects
Authors: Camargo Suzana J. , Robertson Andrew W. , Barnston Anthony G. , Ghil Michael
Published: June 2008

A probabilistic clustering technique is used to describe tropical cyclone tracks in the eastern North Pacific, on the basis of their shape and location. The best track data set is decomposed in terms of three clusters; these clusters are analyzed in terms of genesis location, trajectory, landfall, intensity, seasonality, and their relationships with the El Niño–Southern Oscillation (ENSO) and Madden‐Julian Oscillation (MJO). Longitudinal track location plays a strong discriminating role in the regression mixture model's solution, with the average track orientation becoming more zonal toward the west. This progression encapsulates well the relationship between tropical cyclones over the eastern tropical Pacific and the MJO or ENSO. Two of the clusters describe tropical cyclones (TCs) with tracks that lie near the coast of Mexico and Central America. The most frequent cluster contains tracks that trend west‐northwestward, while the second most frequent one has genesis locations that lie slightly to the southeast of those in the most frequent cluster and tracks that run typically parallel to the Central American coast. This second cluster is shown to be significantly associated with the westerly phase of the MJO. The third, least frequent cluster contains TCs with westward trajectories over the central and eastern equatorial Pacific; some of these TCs have an impact on Hawaii and other islands, as far as the central and western North Pacific regions. The least frequent cluster is strongly related to ENSO, while the others are not; it occurs significantly more frequently during El Niño conditions. Examination of the large‐scale patterns of atmospheric circulation and sea surface temperature associated with each of our three clusters are consistent with previous studies. Anomalous low‐level westerly zonal winds from the monsoon trough and MJO meet anomalous easterlies near the region of genesis in each cluster.
Parametric analysis of positive amplitude electron acoustic solitary waves in a magnetized plasma and its application to boundary layers
Authors: Ghosh S. S. , Pickett J. S. , Lakhina G. S. , Winningham J. D. , Lavraud B. , Décréau P. M. E.
Published: June 2008

The existence domain of a fully nonlinear positive amplitude electron acoustic solitary wave has been studied in a four‐component plasma composed of warm magnetized electrons, warm electron beam, and energetic multi‐ion species with ions hotter than the electrons (Ti > Te). A Sagdeev pseudopotential technique has been used to obtain the nonlinear evolution equation for the wave propagating obliquely with the ambient magnetic field. It is observed that the ion temperatures and concentrations play a crucial role in determining the characteristics and the existence domain of the electron acoustic solitary wave. With a large cold ion population and/or a large cold to hot ion temperature ratio, the plasma tends to behave like a single ion‐dominated one. The corresponding Sagdeev pseudopotential shows an extremely narrow and deep profile producing small‐amplitude, narrow width, spiky solitary waves. Such solutions are found to be applicable in the bow shock, magnetosheath, and cusp regions. Comparison with CLUSTER observations agrees well with the analytical model. It has been shown that in the magnetosheath, cooler He2+ ions are necessary to produce a positive polarity solution while a hotter species may produce a compressive (negative polarity) solution.
Landscape‐scale extent, height, biomass, and carbon estimation of Mozambique's mangrove forests with Landsat ETM+ and Shuttle Radar Topography Mission elevation data
Authors: Fatoyinbo Temilola E. , Simard Marc , Washington‐Allen Robert A. , Shugart Herman H.
Published: June 2008

Mangroves are salt tolerant plants that grow within the intertidal zone along tropical and subtropical coasts. They are important barriers for mitigating coastal disturbances, provide habitat for over 1300 animal species and are one of the most productive ecosystems. Mozambique's mangroves extend along 2700 km and cover one of the largest areas in Africa. The purpose of this study was to determine the countrywide mean tree height spatial distribution and biomass of Mozambique's mangrove forests using Landsat ETM+ and Shuttle Radar Topography Mission (SRTM) data. The SRTM data were calibrated using the Landsat derived land‐cover map and height calibration equations. Stand‐specific canopy height‐biomass allometric equations developed from field measurements and published height‐biomass equations were used to calculate aboveground biomass of the mangrove forests on a landscape scale. The results showed that mangrove forests covered a total of 2909 km2 in Mozambique, a 27% smaller area than previously estimated. The SRTM calibration indicated that average tree heights changed with geographical settings. Even though the coast of Mozambique spans across 16 degrees latitude, we did not find a relationship between latitude and biomass. These results confirm that geological setting has a greater influence than latitude alone on mangrove production. The total mangrove dry aboveground biomass in Mozambique was 23.6 million tons and the total carbon was 11.8 million tons.
Interdecadal‐decadal climate variability from multicoral oxygen isotope records in the South Pacific Convergence Zone region since 1650 A.D.
Authors: Linsley Braddock K. , Zhang Peipei , Kaplan Alexey , Howe Stephen S. , Wellington Gerard M.
Published: June 2008

