bluuebunny/crossref_metadata_2025 huggingface dataset:
Holocene Alluvial Stratigraphy in the Upper Susquehanna River Basin, New York
Authors: Scully Richard W. , Arnold Richard W.
Published: December 2004

Two alluvial terraces and the present flood plain were studied at two locations along the Susquehanna and Unadilla Rivers in south-central New York state. They have formed since deglaciation and incision of the stream channels into the valley train deposits. The higher terrace has noncumulative soil profiles with well-developed color B horizons predominantly of silt loam and very fine sandy loam. The terrace is weathered to a degree similar to nearby glacial outwash terraces that have caps of similarly textured sediments. Incision that produced the terrace occurred before 9705 ± 130 yr B.P. The lower terrace is characterized by relatively thick, vertical-accretion deposits of silt loam that contain sequences of thin, buried A, color B, and C horizons. They were formed between about 3240 ± 110 (14C data of soil humin) and 235 ± 80 yr B.P. Deposits above the 235 ± 80 yr B.P. stratum are unweathered. The soil stratigraphy and 14C dates of soil humin from buried A horizons are surprisingly well correlated between sites. Most sediments of the present flood plain have been deposited since 1120 ± 80 yr B.P. Incipient A horizons and oxidation of inherited organic matter in the subsoil are the only evidence of pedogenesis in the flood-plain deposits that are older than 275 ± 80 yr B.P. The most recent flood-plain fill deposited since then is unaltered. These youngest sediments of the flood plain along with the youngest veneer of vertical-accretion deposits on the lowest terrace are associated with an increased rate of deposition largely attributable to clearing of the forests by settlers, beginning in the late 1700s. Comparison of the alluvial stratigraphy with the radiocarbon-dated pollen stratigraphy of southwestern New York (Miller 1973) reveals some apparent time correlations between alluvial events and vegetation changes. This gives reason to speculate that climatic change or forest catastrophes such as disease or drought are causes of some of the alluvial events.
Old Crow Tephra Found at the Palisades of the Yukon, Alaska
Authors: Begét James , Edwards Mary , Hopkins David , Keskinen Mary , Kukla George
Published: December 2004

A 20-cm-thick volcanic ash layer at the Palisades along the Yukon River is geochemically correlated with the Old Crow tephra. A buried organic and wood-rich layer above the Old Crow tephra probably records the last interglaciation. The recognition of the Old Crow tephra provides the first chronologic information on the age of the thick sequence of Pleistocene sediments at the Palisades, an important ice-age mammal site in central Alaska and a key locality for the reconstruction of the history of the Yukon River and the last interglaciation in central Alaska.
Identification of a putative p53 binding sequence within the human mitochondrial genome
Authors: Heyne K. , Mannebach S. , Wuertz E. , Knaup K.X. , Mahyar-Roemer M. , Roemer K.
Published: December 2004

A small fraction of the total cellular amount of nuclear transcription factor p53 seems to be located at and within mitochondria. Transcription factors of the steroid receptor superfamily that, like p53, lack a classical mitochondrial leader sequence are nonetheless imported into mitochondria where they regulate mtDNA transcription through binding to specific recognition sequences. Here, we examined seven candidate sequences from the human mitochondrial genome with similarity to the consensus p53 binding motif. Two imperfect half‐sites at coordinate 1553 with homology to the nuclear IGF‐BP3 box A binding sequence are demonstrated to confer responsivity to p53 and the p53 relatives p73α and β in the context of the cell nucleus. Mitochondrial p53 may thus bind directly to mtDNA and, perhaps, be involved in the regulation of mitochondrial transcription/replication.
Identification of a cysteine residue important for the ATPase activity of C. elegans fidgetin homologue
Authors: Yakushiji Yasufumi , Yamanaka Kunitoshi , Ogura Teru
Published: December 2004

Based on the amino acid alignment, Caenorhabditis elegans F32D1.1 was identified to be a homologue of the mammalian fidgetin. We produced and purified the F32D1.1 protein by using a baculovirus‐expression system. F32D1.1 has an ATPase activity, which is sensitive to N‐ethylmaleimide. K
m and V
max for the ATPase activity of F32D1.1 were estimated to be 0.44 mM and 225 nmol/mg/min, respectively. When the cysteine at the position of 368 was mutated to alanine, the ATPase activity was greatly decreased; V
max was decreased to one‐sixth, while K
m remained similar. These results suggest that the unique position of cysteine 368, located immediately downstream of the Walker A motif, plays an important role in the ATP hydrolysis process of C. elegans F32D1.1 protein.
Factors associated with inadequate prenatal care in Ecuadorian women
Authors: Paredes I. , Hidalgo L. , Chedraui P. , Palma J. , Eugenio J.
Published: December 2004

Background

Although inadequate prenatal care has been associated with adverse perinatal outcomes, reports on the factors associated with poor prenatal care in developing Latin American countries are scarce.

Objective

To determine factors associated with inadequate prenatal care among women from low socioeconomic circumstances.

Method

Women delivered after a pregnancy duration of more than 20 weeks at the Enrique C. Sotomayor Obstetrics and Gynecology Hospital, Guayaquil, Ecuador, were surveyed. The questionnaire collected sociodemographic data and reasons for having inadequate prenatal care. Adequacy of prenatal care was measured with the Kessner index and correlated to the sociodemographic data.

