bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating the energy flux from the wind to ocean inertial motions: The sensitivity to surface wind fields
Authors: Jiang Jing , Lu Youyu , Perrie Will
Published: August 2005

The energy flux from the wind to ocean inertial motions is estimated using three wind products in comparison to the benchmark NCEP winds: (1) corrected NCEP winds, based on scatterometer measurements (Large and Yeager, 2004), increase the energy flux by 50% globally and by 30% at mid‐latitudes, (2) blended QSCAT/NCEP winds double the energy flux at mid‐latitudes, and lead to much larger increases at high latitudes and near the equator, (3) enhanced NCEP winds in the North Atlantic Ocean, through a kinematic reanalysis procedure (Swail and Cox, 2000), increase the energy flux by 30%. We conclude that estimates of the energy fluxes are quite sensitive to wind errors and spatial resolution. NCEP winds provide a lower bound estimate of wind energy flux into ocean near‐inertial motions.
Increased temperature sensitivity and divergent growth trends in circumpolar boreal forests
Authors: Wilmking M. , D'Arrigo R. , Jacoby G. C. , Juday G. P.
Published: August 2005

Tree rings have been used to both reconstruct past climate, and to estimate and project carbon uptake of forest ecosystems. Here we show that large groups of trees of the dominant tree species within widely‐distributed circumpolar forest sites show opposing growth trends during recent warming. These opposing growth trends are present at a sub‐chronology level and, if averaged into chronologies, may have contributed to the widely reported overall decreased temperature sensitivity of high‐latitude chronologies over recent decades. Unlike previous studies, we find that temperature sensitivity has actually increased for most individual trees at these sites. This recent, widespread divergence in growth response seems unique over the past three centuries, and may relate to different microsite responses of individual trees to temperature‐induced drought stress or other factors. This divergence needs to be taken into account in dendroclimatic reconstructions, estimations of global warming impacts, and carbon uptake projections.
Experimental evidence of perturbed odd hydrogen and chlorine chemistry after the October 2003 solar proton events
Authors: von Clarmann T. , Glatthor N. , Höpfner M. , Kellmann S. , Ruhnke R. , Stiller G. P. , Fischer H. , Funke B. , Gil‐López S. , López‐Puertas M.
Published: August 2005

Time series of stratospheric ClO and HOCl have been measured with the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on board the Environmental Satellite (ENVISAT) during the solar storm episode in October/November 2003. A remarkable enhancement of ClO mean values (averaged over latitudes poleward from 70°N) was found, reaching values of more than 0.2 ppbv and even 0.4 ppbv when only nighttime measurements are considered. HOCl was found to increase by up to more than 0.3 ppbv at altitudes above 32 km. This gives indirect proof of enhanced odd hydrogen abundances as a consequence of the solar proton events between 27 and 31 October 2003. Simultaneous increase of both ClO and HOCl hints at HCl destruction either through OH or directly via ion cluster chemistry. When HOCl and ClO mixing ratios decreased, most probably due to then lowered odd hydrogen abundances, large amounts of ClONO2 (polar cap averages enhanced by up to 0.4 ppbv) in early November indicate that ClO then was buffered in this reservoir. Daytime Antarctic ClO enhancements reach 0.2 ppbv and are largest above approximately 40 km. The largest response of Antarctic nighttime ClO is seen at 35 km altitude, where the enhancement reaches 0.3 ppbv. HOCl enhancement in the southern stratosphere was weaker by approximately a factor of two compared with the northern counterpart. The most prominent HOCl increase in the southern stratosphere was observed in subpolar regions between 60°S and 70°S.
Ozone variability in the marine boundary layer of the eastern Mediterranean based on 7‐year observations
Authors: Gerasopoulos E. , Kouvarakis G. , Vrekoussis M. , Kanakidou M. , Mihalopoulos N.
Published: August 2005

A 7‐year time series (1997–2004) of surface ozone at Finokalia, Crete, in the eastern Mediterranean, was analyzed to investigate the mechanisms that control ozone levels and variability in the area. Transport from the European continent was identified as the main mechanism that controls ozone levels in the eastern Mediterranean, especially during summer when ozone presents a summer maximum (July) of 58 ± 10 ppbv. Radon 222 has been proved a useful tool for the verification of the continental origin of ozone. The role of local photochemistry and pollution becomes important under western flow and stagnant wind conditions. For the whole period, a profound ozone‐decreasing trend was also observed with a decline of 1.64 ± 0.15 ppbv yr−1, or 3.1% per year. The sharp decline of ozone during the first 5 years (i.e., 3.4 ± 0.2 ppbv yr−1 or 5.6% per year for 1998–2002) has been succeeded by an abrupt increase in 2003 (to the 1999 ozone levels), followed by a return to the “regular” ozone declining levels in 2004. The rates of the decline were higher for the spring and summer concentrations. In parallel with the ozone decline, a shift of the maximum ozone concentrations from summer to spring, attributed to a continuous decrease of the summer ozone concentrations, was also observed, with the year 2002 presenting a clear spring maximum. The decline of ozone and the shift of its maximum to spring could be related to the reduction of ozone precursors that occurred both in western/central and eastern European countries. The severe weather phenomena that influenced mainly central Europe in summer 2002 have also affected ozone measurements at Finokalia, since the induced meteorological disturbance caused the prevalence of NW winds instead of the dominant NE flow.
The effect of the torsional and stretching vibrations of C2H6 on the H+C2H6→H2+C2H5 reaction
Authors: Kerkeni Boutheïna , Clary David C.
Published: August 2005

