bluuebunny/crossref_metadata_2025 huggingface dataset:
Fully resolved simulations of particle-turbulence interaction
Authors: BURTON TRISTAN M. , EATON JOHN K.
Published: December 2005

The interaction between a fixed particle and decaying homogeneous isotropic turbulence is studied numerically using an overset grid that provides resolution of all scales of fluid motion. A description of the numerical technique and validation of the solution procedure are presented. An ensemble of 64 simulations with the particle in different regions of the flow is computed. The particle diameter in the simulations is approximately twice the size of the unladen Kolmogorov length scale, and the maximum value of the particle Reynolds numbers due to the turbulent fluctuations is close to 20. Ensemble averages of quantities from the numerical solutions are used to investigate the turbulence modification and the fluid forces on the particle. Volume-averaged profiles of the turbulent kinetic energy and dissipation rate from the overset grid simulations reveal that the displacement of fluid by the particle and the formation of the boundary layer at the particle surface lead to turbulence modification in a local region. Time histories of the force applied to the particle from each overset grid simulation are compared to those predicted by a particle equation of motion. The particle equation of motion is shown to underpredict the root mean square (RMS) force applied to the particle by the turbulence. RMS errors between the forces from the overset grid simulation and those predicted by the particle equation of motion are shown to be between 15% and 30% of the RMS force on the particle. The steady viscous drag force is shown to be the dominant term in the particle equation of motion while the history integral term is negligible.
The drag on a microcantilever oscillating near a wall
Authors: CLARKE R. J. , COX S. M. , WILLIAMS P. M. , JENSEN O. E.
Published: December 2005

Motivated by devices such as the atomic force microscope, we compute the drag experienced by a cylindrical body of circular or rectangular cross-section oscillating at small amplitude near a plane wall. The body lies parallel to the wall and oscillates normally to it; the body is assumed to be long enough for the dominant flow to be two-dimensional. The flow is parameterized by a frequency parameter $\gamma^2$ (a Strouhal number) and the wall–body separation $\Delta$ (scaled on body radius). Numerical solutions of the unsteady Stokes equations obtained using finite-difference computations in bipolar coordinates (for circular cross-sections) and boundary-element computations (for rectangular cross-sections) are used to determine the drag on the body. Numerical results are validated and extended using asymptotic predictions (for circular cylinders) obtained at all extremes of $(\gamma,\Delta)$-parameter space. Regions in parameter space for which the wall has a significant effect on drag are identified.
The air bubble entrapped under a drop impacting on a solid surface
Authors: THORODDSEN S. T. , ETOH T. G. , TAKEHARA K. , OOTSUKA N. , HATSUKI Y.
Published: December 2005

We present experimental observations of the disk of air caught under a drop impacting onto a solid surface. By imaging the impact through an acrylic plate with an ultra-high-speed video camera, we can follow the evolution of the air disk as it contracts into a bubble under the centre of the drop. The initial size and contraction speed of the disk were measured for a range of impact Weber and Reynolds numbers. The size of the initial disk is related to the bottom curvature of the drop at the initial contact, as measured in free-fall. The initial contact often leaves behind a ring of micro-bubbles, marking its location. The air disk contracts at a speed comparable to the corresponding air disks caught under a drop impacting onto a liquid surface. This speed also seems independent of the wettability of the liquid, which only affects the azimuthal shape of the contact line. For some impact conditions, the dynamics of the contraction leaves a small droplet at the centre of the bubble. This arises from a capillary wave propagating from the edges of the contracting disk towards the centre. As the wave converges its amplitude grows until it touches the solid substrate, thereby pinching off the micro-droplet at the plate, in the centre of the bubble. The effect of increasing liquid viscosity is to slow down the contraction speed and to produce a more irregular contact line leaving more micro-bubbles along the initial ring.
Ca2+–Surfactant Interactions Affect Enzyme Stability in Detergent Solutions
Authors: Stoner Michael R. , Dale Douglas A. , Gualfetti Peter J. , Becker Todd , Randolph Theodore W.
Published: December 2005

Detergent proteases and amylases generally bind Ca2+ ions. These bound ions enhance enzyme stability, reducing the rates of degradative reactions such as unfolding and proteolysis. Thus, surfactant aggregates, such as micelles, affect protease and amylase stability indirectly, by competing with the enzymes for Ca2+ ions. Dissociation constants for Ca2+ interactions with anionic surfactant micelles are in the 10−3 to 10−2 M range. These interactions are weak relative to enzyme‐Ca2+ interactions (Kd of order 10−6 M). However, surfactant is typically present at much higher concentration than enzyme, and it is the Ca2+–micelle equilibrium that largely determines the amount of free Ca2+ available for binding to enzymes. The problem of surfactant‐mediated Ca2+ removal from enzymes can be avoided by adding calcium to a detergent formulation in an amount such that the concentration of free Ca2+ is around 10−5M.
Mass Transfer of Terpenes through a Silicone Rubber Membrane in a Liquid‐Liquid Contacting System
Authors: Boontawan Apichat , Stuckey David C.
Published: December 2005

