bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential effects of the vascular endothelial growth factor receptor inhibitor PTK787/ZK222584 on tumor angiogenesis and tumor lymphangiogenesis
Authors: Schomber Tibor , Zumsteg Adrian , Strittmatter Karin , Crnic Ivana , Antoniadis Helena , Littlewood-Evans Amanda , Wood Jeanette , Christofori Gerhard 
Published: January 2009

Abstract
Halting tumor growth by interfering with tumor-induced angiogenesis is an attractive therapeutic approach. Such treatments include humanized antibodies blocking the activity of vascular endothelial growth factor (VEGF)-A (bevacizumab), soluble VEGF receptor (VEGFR) constructs (VEGF-Trap), or small-molecule inhibitors of VEGFR signaling, including PTK787/ZK222584 (PTK/ZK), sorafenib, and sunitinib. PTK/ZK has been shown previously to specifically block VEGF-induced phosphorylation of VEGFR-1, -2 and -3 and thereby to inhibit endothelial cell proliferation, differentiation, and tumor angiogenesis. We have investigated the effect of PTK/ZK on tumor angiogenesis and tumor lymphangiogenesis using the Rip1Tag2 transgenic mouse model of pancreatic β cell carcinogenesis. In Rip1Tag2 mice, tumor angiogenesis is predominantly mediated by VEGF-A, and as expected, PTK/ZK efficiently impaired tumor blood vessel angiogenesis and tumor growth. Double-transgenic Rip1Tag2;Rip1VEGF-C and Rip1Tag2;Rip1VEGF-D mice not only exhibit VEGF-A-dependent blood vessel angiogenesis but also tumor lymphangiogenesis induced by the transgenic expression of VEGF-C or -D. In these mouse models, PTK/ZK also repressed tumor blood vessel angiogenesis and tumor growth yet failed to affect tumor lymphangiogenesis and lymphogenic metastasis. Adenoviral delivery of soluble VEGFR-3 also did not prevent tumor lymphangiogenesis in these mice. In contrast, spontaneous tumor lymphangiogenesis, as observed by the stochastic expression of VEGF-C and -D in tumors of neural cell adhesion molecule-deficient Rip1Tag2 mice, was repressed by PTK/ZK and soluble VEGFR-3. The results indicate that the time of onset and the levels of VEGF-C/D expression may be critical variables in efficiently repressing tumor lymphangiogenesis and that pathways other than VEGFR signaling may be involved in tumor lymphangiogenesis. [Mol Cancer Ther 2009;8(1):55–63]
In vivo target-specific activatable near-infrared optical labeling of humanized monoclonal antibodies
Authors: Ogawa Mikako , Regino Celeste A.S. , Choyke Peter L. , Kobayashi Hisataka 
Published: January 2009

Abstract
Imaging with labeled monoclonal antibodies may be useful in detecting, staging, and monitoring tumors. Despite their high affinity and specificity, a critical limitation of antibody imaging is the high background signal due to prolonged clearance from the blood, which reduces the tumor-to-background ratio. To address this problem, we developed a molecular imaging probe consisting of multiple self-quenching fluorophores [Cy5.5 or Alexa Fluor 680 (Alexa680)] conjugated to a monoclonal antibody (trastuzumab) to synthesize Tra-Cy5.5(SQ) or Tra-Alexa680(SQ), respectively. This agent only becomes fluorescently “active” after cellular internalization but is quenched in the unbound state leading to high tumor-to-background ratios. The in vitro quenching capacity for both conjugates was ∼9-fold. In vivo imaging experiments were done in mice bearing both 3T3/HER-2+ and BALB/3T3/ZsGreen/HER-2− xenografts. Tra-Alexa680(SQ) produced specific enhancement in the 3T3/HER-2+ tumors but not in the HER-2− control tumors. However, Tra-Cy5.5(SQ) produced nonspecific enhancement in both 3T3/HER-2+ and control tumors. In conclusion, whereas Cy5.5-conjugates produced nonspecific results as well as rapid liver accumulation, conjugating multiple Alexa680 molecules to a single monoclonal antibody resulted in a near-infrared optical agent that activated within specific target tumors with high tumor-to-background ratio with considerable potential for clinical translation. [Mol Cancer Ther 2009;8(1):232–9]
On the Combined Effects of Turbulence and Gravity on Droplet Collisions in Clouds: A Numerical Study
Authors: Woittiez Eric J. P. , Jonker Harm J. J. , Portela Luís M. 
Published: January 2009