In the South Pacific, interdecadal‐decadal oceanic and atmospheric variability, referred to as the Interdecadal Pacific Oscillation (IPO), is most pronounced in the South Pacific Convergence Zone (SPCZ) salinity front region. Here we have used annual average oxygen isotope (δ18O) time series from five coral cores collected from Fiji and Tonga in this region to construct a Fiji‐Tonga Interdecadal‐Decadal Pacific Oscillation (F‐T IDPO) index of low‐frequency (>9 and <55 years) climate variability back to 1650 A.D. We first demonstrate the consistency between this F‐T IDPO index and a mean sea level (MSL) pressure‐based SPCZ position index (SPI) (1891–2000), thus verifying the ability of coral δ18O to record past interdecadal‐decadal climatic variations in this region back to 1891. The F‐T IDPO index is then shown to be synchronous with the IPO index (1856–2000), suggesting that this coral‐based index effectively represents the interdecadal‐decadal scale climate variance back to 1650. The regularity of the F‐T IDPO index indicates that interdecadal‐decadal variability in the SPCZ region has been relatively constant over the past 350 years with a mean frequency of ∼20 years (variance peaks near 11 and 35 years). There is a consistent antiphase correlation of the F‐T IDPO index and the interdecadal‐decadal components in equatorial Pacific coral δ18O series from Maiana and Palmyra. This observation indicates that the eastward expansion (westward contraction) of the eastern salinity front of the Western Pacific Warm Pool (WPWP) occurs simultaneously (±<1 year) with the westward (eastward) shift of the SPCZ salinity front during positive IPO (negative IPO) phases. This is the same relationship observed during the phases of the El Niño Southern Oscillation.
Determination of the sea surface emissivity at L‐band and application to SMOS salinity retrieval algorithms: Review of the contributions of the UPC‐ICM
Authors: Camps A. , Font J. , Vall‐llossera M. , Corbella I. , Duffo N. , Torres F. , Blanch S. , Aguasca A. , Villarino R. , Gabarró C. , Enrique L. , Miranda J. , Sabia R. , Talone M.
Published: June 2008

This work describes the main effects that have to be taken into account to model the sea surface emission at L‐band, and the existing approaches to perform the sea surface salinity retrieval from multiangular radiometric measurements. This manuscript reviews the activities carried out in these fields during the past years by the Universitat Politècnica de Catalunya (UPC) in collaboration with the Institut de Ciències del Mar (ICM ‐ CSIC). They cover the precise measurement of the dielectric permittivity of the seawater at L‐band, the sea surface emissivity (including the effect of wind‐driven waves, swell, currents, rain, and oil spills), the comparison of experimental data with numerical models, and the development of sea surface salinity retrieval algorithms for SMOS using multiangular radiometric data. The first salinity retrievals using 2D aperture synthesis radiometry are also presented.
Improving human interferon‐β production in mammalian cell lines by insertion of an intronic sequence within its naturally uninterrupted gene
Authors: Zago Paola , Baralle Marco , Ayala Youhna M. , Skoko Natasa , Zacchigna Serena , Buratti Emanuele , Tisminetzky Sergio
Published: June 2008

Human β‐interferon is used extensively as a therapeutic agent in a wide variety of diseases, ranging from multiple sclerosis to viral infections. At present, the most common source of interferon‐β is derived from CHO (Chinese‐hamster ovary) cells. Interestingly, however, the IFNB gene is characterized by a lack of intronic sequences and therefore does not undergo splicing during its expression pathway. As nuclear processing of pre‐mRNA molecules has often been demonstrated to improve production yields of recombinant molecules, we have inserted a heterologous intronic sequence at different positions within the IFNB gene and analysed its effects on protein production. The results obtained in the present study show that the position of intron insertion has profound effects on the expression levels of the IFNB gene and on the nuclear/cytoplasm distribution levels of its mRNA as determined by FISH (fluorescent in situ hybridization) analysis of stably transfected clones. In conclusion, our results provide additional evidence that insertion of intronic sequences may be used to improve protein expression efficiency also in molecules that do not normally undergo any splicing process.
The effect of forward scattered light on the extinction of aerosols in a White type optical cell
Authors: Barkey Brian , Curtis Daniel B. , Paulson Suzanne E.
Published: June 2008

Photons are traced through a simplified White type cell to determine the adjustment to compensate for detected forward scattered light in measuring aerosol optical depth. Verification is performed by comparing the optical depth determined from optical extinction with that calculated from the measured concentration of monodisperse polystyrene latex (PSL) spheres. As the adjustments derived for representative urban and marine aerosols are similar to or larger than those required for the PSL spheres, forward scattered light needs to be considered for real world conditions with our instrument. Although the described adjustment is specific to this instrument, it is shown that it may be significant for other detection geometries.
Nonlinear electron magnetohydrodynamics physics. IV. Whistler instabilities
Authors: Urrutia J. M. , Stenzel R. L. , Strohmaier K. D.
Published: June 2008

A very large low-frequency whistler mode is excited with magnetic loop antennas in a uniform laboratory plasma. The wave magnetic field exceeds the ambient field causing in one polarity a field reversal, and a magnetic topology resembling that of spheromaks in the other polarity. These propagating “whistler spheromaks” strongly accelerate the electrons and create non-Maxwellian distributions in their toroidal current ring. It is observed that the locally energized electrons in the current ring excite new electromagnetic instabilities and emit whistler modes with frequencies unrelated to the applied frequency. Emissions are also observed from electrons excited in X-type neutral lines around the antenna. The properties of the excited waves such as amplitudes, frequency spectra, field topologies, propagation, polarization, growth, and damping have been investigated. The waves remain linear (Bwave⪡B0) and convert a small part of the electron kinetic energy into wave magnetic energy (Bwave2∕2μ0⪡nkTe).
A quantitative analytical model for static dipolar disorder broadening of the density of states at organic heterointerfaces
Authors: Richards Tim , Bird Matthew , Sirringhaus Henning
Published: June 2008

