bluuebunny/crossref_metadata_2025 huggingface dataset:
Free radical biology – terminology and critical thinking
Authors: Azzi Angelo , Davies Kelvin J.A , Kelly Frank
Published: January 2004

What is an antioxidant? Can one, at a cellular level, speak of direct and indirect antioxidants? Can oxidative stress be quantified and characterized? What are the oxidant species that may have regulatory functions in a cell? Since the above concepts have become of frequent use in all Journals it may be appropriate if some critical thinking outlined in this review could become available to a broad public.
PPARγ mediates NSAIDs‐induced upregulation of TFF2 expression in gastric epithelial cells
Authors: Shimada Tadahito , Koitabashi Ayako , Fujii Yoichiro , Hashimoto Takashi , Hosaka Kumi , Tabei Kyoko , Namatame Takashi , Yoneda Masashi , Hiraishi Hideyuki , Terano Akira
Published: January 2004

Trefoil factor family (TFF) is a group of peptides that play critical roles in maintaining gastric mucosal integrity. In real‐time quantitative reverse transcription‐polymerase chain reaction (RT‐PCR) and reporter gene assays, we show that indomethacin and aspirin upregulate TFF2 expression in MKN45 gastric cells. These drugs also activated peroxisome proliferator‐activated receptor γ (PPARγ) at concentration ranges that increase TFF2 expression, and upregulated TFF2 expression was suppressed by GW9662, a specific inhibitor of PPARγ. These results suggest that indomethacin and aspirin upregulate gastric expression of TFF2 through activation of PPARγ. This mechanism may be important in reducing the extent of gastric mucosal injury caused by the administration of non‐steroidal anti‐inflammatory drugs (NSAIDs).
Aryl hydrocarbon receptor‐mediated suppression of GH receptor and Janus kinase 2 expression in mice
Authors: Nukaya Manabu , Takahashi Yoshiki , Gonzalez Frank J , Kamataki Tetsuya
Published: January 2004

Differential mRNA display revealed that a cDNA encoding the major urinary protein 2 (MUP2) that belongs to the lipocalin superfamily was absent in livers of mice treated with 3‐methylcholanthrene (MC). The expression of MUP2 is known to be stimulated by growth hormone (GH), through the GH receptor (GHR), Janus kinase 2 (JAK2) and signal transducer and activator of transcription 5 (STAT5) signal transduction pathway. Since MC is an aryl hydrocarbon receptor (AhR) ligand, the effects of MC treatment on the expression of GHR, JAK2 or STAT5 in the livers of wild‐type or AhR‐null mice were examined. The result indicated that the expression of GHR and JAK2 mRNA was greatly decreased by MC in wild‐type mice but not in AhR‐null mice. In addition, the binding activity of STAT5 bound to STAT5‐binding element was reduced after MC treatment in wild‐type mice but not in AhR‐null mice. Based on these results, we conclude that the suppression of MUP2 mRNA expression by MC is caused by the AhR‐mediated disruption of the GH signaling pathway. Possible mechanism(s) by which exposure to aromatic hydrocarbons causes a decrease in the body weight of mice, which has been referred to as wasting syndrome, will also be discussed.
Functional properties of soybean nodulin 26 from a comparative three‐dimensional model
Authors: Biswas Sampa
Published: January 2004

A model of the nodulin 26 channel protein has been constructed based on comparative modeling and molecular dynamics simulations. Structural features of the protein indicate a selectivity filter that differs from those of the known structures of Escherichia coli glycerol facilitator and mammalian aquaporin 1. The model structure also reveals important roles of Ser207 and Phe96 in ligand binding and transport.
LACTATIONAL AMENORRHOEA IN WELL-NOURISHED TOBA WOMEN OF FORMOSA, ARGENTINA
Authors: VALEGGIA CLAUDIA , ELLISON PETER T.
Published: January 2004

The proximate causes of the contraceptive effect of lactation are still a matter of productive debate. This study sought to disentangle the relative impact that intense breast-feeding practices and maternal nutrition have on the regulation of ovarian function in nursing women. A mixed-longitudinal, direct-observational, prospective study was conducted of the return to postpartum fecundity in 113 breast-feeding, well-nourished Toba women. A sub-sample of 70 women provided data on nursing behaviour, daily activities, diet quality and urinary levels of oestrone and progesterone metabolites. Well-nourished, intensively breast-feeding Toba women experienced a relatively short period of lactational amenorrhoea (10·2±4·3 months) and a high lifetime fertility (TFR=6·7 live births/woman). Duration of lactational amenorrhoea was not correlated with any of the nursing parameters under study or with static measures of maternal nutritional status. The results indicated that the pattern of resumption of postpartum fertility could be explained, at least partly, by differences in individual metabolic budgets. Toba women resumed postpartum ovulation after a period of sustained positive energy balance. As the relative metabolic load hypothesis suggests, the variable effect of lactation on postpartum fertility may not depend on the intensity of nursing per se but rather on the energetic stress that lactation represents for the individual mother.
A numerical method of moments for solute transport in a porous medium with multiscale physical and chemical heterogeneity
Authors: Wu Jichun , Hu Bill X. , He Changming
Published: January 2004

