bluuebunny/crossref_metadata_2025 huggingface dataset:
Short‐term variation of the s = 1 nonmigrating semidiurnal tide during the 2002 stratospheric sudden warming
Authors: Chang Loren C. , Palo Scott E. , Liu Han‐Li
Published: February 2009

In this study, the NCAR Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIME‐GCM) is used to examine short‐term changes in the global structure of the migrating and s = 1 nonmigrating semidiurnal tides in a model run approximating the 2002 Southern Hemisphere stratospheric sudden warming. The TIME‐GCM is found to resolve an s = 1 nonmigrating semidiurnal tide with latitudinal structure similar to that of prior studies and with global structure in the MLT region strongly correlated with Southern Hemisphere planetary wave 1 (PW1) wave events, prior to equinox. Comparison with a control run with no planetary wave activity, Eliassen‐Palm flux, and correlation analysis of the s = 1 semidiurnal tide structure suggest that the wave propagates from the source region in the winter hemisphere stratosphere into both the summer and winter lower thermospheres. The amplitudes of the migrating semidiurnal tide in the Southern Hemisphere are anticorrelated with the nonmigrating tide, suggesting significant energy loss due to nonmigrating tidal generation, a result not previously seen. The amplitude of the s = 1 nonmigrating semidiurnal tide from TIME‐GCM is also compared with data from the South Pole meteor radar system. While the observations show bursts of nonmigrating tidal activity correlated to PW1 activity of comparable amplitudes to the model results, these events do not always appear at the same times as those in the model. This suggests that while the processes generating the nonmigrating tide in TIME‐GCM are realistic, the TIME‐GCM run itself displays differences in time evolution compared to the observations during this time.
Response of coastal Antarctic phytoplankton to solar radiation and ammonium manipulation: An in situ mesocosm experiment
Authors: Agustí Susana , Duarte Carlos M. , Llabrés Moira , Agawin Nona S. R. , Kennedy Hilary
Published: February 2009

We tested the role of solar irradiance and ammonium inputs on phytoplankton bloom formation in Antarctic coastal waters (62°39.576′ S; 60°22.408′ W, Livingston Island, South Sethlands) through the combination of a large‐scale, in situ mesocosm experiment and a small‐scale experiment. Phytoplankton growth, nutrient use, and biomass development remained low at ambient irradiances and increased greatly (greater than thirtyfold) to yield large (up to 93 μg chlorophyll a l−1) phytoplankton blooms in response to moderate shading. The phytoplankton communities tested were light limited when irradiance was reduced below 30% of the incident irradiance and stressed by high irradiance at the full ambient irradiance. Ammonium additions greatly stimulated phytoplankton growth, biomass, and stimulated the use of the large nitrate pool present in the Antarctic waters and lead to a decline in the specific UV absorption by mycosporine‐like amminoacids. The small‐scale experiment confirmed the role of UV irradiance in inhibiting phytoplankton growth and the capacity of ammonium inputs to overcome this inhibition. The alleviation of the high‐irradiance stress by ammonium additions provided evidence of a key role of ammonium inputs in allowing phytoplankton to resume growth and nutrient use. The results demonstrate that there is a narrow window of irradiance where phytoplankton growth is adequate and that coastal Antarctic phytoplankton communities, examined here, are either light limited or stressed by high irradiance at irradiances outside this range. More research is needed to analyze the interplay between light climate, ammonium, and bloom initiation in Antarctic coastal waters to test the generality of the results obtained.
Impact of ambient temperature on evaporation from surface‐exposed fractures
Authors: Kamai Tamir , Weisbrod Noam , Dragila Maria Inés
Published: February 2009

Surface‐exposed fractures (SEFs) form a unique link between the atmosphere and the deep vadose zone. Quantifying evaporation and salt‐accumulation rates within these SEFs is essential for understanding processes leading to groundwater salinization and contamination via these fractures. In this study, evaporation from SEFs (ESEFs) was quantified, mainly as a function of ambient atmospheric temperature, by using large‐scale laboratory experiments and measuring evaporation under controlled conditions. In addition, ESEF was theoretically quantified based on the physical processes that govern it. The theoretical model was used to analyze ESEF rates as a function of ambient temperature, temperature gradient, fracture‐aperture, and matrix pore size. ESEF was experimentally found to increase as the ambient temperature decreased. Measured evaporation rates were between about 110 and 260 g d−1 per square meter of fracture surface, for temperature differences between rock‐bottom and the atmosphere of 0° and 13°C, respectively. Comparing these values with model results suggests that convection is the driving process for enhanced evaporation at low ambient temperatures. Finally, we show that ESEF rates decrease as a result of salt precipitation. During a ∼9‐month period, with an imposed temperature difference of 13°C, ESEF decreased from ∼260 to ∼95 g d−1 m−2 due to salt accumulation near and on the fracture surfaces. Evaporation rates began decreasing after about 100 g m−2 of salt had precipitated and decreased to less than 50% of the initial rate after 160 g m−2 of salt had precipitated. We thus show that not only temperature, but also salt precipitation, largely affect ESEF rates.
Electrochemical corrosion behavior of Nd–Fe–B permanent magnets with modified microstructure
Authors: Liu W. Q. , Yue M. , Zhang D. T. , Zhang J. X. , Liu X. B.
Published: February 2009

