bluuebunny/crossref_metadata_2025 huggingface dataset:
Diurnal nonmigrating tides from TIMED Doppler Interferometer wind data: Monthly climatologies and seasonal variations
Authors: Oberheide J. , Wu Q. , Killeen T. L. , Hagan M. E. , Roble R. G.
Published: September 2006

TIMED Doppler Interferometer (TIDI) measurements of zonal and meridional winds in the mesosphere/lower thermosphere are analyzed for diurnal nonmigrating tides (June 2002 to June 2005). Climatologies of monthly mean amplitudes and phases for seven tidal components are presented at altitudes between 85 and 105 km and latitudes between 45°S and 45°N (westward propagating wave numbers 2, 3, and 4; the standing diurnal tide; and eastward propagating wave numbers 1, 2, and 3). The observed seasonal variations agree well with 1991–1994 UARS results at 95 km. Comparisons between the TIDI results and global scale wave model (GSWM) and thermosphere‐ionosphere‐mesosphere‐electrodynamics general circulation model (TIME‐GCM) tidal predictions indicate that the large eastward propagating wave number 3 amplitude is driven by tropical tropospheric latent heat release alone. In contrast, latent heating and planetary wave/migrating tidal interactions are equally important to westward 2 and standing diurnal tidal forcing. There is good quantitative agreement between TIDI and the model predictions during equinox, but the latter tend to underestimate the westward 2 and standing diurnal tide during solstice. Neither model reproduces the observed seasonal variations of the eastward propagating components.
Soft X‐ray irradiances during solar flares observed by TIMED‐SEE
Authors: Rodgers E. M. , Bailey S. M. , Warren H. P. , Woods T. N. , Eparvier F. G.
Published: September 2006

Observations from the Thermosphere Ionosphere Mesosphere Energetics Dynamics–Solar Extreme Ultraviolet Experiment (TIMED‐SEE) are analyzed to determine the solar soft X‐ray energy emission during a solar flare. The TIMED‐SEE X‐ray ultraviolet Photometer System (XPS) detectors utilize broadband photodiodes that observe from 0.1 to 27 nm. The XPS observed 29 flares of various strengths over a 6‐month period in 2002. We describe an emission measure technique to interpret the broadband observations and determine a best fit flare spectrum. This technique is applied to the 29 flares observed by the XPS. Our results show that most of the enhancement in the solar spectrum during a flare comes from the 0–2 nm wavelength range. We also show that the XPS calculated 0.1–0.8 nm irradiance for brighter M‐class and X‐class flares is in good agreement with the Geostationary Operational Environmental Satellites (GOES) observed 0.1–0.8 nm irradiance. Also, the XPS 0–7 nm flare irradiance is well correlated with the 0.1–0.8 nm irradiance observed by GOES. We show that the total 0–7 nm irradiance of smaller X‐class flares (X1–X5) calculated at the time of the XPS observation provides 2–3 times the energy of the quiet Sun 0–7 nm irradiance.
Stellar occultations at UV wavelengths by the SPICAM instrument: Retrieval and analysis of Martian haze profiles
Authors: Montmessin F. , Quémerais E. , Bertaux J. L. , Korablev O. , Rannou P. , Lebonnois S.
Published: September 2006

Observations made by the SPICAM ultraviolet spectrometer on board the Mars Express orbiter are presented. We focus on several hundreds of atmospheric profiles which have been collected over 3/4 of a Martian year by making use of the stellar occultation technique. The typical structure of the Martian haze possesses at least one discrete layer (60% of all cases) standing over an extended portion wherein opacity continuously increases down to the surface. Differences of morphology are, however, noted between profiles observed near the equator and profiles collected elsewhere. The Martian haze exhibits a pronounced seasonal signal manifested by variations of the maximum elevation at which particles are observed. For reasons related to both convective activity and changes in the hygropause level, cold regions display a much lower hazetop than warm regions. Using UV spectrometry data, we put constraints on haze microphysical properties. Vertical variations of particle size are keyed to variations of opacity; e.g., an increase of particle size is systematically observed near extinction peaks. This is the likely consequence of cloud formation which results into a local increase of particle cross section. Despite marked differences of aerosol profiles between low and high latitudes, haze properties above 60 km remain invariant, possibly reflecting the long‐term presence of a background submicronic particle population. Several profiles have been analyzed in more detail to extract properties of detached cloud layers lofted above 40 km. Their optical depth ranges between 0.01 and 0.1 in the visible. Estimation of cloud particle size is technically restricted because of SPICAM wavelength sampling, but it generally yields a minimum radius value of about 0.3 μm, while several estimates are consistent with a robust 0.1–0.2 μm. This crystal size, significantly smaller than the 1 to 4 μm associated with recently classified type I and II clouds, suggests that a different class of clouds, henceforth type III clouds, can be extracted from our data. Observations made in the southern winter polar night indicate a very distinct aerosol behavior where particles are less abundant (τ < 0.1), confined to lower heights (vertical profile consistent with a Conrath parameter exceeding 0.04) and made of particles having a radius on the order of 0.1 μm. This shows that the Martian polar night is a region with a very clean atmosphere and with a distinct type of aerosols.
Mercury and monomethylmercury in fluids from Sea Cliff submarine hydrothermal field, Gorda Ridge
Authors: Lamborg Carl H. , Von Damm Karen L. , Fitzgerald William F. , Hammerschmidt Chad R. , Zierenberg Robert
Published: September 2006

