bluuebunny/crossref_metadata_2025_split huggingface dataset:
The analysis of doxorubicin resistance in human breast cancer cells using antibody microarrays
Authors: Smith Laura , Watson Mark B. , O'Kane Sara L. , Drew Philip J. , Lind Michael J. , Cawkwell Lynn 
Published: August 2006

Abstract
Doxorubicin is considered to be the most effective agent in the treatment of breast cancer patients. Unfortunately, resistance to this agent is common, representing a major obstacle to successful treatment. The identification of novel biomarkers that are able to predict treatment response may allow therapy to be tailored to individual patients. Antibody microarrays provide a powerful new technique, enabling the global comparative analysis of many proteins simultaneously. This technology may identify a panel of proteins to discriminate between drug-resistant and drug-sensitive samples. The Panorama Cell Signaling Antibody Microarray was exploited to analyze the MDA-MB-231 breast cancer cell line and a novel derivative, which displays significant resistance to doxorubicin at clinically relevant concentrations. The microarray comprised 224 antibodies selected from a variety of pathways, including apoptotic and cell signaling pathways. A standard ≥2.0-fold cutoff value was used to determine differentially expressed proteins. A decrease in the expression of mitogen-activated protein kinase–activated monophosphotyrosine (phosphorylated extracellular signal-regulated kinase; 2.8-fold decrease), cyclin D2 (2.5-fold decrease), cytokeratin 18 (2.5-fold decrease), cyclin B1 (2.4-fold decrease), and heterogeneous nuclear ribonucleoprotein m3-m4 (2.0-fold decrease) was associated with doxorubicin resistance. Western blotting was exploited to confirm results from the antibody microarray experiment. These results suggest that antibody microarrays can be used to identify novel biomarkers and further validation may reveal mechanisms of chemotherapy resistance and identify potential therapeutic targets. [Mol Cancer Ther 2006;5(8):2115–20]
Influence of Initial Conditions on Summer Precipitation Simulations over the United States and Mexico
Authors: Mo Kingtse C. , Schemm J. E. , Kim H. , Higgins W. R. 
Published: August 2006

Abstract
The impact of initial conditions on summer precipitation over North America for July–September was examined by comparing long-term simulations of the Atmospheric Model Intercomparison Project (AMIP) runs with the ensemble simulations (SIMUs) initialized at the end of June each year. Both types of simulations use the observed SSTs as boundary conditions, and hence, the differences are a result of the initial conditions. Experiments were performed using the NCEP Global Forecast System (GFS) T126L28 model with 28 vertical levels. Over the monsoon core region, the model has the correct relationship between evaporation (E) and soil moisture and the T126 model has enough horizontal resolution to simulate the moisture transport from the Gulf of California. Over the Great Plains, the model has dry and warm biases. These biases are larger in the AMIP runs in comparison with the SIMU. Two major model errors contribute to the biases: 1) the deep soil layer (10–200 cm) is far too dry and does not have enough variability; and 2) the model does not have the correct relationship between E and soil moisture at the top level 10 cm (SM10cm). The linear E–SM10cm relationship in the model has a large slope in spring and early summer. Evaporation tends to drop too sharply and too quickly during the model dry periods; it does increase during rainfall periods, but the model still has an overall deficit in E. The SIMU runs have better estimated E values supplied by the initial conditions and the surface conditions deteriorate slow enough to have better seasonal mean summer E and precipitation than the AMIP runs. The results here may be model dependent. For the GFS model, the initial conditions supply better estimates of soil moisture and surface fluxes at the beginning of a simulation, which compensates for model errors.
Spatial and Temporal Variability of Nonfreezing Drizzle in the United States and Canada
Authors: Sears-Collins Addison L. , Schultz David M. , Johns Robert H. 
Published: August 2006

