bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic characterisation of pancreatic islet β-cells stimulated with pancreatic carcinoma cell conditioned medium
Authors: Song G , Cui Y , Zhong N , Han J 
Published: April 2009

Aim:To characterise the protein expression profiles of pancreatic islet β-cells affected by cancer cells, and to identify the potential islet molecules related to pancreatic cancer-associated diabetes.Methods:The cellular proteins of islet β-cell line INS-1 in response to conditioned medium (CM) prepared from pancreatic cancer cells were analysed using fluorescence-labelled 2D gel-based proteomics (2D-DIGE).Results:10 proteins were over-expressed and five were under-expressed in cancer CM-stimulated β-cells. Five differently expressed proteins were selected for further validation by Western blot analysis. HSP60 and peripherin, which have previously been reported to be associated with type 1 diabetes, and Prp19, a DNA repair protein, were up-regulated in INS-1 cells after cancer cell CM stimulation; HMOX1 and GRP78 were down-regulated. The islets adjacent to human pancreatic carcinomas showed increased peripherin expression than normal pancreatic islets.Conclusion:These results provide new information regarding the regulation of protein expression in pancreatic cancer-associated diabetes.
Under what conditions do patients want to be informed about their risk of a complication? A vignette study
Authors: Janssen N B A T , Oort F J , Fockens P , Willems D L , de Haes H C J M , Smets E M A 
Published: April 2009

Background:Discussing treatment risks has become increasingly important in medical communication. Still, despite regulations, physicians must decide how much and what kind of information to present.Objective:To investigate patients’ preference for information about a small risk of a complication of colonoscopy, and whether medical and personal factors contribute to such preference. To propose a disclosure policy related to our results.Design:Vignettes study.Setting:Department of Gastroenterology, Academic Medical Centre, the Netherlands.Patients:810 consecutive colonoscopy patients.Intervention:A home-sent questionnaire containing three vignettes. Vignettes varied in the indication for colonoscopy, complication severity and level of risk. Patients were invited to indicate their wish to be informed and the importance of such information. In addition, sociodemograhic, illness-related and psychological characteristics were assessed.Main outcome measurements:Wish to be informed and importance of information.Results:Of 810 questionnaires, 68% were returned. Patients generally wished to be informed about low-risk complications, regardless of the indication for colonoscopy or the severity of the complication. The level of risk did matter, though (OR = 2.48, SE = 0.28, p = 0.001). The information was considered less important if done for population screening purposes or diagnosis of colon cancer, if the complication was less severe (bleeding) and if the risk was smaller (0.01% and 0.1%). Patients’ information preference was also related to age, mood and coping style.Limitations:Difficulty of vignettes.Conclusions:Patients generally wish to be informed about all possible risks. However, this might become uninformative. A stepwise approach is suggested.
Runoff and inorganic nitrogen export from Boreal Plain watersheds six years after wildfire and one year after harvest
Authors: Pelster David E. , Burke Janice M. , Prepas Ellie E. 
Published: April 2009

This investigation in the Swan Hills, Alberta, located on the Canadian Boreal Plain, examined May through October runoff before, during and six years after wildfire in a 4th order watershed, compared to a 3rd order reference watershed. It also examined runoff and inorganic nitrogen flow-weighted mean concentration and areal export for 1 year after winter harvest in four 1st order watersheds compared to five reference 1st and 2nd order watersheds. Runoff and areal exports were normalized to precipitation at each site. Runoff impact ratios (year 1 post-disturbance value divided by the pre-disturbance value) for burned and harvested watersheds were 60 and 70% higher, respectively, than reference watersheds (P = 0.06). Runoff from the burned watershed remained elevated 6 years after fire. A trend for higher nitrate and ammonium concentrations, combined with higher runoff yielded impact ratios for areal ammonium and nitrate exports that were 130 and 170% higher, respectively, in harvested than reference watersheds (P = 0.08 for both). The proportion of the watershed harvested was positively related to runoff (r2 = 0.94, P = 0.03) and ammonium impact ratios (r2 = 0.96, P = 0.02), but not nitrate impact ratios (P = 0.30). Areal nitrate export in snowmelt was low in harvested watersheds compared to their pre-harvest condition and to reference watersheds.
Effect of watershed subdivision on water-phase phosphorus modelling: An artificial neural network modelling application
Authors: Nour Mohamed H. , Smith Daniel W. , El-Din Mohamed Gamal , Prepas Ellie E. 
Published: April 2009

This study is an effort to incorporate low-cost time-variant remote sensing (RS) information in watershed-scale total phosphorus (TP) modelling. Four watershed subdivisions were delineated to assess the impact of watershed subdivision on the prediction accuracy of TP concentration in stream water. Four TP artificial neural network (ANN) models were designed to incorporate RS data into a semi-distributed approach. The remotely derived enhanced vegetation index and the normalized difference water index were successful in representing vegetation dynamics in the devised models. The models were applied to a 15.6 km2 watershed in the Canadian Boreal Plain. Eight measures of goodness-of-fit statistics were used for model evaluation. Although statistical model evaluation did favour the finest resolution in this case study, the differences in performance indicators among the four models were insignificant for any practical application. The encouraging results from this exercise demonstrate the applicability of the ANN semi-distributed modelling approach and the usefulness of RS data in simulating TP dynamics. Such models can potentially serve as valuable tools for watershed-scale forest management.
Towards a generic neural network model for the prediction of daily streamflow in ungauged boreal plain watersheds
Authors: Nour Mohamed H. , Smith Daniel W. , Gamal El-Din Mohamed , Prepas Ellie E. 
Published: April 2009