Submarine hydrothermal systems are hypothesized to be a potentially important source of monomethylmercury (MMHg) to the ocean, yet the amount of MMHg in vent fluids is unknown. Here, we report total Hg and MMHg concentrations in hydrothermal vent fluids sampled from the Sea Cliff site on the Gorda Ridge. MMHg is the dominant Hg species, and levels of total Hg are enhanced slightly compared to seawater. Hg is enriched in deposits surrounding the site, suggesting near‐field deposition from fluid plumes, with rapid MMHg demethylation and scavenging of Hg(II) complexes. Assuming the flux of MMHg from Sea Cliff is representative of global submarine hydrothermal inputs, we estimate a flux of 0.1–0.4 Mmoles y−1, which may be attenuated by scavenging near the vents. However, deep waters are not typically known to be elevated in Hg, and thus we suggest that hydrothermal systems are not significant sources of MMHg to commercial fisheries.
Short‐term slow slip and correlated tremor episodes in the Tokai region, central Japan
Authors: Hirose Hitoshi , Obara Kazushige
Published: September 2006

We observe the related phenomenon of short‐term slow slip event (SSE) and low‐frequency nonvolcanic tremor on the deeper extension of the 1944 Tonankai and the anticipated Tokai earthquake rupture areas, central Japan. Japan nation‐wide seismometer and tiltmeter array, NIED Hi‐net has recorded these correlated episodes of SSE and tremor, known as episodic tremor and slip (ETS) in 2004 and 2005. The events are located on two areas in the Tokai region, one is near the Shima peninsula, and the other is around the Aichi area. Both episodes have a typical duration of 2–3 days and released seismic moment corresponding to Mw ∼ 6.0. Moreover, these episodes repeatedly occur with a recurrence interval of about six months in both areas. This evidence suggests that the coincidence between the SSE and the tremor is a characteristic behavior in the whole tremor belt‐like zone in the Nankai trough subduction zone.
Geographic variability in the export of moist static energy and vertical motion profiles in the tropical Pacific
Authors: Back L. E. , Bretherton C. S.
Published: September 2006

Column‐integrated moist static energy (MSE) budgets were calculated using daily data from three reanalyses (1998–2001) and ISCCP radiative cooling. The MSE export by the circulation was separated into vertical and horizontal MSE advection components in order to examine how observationally‐derived vertical motion profiles affect gross moist stability calculations. In a 2000 km‐wide region in the central‐eastern Pacific ITCZ, vertical motions import MSE, implying a negative gross moist stability. Horizontal MSE advection is negative and of similar magnitude to vertical MSE advection in rainy regions. Geographic differences in export of MSE by the vertical circulation are primarily due to differences in the shape of the vertical motion profile. In the west Pacific warm pool rainy regions, mean horizontal convergence extends up to 300 mb, while in parts of the Pacific ITCZ where meridional SST gradients are strong, the vertical motion profile is bottom‐heavy, with convergence below 800 mb and divergence above. On daily timescales, the mode of vertical motion variability has little dependence on precipitation rate and is consistent with observed regional differences in the vertical structure of TRMM PR reflectivities.
Tropical dendrochemistry: A novel approach to estimate age and growth from ringless trees
Authors: Poussart P. M. , Myneni S. C. B. , Lanzirotti A.
Published: September 2006

Although tropical forests play an active role in the global carbon cycle and climate, their growth history remains poorly characterized compared to other ecosystems on the planet. Trees are prime candidates for the extraction of paleoclimate archives as they can be probed sub‐annually, are widely distributed and can live for over 1400 years [Chambers et al., 1998]. However, dendrochronological techniques have found limited applications in the tropics because trees often lack visible growth rings (Whitmore, 1990). Alternative methods exist (dendrometry (DaSilva et al., 2002), radio‐ and stable isotopes (Evans and Schrag, 2004; Poussart et al., 2004; Poussart and Schrag, 2005), but the derived records are either of short‐duration, lack seasonal resolution or are prohibitively labor intensive to produce. Here, we show the first X‐ray microprobe synchrotron record of calcium (Ca) from a ringless Miliusa velutina tree from Thailand and use it to estimate the tree's age and growth history. The Ca age model agrees within ≤2 years of bomb‐radiocarbon age estimates and confirms that the cycles are seasonal. The amplitude of the Ca annual cycle is correlated significantly with growth and annual Ca maxima correlate with the amount of dry season rainfall. Synchrotron measurements are fast and producing sufficient numbers of replicated multi‐century tropical dendrochemical climate records now seems analytically feasible.
Grad‐Shafranov reconstruction: An overview
Authors: Sonnerup Bengt U. Ö. , Hasegawa Hiroshi , Teh Wai‐Leong , Hau Lin‐Ni
Published: September 2006

