bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of epidermal growth factor receptor in relation toBRCA1status, basal-like markers and prognosis in breast cancer
Authors: Arnes J B , Bégin L R , Stefansson I , Brunet J-S , Nielsen T O , Foulkes W D , Akslen L A 
Published: August 2008

Aims:BRCA1-related breast cancer is associated with a basal-like phenotype, and is frequently oestrogen receptor (ER) and HER2 negative. The expression of epidermal growth factor receptor (EGFR) has been considered to be one component of the basal-like phenotype, but no standard criteria exist. This study investigates the relationship between EGFR expression,BRCA1status and basal markers with respect to clinicopathological associations and prognosis, in addition to evaluating different criteria for EGFR assessment by immunohistochemistry.Methods:A tissue microarray comprising 230 available cases, from a series of primary invasive breast cancer diagnosed in Ashkenazi Jewish women during 1980–1995, was stained for EGFR using the Dako PharmDX kit, and evaluated by Webslide virtual microscopy.Results:EGFR was positive in 9–19% according to different criteria. Expression was associated withBRCA1carrier status and basal-like markers as negative ER, positive cytokeratin 5/6 and positive P-cadherin staining. EGFR was prognostically significant by univariate and multivariate analysis within the group carrying germ-lineBRCA1mutations. Histological grade, axillary lymph node status and P-cadherin status had significant independent value in the final multivariate model including all cases, whereas EGFR was not significant in this model. All five scoring systems gave comparable results concerning clinicopathological associations and patient outcome, although the most restrictive criteria (EGFR-HI) tended to be most sensitive in predictingBRCA1status, a basal phenotype, and patient prognosis.Conclusions:EGFR expression, being present in 9–19% of the cases, was prognostically significant amongBRCA1mutated cases only. In multivariate survival analysis of all cases, no independent effect was seen. However, EGFR immunostaining might be relevant to predict the response to targeted therapy, and this should be studied further.
A Climatology of Ocean–Atmosphere Heat Flux Estimates over the Great Barrier Reef and Coral Sea: Implications for Recent Mass Coral Bleaching Events
Authors: Weller Evan , Nunez Manuel , Meyers Gary , Masiri Itsara 
Published: August 2008

Abstract
A regional-scale estimate of the surface heat budget of the Great Barrier Reef and Coral Sea (10°–26°S, 142°–155°E) has been developed for the period 1995–2005 in the hope of understanding the trends of sea surface temperatures and the surface heat balance. This report describes the methodology to acquire input parameters from satellite observations, the resultant individual components of the surface heat budget, and their validation with existing datasets and surface measurements.
The accuracy of individual flux components of the heat budget were analyzed with an array of surface measurements. Derived monthly averaged latent and sensible heat flux estimates show RMS errors of approximately 25.2 and 3.4 W m−2, respectively. Monthly averaged longwave and shortwave radiation flux estimates show RMS errors of approximately 6.7 and 13.3 W m−2, respectively. These improved estimates allow a higher confidence in studies that examine recent sea surface temperature (SST) trends and observed mass coral bleaching for the region.
It is proposed that the greatest uptake of heat occurs over the spring/summer period in the central and southern regions of the Great Barrier Reef, agreeing well with areas where anomalously high sea surface temperatures are observed and where the most significant coral bleaching has occurred, and not in the most northern, more tropical region, as might be expected. The surface heat budget climatology was used to examine the mass bleaching episode that occurred in 2002. Results show that areas of maximum and minimum bleaching are better discriminated by the anomaly from mean seasonal values in the net surface heat flux (QNET), with accuracy of 86% and 79%, respectively, than by absolute QNET, absolute SST, or SST anomaly. Possible reasons for this are discussed.
An Investigation of Warm-Season Spatial Rainfall Variability in Oklahoma City: Possible Linkages to Urbanization and Prevailing Wind
Authors: Hand Lauren M. , Shepherd J. Marshall 
Published: August 2008