Results

During the study period, 1016 pregnant women were surveyed. Among them, there were adolescents (23.7%), primigravidas (30.8%), and women with a high‐risk pregnancy (29.3%). According to the Kessner index, prenatal care was considered adequate or inadequate in 24.5% and 75.5% of cases, respectively. Knowledge regarding the importance of adequate prenatal care and the effects of poor prenatal care was lower among women who had received inadequate prenatal care. The women that were considered to have had adequate prenatal care had at least one visit, and they were more often cared for by a specialist than women who considered having inadequate prenatal care. The three most important reasons associated to inadequate prenatal care in this series (n=767), were economic difficulties having to care for a small child, and transportation difficulties. Logistic regression analysis determined that women with undesired pregnancies who resided in rural areas and were para 5 or higher had an increased risk of inadequate prenatal care. On the other hand, an adverse outcome to a prior pregnancy (abortion, intrauterine fetal demise, or ectopic pregnancy) decreased this risk. Marital status and educational level were confounding factors.

Conclusions

Although prenatal care at our institution is free, adequacy was thought to be low. The main factors associated with poor prenatal care were mostly conditions related to poverty.
Longitudinal variability of equatorial plasma bubbles observed by DMSP and ROCSAT‐1
Authors: Burke W. J. , Gentile L. C. , Huang C. Y. , Valladares C. E. , Su S. Y.
Published: December 2004

We compare observations of equatorial plasma bubbles (EPBs) by polar‐orbiting satellites of the Defense Meteorological Satellite Program (DMSP) with plasma density measurements from the Republic of China Satellite (ROCSAT‐1) in a low‐inclination orbit. DMSP data were acquired in the evening sector at low magnetic latitudes between 1989 and 2002. ROCSAT‐1 plasma densities were measured in March and April of 2000 and 2002. Observations of individual EPBs detected by both ROCSAT‐1 and DMSP were well correlated when satellite orbital paths crossed the same longitude within approximately ±15 min. We compiled a statistical database of ROCSAT‐1 EPB occurrence rates sorted by magnetic local time (MLT), magnetic latitude, and geographic longitude. The rate of ROCSAT‐1 EPB encounters at topside altitudes rose rapidly after 1930 MLT and peaked between 2000 and 2200 MLT, close to the orbital planes of DMSP F12, F14, and F15. EPB encounter rates have Gaussian distributions centered on the magnetic equator with half widths of ∼8°. Longitudinal distributions observed by ROCSAT‐1 and DMSP are qualitatively similar, with both showing significantly fewer occurrences than expected near the west coast of South America. A chain of GPS receivers extending from Colombia to Chile measured a west‐to‐east gradient in S4 indices that independently confirms the existence of a steep longitudinal gradient in EPB occurrence rates. We suggest that precipitation of energetic particles from the inner radiation belt causes the dearth of EPBs. Enhancements in the postsunset ionospheric conductance near the South Atlantic Anomaly cause a decrease in growth rate for the generalized Rayleigh‐Taylor instability. Results indicate substantial agreement between ROCSAT‐1 and DMSP observations and provide new insights on EPB phenomenology.
Open‐boundary modal analysis: Interpolation, extrapolation, and filtering
Authors: Lekien F. , Coulliette C. , Bank R. , Marsden J.
Published: December 2004

Increasingly accurate remote sensing techniques are available today, and methods such as modal analysis are used to transform, interpolate, and regularize the measured velocity fields. Until recently, the modes used did not incorporate flow across an open boundary of the domain. Open boundaries are an important concept when the domain is not completely closed by a shoreline. Previous modal analysis methods, such as those of Lipphardt et al. (2000), project the data onto closed‐boundary modes, and then add a zero‐order mode to simulate flow across the boundary. Chu et al. (2003) propose an alternative where the modes are constrained by a prescribed boundary condition. These methods require an a priori knowledge of the normal velocity at the open boundary. This flux must be extrapolated from the data or extracted from a numerical model of a larger‐scale domain, increasing the complexity of the operation. In addition, such methods make it difficult to add a threshold on the length scale of open‐boundary processes. Moreover, the boundary condition changes in time, and the computation of all or some modes must be done at each time step. Hence real‐time applications, where robustness and efficiency are key factors, were hardly practical. We present an improved procedure in which we add scalable boundary modes to the set of eigenfunctions. The end result of open‐boundary modal analysis (OMA) is a set of time and data independent eigenfunctions that can be used to interpolate, extrapolate and filter flows on an arbitrary domain with or without flow through segments of the boundary. The modes depend only on the geometry and do not change in time.
Mixed layer depth over the global ocean: An examination of profile data and a profile‐based climatology
Authors: de Boyer Montégut Clément , Madec Gurvan , Fischer Albert S. , Lazar Alban , Iudicone Daniele
Published: December 2004