We present a three-dimensional quantum scattering model to treat reactions of the type H+C2H6→H2+C2H5. The model allows the torsional and the stretching degrees of freedom to be treated explicitly. Zero-point energies of the remaining modes are taken into account in electronic structure calculations. An analytical potential-energy surface was developed from a minimal number of ab initio geometry evaluations using the CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ level of theory. The reaction is endothermic by 1.5kcalmol−1 and exhibits a vibrationally adiabatic barrier of 12.0kcalmol−1. The results show that the torsional mode influences reactivity when coupled with the vibrational C–H stretching mode. We also found that ethyl radical products are formed internally excited in the torsional mode.
Branching ratio deviations from statistical behavior in core photoionization
Authors: Di Tommaso Devis , Decleva Piero
Published: August 2005

Accurate calculations of carbon 1s photoionization cross sections have been performed at the density functional level with the B-spline linear combination of atomic orbitals approach. The molecules considered are FCCH, FCCCH3, FCCCN, F2CCH2, CF3COOCH2CH3, and C3H5O. The variation of the branching ratios relative to inequivalent C 1s ionizations have been evaluated from threshold to about 100 eV photoelectron kinetic energy. Large deviations from the statistical ratios are observed at low energies, which remain often significant several tens of eV above threshold. The importance of taking into account core branching ratios for peak deconvolution and quantitative analysis, as well as an additional tool for structural information, is pointed out. Strong shape resonant effects are found to largely cancel in branching ratios. Their nature and variation along the series is analyzed in the framework of excitations into σ* valence orbitals.
A comparative study of cluster-surface collisions: Molecular-dynamics simulations of (H2O)1000 and (SO2)1000
Authors: Tomsic A. , Gebhardt C. R.
Published: August 2005

A classical molecular-dynamics study of (H2O)1000 and (SO2)1000 clusters impacting with velocities between 6×102 and 8×103m∕s at normal incidence on a repulsive target is presented. Using the ratio of total kinetic energy to total binding energy of the cluster as a scaling parameter, a general description of the fragmentation dynamics as well as the final fragment size distributions is achieved for the different systems. With increasing ratio, the angular distribution of the emitted monomers rapidly shifts from isotropic to anisotropic. At the highest investigated velocities, a tendency to recover more isotropic distributions is observed. Comparable transient compression of the impacting cluster is reached, on the other hand, for the same, unscaled collision velocities in both systems. For both H2O and SO2 the obtained internal temperatures of the cluster fragments are found to be independent of impact energy and close to the boiling temperature of the respective systems.
The effect of adsorbed oxygen on the surface potential of n-GaAs(110)
Authors: Nevo Iftach , Aloni Shaul , Cohen Sidney R. , Hasse Gaddi
Published: August 2005

Potential variations on semiconductor surfaces are often mapped using a combination of constant current topographic and local surface photovoltage (SPV) imaging. SPV imaging provides a direct measurement of surface-potential variations at large lateral distances from a charged defect or adsorbate. However, directly above the defect, variations in the SPV signal need to be interpreted in terms of surface screening, traps, and band bending. We have examined these effects using isolated oxygen atoms on a GaAS(110) surface, which is free of surface states. We interpret variations in the SPV signal in terms of a simple electrostatic model which considers the oxygen-induced Coulomb potential and corresponding image potential, both of which affect the surface density of states.
Magnetoresistance and electrical hysteresis in stable half-metallic La0.7Sr0.3MnO3 and Fe3O4 nanoconstrictions
Authors: Céspedes O. , Watts S. M. , Coey J. M. D. , Dörr K. , Ziese M.
Published: August 2005

We have studied the transport properties of mechanically stable Fe3O4 and La0.7Sr0.3MnO3 nanoconstrictions patterned by focused ion-beam milling. The magnetoresistance decreases with the square of the applied voltage and scales with the resistance of the constriction, with values up to 8000% for magnetite and 100% for La0.7Sr0.3MnO3. These results are interpreted within a model for domain-wall magnetoresistance. Some samples exhibit electrical hysteresis with discrete changes of resistance that disappear in the presence of a magnetic field, indicating domain-wall displacement driven by a spin-polarized current.
Synthesis of Si-Ge nanoscale structures via deposition of single-source (GeH3)4−nSiHn hydrides
Authors: Hu Changwu , Tsong I. S. T. , D’Costa V. , Menéndez J. , Crozier P. A. , Tolle J. , Kouvetakis J.
Published: August 2005

Growth of nanoscale islands with distinct Si0.33Ge0.67, Si0.25Ge0.75, and Si0.20Ge0.80 compositions and uniform sizes is conducted on Si(100) via dehydrogenation of the single-source hydrides (H3Ge)2SiH2, (H3Ge)3SiH, and (H3Ge)4Si, respectively. High-spatial-resolution electron energy loss spectroscopy and Raman spectroscopy indicate homogeneous elemental concentrations within and among islands and confirm that their Si-Ge content is predetermined by the stoichiometry of the corresponding precursors. Z-contrast electron microscopy reveals distinct and perfectly epitaxial islands with atomically sharp interfaces grown via a smooth and continuous wetting layer ∼10Å thick. Cross-sectional electron microscopy shows monomodal distributions of islands with defect-free microstructures. Low-energy electron microscopy studies of the film formation reveal that the growth proceeds via the Stranski-Krastanov mode. Assemblies of coherent quantum dots with highly controlled Ge-rich concentrations produced by this method are desirable for their potentially useful optical properties.
Imaging the life story of nanotube devices
Authors: Yuzvinsky T. D. , Mickelson W. , Aloni S. , Konsek S. L. , Fennimore A. M. , Begtrup G. E. , Kis A. , Regan B. C. , Zettl A.
Published: August 2005

