bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signal Transducer and Activator of Transcription 3 Is Required for Hypoxia-Inducible Factor-1α RNA Expression in Both Tumor Cells and Tumor-Associated Myeloid Cells
Authors: Niu Guilian , Briggs Jon , Deng Jiehui , Ma Yihong , Lee Heehyoung , Kortylewski Marcin , Kujawski Maciej , Kay Heidi , Cress W. Douglas , Jove Richard , Yu Hua 
Published: July 2008

Abstract
Hypoxia-inducible factor 1 (HIF-1) is a potent tumorigenic factor. Its α subunit (HIF-1α), which is tightly regulated in normal tissues, is elevated in tumors due to hypoxia and overactive growth signaling pathways. Although much is known about HIF-1α regulation in cancer cells, crucial molecular targets that affect HIF-1α levels modulated by both hypoxia and oncogenic signaling pathways remain to be identified. Additionally, whether and how the tumor microenvironment contributes to HIF-1α accumulation is unclear. This study shows a novel mechanism by which HIF-1α availability is regulated in both cancer cells and in myeloid cells in the tumor microenvironment. We show a requirement of signal transducer and activator of transcription 3 (Stat3) for HIF-1α RNA expression under both hypoxia and growth signaling conditions. Furthermore, tumor-derived myeloid cells express elevated levels of HIF-1α mRNA relative to their counterparts from normal tissues in a Stat3-dependent manner. Additionally, Stat3 activity in the nontransformed cells in the tumor milieu affects HIF-1α RNA expression of the entire growing tumor. Consistent with a role of Stat3 in regulating HIF-1α RNA transcription, elevated Stat3 activity increases HIF-1α promoter activity, and Stat3 protein binds to the HIF-1α promoter in both transformed cells and in growing tumors. Taken together, these findings show a novel mode by which HIF-1α is regulated not only in cancer cells but also in the tumor-associated inflammatory cells, suggesting Stat3 as an important molecular target for inhibiting the oncogenic potential of HIF-1 induced by both hypoxia and overactive growth signaling pathways prevalent in cancer. (Mol Cancer Res 2008;6(7):1099–105)
Gain-of-Function Mutations in the Extracellular Domain of KIT Are Common in Canine Mast Cell Tumors
Authors: Letard Sébastien , Yang Ying , Hanssens Katia , Palmérini Fabienne , Leventhal Phillip S. , Guéry Stéphanie , Moussy Alain , Kinet Jean-Pierre , Hermine Olivier , Dubreuil Patrice 
Published: July 2008

Abstract
In the current study, we examined the types and frequency of KIT mutations in mast cell tumors from 191 dogs. Sequencing of reverse transcription-PCR products revealed alterations in 50 (26.2%) of the dogs. Most mutations were in exon 11 (n = 32), and of these, most were internal tandem duplications (n = 25) between residues 571 and 590. Within exon 11, there were two hotspots for mutations at codons 555-559 and 571-590. In addition, nine dogs had mutations in exon 8 and eight had mutations in exon 9. We selected the two most common mutants and two representative exon 11 mutants for further analysis. When expressed in Ba/F3 cells, they were constitutively tyrosine phosphorylated and induced growth factor–independent cell proliferation. AG1296, a tyrosine kinase inhibitor, dose dependently inhibited both the tyrosine phosphorylation of these mutants and their induction of growth factor–independent proliferation. This study shows that activating mutations in not only exon 11 but also exons 8 and 9 are common in canine mast cell tumors. These results also show that Ba/F3 cells can be used for the direct characterization of canine KIT mutants, eliminating the need to make equivalent mutations in the mouse or human genes. (Mol Cancer Res 2008;6(7):1137–45)
Momentum and Energy Transport by Gravity Waves in Stochastically Driven Stratified Flows. Part II: Radiation of Gravity Waves from a Gaussian Jet
Authors: Bakas Nikolaos A. , Farrell Brian F. 
Published: July 2008