A new 2° resolution global climatology of the mixed layer depth (MLD) based on individual profiles is constructed. Previous global climatologies have been based on temperature or density‐gridded climatologies. The criterion selected is a threshold value of temperature or density from a near‐surface value at 10 m depth (ΔT = 0.2°C or Δσθ = 0.03 kg m−3). A validation of the temperature criterion on moored time series data shows that the method is successful at following the base of the mixed layer. In particular, the first spring restratification is better captured than with a more commonly used larger criteria. In addition, we show that for a given 0.2°C criterion, the MLD estimated from averaged profiles results in a shallow bias of 25% compared to the MLD estimated from individual profiles. A new global seasonal estimation of barrier layer thickness is also provided. An interesting result is the prevalence in mid‐ and high‐latitude winter hemispheres of vertically density‐compensated layers, creating an isopycnal but not mixed layer. Consequently, we propose an optimal estimate of MLD based on both temperature and density data. An independent validation of the maximum annual MLD with oxygen data shows that this oxygen estimate may be biased in regions of Ekman pumping or strong biological activity. Significant differences are shown compared to previous climatologies. The timing of the seasonal cycle of the mixed layer is shifted earlier in the year, and the maximum MLD captures finer structures and is shallower. These results are discussed in light of the different approaches and the choice of criterion.
GOES 8 aerosol optical thickness assimilation in a mesoscale model: Online integration of aerosol radiative effects
Authors: Wang Jun , Nair U. S. , Christopher Sundar A.
Published: December 2004

To investigate the importance of aerosol radiative effects in the troposphere, numerical simulation of a dust event during the Puerto Rico Dust Experiment is presented by using the Colorado State University Regional Atmospheric Modeling System (RAMS). Through assimilation of geostationary satellite‐derived aerosol optical thickness (AOT) into the RAMS, spatial and temporal aerosol distribution is optimally characterized, facilitating direct comparison with surface observations of downwelling radiative energy fluxes and 2 m air temperature that is not possible with a free‐running mesoscale model. Two simulations with and without consideration of aerosol radiative effects are performed. Comparisons against observations show that direct online integration of aerosol radiative effects produces realistic downwelling shortwave and longwave fluxes at the surface but minimal improvement on 2 m air temperature at the observation location. Numerical simulations show that for the dust loading considered in this study (AOT = 0.45 at 0.67 μm), if the dust radiative effects are not properly represented, the uncertainty in the simulated AOT is about ±5 to ±10%, the surface radiative energy is overestimated by 30–40 W m−2 during the day and underestimated by 10 W m−2 during the night, and the bias in air temperatures near the surface could be up to ±0.5°C, though these biases also depend on local time, AOT values, and surface properties. The results from this study demonstrate that the assimilation of satellite aerosol retrievals not only improves the aerosol forecasts but also has the potential to reduce the uncertainties in modeling the surface energy budget and other associated atmospheric processes.
Energy enhancements of gravity waves in the Antarctic lower stratosphere associated with variations in the polar vortex and tropospheric disturbances
Authors: Yoshiki Motoyoshi , Kizu Nobuhiko , Sato Kaoru
Published: December 2004

Gravity waves in the Antarctic lower stratosphere are examined using original operational radiosonde data obtained at Syowa Station (69.0°S, 39.6°E) with fine vertical resolution. In the lower stratosphere the temporal variation in gravity wave energy depends on height. In the height region of 13–15 km, just above the tropopause, the seasonal variation in gravity wave energy is not evident. The wave energy is rather enhanced when the absolute value of potential vorticity in the upper troposphere becomes small over Syowa Station. This fact implies that tropospheric disturbances affect the dynamical processes of gravity waves there. However, the gravity wave energy in the height region of 15–25 km shows clear seasonal variation having a maximum in spring. The time variation in gravity wave energy is examined in detail in terms of the polar vortex by using the equivalent latitude coordinate. Energy enhancements occur when the edge of the polar vortex approaches Syowa Station, and the enhancements are especially large when the polar vortex breaks down in spring. These results suggest that height variation in the background atmosphere leads to the difference of wave characteristics between the two height regions. The enhancements of wave energy are partly explained as modification of the wave structure by the background wind speed and the static stability, but it is also likely that enhancements of wave activity contribute to the energy enhancement at the edge of the polar vortex in spring.
Gated four-probe measurements on pentacene thin-film transistors: Contact resistance as a function of gate voltage and temperature
Authors: Pesavento Paul V. , Chesterfield Reid J. , Newman Christopher R. , Frisbie C. Daniel
Published: December 2004

We describe gated four-probe measurements designed to measure contact resistance in pentacene-based organic thin-film transistors (OTFTs). The devices consisted of metal source and drain electrodes contacting a 300-Å-thick pentacene film thermally deposited on Al2O3 or SiO2 dielectrics with a p-doped Si substrate serving as the gate electrode. Voltage-sensing leads extending into the source-drain channel were used to monitor potentials in the pentacene film while passing current during drain voltage (VD) or gate voltage (VG) sweeps. We investigated the potential profiles as a function of contact metallurgy (Pt, Au, Ag, and Ca), substrate chemistry, VG, and temperature. The contact-corrected linear hole mobilities were as high as 1.75cm2∕Vs and the film sheet resistance and specific contact resistance were as low as 600kΩ∕◻ and 1.3kΩ-cm, respectively, at high gate voltages. In the temperature range of 50–200K, the pentacene OTFTs displayed an activated behavior with activation energies of 15–30meV. Importantly, the activation energy associated with the contact resistance showed no dependence on contact metal type at high gate voltage. Also, the activation energies of the contact resistance and film resistance were approximately the same. Above approximately 200K and below 50K, the mobility was essentially temperature independent.
Polarization filtering by nonpolar M-plane GaN films on LiAlO2
Authors: Misra Pranob , Sun, Yue Jun , Brandt Oliver , Grahn Holger T.
Published: December 2004