Abstract
This study used 9 yr (1998–2006) of warm-season (June–September) mean daily cumulative rainfall data from both the Tropical Rainfall Measuring Mission (TRMM) Multisatellite Precipitation Analysis and rain gauge stations to examine spatial variability in warm-season rainfall events around Oklahoma City (OKC). It was hypothesized that with warm-season rainfall variability, under weakly forced conditions, a rainfall anomaly would be present in climatological downwind areas of OKC. Results from both satellite and gauge-based analyses revealed that the north-northeastern (NNE) regions of the metropolitan OKC area were statistically wetter than other regions. Climatological sounding and reanalysis data revealed that, on average, the NNE area of OKC was the climatologically downwind region, confirming that precipitation modification by the urban environment may be more dominant than agricultural/topographic influences on weakly forced days. The study also established that satellite precipitation estimates capture spatial rainfall variability as well as traditional ground-based resources do. TRMM products slightly underestimate the precipitation recorded by gauges, but the correlation R improves dramatically when the analysis is restricted to mean daily rainfall estimates from OKC urban grid cells containing multiple gauge stations (R2 = 0.878). It was also quantitatively confirmed, using a relatively new concentration factor analysis, that prevailing wind–rainfall yields were consistent with the overall framework of an urban rainfall effect. Overall, the study establishes a prototype method for utilizing satellite-based rainfall estimates to examine rainfall modification by urbanization on global scales and in parts of the world that are not well instrumented with rain gauge or radar networks.
Planetary Wave Breaking and Tropospheric Forcing as Seen in the Stratospheric Sudden Warming of 2006
Authors: Coy Lawrence , Eckermann Stephen , Hoppel Karl 
Published: August 2008

Abstract
The major stratospheric sudden warming (SSW) of January 2006 is examined using meteorological fields from Goddard Earth Observing System version 4 (GEOS-4) analyses and forecast fields from the Navy Operational Global Atmospheric Prediction System–Advanced Level Physics, High Altitude (NOGAPS-ALPHA). The study focuses on the upper tropospheric forcing that led to the major SSW and the vertical structure of the subtropic wave breaking near 10 hPa that moved low tropical values of potential vorticity (PV) to the pole. Results show that an eastward-propagating upper tropospheric ridge over the North Atlantic with its associated cold temperature perturbations (as manifested by high 360-K potential temperature surface perturbations) and large positive local values of meridional heat flux directly forced a change in the stratospheric polar vortex, leading to the stratospheric subtropical wave breaking and warming. Results also show that the anticyclonic development, initiated by the subtropical wave breaking and associated with the poleward advection of the low PV values, occurred over a limited altitude range of approximately 6–10 km. The authors also show that the poleward advection of this localized low-PV anomaly was associated with changes in the Eliassen–Palm (EP) flux from equatorward to poleward, suggesting an important role for Rossby wave reflection in the SSW of January 2006. Similar upper tropospheric forcing and subtropical wave breaking were found to occur prior to the major SSW of January 2003.
A 10–15-Yr Modulation Cycle of ENSO Intensity
Authors: Sun Fengpeng , Yu Jin-Yi 
Published: August 2008

Abstract
This study examines the slow modulation of El Niño–Southern Oscillation (ENSO) intensity and its underlying mechanism. A 10–15-yr ENSO intensity modulation cycle is identified from historical and paleoclimate data by calculating the envelope function of boreal winter Niño-3.4 and Niño-3 sea surface temperature (SST) indices. Composite analyses reveal interesting spatial asymmetries between El Niño and La Niña events within the modulation cycle. In the enhanced intensity periods of the cycle, El Niño is located in the eastern tropical Pacific and La Niña in the central tropical Pacific. The asymmetry is reversed in the weakened intensity periods: El Niño centers in the central Pacific and La Niña in the eastern Pacific. El Niño and La Niña centered in the eastern Pacific are accompanied with basin-scale surface wind and thermocline anomalies, whereas those centered in the central Pacific are accompanied with local wind and thermocline anomalies. The El Niño–La Niña asymmetries provide a possible mechanism for ENSO to exert a nonzero residual effect that could lead to slow changes in the Pacific mean state. The mean state changes are characterized by an SST dipole pattern between the eastern and central tropical Pacific, which appears as one leading EOF mode of tropical Pacific decadal variability. The Pacific Walker circulation migrates zonally in association with this decadal mode and also changes the mean surface wind and thermocline patterns along the equator. Although the causality has not been established, it is speculated that the mean state changes in turn favor the alternative spatial patterns of El Niño and La Niña that manifest as the reversed ENSO asymmetries. Using these findings, an ENSO–Pacific climate interaction mechanism is hypothesized to explain the decadal ENSO intensity modulation cycle.
A Simple Atmospheric Model of the Local and Teleconnection Responses to Tropical Heating Anomalies
Authors: Lee Sang-Ki , Wang Chunzai , Mapes Brian E. 
Published: August 2008