Most of the currently available streamflow neural network models are either recurrent neural networks or feed-forward multi-layer perceptron (FF-MLP) requiring past flow values for lead time prediction. These models cannot be used for modelling ungauged watersheds because past flow values are not available in such cases. This study proposes a FF-MLP algorithm that relies only on low-cost, readily available meteorological data and careful time series manipulation prior to model building, and thus, is suitable for modelling streamflow in ungauged watersheds. The proposed approach was tested on four watersheds (5 to 130 km2) in the Canadian Boreal forest and was found to provide an efficient modelling alternative for daily streamflow predictions. To assess the possibility of successful model transferability from a gauged watershed to a hydrologically similar ungauged watershed, a new remotely sensed hydrologic similarity measure — SWMIR_SI — was proposed and was found to provide a successful indicator of basin similarity. The square of Pearson’s correlation coefficient, r2, was evaluated to exceed 0.71 when SWMIR_SI was regressed to models’ “goodness-of-fit” statistics reflecting the usefulness of the approach.
Modification of SWAT for modelling streamflow from forested watersheds on the Canadian Boreal Plain
Authors: Watson Brett M. , McKeown Ruth A. , Putz Gordon , MacDonald J. Douglas 
Published: April 2009

Several modifications were made to the Soil and Water Assessment Tool (SWAT) to better represent processes occurring within forested watersheds on the Boreal Plain in Canada. The modified model, called SWATBF, was applied to the Willow Creek watershed (15.1 km2) in north central Alberta. The performance of the model for the calibration period (2001–2003) was good with coefficients of efficiency of 0.89 and 0.81 being achieved for the prediction of monthly and daily runoff, respectively. However, it was found that SWATBF did not perform as well for the validation period (2004–2006) with the monthly and daily coefficients of efficiency being 0.44 and 0.27, respectively. Potential sources of error to explain the decline in model performance for the validation period are discussed. SWATBF has the potential to be used as a tool by forest managers for predicting the effects of land use change on the Boreal Plain provided that it can be satisfactorily validated.
A GPU-BASED ALGORITHM FOR APPROXIMATELY FINDING THE LARGEST COMMON POINT SET IN THE PLANE UNDER SIMILARITY TRANSFORMATION
Authors: AIGER DROR , KEDEM KLARA 
Published: April 2009

We consider the following geometric pattern matching problem: Given two sets of points in the plane, P and Q, and some (arbitrary) δ > 0, find the largest subset B ⊂ P and a similarity transformation T (translation, rotation and scale) such that h(T(B),Q) < δ, where h(.,.) is the directional Hausdorff distance. This problem stems from real world applications, where δ is determined by the practical uncertainty in the position of the points (pixels). We reduce the problem to finding the depth (maximally covered point) of an arrangement of polytopes in transformation space. The depth is the cardinality of B, and the polytopes that cover the deepest point correspond to the points in B. We present an algorithm that approximates the maximum depth with high probability, thus getting a large enough common point set in P and Q. The algorithm is implemented in the GPU framework, thus it is very fast in practice. We present experimental results and compare their runtime with those of an algorithm running on the CPU.
E2F1 Expression Is Deregulated and Plays an Oncogenic Role in Sporadic Burkitt's Lymphoma
Authors: Molina-Privado Irene , Rodríguez-Martínez María , Rebollo Patricia , Martín-Pérez Daniel , Artiga María-Jesús , Menárguez Javier , Flemington Erik K. , Piris Miguel A. , Campanero Miguel R. 
Published: April 2009

Abstract
Current treatments of sporadic Burkitt's lymphoma (sBL) are associated with severe toxicities. A better understanding of sBL formation would facilitate development of less toxic therapies. The etiology of sBL remains, however, largely unknown, C-MYC up-regulation being the only lesion known to occur in all sBL cases. Several studies examining the role of C-MYC in the pathogenesis of BL have concluded that C-MYC translocation is not the only critical event and that additional unidentified factors are expected to be involved in the formation of this tumor. We herein report that a gene distinct from C-MYC, E2F1, is involved in the formation of all or most sBL tumors. We found that E2F1 is highly expressed in Burkitt's lymphoma cell lines and sBL lymphoma specimens. Our data indicate that its elevated expression is not merely the consequence of the presence of more cycling cells in this tumor relative to other cell lines or to other neoplasias. In fact, we show that reduction of its expression in sBL cells inhibits tumor formation and decreases their proliferation rate. We also provide data suggesting that E2F1 collaborates with C-MYC in sBL formation. E2F1 expression down-regulation did not affect, however, the proliferation of human primary diploid fibroblasts. Because E2F1 is not needed for cell proliferation of normal cells, our results reveal E2F1 as a promising therapeutic target for sBL. [Cancer Res 2009;69(9):4052–8]
Effects of potential predator and competitor cues and sibship on wood frog (Rana sylvatica) embryos
Authors: Dibble Christopher , Kauffman Jamie , Zuzik Evan , Smith Geoffrey , Rettig Jessica 
Published: May 2009