The anisotropic optical properties and polarization filtering are investigated for strained M-plane GaN films as a function of the angle of the in-plane polarization vector. Since the c axis of the underlying wurtzite crystal structure lies in the film plane, its symmetry is reduced in comparison to conventional C-plane films, giving rise to an in-plane polarization anisotropy. This anisotropy is further enhanced by the anisotropic compressive in-plane strain, which occurs due to the lattice mismatch between the GaN film and the substrate LiAlO2. In addition to linear birefringence, the film also exhibits linear dichroism, resulting in a polarization filtering of an incident, linearly polarized light beam after transmission. This filtering manifests itself as a rotation of the polarization vector towards the c axis and can be as large as 80°. We compare the measured polarization rotation with calculated values taking into account the birefringence of the GaN film. In the energy range where the filtering is most effective, the birefringence almost disappears and can therefore be neglected for the determination of the rotation angle. Finally, the rotation, which is determined by the transmittance for the two orthogonal polarization directions, can be very well approximated by the product of the film thickness and the difference of the absorption coefficients for the two polarization directions.
Island growth as a growth mode in atomic layer deposition: A phenomenological model
Authors: Puurunen Riikka L. , Vandervorst Wilfried
Published: December 2004

Atomic layer deposition (ALD) has recently gained world-wide attention because of its suitability for the fabrication of conformal material layers with thickness in the nanometer range. Although the principles of ALD were realized about 40 years ago, the description of many physicochemical processes that occur during ALD growth is still under development. A constant amount of material deposited in an ALD reaction cycle, that is, growth-per-cycle (GPC), has been a paradigm in ALD through decades. The GPC may vary, however, especially in the beginning of the ALD growth. In this work, a division of ALD processes to four classes is proposed, on the basis of how the GPC varies with the number of ALD reaction cycles: linear growth, substrate-enhanced growth, and substrate-inhibited growth of type 1 and type 2. Island growth is identified as a likely origin for type 2 substrate-inhibited growth, where the GPC increases and goes through a maximum before it settles to a constant value characteristic of a steady growth. A simple phenomenological model is developed to describe island growth in ALD. The model assumes that the substrate is unreactive with the ALD reactants, except for reactive defects. ALD growth is assumed to proceed symmetrically from the defects, resulting islands of a conical shape. Random deposition is the growth mode on the islands. The model allows the simulation of GPC curves, surface fraction curves, and surface roughness, with physically significant parameters. When the model is applied to the zirconium tetrachloride/water and the trimethylaluminum/water ALD processes on hydrogen-terminated silicon, the calculated GPC curves and surface fractions agree with the experiments. The island growth model can be used to assess the occurrence of island growth, the size of islands formed, and point of formation of a continuous ALD-grown film. The benefits and limitations of the model and the general characteristics of type 2 substrate-inhibited ALD are discussed.
Correlation of properties with preferred orientation in coagulated and stretch-aligned single-wall carbon nanotubes
Authors: Badaire Stéphane , Pichot Vincent , Zakri Cécile , Poulin Philippe , Launois Pascale , Vavro Juraj , Guthy Csaba , Chen Michelle , Fischer John E.
Published: December 2004

We report structure-property correlations in single-wall carbon nanotube (SWNT) fibers, among electrical, thermal, and chemical parameters with respect to stretch-induced preferential SWNT alignment along the fiber axis. Purified HiPco (high-pressure CO) conversion tubes are dispersed with the aid of an anionic surfactant and coagulated in the co-flowing stream of an adsorbing polymer. The fibers are then dried, rewetted under tensile load, and redried to improve the alignment. Complete removal of the polymer was assured by annealing in hydrogen at 1000°C. The degree of alignment was determined by x-ray scattering from individual fibers using a two-dimensional detector. The half width at half maximum describing the axially symmetric distribution of SWNT axes decreases linearly from 27.5° in the initial extruded fiber to 14.5° after stretching by 80%. The electrical resistivity ρ at 300K decreases overall by a factor ∼4 with stretching, for both as-spun composite and polymer-free annealed fibers. However, the temperature dependence ρ(T) is markedly different for the two, implying different electron-transport mechanisms with and without the polymer. Thermal conductivity also improves with increasing alignment, while the absolute values are limited by the disordered network of finite length tubes and bundles. Comparisons are made with results from similar fibers spun from oleum and with magnetically aligned buckypapers.
Mössbauer transmission and back scattered conversion electron study of Fe nanowires encapsulated in multiwalled carbon nanotubes
Authors: Ruskov T. , Asenov S. , Spirov I. , Garcia C. , Mönch I. , Graff A. , Kozhuharova R. , Leonhardt A. , Mühl T. , Ritschel M. , Schneider C. M. , Groudeva-Zotova S.
Published: December 2004