In this study, geostatistical and stochastic methods are used to study groundwater flow and solute transport in a multiscale heterogeneous formation. The formation is composed of various materials, and distributions of conductivity and chemical sorption coefficient within each material are heterogeneous. The random distributions of materials in the formation are characterized by an indicator function. The conductivity and chemical sorption coefficient fields in each material are assumed to be statistically stationary. On the basis of these assumptions a general expression is derived for the covariance function of the composite field in terms of the covariance of the indicator variable and the properties of the composite materials. Darcy's law and perturbation method are applied to develop the covariance of the retarded velocity. The numerical method of moments [Zhang et al., 2000; Wu et al., 2003a, 2003b] is used to study the effects of various uncertain parameters on flow and transport predictions. Case studies have been conducted to investigate the influences of a medium's physical and chemical heterogeneity and nonstationarity on solute flux prediction. The study results indicate that the large‐scale heterogeneity dominates the effects on flow and solute transport processes, and the effect of small‐scale heterogeneity is secondary. It is also shown from the case studies that the numerical method of moments is applicable to studying flow and solute transport in complex subsurface environments, especially for the uncertainty analysis. Monte Carlo simulation is also conducted, and the results are compared with those obtained through method of moment. The calculation results of the mean total solute flux by the two methods match very well, but the variance of total solute flux obtained by the method of moments is smaller than that by the Monte Carlo method, especially for the cases with large total variances of the conductivity and sorption coefficient. In comparison with the Monte Carlo simulation, the method of moments is much more efficient in calculation.
What controls the apparent timescale of solute mass transfer in aquifers and soils? A comparison of experimental results
Authors: Haggerty Roy , Harvey Charles F. , Freiherr von Schwerin Claudius , Meigs Lucy C.
Published: January 2004

Estimates of mass transfer timescales from 316 solute transport experiments reported in 35 publications are compared to the pore‐water velocities and residence times, as well as the experimental durations. New tracer experiments were also conducted in columns of different lengths so that the velocity and the advective residence time could be varied independently. In both the experiments reported in the literature and the new experiments, the estimated mass transfer timescale (inverse of the mass‐transfer rate coefficient) is better correlated to residence time and the experimental duration than to velocity. Of the measures considered, the experimental duration multiplied by 1 + β (where β is the capacity coefficient, defined as the ratio of masses in the immobile and mobile domains at equilibrium) best predicted the estimated mass transfer timescale. This relation is consistent with other work showing that aquifer and soil material commonly produce multiple timescales of mass transfer.
Steady plumes in viscously stratified, vigorously convecting, three‐dimensional numerical mantle convection models with mobile plates
Authors: Lowman Julian P. , King Scott D. , Gable Carl W.
Published: January 2004

We present results from three‐dimensional (3‐D) Cartesian geometry computations featuring vigorous (high Rayleigh number) mantle convection in a system incorporating stiff tectonic plates with dynamically determined, time‐dependent velocities. We track plume‐related hot spot motion while calculating associated synthetic hot spot tracks, allowing us to estimate plume migration rates relative to plate motion rates. Plate‐like surface motion is achieved explicitly by specifying both the plate geometry and rigidity; however, plate velocities evolve dynamically in response to the buoyancy distribution within the convecting system, including buoyancy within the plate itself. We find that convection is characterized by downwelling sheets and varying numbers of 3‐D upwelling structures when the lower mantle to upper mantle viscosity ratio is varied from 9 to 90. As the lower mantle viscosity is increased relative to the upper mantle viscosity, the upwellings in the calculations evolve into vigorous (active) plumes characterized by long, narrow, thermal conduits with broad, disk‐like heads. The total number, shape, and persistence of the plumes are affected by the specified viscosity stratification in the calculations. Our findings indicate that hot spots associated with mantle plumes drift by smaller distances in comparable amounts of time when the lower mantle viscosity is increased relative to the upper mantle viscosity. In cases with a high lower mantle to upper mantle viscosity ratio, the depth of the flow aligned with plate motion is diminished and the plate‐scale return flow is integrated into a deep, unorganized, sluggish layer. As a result, plume conduit morphology in the lower mantle of such calculations is less influenced by plate motion than in calculations with a small difference between upper mantle and lower mantle viscosity. For lower mantle viscosities 30 times and 90 times greater than the upper mantle viscosity, the lower mantle velocity field is dominated locally by active plumes anchored in the lower thermal boundary layer of the convecting system and plume migration rates are typically only about 10% of the overriding plate velocity. In such cases, we also find that plume‐related hot spots persist for periods that we estimate to be between 0.55 and 1.1 plume‐transit times.
Rotational Raman Lidar measurements of atmospheric temperature in the UV
Authors: Di Girolamo P. , Marchese R. , Whiteman D. N. , Demoz B. B.
Published: January 2004

Measurements of atmospheric temperature have been performed by the NASA Scanning Raman Lidar based on the application of the pure rotational Raman (RR) technique. These measurements represent to our knowledge the first successful lidar measurements of temperature using the RR technique in the UV region, where eye‐safe concerns are far less stringent than in the visible and IR. While the system configuration was unoptimized for temperature measurements, nevertheless results were achieved that demonstrate the feasibility of the RR technique for meteorological and climatological applications. Based on 90 minutes data averaging, lidar measurements extend up to 23 km, with RMS deviation between lidar and simultaneous radiosondes not exceeding 1.2 K and average bias smaller than 0.5 K. Simulations reveal that the RR technique in the UV has the potential for providing accurate measurements throughout the troposphere, with appreciable improvement with respect to visible systems for daytime operation.
Bias characteristics in the AVHRR sea surface temperature
Authors: Zhang Huai‐Min , Reynolds Richard W. , Smith Thomas M.
Published: January 2004

