bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of Flood Water Infiltration and Ground Water Recharge in Hyperarid Desert
Authors: Dahan Ofer , Tatarsky Boaz , Enzel Yehouda , Kulls Christoph , Seely Mary , Benito Gererdo 
Published: January 2008

AbstractA study on flood water infiltration and ground water recharge of a shallow alluvial aquifer was conducted in the hyperarid section of the Kuiseb River, Namibia. The study site was selected to represent a typical desert ephemeral river. An instrumental setup allowed, for the first time, continuous monitoring of infiltration during a flood event through the channel bed and the entire vadose zone. The monitoring system included flexible time domain reflectometry probes that were designed to measure the temporal variation in vadose zone water content and instruments to concurrently measure the levels of flood and ground water. A sequence of five individual floods was monitored during the rainy season in early summer 2006. These newly generated data served to elucidate the dynamics of flood water infiltration. Each flood initiated an infiltration event which was expressed in wetting of the vadose zone followed by a measurable rise in the water table. The data enabled a direct calculation of the infiltration fluxes by various independent methods. The floods varied in their stages, peaks, and initial water contents. However, all floods produced very similar flux rates, suggesting that the recharge rates are less affected by the flood stages but rather controlled by flow duration and available aquifer storage under it. Large floods flood the stream channel terraces and promote the larger transmission losses. These, however, make only a negligible contribution to the recharge of the ground water. It is the flood duration within the active streambed, which may increase with flood magnitude that is important to the recharge process.
Time variation of some selected topics in bioethical publications
Authors: Cohen C , Vianna J A R , Battistella L R , Massad E 
Published: January 2008

Objective:To analyse the time variation of topics in bioethical publications as a proxy of the relative importance.Methods:We searched the Medline database for bioethics publications using the words “ethics or bioethics”, and for 360 specific topics publications, associating Medical Subject Heading topic descriptors to those words. We calculated the ratio of bioethics publications to the total publications of Medline, and the ratio of each topic publications to the total bioethics publications, for five-year intervals, from 1970 to 2004. We calculated the time variation of ratios, dividing the difference between the highest and lowest ratio of each topic by its highest ratio. Four topics were described, selected to illustrate different patterns of variation: “Induced Abortion”, “Conflict of Interest”, “Acquired Immunodeficiency Syndrome”, “Medical Education.”Results:The ratio of bioethics publications to total Medline publications increased from 0.003 to 0.012. The variation of the topic’s ratios was higher than 0.7 for 68% of the topics. The Induced Abortion ratios decreased from 0.12 to 0.02. Conflict of Interest ratios increased from zero to 0.07. The Acquired Immunodeficiency Syndrome ratios were nearly zero in the first three intervals, had a peak of 0.06 during 1985–9, followed by a decrease to 0.01. Medical Education ratios varied few, from 0.04 to 0.03.Conclusions:There was an increase of bioethical publications in the Medline database. The topics in bioethics literature have an important time variation. Some factors were suggested to explain this variation: current legal cases, resolution of the issue, saturation of a discussion and epidemiologic importance.
Down-Regulation of Mcl-1 by Small Interfering RNA Sensitizes Resistant Melanoma Cells to Fas-Mediated Apoptosis
Authors: Chetoui Nizar , Sylla Khaoussou , Gagnon-Houde Jean-Vincent , Alcaide-Loridan Catherine , Charron Dominique , Al-Daccak Reem , Aoudjit Fawzi 
Published: January 2008