Understanding the electronic structure of organic-organic heterointerfaces is crucial for many device applications of organic semiconductors. Here we have developed a simple analytical model to describe the effect of static dipolar disorder in a polymer dielectric on the density of states of an adjacent organic semiconductor. The degree of energetic disorder varies strongly with distance from the interface. Using a simple mobility model, we have been able to explain quantitatively both the magnitude as well as the gate voltage dependence of the field-effect mobility for polymer gate dielectrics with different dielectric constants.
p
-type field-effect transistor of NiO with electric double-layer gating
Authors: Shimotani Hidekazu , Suzuki Hirotaka , Ueno Kazunori , Kawasaki Masashi , Iwasa Yoshihiro
Published: June 2008

Electric double-layer transistors have recently attracted a growing interest because of their low operating voltage and capacity for accumulation of high carrier density. Here, we demonstrate an electric double-layer transistor with a NiO single-crystal Mott insulator that displays a p-type behavior with a field-effect mobility and on/off ratio of 1.6×10−4cm2∕Vs and 130, respectively. Despite relatively poor device performance, the present results demonstrate that the electric double-layer transistor is not limited to normal band insulators but is achievable using Mott insulators, in which electrostatic doping is of significant interest.
Dipole switching in large molecules described by explicitly time-dependent configuration interaction
Authors: Krause Pascal , Klamroth Tillmann
Published: June 2008

In this paper, we report laser-driven charge transfer simulations for Li-(Ph)n-CN (n=1,2,3) using the time-dependent configuration interaction single approach. These molecules serve as systematically extendable model systems, in order to investigate the selectivity, and thus controllability, of an ultrashort laser-induced electronic excitation as a function of the molecular size. For example, such control would be needed if a small electronic molecular switch is connected to a larger molecular device. We demonstrate that for larger molecules, the selectivity of the electronic transition is considerably reduced even for rather long pulses due to dynamic polarizations of the molecules. We also show that these dynamic polarizations might be substantially underestimated in few state models.
Ab initio study of the KrH+ photodissociation
Authors: Alekseyev Aleksey B. , Buenker Robert J. , Liebermann Heinz-Peter
Published: June 2008

The multireference spin-orbit configuration interaction method is employed to calculate potential energy curves for the ground and low-lying excited states of the KrH+ cation. For the first time, the spin-orbit interaction is taken into account and electric dipole moments are computed for transitions to the states responsible for the first absorption continuum (A band) of KrH+. On this basis, the partial and total absorption spectra in this energy range are obtained. It is shown that the A-band absorption is dominated by the parallel AΣ+1←XΣ+1 transition. In the low-energy part of the band (<83×103cm−1) the absorption is mainly caused by the spin-forbidden bΠ0+3←XΣ+1 excitation, while perpendicular transitions to the BΠ1 and bΠ13 states are significantly weaker. The branching ratio Γ for the photodissociation products is calculated and it is shown to increase smoothly from 0 in the red tail of the band to 1 at E⩾90×103cm−1. The latter value corresponds to the exclusive formation of the spin-excited Kr+(P1∕22) ions, which may be used to obtain laser generation on the Kr+(P1∕22–P3∕22) transition.
Rotational and vibrational state distributions of NaH in the reactions of Na(4S2,3D2,and6S2) with H2: Insertion versus harpoon-type mechanisms
Authors: Chang Yuan-Pin , Hsiao Ming-Kai , Liu Dean-Kuo , Lin King-Chuen
Published: June 2008

By using a pump-probe technique, the nascent rotational and vibrational state distributions of NaH are obtained in the Na(4S2,3D2,and6S2) plus H2 reactions. The rotational distributions for the Na(4S2,3D2) reactions yield a bimodal feature with a major component peaking at J=20–22, similar to that obtained previously in the 4P2 reaction, whereas the Na(6S2) reaction gives rise to a distinct distribution with a much lower rotational temperature. The vibrational populations (v=0–4) for these 4S2, 3D2, and 6S2 reactions are characterized by corresponding temperatures of 1692±120, 819±35, and 5329±350K. Due to a significant contribution of configurational mixing between different states with the same symmetry, the collision species initiated from the 4S2 and 3D2 states are anticipated to track along the entrance surface in a near C2v symmetry, then undergo nonadiabatic transition to the inner limb of the reactive 2A′ surface. In contrast, the reaction pathway for the Na(6S2) state with a significantly reduced ionization energy is anticipated to follow a harpoon-type mechanism via a (near) collinear configuration. The increased atomic size of Na may hinder the insertion approach.
Analytical carbon-oxygen reactive potential
Authors: Kutana A. , Giapis K. P.
Published: June 2008

We present a reactive empirical potential with environment-dependent bond strengths for the carbon-oxygen (CO) system. The distinct feature of the potential is the use of three adjustable parameters characterizing the bond: the strength, length, and force constant, rather than a single bond order parameter, as often employed in these types of potentials. The values of the parameters are calculated by fitting results obtained from density functional theory. The potential is tested in a simulation of oxidative unzipping of graphene sheets and carbon nanotubes. Previous higher-level theoretical predictions of graphene unzipping by adsorbed oxygen atoms are confirmed. Moreover, nanotubes with externally placed oxygen atoms are found to unzip much faster than flat graphene sheets.
Ge-vacancy pair in Ge-doped Czochralski silicon
Authors: Chen Jiahe , Wu Taiquan , Ma Xiangyang , Wang Lei , Yang Deren
Published: June 2008