Terpenoids are important compounds for the fragrance industry, and recently, biocatalytic methods have been developed to produce them from cheap monoterpenes, such as α‐pinene oxide. The biotransformation of α‐pinene oxide using resting cells of Pseudomonas fluorescensNCIMB 11671 produces isonovalal (cis‐2‐methyl‐5‐isopropylhexa‐2,5‐dienal), which is a fragrance. However, this biotransformation has technical problems including the following: α‐pinene oxide undergoes autoxidation in water and light; it is hydrophobic and relatively toxic to the biocatalyst; and it suffers from product inhibition. Therefore, removal of isonovalal as it is formed should reduce its toxicity and increase volumetric productivity and production yield. Aqueous‐organic two‐phase (AOTP) systems can be used in the biotransformation of hydrophobic substrates and can protect biocatalysts from toxic substrates and products. However, the formation of stable emulsions makes further downstream processing and continuous operation difficult. One solution to these problems is to use a solid‐phase membrane between the aqueous and organic phases in a Membrane Bioreactor for Biotransformation (MBB). Since there are no data in the literature on the behavior of terpenes and terpenoids with solid‐phase membranes, or their mass transfer behavior, the objective of this work was to measure these parameters for a wide range of compounds so as to be able to design an MBB, and to gain a greater understanding of their behavior in these types of systems. Organic/aqueous (Porgaq) and membrance/aqueous (Pmemaq) partition coefficients were measured first, and subsequently used to quantify the overall mass transfer coefficients (kov). The overall mass transfer coefficient (kov) of α‐pinene oxide through the membrane was found to be 2.5 × 10−5 m·s−1 using thicknesses of both 250 and 1000 μm. Extraction kinetics were successfully described using a resistance‐in‐series model and were controlled by the aqueous boundary layer and/or membrane resistance (kmem), while organic film resistance played an insignificant role. Aqueous film resistance (kaq) was found to be the limiting step for mono‐ and diterpenes, and the effect of the hydrodynamics on kov was successfully predicted using a Wilson plot. However, the extraction kinetics of larger terpenes, such as steroids, were influenced solely by the kmem, suggesting that membrane diffusivity also depended on the size of the permeating molecule. Finally, the influence of other terpene byproducts on the flux of α‐pinene oxide was investigated and found to decrease the flux into the organic phase by up to 10%.
Enhanced Production of the Polysaccharide Arabinogalactan Using Immobilized Cultures of Tinospora cordifolia by Elicitation and In Situ Adsorption
Authors: Roja G. , Bhangale A. S. , Juvekar A. R. , Eapen S. , Dapos;Souza S. F.
Published: December 2005

Immobilized callus cultures of Tinospora cordifolia (Willd) Miers ex Hooks and Thoms were investigated to find out the combined effect of elicitation, cell permeabilization with chitosan and in situ product recovery by polymeric neutral resin‐like Diaion HP 20. In this study, callus cultures of T. cordifolia were immobilized using sodium alginate and calcium chloride and the beads were cultured in Murashige and Skoogapos;s basal medium along with benzyl adenine (BA), 2,4‐dichlorophenoxy acetic acid (2,4‐D) and 3% sucrose. The immobilized cultures, when subjected to elicitation and cell permeabilization with chitosan and in situ removal of the secondary metabolites by addition of resin, showed a 10‐fold increase in production of arabinogalactan (0.490% dry weight) as compared to respective controls devoid of resin and chitosan. This indicates that in situ adsorption may have reduced the feedback inhibition caused by accumulation of secondary metabolites in the media, while the dual effect of elicitation and cell permeabilization by chitosan may have released the intracellular (secreted) berberine and the polysaccharide arabinogalactan, respectively.
Metabolic Control Analysis of Aspergillus nigerl‐Arabinose Catabolism
Authors: de Groot Marco J. L. , Prathumpai Wai , Visser Jaap , Ruijter George J. G.
Published: December 2005

A mathematical model of the l‐arabinose/d‐xylose catabolic pathway of Aspergillus nigerwas constructed based on the kinetic properties of the enzymes. For this purpose l‐arabinose reductase, l‐arabitol dehydrogenase and d‐xylose reductase were purified using dye‐affinity chromatography, and their kinetic properties were characterized. For the other enzymes of the pathway the kinetic data were available from the literature. The metabolic model was used to analyze flux and metabolite concentration control of the l‐arabinose catabolic pathway. The model demonstrated that flux control does not reside at the enzyme following the intermediate with the highest concentration, l‐arabitol, but is distributed over the first three steps in the pathway, preceding and following l‐arabitol. Flux control appeared to be strongly dependent on the intracellular l‐arabinose concentration. At 5 mM intracellular l‐arabinose, a level that resulted in realistic intermediate concentrations in the model, flux control coefficients for l‐arabinose reductase, l‐arabitol dehydrogenase and l‐xylulose reductase were 0.68, 0.17 and 0.14, respectively. The analysis can be used as a guide to identify targets for metabolic engineering aiming at either flux or metabolite level optimization of the l‐arabinose catabolic pathway of A. niger. Faster l‐arabinose utilization may enhance utilization of readily available organic waste containing hemicelluloses to be converted into industrially interesting metabolites or valuable enzymes or proteins.
Polysaccharide Hydrolysis Accelerated by Adding Carbon Dioxide under Hydrothermal Conditions
Authors: Miyazawa Tetsuya , Funazukuri Toshitaka
Published: December 2005