Live imaging of operating multiwall carbon nanotube (MWCNT-) based electronic devices is performed by high resolution transmission electron microscopy. Our measurements allow us to correlate electronic transport with changes in device structure. Surface contamination, contact annealing, and sequential wall removal are observed. Temperature profiles confirm diffusive conduction in MWCNTs in the high bias limit. This technique provides a general platform for studying nanoscale systems, where geometric configuration and electronic transport are intimately connected.
Ultrafast traveling-wave electro-optic deflector using domain-engineered LiTaO3 crystal
Authors: Hisatake Shintaro , Shibuya Kyoji , Kobayashi Tetsuro
Published: August 2005

We report a traveling-wave electro-optic sinusoidal deflector which operates in a picosecond time scale. The deflector is fabricated by use of simple domain-engineering processes in a LiTaO3 electro-optic crystal. The shape of the domain inverted region in a traveling-wave electro-optic phase modulator is theoretically designed in consideration of velocity mismatch between an optical group velocity and a microwave phase velocity in a crystal for spatial linear distribution of the modulation index within an optical beam cross section. At a deflection period of 61.5 ps, the maximum resolvable spot number of 13.0±0.6 is demonstrated. Our EOD can be applicable to time-space optical information processing systems with the minimum temporal resolution of 1.5 ps.
Direct comparison of threshold and gain characteristics of 1300 nm GaInNAs lasers with GaNAs and GaAs barriers
Authors: Wei Y. Q. , Fu Y. , Wang X. D. , Modh P. , Hedekvist P. O. , Gu Q. F. , Sadeghi M. , Wang S. M. , Larsson A.
Published: August 2005

The threshold and gain characteristics of GaInNAs single quantum well (QW) lasers with GaNAs and GaAs barriers, both emitting at 1300 nm, have been compared. The threshold current density for the laser with GaAs barriers is twice as high, presumably because of a higher monomolecular recombination rate caused by the higher N concentration in the QW. A significant difference in the spectral gain characteristics was also observed. Calculations show that this is due to a modification of the confinement potential for the conduction band electrons when incorporating N in the barriers and reducing the N concentration in the QW. An additional inhomogeneous broadening also had to be included in the calculations to obtain quantitative agreement between measured and calculated gain spectra.
Sexual diploid and apomictic tetraploid races in Thrasya petrosa (Gramineae)
Authors: Acuña Carlos A. , Martínez Eric J. , Quarin Camilo L.
Published: August 2005

Thrasya petrosa (Trin.) Chase is the most widespread species of a grass genus indigenous to the New World. Genetic systems in diploid (2n=2x=20) and tetraploid (2n=4x=40) races of T. petrosa were investigated. The diploid race exhibited embryological development typical of sexual reproduction, but failed to produce seed because of self-incompatibility, whereas the tetraploid showed embryological pathways characteristic of facultative apomixis. Consequently, some ovules showed a normal meiotic embryo sac, others had one to several aposporous sacs, and, finally, some ovules had one or more aposporous sacs beside the meiotic one. A uniform progeny test assisted by molecular markers confirmed that the main reproductive mode for the tetraploid race was apomixis, despite some sexual reproductive structures observed by cytoembryological analyses. The chromosome pairing patterns at meiosis suggested that autoploidy was the genetic origin of the tetraploid races of T. petrosa. In addition, the close relationship between Thrasya Kunth and Paspalum L. previously supported by phylogenetic analyses is further sustained by the particular genetic system shared by the two genera. The system involves co-specific sexual self-incompatible diploids and apomictic, pseudogamous and self-compatible polyploids.
Neuronal ELAV proteins enhance mRNA stability by a PKCα-dependent pathway
Authors: Pascale Alessia , Amadio Marialaura , Scapagnini Giovanni , Lanni Cristina , Racchi Marco , Provenzani Alessandro , Govoni Stefano , Alkon Daniel L. , Quattrone Alessandro
Published: August 2005

More than 1 in 20 human genes bear in the mRNA 3′ UTR a specific motif called the adenine- and uridine-rich element (ARE), which posttranscriptionally determines its expression in response to cell environmental signals. ELAV (embryonic lethal abnormal vision) proteins are the only known ARE-binding factors that are able to stabilize the bound mRNAs, thereby positively controlling gene expression. Here, we show that in human neuroblastoma SH-SY5Y cells, neuron-specific ELAV (nELAV) proteins (HuB, HuC, and HuD) are up-regulated and redistributed by 15 min of treatment with the activators of PKC phorbol esters and bryostatin-1. PKC stimulation also induces nELAV proteins to colocalize with the translocated PKCα isozyme preferentially on the cytoskeleton, with a concomitant increase of nELAV threonine phosphorylation. The same treatment promotes stabilization of growth-associated protein 43 (GAP-43) mRNA, a well known nELAV target, and induces an early increase in GAP-43 protein concentration, again only in the cytoskeletal cell fraction. Genetic or pharmacological inactivation of PKCα abolishes nELAV protein cytoskeletal up-regulation, GAP-43 mRNA stabilization, and GAP-43 protein increase, demonstrating the primary role of this specific PKC isozyme in the cascade of nELAV recruitment. Finally,in vivoPKC activation is associated with an up-regulation of nELAV proteins in the hippocampal rat brain. These findings suggest a model for gene expression regulation by nELAV proteins through a PKCα-dependent pathway that is relevant for the cellular programs in which ARE-mediated control plays a pivotal role.
Homological methods for hypergeometric families
Authors: Matusevich Laura , Miller Ezra , Walther Uli
Published: August 2005