The potential configurations of Ge-vacancy pairs in a Ge-doped Czochralski Si (GCz-Si) crystal have been identified through first-principles theory using a total-energy pseudopotential method. The Ge atoms in the GCz-Si lattice are suggested to aggregate with the vacancy/vacancies to generate the Ge-related complexes. The total energy of the GCz-Si lattice configuration containing multivacancies decreases with the reduction of bond lengths among the vacancies and decreases with the reduction of bond lengths between the Ge atom and the vacancies. It is suggested that the Ge atom introduced in the GCz-Si crystal tends to accumulate with the vacancy and then seeds for the Ge-vacancy pairs.
Thermomigration induced degradation in solder alloys
Authors: Basaran Cemal , Li Shidong , Abdulhamid Mohd F.
Published: June 2008

Miniaturization of electronics to the nanoscale brings new challenges. Because of their small size and immense information and power processing capacity, large temperature gradients exist across nanoelectronics and power electronics solder joints. In this paper, a fully coupled thermomechanical-diffusion model is introduced to study the thermomigration induced strength degradation. A nonlinear viscoplastic material model with kinematic and isotropic hardening features is utilized. The model takes into account microstructural evolution of the material. A grain coarsening capability is built into the model to study its influence on thermomigration in solder alloys. The model is validated by comparing the simulation results with experimental data.
Radiative recombination spectra of p-type δ-doped GaAs∕AlAs multiple quantum wells near the Mott transition
Authors: Kundrotas J. , Čerškus A. , Valušis G. , Lachab M. , Khanna S. P. , Harrison P. , Linfield E. H.
Published: June 2008

Photoluminescence (PL) spectra of beryllium δ-doped GaAs∕AlAs multiple quantum wells are studied over a range of doping concentrations. Possible mechanisms for carrier recombination, both above and below the Mott metal-insulator transition, are discussed. In 15nm width Be δ-doped GaAs∕AlAs quantum wells, it is found that the Mott transition can be observed if the acceptor concentration (NBe)⩾3×1012cm−2. At doping concentrations near the Mott transition band the PL spectra are dominated by excitons-bound-to-acceptor impurity recombinations. Above the Mott transition, the radiative recombination of free electrons with a two-dimensional hole gas is found to be the dominant recombination mechanism.
Greatly decreased critical current density anisotropy in YBa2Cu3O6+x thin films ablated from nanocrystalline and BaZrO3-doped nanocrystalline targets
Authors: Paturi P. , Irjala M. , Huhtinen H.
Published: June 2008

The anisotropy of the critical current density Jc was determined from angular critical current measurements for YBa2Cu3O6+x (YBCO) thin films laser deposited from a nanograined and a BaZrO3-doped nanograined target. In quantitative analysis using Blatter scaling the effective Jc anisotropy was found to be much smaller than for standard YBCO films.
Effective elastic constants in acoustoelasticity
Authors: Duquennoy Marc , Ouaftouh Mohammadi , Devos Dany , Jenot Frédéric , Ourak Mohamed
Published: June 2008

In the context of studies on ultrasonic wave propagation in stressed media (acoustoelasticity), a classic formalism can be considered (second order) by replacing the elastic constants with effective elastic constants (EECs) for which the influence of stress is taken into account. Up until now, this formalism presented some limitations since certain EEC split, which meant the authors have to consider the pseudo-orthotropy or pseudohexagonality to describe the symmetry of the materials with respect to ultrasonic wave propagation. In this letter, the possibility of avoiding these degenerations by carrying out the developments using the natural coordinates of the material is shown.
Impact of elemental arsenic on electrical characteristics of metal-oxide-semiconductor capacitors on GaAs using atomic-layer deposited HfO2 gate dielectric
Authors: Suri Rahul , Lichtenwalner Daniel J. , Misra Veena
Published: June 2008

The interface between HfO2 and sulfur-passivated GaAs was analyzed after atomic-layer deposition (ALD) and postdeposition annealing (PDA) using x-ray photoelectron spectroscopy. The HfO2 ALD process resulted in elemental arsenic buildup at the interface. Electrical measurements confirmed that the elemental arsenic caused anomalously large values for equivalent oxide thickness (EOT), hysteresis, and frequency dispersion in accumulation. Arsenic outdiffusion after PDA lowered the EOT but increased the gate leakage. Annealing the (NH4)2S-treated GaAs prior to ALD yielded an EOT of 1.85nm and leakage of 6.6×10−4A∕cm2 at Vg=Vfb−1V. This modified passivation scheme looks promising for achieving a high-quality HfO2∕GaAs interface.
Enhancing effects of microcavities on shear-horizontal surface acoustic wave sensors: A finite element simulation study
Authors: Cular Stefan , Sankaranarayanan Subramanian K. R. S. , Bhethanabotla Venkat R.
Published: June 2008