Polysaccharides such as agar, guar gum, starch, and xylan were hydrolyzed to produce mono‐ and oligosaccharides under hydrothermal conditions with and without carbon dioxide in a small batch reactor. The molecular weight distributions of the polysaccharide hydrolyzates shifted to lower molecular weights by increasing the carbon dioxide load, corresponding to higher pressures of carbon dioxide. For example, the yield of glucose produced from the hydrolysis of starch at 200 °C was increased significantly from 3.7% to 53.0% (on a carbon weight basis) of the initial polysaccharide by increasing carbon dioxide load in a reaction time of 15 min. Carbonic acid generated from water and carbon dioxide appeared to lower the pH of high‐temperature and high‐pressure water. Polysaccharide hydrolysis under hydrothermal conditions in the presence of carbon dioxide is an environmentally benign method to produce mono‐ and oligosaccharides because the process does not require the use of conventional acids and bases followed by neutralization and separation.
Variables That Affect Xylitol Production from Sugarcane Bagasse Hydrolysate in a Zeolite Fluidized Bed Reactor
Authors: Santos Júlio C. , Mussatto Solange I. , Cunha Mário A. A. , Silva Silvio S.
Published: December 2005

The operational conditions for xylitol production by fermentation of sugarcane bagasse hydrolysate in a fluidized bed reactor with cells immobilized on zeolite were evaluated. Fermentations were carried out under different conditions of air flowrate (0.0125–0.0375 vvm), zeolite mass (100–200 g), initial pH (4–6), and xylose concentration (40–60 g/L), according to a 24 full factorial design. The air flowrate increase resulted in a metabolic deviation from product to biomass formation. On the other hand, the pH increase favored both the xylitol yield (YP/S) and volumetric productivity (QP), and the xylose concentration increase positively influenced the xylitol concentration. The best operational conditions evaluated were based on the use of an air flowrate of 0.0125 vvm, 100 g of zeolite, pH 6, and xylose concentration of 60 g/L. Under these conditions, 38.5 g/L of xylitol were obtained, with a YP/S of 0.72 g/g, QP of 0.32 g/L·h, and cell retention of 25.9%.
Control of Recombinant Monoclonal Antibody Effector Functions by Fc N‐Glycan Remodeling in Vitro
Authors: Hodoniczky Jason , Zheng Yuan Zhi , James David C.
Published: December 2005

N‐Glycans at Asn297 in the Fc domain of IgG molecules are required for Fc receptor‐mediated effector functions such as antibody‐dependent cell‐mediated cytotoxicity (ADCC) and complement‐dependent cytotoxicity (CDC). In this study we have specifically remodeled the Fc N‐glycans of intact recombinant IgG1 therapeutic monoclonal antibody (Mab) products, Rituxan and Herceptin, with a soluble recombinant rat β‐1,4‐N‐acetylglucosaminyltransferase III (rGnTIII) produced by baculovirus‐infected insect cells. N‐Glycan remodeling in vitro permitted a controlled and selective transfer of a bisecting β1,4‐linked GlcNAc to the core β‐linked mannose of degalactosylated Mab N‐glycans to yield Mabs varying in bisecting GlcNAc content from 31% to 85%. This was confirmed by analysis of N‐glycans by both normal phase HPLC and MALDI‐MS, the latter yielding the expected mass increase of 203.2 Da with no other oligosaccharide modifications evident. ADCC of remodeled Rituxan and Herceptin Mabs was determined using peripheral blood mononuclear cells as effectors and either CD20+ (SKW6.4 and SU‐DHL‐4) or Her2+ (SKBR‐3) target cells, respectively. A conserved 10‐fold increase in ADCC was observed for both remodeled therapeutic Mabs with high (>80%) bisecting GlcNAc content. In contrast, although the presence of a bisecting GlcNAc had minimal effect on CDC, degalactosylation of Rituxan reduced CDC by approximately half, relative to unmodified (variably galactosylated) control Mab. In summary, our data suggests that in vitro remodeling of therapeutic Mab Fc N‐glycans may be utilized to control the therapeutic efficacy of Mabs in vivo and to offer a more “humanized” glycoform profile for recombinant Mab products.
Identification of Candida albicans Genes that Induce Saccharomyces cerevisiae Cell Adhesion and Morphogenesis
Authors: Li Fang , Palecek Sean P.
Published: December 2005

Morphogenesis and adhesion to host tissues and medical devices contribute to the virulence of Candida albicans, the most common fungal pathogen isolated from humans. However, identification of molecular mechanisms of C. albicans adhesion and morphogenesis has been impaired by the lack of effective molecular and genetic tools available for this organism. Saccharomyces cerevisiae provides an attractive model system for studying C. albicans adhesion and morphogenesis because of its well‐characterized genetics and gene expression systems. To gain insight into the genetic mechanisms of C. albicans adhesion and morphogenesis, we used a parallel plate flow chamber to screen and quantitatively characterize attachment to polystyrene of an adhesion‐deficient nonfilamentous flo8Δ S. cerevisiae strain expressing a C. albicans genomic library. We identified six C. albicans genes that are capable of promoting cell adhesion and pseudohyphal development in S. cerevisiae. We also analyzed the ability of these adhesion‐promoting genes to regulate the expression of FLO11,which encodes an endogenous S. cerevisiaeadhesin. One C. albicansgene, EAP1, appears to directly mediate adhesion and morphogenesis while the remaining five (EAP2, SWI1, MSB1, AAF1, and TEC1) upregulate expression of endogenous S. cerevisiae adhesins. These results suggest that S. cerevisiaeis a useful system for molecular characterization of factors that regulate C. albicansadhesion and morphogenesis and that parallel plate flow chamber‐based adhesion assays can be used in conjunction with genetic screens to identify molecular mechanisms regulating fungal cell adhesion.
Simulations of Chesapeake Bay estuary: Sensitivity to turbulence mixing parameterizations and comparison with observations
Authors: Li Ming , Zhong Liejun , Boicourt William C.
Published: December 2005