Polarization curve and electrochemical impedance spectroscopy tests have been applied to investigate the corrosion kinetics for both spark plasma sintered (SPS) and conventional sintered Nd–Fe–B magnets in different electrolytes. Effect of microstructure modification on the chemical stability of the magnets was discussed. Both magnets exhibit evident passive behavior in alkaline electrolyte but are susceptible to corrosion in weak acid and saline electrolytes. SPS magnets are more corrosion resistant than conventional sintered magnets due to a remarkable microstructure modification formed in the SPS process. Further investigation shows that the unique microstructure in SPS magnets effectively restrains the aggressive intergranular corrosion which takes place along Nd-rich phases in conventional magnets.
Molecular mobility and Li+ conduction in polyester copolymer ionomers based on poly(ethylene oxide)
Authors: Fragiadakis Daniel , Dou Shichen , Colby Ralph H. , Runt James
Published: February 2009

We investigate the segmental and local dynamics as well as the transport of Li+ cations in a series of model poly(ethylene oxide)-based single-ion conductors with varying ion content, using dielectric relaxation spectroscopy. We observe a slowing down of segmental dynamics and an increase in glass transition temperature above a critical ion content, as well as the appearance of an additional relaxation process associated with rotation of ion pairs. Conductivity is strongly coupled to segmental relaxation. For a fixed segmental relaxation frequency, molar conductivity increases with increasing ion content. A physical model of electrode polarization is used to separate ionic conductivity into the contributions of mobile ion concentration and ion mobility, and a model for the conduction mechanism involving transient triple ions is proposed to rationalize the behavior of these quantities as a function of ion content and the measured dielectric constant.
The magnetocaloric effect in materials with a second order phase transition: Are TC and Tpeak necessarily coincident?
Authors: Franco V. , Conde A. , Kuz’min M. D. , Romero-Enrique J. M.
Published: February 2009

Using the Arrott–Noakes equation of state it is shown that the Curie point (TC) and the temperature where the magnetic entropy change is maximum (Tpeak) coincide only in the mean field approximation, but the Heisenberg model implies that Tpeak>TC even for homogeneous materials. The distance between Tpeak and TC increases with applied magnetic field following a power law. In both cases, TC corresponds to a singular point in the temperature dependence of the magnetic entropy change. The field dependence of the magnetic entropy change is exactly the same at the Curie temperature and at the temperature of the peak.
Characterization of narrow-band terahertz shaping in periodically poled Mg:LiNbO3 using multipulse pump probe
Authors: Liu W. M. , Guo H. C. , Kitaeva G. Kh. , Tuchak A. N. , Yan Y. H. , Tang S. H.
Published: February 2009

By using a multipulse femtosecond pump-probe technique, we achieved an in situ characterization of terahertz wave shaping in the periodically poled Mg:LiNbO3 crystal. The analysis method, which includes fast-Fourier transform (frequency spectrum) and Morlet wavelet transform (time-frequency spectrum) that detailed information on the shaping of the terahertz waves, is demonstrated.
Influence of the demagnetizing field on the determination of the magnetocaloric effect from magnetization curves
Authors: Caballero-Flores R. , Franco V. , Conde A. , Kiss L. F.
Published: February 2009

The influence of the demagnetizing factor (N) on the magnetic entropy change (ΔSM) curves is studied for materials with a second order phase transition. For this purpose, a soft magnetic amorphous ribbon is measured for different orientations of the magnetic field with respect to the plane of the sample. For temperatures below the Curie temperature (TC), the increase in N causes a decrease in ΔSM, while for temperatures above TC no change in the shape of the curves has been found for the different orientations, as expected. In order to eliminate this influence of N and compare the ΔSM(T) curves for samples with different shapes, the recently proposed universal curve for the magnetocaloric effect can be used.
Surface plasmon effects excitation from three-pair arrays of silver-shell nanocylinders
Authors: Chau Yuan-Fong , Yeh Han-Hsuan , Tsai Din Ping
Published: February 2009

Surface plasmon effects excitation from the three-pair arrays of silver-shell nanocylinders are investigated numerically by using the finite-element method. Effects from different illumination wavelengths, interparticle distance, interpair distance, and the radii of air hole in nanocylinders are studied. Compared to the three-pair arrays of solid silver cylinder, the near-field optical response of the shell exhibits electric field enhancements and redshift which are found to be strongly influenced by tuning the radius of the air-hole in the nanocylinders.
Dust voids in collision-dominated plasmas with negative ions
Authors: Zheng Xiang , Chen Yinhua , Hu Zuquan , Wang Guanwen , Huang Feng , Dong Chuanfei , Yu M. Y.
Published: February 2009

Using fluid theory, the properties of voids in collision-dominated plasmas containing negative ions are studied. The profiles of the charged-particle densities in the void region are obtained. It is also shown that with an increase of the negative-ion concentration, the electric field, the ion drift velocity, the dust charge at the void edge, as well as the void size decrease.
Dominant reaction pathways in high-dimensional systems
Authors: Autieri E. , Faccioli P. , Sega M. , Pederiva F. , Orland H.
Published: February 2009