We analyze the behavior of the holonomic rank in families of holonomic systems over complex algebraic varieties by providing homological criteria for rank-jumps in this general setting. Then we investigate rank-jump behavior for hypergeometric systems 

H
A

(
β
)

H_A(\beta )

arising from a

d
×
n

d \times n

integer matrix 

A
A

and a parameter

β
∈

C

d

\beta \in \mathbb {C}^d

. To do so we introduce an Euler–Koszul functor for hypergeometric families over 

C

d

\mathbb {C}^d

, whose homology generalizes the notion of a hypergeometric system, and we prove a homology isomorphism with our general homological construction above. We show that a parameter

β
∈

C

d

\beta \in \mathbb {C}^d

is rank-jumping for

H
A

(
β
)

H_A(\beta )

if and only if

β
\beta

lies in the Zariski closure of the set of

C

d

\mathbb {C}^d

-graded degrees 

α
\alpha

where the local cohomology

⨁

i
>
d

H

m

i

(

C

[

N

A
]

)
α

\bigoplus _{i > d} H^i_\mathfrak m(\mathbb {C}[\mathbb {N} A])_\alpha

of the semigroup ring

C

[

N

A
]

\mathbb {C}[\mathbb {N} A]

supported at its maximal graded ideal 

m

\mathfrak m

is nonzero. Consequently,

H
A

(
β
)

H_A(\beta )

has no rank-jumps over 

C

d

\mathbb {C}^d

if and only if

C

[

N

A
]

\mathbb {C}[\mathbb {N} A]

is Cohen–Macaulay of dimension 

d
d

.
The cohomological equation for Roth-type interval exchange maps
Authors: Marmi S. , Moussa P. , Yoccoz J.-C.
Published: August 2005

We exhibit an explicit class of minimal interval exchange maps (i.e.m.’s)

T
T

for which the cohomological equation
\[

Ψ
−
Ψ
∘
T
=
Φ

\Psi -\Psi \circ T=\Phi

\]
has a bounded solution

Ψ
\Psi

provided that the datum

Φ
\Phi

belongs to a finite codimension subspace of the space of functions having on each interval a derivative of bounded variation. The proof is purely dynamical and is based on a renormalization argument and on Gottshalk-Hedlund’s theorem. If the datum is more regular the loss of differentiability in solving the cohomological equation will be the same. The class of interval exchange maps is characterized in terms of a diophantine condition of Roth type imposed to an acceleration of the Rauzy-Veech-Zorich continued fraction expansion associated to

T
T

. More precisely one must impose a growth rate condition for the matrices appearing in the continued fraction algorithm together with a spectral gap condition (which guarantees unique ergodicity) and a coherence condition. We also prove that the set of Roth-type interval exchange maps has full measure. In the appendices we construct concrete examples of Roth-type i.e.m.’s and we show how the growth rate condition alone does not imply unique ergodicity.
Simple Hironaka resolution in characteristic zero
Authors: Włodarczyk Jarosław
Published: August 2005

Building upon work of Villamayor and Bierstone-Milman we give a proof of the canonical Hironaka principalization and desingularization. The idea of “homogenized ideals" introduced in the paper gives a priori the canonicity of the algorithm and radically simplifies the proof.
A geometric invariant-based framework for the analysis of protein conformational space
Authors: Tendulkar Ashish V. , Sohoni Milind A. , Ogunnaike Babatunde , Wangikar Pramod P.
Published: August 2005

Motivation: Characterization of the restricted nature of the protein local conformational space has remained a challenge, thereby necessitating a computationally expensive conformational search in protein modeling. Moreover, owing to the lack of unilateral structural descriptors, conventional data mining techniques, such as clustering and classification, have not been applied in protein structure analysis.

Results: We first map the local conformations in a fixed dimensional space by using a carefully selected suite of geometric invariants (GIs) and then reduce the number of dimensions via principal component analysis (PCA). Distribution of the conformations in the space spanned by the first four PCs is visualized as a set of conditional bivariate probability distribution plots, where the peaks correspond to the preferred conformations. The locations of the different canonical structures in the PC-space have been interpreted in the context of the weights of the GIs to the first four PCs. Clustering of the available conformations reveals that the number of preferred local conformations is several orders of magnitude smaller than that suggested previously.

Contact:  pramodw@iitb.ac.in

Supplementary information:  www.it.iitb.ac.in/~ashish/bioinfo2005/
Estimating Regression Models in Which the Dependent Variable Is Based on Estimates
Authors: Lewis Jeffrey B. , Linzer Drew A.
Published: August 2005

Researchers often use as dependent variables quantities estimated from auxiliary data sets. Estimated dependent variable (EDV) models arise, for example, in studies where counties or states are the units of analysis and the dependent variable is an estimated mean, proportion, or regression coefficient. Scholars fitting EDV models have generally recognized that variation in the sampling variance of the observations on the dependent variable will induce heteroscedasticity. We show that the most common approach to this problem, weighted least squares, will usually lead to inefficient estimates and underestimated standard errors. In many cases, OLS with White's or Efron heteroscedastic consistent standard errors yields better results. We also suggest two simple alternative FGLS approaches that are more efficient and yield consistent standard error estimates. Finally, we apply the various alternative estimators to a replication of Cohen's (2004) cross-national study of presidential approval.
Can a fibrillar interface be stronger and tougher than a non-fibrillar one?
Authors: Tang Tian , Hui Chung-Yuen , Glassmaker Nicholas J
Published: August 2005