Shear-horizontal surface acoustic wave (SAW) sensors with microcavities in the delay paths of 36° YX-LiTaO3 substrate were studied using finite element methods. Microcavities of square cross sections of sizes λ∕4 and λ∕2 and of different depths were located in the middle of the delay path. Simulation results for nonfilled and polystyrene-filled microcavity devices were compared with standard delay line shear-horizontal SAW, optimized Love-wave, and etched grating sensors. We found that the best case microcavities studied reduce insertion loss by 19.25dB from 33.28dB and exhibit velocity sensitivity 4.83 times larger than that of the standard SAW sensor simulated.
Tuning of spin polarization in ferromagnetic resonant tunneling diode by varying δ doping
Authors: Qiu Z. J. , Zhang S.-L. , Liu R.
Published: June 2008

GaMnN ferromagnetic resonant tunneling diode, incorporating δ doping is theoretically investigated. A clear spin splitting current is observed when an optimal δ doping concentration is assumed. Compared to non δ doping case, the spin-down polarization can be enhanced 2–3 times at the doping concentration of 7×1011cm−2. In addition, spin-down peak current is also increased ∼30%. These results demonstrate that δ doping is a flexible and feasible way to tune electron spin polarization.
Local environment dependent linewidth of plasmon absorption in gold nanoshell: Effects of local field polarization
Authors: Zhu Jian
Published: June 2008

The linewidth of the plasmon absorption of a gold nanoshell was theoretically studied by using a Drude model and quasistatic approximation. Increasing the dielectric constant of the core or surrounding can broaden the absorption peak linearly. A mechanism based on the polarization direction of the local electric field in the gold shell was investigated to illuminate the effect of dielectric constant on the broadening of the plasmon absorption. The perpendicular local field enhances the scattering of the oscillatory electrons and brings a loss of electron phase coherence, which in turn results in a broadening of the plasmon absorption linewidth.
The effect of finishing diet and meat cuts on the attributes of four processed products from bull beef
Authors: Farouk M. M. , Podmore C. , Boom C. , Sheath G.
Published: June 2008

Breakfast beef, stir-fry, pot-roast and oven-roast meats were prepared from the brisket, clod, inside round and knuckle of bulls on two pasture-based finishing diets (6 weeks of grain supplement before slaughter or no supplement). Diet affected the fatness of the raw meat but had no significant effect on the attributes assessed by the in-house consumer or trained panel. Stir fry from brisket, and pot roast and oven roast from brisket and clod, had higher (P < 0.001) cook yields than similar products from the other cuts. Overall, the order of acceptability of cuts with the appropriate inputs for processing the four products as determined by taste panels was: clod > knuckle > inside round > brisket; and that of product acceptability with appropriate processing was breakfast beef > oven roast > pot roast > stir fry. Female in-house consumer panellists assigned lower acceptability scores to the beef products than their male counterparts (P < 0.05). Because none of the muscles or products made from the muscles were totally rejected by the consumer panel (overall scores range from 4.2 to 7.0), there is potential to add value to these cuts through further processing.
Effect of birthweight on survival in triplet-born lambs
Authors: Morel P. C. H. , Morris S. T. , Kenyon P. R.
Published: June 2008

Lambing percentage is the main contributor to higher profit on New Zealand sheep farms and has increased from 98% in 1960 to 124% in 2006. As ewe litter size increases so does the proportion of triplet-born lambs and consequently preweaning mortality rate. The purpose of this study was to investigate the effect of birthweight (BWT) on survival in triplet-born lambs within and among litters.
Data from a total of 594 triplet crossbreed lambs born to mixed-age ewes was analysed. For the statistical analysis, the lambs were allocated according to their BWT, and within the litter were then allocated to three BWT groups (light, medium and heavy). The following parameters were calculated: total litter BWT (TBWT), percentage of TBWT for each lamb (PBWT = BWT/TBWT), coefficient of variation for BWT within litter and lamb average daily gain from birth to weaning.
The mortality rate for the light, medium and heavy lambs was 56, 40 and 28%, respectively, and consequently the lightest lamb in a litter was 3.2 times more likely to die than the heaviest lamb. In the light lamb group, as BWT increased mortality decreased (P = 0.006), for medium lambs BWT did not influence mortality (P = 0.88) and in the heavy group there was a trend of increased BWT associated with increased mortality (P = 0.10). The negative relationship between lamb mortality and PBWT was identical in the three BWT groups (P < 0.0001). The effect of BWT on lamb mortality became non-significant when PBWT was fitted in the same model. This means that, in triplet-born lambs, mortality is not influenced by the BWT of the lamb itself, but by the BWT of its littermates. It can be calculated that a 4-kg lamb has a 24% chance of surviving in a litter of 16 kg, a 60% chance in a litter of 12 kg and an 87% chance of surviving in a litter of 8 kg. It is concluded that reducing the variation in BWT within a litter, or specifically managing the lightest lamb at birth, will increase the competitive ability for survival of each lamb and, therefore, decrease overall mortality and further improve farm profitability.
A training program to improve milk production in the developing Chinese dairy industry
Authors: Bush R. D. , House J. K. , Hamilton B. , Wynn P. C.
Published: June 2008

The Chinese government has been concerned about the inability of Holstein heifers imported from Australia to perform to their genetic potential. Therefore, the Australian government initiated an extension program to address the nutritional, environmental and health management of these animals. This involved developing appropriate resources and providing on-site training at workshops in four Chinese provinces (Xinjiang, Inner Mongolia, Hebei and Heilongjiang) that have been the major recipients of Australian cattle and together account for 65% of China’s dairy herd. Training resources were developed in the form of a comprehensive reference manual, a set of 12 applied fact sheets and an interactive DVD. Training has been delivered to over 285 key dairy extension workers and farmers from across China, with over 90% of participants giving a positive appraisal for all workshop sessions. The growth of dairy farming in China is likely to be the key driver of continued demand for dairy heifers from Australia and associated support for training, which must now be the initiative of the Chinese government.
Development and validation of a simple technique for logging body temperature in free-ranging cattle
Authors: Lea J. M. , Niemeyer D. D. O. , Reed M. T. , Fisher A. D. , Ferguson D. M.
Published: June 2008