Grad‐Shafranov reconstruction is a data analysis tool for the reconstruction of two‐dimensional (2‐D) coherent field and flow structures from data collected as the structures move past an observing platform. To date, the method has been applied with good success to reconstruct magnetohydrostatic structures in Earth's magnetopause, in the solar wind, and in the geomagnetic tail, as the structures move past one or more observing spacecraft. However, with suitable modification, the reconstruction method can be extended to other applications, three of which are presented here: 2‐D magneto‐hydrodynamic structures in which dynamically important field‐aligned flow is present, 2‐D flow transverse to the magnetic field in the magnetospheric low‐latitude boundary layer, and 2‐D ordinary gasdynamic/hydrodynamic flow. We develop the fundamental equations required in the reconstructions, both for isotropic pressure and, in Appendix A, for the case where the pressures parallel and perpendicular to the magnetic field are described by the double‐polytropic laws. Applications to actual or simulated data are discussed but not included in the present paper.
Ab initio calculations on SF2 and its low-lying cationic states: Anharmonic Franck-Condon simulation of the uv photoelectron spectrum of SF2
Authors: Lee Edmond P. F. , Mok Daniel K. W. , Chau Foo-tim , Dyke John M.
Published: September 2006

Geometry optimization calculations were carried out on the X̃A11 state of SF2 and the X̃B12, ÃA12, B̃B22, C̃B22, D̃A12, and ẼA22 states of SF2+ employing the restricted-spin coupled-cluster single-double plus perturbative triple excitation [RCCSD(T)] method and basis sets of up to the augmented correlation-consistent polarized quintuple-zeta [aug-cc-pV(5+d)Z] quality. Effects of core electron (S 2s22p6 and F 1s2 electrons) correlation and basis set extension to the complete basis set limit on the computed minimum-energy geometries and relative electronic energies (adiabatic and vertical ionization energies) were investigated. RCCSD(T) potential energy functions (PEFs) were calculated for the X̃A11 state of SF2 and the low-lying states of SF2+ listed above employing the aug-cc-pV(5+d)Z and aug-cc-pV5Z basis sets for S and F, respectively. Anharmonic vibrational wave functions of these neutral and cationic states of SF2, and Franck-Condon (FC) factors of the lowest four one-electron allowed neutral photoionizations were computed employing the RCCSD(T) PEFs. Calculated FC factors with allowance for Duschinsky rotation and anharmonicity were used to simulate the first four photoelectron bands of SF2. The agreement between the simulated and observed first bands in the HeI photoelectron spectrum reported by de Leeuw et al. [Chem. Phys. 34, 287 (1978)] is excellent. Our calculations largely support assignments made by de Leeuw et al. on the higher ionization energy bands of SF2.
Experiment for measurements of the gas breakdown statistics by ramp voltage pulses
Authors: Marković V. Lj. , Stamenković S. N. , Gocić S. R. , Petrović Z. Lj.
Published: September 2006

In the first part of this article the electronic automatic system for the measurements of dynamic breakdown voltages Ub with linearly rising (ramp) pulses is presented. It generates the sequence of ramp pulses with subvoltage level Usub≈0 during the relaxation time τ of the tube, and the ramp pulses start from the static breakdown voltage Us, thus enabling the correct study of electrical breakdowns and relaxation in gases. In the second part the measurements in argon with and without a voltage during the off period of the pulse are analyzed. The influence of the subvoltage on the mean value of the breakdown voltage Ub¯ as a function of the rise rate k, on the statistical Ub distributions and on the afterglow kinetics is also discussed.
A dependence of carbon impurity transport coefficients on fuel ions in hydrogen and helium plasmas of Large Helical Device
Authors: Nozato H. , Morita S. , Goto M. , Takase Y. , Ejiri A. , Amano T. , Tanaka K. , Inagaki S. ,   LHD Experimental Group
Published: September 2006

Impurity transport of carbon has been studied using a new method combined carbon pellet injection with high-spatial resolution bremsstrahlung measurement on the Large Helical Device [A. Iiyoshi et al., Fusion Technol. 17, 169 (1990)]. The carbon pellets are injected into a steady phase in neutral beam heated discharges with a standard configuration of Rax=3.6m. The particle transport coefficients (diffusion coefficient D and convective velocity V) are inferred using a diffusive/convective model. The results are compared between hydrogen and helium plasmas. As a result, it is found that the analyzed D has a constant radial profile with almost closed values of 0.2m2∕s in both plasmas. On the other hand, the inward V is required only at the plasma outer region (ρ>0.6) where the electron density gradient exits, and the inward V in helium plasmas (−0.4m∕s at ρ=0.8 and ne∼4.0×1019m−3) is nearly half as much as that in hydrogen plasmas (−0.7m∕s). This difference of the inward V between hydrogen and helium plasmas suggests a dependence on the charge state of fuel ions predicted from neoclassical theory.
Ethernet based list processing controller for high speed data acquisition systems
Authors: Subramaniam E. T. , Rani Kusum , Ajith Kumar B. P. , Bhowmik R. K.
Published: September 2006

CAMAC standard crates and modules continue to be used for nuclear and high energy physics experiments and test setups. They provide unbeaten performance in high precision measurements, flexibility and simplicity in the design of modules. We have designed and fabricated a new type of CAMAC crate controller with list processing capability to maximize the data throughput, event rate handling capability, while simultaneously simplifying software development efforts for data acquisition systems, also maintain complete compliance with CAMAC standards and ability to utilize all existing CAMAC compliant modules. The throughput increase is achieved by eliminating the arbitration between the CAMAC crate controller and list processing modules by integrating the list processor (auxiliary crate controller) and the crate controller. The event rate handling capability is increased by advanced list processing techniques such as Q-stop and hit-pattern based list processing. The resulting ethernet based list processing crate controller can transfer up to 1700 kbytes/s reaching up to hundreds of kilo events̸s in 16bit transfer mode from CAMAC modules measured at the analysis engine end. This makes it suitable for use in experimental systems, where a large number of signals with high event rates need to be collected with high precision.
A semi-analytic model for localized variable charge dust acoustic waves
Authors: Tribeche Mouloud , Gougam Leila Ait , Aoutou Kamal
Published: September 2006