Elasticity analysis and finite element simulations are carried out to study the strength of an elastic fibrillar interface. The fibrils are assumed to be in perfect contact with a rigid substrate. The adhesive interaction between the fibrils and the substrate is modelled by the Dugdale–Barenblatt model (DB). The condition for a fibrillar interface to be stronger than a non-fibrillar one is obtained for two regimes: (i) small fibril or flaw insensitive regime; (ii) large fibril or flaw sensitive regime. The transition between the two regimes is characterized by a dimensionless parameter that incorporates the material constants of the elastic fibrils and interfacial properties. The condition for a fibrillar interface to be tougher is also given. Lateral collapse is found to be detrimental to the strength and toughness of a fibrillar interface.
PrP glycoforms are associated in a strain-specific ratio in native PrPSc
Authors: Khalili-Shirazi Azadeh , Summers Linda , Linehan Jacqueline , Mallinson Gary , Anstee David , Hawke Simon , Jackson Graham S. , Collinge John
Published: August 2005

Prion diseases involve conversion of host-encoded cellular prion protein (PrPC) to a disease-related isoform (PrPSc). Using recombinant humanβ-PrP, a panel of monoclonal antibodies was produced that efficiently immunoprecipitated native PrPScand recognized epitopes between residues 93–105, indicating for the first time that this region is exposed in both human vCJD and mouse RML prions. In contrast, monoclonal antibodies raised to humanα-PrP were more efficient in immunoprecipitating PrPCthan PrPSc, and some of them could also distinguish between different PrP glycoforms. Using these monoclonal antibodies, the physical association of PrP glycoforms was studied in normal brain and in the brains of humans and mice with prion disease. It was shown that while PrPCglycoforms can be selectively immunoprecipitated, the differentially glycosylated molecules of native PrPScare closely associated and always immunoprecipitate together. Furthermore, the ratio of glycoforms comprising immunoprecipitated native PrPScfrom diverse prion strains was similar to those observed on denaturing Western blots. These studies are consistent with the view that the proportion of each glycoform incorporated into PrPScis probably controlled in a strain-specific manner and that each PrPScparticle contains a mixture of glycoforms.
Analysis of the epidemiological dynamics during the 1982–1983 epidemic of foot-and-mouth disease in Denmark based on molecular high-resolution strain identification
Authors: Christensen Laurids S. , Normann Preben , Thykier-Nielsen Søren , Sørensen Jens H. , de Stricker Karin , Rosenørn Stig
Published: August 2005

An epidemic of foot-and-mouth disease (FMD) causing a total of 23 cases in 1982–1983, primarily on the island of Funen, Denmark, was subjected to molecular epidemiological investigations. In an attempt to exploit the quasi-species nature of foot-and-mouth disease virus strains for molecular high-resolution strain identification in order to analyse the dynamics of this epidemic, full-length VP1 coding regions were sequenced for 17 isolates collected at different farms during the epidemic. The sequence information together with epidemiological information gathered during the epidemic suggests that the epidemic was caused by at least three introductions across Danish borders and one case of airborne transmission between two islands in Denmark over a distance of 70 km. The assortment of nucleotide markers among the three strains is indicative of common recombination events in their evolutionary history, and the prerequisite of co- or superinfection of animals with variant strains in turn implies that they have a common source or epidemiologically related sources originating from an area with endemic FMD.
Sheep scrapie susceptibility-linked polymorphisms do not modulate the initial binding of cellular to disease-associated prion protein prior to conversion
Authors: Rigter Alan , Bossers Alex
Published: August 2005

Conversion of the host-encoded protease-sensitive cellular prion protein (PrPC) into the scrapie-associated protease-resistant isoform (PrPSc) of prion protein (PrP) is the central event in transmissible spongiform encephalopathies or prion diseases. Differences in transmissibility and susceptibility are largely determined by polymorphisms in PrP, but the exact molecular mechanism behind PrP conversion and the modulation by disease-associated polymorphisms is still unclear. To assess whether the polymorphisms in either PrPC or PrPSc modulate the initial binding of PrPC to PrPSc, several naturally occurring allelic variants of sheep PrPC and PrPSc that are associated with differential scrapie susceptibility and transmissibility [the phylogenetic wild-type (ARQ), the codon 136Val variant (VRQ) and the codon 171Arg variant (ARR)] were used. Under cell-free PrP conversion conditions known to reproduce the observed in vivo differential scrapie susceptibility, it was found that the relative amounts of PrPC allelic variants bound by various allelic PrPSc variants are PrP-specific and have comparable binding efficiencies. Therefore, the differential rate-limiting step in conversion of sheep PrP variants is not determined by the initial PrPC–PrPSc-binding efficiency, but seems to be an intrinsic property of PrPC itself. Consequently, a second step after PrPC–PrPSc-binding should determine the observed differences in PrP conversion efficiencies. Further study of this second step may provide a future tool to determine the mechanism underlying refolding of PrPC into PrPSc and supports the use of conversion-resistant polymorphic PrPC variants as a potential therapeutic approach to interfere with PrP conversion in transmissible spongiform encephalopathy development.
Identification of classical swine fever virus protein E2 as a target for cytotoxic T cells by using mRNA-transfected antigen-presenting cells
Authors: Ceppi M. , de Bruin M. G. M. , Seuberlich T. , Balmelli C. , Pascolo S. , Ruggli N. , Wienhold D. , Tratschin J. D. , McCullough K. C. , Summerfield A.
Published: August 2005