This series of experiments was undertaken to develop a low animal impact, inexpensive and simple method of continuous logging of body temperature in free-ranging adult cattle for periods up to 7 days. Two different types of logger (iButton and Vemco minilogger) and three different methods of attachment (surgical implant, anal girth strap and anal tail attachment) for the iButton were investigated. The technique based on the iButton temperature logger, secured to the tail head was the most effective. This technique required minimal animal handling and provided reliable and accurate measurement of temperature in freely behaving cattle.
Abundance, spatial distribution and habitat relationships of echinoderms in the Cabo Verde Archipelago (eastern Atlantic)
Authors: Entrambasaguas Laura , Pérez-Ruzafa Ángel , García-Charton Jose A. , Stobart Ben , Bacallado Juan José
Published: June 2008

The analysis of spatial variability in distribution and abundance of echinoderms may help in identifying the range of processes that can explain the observed patterns of this important component of benthic communities. The distribution and abundance of the echinoderm assemblage inhabiting the shallow rocky reefs at the Cabo Verde archipelago (where few studies other than descriptive ones have been performed until now) was quantified at three spatial scales (among islands, between locations within islands, and among replicates), at two depth strata, and related to fine-scale variation of habitat structure. Total echinoderm abundance and the abundance of the sea urchins Diadema antillarum and Eucidaris tribuloides, and the holothurian Euapta lappa were heterogeneous at the largest considered scale. Most species and habitat descriptors exhibited spatial variability at finer scales. There were significant relationships between habitat architecture and depth and both assemblage parameters and species abundances. Although the effects of habitat structure were species-specific, the probability of occurrence of Asteroidea, Ophiuroidea and Holothuroidea species was higher in heterogeneous habitats. Meanwhile Echinoidea and Holothuroidea species showed higher correlations to complex habitats. The observed spatial patterns are inferred to reflect behavioural responses to fine-scale microhabitat complexity, as well as broad-scale oceanic variables and recruitment dynamics.
Genetic stock structure of blue-eye trevalla (Hyperoglyphe antarctica) and warehous (Seriolella brama and Seriolella punctata) in south-eastern Australian waters
Authors: Robinson Nick , Skinner Alexandra , Sethuraman Lakshmi , McPartlan Helen , Murray Neil , Knuckey Ian , Smith David C. , Hindell Jeremy , Talman Sonia
Published: June 2008

Blue-eye trevalla (Hyperoglyphe antarctica), blue warehou (Seriolella brama) and silver warehou (Seriolella punctata) from the family Centrolophidae are three commercially important species in the Australian fishery. These species are currently managed as single stocks. We tested the hypothesis that patterns of phenotypic structuring in these species reflect underlying genetic stock structure using an analysis of mitochondrial DNA control region sequences. The analysis revealed high levels of haplotype diversity within populations. The most common haplotypes for the species occurred in all geographical locations sampled. For S. brama, although structuring was not significant after Bonferroni correction, differences between two sites were sufficient to warrant caution in the management of fishery zones for this species. There were also some indications of structuring when sites were grouped into common regions. Demographic analysis suggested that S. brama might have had a history of population bottlenecks followed by sudden population expansion, potentially contributing to genetic structuring in the fishery. No structuring was detected for H. antarctica and S. punctata. The present study highlights the need for, and the utility of, multiple sources of information, that is, genetic, phenotypic, behavioural and ecological, when managing marine fisheries and the need to take a cautionary approach to the interpretation of genetic data for fisheries management.
The associative nature of adenylyl transfer catalyzed by T4 DNA ligase
Authors: Cherepanov Alexey V. , Doroshenko Elena V. , Matysik Jörg , de Vries Simon , de Groot Huub J. M.
Published: June 2008

DNA ligase seals nicks in dsDNA using chemical energy of the phosphoanhydride bond in ATP or NAD
+
and assistance of a divalent metal cofactor Mg
2+
. Molecular details of ligase catalysis are essential for understanding the mechanism of metal-promoted phosphoryl transfer reactions in the living cell responsible for a wide range of processes, e.g., DNA replication and transcription, signaling and differentiation, energy coupling and metabolism. Here we report a single-turnover
31
P solid-state NMR study of adenylyl transfer catalyzed by DNA ligase from bacteriophage T4. Formation of a high-energy covalent ligase–nucleotide complex is triggered
in situ
by the photo release of caged Mg
2+
, and sequentially formed intermediates are monitored by NMR. Analyses of reaction kinetics and chemical-shift changes indicate that the pentacoordinated phosphorane intermediate builds up to 35% of the total reacting species after 4–5 h of reaction. This is direct experimental evidence of the associative nature of adenylyl transfer catalyzed by DNA ligase. NMR spectroscopy in rotating solids is introduced as an analytical tool for recording molecular movies of reaction processes. Presented work pioneers a promising direction in structural studies of biochemical transformations.
4D visualization of embryonic, structural crystallization by single-pulse microscopy
Authors: Kwon Oh-Hoon , Barwick Brett , Park Hyun Soon , Baskin J. Spencer , Zewail Ahmed H.
Published: June 2008