Regional Ocean Modeling System (ROMS) is used to develop a new three‐dimensional hydrodynamic model for the Chesapeake Bay estuary. Hindcast simulations are conducted for 2 years with markedly different annual river discharges and are compared with time series measurements and high‐resolution hydrographic data. The model shows skill in reproducing observed temporal variability in sea level height, salinity, and subtidal current. The agreement with observations is better in the normal runoff year 1997 than in the high runoff year 1996. The model qualitatively reproduces the along‐channel and cross‐channel salinity distributions during low‐to‐medium runoff periods. However, during high runoff periods it predicts weaker stratification and a more diffuse halocline than shown by observations. This model/data discrepancy is related to the deficiency of turbulent mixing parameterizations in strong stratification. We have experimented with four turbulence closure schemes (Mellor‐Yamada/k‐kl, k‐ɛ, k‐ω, and KPP models) in ROMS but found little difference in the model results. However, vertical stratification shows a strong sensitivity to the background diffusivity. The vertical diffusivity inferred from the model is found to be set by the background diffusivity except in the surface and bottom boundary layers where the turbulence schemes produce similar diffusivity distributions. Among the schemes explored, KPP and k‐kl scheme with a background diffusivity of 10−5 or 10−6 m2 s−1 provide the best simulations of the Chesapeake Bay estuary. Both the model sensitivity study and model/data comparison highlight the importance of obtaining a more realistic parameterization for turbulence mixing in a strong pycnocline.
A comparison of experimental and natural drainage basin morphology across a range of scales
Authors: Niemann Jeffrey D. , Hasbargen Leslie E.
Published: December 2005

Numerous quantitative models have been developed to simulate the long‐term evolution of river basin topography. Most of these models reach an equilibrium state when the base level is lowered at a constant rate and the substrate and climate are constant in time. At equilibrium the erosion balances the base level lowering, so the topography remains frozen in time. However, some recent laboratory experiments contradict this behavior. In these experiments the space‐time mean erosion rate balances the base level lowering rate, but the actual erosion rates are highly variable in space and time. Consequently, the channel networks are substantially mobile. The experimental flow conditions are approximately similar but not dynamically equivalent to those in nature, so it is unclear whether the observed dynamics are representative. This paper examines whether the processes occurring in the experiments produce basins that are geometrically similar to typical natural basins. To make this comparison, the conceptual framework of scaling invariance is used. Many similarities are observed, but we find that the experimental basins are slightly more elongated across a range of scales than the natural basins we consider and the relationship between channel slope and drainage area exhibits a break that is not found in the natural basins we analyze. In the experiments the slopes of small channels also depend on the proximity of large channels. This dependency is more pronounced for experiments with more mobile channel networks, and it is not observed in most of the natural basins we analyze.
Spectral analysis of ground penetrating radar response to thin sedimentary layers
Authors: Guha S. , Kruse S. E. , Wright E. E. , Kruse U. E.
Published: December 2005

Ground penetrating radar (GPR) systems utilized in studies of sedimentary deposits generate wavelengths (tens of centimeters) that are commonly much longer than the thickness of bedding (often millimeters to centimeters) within the target strata. Where this is the case, radar profiles represent interference patterns. Simple models of radar response to sequences of thin beds such as those found in coastal deposits show potentially detectable spectral shifts toward higher frequencies in radar returns. Spectral analysis of radar data over barrier beach deposits at Waites Island, South Carolina, shows that returns from packages with heavy mineral laminations are shifted toward higher frequencies relative to returns from more isolated contacts. Such spectral shifts may be useful as an indicator of fine‐scale layering on radar profiles.
The contribution of AIRS data to the estimation of CO2 sources and sinks
Authors: Chevallier Frédéric , Engelen Richard J. , Peylin Philippe
Published: November 2005

The analysis of radiance measurements from the Atmospheric Infra‐Red Sounder (AIRS) has been providing the first global maps of CO2 concentrations in the cloud‐free upper troposphere. This paper explores the usefulness of this data for the estimation of CO2 surface fluxes. It appears that atmospheric mixing makes the upper tropospheric CO2 concentrations rather zonal, which indicates that AIRS data inform about very broad features of the surface fluxes only. Further, such a small variability imposes a stringent constraint on the size of retrieval biases and of transport model biases for the estimation of CO2 surface fluxes. We show that latitude‐dependent biases larger than a few tenths of a particle per million (ppm), at least south of 25°N, would harm the inversions. Significant improvements to the concentration retrieval algorithms and to the transport models are a prerequisite for the inversion of surface fluxes from AIRS.
ICESat sea level comparisons
Authors: Urban Timothy J. , Schutz Bob E.
Published: December 2005

ICESat calculations of sea level and mesoscale variability are demonstrated and compared to calculations from TOPEX altimetry. In particular, we examine the accuracy of the ICESat Laser 2a Release 21 GLA15 ocean elevations. A global ICESat ocean elevation bias of −10.0 ± 1.0 cm (low) was found with respect to TOPEX, obtained with a reference mean sea surface (MSS). Dual‐satellite (ICESat ‐ TOPEX) crossovers independently verify this bias, having a mean of −11.7 ± 1.8 cm. The origin of this bias is unknown, although it may be related to sea state. Release 21 improvements have mitigated ICESat's thermally‐induced day/night laser pointing variations to 1 to 2 cm in elevation. The average daily single‐satellite internal crossover RMS is 12 cm for ICESat, 7 cm for TOPEX. ICESat laser altimetry is able to match TOPEX detection of major sea level anomaly and mesoscale variability features on a global scale.
Electrostatic electron cyclotron harmonic instability due to energetic electrons in Jupiter's magnetosphere
Authors: Tripathi A. K. , Singhal R. P.
Published: December 2005