Vaccination of pigs againstClassical swine fever virus(CSFV) by using live-virus vaccines induces early protection before detectable humoral immune responses. Immunological analyses indicate that this is associated with T-cell activation, underlining the importance of targeting cytotoxic T-lymphocyte (CTL) responses for vaccine improvement. Antigen-presenting cells (APCs) transfected with mRNA encoding structural protein E2 or non-structural viral proteins NS3–NS4A were used to identify viral genes encoding CTL epitopes. Monocyte-derived dendritic cells (DCs) and fibrocytes served as the APCs.In vitrotranslation of the mRNA and microscopic analysis of transfected cells demonstrated that E2 and NS3–NS4A could be identified. APCs transfected with either of the mRNA molecules restimulated CSFV-specific T cells to produce gamma interferon and specific cytotoxic activity against CSFV-infected target cells. The presence of CTL epitopes on E2 was confirmed by using d/d-haplotype MAX cells expressing E2 constitutively as target cells in d/d-haplotype CTL assays. A potent CTL activity against E2 was detected early (1–3 weeks) after CSFV challenge. This work corroborates the existence of CTL epitopes within the non-structural protein domain NS3–NS4A of CSFV. Furthermore, epitopes on the E2 protein can also now be classified as targets for CTLs, having important implications for vaccine design, especially subunit vaccines. As for the use of mRNA-transfected APCs, this represents a simple and efficient method to identify viral genes encoding CTL epitopes in outbred populations.
Molecular characterization of the major capsid protein VP6 of bovine group B rotavirus and its use in seroepidemiology
Authors: Tsunemitsu Hiroshi , Kamiyama Mariko , Kawashima Kenji , Katsuda Ken , Kohmoto Mariko , Saif Linda J. , Shouji Tomotaro , Onodera Toshiyuki
Published: August 2005

The major inner capsid protein (VP6) gene of the bovine group B rotavirus (GBR) Nemuro strain is 1269 nt in length and contains one open reading frame encoding 391 aa. Nucleotide and amino acid sequence identities of the Nemuro VP6 gene compared with the published corresponding human and rodent GBR genes were respectively 66–67 and 70–72 %, which are notably lower than those between human and rodent viruses (72–73 and 83–84 %, respectively). Overall identities of VP6 genes among GBRs were substantially lower than those among both group A rotaviruses (GARs) and group C rotaviruses (GCRs) derived from different species of mammals. These results demonstrate that bovine GBR is remarkably distinct from other GBRs and that GBRs from different species may have had a longer period of divergence than GARs and GCRs. Recombinant VP6 was generated with a baculovirus expression system and used for an ELISA to detect GBR antibodies. All 13 paired sera from adult cows with GBR-induced diarrhoea in the field showed antibody responses in the ELISA. In serological surveys of GBR infection using the ELISA, 47 % of cattle sera were positive for GBR antibodies, with a higher antibody prevalence in adults than in young cattle. In pigs, a high prevalence of GBR antibodies (97 %) was detected in sera from sows. These results suggest that GBR infection is common in cattle and pigs, notwithstanding the scarcity of reports of GBR detection in these species to date.
Differential splicing of E6 within human papillomavirus type 18 variants and functional consequences
Authors: De la Cruz-Hernández Erick , García-Carrancá Alejandro , Mohar-Betancourt Alejandro , Dueñas-González Alfonso , Contreras-Paredes Adriana , Pérez-Cardenas Enrique , Herrera-Goepfert Roberto , Lizano-Soberón Marcela
Published: August 2005

Persistent infections of the uterine cervix with ‘high-risk’ human papillomavirus (HPV) are now recognized as necessary for the development of cervical cancer. Among them, HPV types 16 and 18 exhibit numerous variants associated with different risks for cervical cancer development. In this study, the questions of whether different HPV type 18 variants exhibit changes in early gene transcription and the molecular mechanisms underlying these differences were investigated. It was shown that, indeed, type 18 variants exhibited singular differences in E6 transcripts in vivo. Higher levels of the E6*I transcript were detected regularly in clones harbouring the African variant, as opposed to low levels of this transcript detected in clones containing the reference clone (Asian–Amerindian), where significantly higher levels of full-length E6 transcript were usually observed. As a direct consequence, higher levels of p53 protein were found in the presence of African E6, as opposed to the low levels of p53 observed with the Asian–Amerindian E6. These variations in consequence affected the levels of cellular proteins regulated by p53, such as Bax. Similar changes in the relative levels of E6 transcripts were observed when tumours containing type 18 E6 variants were analysed. The different ability of cells containing variant E6 genes to form tumours in nude mice was suggested by the fact that tumour volumes were considerably higher when cells expressed the Asian–Amerindian E6. Mutagenesis analysis of the reference clone showed that a C491A change reverts the phenotype. These results suggest that different splicing patterns of E6 within HPV type 18 variants may possibly have biological implications in viral tumorigenesis.
Identification and real-time PCR quantification of Phocine distemper virus from two colonies of Scottish grey seals in 2002
Authors: Hammond John A. , Pomeroy Patrick P. , Hall Ailsa J. , Smith Valerie J.
Published: August 2005

The North Sea European harbour seal (Phoca vitulina) population has endured two phocine distemper virus (PDV) epidemics in 1988 and 2002. The grey seal (Halichoerus grypus) is a sympatric seal species that shows little or no mortality from PDV. Two Scottish grey seal breeding colonies were sampled for evidence of PDV infection approximately 2 months after the peak of the 2002 epidemic. In both colonies, a proportion of mothers (13/109) and pups (6/84) tested positive for PDV in their leukocytes. All infected animals were asymptomatic and completed the breeding season successfully. These results illustrate that grey seals come into contact with infectious seals and can become infected themselves without experiencing acute effects. In some seals the virus is able to replicate from the primary site of infection. This study provides evidence that grey seals may have an active role in the spread of PDV during an epidemic.
Early endocytosis pathways in SSN-1 cells infected by dragon grouper nervous necrosis virus
Authors: Liu Wangta , Hsu Chi-Hsin , Hong Yi-Ren , Wu Shu-Chuan , Wang Chun-Hsiung , Wu Yi-Min , Chao Chia-Ben , Lin Chan-Shing
Published: August 2005