Abstract
Resistance of malignant melanoma cells to Fas-mediated apoptosis is among the mechanisms by which they escape immune surveillance. However, the mechanisms contributing to their resistance are not completely understood, and it is still unclear whether antiapoptotic Bcl-2–related family proteins play a role in this resistance. In this study, we report that treatment of Fas-resistant melanoma cell lines with cycloheximide, a general inhibitor of de novo protein synthesis, sensitizes them to anti-Fas monoclonal antibody (mAb)–induced apoptosis. The cycloheximide-induced sensitization to Fas-induced apoptosis is associated with a rapid down-regulation of Mcl-1 protein levels, but not that of Bcl-2 or Bcl-xL. Targeting Mcl-1 in these melanoma cell lines with specific small interfering RNA was sufficient to sensitize them to both anti-Fas mAb-induced apoptosis and activation of caspase-9. Furthermore, ectopic expression of Mcl-1 in a Fas-sensitive melanoma cell line rescues the cells from Fas-mediated apoptosis. Our results further show that the expression of Mcl-1 in melanoma cells is regulated by the mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) and not by phosphatidylinositol 3-kinase/AKT signaling pathway. Inhibition of ERK signaling with the mitogen-activated protein/ERK kinase-1 inhibitor or by expressing a dominant negative form of mitogen-activated protein/ERK kinase-1 also sensitizes resistant melanoma cells to anti-Fas mAb-induced apoptosis. Thus, our study identifies mitogen-activated protein kinase/ERK/Mcl-1 as an important survival signaling pathway in the resistance of melanoma cells to Fas-mediated apoptosis and suggests that its targeting may contribute to the elimination of melanoma tumors by the immune system. (Mol Cancer Res 2008;6(1):42–52)
The Osterix Transcription Factor Down-Regulates Interleukin-1α Expression in Mouse Osteosarcoma Cells
Authors: Cao Ying , Jia Shu-Fang , Chakravarty Geetika , de Crombrugghe Benoit , Kleinerman Eugenie S. 
Published: January 2008

Abstract
K7M2 mouse osteosarcoma cells form lytic tumors and are deficient in osterix (Osx), a zinc finger–containing transcription factor required for osteoblast differentiation and bone formation. Our previous studies showed that replacement of Osx suppresses lytic bone destruction. Cytokines, including interleukin (IL)-1α, IL-6, IL-11, and prostaglandin E2, have been shown to stimulate osteoclast activity. We showed that IL-1α production by K7M2 cells was significantly suppressed following Osx transfection through a transcription-mediated mechanism. Osx had no effect on IL-6, IL-11, or prostaglandin E2. Site-directed mutagenesis and chromatin immunoprecipitation indicated that Osx down-regulated IL-1α through an Sp1-binding site on the IL-1α promoter. Inhibiting Osx by small interfering RNA in two cell lines (Dunn and DLM8) that expressed high levels of Osx led to enhanced IL-1α promoter activity and protein production and altered the phenotype from blastic to lytic. These data suggest that Osx down-regulates IL-1α expression in mouse osteosarcoma cells via transcriptional repression of IL-1α and this may in turn affect the lytic activity of the tumor cells. (Mol Cancer Res 2008;6(1):119–26)
Sustained VEGF Blockade Results in Microenvironmental Sequestration of VEGF by Tumors and Persistent VEGF Receptor-2 Activation
Authors: Kadenhe-Chiweshe Angela , Papa Joey , McCrudden Kimberly W. , Frischer Jason , Bae Jae-O , Huang Jianzhong , Fisher Jason , Lefkowitch Jay H. , Feirt Nikki , Rudge John , Holash Jocelyn , Yancopoulos George D. , Kandel Jessica J. , Yamashiro Darrell J. 
Published: January 2008

AbstractVascular endothelial growth factor (VEGF) blockade has been validated clinically as a treatment for human cancers, yet virtually all patients eventually develop progressive disease during therapy. In order to dissect this phenomenon, we examined the effect of sustained VEGF blockade in a model of advanced pediatric cancer. Treatment of late-stage hepatoblastoma xenografts resulted in the initial collapse of the vasculature and significant tumor regression. However, during sustained treatment, vessels recovered, concurrent with a striking increase in tumor expression of perlecan, a heparan sulfate proteoglycan. Whereas VEGF mRNA was expressed at the periphery of surviving clusters of tumor cells, both secreted VEGF and perlecan accumulated circumferential to central vessels. Vascular expression of heparanase, VEGF receptor-2 ligand binding, and receptor activation were concurrently maintained despite circulating unbound VEGF Trap. Endothelial survival signaling via Akt persisted. These findings provide a novel mechanism for vascular survival during sustained VEGF blockade and indicate a role for extracellular matrix molecules that sequester and release biologically active VEGF. (Mol Cancer Res 2008;6(1):1–9)
A JNK1/AP-1–Dependent, COX-2 Induction Is Implicated in 12-O-Tetradecanoylphorbol-13-Acetate–Induced Cell Transformation through Regulating Cell Cycle Progression
Authors: Zhang Dongyun , Li Jingxia , Song Lun , Ouyang Weiming , Gao Jimin , Huang Chuanshu 
Published: January 2008