Fe 57 transmission Mössbauer spectroscopy (TMS) and back scattered conversion electron Mössbauer spectroscopy (CEMS) measurements were carried out on Fe-filled multiwalled carbon nanotubes (Fe-MWCNTs) grown by chemical vapor deposition with ferrocene as precursor. Samples of Fe-MWCNTs material deposited on the inner wall of the quartz tube reactor and samples of aligned Fe-MWCNTs grown perpendicularly to the oxidized Si substrate were characterised by the TMS method. The data show that Fe phases encapsulated within the carbon nanotubes comprise α-Fe, γ-Fe, and Fe3C in different percentage ratio depending on the sample preparation. These results are in a good accordance with the previously measured magnetic characteristics and with the structural data found by x-ray diffraction as well by selected area electron diffraction methods and allow a new complementary characterization of the Fe(Fe-alloy)-MWCNT systems. The CEMS method applied for the characterization of metal containing MWCNTs reveals that close to the top surface of the aligned Fe-MWCNTs samples only the γ-Fe phase is found. This technique shows an additional potential for further investigation of the spatial distribution of the crystalline phases in the depth of aligned Fe-MWCNT samples.
Real-time observation of initial stages of copper film growth on silicon oxide using reflection high-energy electron diffraction
Authors: Drotar Jason T. , Lu T.-M. , Wang G.-C.
Published: December 2004

We have studied, in real time, the evolution of a thin (less than 200Å) copper film deposited onto an oxidized silicon surface using reflection high-energy electron diffraction. We show that quantitative measurements of island size and shape as functions of time are possible and the results are presented. While the film texture is initially random, texture competition leads to an absence of the low-energy (111) and (200) oriented grains for later times. It is also found that the film surface is composed of facets that increase in size with time. This behavior is explained in terms of facet coalescence.
Mechanisms of the refractive index change in femtosecond laser-irradiated Au3+-doped silicate glasses
Authors: Zhao Quan-Zhong , Qiu Jian-Rong , Jiang Xiong-Wei , Zhao Chong-Jun , Zhu Cong-Shan
Published: December 2004

We report on the refractive index change in Au3+-doped silicate glasses irradiated by a femtosecond laser and successive heat treatment. The refractive index of the irradiated area increased after the femtosecond laser irradiation and decreased with increasing annealing temperature up to 450°C and then increased again with increasing annealing temperature. Absorption spectra of the glass samples before and after femtosecond laser irradiation and after further annealing manifested the formation of color centers after laser irradiation, disappearance of color centers after annealing at 300°C, and precipitation of gold nanoparticles after annealing at high temperature. The mechanisms of the observed phenomena are discussed.
Hydrogen diffusion at moderate temperatures in p-type Czochralski silicon
Authors: Huang Y. L. , Ma Y. , Job R. , Ulyashin A. G.
Published: December 2004

In plasma-hydrogenated p-type Czochralski silicon, rapid thermal donor (TD) formation is achieved, resulting from the catalytic support of hydrogen. The n-type counter doping by TD leads to a p-n junction formation. A simple method for the indirect determination of the diffusivity of hydrogen via applying the spreading resistance probe measurements is presented. Hydrogen diffusion in silicon during both plasma hydrogenation and post-hydrogenation annealing is investigated. The impact of the hydrogenation duration, annealing temperature, and resistivity of the silicon wafers on the hydrogen diffusion is discussed. Diffusivities of hydrogen are determined in the temperature range 270–450°C. The activation energy for the hydrogen diffusion is deduced to be 1.23eV. The diffusion of hydrogen is interpreted within the framework of a trap-limited diffusion mechanism. Oxygen and hydrogen are found to be the main traps.
Comparison between radical- and energetic ion-induced growth of SiCxNy films in plasma immersion ion implantation and deposition
Authors: Afanasyev-Charkin I. V. , Nastasi M.
Published: December 2004

Ternary SiCxNy compounds are materials with some remarkable properties such as high oxidation resistance and high hardness. In this work we compare the properties of SiCxNy films obtained using radio-frequency (rf) and pulsed glow discharge (PGD) plasmas with combinations of SiH4, C2H2, N2, and Ar source gases. The pulsed voltage used for the rf deposition was 200V and for the PGD deposition it was 4kV. During the rf growth, the growth takes place mostly by attaching neutral radicals to form chemical bonds. In the PGD method, the deposition takes place by subplantation and surface activation by energetic ions. We show that in the case of low-energy RF deposition, a high relative number of C–N bonds with sp3 hybridization is formed and very few Si–C bonds can be observed. Apparently the growth of carbon nitride and silicon nitride networks takes place independently. This indicates that SiH3 radicals attach to the dangling bonds of silicon and nitrogen, whereas C2H radicals attach to the dangling bonds of carbon and nitrogen. During pulsed glow discharge deposition, bonds between all three components are formed apparently by means of subplantation and damage-induced disorder. The hardness of the PGD films exceed that of the RF films, showing that to form a dense SiCxNy film one has to either supply energy during the growth of the films by heating the substrate, as in the case of chemical vapor deposition or by using energetic ions.
Residual stresses in sputter-deposited copper/330 stainless steel multilayers
Authors: Zhang X. , Misra A.
Published: December 2004