Abstract
A climatology of nonfreezing drizzle is created using surface observations from 584 stations across the United States and Canada over the 15-yr period 1976–90. Drizzle falls 50–200 h a year in most locations in the eastern United States and Canada, whereas drizzle falls less than 50 h a year in the west, except for coastal Alaska and several western basins. The eastern and western halves of North America are separated by a strong gradient in drizzle frequency along roughly 100°W, as large as about an hour a year over 2 km. Forty percent of the stations have a drizzle maximum from November to January, whereas only 13% of stations have a drizzle maximum from June to August. Drizzle occurrence exhibits a seasonal migration from eastern Canada and the central portion of the Northwest Territories in summer, equatorward to most of the eastern United States and southeast Canada in early winter, to southeastern Texas and the eastern United States in late winter, and back north to eastern Canada in the spring. The diurnal hourly frequency of drizzle across the United States and Canada increases sharply from 0900 to 1200 UTC, followed by a steady decline from 1300 to 2300 UTC. Diurnal drizzle frequency is at a maximum in the early morning, in agreement with other studies.
Drizzle occurs during a wide range of atmospheric conditions at the surface. Drizzle has occurred at sea level pressures below 960 hPa and above 1040 hPa. Most drizzle, however, occurs at higher than normal sea level pressure, with more than 64% occurring at a sea level pressure of 1015 hPa or higher. A third of all drizzle falls when the winds are from the northeast quadrant (360°–89°), suggesting that continental drizzle events tend to be found poleward of surface warm fronts and equatorward of cold-sector surface anticyclones. Two-thirds of all drizzle occurs with wind speeds of 2.0–6.9 m s−1, with 7.6% in calm wind and 5% at wind speeds ⩾ 10 m s−1. Most drizzle (61%) occurs with visibilities between 1.5 and 5.0 km, with only about 20% occurring at visibilities less than 1.5 km.
Toward an Integrated Seasonal Forecasting System for South America
Authors: Coelho C. A. S. , Stephenson D. B. , Balmaseda M. , Doblas-Reyes F. J. , van Oldenborgh G. J. 
Published: August 2006

Abstract
This study proposes an objective integrated seasonal forecasting system for producing well-calibrated probabilistic rainfall forecasts for South America. The proposed system has two components: (i) an empirical model that uses Pacific and Atlantic sea surface temperature anomalies as predictors for rainfall and (ii) a multimodel system composed of three European coupled ocean–atmosphere models. Three-month lead austral summer rainfall predictions produced by the components of the system are integrated (i.e., combined and calibrated) using a Bayesian forecast assimilation procedure. The skill of empirical, coupled multimodel, and integrated forecasts obtained with forecast assimilation is assessed and compared. The simple coupled multimodel ensemble has a comparable level of skill to that obtained using a simplified empirical approach. As for most regions of the globe, seasonal forecast skill for South America is low. However, when empirical and coupled multimodel predictions are combined and calibrated using forecast assimilation, more skillful integrated forecasts are obtained than with either empirical or coupled multimodel predictions alone. Both the reliability and resolution of the forecasts have been improved by forecast assimilation in several regions of South America. The Tropics and the area of southern Brazil, Uruguay, Paraguay, and northern Argentina have been found to be the two most predictable regions of South America during the austral summer. Skillful rainfall forecasts are generally only possible during El Niño or La Niña years rather than in neutral years.
Extreme Anomalous Atmospheric Circulation in the West Antarctic Peninsula Region in Austral Spring and Summer 2001/02, and Its Profound Impact on Sea Ice and Biota*
Authors: Massom Robert A. , Stammerjohn Sharon E. , Smith Raymond C. , Pook Michael J. , Iannuzzi Richard A. , Adams Neil , Martinson Douglas G. , Vernet Maria , Fraser William R. , Quetin Langdon B. , Ross Robin M. , Massom Yuko , Krouse H. Roy 
Published: August 2006