In many physical and biological systems the transition from an amorphous to ordered native structure involves complex energy landscapes, and understanding such transformations requires not only their thermodynamics but also the structural dynamics during the process. Here, we extend our 4D visualization method with electron imaging to include the study of irreversible processes with a single pulse in the same ultrafast electron microscope (UEM) as used before in the single-electron mode for the study of reversible processes. With this augmentation, we report on the transformation of amorphous to crystalline structure with silicon as an example. A single heating pulse was used to initiate crystallization from the amorphous phase while a single packet of electrons imaged selectively in space the transformation as the structure continuously changes with time. From the evolution of crystallinity in real time and the changes in morphology, for nanosecond and femtosecond pulse heating, we describe two types of processes, one that occurs at early time and involves a nondiffusive motion and another that takes place on a longer time scale. Similar mechanisms of two distinct time scales may perhaps be important in biomolecular folding.
Saccharides cross-reactive with
Bacillus anthracis
spore glycoprotein as an anthrax vaccine component
Authors: Kubler-Kielb Joanna , Vinogradov Evgeny , Hu Haijing , Leppla Stephen H. , Robbins John B. , Schneerson Rachel
Published: June 2008

Bacillus anthracis
is a spore-forming bacterium that causes anthrax in humans and in other mammals. The glycoprotein BclA (
Bacillus
collagen-like protein of
anthracis
) is a major constituent of the exosporium, the outermost surface of
B. anthracis
spores. The glycosyl part of BclA is an oligosaccharide composed of 2-
O
-methyl-4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-
d
-glucose, referred to as anthrose, and three rhamnose residues. A structure similar to anthrose, 4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-
d
-glucose is found in the side chain of the capsular polysaccharide (CPS) of
Shewanella
spp. MR-4. Under certain growth conditions the bacteria produce a variant CPS lacking one methyl group on the hydroxybutyrate, 4-(3-hydroxybutanamido)-4,6-dideoxy-
d
-glucose. Contrary to anthrose, neither of the
Shewanella
CPSs is 2-
O
methylated. Here, we report that both
Shewanella
CPS variants react with anti-
B. anthracis
spore sera. We also found that these antisera reacted with flagellae of
Pseudomonas syringae
, reported to be glycosylated with a similar terminal saccharide, 4-(3-hydroxybutanamido)-4,6-dideoxy-2-
O
-methyl-
d
-glucose. Sera produced by immunization with
Shewanella
or
P. syringae
cells bound to
B. anthracis
spores but not to
Bacillus cereus
spores in a fluorescent microscopy assay. These experiments show that methylation of the anthrose at the
O-
2 of the sugar ring and at the
C
-3 of 3-hydroxybutyrate are not essential for induction of cross-reactive antibodies. We report the preparation, characterization, and antibody responses to protein conjugates of the two variants of
Shewanella
CPS. Both conjugates induced antibodies that bound to both
Shewanella
CPS variants by ELISA and to
B. anthracis
spores, as detected by fluorescent microscopy. We propose the use of
Shewanella
CPS conjugates as a component of an anthrax vaccine.
Epidemiology of Sepsis in the Valencian Community (Spain), 1995–2004
Authors: Ballester Juan Carlos Andreu , Ballester Ferran , Sánchez Antonio González , Quilis Amadeo Almela , Rubio Enrique Colomer , Otero Carlos Peñarroja
Published: June 2008

Objective.

To study the incidence of sepsis in the Valencian Community (Spain) during a period of 10 years (1995–2004).

Methods.

We downloaded data on discharge diagnoses of septicemia in all 26 public hospitals in the Valencian Community during the 10-year study period, as well as the additional discharge diagnoses of each patient.

Results.

We identified 33,767 cases of sepsis during the study period. The age-standardized incidence rates among men increased from 64.11 (95% confidence interval [CI], 60.37–67.85) cases per 100,000 population in 1995 to 114.02 (95% CI, 109.02–118.50) cases per 100,000 population in 2004 (P < .001), and those among women increased from 45.08 (95% CI, 42.01–48.15) cases per 100,000 population in 1995 to 83.62 (95% CI, 79.85–87.39) cases per 100,000 population in 2004 (P < .001). Gram-negative bacteria were the most frequently involved microorganisms (in 21.4% of cases), and there was a significant increase in the number of sepsis cases caused by these organisms from 1999 onward. The mortality rate was approximately 42.5% among patients hospitalized for sepsis, and mortality was associated with organ failure. In addition, mortality was associated with the microorganism responsible not being known, with infection due to fungi, and with polymicrobial sepsis.

Conclusions.