A semi-analytic model for nonlinear variable charge dust acoustic waves is outlined. It is shown that rarefactive variable charge dust acoustic solitons involving cusped density humps can exist. The effects of dust dynamics as well as equilibrium dust charge on these nonlinear localized structures are briefly discussed.
Orbital disproportionation and spin crossover as a pseudo Jahn-Teller effect
Authors: Garcia-Fernandez P. , Bersuker Isaac B. , Boggs James E.
Published: September 2006

It is shown that in systems with electronic half-closed-shell configurations of degenerate orbitals, e2 and t3 (which have totally symmetric charge distribution), ground state distortions from high-symmetry geometries may occur due to a strong pseudo Jahn-Teller effect (PJTE) in the excited states, resulting also in a novel phenomenon of PJT-induced spin crossover. There is no JTE neither in the ground state term nor in the excited terms (including degenerate terms) of these configurations but a strong PJT mixing between two excited states [(E1+A1)⊗e and (T12+T22)⊗e in the e2 and t3 cases, respectively] pushes down the lower term to cross the ground state of the undistorted system and to form the global minimum with a distorted geometry. The analysis of the electronic structure of this distorted configuration shows that it is accompanied by orbital disproportionation: instead of proportional population of all degenerate orbitals by one electron each (as in the ground state of the undistorted system that follows Hund’s rule), two electrons with opposite spins occupy one orbital, resulting in transformations of the type (eθ↑;eε↑)→(eθ↑;eθ↓) for e2 and (tx↑;ty↑;tz↑)→(tx↑;tx↓;tz↑) for t3 systems. Since the two geometry configurations, undistorted and distorted, appertain to different electronic terms that have different spin states, the formation of the global minimum with the distorted configuration is accompanied by a spin crossover. Distinguished from the known spin-crossover phenomenon in some transition metal compounds, the two states with different spin in the PJT-induced spin crossover have also different nuclear configurations, undistorted and distorted, that coexist with a relatively small energy difference. The change of configuration reduces significantly the rate of relaxation between the two states; the relaxation is further reduced by the lower spin-orbital coupling in the light-atom systems as compared with transition metal compounds. This means that there may be systems for which the switch between the two states (in both directions) under perturbations may be observed as a single-molecule phenomenon. Systems with half-closed-shell electronic configurations e2 and t3 are available in a variety of molecules from different classes, organic and inorganic; the theory is illustrated here by ab initio calculations for a series of molecular systems, including Si3, Si3C, CuF3, Na3, Si4, Na4, Na4−, and C603−, which are in agreement with the experimental data available.
New Aminophenylsilsesquioxanes—Synthesis, Properties, and Epoxy Nanocomposites
Authors: Takahashi Kunio , Sulaiman Santy , Katzenstein Joshua M. , Snoblen Stephanie , Laine Richard M.
Published: September 2006

New aminophenylsilsesquioxanes, dodecaaminophenylsilsesquioxane (NH2PhSiO1.5)12 (DAPS), and hexadecaaminooctaphenylsilsesquioxane ((NH2)2PhSiO1.5)8 (HDAPS), were prepared from dodecaphenylsilsesquioxane (PhSiO1.5)12 (DPS), and octaphenylsilsesquioxane (PhSiO1.5)8 (OPS), by nitration in fuming HNO3, followed by reduction with HCO2H/Et3N/Pd/C. The effects of the cage structure and numbers of NH2 groups on the chemical and physical properties of these compounds were compared with octaaminophenylsilsesquioxane (NH2PhSiO1.5)8 (OAPS), and analogous epoxy resin nanocomposites. The cage structure does not affect nitration patterns (primarily meta and para), but affects coefficients of thermal expansion (CTEs), likely because of overall crosslink densities and because of the epoxy tether structures joining cube vertices. CTEs as low as 25 ± 2 ppm°C–1 were found, perhaps the lowest reported for an unfilled epoxy resin. The thermal stabilities of synthesized HDAPS epoxy nanocomposites were 20–30°C lower than those made with OAPS. This result may be a consequence of less-complete curing due to gelation before stoichiometric curing, caused by the much higher crosslink densities in OAPS.
Chemiluminescence as a Probe of Polymer Oxidation
Authors: Blakey Idriss , Goss Ben , George Graeme
Published: September 2006

Many oxidation reactions of organic materials, including polymers, are accompanied by the emission of weak chemiluminescence (CL). From a study of the mechanism of this weak CL, it is shown that the time development of the CL intensity may provide the kinetics of the oxidation reaction and is thus a sensitive probe of the degradation of the material. The intensity of emission reflects the concentration of peroxidic species in the material. Whereas the kinetics of the oxidation may be described by a series of elementary, homogeneous free radical reactions, the use of imaging techniques has shown that the oxidation of polymers such as polypropylene is highly heterogeneous. A model that describes the oxidation as spreading through the material as an infection from a number of initiating sites is able to rationalize these observations and provide a new approach to the prediction of the useful lifetime of a polymeric material.
Carving Out Niches for Nanostructures: Implementation and Interplay of Building Blocks, Methods, and Tools
Authors: Harth Eva , Croce Teresa A.
Published: September 2006