Electrostatic electron cyclotron harmonic instability in the magnetosphere of Jupiter is investigated using a kappa distribution with loss cone for energetic electrons in the tail of the distribution function. Temporal growth rates are calculated at two representative radial distances characterized by different temperatures of the thermal electron population. It is found that the frequency within the harmonic band shifts to a lower value as the temperature of the thermal electron population increases. Furthermore, higher harmonic bands are damped faster as the angle between the wave normal and the ambient magnetic field is decreased. Calculations are performed by changing various parameters appearing in the distribution function. The present study may be helpful in accounting for some of the observed features of the electron cyclotron harmonic bands in the magnetosphere of Jupiter. The observed features are as follows: (1) Maximum amplitudes are usually seen in the first harmonic band and at the highest frequency of emission near upper hybrid resonance, (2) Emissions are greatest at smaller radial distances and decrease with increasing distance, (3) The amplitude is observed to fluctuate over more than an order of magnitude on timescales of several seconds.
A numerical investigation of the phytoplankton bloom in the Bay of Bengal during Northeast Monsoon
Authors: Vinayachandran P. N. , McCreary Julian P. , Hood Raleigh R. , Kohler Kevin E.
Published: December 2005

A 4.5‐layer model of the Indian Ocean coupled to a four‐component (NPZD) ecosystem model is used to study the phytoplankton bloom in the Bay of Bengal during the Northeast Monsoon of 1996. The model realistically simulates the surface chlorophyll bloom observed by satellite‐derived ocean‐color images in the western Bay of Bengal during that time. It also reproduces the subsurface chlorophyll maximum present earlier in the fall. The terms in the phytoplankton equation for the model's mixed layer show that the surface bloom is caused by the entrainment not only of subsurface nutrients but also of phytoplankton from the subsurface maximum. To our knowledge, this study is the first to report enrichment of surface chlorophyll by entrainment of the subsurface maximum. Upwelling caused by Ekman pumping and mixed layer entrainment occurring over an already shallow thermocline drives the vertical fluxes. An intense wind event from 26 November to 5 December also generated favorable conditions for the formation of a phytoplankton bloom.
Relationships between radiosonde and RUC‐2 meteorological conditions and cloud occurrence determined from ARM data
Authors: Minnis Patrick , Yi Yuhong , Huang Jianping , Ayers Kirk
Published: December 2005

Relationships between modeled and measured meteorological state parameters and cloudy and cloud‐free conditions are examined using data taken over the ARM (Atmospheric Radiation Measurement) Southern Great Plains Central Facility between 1 March 2000 and 28 February 2001. Cloud vertical layering was determined from the Active Remotely Sensed Cloud Location product based on the ARM active sensor measurements. Both temperature and relative humidity (RH) observations from balloon‐borne Vaisala RS80‐15LH radiosonde (SONDE) and the Rapid Update Cycle (RUC) 40‐km resolution model are highly correlated, but the SONDE RHs generally exceed those from RUC. Inside cloudy layers, the RH from SONDE is 2–14% higher than the RH from RUC at all pressure levels. Although the layer mean RH within clouds is much greater than the layer mean RH outside clouds or in clear skies, RH thresholds chosen as a function of temperature can more accurately diagnose cloud occurrence for either data set than a fixed RH threshold. For overcast clouds (cloud amount greater than or equal to 90%), it was found that the 50% probability RH threshold for diagnosing a cloud, within a given upper tropospheric layer, is roughly 90% for the SONDE and 80% for RUC data. For partial cloud cover (cloud amount is less than 90%), the SONDE RH thresholds are close to those for RUC at a given probability in upper tropospheric layers. Cloud probability was found to be only minimally dependent on vertical velocity. In the upper troposphere, SONDE ice‐supersaturated air occurred in 8 and 35% of the clear and cloudy layers, respectively. The RH was distributed exponentially in the ice supersaturated layers as found in previous studies. The occurrence of high‐altitude, ice‐supersaturated layers in the RUC data was roughly half of that in the SONDE data. Optimal thresholds were derived as functions of temperature to define the best RH thresholds for accurately determining the mean cloud cover. For warm clouds the typical SONDE threshold exceeds 87%, while the RH thresholds for cold clouds are typically less than 80% and greater than 90% with respect to liquid and ice water, respectively. Preliminary comparisons with satellite data suggest that the relationships between cloudiness and RH and T determined here could be useful for improving the characterization of cloud vertical structure from satellite data by providing information about low‐level clouds that were obscured by high‐level clouds viewed by the satellite. The results have potential for improving computations of atmospheric heating rate profiles and estimates of aircraft icing conditions. Similar analyses are recommended for later versions of the RUC analyses and forecasts.
Late Pliocene‐Pleistocene changes in mass accumulation rates of eolian deposits on the central Chinese Loess Plateau
Authors: Sun Youbin , An Zhisheng
Published: November 2005