Many fish undergo betanodavirus infection. To study the infection process of dragon grouper nervous necrosis virus (DGNNV), native virus and virus-like particles (VLPs) were used to analyse the binding and internalization in SSN-1 cells. The binding of DGNNV and VLPs to SSN-1 cells was demonstrated using Western blotting and immunofluorescence microscopy. As estimated by indirect ELISA, the DGNNV particles bound SSN-1 cells in a dose-dependent manner up to 8×104 particles per cell. The binding of VLPs was sensitive to neuraminidase and tunicamycin, suggesting that cell-surface sialic acid is involved in binding. The penetration of DGNNV into cells, which was monitored by electron microscopy, appeared to occur mainly via the spherical pit and membrane ruffling pathways. Occasionally, a spherical pit was engulfed by membrane ruffling so as to form a large figure-of-eight-shaped vesicle with an open connection. Our observations suggest that DGNNV utilizes both micro- and macropinocytosis pathways to enter SSN-1 cells.
Characterization of the triplet repeats in the central domain of the γ
134·5 protein of herpes simplex virus 1
Authors: Jing Xianghong , He Bin
Published: August 2005

The γ
134·5 protein of herpes simplex virus 1 (HSV-1) consists of an amino-terminal domain, a central domain with triplet repeats (Ala–Thr–Pro) and a carboxyl-terminal domain. The triplet repeats are a unique feature of the γ
134·5 protein encoded by HSV-1, but the number of repeats varies among different strains. Notably, the central domain containing the triplet repeats is implicated in neuroinvasion. In this report, it has been shown that partial or full deletion of triplet repeats, i.e. from ten to either three or zero, in the γ
134·5 protein has no effect on the virus response to interferon. The triplet deletion mutants replicate efficiently in CV-1 and mouse 10T1/2 cells. However, in mouse 3T6 cells, these mutants grow with delayed growth kinetics. This decrease in growth, compared with wild-type HSV-1(F), does not result from failure of the virus to suppress the RNA-dependent protein kinase response, but rather from a delay in virus release or egress. Accordingly, these mutant viruses are predominantly present within infected cells. These results indicate that deletions in the central domain of the γ
134·5 protein impair virus egress, but not virus response to interferon.
Specific and common changes in Nicotiana benthamiana gene expression in response to infection by enveloped viruses
Authors: Senthil G. , Liu H. , Puram V. G. , Clark A. , Stromberg A. , Goodin M. M.
Published: August 2005

Microarrays derived from Solanum tuberosum expressed sequence tags were used to test the hypothesis that genetically distinct enveloped viruses elicit unique changes in Nicotiana benthamiana gene expression. The results of our study, which included Sonchus yellow net virus (SYNV), a plant rhabdovirus that replicates in the nucleus of infected cells, and Impatiens necrotic spot virus (INSV), a plant bunyavirus that replicates in the cytoplasm, were consistent with this hypothesis. Statistically significant changes (P⩽0·01) in the expression of 275, 2646 and 4165 genes were detected in response to INSV at 2, 4 and 5 days post-inoculation (d.p.i.), respectively. In contrast, 35, 665 and 1458 genes were expressed differentially in response to SYNV at 5, 11 and 14 d.p.i., respectively. The microarray results were verified by Northern hybridization using a subset of these genes as probes. Notably, INSV, but not SYNV, induced expression of small heat-shock protein genes to high levels. In contrast to SYNV, infection by INSV resulted in downregulation of all histone genes, of which the downregulation of histone 2b expression to very low levels was confirmed by Northern hybridization. The expression of a putative WRKY transcription factor at 11 d.p.i., but not at 5 or 14 d.p.i., in SYNV-infected tissue suggested that the temporal response to virus infection was identified readily using our experimental design. Overall, infection by INSV resulted in larger fold changes in host gene expression relative to infection by SYNV. Taken together, the present data demonstrate differential responses of a common host to two genetically distinct viruses.
Increasing seroprevalence of Human herpesvirus 8 (HHV-8) with age confirms HHV-8 endemicity in Amazon Amerindians from Brazil
Authors: Cunha A. M. G. , Caterino-de-Araujo A. , Costa S. C. B. , Santos-Fortuna E. , Boa-Sorte N. C. A. , Gonçalves M. S. , Costa F. F. , Galvão-Castro B.
Published: August 2005

Human herpesvirus 8 (HHV-8) seroprevalences were determined in two isolated Amazon Amerindian tribes, according to age, gender and familial aggregation. Plasma and serum samples obtained from 982 Amazon Amerindians (664 Tiriyó and 318 Waiampi) were tested for antibodies against lytic and latent HHV-8 antigens by using ‘in-house’ immunofluorescence assays. Overall, HHV-8 seroprevalence was 56·8 % (57·4 % in the Tiriyó tribe and 55·7 % in the Waiampi tribe). Seroprevalence was independent of gender and increased linearly with age: it was 35·0 % among children aged 2–9 years, 51·4 % in adolescents (10–19 years), 72·9 % in adults and 82·3 % in adults aged >50 years. Interestingly, 44·4 % of children under 2 years of age were HHV-8-seropositive. No significant differences in seroprevalence between tribes and age groups were detected. It is concluded that HHV-8 is hyperendemic in Brazilian Amazon Amerindians, with vertical and horizontal transmission during childhood, familial transmission and sexual contact in adulthood contributing to this high prevalence in these isolated populations.
Analysis of the binding of hepatitis C virus genotype 1a and 1b E2 glycoproteins to peripheral blood mononuclear cell subsets
Authors: Yamada Eriko , Montoya Maria , Schuettler Christian G. , Hickling Timothy P. , Tarr Alexander W. , Vitelli Alessandra , Dubuisson Jean , Patel Arvind H. , Ball Jonathan K. , Borrow Persephone
Published: August 2005