The number and diversity of techniques to create well-defined polymeric architectures has set the foundation to reinvent macromolecular chemistry’s tenor. This development offers the chance to build refined structures with multifaceted, cross-disciplinary applications. We discuss a few advances in the design and development of selected nanoobjects with far-reaching potential. Herein, well-defined building blocks and introduced methods to establish three-dimensional architectures will be presented. Sequential attachment strategies and tools taken from biological chemistries achieve new levels of specificity.
The p47 GTPases
Igtp
and
Irgb10
map to the
Chlamydia trachomatis
susceptibility locus
Ctrq-3
and mediate cellular resistance in mice
Authors: Bernstein-Hanley Isaac , Coers Jörn , Balsara Zarine R. , Taylor Gregory A. , Starnbach Michael N. , Dietrich William F.
Published: September 2006

Infections caused by the bacteria
Chlamydia trachomatis
contribute to diverse pathologies in a variety of human populations. We previously used a systemic model of
C. trachomatis
infection in mice to map three quantitative trait loci that influence
in vivo
susceptibility differences between the C57BL/6J and C3H/HeJ inbred strains of mouse. One of these quantitative trait loci,
Ctrq-3
, influences an IFN-γ-dependent susceptibility difference in primary embryonic fibroblasts isolated from these strains. Here we use fine structure mapping in congenic fibroblasts carrying DNA from the susceptible parent to localize the effect of
Ctrq-3
to a 1.2-megabase interval of genomic DNA that contains
Irgb10
and
Igtp
, two members of the IFN-γ-inducible p47 family of GTPases. This class of proteins has been widely implicated in resistance to intracellular pathogens in mice. We analyzed expression of
Irgb10
and
Igtp
in parental and congenic embryonic fibroblasts treated with IFN-γ and found that relatively resistant fibroblasts express more
Irgb10
than relatively susceptible fibroblasts. However, we also found that abolishing the expression of either
Irgb10
or
Igtp
increases susceptibility of embryonic fibroblasts to
C. trachomatis
. Thus, we conclude that, although a difference in
Irgb10
expression is likely responsible for the effect of
Ctrq-3
on susceptibility to
C. trachomatis
, both genes play a role in intracellular resistance to
C. trachomatis
.
Evolution of protein structural classes and protein sequence families
Authors: Choi In-Geol , Kim Sung-Hou
Published: September 2006

In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four “allowed” regions of the protein structure space, “structural selection,” an important component of natural selection in gene evolution. Our studies on tracing the “common structural ancestor” for each protein sequence family of known structure suggest that: (
i
) recently emerged proteins belong mostly to three classes; (
ii
) the proteins that emerged earlier evolved to gain a new class; and (
iii
) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were “born” at different evolutionary times, not traceable to one or two ancestral proteins: “the multiple birth model” for the evolution of protein sequence families.
Identification of biomarkers that distinguish human papillomavirus (HPV)-positive versus HPV-negative head and neck cancers in a mouse model
Authors: Strati Katerina , Pitot Henry C. , Lambert Paul F.
Published: September 2006

Head and neck squamous cell carcinoma (HNSCC) is a leading cause of cancer mortality worldwide. Recent reports have associated a subset of HNSCC with high-risk human papillomaviruses (HPVs), particularly HPV16, the same subset of HPVs responsible for the majority of cervical and anogenital cancers. In this study we describe a mouse model for HPV-associated HNSCC that employs mice transgenic for the HPV16 oncogenes E6 and E7. In these mice, E6 and E7 induce aberrant epithelial proliferation and, in the presence of a chemical carcinogen, they increase dramatically the animal's susceptibility to HNSCC. The cancers arising in the HPV16-transgenic mice mirror the molecular and histopathological characteristics of human HPV-positive HNSCC that distinguish the latter from human HPV-negative HNSCC, including overexpression of p16 protein and formation of more basaloid cancers. This validated model of HPV-associated HNSCC provides the means to define the contributions of individual HPV oncogenes to HNSCC and to understand the molecular basis for the differing clinical properties of HPV-positive and HPV-negative human HNSCC. From this study, we identify minichromosome maintenance protein 7 (MCM7) and p16 as potentially useful biomarkers for HPV-positive head and neck cancer.
Progestin negatively affects hearing in aged women
Authors: Guimaraes Patricia , Frisina Susan T. , Mapes Frances , Tadros Sherif F. , Frisina D. Robert , Frisina Robert D.
Published: September 2006