This paper is devoted to the development of a theoretical and computational framework denominated dominant reaction pathways (DRPs) to efficiently sample the statistically significant thermally activated reaction pathways, in multidimensional systems. The DRP approach is consistently derived from the Langevin equation through a systematic expansion in the thermal energy, kBT. Its main advantage with respect to existing simulation techniques is that it provides a natural and rigorous framework to perform the path sampling using constant displacement steps, rather than constant time steps. In our previous work, we have shown how to obtain the set of most probable reaction pathways, i.e., the lowest order in the kBT expansion. In this work, we show how to compute the corrections to the leading order due to stochastic fluctuations around the most probable trajectories. We also discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations, which are representative of the transition state ensemble. We illustrate how our method works in practice by studying the diffusion of a point particle in a two-dimensional funneled external potential.
Controlling two-photon photoemission using polarization pulse shaping
Authors: Golan B. , Fradkin Z. , Kopnov G. , Oron D. , Naaman R.
Published: February 2009

Our understanding of processes involved in two-photon photoemission (2PPE) from surfaces can be tested when we try to exercise control over the electron emission. In the past, coherently controlled 2PPE has been demonstrated using very short pulses and single crystal surfaces. Here we show that by applying polarization pulse shaping on surfaces, it is possible to vary both the angular distribution of the emitted photoelectrons and the total photoemission yield. The presented 2PPE experimental setup introduces pulse shaping in the visible range, which is a unique property that allows control of polarization. We relate the ability to use polarization as a means of control to the surface corrugation.
Heat flux sensor calibration using noninteger system identification: Theory, experiment, and error analysis
Authors: Gardarein Jean-Laurent , Battaglia Jean-Luc , Löhle Stefan
Published: February 2009

This paper concerns the improvement of the calibration technique of null point calorimeters generally used in high enthalpy plasma flows. Based on the linearity assumption, this technique leads to calculate the impulse response that relates the heat flux at the tip of the sensor according to the temperature at the embedded thermocouple close to the heated surface. The noninteger system identification (NISI) procedure is applied. The NISI technique had been well described in previous study. The present work focuses on the accuracy of the identified system in terms of absorbed heat flux during the calibration experiment and of the estimated parameters in the model. The impulse response is thus calculated along with its associated standard deviation. Furthermore, this response is compared with that of the one-dimensional semi-infinite medium, which is classically used in practical applications. The asymptotic behavior of the identified system at the short times is analyzed for a better understanding of the noninteger identified system. Finally, the technique was applied to a new sensor geometry that has been developed particularly for high enthalpy plasma flows and it is shown that the method can be applied to any geometry suitable for a certain test configuration.
Field orientation dependent vortex formation in individual multilayer triangular rings
Authors: Jain S. , Adeyeye A. O.
Published: February 2009

We present the giant magnetoresistance responses of individual pseudo-spin-valve triangular ring using synchronous transport measurement technique. We observed that unlike single layer triangular rings, the formation of intermediate vortex state is strongly dependent on the applied field orientation (θ). For nπ/6<θ<(n+1)π/6, n=0,1,2…, the Co layer in the ring undergoes a transition from forward onion state to reverse onion state via an intermediate vortex state, otherwise there is a direct transition from forward onion state to reverse onion states. This phenomenon in triangular rings may be useful for applications in future spin logic devices.
Obdurate Pains, Transient Intensities: Affect and the Chronically Pained Body
Authors: Bissell David
Published: February 2009

In contrast to other discourse-centric explorations, I rethink the embodied experience of chronic pain through an affective ontology. Drawing on intensity, as a way of coming to know the qualitative experiential dimension of affect as diminished or heightened, I explore some of the complex relationships between intensity, desirability, and intentionality that cohere around pained bodies. In contrast to transient pain, chronic pain is presented as an undesirable affective intensity that has no recourse to intentionality and meaning but territorialises the body in ways that prevent other intensities from taking hold. Through an encounter with a pain-management programme, I explore a number of strategies for deterritorialising the chronically pained body in order to open it up to more desirable intensities. I argue that ultimately it is the progressive vulnerability and openness that deterritorialisation promises that is the key to becoming otherwise.
Total Factor Productivity, Efficiency, and Technological Change in the European Regions: A Nonparametric Approach
Authors: Ezcurra Roberto , Iraizoz Belen , Pascual Pedro
Published: February 2009

This paper examines the global trend of total factor productivity, efficiency, and technological change in the European Union regions over the period 1986–2004, using the Malmquist index computed by data envelopment analysis. The results reveal the important role played by technical efficiency in explaining total factor productivity growth in the European Union. For this reason, in a second stage, we investigate existing regional disparities in efficiency levels across the European regions, using a nonparametric methodology that allows us to study the dynamics of the entire cross-sectional distribution. Estimates show the presence of a process of convergence in efficiency levels over the sample period, despite a relatively low degree of intradistribution mobility. In order to complete these results, factors such as the geographical location of the various regions, country-specific characteristics, or the sectoral composition of economic activity were examined for their role in explaining the observed disparities.
The Intercorporeal Emergence of Landscape: Negotiating Sight, Blindness, and Ideas of Landscape in the British Countryside
Authors: Macpherson Hannah
Published: February 2009