To provide possible means to improve future satellite SST retrieval algorithms and to provide data users with error information, spatiotemporal bias patterns in the 1982–2002 NOAA operational AVHRR SST were characterized. At the start of one (NOAA‐14) satellite mission, typical global average biases were about −0.05°C, and gradually increased during the satellite mission. Normally global averages rarely exceeded 0.2°C, due to cancellation of larger biases of opposite signs in different regions. Biases were inhomogeneous and locally exceeded 0.5°C even in the 21‐year time mean. Large irregular biases were due to stratospheric aerosols from volcanic eruptions. Seasonal biases were strongly related to local weather phenomena, such as seasonal dust aerosols and cloud covers. The findings suggest that future satellite SST retrieval algorithms should be time and space dependent.
A study of the electrical charging of the Rosetta orbiter: 2. Experimental tests in a laboratory plasma
Authors: Berthelier Jean‐Jacques , Roussel Jean‐François
Published: January 2004

Following the numerical simulation presented in the companion paper, we have performed experimental tests in a plasma simulation chamber to check the results of the numerical model and validate its capability to properly predict the electrical equilibrium of the Rosetta orbiter. Since low temperature cometary plasmas cannot be directly reproduced in such a chamber, we conducted the tests in plasmas with scaled characteristics deduced by considering similarity laws as is done in wind tunnel experiments. A mock‐up of the Rosetta orbiter and solar panels was constructed with the capability of measuring collected currents over the various faces of the mock‐up. These measurements included the possibility of observations on finer scales typical of ion collection as measured by ion energy analysers. This series of tests has allowed us to validate the performances and the predictions of the model presented in the companion paper.
A study of the electrical charging of the Rosetta orbiter: 1. Numerical model
Authors: Roussel Jean‐François , Berthelier Jean‐Jacques
Published: January 2004

Charging of spacecraft in terrestrial or planetary ionospheres and magnetospheres is a well‐known effect which may have detrimental consequences for in‐situ plasma measurements. The case of the Rosetta mission is of particular importance because the expected temperatures of cometary ions and electrons in the inner coma of comet Wirtanen are very low. For this reason, we have undertaken a numerical simulation study of the electrical equilibrium of the Rosetta spacecraft in various conditions during its operational phase in order to determine its floating potential and the structure of the surrounding plasma sheath. The results of this study demonstrate that the electric equilibrium of the spacecraft is essentially controlled by the photoelectron current emitted by its very large solar panels. Only very close to the nucleus the expected plasma density is large enough to allow the spacecraft to collect enough thermal electrons to stay within a few kTe from the plasma potential. At larger distances it will float positive and at high potentials compared with the characteristic energy of cometary particles, thus hindering reliable ion measurements. A possible way to circumvent this effect is suggested by our numerical model. It relies on disconnecting the sunlit surface of the solar panels from the spacecraft ground. With such a grounding scheme the equilibrium electric potential of the spacecraft would stay at moderate values compatible with thermal ion measurements.
Neutral atom imaging of solar wind interaction with the Earth and Venus
Authors: Fok M.‐C. , Moore T. E. , Collier M. R. , Tanaka T.
Published: January 2004

Observations from the Low‐Energy Neutral Atom (LENA) imager on the Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE) mission have emerged as a promising new tool for studying the solar wind interaction with the terrestrial magnetosphere. Strong LENA emissions are seen from the magnetosheath during magnetic storms, especially during high solar wind dynamic pressure when the magnetopause is strongly compressed and the magnetosheath penetrates deeply into the exosphere. Venus, unlike the Earth, has no intrinsic magnetic field, so the solar wind penetrates deeply and interacts directly with its upper atmosphere. Energy transfer processes enhance atomic escape and thus play a potentially important role in the evolution of the atmosphere. We have performed simulations of the solar wind interaction with both Earth and Venus and compared the results to LENA observations at the Earth. Low‐energy neutral atom emissions from Venus are calculated based on the global MHD model of Tanaka. We found the simulated energetic neutral atom (ENA) emissions from Venus magnetosheath are comparable or greater than for the Earth. The Venus ionopause is clearly seen in the modeled oxygen ENA images. This simulation work demonstrates the feasibility of remotely sensing the Venusian solar wind interaction and resultant atmospheric escape using fast neutral atom imaging.
Stabilization of right‐hand polarized beam plasma instabilities due to a large‐amplitude left‐hand polarized wave: A simulation study
Authors: Araneda J. A. , Gomberoff L.
Published: January 2004

It has been recently shown that the presence of large amplitude left‐hand polarized waves can change the linear properties of ion‐beam plasma electromagnetic instabilities [Gomberoff, 2003]. Thus, it was shown that in the presence of large amplitude Alfvén or ion‐cyclotron waves, linear beam‐plasma right‐hand polarized instabilities tend to be stabilized. In particular, when the nonlinear wave amplitude exceeds a threshold value, the linear instability can be completely stabilized. Here, by using computer simulation techniques based upon a one‐dimensional hybrid code, we confirm these results.
Quiet‐time seasonal behavior of the thermosphere seen in the far ultraviolet dayglow
Authors: Strickland D. J. , Meier R. R. , Walterscheid R. L. , Craven J. D. , Christensen A. B. , Paxton L. J. , Morrison D. , Crowley G.
Published: January 2004