Female hormone influences on auditory system aging are not completely understood. Because of widespread clinical use of hormone replacement therapy (HRT), it is critical to understand HRT effects on sensory systems. The present study retrospectively analyzed and compared hearing abilities among 124 postmenopausal women taking HRT, treated with estrogen and progestin (E+P;
n
= 32), estrogen alone (E;
n
= 30), and a third [non-hormone replacement therapy (NHRT;
n
= 62)] control group. Subjects were 60–86 years old and were matched for age and health status. All had relatively healthy medical histories and no significant noise exposure, middle-ear problems, or major surgeries. Hearing tests included pure-tone audiometry, tympanometry, distortion-product otoacoustic emissions (DPOAEs), transient otoacoustic emissions, and the hearing-in-noise test (HINT). The HINT tests for speech perception in background noise, the major complaint of hearing-impaired persons. Pure-tone thresholds in both ears were elevated (poorer) for the E+P relative to the E and control groups. For DPOAEs, the E+P group presented with lower (worse) levels than the E and control groups, with significant differences for both ears. For the HINT results, the E+P group had poorer speech perception than the E and control groups across all background noise speaker locations and in quiet. These findings suggest that the presence of P as a component of HRT results in poorer hearing abilities in aged women taking HRT, affecting both the peripheral (ear) and central (brain) auditory systems, and it interferes with the perception of speech in background noise.
Genotype turnover by reassortment of replication complex genes from avian Influenza A virus
Authors: Macken Catherine A. , Webby Richard J. , Bruno William J.
Published: September 2006

Reassortment among the RNA segments of Influenza A virus caused the two most recent human influenza pandemics; recently, reassortment has generated viral genotypes associated with outbreaks of avian H5N1 influenza in Asia and Europe. A statistical analysis has been developed for the systematic identification and characterization of reassortant viruses. The analysis was applied to the genes of the replication complex of 152 avian influenza A viruses isolated between 1966 and 2004 from predominantly terrestrial and domestic aquatic avian species. The results indicated that reassortment among these genes was pervasive throughout this period and throughout both the Eurasian and North American lineages of the virus. Evidence is presented that the circulating genotypes of the replication complex are being replaced continually by novel genotypes created by reassortment. No constraints for coordinated reassortment among genes of the replication complex were evident; rather, reassortment almost always proceeded one segment at a time. A maximum-likelihood estimate of the rate of reassortment was derived. For significantly diverged Asian avian influenza A viruses from the period 1991–2004, it was estimated that the median duration between creation of a new genotype and its next segment reassortment was 3 years. Reassortments that introduced previously unobserved influenza genetic material were detected. These findings point to substantial potential for rapid generation of novel avian influenza A viruses, emphasizing the importance of intensive surveillance of these host species in preparation for a possible pandemic.
Priming with DNA encoding E2 and boosting with E2 protein formulated with CpG oligodeoxynucleotides induces strong immune responses and protection from Bovine viral diarrhea virus in cattle
Authors: Liang Rong , van den Hurk Jan V. , Babiuk Lorne A. , van Drunen Littel-van den Hurk Sylvia
Published: September 2006

The objective of this study was to develop an optimal vaccination strategy forBovine viral diarrhea virus(BVDV). The E2 protein of BVDV plays a major protective role against BVDV infection. In order to be able to compare DNA, protein and DNA prime–protein boost regimens, a plasmid was constructed encoding a secreted form of the NADL strain E2 protein (pMASIA-tPAsΔE2). Furthermore, a pure secreted recombinant ΔE2 (rΔE2) protein was produced. The rΔE2 protein was formulated with a combination of Emulsigen and CpG oligodeoxynucleotide. Groups of calves were immunized with pMASIA-tPAsΔE2 or with rΔE2, or first with pMASIA-tPAsΔE2 and then with rΔE2. To evaluate the protection against BVDV, calves were challenged with BVDV strain NY-1 after the last immunization. Although all immunized calves developed humoral and cellular immune responses, the antibody responses in the DNA prime–protein boost group were stronger than those elicited by either the DNA vaccine or the protein vaccine. In particular, E2-specific antibody titres were enhanced significantly after boosting the ΔE2 DNA-primed calves with rΔE2 protein. Moreover, protection against BVDV challenge was obtained in the calves treated with the DNA prime–protein boost vaccination regimen, as shown by a significant reduction in weight loss, viral excretion and lymphopenia, compared with the unvaccinated calves and the animals immunized with the DNA or protein only. These results demonstrate the advantage of a DNA prime–protein boost vaccination approach in an outbred species.
Genetic variation of populations of Citrus psorosis virus
Authors: Martín Susana , García María Laura , Troisi Antonella , Rubio Luis , Legarreta Gonzalo , Grau Oscar , Alioto Daniela , Moreno Pedro , Guerri José
Published: September 2006

Citrus psorosis virus(CPsV), the type species of genusOphiovirus, has a segmented, negative-stranded RNA genome. We examined the population structure and genetic variation of CPsV in three coding regions located in RNAs 1, 2 and 3, analysing 22 isolates from Argentina, California, Florida, Italy and Spain. Most isolates contained a predominant sequence and some minor variants. Estimations of the genetic diversity and phylogenetic clustering of isolates disclosed two populations, one comprising isolates from Spain, Italy, Florida and California and the other including the Argentinean isolates. Isolate CPV-4 (from Texas) included for comparison was distant from both groups, suggesting that it belongs to a third group. The low ratio between non-synonymous and synonymous nucleotide substitutions indicated strong selection for amino acid sequence conservation, particularly in the coat protein gene. Incongruent phylogenetic relationships in different genomic regions suggested that exchange of genomic segments may have contributed to CPsV evolution.
Antiviral action of nitric oxide on dengue virus type 2 replication
Authors: Takhampunya Ratree , Padmanabhan R. , Ubol Sukathida
Published: September 2006