In this paper I explore some of the ways in which people with visual impairments see landscape and participate in visual cultures of landscape apprehension. I draw on ethnographic and interview material, developed while acting as a sighted guide for specialist blind and visually impaired walking groups who visit the landscapes of the Lake District and Peak District in Britain. Through this research material I show how landscape is likely to become present for people with blindness or visual impairment through both their individual capacities for sight and a complex mix of discursive, material, social, and historical relations. Specifically, I argue that there is an intercorporeal, collective dimension to this emergence of landscape and this intercorporeality is evident at both a perceptual and a discursive level. I suggest that future research needs to attend further to how landscape emerges and becomes present through intercorporeal processes.
Residential Choice, the Built Environment, and Nonwork Travel: Evidence Using New Data and Methods
Authors: Chatman Daniel G
Published: February 2009

Residents of dense, mixed-use, transit-accessible neighborhoods use autos less. Recent studies have suggested that this relationship is partly because transit-preferring and walk-preferring households seek and find such neighborhoods. If this is so, and if the number of such households is small, policies to alter the built environment may not influence auto use very much. I argue that many of these studies are inconclusive on methodological grounds, and that more research is needed. A purpose-designed survey of households in two urban regions in California is investigated, with the aid of a new methodological approach. I find that most surveyed households explicitly consider travel access of some kind when choosing a neighborhood, but that this process of residential self-selection does not bias estimates of the effects of the built environment very much. To the extent that it does exert an influence, the bias results both in underestimates and overestimates of the effects of the built environment, contrary to previous research. The analysis not only implies a need for deregulatory approaches to land-use and transportation planning, but also suggests that there may be value in market interventions such as subsidies and new prescriptive regulations.
The reciprocal coordination and mechanics of molecular motors in living cells
Authors: Laib Jeneva A. , Marin John A. , Bloodgood Robert A. , Guilford William H.
Published: February 2009

Molecular motors in living cells are involved in whole-cell locomotion, contractility, developmental shape changes, and organelle movement and positioning. Whether motors of different directionality are functionally coordinated in cells or operate in a semirandom “tug of war” is unclear. We show here that anterograde and retrograde microtubule-based motors in the flagella of
Chlamydomonas
are regulated such that only motors of a common directionality are engaged at any single time. A laser trap was used to position microspheres on the plasma membrane of immobilized paralyzed
Chlamydomonas
flagella. The anterograde and retrograde movements of the microsphere were measured with nanometer resolution as microtubule-based motors engaged the transmembrane protein FMG-1. An average of 10 motors acted to move the microsphere in either direction. Reversal of direction during a transport event was uncommon, and quiescent periods separated every transport event, suggesting the coordinated and exclusive action of only a single motor type. After a jump to 32 °C, temperature-sensitive mutants of kinesin-2 (
fla10
) showed exclusively retrograde transport events, driven by 7 motors on average. These data suggest that molecular motors in living cells can be reciprocally coordinated to engage simultaneously in large numbers and for exclusive transport in a single direction, even when a mixed population of motors is present. This offers a unique model for studying the mechanics, regulation, and directional coordination of molecular motors in a living intracellular environment.
Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene
Fv1
in the genus
Mus
Authors: Yan Yuhe , Buckler-White Alicia , Wollenberg Kurt , Kozak Christine A.
Published: February 2009

The
Fv1
virus resistance gene is a coopted endogenous retrovirus (ERV) sequence related to the
gag
gene of the MuERV-L ERV family. Three major
Fv1
resistance alleles have been identified in laboratory mice, and they target virus capsid genes to produce characteristic patterns of resistance to mouse leukemia viruses (MLVs). We identified
Fv1
in 3 of the 4
Mus
subgenera; its absence from
Coelomys
and 1 of 3 species of
Pyromys
indicate
Fv1
was acquired shortly after the origin of the
Mus
genus. We sequenced
Fv1
genes from 21 mice representative of the major taxonomic groups of
Mus
. Two lines of evidence indicate that
Fv1
has had antiviral function for 7 million years of evolution. First, 2 species of African pygmy mice (subgenus
Nannomys
) show an
Fv1
-like MLV resistance, and transduced cells expressing the
Nannomys Fv1
gene reproduce this resistance pattern. Second, sequence comparisons suggest that
Fv1
has been involved in genetic conflicts throughout
Mus
evolution. We found evidence for strong positive selection of
Fv1
and identified 6 codons that show evidence of positive selection: 3 codons in the C-terminal region including 2 previously shown to contribute to
Fv1
restriction in laboratory mice, and 3 codons in a 10-codon segment overlapping the major homology region of
Fv1
; this segment is known to be involved in capsid multimerization. This analysis suggests that
Fv1
has had an antiviral role throughout
Mus
evolution predating exposure of mice to the MLVs restricted by laboratory mouse
Fv1
, and suggests a mechanism for
Fv1
restriction.
Matrix product simulations of non-equilibrium steady states of quantum spin
chains
Authors: Prosen Tomaž , Žnidarič Marko
Published: February 2009