Abstract
This paper examines the combined influences of turbulence and gravity on droplet collision statistics in turbulent clouds by means of direct numerical simulation (DNS). The essential microphysical mechanisms that determine the geometric collision kernel are explored by studying how gravity affects droplet relative velocities and preferential concentration of both monodisperse and bidisperse droplet distributions. To this end, collision statistics of large amounts of droplets with radii ranging from 10 to 90 μm, driven by a turbulent flow field and gravity, are calculated. The flow is homogeneous and isotropic and has a dissipation rate of ε = 4.25 × 10−2 m2 s−3. The results show that in the calculation of collision statistics, the interplay between gravity and turbulence is an essential element and not merely an addition of separate phenomena. For example, the presence of gravity leads to clustering of large droplets interacting with the larger scales of turbulence in the DNS. The collision statistics of a bidisperse droplet distribution, even with a very small radius difference, shows profoundly different behavior than the monodisperse case.
Reconstructing the Past Wind Stresses over the Tropical Pacific Ocean from 1875 to 1947
Authors: Deng Ziwang , Tang Youmin 
Published: January 2009

Abstract
An important step in understanding the climate system is simulating and studying the past climate variability, using oceanic models, atmospheric models, or both. Toward this goal, long-term wind stress data, as the forcing of oceanic or climate models, are often required. In this study, the possibility of reconstructing the past winds of the tropical Pacific Ocean using historical sea surface temperature (SST) and sea level pressure (SLP) datasets was explored. Four statistical models, based on principal component (PC) regression and singular vector decomposition (SVD), were developed for reconstructing monthly pseudo wind stress over the tropical Pacific for the period 1875–1947. The high-frequency noise was removed from the raw data prior to the reconstruction. These models are SST-based PC regression (model 1), SLP-based PC regression (model 2), SST-based SVD (model 3), and SLP-based SVD (model 4). The results show that reconstructed wind stresses from all models can account for more than one-half of the total variances. In general, the SLP is better than SST as a predictor and the SVD method is superior to the PC regression. Forced by these reconstructed wind stresses, an oceanic general circulation model can simulate realistic interannual variability of the tropical Pacific SST. However, the wind stress reconstructed by SST-based models leads to better simulation skill in comparison with that from SLP-based models. Last, a long-term wind stress dataset was constructed for the period from 1875 to 1947 by the SST-based SVD model, which provides a useful tool for studying the past climate variability over the tropical Pacific, especially for El Niño–Southern Oscillation.
Cloud Microphysics Impact on Hurricane Track as Revealed in Idealized Experiments
Authors: Fovell Robert G. , Corbosiero Kristen L. , Kuo Hung-Chi 
Published: January 2009

Abstract
Analyses of tropical cyclones created in an idealized environment reveal how and why cloud microphysical assumptions can influence storm motion, including speed and direction. It is well known that in the absence of a mean flow, a leading factor in storm propagation is the establishment of “beta gyres” owing to planetary vorticity advection by the storm’s circulation. Previous research demonstrated that tangential winds well beyond the core influence storm motion by helping to determine the gyres’ orientation and intensity.
Microphysical assumptions, especially involving average particle fall speeds, can strongly influence the winds at outer radius. More specifically, microphysics modulates the radial distribution of column-average virtual temperature, which largely determines the radial surface pressure gradient and therefore the winds because they tend to be in gradient balance beyond the core. Microphysics schemes can differ markedly with respect to average fall speed, depending on the complexity of the scheme and how interactions among condensation types are handled. Average fall speed controls the outward movement of particles produced in the eyewall into the anvil, where they can influence the environment through cloud–radiative interactions and phase changes.
With the assistance of some special sensitivity tests, the influence of microphysics and fall speed on radial temperature gradients, leading to different outer wind strengths and tracks, is shown. Among other things, this work demonstrates that the treatment of outer rainbands in operational models can potentially influence how simulated storms move, thus affecting position forecasts.
Baroclinic Instability in the Eady Model: Interpretations
Authors: Egger Joseph 
Published: January 2009