AbstractExceptional sea ice conditions occurred in the West Antarctic Peninsula (WAP) region from September 2001 to February 2002, resulting from a strongly positive atmospheric pressure anomaly in the South Atlantic coupled with strong negative anomalies in the Bellingshausen–Amundsen and southwest Weddell Seas. This created a strong and persistent north-northwesterly flow of mild and moist air across the WAP. In situ, satellite, and NCEP–NCAR Reanalysis (NNR) data are used to examine the profound and complex impact on regional sea ice, oceanography, and biota. Extensive sea ice melt, leading to an ocean mixed layer freshening and widespread ice surface flooding, snow–ice formation, and phytoplankton growth, coincided with extreme ice deformation and dynamic thickening. Sea ice dynamics were crucial to the development of an unusually early and rapid (short) retreat season (negative ice extent anomaly). Strong winds with a dominant northerly component created an unusually compact marginal ice zone and a major increase in ice thickness by deformation and over-rafting. This led to the atypical persistence of highly compact coastal ice through summer. Ecological effects were both positive and negative, the latter including an impact on the growth rate of larval Antarctic krill and the largest recorded between-season breeding population decrease and lowest reproductive success in a 30-yr Adélie penguin demographic time series. The unusual sea ice and snow cover conditions also contributed to the formation of a major phytoplankton bloom. Unexpectedly, the initial bloom occurred within compact sea ice and could not be detected in Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) ocean color data. This analysis demonstrates that sea ice extent alone is an inadequate descriptor of the regional sea ice state/conditions, from both a climatic and ecological perspective; further information is required on thickness and dynamics/deformation.
Predictability Loss in an Intermediate ENSO Model due to Initial Error and Atmospheric Noise*
Authors: Karspeck Alicia R. , Kaplan Alexey , Cane Mark A. 
Published: August 2006

AbstractThe seasonal and interannual predictability of ENSO variability in a version of the Zebiak–Cane coupled model is examined in a perturbation experiment. Instead of assuming that the model is “perfect,” it is assumed that a set of optimal initial conditions exists for the model. These states, obtained through a nonlinear minimization of the misfit between model trajectories and the observations, initiate model forecasts that correlate well with the observations. Realistic estimates of the observational error magnitudes and covariance structures of sea surface temperatures, zonal wind stress, and thermocline depth are used to generate ensembles of perturbations around these optimal initial states, and the error growth is examined. The error growth in response to subseasonal stochastic wind forcing is presented for comparison.In general, from 1975 to 2002, the large-scale uncertainty in initial conditions leads to larger error growth than continuous stochastic forcing of the zonal wind stress fields. Forecast ensemble spread is shown to depend most on the calendar month at the end of the forecast rather than the initialization month, with the seasons of greatest spread corresponding to the seasons of greatest anomaly variance. It is also demonstrated that during years with negative (and rapidly decaying) Niño-3 SST anomalies (such as the time period following an El Niño event), there is a suppression of error growth. In years with large warm ENSO events, the ensemble spread is no larger than in moderately warm years. As a result, periods with high ENSO variance have greater potential prediction utility.In the realistic range of observational error, the ensemble spread has more sensitivity to the initial error in the thermocline depth than to the sea surface temperature or wind stress errors. The thermocline depth uncertainty is the principal reason why initial condition uncertainties are more important than wind noise for ensemble spread.
The Evolution and Demise of North Brazil Current Rings*
Authors: Fratantoni David M. , Richardson Philip L. 
Published: August 2006

AbstractSubsurface float and surface drifter observations illustrate the structure, evolution, and eventual demise of 10 North Brazil Current (NBC) rings as they approached and collided with the Lesser Antilles in the western tropical Atlantic Ocean. Upon encountering the shoaling topography east of the Lesser Antilles, most of the rings were deflected abruptly northward and several were observed to completely engulf the island of Barbados. The near-surface and subthermocline layers of two rings were observed to cleave or separate upon encountering shoaling bathymetry between Tobago and Barbados, with the resulting portions each retaining an independent and coherent ringlike vortical circulation. Surface drifters and shallow (250 m) subsurface floats that looped within NBC rings were more likely to enter the Caribbean through the passages of the Lesser Antilles than were deeper (500 or 900 m) floats, indicating that the regional bathymetry preferentially inhibits transport of intermediate-depth ring components. No evidence was found for the wholesale passage of rings through the island chain.
Sea Surface Temperature Variability along the Path of the Antarctic Circumpolar Current
Authors: Verdy Ariane , Marshall John , Czaja Arnaud 
Published: August 2006