A time-dependent density matrix renormalization group method with a matrix product
ansatz is employed for explicit computation of non-equilibrium steady state density
operators of several integrable and non-integrable quantum spin chains, which are driven
far from equilibrium by means of Markovian couplings to external baths at the two ends. It
is argued that even though the time evolution cannot be simulated efficiently due to fast
entanglement growth, the steady states in and out of equilibrium can be typically
accurately approximated, with the result that chains of length of the order of
n≈100
spins are accessible. Our results are demonstrated by performing explicit simulations of
steady states and calculations of energy/spin densities/currents in several problems of heat
and spin transport in quantum spin chains. A previously conjectured relation between
quantum chaos and normal transport is re-confirmed with high accuracy for much larger
systems.
Brazilian Green Propolis: Effects In Vitro and In Vivo on Trypanosoma cruzi
Authors: Salomão Kelly , de Souza Eniuce M. , Henriques-Pons Andrv , Barbosa Helene S. , de Castro Solange L.
Published: February 2009

The composition of a Brazilian green propolis ethanolic extract (Et‐Bra) and its effect on Trypanosoma cruzi trypomastigotes and other pathogenic microorganisms have already been reported. Here, we further investigated Et‐Bra targets in T. cruzi and its effect on experimental infection of mice. The IC50/4 days for inhibition of amastigote proliferation was 8.5 ± 1.8 μg mL−1, with no damage to the host cells. In epimastigotes Et‐Bra induced alterations in reservosomes, Golgi complex and mitochondrion. These effects were confirmed by flow cytometry analysis. In trypomastigotes, Et‐Bra led to the loss of plasma membrane integrity. The in vitro studies indicate that Et‐Bra interferes in the functionality of the plasma membrane in trypomastigotes and of reservosomes and mitochondrion in epimastigotes. Acutely infected mice were treated orally with Et‐Bra and the parasitemia, mortality and GPT, GOT, CK and urea levels were monitored. The extract (25–300 mg kg−1 body weight/day for 10 days) reduced the parasitemia, although not at significant levels; increased the survival of the animals and did not induce any hepatic, muscular lesion or renal toxicity. Since Et‐Bra was not toxic to the animals, it could be assayed in combination with other drugs. Et‐Bra could be a potential metacyclogenesis blocker, considering its effect on reservosomes, which are an important energy source during parasite differentiation.
Estimating legal and illegal catches of Russian sockeye salmon from trade and market data
Authors: Clarke Shelley C. , McAllister Murdoch K. , Kirkpatrick R. Craig
Published: February 2009

Clarke, S. C., McAllister, M. K., and Kirkpatrick, R. C. 2009. Estimating legal and illegal catches of Russian sockeye salmon from trade and market data. – ICES Journal of Marine Science, 66: 532–545. To address concerns about the conservation of Russian sockeye salmon (Oncorhynchus nerka) in the face of potentially large-scale illegal, unreported, and unregulated (IUU) fishing activities, we estimated the quantities of sockeye caught in eastern Russia based on trade data from Japan, China, and Korea. In addition to being a fishery-independent estimate, our approach avoids reliance on Russian customs documentation that may not capture quantities of fish transhipped at sea. Using a Bayesian statistical model, we estimate quantities imported and traded in municipal markets as two separate estimates of the actual Russian sockeye catch. To estimate the “excess” catch deriving from IUU fishing operations, these trade-based estimates of catch are compared with official Russian catch figures. The results support (posterior probabilities 0.72 to >0.99) the hypothesis that there are substantial quantities of excess catch of Russian sockeye making their way to East Asian markets. In the years 2003–2005, the median quantities of annual excess catch were estimated to range from 8000 to 15 000 t, representing a value of US$40–74 million and demonstrating that actual catches are 60–90% above reported levels.
Swine torque teno virus detection in pig commercial vaccines, enzymes for laboratory use and human drugs containing components of porcine origin
Authors: Kekarainen Tuija , Martínez-Guinó Laura , Segalés Joaquim
Published: February 2009

Torque teno viruses (TTVs) are vertebrate infecting, single-stranded circular DNA viruses. Two genetically distinct TTV genogroups (TTV1 and TTV2) infect swine worldwide with high prevalence. Currently, swine TTVs are considered non-pathogenic, although TTV2 has been linked to post-weaning multisystemic wasting syndrome, a porcine circovirus disease. On the other hand, pig materials are an important source of components used in porcine vaccine manufacturing, human drugs and commercial enzyme products. However, there is little information about the possible existence of extraneous viruses in products containing porcine-derived components. In the present study, 26 commercial swine vaccines, seven human drugs and three enzyme products from porcine origin were tested for the presence of TTV1 and TTV2 genomes by PCR. Four vaccines against Mycoplasma hyopneumoniae were positive for TTV2 by PCR. Three M. hyopneumoniae, one porcine parvovirus and one porcine reproductive and respiratory syndrome virus vaccines were PCR positive for TTV1. One human drug contained TTV1 DNA as well as a trypsin enzyme; a porcine-derived elastase product was positive for both TTV genogroups. These results show that swine TTVs are contaminants not only of swine vaccines but also of human drugs containing porcine components and enzymes for laboratory use.
Assessment of recombinant beak and feather disease virus capsid protein as a vaccine for psittacine beak and feather disease
Authors: Bonne Nicolai , Shearer Patrick , Sharp Margaret , Clark Phillip , Raidal Shane
Published: February 2009