Abstract
Interaction between the midlatitude jet and gravity waves is examined, focusing on the nonnormality of the underlying linear dynamics, which plays an essential role in processing the wave activity and selecting structures that dominate wave momentum and energy transport. When the interior of a typical midlatitude jet is stochastically forced, waves with short horizontal wavelength are trapped inside the jet and deposit momentum and energy at jet interior critical levels. Longer waves transport momentum and energy away from the jet, and the resulting momentum flux divergence produces a significant deceleration of the tropospheric and lower-stratospheric jet. This induced drag is found to depend on the shape of the jet and on the horizontal wavelength of the excited waves, reaching a maximum at wavelength λx = 20 km and leading to a deceleration O(1) m s−1 day−1 for a stochastic forcing rate of 0.1 W m−2 distributed over the height of the jet. This deceleration is robust to changes in static stability but is reduced when the stochastic forcing is correlated over too long a time.
Implications of gravity wave absorption for middle-atmosphere circulation are discussed, focusing on differences implied for acceleration of the winter and summer midlatitude upper-stratospheric jets. The tropospheric flow is found not only to passively filter transiting waves, but also to amplify portions of the wave spectrum in conjunction with the distributed forcing, leading to enhanced gravity wave momentum and energy fluxes in agreement with observations linking middle-atmosphere enhanced variance with regions of high jet velocities.
Morphology of Tropical Upwelling in the Lower Stratosphere
Authors: Geller Marvin A. , Zhou Tiehan , Hamilton Kevin 
Published: July 2008

Abstract
Sensitivity tests of a mechanistic model of the mean meridional circulation driven by specified eddy forcing are conducted to investigate how the morphology of tropical upwelling in the lower stratosphere is related to the structure of the forcing expected to be associated with the stratospheric surf zone. The basic morphology of tropical upwelling is found to be similar among the mechanistic model forced with reasonable eddy fluxes, the Geophysical Fluid Dynamics Laboratory (GFDL) SKYHI GCM, U.K. Met Office (UKMO) analyses, and other climate models, indicating the robustness of the upwelling features. Atmospheric data are analyzed to characterize the interannual variability of wave drag. The influence of such variations on the interannual variability of tropical upwelling in the lower stratosphere is explored, which may help explain the observed interannual variability of stratospheric water vapor.
Analytical Solutions to the Stochastic Kinetic Equation for Liquid and Ice Particle Size Spectra. Part I: Small-Size Fraction
Authors: Khvorostyanov Vitaly I. , Curry Judith A. 
Published: July 2008

AbstractThe kinetic equation of stochastic condensation for cloud drop size spectra is extended to account for crystalline clouds and also to include the accretion–aggregation process. The size spectra are separated into small and large size fractions that correspond to cloud drops (ice) and rain (snow). In Part I of this two-part paper, analytical solutions are derived for the small-size fractions of the spectra that correspond to cloud drops and cloud ice particles that can be identified with cloud liquid water or cloud ice water content, and used in bulk microphysical schemes employed in cloud and climate models. Solutions for the small-size fraction have the form of generalized gamma distributions. Simple analytical expressions are found for parameters of the gamma distributions that are functions of quantities that are available in cloud and climate models: liquid or ice water content and its vertical gradient, mean particle radius or concentration, and supersaturation or vertical velocities. Equations for the gamma distribution parameters provide an explanation of the dependence of the observed spectra on atmospheric dynamics, cloud temperature, and cloud liquid water or ice water content. The results are illustrated with example calculations for a crystalline cloud. The analytical solutions and expressions for the parameters presented here can be used for parameterization of the small-size fraction size spectra in liquid and crystalline clouds and related quantities (e.g., optical properties, lidar, and radar reflectivities).
Analytical Solutions to the Stochastic Kinetic Equation for Liquid and Ice Particle Size Spectra. Part II: Large-Size Fraction in Precipitating Clouds
Authors: Khvorostyanov Vitaly I. , Curry Judith A. 
Published: July 2008