Abstract
Cyclooxygenase-2 (COX-2) is reported to be one of the early-response gene products induced by 12-O-tetradecanoylphorbol-13-acetate (TPA). However, the relevance of COX-2 in TPA-induced cell transformation and the underlying mechanisms remains to be explored. Initially, we verified COX-2 induction after TPA treatment in mouse embryonic fibroblasts (MEF) and mouse epidermal cells Cl 41. More importantly, introduction of COX-2 small interfering RNA in MEFs or Cl 41 cells suppressed the cell transformation caused by TPA treatment. This inhibition could be reversed by overexpression of human full-length COX-2, indicating that COX-2 is at least one of the critical molecules involved in TPA-induced cell transformation. We further showed that TPA-promoted cell cycle progression was partially suppressed by COX-2 small interfering RNA, indicating that COX-2 also participated in TPA-associated cell cycle progression. Investigation of the upstream signaling pathways revealed that c-Jun-NH2-kinase 1 (JNK1), but not JNK2, played important roles in COX-2 induction, because knockout of JNK1 gene rather than JNK2 gene markedly impaired COX-2 induction. Furthermore, inhibition of c-Jun/activator protein 1 pathway or JNKs/c-Jun pathway by overexpression of dominant negative mutants of c-Jun, or MKK4 and MKK7 together, resulted in impairment of COX-2 induction, suggesting that JNK1/c-Jun/activator protein 1 pathway is involved in TPA-associated COX-2 induction. In contrast, IKK/p65 nuclear factor-κB pathway was not implicated because knockout of IKKα, IKKβ, or p65 gene did not affect COX-2 induction although nuclear factor-κB was activated by TPA. In addition, the TPA-promoted cell cycle progression was found impaired in JNK1-deficient, but not in JNK2-deficient, MEFs. Our results show that JNK1-associated COX-2 induction is implicated in TPA-associated cell transformation and cell cycle progression. (Mol Cancer Res 2008;6(1):165–74)
Cloud Detection with MODIS. Part II: Validation
Authors: Ackerman S. A. , Holz R. E. , Frey R. , Eloranta E. W. , Maddux B. C. , McGill M. 
Published: January 2008

Abstract
An assessment of the performance of the Moderate Resolution Imaging Spectroradiometer (MODIS) cloud mask algorithm for Terra and Aqua satellites is presented. The MODIS cloud mask algorithm output is compared with lidar observations from ground [Arctic High-Spectral Resolution Lidar (AHSRL)], aircraft [Cloud Physics Lidar (CPL)], and satellite-borne [Geoscience Laser Altimeter System (GLAS)] platforms. The comparison with 3 yr of coincident observations of MODIS and combined radar and lidar cloud product from the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Program Southern Great Plains (SGP) site in Lamont, Oklahoma, indicates that the MODIS algorithm agrees with the lidar about 85% of the time. A comparison with the CPL and AHSRL indicates that the optical depth limitation of the MODIS cloud mask is approximately 0.4. While MODIS algorithm flags scenes with a cloud optical depth of 0.4 as cloudy, approximately 90% of the mislabeled scenes have optical depths less than 0.4. A comparison with the GLAS cloud dataset indicates that cloud detection in polar regions at night remains challenging with the passive infrared imager approach.
In anticipation of comparisons with other satellite instruments, the sensitivity of the cloud mask algorithm to instrument characteristics (e.g., instantaneous field of view and viewing geometry) and thresholds is demonstrated. As expected, cloud amount generally increases with scan angle and instantaneous field of view (IFOV). Nadir sampling represents zonal monthly mean cloud amounts but can have large differences for regional studies when compared to full-swath-width analysis.
The Slope of Moist Symmetric Instability with Water Loading
Authors: Fantini Maurizio , Malguzzi Piero 
Published: January 2008