Abstract
A minimal complexity model of both the local and remote stationary responses of the atmosphere to tropical heating anomalies is described and demonstrated. Two levels are recast as baroclinic and barotropic components with thermal advection in the tropics neglected. The model is linearized about some idealized and realistic background wind fields and forced with a localized heating for illustration. In the tropics, the baroclinic responses are familiar from the Matsuno–Gill model; these excite barotropic responses by advective interactions with vertical background wind shear. The barotropic signals are in turn transmitted to high latitudes only in the presence of barotropic background westerly winds. For an El Niño–like equatorial heating, the barotropic response has anticyclones to the north and south of the heating reinforcing (opposing) the anticyclonic (cyclonic) baroclinic gyres in the upper (lower) troposphere. With realistic background flows, the model reproduces the hemispheric asymmetry of ENSO teleconnections. Further experiments show that the winter hemisphere is favored mainly because the summer hemispheric subtropical jet is farther from the heating latitude, suggesting that the summer hemisphere can still host robust stationary Rossby waves if the heating occurs in the vicinity of the jet. As an example, it is shown that summer heating over the Atlantic warm pool (AWP) can have a remote influence on the summer climate of North America and Europe.
An Evaluation of Calibration Techniques for In Situ Carbon Dioxide Measurements Using a Programmable Portable Trace-Gas Measuring System
Authors: Burns Sean P. , Delany Anthony C. , Sun Jielun , Stephens Britton B. , Oncley Steven P. , Maclean Gordon D. , Semmer Steven R. , Schröter Joel , Ruppert Johannes 
Published: August 2008

Abstract
The construction and deployment of a portable trace-gas measurement system (TGaMS) is described. The air-collection system (dubbed HYDRA) collects air samples from 18 different locations and was connected to either one or two LI-COR LI-7000 gas analyzers to measure CO2. An in situ “field calibration” method, that uses four calibration gases with an uncertainty on the order of ±0.1 μmol mol−1 relative to the WMO CO2 mole fraction scale, revealed CO2 output from the LI-7000 had a slightly nonlinear relationship relative to the CO2 concentration of the calibration gases. The sensitivity of the field-calibrated CO2 to different forms of the field-calibration equation is investigated. To evaluate TGaMS performance, CO2 from collocated inlets, portable gas cylinders, and nearby independent CO2 instruments are compared. Results are as follows: 1) CO2 measurements from HYDRA multiple inlets are feasible with a reproducibility of ±0.4 μmol mol−1 (based on the standard deviation of the CO2 difference between collocated inlets when HYDRA was operating with two LI-7000s); 2) CO2 differences among the various field-calibration equations were on the order of ±0.3 μmol mol−1; and 3) comparison of midday hourly CO2 measurements at 30 m AGL between TGaMS and an independent high-accuracy CO2 measurement system (within 300 m of TGaMS) had a median difference and standard deviation of 0.04 ± 0.81 μmol mol−1 over two months.
Development of a Long-Range Lightning Detection Network for the Pacific: Construction, Calibration, and Performance*
Authors: Pessi Antti T. , Businger Steven , Cummins K. L. , Demetriades N. W. S. , Murphy M. , Pifer B. 
Published: August 2008