Abstract
The spatial and temporal distributions of sea surface temperature (SST) anomalies in the Antarctic Circumpolar Current (ACC) are investigated, using monthly data from the NCEP–NCAR reanalysis for the period 1980–2004. Patterns of atmospheric forcing are identified in observations of sea level pressure and air–sea heat fluxes. It is found that a significant fraction of SST variability in the ACC can be understood as a linear response to surface forcing by the Southern Annular Mode (SAM) and remote forcing by ENSO. The physical mechanisms rely on the interplay between atmospheric variability and mean advection by the ACC. SAM and ENSO drive a low-level anomalous circulation pattern localized over the South Pacific Ocean, inducing surface heat fluxes and Ekman heat advection anomalies. A simple model of SST propagating in the ACC, forced with heat fluxes estimated from the reanalysis, suggests that surface heat fluxes and Ekman heat advection are equally important in driving the observed SST variability. Further diagnostics indicate that SST anomalies, generated mainly upstream of Drake Passage, are subsequently advected by the ACC and damped after a couple of years. It is suggested that SST variability along the path of the ACC is largely a passive response of the oceanic mixed layer to atmospheric forcing.
Three-Dimensional Wind-Driven Coastal Circulation past a Headland
Authors: Winant Clinton D. 
Published: August 2006

AbstractLocal velocities and the trajectories of fluid parcels forced by wind blowing over a continental shelf, in the vicinity of a headland, are described with a linear, steady, three-dimensional barotropic model. The dynamical balance that governs the transport is similar to the wind-driven general circulation, because the varying bottom depth acts in the same way as meridional variation in the rotation rate. Far from the headland the circulation is independent of alongshore position, and the transport is parallel to the coast. The alongshore pressure gradient is a significant term in the alongshore momentum balance. Near the headland, the amplitude of the circulation, including the vertical motion, is larger on the upwave side (the side toward which a Kelvin wave would travel) than on the downwave side. On the upwave side, the flow adjusts to the presence of the headland over a distance of order δEB*, where δE is the ratio of the Ekman depth to the maximum shelf depth and B* is the width of the shelf. Fluid parcels that upwell on the upwave side are drawn from deeper depths than parcels that upwell at other alongshore locations. On the downwave side the flow adjusts over a relatively long distance, of order δ−1EB*.
Thermally Driven Exchanges between a Coral Reef and the Adjoining Ocean
Authors: Monismith Stephen G. , Genin Amatzia , Reidenbach Matthew A. , Yahel Gitai , Koseff Jeffrey R. 
Published: August 2006

Abstract
In this paper hydrographic observations made over a fringing coral reef at the northern end of the Gulf of Aqaba near Eilat, Israel, are discussed. These data show exchange flows driven by the onshore–offshore temperature gradients that develop because shallow regions near shore experience larger temperature changes than do deeper regions offshore when subjected to the same rate of heating or cooling. Under heating conditions, the resulting vertically sheared exchange flow is offshore at the surface and onshore at depth, whereas when cooling dominates, the pattern is reversed. For summer conditions, heating and cooling are both important and a diurnally reversing exchange flow is observed. During winter conditions, heating occupies a relatively small fraction of the day, and only the cooling flow is observed. When scaled by ΔV, the observed profiles of the cross-shore during cooling velocity collapse onto a single curve. The value of ΔV depends on the convective velocity scale uf and the bottom slope β through the inertial scaling, ΔV ∼ β−1/3uf first proposed by Phillips in the 1960s as a model of buoyancy-driven flow in the Red Sea. However, it is found that turbulent stresses associated with the longshore tidal flows and unsteadiness due to the periodic nature of the buoyancy forcing can act to weaken the sheared exchange flow. Nonetheless, the measured exchange flow transport agrees well with previous field and laboratory work. The paper is concluded by noting that the “thermal siphon” observed on the Eilat reef may be a relatively generic feature of the nearshore physical oceanography of reefs and coastal oceans in general.
Laboratory and Analytical Model Studies of the Faroe Bank Channel Deep-Water Outflow
Authors: Davies P. A. , Wåhlin A. K. , Guo Y. 
Published: August 2006