Hepatitis C virus (HCV) binding to hepatocytes is thought to be mediated via interaction of the E2 glycoprotein with (co-)receptors including CD81 and scavenger receptor class B type I (SR-BI). Here, the expression of CD81 and SR-BI was analysed on peripheral blood mononuclear cell (PBMC) subsets, and the binding of genotype 1 soluble truncated E2 (sE2) proteins to these cells was investigated. All PBMC subsets expressed CD81, although at varying levels. In contrast, SR-BI was only detected on monocytes and dendritic cells (DCs). The genotype 1a H77c sE2 protein showed higher PBMC binding than other genotype 1a/b sE2s. H77c sE2 binding to different PBMC subsets largely paralleled their level of CD81 expression, and could be inhibited by blocking E2–CD81 interaction. However, those PBMC subsets reported to be infected by HCV in vivo (monocytes, DCs and B cells) also exhibited residual, CD81-independent binding, indicating roles for SR-BI/other receptor(s) in mediating haematopoietic cell infection.
DNA methylation profiles of differentiated‐type gastric carcinomas with distinct mucin phenotypes
Authors: Motoshita Junichi , Oue Naohide , Nakayama Hirofumi , Kuraoka Kazuya , Aung Phyu Phyu , Taniyama Kiyomi , Matsusaki Keisuke , Yasui Wataru
Published: August 2005

Gastric carcinomas (GC) are classified into four phenotypes according to mucin expression. Previous studies revealed the association of distinct genetic profiles in GC with mucin phenotypic expression; however, the roles of epigenetic changes, such as DNA methylation, are poorly understood. We examined whether the phenotypic expression of GC was associated with DNA methylation of hMLH1, MGMT, p16INK4a, RAR‐beta or CDH1. Expression of HGM, M‐GGMC‐1, MUC2, and CD10 was analyzed immunohistochemically in 33 advanced GC with differentiated histology. HGM was expressed in 14 (42.4%) cases, M‐GGMC‐1 in five (15.2%) cases, MUC2 in 15 (45.5%) cases and CD10 in 18 (54.5%) cases. DNA methylation was detected in five (15.2%) cases for hMLH1, 11 (33.3%) cases for MGMT, 13 (39.4%) cases for p16INK4a, 17 (51.5%) cases for RAR‐beta and 14 (42.4%) cases for CDH1 by bisulfite‐polymerase chain reaction and methylation‐specific polymerase chain reaction. DNA methylation of hMLH1 occurred more frequently in MUC2‐negative GC than in MUC2‐positive GC (P = 0.0488, Fisher's exact test). In contrast, MGMT was more frequently methylated in MUC2‐positive GC than in MUC2‐negative GC (P = 0.0078, Fisher's exact test). There was no correlation between gastric or intestinal‐markers and methylation of the p16INK4a, RAR‐beta and CDH1 genes. These results indicate that DNA methylation of specific genes, such as hMLH1 and MGMT, may be involved partly in the distinct phenotypic expression of GC. (Cancer Sci 2005; 96: 474 –479)
Stimulation of CD30 in anaplastic large cell lymphoma leads to production of nuclear factor‐κB p52, which is associated with hyperphosphorylated Bcl‐3
Authors: Nishikori Momoko , Ohno Hitoshi , Haga Hironori , Uchiyama Takashi
Published: August 2005

Anaplastic large cell lymphoma (ALCL) and Hodgkin lymphoma (HL) express CD30 at high levels, but stimulation of this molecule has been reported to induce contradictory effects. To elucidate the molecular mechanism of CD30‐mediated apoptosis of ALCL, we compared the gene expression profiles of t(2;5)(p23;q35)‐positive ALCL with those of HL altered by CD30 agonistic stimulation. The results showed that BCL3, the high‐level expression of which in ALCL was previously reported, was further upregulated in response to CD30 stimulation, along with several pro‐apoptotic genes. Bcl‐3 protein was present as an intermediate phospho‐form in the resting‐state ALCL, becoming hyperphosphorylated (Bcl‐3P) upon stimulation. We next found that the stimulation promoted de novo synthesis of the nuclear factor (NF)‐κB2/p100 precursor as well as processing to p52, and a series of immunoprecipitation and western blotting analyses consistently showed association of Bcl‐3P with p52 in CD30‐stimulated ALCL. An electrophoretic mobility shift assay revealed the induction of κB binding activity of the p52 homodimer, and nuclear colocalization of Bcl‐3 and p52 was demonstrated in anaplastic lymphoma kinase‐positive ALCL tumor tissues by immunohistochemistry. As Bcl‐3 can act as an antirepressor or transactivator or both, we propose that the (p52)2/Bcl‐3P ternary complex, which is specifically induced in CD30‐stimulated ALCL, can modulate expression of apoptosis‐related genes regulated by NF‐κB, thereby accounting for CD30‐mediated apoptosis of ALCL. (Cancer Sci 2005; 96: 487–497)