Abstract
The mechanism of baroclinic instability in the Eady model is interpreted by explicitly calculating the ageostrophic circulations related to the model’s hyperbolic basic functions. It is advantageous to perform the analysis at the midlevel where the model’s “barotropic” mode provides the streamfunction and the “baroclinic” mode represents the temperature. These modes interact and instability occurs if the horizontal advection of background potential temperature by the barotropic mode dominates over the vertical one because of the same mode at the midlevel. A rather simple picture of the stable as well as the unstable flow configurations emerges. Other interpretations are discussed briefly.
A Homogeneous Stochastic Model of the Madden–Julian Oscillation
Authors: Jones Charles 
Published: January 2009

Abstract
This paper presents a new empirical model to simulate the Madden–Julian oscillation (MJO), which is the most prominent mode of tropical intraseasonal variability. Zonal wind components at 850 and 200 hPa from reanalysis (1948–2007) and outgoing longwave radiation from satellites (1979–2007) are used to identify MJOs and characterize their statistical properties.
The temporal variability of the MJO is represented with a nine-state first-order Markov chain in which state 0 represents quiescent days and states 1–8 are phases of the MJO when it is active. Transition probabilities are estimated based on the historical record of MJO events, and sensitivity tests were performed to evaluate the best estimates for a homogeneous model. Once the model simulates time series of phase transitions, composites of convective and circulation anomalies determine the spatial structure of the events. The amplitudes of the MJOs are stochastically generated with an amplitude factor that has a Gaussian frequency distribution.
MJO events generated by the homogeneous stochastic model occur irregularly in time and can appear as single isolated events or sequences of successive MJOs. The MJO in the model can have different eastward propagations and the zonal scale is consistent with the observations. The simulated MJOs have different durations (30–90 days), and each event can be stronger or weaker than the mean composite according to a normal distribution. The results show that the homogeneous stochastic model simulates the irregularity of the MJO and model biases are small. Possible applications and future extensions of the homogeneous stochastic model are discussed.
On the Relationship between Synoptic Wintertime Atmospheric Variability and Path Shifts in the Gulf Stream and the Kuroshio Extension
Authors: Joyce Terrence M. , Kwon Young-Oh , Yu Lisan 
Published: January 2009

Abstract
Coherent, large-scale shifts in the paths of the Gulf Stream (GS) and the Kuroshio Extension (KE) occur on interannual to decadal time scales. Attention has usually been drawn to causes for these shifts in the overlying atmosphere, with some built-in delay of up to a few years resulting from propagation of wind-forced variability within the ocean. However, these shifts in the latitudes of separated western boundary currents can cause substantial changes in SST, which may influence the synoptic atmospheric variability with little or no time delay. Various measures of wintertime atmospheric variability in the synoptic band (2–8 days) are examined using a relatively new dataset for air–sea exchange [Objectively Analyzed Air–Sea Fluxes (OAFlux)] and subsurface temperature indices of the Gulf Stream and Kuroshio path that are insulated from direct air–sea exchange, and therefore are preferable to SST. Significant changes are found in the atmospheric variability following changes in the paths of these currents, sometimes in a local fashion such as meridional shifts in measures of local storm tracks, and sometimes in nonlocal, broad regions coincident with and downstream of the oceanic forcing. Differences between the North Pacific (KE) and North Atlantic (GS) may be partly related to the more zonal orientation of the KE and the stronger SST signals of the GS, but could also be due to differences in mean storm-track characteristics over the North Pacific and North Atlantic.
Analyzing the Concurrence of Meteorological Droughts and Warm Periods, with Implications for the Determination of Evaporative Regime
Authors: Koster R. D. , Schubert S. D. , Suarez M. J. 
Published: January 2009

Abstract
The hydroclimatic conditions under which a seasonal meteorological drought (below-normal seasonal rainfall) can induce an increase in seasonal air temperature are investigated, first with an atmospheric general circulation model (AGCM) and then with observations. Geographical differences in the dryness–warmth connection abound in the AGCM; in the United States, for example, identified evaporative controls tend to tie meteorological droughts to warmer temperatures in the South but not in the Northeast. The strong agreement between AGCM and observations-based geographical patterns of drought-induced warming supports the idea that the same evaporative controls are also present in nature. A powerful side benefit of the analysis of drought-induced warming is a Northern Hemisphere map, derived solely from observations, showing where total boreal summer evaporation is controlled by soil moisture, energy availability, or both.
PDFs of Tropical Tropospheric Humidity: Measurements and Theory
Authors: Ryoo Ju-Mee , Igusa Takeru , Waugh Darryn W. 
Published: January 2009