Beak and feather disease virus (BFDV) is a significant pathogen of wild Australasian and African psittacine birds. We assessed the immunogenicity of recombinant BFDV capsid (recBFDVcap) to protect against the development of psittacine beak and feather disease (PBFD). Long-billed corellas (Cacatua tenuirostris) (n=13) received (by injection) 1 ml vaccine containing 10 μg recBFDVcap on day 0 and 0.4 ml vaccine containing 66.8 μg recBFDVcap on day 11. All vaccinated corellas and five non-vaccinated control corellas were given 0.4 ml BFDV suspension [titre=log212 haemagglutination units (HAU) 50 μl−1] intramuscularly and 0.1 ml orally 16 days after booster vaccination. Blood was collected during the vaccination period and blood and feathers were collected after BFDV administration. Testing of blood samples included BFDV DNA detection by PCR and quantitative PCR (qPCR) as well as antibody detection by haemagglutination inhibition (HI) and on feather samples, BFDV DNA and antigen was detected by haemagglutination (HA) and qPCR. Four of 97 blood samples collected from vaccinated birds after virus challenge tested positive by PCR, whereas 17 of 35 samples taken from non-vaccinated control corellas tested positive. Vaccinated birds did not develop feather lesions, had only transient PCR-detectable viraemia and had no evidence of persistent infection 270 days post-challenge using PCR, histopathology and immunohistochemistry. Non-vaccinated control corellas developed transient feather lesions and had PCR, HI and HA test results consistent with PBFD. They were BFDV PCR-positive for up to 41 days post-challenge and qPCR demonstrated reduced virus replication in vaccinated birds compared with non-vaccinated control birds.
Poly(A)-binding protein binds to the non-polyadenylated 3′ untranslated region of dengue virus and modulates translation efficiency
Authors: Polacek Charlotta , Friebe Peter , Harris Eva
Published: February 2009

Poly(A)-binding protein (PABP) is a key player in mRNA circularization and translation initiation of polyadenylated mRNAs. It simultaneously binds the 3′ poly(A) tail of an mRNA and eukaryotic initiation factor 4G (eIF4G), which forms part of the translation initiation complex assembling at the 5′end, thus circularizing the RNA molecule and enhancing translation initiation. Here, we report the binding of PABP to the non-polyadenylated 3′end of dengue virus (DENV) RNA. PABP binds the DENV 3′ untranslated region (3′UTR) internally, upstream of the conserved 3′stem–loop near the two dumb-bell structures, and can be displaced by poly(A) RNA. The PABP-specific translation inhibitor PABP-interacting protein 2 (Paip2) interferes with the DENV 3′UTR–PABP interaction, andin vitrotranslation of DENV reporter RNAs in baby hamster kidney cell extracts is inhibited by Paip2 in a dose-dependent manner. Our findings show an expanded translation mechanism for PABP, binding to a viral RNA lacking a terminal poly(A) tail.
Cryo-electron tomography of porcine reproductive and respiratory syndrome virus: organization of the nucleocapsid
Authors: Spilman Michael S. , Welbon Craig , Nelson Eric , Dokland Terje
Published: February 2009

Porcine reproductive and respiratory virus (PRRSV) is an enveloped positive-sense RNA virus of the family Arteriviridae that causes severe and persistent disease in pigs worldwide. The PRRSV virion consists of a lipid envelope that contains several envelope proteins surrounding a nucleocapsid core that encapsidates the RNA genome. To provide a better understanding of the structure and assembly of PRRSV, we have carried out cryo-electron microscopy and tomographic reconstruction of virions grown in MARC-145 cells. The virions are pleomorphic, round to egg-shaped particles with an average diameter of 58 nm. The particles display a smooth outer surface with only a few protruding features, presumably corresponding to the envelope protein complexes. The virions contain a double-layered, hollow core with an average diameter of 39 nm, which is separated from the envelope by a 2–3 nm gap. Analysis of the three-dimensional structure suggests that the core is composed of a double-layered chain of nucleocapsid proteins bundled into a hollow ball.
Absence of spontaneous disease and comparative prion susceptibility of transgenic mice expressing mutant human prion proteins
Authors: Asante Emmanuel A. , Gowland Ian , Grimshaw Andrew , Linehan Jacqueline M. , Smidak Michelle , Houghton Richard , Osiguwa Olufunmilayo , Tomlinson Andrew , Joiner Susan , Brandner Sebastian , Wadsworth Jonathan D. F. , Collinge John
Published: February 2009

Approximately 15 % of human prion disease is associated with autosomal-dominant pathogenic mutations in the prion protein (PrP) gene. Previous attempts to model these diseases in mice have expressed human PrP mutations in murine PrP, but this may have different structural consequences. Here, we describe transgenic mice expressing human PrP with P102L or E200K mutations and methionine (M) at the polymorphic residue 129. Although no spontaneous disease developed in aged animals, these mice were readily susceptible to prion infection from patients with the homotypic pathogenic mutation. However, while variant Creutzfeldt–Jakob disease (CJD) prions transmitted infection efficiently to both lines of mice, markedly different susceptibilities to classical (sporadic and iatrogenic) CJD prions were observed. Prions from E200K and classical CJD M129 homozygous patients, transmitted disease with equivalent efficiencies and short incubation periods in human PrP 200K, 129M transgenic mice. However, mismatch at residue 129 between inoculum and host dramatically increased the incubation period. In human PrP 102L, 129M transgenic mice, short disease incubation periods were only observed with transmissions of prions from P102L patients, whereas classical CJD prions showed prolonged and variable incubation periods irrespective of the codon 129 genotype. Analysis of disease-related PrP (PrPSc) showed marked alteration in the PrPSc glycoform ratio propagated after transmission of classical CJD prions, consistent with the PrP point mutations directly influencing PrPSc assembly. These data indicate that P102L or E200K mutations of human PrP have differing effects on prion propagation that depend upon prion strain type and can be significantly influenced by mismatch at the polymorphic residue 129.
The Fourier transforms of curves and filaments and their application to low-resolution protein crystallography
Authors: Hausrath Andrew C. , Goriely Alain
Published: February 2009