The TIMED/GUVI instrument is a far ultraviolet spectrograph that obtains images in five spectrally resolved wavelength channels. These images yield information on the dayside composition, temperature, solar EUV flux, large‐scale wave structures, and auroral processes. In this paper we present an overview analysis of Earth‐disk images for four seasons (March, July, and September 2002 and January 2003). Days were selected during geomagnetically quiet periods when the Sun was nearly in the orbital plane (noon orbits). Two of GUVI's five channels (designated as 135.6 and LBHS and dominated by OI 135.6 nm and short wavelength N2 LBH band emission, respectively) are used when the instrument is in its imaging mode. These data are used to derive O/N2 (column density ratio referenced to an N2 column density of 1017 cm−2). The AURIC model is used to generate a lookup table that relates O/N2 to the ratio of 135.6 to LBHS for a given solar zenith angle. Global images of derived O/N2 (designated as GUVI O/N2) are presented for the 4 days. The initial validation of the retrieved composition ratio comes from comparison with the NRLMSIS model. Good overall qualitative agreement is obtained between GUVI and NRLMSIS. Both data and model exhibit similar latitudinal behaviors on the near‐solstice days, namely a distinct gradient with O/N2 decreasing from the winter to the summer hemisphere. Reductions in O/N2 in the vicinity of magnetic poles are seen in both GUVI and NRLMSIS images. Globally, O/N2 is smaller at the solstices and may be explained by the “thermospheric spoon” mechanism discussed by Fuller‐Rowell [1998]. Alternatively, the greater overall values at the equinoxes may arise in part from global response to greater Joule heating at these times of the year. The sensitivity of O/N2 to scalings of the N2 LBH cross section and solar EUV below 20 nm is also addressed in response to recent papers on these topics. This initial look at the GUVI data demonstrates great promise of FUV remote sensing as a way to observe thermospheric composition changes over broad geographic scales.
Temperature fields generated by the elastodynamic propagation of shear cracks in the Earth
Authors: Fialko Yuri
Published: January 2004

Thermal perturbations associated with seismic slip on faults may significantly affect the dynamic friction and the mechanical energy release during earthquakes. This paper investigates details of the coseismic temperature increases associated with the elastodynamic propagation of shear cracks and effects of fault heating on the dynamic fault strength. Self‐similar solutions are presented for the temperature evolution on a surface of a mode II shear crack and a self‐healing pulse rupturing at a constant velocity. The along‐crack temperature distribution is controlled by a single parameter, the ratio of the crack thickness to the width of the conductive thermal boundary layer,. For “thick” cracks, or at early stages of rupture (> 1), the local temperature on the crack surface is directly proportional to the amount of slip. For “thin” cracks, or at later times (< 1), the temperature maximum shifts toward the crack tip. For faults having slip zone thickness of the order of centimeters or less, the onset of thermally induced phenomena (e.g., frictional melting, thermal pressurization, etc.) may occur at any point along the rupture, depending on the degree of slip localization and rupture duration. In the absence of significant increases in the pore fluid pressure, localized fault slip may raise temperature by several hundred degrees, sufficient to cause melting. The onset of frictional melting may give rise to substantial increases in the effective fault strength due to an increase in the effective fault contact area, and high viscosity of silicate melts near solidus. The inferred transient increases in the dynamic friction (“viscous braking”) are consistent with results of high‐speed rock sliding experiments and might explain field observations of the fault wall rip‐out structures associated with pseudotachylites. Possible effects of viscous braking on the earthquake rupture dynamics include (1) delocalization of slip and increases in the effective fracture energy, (2) transition from a crack‐like to a pulse‐like rupture propagation, or (3) ultimate rupture arrest. Assuming that the pulse‐like ruptures heal by incipient fusion, the seismologic observations can be used to place a lower bound on the dynamic fault friction. This bound is found to be of the order of several megapascals, essentially independent of the earthquake size. Further experimental and theoretical studies of melt rheology at high strain rates are needed to quantify the effects of melting on the dynamic fault strength.
Low‐frequency sea waves generated by atmospheric convection cells
Authors: de Jong M. P. C. , Battjes J. A.
Published: January 2004

The atmospheric origin of low‐frequency sea waves that cause seiches in the Port of Rotterdam is investigated using hydrological and meteorological observations. These observations, combined with weather charts, show that all significant seiche events coincide with the passage of a low‐pressure area and a cold front. Following these front passages, increased wind speed fluctuations occur with periods on the order of 1 hour. The records show that enhanced low‐frequency wave energy at sea and the seiche events in the harbor occur more or less simultaneously with these strong wind speed fluctuations. These oscillatory wind speed changes are due to convection cells that arise in an unstable lower atmosphere in the area behind a cold front, where cold air moves over the relatively warm sea surface. It is shown that the moving system of a cold front and trailing convection cells generates forced low‐frequency waves at sea that can cause seiche events inside the harbor. The occurrence of such events may be predictable operationally on the basis of a criterion for the difference in temperature between the air in the upper atmosphere and the water at the sea surface.
Development and application of the Model of Aerosol Dynamics, Reaction, Ionization, and Dissolution (MADRID)
Authors: Zhang Yang , Pun Betty , Vijayaraghavan Krish , Wu Shiang‐Yuh , Seigneur Christian , Pandis Spyros N. , Jacobson Mark Z. , Nenes Athanasios , Seinfeld John H.
Published: January 2004