Abstract
The spatial variations in the probability density functions (PDFs) of relative humidity (RH) in the tropical and subtropical troposphere are examined using observations from the Atmospheric Infrared Sounder (AIRS) and the Microwave Limb Sounder (MLS) instruments together with a simple statistical model. The model, a generalization of that proposed by Sherwood et al., assumes the RH is determined by a combination of drying by uniform subsidence and random moistening events and has two parameters: r, the ratio of the drying time by subsidence to the time between moistening events, and k, a measure of the variability of the moistening events. The observations show that the characteristics of the PDFs vary between the tropics and subtropics, within the tropics or subtropics, and with altitude. The model fits the observed PDFs well, and the model parameters concisely characterize variations in the PDFs and provide information on the processes controlling the RH distributions. In tropical convective regions, the model PDFs that match the observations have large r and small k, indicating rapid random remoistening, which is consistent with direct remoistening in convection. In contrast, in the nonconvective regions there are small r and large k, indicating slower, less random remoistening, consistent with remoistening by slower, quasi-horizontal transport. The statistical model derived will be useful for quantifying differences between, or temporal changes in, RH distributions from different datasets or models, and for examining how changes in physical processes could alter the RH distribution.
Dynamics of Late Spring Rainfall Reduction in Recent Decades over Southeastern China
Authors: Qiu Yun , Cai Wenju , Guo Xiaogang , Pan Aijun 
Published: January 2009

Abstract
Since 1951, late spring (May) rainfall over southeastern China (SEC) has decreased by more than 30% from its long-term average, in contrast to a rainfall increase in boreal summer. The dynamics have yet to be fully determined. This paper shows that as the Indo-Pacific enters into a La Niña phase, significant negative mean sea level pressure (MSLP) anomalies grow over the Indian Ocean and the western Pacific sector. The associated large-scale southwesterly anomalies transport moisture to the nearby South China Sea and the SEC region, contributing to a higher rainfall. A presence of a Philippine Sea anticyclonic (PSAC) pattern, arising from a decaying El Niño, strengthens the rain-conducive flow to SEC, but it is not a necessary condition. During the past decades, an increase in protracted El Niño events accompanied by a reduction in La Niña episodes has contributed to the May rainfall decline. The extent to which climate change is contributing is discussed.
Seasonal-to-Interannual Variability of Ethiopia/Horn of Africa Monsoon. Part I: Associations of Wavelet-Filtered Large-Scale Atmospheric Circulation and Global Sea Surface Temperature
Authors: Segele Zewdu T. , Lamb Peter J. , Leslie Lance M. 
Published: January 2009

Abstract
Horn of Africa rainfall varies on multiple time scales, but the underlying climate system controls on this variability have not been examined comprehensively. This study therefore investigates the linkages between June–September Horn of Africa (especially Ethiopian) rainfall and regional atmospheric circulation and global sea surface temperature (SST) variations on several key time scales. Wavelet analysis of 5-day average or monthly total rainfall for 1970–99 identifies the dominant coherent modes of rainfall variability. Several regional atmospheric variables and global SST are then identically wavelet filtered, based on the rainfall frequency bands. Regression, correlation, and composite analyses are subsequently used to identify the most important rainfall–climate system time-scale relationships.
The results show that Ethiopian monsoon rainfall variation is largely linked with annual time-scale atmospheric circulation patterns involving variability in the major components of the monsoon system. Although variability on the seasonal (75–210 days), quasi-biennial (QB; 1.42–3.04 yr), and El Niño–Southern Oscillation (ENSO; 3.04–4.60 yr) time scales accounts for much less variance than the annual mode (210 days–1.42 yr), they significantly affect Ethiopian rainfall by preferentially modulating the major regional monsoon components and remote teleconnection linkages. The seasonal time scale largely acts in phase with the annual mode, by enhancing or reducing the lower-tropospheric southwesterlies from the equatorial Atlantic during wet or dry periods. The wet QB phase strengthens the Azores and Saharan high and the tropical easterly jet (TEJ) over the Arabian Sea, while the wet ENSO phase enhances the Mascarene high, the TEJ, and the monsoon trough more locally. The effects of tropical SST on Ethiopian rainfall also are prominent on the QB and ENSO time scales. While rainfall–SST correlations for both the QB and ENSO modes are strongly positive (negative) over the equatorial western (eastern) Pacific, only ENSO exhibits widespread strong negative correlations over the Indian Ocean. Opposite QB and ENSO associations tend to characterize dry Ethiopian conditions. The relationships identified on individual time scales now are being used to develop and validate statistical prediction models for Ethiopia.
Efficiency of Mixing Forced by Unsteady Shear Flow
Authors: Inoue Ryuichiro , Smyth William D. 
Published: January 2009