A numerical method for computing the Fourier transform of an arbitrary space curve is described. The method is applicable to all sufficiently smooth curves and relies on the local geometric parameters describing a curve. The numerical results for a helical curve are compared with the exact analytical theory for the transform of a helix. It is shown that the transform of a filamentary density distribution radially symmetric around a curve is equivalent to the transform of that curve scaled by an appropriately defined weight function. These filamentary density distributions in conjunction with the numerical transform evaluation method can be used for simulating low-resolution diffraction data for protein crystals. Crystallographic structure factors obtained from a filament model representing a simple three-helix-bundle protein are compared with those calculated from conventional coordinate models. At low resolution, the filamentary representation provides an excellent approximation of the structure factors obtained from the standard coordinate model, but requires far fewer independent parameters.
The undesirable effects of neuromuscular blocking drugs
Authors: Claudius C. , Garvey L. H. , Viby‐Mogensen J.
Published: February 2009

Neuromuscular blocking drugs are designed to bind to the nicotinic receptor at the neuromuscular junction. However, they also interact with other acetylcholine receptors in the body. Binding to these receptors causes adverse effects that vary with the specificity for the cholinergic receptor in question. Moreover, all neuromuscular blocking drugs may cause hypersensitivity reactions. Often the symptoms are mild and self‐limiting but massive histamine release can cause systematic reactions with circulatory and respiratory symptoms and signs. At the end of anaesthesia, no residual effect of a neuromuscular blocking drug should be present. However, the huge variability in response to neuromuscular blocking drugs makes it impossible to predict which patient will suffer postoperative residual curarization. This article discusses the undesirable effects of the currently available neuromuscular blocking drugs including the definitions, diagnosis and causes of hypersensitivity reactions and postoperative residual curarisation.
Antagonism of non‐depolarising neuromuscular block: current practice
Authors: Kopman A. F. , Eikermann M.
Published: February 2009

There is now mounting evidence that even small degrees of postoperative residual neuromuscular block increases the incidence of adverse respiratory events in the Post Anaesthesia Care Unit and may increase longer‐term morbidity as well. In the absence of quantitative neuromuscular monitoring, residual block is easily missed. A very strong case can be made for the routine administration of a non‐depolarising antagonist unless it can be objectively demonstrated that complete recovery has occurred spontaneously. However, the use of acetylcholinesterase inhibitors is associated with the potential for cardiovascular and respiratory side‐effects, so there are cogent reasons for using low doses when the level of neuromuscular block is not intense. As little as 0.015–0.025 mg.kg−1 of neostigmine is required at a train‐of‐four count of four with minimal fade, whereas 0.04–0.05 mg.kg−1 is needed at a train‐of‐four count of two or three. If only a single twitch or none at all can be evoked, neostigmine should not be expected to promptly reverse neuromuscular block, and antagonism is best delayed till a train‐of‐four‐count of two is achieved.
Cyclodextrins and the emergence of sugammadex
Authors: Booij L. H. D. J.
Published: February 2009

Residual paralysis, with its subsequent postoperative pulmonary sequelae, is one of the major complications of anaesthesia, and was recognised shortly after the introduction of neuromuscular blocking drugs into routine clinical practice. Although its incidence decreased with the introduction of intermediate duration drugs, and further diminished with routine neuromuscular monitoring and reversal with cholinesterase inhibitors, residual paralysis still remained a problem. In the search for alternatives to stop the effect of neuromuscular blocking drugs and to match their duration of action to clinical need, chelation of the non‐depolarising neuromuscular blocking drugs was considered. It was recognised that cyclodextrins could encapsulate steroidal molecules and thereby inactivate the aminosteroidal neuromuscular blocking drugs. In order to improve the binding of rocuronium to the cyclodextrin and to increase the compound’s water solubility, the molecule was modified. This led to the development of sugammadex (Org 25969), a modified γ‐cyclodextrin. The modification of the molecule and the initial in vitro studies that led toin vivoand later human studies of this conceptually new drug for anaesthesia are described.
Goodbye Suxamethonium!
Authors: Lee C.
Published: February 2009

No drugs in anaesthesia are more problematic than suxamethonium. Yet, no drugs have survived as suxamethonium does in spite of crisis after crisis, and attempt after attempt at its replacement. For decades, suxamethonium has taught us neuromuscular pharmacology and provided us with an encyclopaedia of side effects, while benefiting millions and millions of our anaesthetised patients. With the arrival of sugammadex, it finally appears that suxamethonium can be retired. Suxamethonium has done its job and seen its days! The present review is intended to offer a eulogy for suxamethonium.
Post‐thrombotic syndrome: prevalence, prognostication and need for progress
Authors: Prandoni Paolo , Kahn Susan R.
Published: February 2009