AbstractThe stochastic kinetic equation is solved analytically for precipitating particles that can be identified as rain, snow, and graupel. The general solution for the size spectra of the large-size particles is represented by the product of an exponential term and a term that is an algebraic function of radius. The slope of the exponent consists of the Marshall–Palmer slope and an additional integral that is a function of the radius. Both the integral and algebraic terms depend on the condensation and accretion rates, vertical velocity, turbulence coefficient, terminal velocity of the particles, and the vertical gradient of the liquid (ice) water content. At sufficiently large radii, the radius dependence of the algebraic term is a power law, and the spectra have the form of gamma distributions. Simple analytical expressions are derived for the slopes and indices of the size distributions. These solutions provide explanations of the observed dependencies of the cloud particle spectra in different phases and size regimes on temperature, height, turbulence, vertical velocities, liquid or ice water content, and other cloud properties. These analytical solutions and expressions for the slopes and shape parameters can be used for parameterization of the spectra of precipitating particles and related quantities (e.g., optical properties, radar reflectivities) in bulk cloud microphysical parameterizations and in remote sensing techniques.
On the Climate Impact of Surface Roughness Anomalies
Authors: Kirk-Davidoff Daniel B. , Keith David W. 
Published: July 2008

Abstract
Large-scale deployment of wind power may alter climate through alteration of surface roughness. Previous research using GCMs has shown large-scale impacts of surface roughness perturbations but failed to elucidate the dynamic mechanisms that drove the observed responses in surface temperature. Using the NCAR Community Atmosphere Model in both its standard and aquaplanet forms, the authors have explored the impact of isolated surface roughness anomalies on the model climate. A consistent Rossby wave response in the mean winds to roughness anomalies across a range of model implementations is found. This response generates appreciable wind, temperature, and cloudiness anomalies. The interrelationship of these responses is discussed, and it is shown that the magnitude of the responses scales with the horizontal length scale of the roughened region, as well as with the magnitude of the roughness anomaly. These results are further elucidated through comparison with results of a series of shallow-water model experiments.
A Modified Dynamic Framework for the Atmospheric Spectral Model and Its Application
Authors: Wu Tongwen , Yu Rucong , Zhang Fang 
Published: July 2008

Abstract
This paper describes a dynamic framework for an atmospheric general circulation spectral model in which a reference stratified atmospheric temperature and a reference surface pressure are introduced into the governing equations so as to improve the calculation of the pressure gradient force and gradients of surface pressure and temperature. The vertical profile of the reference atmospheric temperature approximately corresponds to that of the U.S. midlatitude standard atmosphere within the troposphere and stratosphere, and the reference surface pressure is a function of surface terrain geopotential and is close to the observed mean surface pressure. Prognostic variables for the temperature and surface pressure are replaced by their perturbations from the prescribed references. The numerical algorithms of the explicit time difference scheme for vorticity and the semi-implicit time difference scheme for divergence, perturbation temperature, and perturbation surface pressure equation are given in detail. The modified numerical framework is implemented in the Community Atmosphere Model version 3 (CAM3) developed at the National Center for Atmospheric Research (NCAR) to test its validation and impact on simulated climate. Both the original and the modified models are run with the same spectral resolution (T42), the same physical parameterizations, and the same boundary conditions corresponding to the observed monthly mean sea surface temperature and sea ice concentration from 1971 to 2000. This permits one to evaluate the performance of the new dynamic framework compared to the commonly used one. Results show that there is a general improvement for the simulated climate at regional and global scales, especially for temperature and wind.
Intertropical Convergence Zones during the Active Season in Daily Data
Authors: Magnusdottir Gudrun , Wang Chia-Chi 
Published: July 2008