Abstract
The waveguide between the earth’s surface and the ionosphere allows very low-frequency (VLF) emissions generated by lightning, called sferics, to propagate over long distances. The new Pacific Lightning Detection Network (PacNet), as a part of a larger long-range lightning detection network (LLDN), utilizes this attribute to monitor lightning activity over the central North Pacific Ocean with a network of ground-based lightning detectors that have been installed on four widely spaced Pacific islands (400–3800 km). PacNet and LLDN sensors combine both magnetic direction finding (MDF) and time-of-arrival (TOA)-based technology to locate a strike with as few as two sensors. As a result, PacNet/LLDN is one of the few observing systems, outside of geostationary satellites, that provides continuous real-time data concerning convective storms throughout a synoptic-scale area over the open ocean.
The performance of the PacNet/LLDN was carefully assessed. Long-range lightning flash detection efficiency (DE) and location accuracy (LA) models were developed with reference to accurate data from the U.S. National Lightning Detection Network (NLDN). Model calibration procedures are detailed, and comparisons of model results with lightning observations from the PacNet/LLDN in correlation with NASA’s Lightning Imaging Sensor (LIS) are presented. The daytime and nighttime flash DE in the north-central Pacific is in the range of 17%–23% and 40%–61%, respectively. The median LA is in the range of 13–40 km. The results of this extensive analysis suggest that the DE and LA models are reasonably able to reproduce the observed performance of PacNet/LLDN.
The implications of this work are that the DE and LA model outputs can be used in quantitative applications of the PacNet/LLDN over the North Pacific Ocean and elsewhere. For example, by virtue of the relationship between lightning and rainfall rates, these data also hold promise as input for NWP models as a proxy for latent heat release in convection. Moreover, the PacNet/LLDN datastream is useful for investigations of storm morphology and cloud microphysics over the central North Pacific Ocean. Notably, the PacNet/LLDN lightning datastream has application for planning transpacific flights and nowcasting of squall lines and tropical storms.
Spectral Partitioning and Identification of Wind Sea and Swell
Authors: Portilla Jesús , Ocampo-Torres Francisco J. , Monbaliu Jaak 
Published: August 2008

AbstractIn this paper, different partitioning techniques and methods to identify wind sea and swell are investigated, addressing both 1D and 2D schemes. Current partitioning techniques depend largely on arbitrary parameterizations to assess if wave systems are significant or spurious. This makes the implementation of automated procedures difficult, if not impossible, to calibrate. To avoid this limitation, for the 2D spectrum, the use of a digital filter is proposed to help the algorithm keep the important features of the spectrum and disregard the noise. For the 1D spectrum, a mechanism oriented to neglect the most likely spurious partitions was found sufficient for detecting relevant spectral features. Regarding the identification of wind sea and swell, it was found that customarily used methods sometimes largely differ from one another. Evidently, methods using 2D spectra and wind information are the most consistent. In reference to 1D identification methods, attention is given to two widely used methods, namely, the steepness method used operationally at the National Data Buoy Center (NDBC) and the Pierson–Moskowitz (PM) spectrum peak method. It was found that the steepness method systematically overestimates swell, while the PM method is more consistent, although it tends to underestimate swell. Consistent results were obtained looking at the ratio between the energy at the spectral peak of a partition and the energy at the peak of a PM spectrum with the same peak frequency. It is found that the use of partitioning gives more consistent identification results using both 1D and 2D spectra.
Automated Processing of Sea Surface Images for the Determination of Whitecap Coverage
Authors: Callaghan Adrian H. , White Martin 
Published: August 2008

Abstract
Sea surface images have been collected to determine the percentage whitecap coverage (W) since the late 1960s. Image processing methods have changed dramatically since the beginning of whitecap studies. An automated whitecap extraction (AWE) technique has been developed at the National University of Ireland, Galway, that allows images to be analyzed for percentage whitecap coverage without the need of a human analyst. AWE analyzes digital images and determines a suitable threshold with which whitecaps can be separated from unbroken background water. By determining a threshold for each individual image, AWE is suitable for images obtained in conditions of changing ambient illumination. AWE is also suitable to process images that have been taken from both stable and nonstable platforms (such as towers and research vessels, respectively). Using techniques based on derivative analysis, AWE provides an objective method to determine an appropriate threshold for the identification of whitecaps in sea surface images without the need for a human analyst. The automated method allows large numbers of images to be analyzed in a relatively short amount of time. AWE can be used to analyze hundreds of images per individual W data point, which produces more convergent values of W.
Evaluation of in-vivo animal and in-vitro models for prediction of dermal absorption in man
Authors: Jakasa I , Kezic S 
Published: August 2008