AbstractIdealized numerical experiments, supported by analytic considerations, are performed to determine the preferred direction of symmetric instability when water loading is considered. It is concluded that the most unstable direction is tangent to a surface of neutral buoyancy, which can be defined numerically from the water content of lifted air, and coincides with the tangent to saturated isentropes only when all condensed water is precipitated out, consistent with the thermodynamic approximations made in the definition of equivalent potential temperature.In more common situations, when part or all of the condensed water is retained in the cloud, the orientation of symmetrically unstable normal modes is much more slanted toward the horizontal, to the point that regions of the atmosphere, diagnosed as unstable from the consideration of equivalent potential temperature and vorticity, can in fact be stable.
Tropical and Stratospheric Influences on Extratropical Short-Term Climate Variability
Authors: Newman Matthew , Sardeshmukh Prashant D. 
Published: January 2008

Abstract
The relative impacts of tropical diabatic heating and stratospheric circulation anomalies on wintertime extratropical tropospheric variability are investigated in a linear inverse model (LIM) derived from the observed zero lag and 5-day lag covariances of 7-day running mean departures from the annual cycle. The model predicts the covariances at all other lags. The predicted and observed lag covariances are generally found to be in excellent agreement, even at the much longer lag of 21 days. This validates the LIM’s basic premise that the dynamics of weekly averages are effectively linear and stochastically driven, which justifies further linear diagnosis of the system.
Analysis of interactions among the LIM’s variables shows that tropical diabatic heating greatly enhances persistent variability over most of the Northern Hemisphere, especially over the Pacific Ocean and North America. Stratospheric effects are largely confined to the polar region, where they ensure that the dominant pattern of sea level pressure variability is the annular Arctic Oscillation rather than the more localized North Atlantic Oscillation. Over the North Atlantic, both effects are important, although some of the stratospheric influence is ultimately traceable to tropical forcing. In general, the tropically forced anomalies extend through the depth of the troposphere and into the stratosphere, whereas stratospherically generated anomalies tend to be largest at the surface and relatively weak at midtropospheric levels. Some persistent variability is, however, found even in the absence of these “external” forcings, especially near the amplitude maxima of the leading eigenmodes of the internal extratropical tropospheric evolution operator. One of these eigenmodes has a circumglobal zonal wavenumber-5 structure with maxima over the Arabian Sea and the central Pacific, and two others are associated with north–south dipole variations across the North Atlantic jet. Overall, tropical influences are generally found to be larger than stratospheric influences on extratropical tropospheric variability and have a pronounced impact on the persistent, and therefore the potentially predictable, portion of that variability.
Evaluation of the NOHRSC Snow Model (NSM) in a One-Dimensional Mode
Authors: Rutter Nick , Cline Don , Li Long 
Published: January 2008

Abstract
The National Operational Hydrologic Remote Sensing Center (NOHRSC) Snow Model (NSM) is an energy- and mass-balance model used by the National Oceanic and Atmospheric Administration’s National Weather Service for moderate-resolution spatially distributed snow analysis and data assimilation over the United States. The NSM was evaluated in a one-dimensional mode using meteorological and snowpit observations from five sites in Colorado collected during 2002–03. Four parameters estimated by the NSM [snow water equivalent (SWE), snow depth, average snowpack temperature, and snow surface temperature] were compared with snowpit observations and with estimates from another snow energy and mass-balance model, SNTHERM. Root-mean-squared differences (RMSDs) between snowpit SWE observations (January–June) at all sites and estimates from the NSM were about 11% (RMSD = 0.073 m) of the average maximum observed SWE from all sites of 0.694 m. SNTHERM exhibited only a slightly better agreement (RMSD = 0.066 m). During the winter and early spring period before snowpacks became isothermal at 273.15 K, both NSM and SNTHERM simulated significantly cooler average snowpack temperatures than observed (RMSD = 3 and 2 K, respectively). During this snow accumulation period estimates of SWE by both models were very similar. Differences in modeled SWE were traced to short periods (5–21 days) during isothermal conditions in early spring when the two models diverged. These events caused SWE differences that persisted throughout the ablation period and resulted in a range in melt-out times of 0.2–7.2 days between depth observations and modeled estimates. The divergence in SWE resulted from differences in snowmelt fluxes estimated by the two models, which are suggested to result from 1) liquid water fractions within a snowpack being estimated by the NSM using an internal energy method and by SNTHERM using a semiempirical temperature-based approach, and 2) SNTHERM, but not the NSM, accounting for the small liquid water fraction that coexists in equilibrium with snow when the snowpack surface is dry (&lt;273.15 K).
Model Performance of Downscaling 1999–2004 Hydrometeorological Fields to the Upper Rio Grande Basin Using Different Forcing Datasets
Authors: Li J. , Gao X. , Sorooshian S. 
Published: January 2008