The evolution of residual stresses as a function of bilayer period from 10nmto1μm in sputter-deposited Cu/330 stainless-steel (SS) multilayered films is evaluated by the substrate curvature technique. The multilayer stress evolution is compared with residual stresses in single layer Cu films and single layer 330 SS films, also measured by substrate curvature technique, with respective film thicknesses varying from 5to500nm. Both single layer and multilayer films exhibit high tensile residual stresses that increase with decreasing layer thickness, but are found to be lower than the respective yield strengths. The intrinsic tensile residual stress evolution with film thickness is explained using the island coalescence model. The difference between the multilayer residual stress and the average residual stresses in single-layered Cu and 330 SS films is interpreted in terms of interface stress.
Adsorption, desorption, and interdiffusion in atomic layer epitaxy of CdTe and CdZnTe
Authors: Larramendi E. M. , de Melo O. , Hernández Vélez M. , Tamargo M. C.
Published: December 2004

The mechanisms controlling the growth rate and composition of epitaxial CdTe and Cd1−xZnxTe films were studied. The films were grown by isothermal closed space configuration technique. A GaAs(100) substrate was exposed sequentially to the elemental sources (Zn, Te, and Cd) in isothermal conditions. While growth of ZnTe followed an atomic layer epitaxy (ALE) regime [self-regulated at one monolayer (ML) per cycle]; the CdTe films revealed different growth rates in dependence of the growth parameters (exposure and purge times). Combination of short purge times and larger Cd exposure times led to not self-regulated growth regime for CdTe. This is ascribed to large Cd coverages that were dependent on Cd exposure times (following a Brunauer-Emmett and Teller-type adsorption). However, for longer purge times and∕or short Cd exposure times, an ALE self-regulated regime was achieved with 2ML∕cycle. In this sense, the self-regulation of the growth is limited by desorption, instead of absorption, as in the traditional growth technique. Cd atoms substitution by Zn atoms and subsequent evaporation of surface Cd atoms during Zn exposure has been proved. The influence of these facts on the growth and composition of the alloy is discussed.
Physics of high-pressure helium and argon radio-frequency plasmas
Authors: Moravej M. , Yang X. , Nowling G. R. , Chang J. P. , Hicks R. F. , Babayan S. E.
Published: December 2004

The physics of helium and argon rf discharges have been investigated in the pressure range from 50 to 760Torr. The plasma source consists of metal electrodes that are perforated to allow the gas to flow through them. Current and voltage plots were obtained at different purity levels and it was found that trace impurities do not affect the shape of the curves. The electron temperature was calculated using an energy balance on the unbound electrons. It increased with decreasing pressure from 1.1 to 2.4eV for helium and from 1.1 to 2.0 for argon. The plasma density calculated at a constant current density of 138mA∕cm2 ranged from 1.7×1011 to 9.3×1011cm−3 for helium and from 2.5×1011 to 2.4×1012cm−3 for argon, increasing with the pressure. At atmospheric pressure, the electron density of the argon plasma is 2.5 times that of the helium plasma.
Resistivity and phonon softening in ion-irradiated epitaxial gold films
Authors: Kästle G. , Müller T. , Boyen H.-G. , Klimmer A. , Ziemann P.
Published: December 2004

The influence of ion irradiation-induced defects on the temperature dependence of the resistivity of epitaxial, thin (25nm), and ultrathin (7nm) gold films was investigated. To include surface scattering properly, the analysis was performed with the classical size-effect model of Fuchs–Sondheimer. Values for the residual resistivity, the specularity parameter p, and the Debye temperature were obtained. It turned out that ion irradiation not only leads to an expected increase of the resistivity but also to a modification of electron-phonon scattering. With increasing defect density, the effective Debye temperature was significantly reduced. This reduction was less pronounced for He+ as compared to Ar+ irradiation pointing towards vacancy clustering in the latter case. In ultrathin films (7nm), the Debye temperature is reduced already in the as-prepared state due to an increased surface-to-volume ratio, and ion irradiation-induced defects do not lead to a further reduction.
On the nature of the anisotropy of the resistivity of Nd2−xCexCuO4+δ with different cerium and oxygen concentrations
Authors: Ponomarev A. I. , Charikova T. B. , Ignatenkov A. N. , Tashlykov A. O. , Ivanov A. A.
Published: December 2004

The results of a study of the temperature dependences of the resistivity and its anisotropy coefficient in the normal phase of single-crystal Nd2−xCexCuO4+δ films with different degrees of cerium doping x and oxygen content δ are presented. Two types of films of identical composition are considered, grown with the orientation of the c axis of the crystal perpendicular to and parallel to the plane of the substrate. The parameters found from an analysis of the conductivity and Hall coefficient are presented for the 18 samples studied.
Wavelet analysis and its application in tunneling and x-ray spectroscopy
Authors: Chukalina M. V. , Dubrovskii Yu. V. , Funke H.
Published: December 2004

The capabilities and limitations of wavelet analysis are demonstrated for the illustrative case of two practial applications: investigation of magneto-tunneling signals and the extended x-ray absorption fine structure (EXAFS) of uranium. A brief introduction to wavelet analysis is given. The term “window size” of the mother wavelet function is defined; this concept underlies one of the ideas for a criterion of optimal choice of the mother wavelet function. The capabilities of a software package developed by the authors are demonstrated; this software was used for all the calculations done in the course of this study.
Lentiviral vector delivery of parkin prevents dopaminergic degeneration in an α-synuclein rat model of Parkinson's disease
Authors: Lo Bianco Christophe , Schneider Bernard L. , Bauer Matthias , Sajadi Ali , Brice Alexis , Iwatsubo Takeshi , Aebischer Patrick
Published: December 2004