The rates of hospitalization both for sepsis overall and for severe sepsis in the Valencian Community (Spain) are lower than those in other countries but are increasing, by 5% each year. The increase in the number of cases in which gram-negative bacteria are the cause of sepsis is notable.
Photoelectron Spectroscopy, Photoionization Mass Spectroscopy, and Theoretical Study on CCl3SSCN
Authors: Du Lin , Yao Li , Ge Mao-fa
Published: June 2008

Trichloromethanesulfenyl thiocyanate, CC13SSCN, was generated and studied by photoelectron spectroscopy (PES), photoionization mass spectroscopy (PIMS), and theoretical calculations. This molecule exhibits a gauche conformation, and the torsional angle around S-S bond is 91.4 due to the sulfur-sulfur lone pair interactions. After ionization, the ground-state cationic-radical form of CC13SSCN+ adopts a trans planar main-atom structure with Cs symmetry. The highest occupied molecular orbital (HOMO) of CC13SSCN corresponds to the electrons mainly localized on the sulfur 3p lone pair MO. The first ionization energy is determined to be 10.40 eV.
Photoacoustic and Fluorescence Spectroscopy of Metallomesogens Containing Lanthanide Ions
Authors: Yang Yue-tao , Li Jun-jia , Liu Xiao-jun , Zhang Shu-yi , Liu Jing
Published: June 2008

Metallomesogens Ln(bta)3L2 (Ln3+: La3+, Eu3+, and Ho3+; bta: benzoyltrifluoroacetonate; L: Schiff base) were prepared. Photoacoustic (PA) spectroscopy was used to study physicochemical properties of the liquid crystalline metal complexes. In the region of ligand absorption, PA intensity increases for Eu(bta)3L2, La(bta)3L2, and Ho(bta)3L2, in that order. It is found that the PA intensity of the ligand bears a relation to the intramolecular energy transfer process. For the first time, phase transitions of Eu(bta)3L2 from glass state to smectic A (SmA) phase and SmA phase to isotropic liquid are monitored by PA and fluorescence (FL) spectroscopy from two aspects: nonradiative and radiative transitions. The results show that PA technique may serve as a new tool for investigating the spectral properties and phase transitions of liquid crystals containing metal ions.
Different Domains of the UBL-UBA Ubiquitin Receptor, Ddi1/Vsm1, Are Involved in Its Multiple Cellular Roles
Authors: Gabriely Galina , Kama Rachel , Gelin-Licht Rita , Gerst Jeffrey E.
Published: June 2008

Ddi1/Vsm1 is an ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. Ddi1 possesses three domains: an NH2-terminal ubiquitin-like domain (UBL), a COOH-terminal ubiquitin-associated domain (UBA), and a retroviral aspartyl-protease domain (RVP). Here, we demonstrate the domains involved in homodimerization, checkpoint regulation, localization, and t-SNARE binding. The RVP domain is required for protein homodimerization, whereas the UBL and UBA domains are required for rescue of the pds1-128 checkpoint mutant and enrichment of GFP-Ddi1 in the nucleus. A mutation in aspartate-220, which is necessary for putative aspartyl-protease function, abolished the rescue of pds1-128 cells but not homodimerization. Thus, Ddi1 catalytic activity may be required for checkpoint regulation. The Sso1 t-SNARE-interacting domain maps to residues 344–395 and undergoes phosphorylation on threonines T346 and T348. T348 is necessary for Sso binding, and phosphorylation is important for function, because mutations that lessen phosphorylation (e.g., Ddi1T346A, Ddi1T348A) are unable to facilitate growth of the sec9-4 t-SNARE mutant. In contrast, the overproduction of phosphorylatable forms of Ddi1 (e.g., Ddi1, Ddi1S341A) rescue the growth of sec9-4 cells similar to Sso1 overproduction. Thus, Ddi1 participates in multiple cellular processes via its different domains and phosphorylation may regulate exocytic functions.
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data
Authors: Oh Jung Hun , Kim Young Bun , Gurnani Prem , Rosenblatt Kevin P. , Gao Jean X.
Published: June 2008

Motivation: Diseases normally progress through several stages. Therefore, biomarkers corresponding to each stage may exist. To deal with such a multi-category problem, including sample stage prediction and biomarker selection, we propose methods for classification and feature selection. The proposed classification method is based on two schemes: error-correcting output coding (ECOC) and pairwise coupling (PWC). The final decision for a test sample prediction is an integration of these two schemes. The biomarker pattern for distinguishing each disease category from another one is achieved by the development of an extended Markov blanket (EMB) feature selection method.

Results: In this study, a liver cancer matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) dataset was used, which comprises hepatocellular carcinoma (HCC), cirrhosis, and healthy spectra. Peak patterns were discovered for distinguishing pairwise categories among the three classes. Importance and reliability of individual peaks were presented by the measurements of certain weight values and frequencies. The classification capability of the proposed approach was compared with classical ECOC, random forest, Naive Bayes, and J48 methods.

Availability: Supplementary materials are available at http://visionlab.uta.edu/biomarker/bioinfo.htm

Contact:  gao@uta.edu
Density dependence of developmental instability in a dimorphic ungulate
Authors: Serrano Emmanuel , Angibault Jean-Marc , Cargnelutti Bruno , Hewison A. J. Mark
Published: June 2008

The use of fluctuating asymmetry (FA) for biomonitoring environmental stress is limited by the lack of work on how FA in particular traits responds to specific stresses. Here, by manipulating the number of individuals in an enclosed fallow deer (Dama dama) population, we describe, for the first time, clear density dependence in the FA of juvenile jaw morphology. The impact of high population density on FA was strong for both sexes, supporting the use of FA for indexing environmental stress. In addition, there was some indication that the change in FA was greater in males (43.6%) than females (28.5%). Finally, the ability to buffer density-dependent stress was independent of body condition. We suggest that, under highly limiting conditions, whole cohorts may be unable to buffer against developmental error, irrespective of individual quality.