Abstract
Synoptic-scale variability of vorticity structures in the lower troposphere of the tropics is analyzed in 23 yr of daily averaged high-resolution reanalysis data. The vorticity structures can be divided into zonally elongated vorticity strips, classified as intertropical convergence zones (ITCZs), and more localized maxima, termed westward-propagating disturbances. A composite of such variability is presented for the east to central Pacific and for the east Atlantic/Africa region, both in summer. The composite in the east Pacific is zonally elongated and ITCZ-like, propagating westward over a number of days before dissipating. The spatial structure of the vorticity strip shows the characteristic cyclonic tilt into the latitudinal direction with time that is also seen in modeling experiments. The composite over the Atlantic/Africa region shows two active regions that are correlated on synoptic time scales. The disturbances in the southern region are better developed and longer lasting, even though the time and space scales are smaller than over the east Pacific. Overall, variability over the Atlantic is consistent with variability due to African easterly waves. The double ITCZ in spring in the east Pacific is different from the few earlier studies available. It is stronger south of the equator and located at 10°S, which is farther poleward than earlier studies have indicated. The northern branch that is weak in comparison is located at 5°N. The two branches of the double ITCZ tend to appear in tandem on the 2-week time scale.
Implementing the Delta-Four-Stream Approximation for Solar Radiation Computations in an Atmosphere General Circulation Model
Authors: Ayash Tarek , Gong Sunling , Jia Charles Q. 
Published: July 2008

Abstract
Proper quantification of the solar radiation budget and its transfer within the atmosphere is of utmost importance in climate modeling. The delta-four-stream (DFS) approximation has been demonstrated to offer a more accurate computational method of quantifying the budget than the simple two-stream approximations widely used in general circulation models (GCMs) for radiative-transfer computations. Based on this method, the relative improvement in the accuracy of solar flux computations is investigated in the simulations of the third-generation Canadian Climate Center atmosphere GCM. Relative to the computations of the DFS-modified radiation scheme, the GCM original-scheme whole-sky fluxes at the top of the atmosphere (TOA) show the largest underestimations at high latitudes of a winter hemisphere on the order of 4%–6% (monthly means), while the largest overestimations of the same order are found over equatorial regions. At the surface, even higher overestimations are found, exceeding 20% at subpolar regions of a winter hemisphere. Flux differences between original and DFS schemes are largest in the tropics and at high latitudes, where the monthly zonal means and their dispersions are within 5 W m−2 at the TOA and 10 W m−2 at the surface in whole sky, but differences may be as large as 20 and −40 W m−2. In clear sky, monthly zonal means and their dispersions remain within 2 W m−2, but may be as large as 25 and −12 W m−2. Such differences are found to be mostly determined by variations in cloud optical depth and solar zenith angle, and by aerosol loading in a clear sky.
On the Instability of the African Easterly Jet and the Generation of African Waves: Reversals of the Potential Vorticity Gradient
Authors: Hsieh Jen-Shan , Cook Kerry H. 
Published: July 2008

Abstract
The relationship between the generation of African easterly waves and instability growing in regions with reversed potential vorticity gradients is studied using a regional climate model. Results indicate that the convective generation of potential vorticity (PV) due to the meridional and vertical gradients of diabatic heating in the upper and lower troposphere causes a vertically elongated PV anomaly on the southern flank of the African easterly jet. This PV maximum at 9°N in the midtroposphere, together with a PV minimum near 15°N at lower levels because of dry convection over the Sahara, reverses the meridional PV gradient between 9° and 15°N, which suggests that the zonal flow may be unstable in this region. Analysis of the seasonal mean Eliassen–Palm flux for African waves indicates that wave energy generated convectively through baroclinic overturning in the upper troposphere propagates downward and triggers barotropic conversions south of the jet and baroclinic conversions below and north of the jet.
The barotropic conversion of the jet initiates primarily outside of the region of strengthened reversed potential vorticity (q) gradients, suggesting that this barotropic conversion is a result of convectively induced eddies extracting energy from the zonal flow rather than the release of zonal kinetic energy to the waves in the unstable region. In contrast, the residual barotropic conversion occurs inside the region of reversed q gradients during the waves’ decaying stage when ITCZ convection weakens. The baroclinic instability in the unstable region becomes distinguishable from that due to surface temperature gradients when the surface heat flux is weak, a condition under which the African easterly jet better acts as an internal jet. Thus, this analysis indicates that the shear instability of the jet occurs to sustain the waves at the decaying stage rather than to initiate the waves, since it does not appear strong enough to reenergize the waves.
Effects of erosion and macroalgae on intertidal eelgrass (Zostera marina) in a northeastern Pacific estuary (USA)
Authors: Boese Bruce L. , Robbins Bradley D. 
Published: July 2008