A new aerosol model, the Model of Aerosol Dynamics, Reaction, Ionization, and Dissolution (MADRID) has been developed to simulate atmospheric particulate matter (PM). MADRID and the Carnegie‐Mellon University (CMU) bulk aqueous‐phase chemistry have been incorporated into the three‐dimensional Models‐3/Community Multiscale Air Quality model (CMAQ). The resulting model, CMAQ‐MADRID, is applied to simulate the August 1987 episode in the Los Angeles basin. Model performance for ozone and PM is consistent with current performance standards. However, organic aerosol was underpredicted at most sites owing to underestimation of primary organic PM emissions and secondary organic aerosol (SOA) formation. Nitrate concentrations were also sometimes underpredicted, mainly owing to overpredictions in vertical mixing, underpredictions in relative humidity, and uncertainties in the emissions of primary pollutants. Including heterogeneous reactions changed hourly O3 by up to 17% and 24‐hour average PM2.5, sulfate2.5, and nitrate2.5 concentrations by up to 3, 7, and 19%, respectively. A SOA module with a mechanistic representation provides results that are more consistent with observations than that with an empirical representation. The moving‐center scheme for particle growth predicts more accurate size distributions than a typical semi‐Lagrangian scheme, which causes an upstream numerical diffusion. A hybrid approach that simulates dynamic mass transfer for coarse PM but assumes equilibrium for fine PM can predict a realistic particle size distribution under most conditions, and the same applies under conditions with insignificant concentrations of reactive coarse particles to a bulk equilibrium approach that allocates transferred mass to different size sections based on condensational growth law. In contrast, a simple bulk equilibrium approach that allocates transferred mass based on a given distribution tends to cause a downstream numerical diffusion in the predicted particle size distribution.
Permafrost dynamics in the 20th and 21st centuries along the East Siberian transect
Authors: Sazonova T. S. , Romanovsky V. E. , Walsh J. E. , Sergueev D. O.
Published: January 2004

The East Siberian transect, which has been designated by the International Geosphere‐Biosphere Program (IGBP) as its Far East transect, has unique permafrost conditions. Not only does permafrost underlie the entire transect, but also about one third of the region is underlain by an “ice complex,” consisting of extremely ice‐rich Late Pleistocene sediments. Given the possibility of a predicted future increase in global temperatures, an evaluation of the magnitude of changes in the ground thermal regime becomes desirable for assessments of possible ecosystem responses and impacts on infrastructure. A soil model developed at the Geophysical Institute Permafrost Laboratory was used to simulate the dynamics of the active layer thickness and ground temperature in this transect, both retrospectively and prognostically, using climate forcing from six global climate models (GCMs). Analysis of future permafrost dynamics showed that within the southwestern part of the transect, widespread permafrost thawing from the surface can begin as early as 2050. The spatial extent and temporal dynamics of the zone with thawing permafrost vary significantly among the different GCMs. According to all the GCMs the mean annual ground temperatures could rise by 2°–6°C, and the active layer thickness could increase by 0.5–2 m everywhere within the transect by 2099. However, the increases in mean annual ground temperature and active layer thickness are not uniform in time. Relatively cold and warm periods associated with natural fluctuations in air temperature and precipitation are superimposed on the background warming trend. The most significant increases in mean annual ground temperatures and in the active layer thickness are projected to occur in the southwestern part of the transect and in areas with coarse‐grained sediments, characterized by low water content and high thermal conductivity.
Updated radiative forcing estimates of four halocarbons
Authors: Gohar L. K. , Myhre G. , Shine K. P.
Published: January 2004

There is a large discrepancy (greater than 20%) between two recently published estimates of radiative forcing of four hydrofluorocarbons (HFCs), two of which, HFC‐23 and HFC‐134a, are the most abundant HFCs in the atmosphere. We report an intercomparison, using two different radiative transfer methods, aimed at clarifying the forcing values for HFC‐23 and HFC‐134a, as well as HFC‐227ea and HFC‐32. The calculated global, annual mean radiative forcings differed by 12% or less and are within the expected errors in the radiative forcing estimates.
A combined modeling and measurement technique for estimating windblown dust emissions at Owens (dry) Lake, California
Authors: Gillette Dale , Ono Duane , Richmond Kenneth
Published: January 2004