Abstract
The dependence of mixing efficiency on time-varying forcing is studied by direct numerical simulation (DNS) of Kelvin–Helmholtz (KH) instability. Time-dependent forcing fields are designed to reproduce a wavelike oscillation by solving the equations of motion in a tilted coordinate frame and allowing the tilt angle to vary in time. Mixing efficiency Γc is defined as the ratio of potential energy gain to dissipation, both averaged over one forcing cycle and first examined via parameters characterizing waves: the minimum Richardson number Rimin and the normalized frequency of the forcing ω/N. The effect of Reynolds number Re0 and the initial random disturbance amplitude b are also examined. In the experiments presented, Γc varies between 0.21 and 0.36 and is controlled by the timing of two events: the emergence of KH billows and the arrival of the deceleration of the mean shear by the wavelike forcing. Here, Γc is higher than a canonical value of 0.2 when the deceleration phase of the forcing suppresses the less efficient turbulence after breakdown of KH billows. However, when Rimin and ω/N are small, KH billows start to develop before Rimin is achieved. Therefore, the forcing accelerates the mean shear and thereby sustains turbulence after the breakdown of KH billows. The canonical value is then reproduced in the DNS. Although larger values of Re0 and b intensify the development of KH billows and modify Γc, this effect is less significant when forcing fields act to sustain turbulence. The time-averaged Thorpe scale and Ozmidov scale are also used to see how mixing is modified by forcing fields and compared with past microstructure measurements. It is found that DNS also corresponds to past observations if the forcing accelerates the mean shear to sustain turbulence.
Accelerating Dense-Water Flow down a Slope
Authors: Huthnance John M. 
Published: January 2009

Abstract
Where water is denser on a shallow shelf than in the adjacent deep ocean, it tends to flow down the slope from shelf to ocean. The flow can be in a steady bottom boundary layer for moderate combinations of upslope density gradient −ρx∞ and bottom slope (angle θ to horizontal):Here g is acceleration due to gravity, ρ0 is a mean density, and f is twice the component of the earth’s rotation normal to the sloping bottom. For stronger combinations of the horizontal density gradient and bottom slope, the flow accelerates. Analysis of an idealized initial value problem shows that, when b ≥ 1, there is a bottom boundary layer with downslope flow, intensifying exponentially at a rate fb2(1 + b)−1/2/2, and slower-growing flow higher up. For stronger stratification b &gt; 21/2, that is, a relatively weak Coriolis constraint, the idealized problem posed here may not be the most apposite but suggests that the whole water column accelerates, at a rate [ρ0−1|ρx∞|g sinθ]1/2 if f is negligible.
A New Climatology of Air–Sea Density Fluxes and Surface Water Mass Transformation Rates Constrained by WOCE
Authors: Howe Nicola , Czaja Arnaud 
Published: January 2009

Abstract
Global air–sea heat and freshwater flux data, constrained by World Ocean Circulation Experiment (WOCE) hydrographic section transports, is used to construct a new global density flux climatology. Global transformations calculated using this density flux dataset show two regimes: surface waters with density less than ∼1023.3 kg m−3 are transformed to lighter density classes with a maximum rate of 130 Sv (1 Sv ≡ 106 m3 s−1) at σ ∼ 1021.6 kg m−3, and surface waters with density greater than 1023.3 kg m−3 are transformed to denser density classes with a maximum rate of 100 Sv at σ = 1025.4 kg m−3. At higher density (σ = 1027 kg m−3) the net transformation rates vanish, reflecting heat loss in the Northern Hemisphere balanced by Southern Hemisphere freshening. This results in a kink in the global transformation rate, which is attributed to the presence of Drake Passage. Further analysis of the control run of the third Hadley Centre global climate model, HadCM3, suggests this feature to be robust and to reflect the “channel” geometry of the Southern Ocean and the “basin” geometry of the Northern Hemisphere.