Abstract
Results are described from a combined laboratory and analytical study of the dense, deep-water flow through the Faroe Bank Channel. Archival field data have been used to specify the velocity and density field conditions in an idealized, distorted laboratory model in which the spatial and temporal development of a turbulent, dense source flow has been studied parametrically in terms of the source Rossby and Froude numbers, respectively. Measurements are presented to show that the flow (i) maintains geostrophic balance within the topographically varying channel and (ii) adjusts on the Ekman time scale to changing flow conditions. The outflow structure is shown to consist of a dominant axial (i.e., along channel) core component, with a significant transverse (i.e., side slope) secondary circulation driven by Ekman drainage and topographic divergence processes. Density field measurements are presented to show the mixing occurring between the turbulent outflow and the overlying water mass. Buoyancy anomaly data are derived to quantify the spatial variations of mixing processes along and across the channel. An analytical model based on Ekman dynamics is developed for flow in the channel, and the predictions of the dimensions of the outflow in terms of the external flow and topographic parameters are shown to agree well with the laboratory data.
Decadal Variability in the Formation of the North Pacific Subtropical Mode Water: Oceanic versus Atmospheric Control
Authors: Qiu Bo , Chen Shuiming 
Published: August 2006

Abstract
In situ temperature and altimetrically derived sea surface height data are used to investigate the low-frequency variations in the formation of the North Pacific Ocean Subtropical Mode Water (STMW) over the past 12 yr. Inside the Kuroshio Extension (KE) recirculation gyre where STMW forms, the dominant signal is characterized by a gradual thinning in the late winter mixed layer depth and in the 16°–18°C thermostad layer from 1993 to 1999 and a subsequent steady thickening of these features after 2000. This same decadal signal is also seen in the low-potential-vorticity (PV) STMW layer in the interior subtropical gyre south of the recirculation gyre. By analyzing the air–sea flux data from the NCEP–NCAR reanalysis project, little correlation is found between the decadal STMW signal and the year-to-year changes in the cumulative wintertime surface cooling. In contrast, the decadal signal is found to be closely related to variability in the dynamic state of the KE system. Specifically, STMW formation is reduced when the KE path is in a variable state, during which time high regional eddy variability infuses high-PV KE water into the recirculation gyre, increasing the upper-ocean stratification and hindering the development of a deep winter mixed layer. A stable KE path, on the other hand, favors the maintenance of a weak stratification, leading to a deep winter mixed layer and formation of a thick STMW layer. The relative importance of the surface air–sea flux forcing versus the preconditioning stratification in controlling the variations in the late winter mixed layer depth is quantified using both a simple upper-ocean heat conservation model and a bulk mixed layer model. The majority of the variance (∼80%) is found to be due to the stratification changes controlled by the dynamic state of the KE system.
The Ocean’s Memory of the Atmosphere: Residence-Time and Ventilation-Rate Distributions of Water Masses
Authors: Primeau François W. , Holzer Mark 
Published: August 2006

Abstract
A conceptually new approach to diagnosing tracer-independent ventilation rates is developed. Tracer Green functions are exploited to partition ventilation rates according to the ventilated fluid’s residence time in the ocean interior and according to where this fluid enters and exits the interior. In the presence of mixing by mesoscale eddies, which are reasonably represented by diffusion, ventilation rates for overlapping entry and exit regions cannot meaningfully be characterized by a single rate. It is a physical consequence of diffusive transport that fluid elements that spend an infinitesimally short time in the interior cause singularly large ventilation rates for overlapping entry and exit regions. Therefore, ventilation must generally be characterized by a ventilation-rate distribution, ϕ, partitioned according to the time that the ventilated fluid spends in the interior between successive surface contacts. An offline forward and adjoint time-averaged OGCM is used to illustrate the rich detail that ϕ and the closely related probability density function of residence times ℛ provide on the way the ocean communicates with the surface. These diagnostics quantify the relative importance of various surface regions for ventilating the interior ocean by either exposing old water masses to the atmosphere or by forming newly ventilated ones. The model results suggest that the Southern Ocean plays a dominant role in ventilating the ocean, both as a region where new waters are ventilated into the interior and where old waters are first reexposed to the atmosphere.