Late Pliocene‐Pleistocene changes in the mass accumulation rates (MARs) of eolian deposits on the central Chinese Loess Plateau (CLP) are reconstructed from measured bulk sediment densities combined with sedimentation rates calculated for two loess/red clay sequences. The reconstructed MARs demonstrate that over the past 3600 kyr, distinct aridity‐humidity fluctuations occurred over glacial‐interglacial timescales, and these were superimposed on a gradual long‐term drying trend. Comparisons of the CLP MAR record with the MAR and δ18O records for marine sediments suggest that the development of Northern Hemisphere ice sheets since the late Pliocene has played a part in increasing the aridity of central Asia. In addition, the phased uplift of the Himalaya‐Tibetan Plateau evidently had a profound influence on the aridity of central Asia; this was mediated by variations in the East Asian monsoonal circulation. Correlations among dust records from ice cores, marine sediments, and terrestrial loess over the last several glacial cycles provide compelling evidence that glacial periods are characterized by higher and more variable dust fluxes than interglacial intervals. Synchronous changes in the MAR, grain size, and δ18O records reveal dynamic linkages between Asian interior aridity, paleowind intensity, and ice volume after the onset of major Northern Hemisphere glaciations.
Variability of the mesospheric nightglow sodium D2/D1 ratio
Authors: Slanger T. G. , Cosby P. C. , Huestis D. L. , Saiz‐Lopez A. , Murray B. J. , O'Sullivan D. A. , Plane J. M. C. , Allende Prieto C. , Martin‐Torres F. J. , Jenniskens P.
Published: November 2005

Measurements of the intensity ratio of the 589.0/589.6 nm sodium doublet in the terrestrial nightglow over an 8‐year period, involving >300 separate determinations, have established that it is variable, the value RD = I(D2)/I(D1) lying between 1.2 and 1.8. Sky spectra from the Keck I telescope with the High‐Resolution Échelle Spectrometer (HIRES) échelle spectrograph and the Keck II telescope with the Échellette Spectrograph and Imager (ESI) échelle spectrograph were used in this analysis. The result contrasts with the accepted view, from earlier measurements at midlatitude, that the ratio is 2.0, as expected on statistical grounds. The lack of dependence of the ratio on viewing elevation angle, and hence Na slant column, allows self‐absorption to be ruled out as a cause of the variability. The data suggest a semiannual oscillation in the ratio, maximum at the equinoxes and minimum at the solstices. Airborne measurements over the North Atlantic (40°–50°N) in 2002 show an even larger range in the nightglow ratio and no correlation with the upper mesospheric temperature determined from the OH 6–2 bands. A laboratory study confirms that the ratio does not depend on temperature; however, it is shown to be sensitive to the [O]/[O2] ratio. It is therefore postulated that the variable ratio arises from a competition between O reacting with NaO(A3Σ+), produced from the reaction of Na with O3, to yield D‐line emission with a D2/D1 ratio greater than about 2.0, and quenching by O2 to produce NaO(X2Π), possibly with vibrational excitation, which then reacts with O to produce emission with a ratio of less than 1.3.
Regional advanced very high resolution radiometer–derived climatology of aerosol optical thickness and size
Authors: Geogdzhayev Igor V. , Mishchenko Michael I. , Terez Edward I. , Terez Galina A. , Gushchin Genady K.
Published: December 2005

We have used the NASA Global Energy and Water Cycle Experiment (GEWEX) Global Aerosol Climatology Project data set of retrieved aerosol optical thickness and Ångström exponent to construct and analyze regional aerosol climatologies for a number of areas affected by different aerosol types (such as dust, biomass burning, anthropogenic, or clear maritime aerosols) that exemplify the range of natural aerosol variation. We have found that variations in the number of individual pixels used to calculate monthly means associated with short‐ and long‐term satellite orbit changes and instrument degradation have little effect on global and hemispherical values of the aerosol optical thickness and Ångström exponent. Aerosol loads are found to be higher, and aerosol particles smaller, over the northern Atlantic Ocean off the coast of Europe and the eastern United States, rather than off the west coast, thereby indicating a significant impact of anthropogenic aerosols. The smallest background levels of maritime aerosols are found in the southern Pacific Ocean, with seasonal mean optical thicknesses as low as 0.1. We analyze time series of the aerosol optical thickness in the regions affected by dust outflows from the Sahara and Asian deserts and by biomass burning. An influence of anthropogenic aerosols associated with the high regional industrial activity is apparent in the eastern China Sea. Two distinct periods are identified in satellite and Sun photometer aerosol time series over the Black Sea with transition time around 1993. During the first period the aerosol loads in the region significantly exceeded the hemispherical mean, whereas in the second period they became very close. This change is linked to the reduction of the industrial output in that region.
Oxidation of S(IV) in sea‐salt aerosol at high pH: Ozone versus aerobic reaction
Authors: Hoppel William A. , Caffrey Peter F.
Published: November 2005

The oxidation of dissolved SO2 (as S(IV)) by dissolved O3 is known to increase rapidly with pH and is generally thought to be the mechanism responsible for the oxidation of S(IV) in sea‐salt aerosol at high pH. Recently, Hoppel et al. (2001) have shown that an aerobic reaction studied by Zhang and Millero (1991) increases even more rapidly with pH than O3 oxidation and exceeds that of O3 at pH of about 7.5 to 8.5, depending on the ambient SO2 concentrations. At high pH, both of these oxidation mechanisms proceed so rapidly that the actual rate is constrained by both gas‐phase and aqueous‐phase transport processes. A method of analysis is developed to calculate the transport‐limited reaction rates for both of these mechanisms in sea‐salt aerosol. Even when the unconstrained O3‐S(IV) rate is faster than the aerobic mechanism, aqueous‐phase transport limitations on ozone can slow the constrained O3‐S(IV) rate to the degree that it is slower than the aerobic reaction. In general, the O3‐S(IV) rate is favored over the aerobic mechanism at low SO2 and high O3 concentrations, whereas the aerobic mechanism is favored at high SO2 concentrations. The analysis indicates that the O3‐S(IV) mechanism is more important in the remote regions where the SO2 concentration can be extremely low. When the SO2 concentration approaches 1 ppb or greater the aerobic mechanism is likely to be more important.
Seasonality and weather‐driven variability of transpacific transport
Authors: Holzer Mark , Hall Timothy M. , Stull Roland B.
Published: December 2005