The problem of dust emissions from playa sources is an important one both in terms of human health and in terms of global dust issues, distribution of loess, and mineral cycling. A refined method of modeling atmospheric dust concentrations due to wind erosion was developed using real‐time saltation flux measurements and ambient dust monitoring data at Owens Lake, California. This modeling method may have practical applications for modeling the atmospheric effects of wind erosion in other areas. Windblown dust from the Owens Lake bed often causes violations of federal air quality standards for particulate matter (PM10) that are the highest levels measured in the United States. The goal of this study was to locate dust source areas on the exposed lake bed, estimate their PM10 emissions, and use air pollution modeling techniques to determine which areas caused or contributed to air quality violations. Previous research indicates that the vertical flux of PM10 (Fa) is generally proportional to the total horizontal saltation flux (q) for a given soil texture and surface condition. For this study, hourly PM10 emissions were estimated using Fa = K′ × m15, where m15 is the measured sand flux at 15 cm above the surface, and K′ was derived empirically by comparing air quality model predictions to monitored PM10 concentrations. Hourly sand flux was measured at 135 sites (1 km spacing) on the lake bed, and PM10 was monitored at six off‐lake sites for a 30 month period. K′ was found to change spatially and temporally over the sampling period. These changes appeared to be linked to different soil textures and to seasonal surface changes. K′ values compared favorably with other Fa/q values measured at Owens Lake using portable wind tunnel and micrometeorological methods. Hourly trends for the model‐predicted PM10 concentrations agreed well with monitored PM10 concentrations. Dust production was estimated at 7.2 × 104 t of PM10 for a 12 month period. A single storm accounted for 9% of the annual dust emissions at 6.5 × 103 t. The modeling results were used to identify 77 km2 of dust‐producing areas on the lake bed that will be controlled to attain the federal air quality standard for PM10.
Dense nonaqueous phase liquid (DNAPL) source zone characterization: Influence of hydraulic property correlation on predictions of DNAPL infiltration and entrapment
Authors: Lemke Lawrence D. , Abriola Linda M. , Goovaerts Pierre
Published: January 2004

The influence of aquifer property correlation on multiphase fluid migration and entrapment was explored through the use of correlated and uncorrelated porosity, permeability, and capillary pressure‐saturation (Pc‐Sat) parameter fields in a cross‐sectional numerical multiphase flow model. Data collected from core samples in a nonuniform sandy aquifer were used to generate three‐dimensional aquifer parameter fields. Porosity was assumed to be uniform or simulated using sequential Gaussian simulation (SGS). Permeability (k) was modeled independently of porosity using SGS as well as simulated geostatistical indicator classes derived from measured grain size distribution curves. Retention characteristics were assigned employing Leverett scaling of a representative Pc‐Sat curve to the geostatistical k fields or, alternatively, on the basis of simulated indicator classes and porosity values. Ensemble dense nonaqueous phase liquid (DNAPL) infiltration and entrapment behavior for a hypothetical tetrachloroethylene (PCE) spill was simulated in four sets of two‐dimensional profiles extracted from these realizations. Comparisons of saturation profiles and spatial moments from point source DNAPL infiltration simulations suggest that choices involving the geostatistical algorithm used to model k and the incorporation of variable versus uniform porosity have a smaller influence than choices involving the scaling of capillary retention properties to k. From these simulations it is apparent that the degree of spatial correlation in Pc‐Sat parameters exerts a controlling influence on predicted DNAPL spreading and redistribution in saturated aquifers. The resultant distribution of mass within a DNAPL source zone will have implications for DNAPL recovery and subsequent mass fluxes in remediation operations.
Lattice Boltzmann method for modeling liquid‐vapor interface configurations in porous media
Authors: Sukop Michael C. , Or Dani
Published: January 2004

The lattice Boltzmann method (LBM) has emerged as a powerful tool for simulating the behavior of multiphase fluid systems in complex pore networks. Specifically, the single component multiphase LBM can simulate the interfacial phenomena of surface tension and adsorption and thus be used for modeling fluids such as water and its vapor in porous media. This paper provides an introduction to LBM applications to interface configurations in partially saturated porous media. Key elements of this LBM application are fluid‐fluid and fluid‐solid interactions that successfully mimic the Young‐Laplace equation and liquid film adsorption. LBM simulations of liquid behavior in simple pore geometry considering capillarity and adsorption are in good agreement with analytical solutions and serve as critical first steps toward validating this approach. We demonstrate the usefulness of LBM in constructing virtual liquid retention measurements based on porous media imagery. Results of this study provide a basis for application of LBM to understanding liquid configurations in more complex geometries and clear a path for applications involving interface migration, flow, and transport in partially saturated porous media.
Independent CD28 signaling via VAV and SLP‐76: a model for in trans costimulation
Authors: Rudd Christopher E. , Raab Monika
Published: January 2004

Summary:  The two‐signal theory of T‐cell activation dictates that optimal T‐cell responses are determined by a least two signals, the primary signal provided by the antigen‐receptor complex (TCR/CD3) and the second signal provided by a costimulatory receptor. Recent studies have underlined the importance of in trans costimulation via CD28 in the regulation of transplant rejection. Previous studies have emphasized the ability of CD28 to operate in cis in the amplification of signaling through the T‐cell receptor (TCR). Our recent work has demonstrated that CD28 can activate the lipid kinase phosphatidylinositol 3‐kinase (PI‐3K) and can cooperate with adapters Vav and SLP‐76 to influence the induction of interleukin (IL)‐2 and IL‐4 transcription in the absence of TCR ligation. CD28–PI‐3K binding and CD28–VAV/SLP‐76 cooperativity provide a pathway to account for in trans costimulation in T‐cell immunity.
The PI‐3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3
Authors: Kane Lawrence P. , Weiss Arthur
Published: January 2004