Recently, nitric oxide (NO) has been shown to suppress dengue virus (DENV) RNA and protein accumulation in infected cells. In this report, the potential target of the inhibitory effect of NO was studied at the molecular level. The NO donor,S-nitroso-N-acetylpenicillamine (SNAP), showed an inhibitory effect on RNA accumulation at around 8–14 h post-infection, which corresponded to the step of viral RNA synthesis in the DENV life cycle. The activity of the viral replicase isolated from SNAP-treated DENV-2-infected cells was suppressed significantly compared with that of the negative-controlN-acetyl-dl-penicillamine (NAP)-treated cells. Further investigations on the molecular target of NO action showed that the activity of recombinant DENV-2 NS5 in negative-strand RNA synthesis was affected in the presence of 5 mM SNAP inin vitroRNA-dependent RNA polymerase (RdRp) assays, whereas the RNA helicase activity of DENV-2 NS3 was not inhibited up to a concentration of 15 mM SNAP. These results suggest that the inhibitory effect of NO on DENV infection is partly via inhibition of the RdRp activity, which then downregulates viral RNA synthesis.
Analysis of the subgenomic RNAs and the small open reading frames of Beet black scorch virus
Authors: Yuan Xuefeng , Cao Yunhe , Xi Dehui , Guo Lihua , Han Chenggui , Li Dawei , Zhai Yafeng , Yu Jialin
Published: September 2006

A full-length cDNA of the genome ofBeet black scorch virus(BBSV), isolate Ningxia, was constructed and modified by site-directed mutagenesis to permitin vitrotranscription of mutant viral RNAs. Two subgenomic (sg) RNAs (sgRNA1 and sgRNA2) appeared during BBSV replication. Mutagenesis revealed that sgRNA1 transcription was initiated at G2209within the P82 polymerase subunit open reading frame (ORF) and that transcription of sgRNA2 began at G2526within the nested p7b/p5′ ORF. Initiation-codon shifting or premature termination of translation of the three ORFs (P7a, P7b and P5′) encoded by sgRNA1 indicated that each of the genes was required for localized movement, accumulation of viral RNAs and formation of local lesions on the leaves ofChenopodium amaranticolor. Microscopic observations of the distribution of green fluorescent protein fused to the N-terminal portion of the capsid protein provided additional evidence that the P7a, P7b and P5′ proteins are each required for cell-to-cell movement. In contrast, elimination of sgRNA2 showed that the BBSV coat protein was not required for viral RNA accumulation or the appearance of local lesions onC. amaranticolor. In addition, disruption of the small P5 ORF previously predicted by computer analysis to originate at the C terminus of the P82 ORF had no effect on disease phenotype, suggesting that this ORF may represent a cryptic, non-essential gene. These results show that BBSV has a novel cell-to-cell movement protein organization that differs in size and sequence from that of other viruses.
A minimal region in the NTPase/helicase domain of the TGBp1 plant virus movement protein is responsible for ATPase activity and cooperative RNA binding
Authors: Leshchiner Anna D. , Solovyev Andrey G. , Morozov Sergey Yu. , Kalinina Natalia O.
Published: September 2006

The TGBp1 protein, encoded in the genomes of a number of plant virus genera as the first gene of the ‘triple gene block’, possesses an NTPase/helicase domain characterized by seven conserved sequence motifs. It has been shown that the TGBp1 NTPase/helicase domain exhibits NTPase, RNA helicase and RNA-binding activities. In this paper, we have analysed a series of deletion and point mutants in the TGBp1 proteins encoded by Potato virus X (PVX, genus Potexvirus) and Poa semilatent virus (PSLV, genus Hordeivirus) to map functional regions responsible for their biochemical activities in vitro. It was found that, in both PVX and PSLV, the N-terminal part of the TGBp1 NTPase/helicase domain comprising conserved motifs I, Ia and II was sufficient for ATP hydrolysis, RNA binding and homologous protein–protein interactions. Point mutations in a single conserved basic amino acid residue upstream of motif I had little effect on the activities of C-terminally truncated mutants of both TGBp1 proteins. However, when introduced into the full-length NTPase/helicase domains, these mutations caused a substantial decrease in the ATPase activity of the protein, suggesting that the conserved basic amino acid residue upstream of motif I was required to maintain a reaction-competent conformation of the TGBp1 ATPase active site.
Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family
Authors: Habayeb Mazen S. , Ekengren Sophia K. , Hultmark Dan
Published: September 2006

Several viruses, including picornaviruses, are known to establish persistent infections, but the mechanisms involved are poorly understood. Here, a novel picorna-like virus, Nora virus, which causes a persistent infection in Drosophila melanogaster, is described. It has a single-stranded, positive-sense genomic RNA of 11879 nt, followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RNA-dependent RNA polymerase and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viral sequences. The unusual sequence and genome organization in Nora virus suggest that it belongs to a new family of picorna-like viruses. Surprisingly, Nora virus could be detected in all tested D. melanogaster laboratory stocks, as well as in wild-caught material. The viral titres varied enormously, between 104 and 1010 viral genomes per fly in different stocks, without causing obvious pathological effects. The virus was also found in Drosophila simulans, a close relative of D. melanogaster, but not in more distantly related Drosophila species. It will now be possible to use Drosophila genetics to study the factors that control this persistent infection.
Genetic diversity and phylogeography of cassava mosaic viruses in Kenya
Authors: Bull Simon E. , Briddon Rob W. , Sserubombwe William S. , Ngugi Kahiu , Markham Peter G. , Stanley John
Published: September 2006