We quantify transport from the industrialized regions of E Asia using the transit‐time probability density function, ��, to isolate the role of transport from any other factors, such as chemistry and deposition. Using the offline transport model MATCH driven by NCEP reanalyses, we calculate ��, which is the mass fraction of air that had its last contact with the E‐Asian source region during a given day, for each day of a three‐year period. Ensemble means of �� establish the climatological seasonal‐mean transport from E Asia. Export from the source region is most efficient in spring, with nearly all E‐Asian air involved in transpacific transport. In summer, E‐Asian air is transported aloft across the Pacific and, in nearly equal measure, west over SE Asia to the Middle East. Winter transport is similar to that of spring, except winter has low‐level transport to SE Asia. Fall transport is intermediate between that of summer and winter. For all seasons, the most probable transit times to N America are 6–8 days in the mid‐to‐upper troposphere and approximately one week (two for summer) longer at the surface. The surface signal of E‐Asian air over N America is strongest in spring. Daily variability of transpacific transport is quantified in terms of the transit‐time partitioned burden of E‐Asian air over western N America. The standard deviation of the transit‐time partitioned fluctuations has a nearly universal dependence on the corresponding seasonal‐mean burden. The standard deviation peaks several days before the burden at a transit time of ∼7 days. Lagged event and nonevent composites, based on the western N‐American burden of E‐Asian air, reveal that transport events are associated with dipolar wind perturbations over the eastern Pacific that are positioned and phased to receive enhanced Asian outflow. Surface‐pressure correlations are consistent with an associated strengthened Pacific High and weakened Aleutian Low.
Cross‐sectional and longitudinal profiles of valleys and channels in Xanthe Terra on Mars
Authors: Kereszturi A.
Published: December 2005

On the basis of Mars Orbiter Laser Altimeter data and Viking Orbiter and Mars Global Surveyor images, cross‐sectional and longitudinal profiles of channels and valleys were analyzed in Xanthe Terra on Mars. Concave and convex longitudinal profiles were observed at Bahram and Tyras Valles, respectively, while no general trend was visible at other valleys. The longitudinal profiles also showed signs of knickpoints and some short reaches with increasing elevation in the flow direction. The cross‐sectional profiles of Tyras Valles show more V‐shaped of upper and U‐shaped of lower reaches, but the great variety of profiles of other channels suggests a complex relationship with the regional lithology/topography. Also at Tyras Valles the longitudinal profiles could be divided into upper and lower sections that probably formed at different periods under different conditions. The largest observed valleys contain small, previously unnoticed inner channels. There is no correlation between the shape of cross‐sectional profiles and the direction of curvature of the valley's long axis (left/right or straight), as is found in riverbeds on the Earth, suggesting that the analyzed depressions are probably valleys and not dry riverbeds, but substantial wind‐blown sedimentary infill could have modified their shape too.
Flume investigations into the influence of shear stress history on a graded sediment bed
Authors: Monteith Heather , Pender Gareth
Published: November 2005

A series of flume‐based experiments was undertaken to investigate the effect of below‐threshold antecedent flow conditions on the stability of a graded sediment bed (D16 = 1.8 mm, D50 = 4.8 mm, D84 = 7.8 mm, and σg = 2.08). The experiments revealed that stability is dependent not only on the applied shear stress of the antecedent flow (1.46, 2.08, 2.19, 2.41, and 2.63 N m−2) but also on its duration (0, 15, 30, 60, 1440 and 5760 min). A new stability diagram has been developed to illustrate stress history effects for the graded substrates and hydraulic conditions used in the investigation. The diagram has implications for flume‐based experimental practice, the prediction of sediment transport rates, and sediment management in river restoration.
Prophenoloxidase activation is not required for survival to microbial infections in Drosophila
Authors: Leclerc Vincent , Pelte Nadège , Chamy Laure El , Martinelli Cosimo , Ligoxygakis Petros , Hoffmann Jules A , Reichhart Jean‐Marc
Published: December 2005

The antimicrobial defence of Drosophila relies on cellular and humoral processes, of which the inducible synthesis of antimicrobial peptides has attracted interest in recent years. Another potential line of defence is the activation, by a proteolytic cascade, of phenoloxidase, which leads to the production of quinones and melanin. However, in spite of several publications on this subject, the contribution of phenoloxidase activation to resistance to infections has not been established under appropriate in vivo conditions. Here, we have isolated the first Drosophila mutant for a prophenoloxidase‐activating enzyme (PAE1). In contrast to wild‐type flies, PAE1 mutants fail to activate phenoloxidase in the haemolymph following microbial challenge. Surprisingly, we find that these mutants are as resistant to infections as wild‐type flies, in the total absence of circulating phenoloxidase activity. This raises the question with regard to the precise function of phenoloxidase activation in defence, if any.
Allotopic expression of a mitochondrial alternative oxidase confers cyanide resistance to human cell respiration
Authors: Hakkaart Gerrit A J , Dassa Emmanuel P , Jacobs Howard T , Rustin Pierre
Published: December 2005