Parkinson's disease (PD) is characterized by a progressive loss of midbrain dopamine neurons and the presence of cytoplasmic inclusions called Lewy bodies. Mutations in several genes including α-synuclein and parkin have been linked to familial PD. The loss of parkin's E3-ligase activity leads to dopaminergic neuronal degeneration in early-onset autosomal recessive juvenile parkinsonism, suggesting a key role of parkin for dopamine neuron survival. To evaluate the potential neuroprotective role of parkin in the pathogenesis of PD, we tested whether overexpression of wild-type rat parkin could protect against the toxicity of mutated human A30P α-synuclein in a rat lentiviral model of PD. Animals overexpressing parkin showed significant reductions in α-synuclein-induced neuropathology, including preservation of tyrosine hydroxylase-positive cell bodies in the substantia nigra and sparing of tyrosine hydroxylase-positive nerve terminals in the striatum. The parkin-mediated neuroprotection was associated with an increase in hyperphosphorylated α-synuclein inclusions, suggesting a key role for parkin in the genesis of Lewy bodies. These results indicate that parkin gene therapy may represent a promising candidate treatment for PD.
A novel method reveals that solvent water favors polyproline II over β‐strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)
Authors: Fleming Patrick J. , Fitzkee Nicholas C. , Mezei Mihaly , Srinivasan Rajgopal , Rose George D.
Published: December 2004

In aqueous solution, the ensemble of conformations sampled by peptides and unfolded proteins is largely determined by their interaction with water. It has been a long‐standing goal to capture these solute‐water energetics accurately and efficiently in calculations. Historically, accessible surface area (ASA) has been used to estimate these energies, but this method breaks down when applied to amphipathic peptides and proteins. Here we introduce a novel method in which hydrophobic ASA is determined after first positioning water oxygens in hydrogen‐bonded orientations proximate to all accessible peptide/protein backbone N and O atoms. This conditional hydrophobic accessible surface area is termed CHASA. The CHASA method was validated by predicting the polyproline‐II (PII) and β‐strand conformational preferences of non‐proline residues in the coil library (i.e., non‐α‐helix, non‐β‐strand, non‐β‐turn library derived from X‐ray elucidated structures). Further, the method successfully rationalizes the previously unexplained solvation energies in polyalanyl peptides and compares favorably with published experimentally determined PII residue propensities.

We dedicate this paper to Frederic M. Richards.
Benchmarking B cell epitope prediction: Underperformance of existing methods
Authors: Blythe Martin J. , Flower Darren R.
Published: December 2004

Sequence profiling is used routinely to predict the location of B‐cell epitopes. In the postgenomic era, the need for reliable epitope prediction is clear. We assessed 484 amino acid propensity scales in combination with ranges of plotting parameters to examine exhaustively the correlation of peaks and epitope location within 50 proteins mapped for polyclonal responses. After examining more than 106combinations, we found that even the best set of scales and parameters performed only marginally better than random. Our results confirm the null hypothesis: Single‐scale amino acid propensity profiles cannot be used to predict epitope location reliably. The implication for studies using such methods is obvious.
The length of the reactive center loop modulates the latency transition of plasminogen activator inhibitor‐1
Authors: Na Yu‐Ran , Im Hana
Published: December 2004

Plasminogen activator inhibitor‐1 (PAI‐1) belongs to the serine protease inhibitor (serpin) protein family, which has a common tertiary structure consisting of three β‐sheets and several α‐helices. Despite the similarity of its structure with those of other serpins, PAI‐1 is unique in its conformational lability, which allows the conversion of the metastable active form to a more stable latent conformation under physiological conditions. For the conformational conversion to occur, the reactive center loop (RCL) of PAI‐1 must be mobilized and inserted into the major β‐sheet, A sheet. In an effort to understand how the structural conversion is regulated in this conformationally labile serpin, we modulated the length of the RCL of PAI‐1. We show that releasing the constraint on the RCL by extension of the loop facilitates a conformational transition of PAI‐1 to a stable state. Biochemical data strongly suggest that the stabilization of the transformed conformation is owing to the insertion of the RCL into A β‐sheet, as in the known latent form. In contrast, reducing the loop length drastically retards the conformational change. The results clearly show that the constraint on the RCL is a factor that regulates the conformational transition of PAI‐1.
Crystal structure of the histidine‐containing phosphotransfer protein ZmHP2 from maize
Authors: Sugawara Hajime , Kawano Yoshiaki , Hatakeyama Tomomitsu , Yamaya Tomoyuki , Kamiya Nobuo , Sakakibara Hitoshi
Published: December 2004

In higher plants, histidine‐aspartate phosphorelays (two‐component system) are involved in hormone signaling and stress responses. In these systems, histidine‐containing phosphotransfer (HPt) proteins mediate the signal transmission from sensory histidine kinases to response regulators, including integration of several signaling pathways or branching into different pathways. We have determined the crystal structure of a maize HPt protein, ZmHP2, at 2.2 Å resolution. ZmHP2 has six α‐helices with a four‐helix bundle at the C‐terminus, a feature commonly found in HPt domains. In ZmHP2, almost all of the conserved residues among plant HPt proteins surround this histidine, probably forming the docking interface for the receiver domain of histidine kinase or the response regulator. Arg102 of ZmHP2 is conserved as a basic residue in plant HPt proteins. In bacteria, it is replaced by glutamine or glutamate that form a hydrogen bond to Nδ atoms of the phospho‐accepting histidine. It may play a key role in the complex formation of ZmHP2 with receiver domains.
Computational analysis of the transient movement of helices in sensory rhodopsin II
Authors: Sato Y. , Hata M. , Neya S. , Hoshino T.
Published: December 2004