Abstract
This study downscaled more than five years of data (1999–2004) for hydrometeorological fields over the upper Rio Grande basin (URGB) to a 4-km resolution using a regional model [fifth-generation Pennsylvania State University–National Center for Atmospheric Research (NCAR) Mesoscale Model (MM5, version 3)] and two forcing datasets that include National Centers for Environmental Prediction (NCEP)–NCAR reanalysis-1 (R1) and North America Regional Reanalysis (NARR) data. The long-term high-resolution simulation results show detailed patterns of hydroclimatological fields that are highly related to the characteristics of the regional terrain; the most important of these patterns are precipitation localization features caused by the complex topography. In comparison with station observational data, the downscaling processing, on whichever forcing field is used, generated more accurate surface temperature and humidity fields than the Eta Model and NARR data, although it still included marked errors, such as a negative (positive) bias toward the daily maximum (minimum) temperature and overestimated precipitation, especially in the cold season.
Comparing the downscaling results forced by the NARR and R1 with both the gridded and station observational data shows that under the NARR forcing, the MM5 model produced generally better results for precipitation, temperature, and humidity than it did under the R1 forcing. These improvements were more apparent in winter and spring. During the warm season, although the use of NARR improved the precipitation estimates statistically at the regional (basin) scale, it substantially underestimated them over the southern upper Rio Grande basin, partly because the NARR forcing data exhibited warm and dry biases in the monsoon-active region during the simulation period and improper domain selection. Analyses also indicate that over mountainous regions, both the Climate Prediction Center’s (CPC’s) gridded (0.25°) and NARR forcings underestimate precipitation in comparison with station gauge data.
Normal-Mode Instabilities of a Time-Dependent Coastal Upwelling Jet
Authors: Durski S. M. , Samelson R. M. , Allen J. S. , Egbert G. D. 
Published: January 2008

Abstract
The linear stability of a nearly time-periodic, nonlinear, coastal upwelling–downwelling circulation, over alongshore-uniform topography, driven by a time-periodic wind stress is investigated using numerical methods. The near-periodic alongshore-uniform basic flow is obtained by forcing a primitive equation numerical model of coastal ocean circulation with periodic wind stress. Disturbance growth on this near-periodic flow is explored in linear and nonlinear model simulations. Numerous growing normal modes are found in the linear analyses at alongshore scales between 4 and 24 km. These modes vary in cross-shore structure and timing of maximum disturbance growth rate. One group of modes, in the 6.5–8.5-km alongshore-scale range, bears strong resemblance to the ensemble average disturbance structures observed in perturbed nonlinear model simulations. These modes are of a mixed type, exhibiting both strong baroclinic and barotropic energy exchange mechanisms, with maximum disturbance growth occurring during the transition from upwelling favorable to downwelling favorable winds. Nonlinear disturbance growth is characterized by similar structures at these same scales, but with significant exchange of energy between disturbances at different alongshore scales, such that overall disturbance energy accumulates at the longest (domain) scales, and gradually propagates offshore mainly in the pycnocline over numerous forcing cycles.