Summary Ligation of the T cell receptor for antigen (TCR) and/or costimulatory receptor CD28 results in rapid activation of phosphoinositide‐3 kinase (PI‐3 kinase). It remains unclear, however, precisely how this activation occurs and also how the newly generated phospholipid products trigger the various events associated with T cell activation. Here we discuss the current understanding of how PI‐3 kinase is activated by the TCR and CD28 and what roles its products play in T cell activation. We also review recent advances in understanding the function of Akt in particular, especially its role in CD28 costimulation. Several functional targets of Akt are discussed in this regard: inducible transcription, cell survival, glucose metabolism, and the cellular translational machinery. These pathways have been associated with TCR/CD28 costimulation, and they have also been implicated as targets of Akt.
T cell anergy and costimulation
Authors: Appleman Leonard J. , Boussiotis Vassiliki A.
Published: January 2004

Summary:  T lymphocytes play a key role in immunity by distinguishing self from nonself peptide antigens and regulating both the cellular and humoral arms of the immune system. Acquired, antigen‐specific unresponsiveness is an important mechanism by which T cell responses to antigen are regulated in vivo. Clonal anergy is the term that describes T cell unresponsiveness at the cellular level. Anergic T cells do not proliferate or secrete interleukin (IL)‐2 in response to appropriate antigenic stimulation. However, anergic T cells express the IL‐2 receptor, and anergy can be broken by exogenous IL‐2. Anergy can be induced by submitogenic exposure to peptide antigen in the absence of a costimulatory signal provided by soluble cytokines or by interactions between costimulatory receptors on T cells and counter‐receptors on antigen‐presenting cells. The molecular events that mediate the induction and maintenance of T cell anergy are the focus of this review. The molecular consequences of CD28–B7 interaction are discussed as a model for the costimulatory signal that leads to T cell activation rather than the induction of anergy.
Lipid phosphatases in the regulation of T cell activation: living up to their PTEN‐tial
Authors: Seminario Maria‐Cristina , Wange Ronald L.
Published: January 2004

Summary: The initiating events associated with T activation in response to stimulation of the T cell antigen receptor (TCR) and costimulatory receptors, such as CD28, are intimately associated with the enzymatically catalyzed addition of phosphate not only to key tyrosine, threonine and serine residues in proteins but also to the D3 position of the myo‐inositol ring of phosphatidylinositol (PtdIns). This latter event is catalyzed by the lipid kinase phosphoinositide 3‐kinase (PI3K). The consequent production of PtdIns(3,4)P2 and PtdIns(3,4,5)P3 serves both to recruit signaling proteins to the plasma membrane and to induce activating conformational changes in proteins that contain specialized domains for the binding of these phospholipids. The TCR signaling proteins that are subject to regulation by PI3K include Akt, phospholipase Cγ1 (PLCγ1), protein kinase C ζ (PKC‐ζ), Itk, Tec and Vav, all of which play critical roles in T cell activation. As is the case for phosphorylation of protein substrates, the phosphorylation of PtdIns is under dynamic regulation, with the D3 phosphate being subject to hydrolysis by the 3‐phosphatase PTEN (phosphatase and tensin homolog deleted on chromosome 10), thereby placing PTEN in direct opposition to PI3K. In this review we consider recent data concerning how PTEN may act in regulating the process of T cell activation.
The PKC gene module: molecular biosystematics to resolve its T cell functions
Authors: Baier Gottfried
Published: January 2004

Summary:  The distinct protein kinase C (PKC) multigene family (PKC gene module) is known to be the ‘classic’ intracellular receptor for mitogenic phorbol esters, and it is widely accepted in the scientific community that the ‘PKC effect’ is essential in activation, differentiation, adhesion and motility, as well as in cellular survival, of T cells. Nevertheless, the first concepts about PKC isotype heterogeneity of cellular localization and function emerged only recently, when the PKC‐θ pathways were mapped to critical signaling networks that control T cell receptor (TCR)/CD3‐dependent interleukin (IL)‐2 production and proliferation in T lymphocytes. This review summarizes the current knowledge about T cell expressed PKC gene products, their known and/or suspected regulation and cellular effector pathways, as well as physiological functions in T lymphocytes (as determined by molecular cell biology and ongoing mouse genetic studies). Given PKCs integral role in T cell function but today's very fragmentary molecular understanding of directly PKC‐mediated effector functions in transmembrane signaling, a ‘molecular biosystematics’ approach is suggested to resolve the isotype‐selective functions of this PKC gene family. Such an approach has to be based not only on genomic/cytogenetic analysis to establish its genetic relationships but also on biochemical/cell biology and genetic studies to resolve its functional diversity and, ultimately, nonredundant roles in real T cell physiology.
JNK and p38 MAP kinases in CD4+ and CD8+ T cells
Authors: Rincón Mercedes , Pedraza‐Alva Gustavo
Published: January 2004