Cassava is a major factor in food security across sub-Saharan Africa. However, the crop is susceptible to losses due to biotic stresses, in particular to viruses of the genus Begomovirus (family Geminiviridae) that cause cassava mosaic disease (CMD). During the 1990s, an epidemic of CMD severely hindered cassava production across eastern and central Africa. A significant influence on the appearance of virus epidemics is virus diversity. Here, a survey of the genetic diversity of CMD-associated begomoviruses across the major cassava-growing areas of Kenya is described. Because an initial PCR-restriction fragment-length polymorphism analysis identified a much greater diversity of viruses than assumed previously, representative members of the population were characterized by sequence analysis. The full-length sequences of 109 components (68 DNA-A and 41 DNA-B) were determined, representing isolates of East African cassava mosaic virus and East African cassava mosaic Zanzibar virus, as well as a novel begomovirus species for which the name East African cassava mosaic Kenya virus is proposed. The DNA-B components were much less diverse than their corresponding DNA-A components, but nonetheless segregated into western and eastern (coastal) groups. All virus species and strains encountered showed distinct geographical distributions, highlighting the importance of preventing both the movement of viruses between these regions and the importation of the disease from adjacent countries and islands in the Indian Ocean that would undoubtedly encourage further diversification.
Role of the yellow fever virus structural protein genes in viral dissemination from the Aedes aegypti mosquito midgut
Authors: McElroy Kate L. , Tsetsarkin Konstantin A. , Vanlandingham Dana L. , Higgs Stephen
Published: September 2006

Live-attenuated virus vaccines are key components in controlling arboviral diseases, but they must not disseminate in or be transmitted by mosquito vectors. Although the cycles in which many mosquito-borne viruses are transmitted are well understood, the role of viral genetics in these processes has not been fully elucidated. Yellow fever virus (YFV) is an important arbovirus and the prototype member of the family Flaviviridae. Here, YFV was used in Aedes aegypti mosquitoes as a model to investigate the genetic basis of infection and dissemination in mosquitoes. Viruses derived from infectious clones and chimeric viruses with defined sequential manipulations were used to investigate the influence of specific sequences within the membrane and envelope structural protein genes on dissemination of virus from the mosquito midgut. Substitution of domain III of the envelope protein from a midgut-restricted YFV into a wild-type YFV resulted in a marked decrease in virus dissemination, suggesting an important role for domain III in this process. However, synergism between elements within the flavivirus structural and non-structural protein genes may be necessary for efficient virus escape from the mosquito midgut.
Development of the dodecahedral penton particle from adenovirus 3 for therapeutic application
Authors: Fuschiotti P. , Fender P. , Schoehn G. , Conway J. F.
Published: September 2006

The subviral dodecahedral particle of adenovirus 3, which assembles spontaneously in insect cells expressing the viral penton base protein, shows promise as a vector for drug delivery. Its ability to gain cell entry has been demonstrated and recent structural analysis has outlined details of the interfaces between penton bases and the importance of proteolysis of the penton base N terminus for assembly, providing a basis for understanding particle assembly and stability. Here, work in manipulating the assembly status of the dodecahedron by changing buffer conditions and subsequent success in passively encapsidating a marker molecule is described. This represents an important stage towards development of the dodecahedral particle for use as a delivery vehicle capable of targeting therapeutic molecules to specific cell types.
Preferential association of Hepatitis C virus with apolipoprotein B48-containing lipoproteins
Authors: Diaz Olivier , Delers François , Maynard Marianne , Demignot Sylvie , Zoulim Fabien , Chambaz Jean , Trépo Christian , Lotteau Vincent , André Patrice
Published: September 2006

Hepatitis C virus (HCV) in cell culture has a density comparable to that of other members of the family Flaviviridae, whereas in vivo infectious particles are found partially in low-density fractions, associated with triacylglycerol (TG)-rich lipoproteins (TRLs). In the blood of infected patients, HCV circulates as heterogeneous particles, among which are lipo-viroparticles (LVPs), globular particles rich in TG and containing viral capsid and RNA. The dual viral and lipoprotein nature of LVPs was addressed further with respect to apolipoprotein composition and post-prandial dynamic lipid changes. The TRLs exchangeable apoE, -CII and -CIII, but not the high-density lipoprotein apoA-II, were present on LVPs, as well as the viral envelope proteins. apoB100 and-B48, the two isoforms of the non-exchangeable apoB, were represented equally on LVPs, despite the fact that apoB48 was barely detectable in the plasma of these fasting patients. This indicates that a significant fraction of plasma HCV was associated with apoB48-containing LVPs. Furthermore, LVPs were enriched dramatically and rapidly in triglycerides after a fat meal. As apoB48 is synthesized exclusively by the intestine, these data highlight the preferential association of HCV with chylomicrons, the intestine-derived TRLs. These data raise the question of the contribution of the intestine to the viral load and suggest that the virus could take advantage of TRL assembly and secretion for its own production and of TRL fate to be delivered to the liver.