Abstract
Eelgrass (Zostera marina) in open-coast northeastern Pacific estuaries is primarily intertidal, yet little research has been done on the natural factors controlling its upper intertidal growth limits. This two-year study in the Yaquina Estuary (Newport, Oregon, USA) evaluated the effects of two factors (erosion and macroalgal accumulations) on populations of eelgrass. Six study sites were located on steep (n=3) and shallow (n=3) intertidal slopes. At each site, triplicate plots (9 m2) were placed at five tidal elevations. In the plots, we counted shoots monthly into three categories: vegetative, reproductive, or seedling. Canopy height, blade width, blades per shoot, macroalgal biomass, and an index of erosion were also measured. Yaquina Estuary eelgrass behaves as a perennial in the lower intertidal zone and as an annual in the upper intertidal zone. In the transition between the low and high intertidal zones, there are both perennial (in patches) and annual forms. We suggest that aerial desiccation, macroalgae, and erosion play a role in controlling intertidal eelgrass and that these factors operate in an acute rather than a chronic manner.
Toxicity, morphology and distribution of Pseudo-nitzschia calliantha, P. multistriata and P. multiseries (Bacillariophyta) from the northwestern Sea of Japan
Authors: Orlova Tatiana Yu. , Stonik Inna V. , Aizdaicher Nina A. , Bates Stephen S. , Léger Claude , Fehling Johanna 
Published: July 2008

Abstract
Toxicity, morphology and distribution patterns of three bloom-forming species of the diatom genus Pseudo-nitzschia (potential producers of the neurotoxin domoic acid and causative organisms of amnesic shellfish poisoning) from Peter the Great Bay in the northwestern Sea of Japan are presented. Pseudo-nitzschia
calliantha, P. multistriata and P.
multiseries bloomed in Peter the Great Bay in the fall, with abundances exceeding 106 cells l-1. This is the first report of toxicity in P. multiseries from Russian waters. Domoic acid was found in stationary-phase (days 20–35) cultures of P. multiseries isolated from Peter the Great Bay at concentrations varying between 180 and 5390 ng ml-1 or 2 to 21 pg cell-1, which is in the range reported for other isolates of P. multiseries. The Russian isolate had an increasing ability to produce domoic acid over time in culture rather than the usual trend of decreasing toxicity. No domoic acid was detected (<2 ng ml-1) in cultures of P. calliantha and P. multistriata from the same locality. The Russian isolate of P. multiseries produced gametes when mated with the Canadian strains of the opposite mating type, but they never developed into zygotes, auxospores or large initial cells. This suggests that there might be “cryptic” species within P. multiseries. However, a comparison of molecular and morphometric data between the Russian and Canadian strains showed that they indeed belong to the same species.
A reassessment of Halophila species (Hydrocharitaceae) diversity with special reference to Japanese representatives
Authors: Uchimura Masayuki , Jean Faye Etienne , Shimada Satoshi , Inoue Tetsunori , Nakamura Yoshiyuki 
Published: July 2008

Abstract
In a recent review of the seagrass genus Halophila in Japan, eight taxa including four new species were listed: (i) H. decipiens, (ii) H. minor, (iii) H. major, (iv) H. ovalis, (v) H. mikii, (vi) H. nipponica, (vii) H. okinawensis, and (viii) H. gaudichaudii. In this study, the specific concept of Halophila in Japan as well as some other geographic areas was re-assessed by a combination of nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequence analyses and morphological examinations of both recently collected materials and available type collections. The results confirm the distinctness of the Australian endemic species H. australis and the putative pan-tropical taxon H. decipiens; but also demonstrate conspecificity of: (i) H. minor and H. ovalis; (ii) H. major and H. mikii; and (iii) H. nipponica, H. okinawensis and H. gaudichaudii. As an outcome of this study, we recommend restricting the list of Halophila representatives in Japan to the following four species: (i) H. decipiens, (ii) H. major, (iii) H. ovalis, and (iv) H. nipponica. In addition, we predict the possibility of H. major occurring further south than currently recorded.