Summary:  The c‐Jun aminoterminal kinase (JNK) and p38 mitogen‐activated protein (MAP) kinase signaling pathways have been associated with cell death, differentiation and proliferation. CD4+ and CD8+ T cells have different effector functions after antigen stimulation and control specific aspects of the immune response. The studies carried out in our group indicate that the role of JNK and p38 MAP kinases in CD4+ T cells is different from their role in CD8+ T cells. Moreover, these two pathways are not redundant in either T cell population. We have also shown that p38 MAP kinase regulates early stages of T cell development in the thymus. It is therefore important to consider the specific function of these kinases in each T cell population when pharmacological inhibitors of JNK and p38 MAP kinases are used for therapeutic purposes to control the immune response.
Regulation of cytokine receptor signaling by SOCS1
Authors: Ilangumaran Subburaj , Rottapel Robert
Published: January 2004

Summary:  The suppressor of cytokine signaling (SOCS) family of proteins is a novel class of negative feedback regulators of cytokine receptor signaling. SOCS1 is rapidly induced following stimulation by several type I and type II cytokines, and it attenuates their signaling by its ability to bind and inhibit all four of the Janus family of intracellular tyrosine kinases (JAKs). Studies from our own and other laboratories have documented another important function of SOCS1 in facilitating ubiquitination of protein substrates and their subsequent proteasomal degradation. SOCS1 also functions as a potential tumor suppressor by inhibiting several hematopoietic oncogenes. In addition to these negative regulatory functions, we have recently shown a positive regulatory role for SOCS1 in increasing the stability of major histocompatibility complex (MHC) class II proteins by preventing their degradation. These findings illustrate multiple roles for SOCS1 in cytokine receptor signaling, and provide groundwork for detailed analysis of the role of SOCS1 in pre‐T cell receptor (TCR) and TCR signaling, and regulation of T helper (Th)1 and Th2 differentiation.
Sin: good or bad? A T lymphocyte perspective
Authors: Alexandropoulos Konstantina , Donlin Laura T. , Xing Luzhou , Regelmann Adam G.
Published: January 2004

Summary:  Stimulation of T cells through their antigen receptor induces a multitude of signaling networks that regulate T cell activation in the form of cytokine production and T cell proliferation. Multiple signal integration sites exist along these pathways in the form of multiprotein signaling complexes, the formation of which is facilitated by adapter and scaffold molecules. In recent years a number of adapter and scaffold molecules have been described in T cells and shown to play an integral part in T cell function. Among these molecules are proteins that function as positive or negative regulators of T cell activation downstream of the activated T cell receptor (TCR). Here, we discuss the role of a small family of multiadapter proteins on T cell activation, the p130Cas family, with emphasis on one of its members, Sin (Src‐interacting protein). Our results suggest that Sin inhibits thymocyte development and T cell activation and is a novel negative regulator of T lymphocyte function.
Negative feedback of T cell activation through inhibitory adapters and costimulatory receptors
Authors: Saito Takashi , Yamasaki Sho
Published: January 2004

Summary:  Antigen recognition by the T cell receptor (TCR) complex induces the formation of a TCR signalosome by recruiting various signaling molecules, generating the recognition signals for T cell activation. The activation status and functional outcome are positively and negatively regulated by dynamic organization of the signalosome and by costimulation signals. We have studied the negative regulation of T cell activation, particularly through inhibitory adapters and costimulation receptors that are little expressed in resting cells but are induced upon T cell activation. We described Grb‐associated binder 2 (Gab2) and cytotoxic T lymphocyte antigen‐4 (CTLA‐4) as a representative inhibitory adapter and a negative costimulation receptor, respectively, both of which exhibit negative feedback. Gab2 functions as a signal branch for activation vs. inhibition, as phosphorylation of either Src homology 2 (SH2) domain‐containing leukocyte phosphoprotein of 76 kDa (SLP‐76) or Gab2 by zeta‐associated protein of 70 kDa (ZAP‐70) determines the fate of the response. As a professional inhibitory receptor, CTLA‐4 inhibits T cell response by competition of ligand binding with positive costimulator receptor CD28, and also induces inhibitory signaling. The trafficking and the cell surface expression of CTLA‐4 are dynamically regulated and induced. CTLA‐4 is accumulated in lysosomes and secreted to the T cell–APC contact site upon TCR stimulation. As T cell activation proceeds, these inhibitory adapters and costimulation receptors are induced and suppress/regulate the responses as negative feedback.
Molecular and immunological basis of X‐linked lymphoproliferative disease
Authors: Latour Sylvain , Veillette André
Published: January 2004

Summary:  X‐linked lymphoproliferative (XLP) disease is a human immune dysfunction characterized primarily by an inappropriate response to Epstein–Barr virus infection. In 1998, it was discovered that XLP is caused by inactivating mutations in the SAP/SH2D1A/DSHP gene. This gene codes for an immune cell‐specific polypeptide termed SAP (SLAM‐associated protein) that is composed almost exclusively of an Src homology 2 (SH2) domain. By way of its SH2 domain, SAP interacts with tyrosine‐based motifs located in the cytoplasmic region of members of the SLAM (signaling lymphocyte activation molecule) family of receptors. Recent findings indicate that SAP is required for the function of SLAM‐related receptors, as a consequence of its capacity to promote the recruitment and activation of the Src‐related protein tyrosine kinase FynT, thereby allowing SLAM receptor‐mediated protein tyrosine phosphorylation signals in immune cells. Functional and genetic analyses suggest that the phenotype associated with XLP is caused in large part by defects in the functions of SLAM‐related receptors due to SAP deficiency.