MD simulation of sensory rhodopsin II was executed for three intermediates (ground‐state, K‐state, M‐state) appearing in its photocycle. We observed a large displacement of the cytoplasmic side of helixF only in M‐state among the three intermediates. This displacement was transmitted to TM2, and the cytoplasmic side of TM2 rotated clockwise. These transient movements are in agreement with the results of an EPR experiment. That is, the early stage of signal transduction in a sRII–HtrII complex was successfully reproduced by the in silico MD simulation. By analyzing the structure of the sRII–HtrII complex, the following findings about the photocycle of sRII were obtained: (1) The hydrogen bonds between helixF and other helices determine the direction of the movement of helixF; (2) three amino acids (Arg162, Thr189, Tyr199) are essential for sRII–HtrII binding and contribute to the motion transfer from sRII to HtrII; (3) after the isomerization of retinal, a major conformational change of retinal was caused by proton transfer from Schiff base to Asp75, which, in turn, triggers the steric collision of retinal with Trp171. This is the main reason for the movement of the cytoplasmic side of helixF.
Effect of protease treatment on plasma infectivity in variant Creutzfeldt‐Jakob disease mice
Authors: Yakovleva Oksana , Janiak Anna , McKenzie Carroll , McShane Lisa , Brown Paul , Cervenakova Larisa
Published: December 2004

BACKGROUND:  The emergence of variant Creutzfeldt‐Jakob disease (vCJD) and of a probable transmission of the disease through blood transfusion from a presymptomatic case has underlined the need for a reliable, sensitive, and specific screening test. This study was initiated to explain why attempts to identify protease‐resistant prion protein (PrPres) following treatment with proteinase K (PK) in blood or blood components have so far failed.

STUDY DESIGN AND METHODS:  RIII mice were inoculated intracerebrally (i.c.) with vCJD agent. As soon as some mice became ill, blood from all mice was collected, pooled, and separated into components. Aliquots of plasma were treated with either 100 and 500 µg per mL PK or left untreated. Samples were analyzed for total protein and for PrPres by Western blot with 6H4 antibodies. Infectivity in PK‐treated and untreated samples was bioassayed by i.c. inoculation into healthy mice.

RESULTS:  Estimated infectivity in untreated control plasma was 20.6 IU per mL. Treatment of plasma with 100 or 500 µg per mL PK resulted in estimated infectivity levels of 8.4 and 5.2 IU per mL, respectively. Coomassie staining revealed substantial changes in the protein profile after PK treatment, with massive degradation of proteins at 500 µg per mL PK. No PrPres was detected in plasma samples by Western blotting.

CONCLUSION:  Infectivity in plasma of vCJD‐infected mice showed a trend toward reduction following enzymatic treatment with increasing doses of PK, possibly because of activity against proteolysis‐sensitive isoforms of abnormal prion protein. It is concluded that the use of PK in protocols for the detection of PrPres may decrease the sensitivity of blood‐based assays.
A Dual Role for Interferon‐γ in the Pathogenesis of Sjögren's Syndrome‐Like Autoimmune Exocrinopathy in the Nonobese Diabetic Mouse
Authors: Cha S. , Brayer J. , Gao J. , Brown V. , Killedar S. , Yasunari U. , Peck A. B.
Published: December 2004

Sjögren's syndrome‐like autoimmune exocrinopathy (AEC) in the nonobese diabetic (NOD) mouse progresses from a preimmune phase to an immune phase, resulting in dry mouth and/or dry eyes. In the present study, the impact of the prototypical T‐helper type 1 cytokine, interferon‐gamma (IFN‐γ), on the onset of AEC was investigated using both the IFN‐γ and the IFN‐γ receptor gene knockout mice, NOD.IFN‐γ–/– and NOD.IFN‐γR–/–, respectively. Neither the NOD.IFN‐γ–/– nor the NOD.IFN‐γR–/– mice exhibited increased acinar cell apoptosis and abnormal salivary protein expression, typically observed in parental NOD mice prior to disease. Without these preimmune phase abnormalities, NOD.IFN‐γ–/– and NOD.IFN‐γR–/– mice showed no subsequent autoimmune responses against the salivary glands at 20 weeks. Interestingly, real‐time polymerase chain reaction and electrophoretic gel mobility shift assays suggested that IFN‐γ and STAT1, as well as the transcriptional activity of STAT1 in NOD glands, were increased at birth. Unlike the neonatal submandibular glands of NOD or NOD‐scid mice that show abnormal glandular morphogenesis at birth, the submandibular glands of the newly constructed congenic strain, NOD‐scid.IFN‐γ–/–, were found to be normal. Taken together, IFN‐γ appears to play a critical role not only during the later immune phase of AEC, but also the early preimmune phase, independent of effector functions of immune cells. How exactly IFN‐γ functions during this period remains speculative.