Risk assessment of dermal exposure to chemicals requires percutaneous absorption data to link the external exposure to the systemic uptake. The most reliable data on percutaneous absorption are obtained from in-vivo human volunteer studies. In addition to ethical constrains, the conduct of these studies is not feasible for the large number of industrial chemicals in use today. Therefore, there is an increasing need for alternative methods to determine percutaneous absorption such as in-vitro assays and methods performed in vivo in experimental animals. In this article, recent comparative in-vitro and in-vivo studies on percutaneous absorption have been addressed with emphasis on the factors that may affect the predictive value of the in-vitro models. Furthermore, the use of animal models, in particular the rat skin, in prediction of percutaneous absorption in the human skin has been reviewed. In-vitro assays showed to be largely influenced by the experimental circumstances, such as type and thickness of the skin, receptor fluid, and the way in which percutaneous absorption is calculated. Rat skin showed consistently to be more permeable than human skin. However, the difference between human and rat skin does not show a consistent pattern between chemicals hampering prediction of human percutaneous absorption. To increase predictive value of in-vitro and animal models, the influence of experimental factors on the percutaneous absorption should be systematically investigated by comparison with human in-vivo data, resulting in more prescriptive guidelines.
Improving the applicability of (Q)SARs for percutaneous penetration in regulatory risk assessment
Authors: Bouwman T , Cronin MTD , Bessems JGM , van de Sandt JJM 
Published: August 2008

The new regulatory framework REACH (Registration, Evaluation, and Authorisation of Chemicals) foresees the use of non-testing approaches, such as read-across, chemical categories, structure–activity relationships (SARs) and quantitative structure–activity relationships (QSARs). Although information on skin absorption data are not a formal requirement under REACH, data on dermal absorption are an integral part of risk assessment of substances/products to which man is predominantly exposed via the dermal route. In this study, we assess the present applicability of publicly available QSARs on skin absorption for risk assessment purposes. We explicitly did not aim to give scientific judgments on individual QSARs. A total of 33 QSARs selected from the public domain were evaluated using the OECD (Organisation for Economic Co-operation and Development) Principles for the Validation of (Q)SAR Models. Additionally, several pragmatic criteria were formulated to select QSARs that are most suitable for their use in regulatory risk assessment. Based on these criteria, four QSARs were selected. The predictivity of these QSARs was evaluated by comparing their outcomes with experimentally derived skin absorption data (for 62 compounds). The predictivity was low for three of four QSARs, whereas one model gave reasonable predictions. Several suggestions are made to increase the applicability of QSARs for skin absorption for risk assessment purposes.
Pattern of ziprasidone exposures reported to Texas poison centers, 2001–2005
Authors: Forrester MB 
Published: August 2008

Information on potentially adverse exposures to the atypical antipsychotic drug ziprasidone is limited. This study described the pattern of exposures involving only ziprasidone (isolated exposures) reported to Texas poison control centers during 2001–2005. The mean dose was 666 mg. The patient age distribution was ≤5 years (11%), 6–19 years (30%), and ≥20 years (60%). The exposures were intentional in 53% of the cases. Seventy-five percent of the exposures were managed at health care facilities. The final medical outcome was classified as no effect for 39% of the cases and minor effects for 40% of the cases. Adverse clinical effects were listed for 53% of the patients; the most frequently reported being neurological (42%), cardiovascular (13%), and gastrointestinal (5%). The most frequently listed treatment was decontamination by charcoal (34%) or cathartic (28%). Potentially adverse ziprasidone exposures reported to poison control centers are likely to involve management at a health care facility and involve some sort of adverse clinical effect. With proper treatment, the outcomes of such exposures are generally favorable.