Human mitochondrial respiration is distinct from that of most plants, microorganisms and even some metazoans in that it reduces molecular oxygen only through the highly cyanide‐sensitive enzyme cytochrome c oxidase. Here we show that expression of the cyanide‐insensitive alternative oxidase (AOX), recently identified in the ascidian Ciona intestinalis, is well tolerated by cultured human cells and confers spectacular cyanide resistance to mitochondrial substrate oxidation. The expressed AOX seems to be confined to mitochondria. AOX involvement in electron flow is triggered by a highly reduced redox status of the respiratory chain (RC) and enhanced by pyruvate; otherwise, the enzyme remains essentially inactive. AOX expression promises to be a valuable tool to limit the deleterious consequences of RC deficiency in human cells and whole animals.
A cold‐active pectin lyase from the psychrophilic and basidiomycetous yeast Cystofilobasidium capitatum strain PPY‐1
Authors: Nakagawa Tomoyuki , Nagaoka Toshinori , Miyaji Tatsuro , Tomizuka Noboru
Published: December 2005

In the present study we purified a cold‐active PNL (pectin lyase) from the extracellular fraction of the PPY (pectinolytic and psychrophilic yeast) Cystofilobasidium capitatum strain PPY‐1. The purified PNL has a molecular mass of approx. 42 kDa, and its N‐terminal amino acid sequence is ATGVTGSAYGFATGTTGGGSATPAY, which exhibits 72% identity with that of PNL F from Aspergillus niger. The purified PNL exhibited high activity at 10 °C, although its optimum temperature was 40 °C. Moreover, Km and Vmax for pectin as a substrate were found to have values 36.6 mg/ml and 3000 units/mg respectively. These findings may indicate that this enzyme from strain PPY‐1 is a cold‐active PNL that is able to degrade pectin compounds at low temperature.
Sigma‐1 receptor as regulator of neuronal intracellular Ca2+: clinical and therapeutic relevance
Authors: Monnet François P.
Published: December 2005

Preserving brain function and cognitive faculties during aging and psychiatric diseases (e.g. psychotic, anxiety and affective disorders, dementia) is essential for the self‐reliance and quality of life of patients. Cognitive loss involves not only memory, but also motor function. The decrease of catecholaminergic and excitatory neurotransmissions, as well as of protein phosphorylation, have currently been identified as prominent biological markers of the above‐mentioned diseases. Such deleterious biological events are well known to occur downstream of a progressive decline of intracellular Ca2+ signalling. This latter constitutes a key target for the neuronal plasticity that has also been reported during aging and psychiatric disorders. Most of the medicines used in psychiatry are active on the sigma‐1 receptor. This membrane bound receptor is widely distributed in memory‐associated cortical and motor‐related brainstem areas, prompting the hypothesis that it might contribute to the pathophysiology of these behavioural brain diseases. The sigma‐1 receptor is characterized by a unique mode of action by regulating both Ca2+ entry at the plasma membrane level (i.e. via potassium channels, voltage‐sensitive Ca2+ channels) and Ca2+ mobilization from endoplasmic stores [i.e. via Ins(1,4,5)P3receptors]. This review presents recent data supporting the notion that drugs acting via the endoplasmic reticulum‐coupled sigma‐1 receptor might reverse these deleterious events by restoring both extra‐ and intra‐cellular Ca2+‐dependent neuronal responses.
STAT3-mediated transcription of Bcl-2, Mcl-1 and c-IAP2 prevents apoptosis in polyamine-depleted cells
Authors: Bhattacharya Sujoy , Ray Ramesh M. , Johnson Leonard R.
Published: December 2005

Activation of STAT3 (signal transducer and activator of transcription 3) plays a crucial role in cell survival and proliferation. The aim of the present study was to clarify the role of STAT3 signalling in the protection of polyamine-depleted intestinal epithelial cells against TNF-α (tumour necrosis factor-α)-induced apoptosis. Polyamine depletion by DFMO (α-difluoromethylornithine) caused phosphorylation of STAT3 at Tyr-705 and Ser-727. Phospho-Tyr-705 STAT3 was immunolocalized at the cell periphery and nucleus, whereas phospho-Ser-727 STAT3 was predominantly detected in the nucleus of polyamine-depleted cells. Sustained phosphorylation of STAT3 at tyrosine residues was observed in polyamine-depleted cells after exposure to TNF-α. Inhibition of STAT3 activation by AG490 or cell-membrane-permeant inhibitory peptide (PpYLKTK; where pY represents phospho-Tyr) increased the sensitivity of polyamine-depleted cells to apoptosis. Expression of DN-STAT3 (dominant negative-STAT3) completely eliminated the protective effect of DFMO against TNF-α-induced apoptosis. Polyamine depletion increased mRNA and protein levels for Bcl-2, Mcl-1 (myeloid cell leukaemia-1) and c-IAP2 (inhibitor of apoptosis protein-2). Significantly higher levels of Bcl-2 and c-IAP2 proteins were observed in polyamine-depleted cells before and after 9 h of TNF-α treatment. Inhibition of STAT3 by AG490 and DN-STAT3 decreased Bcl-2 promoter activity. DN-STAT3 decreased mRNA and protein levels for Bcl-2, Mcl-1 and c-IAP2 in polyamine-depleted cells. siRNA (small interfering RNA)-mediated inhibition of Bcl-2, Mcl-1 and c-IAP2 protein levels increased TNF-α-induced apoptosis. DN-STAT3 induced the activation of caspase-3 and PARP [poly(ADP-ribose) polymerase] cleavage in polyamine-depleted cells. These results suggest that activation of STAT3 in response to polyamine depletion increases the transcription and subsequent expression of anti-apoptotic Bcl-2 and IAP family proteins and thereby promotes survival of cells against TNF-α-induced apoptosis.