Despite considerable progress in the diagnosis and treatment of deep‐vein thrombosis (DVT) of the lower extremities, one of every 2–3 patients will develop within 2 years post‐thrombotic sequelae, which are severe in approximately 10% of cases and produce considerable socio‐economic consequences. Among factors potentially related to the development of the post‐thrombotic syndrome (PTS) are older age, obesity, a history of previous ipsilateral DVT, iliac‐femoral location of the current thrombosis, failure to promptly recover from the acute symptoms and insufficient quality of oral anticoagulant therapy. Based on recent findings, the lack of vein recanalization within the first 6 months after DVT appears to be an important predictor of PTS, while the role of venous reflux is controversial. According to the results of recent clinical studies, the prompt administration of adequate compression elastic stockings in patients with symptomatic DVT has the potential to halve the frequency of PTS, and when carefully supervised and instructed to wear proper elastic stockings, more than 50% of patients have the potential to either remain stable or improve during long‐term follow‐up. Nevertheless, due to limitations in current therapies, the management of PTS is demanding and often frustrating. Further research is required to optimize the prevention and management of this common and burdensome complication of DVT.
Genetic diversity and population structure of the threatened Bliss Rapids snail (Taylorconcha serpenticola)
Authors: LIU H.‐P. , HERSHLER R.
Published: February 2009

1. The Bliss Rapids snail is a federally listed yet poorly known small caenogastropod which lives in the Snake River drainage (main stem river and spring‐fed tributaries) of south‐central Idaho. The construction of three large dams along this portion of the Snake River during the 20th century is thought to have fragmented a single, ancestral population of this species into genetically isolated subunits that are vulnerable to extinction. We assessed variation of 11 microsatellite loci within and among 29 samples (820 snails) from across the entire range of the Bliss Rapids snail to assess genetic structure and test whether habitat fragmentation resulting from dam construction has impacted population connectivity.

2. The overall FST (0.15133, P < 0.05) and pairwise comparisons among samples (384/406 significant) indicated extensive population subdivision in general. A consistent trend of isolation by distance trend was not detected by Mantel tests. We found no evidence of reduced genetic diversity attributable to segmentation of the Snake River, and genetic variation among portions of drainage separated by the dams was not significant. Population structuring in spring–tributary habitats was considerably greater than in the main stem river as evidenced by differences in FST (0.18370, 0.06492) and the number of private alleles detected (16, 4), and by the results of an assignment test (69.4%, 58.7% correctly classified to sample of origin) and Bayesian genetic clustering algorithm.

3. Our results provide no evidence that dam construction has genetically impacted extant populations of the Bliss Rapids snail. We speculate that the generally weaker genetic structuring of riverine populations of this species is a result of passive dispersal within the water column, which may enable occasional passage through the dams. The somewhat stronger structuring observed in a portion of the river (Shoshone reach) which receives discharge from many springs may be due to local mixing of main stem and more highly differentiated tributary populations. Our findings parallel recent, genetically based studies of other western North American freshwater gastropods that also demonstrate complex population structure that conflicts with traditional concepts of dispersal ability and sensitivity to putative barriers.
A comparison of the efficacy of conventional and new retreatment instruments to remove gutta‐percha in curved root canals: an ex vivo study
Authors: Çelik Ünal G. , Üreyen Kaya B. , Taç A. G. , Keçeci A. D.
Published: February 2009

Aim  To compare the efficacy of conventional and new retreatment instruments when removing gutta‐percha root fillings in curved root canals.

Methodology  A total of 56 curved molar roots were instrumented with ProFile instruments and filled using system B and Obtura II. The root fillings were removed with manual K‐files and Hedström files (Dentsply Maillefer), ProFile (Dentsply Maillefer), R‐Endo (Micro–Mega) or ProTaper Universal retreatment files (Dentsply Maillefer). Eucalyptol was used as a solvent with all techniques. Bucco‐lingual and proximal radiographs of the roots were exposed and the percentage area of the remaining material was calculated by dividing the area of remaining filling material by the area of canal wall. Data were statistically analysed with Kruskal–Wallis and Mann–Whitney U tests (P = 0.05).

Results  None of the techniques completely removed the root filling materials. No significant differences were found amongst the coronal, middle and apical thirds in both radiographic projections (P > 0.05). In the bucco‐lingual direction, the remaining filling material was significantly less following manual instrumentation than R‐Endo and ProTaper instrumentation (P < 0.05). In the proximal view, it was significantly less following manual and ProFile instrumentation than R‐Endo (P < 0.05). Complete removal of filling material occurred only in three specimens (with manual instruments). Manual instruments were significantly faster than R‐Endo and ProFile (P < 0.05). More procedural errors (five fractured instruments and two perforation) were noted when using ProTaper (P < 0.05).

Conclusions  In this laboratory study in curved molar roots, ProTaper Retreatment and R‐Endo instruments were less effective in removing filling material from canal walls than manual and ProFile instruments.