Abstract
Chemical cues emitted from predators or competitors are often important for
animals living in aquatic ecosystems as they allow potential prey to assess
predation risk and make appropriate risk-sensitive responses. In our
experiment, we examined if wood frog (Rana sylvatica) embryos exposed to
potential predator and competitor cues would alter their time to hatching,
size at hatching, or survivorship. Eggs from four different sibships were
subjected to a variety of cues including dragonfly larvae (potential tadpole
predator), mosquitofish (Gambusia affinis; a non-native potential egg and
tadpole predator), and overwintered tadpoles of Rana sp. (potential
competitors). We found no significant effects of any of the cues. However,
we did find significant variation in mean time to hatching and mean
hatchling size among sibships. Our results suggest that wood frog embryos
may have limited ability to respond to some cues at the embryonic stage, at
least for the concentrations and conditions used in this experiment. Our
results do indicate genetic or parental effects can affect embryonic wood
frog development rate and hatchling size.
Annular Variability and Eddy–Zonal Flow Interactions in a Simplified Atmospheric GCM. Part I: Characterization of High- and Low-Frequency Behavior
Authors: Sparrow Sarah , Blackburn Michael , Haigh Joanna D. 
Published: April 2009

Abstract
Experiments have been performed using a simplified, Newtonian forced, global circulation model to investigate how variability of the tropospheric jet can be characterized by examining the combined fluctuations of the two leading modes of annular variability. Eddy forcing of this variability is analyzed in the phase space of the leading modes using the vertically integrated momentum budget. The nature of the annular variability and eddy forcing depends on the time scale. At low frequencies the zonal flow and baroclinic eddies are in quasi equilibrium and anomalies propagate poleward. The eddies are shown primarily to reinforce the anomalous state and are closely balanced by the linear damping, leaving slow evolution as a residual. At high frequencies the flow is strongly evolving and anomalies are initiated on the poleward side of the tropospheric jet and propagate equatorward. The eddies are shown to drive this evolution strongly: eddy location and amplitude reflect the past baroclinicity, while eddy feedback on the zonal flow may be interpreted in terms of wave breaking associated with baroclinic life cycles in lateral shear.
Causes of Reduced North Atlantic Storm Activity in a CAM3 Simulation of the Last Glacial Maximum
Authors: Donohoe Aaron , Battisti David S. 
Published: April 2009

Abstract
The aim of this paper is to determine how an atmosphere with enhanced mean-state baroclinity can support weaker baroclinic wave activity than an atmosphere with weak mean-state baroclinity. As a case study, a Last Glacial Maximum (LGM) model simulation previously documented to have reduced baroclinic storm activity, relative to the modern-day climate (simulated by the same model), despite having an enhanced midlatitude temperature gradient, is considered. Several candidate mechanisms are evaluated to explain this apparent paradox.
A linear stability analysis is first performed on the jet in the modern-day and the LGM simulation; the latter has relatively strong barotropic velocity shear. It was found that the LGM mean state is more unstable to baroclinic disturbances than the modern-day mean state, although the three-dimensional jet structure does stabilize the LGM jet relative to the Eady growth rate. Next, feature tracking was used to assess the storm track seeding and temporal growth of disturbances. It was found that the reduction in LGM eddy activity, relative to the modern-day eddy activity, is due to the smaller magnitude of the upper-level storms entering the North Atlantic domain in the LGM. Although the LGM storms do grow more rapidly in the North Atlantic than their modern-day counterparts, the storminess in the LGM is reduced because storms seeding the region of enhanced baroclinity are weaker.
Rossby Waves and the Interannual and Interdecadal Variability of Temperature and Salinity off California
Authors: Dottori Marcelo , Clarke Allan J. 
Published: April 2009

Abstract
Previous work has shown that large-scale interannual Rossby waves, largely remotely generated by equatorial winds, propagate westward from the coast off southern California. These waves have a large-scale anomalous alongshore velocity field that is proportional to the time derivative of the interannual sea level anomaly. Using these results, a theory is developed for interannual perturbations to a mean density field that varies both vertically and alongshore, like that for the California Current region off southern California. Because both the anomalous vertical and alongshore currents are proportional to the time derivative of the interannual sea level, the theory suggests that the anomalous currents associated with the Rossby waves, acting on the mean temperature field, should induce temperature fluctuations proportional to the anomalous dynamic height. The alongshore and vertical advections contribute to the temperature fluctuations in the same sense, a higher-than-normal sea level, for example, resulting in downward and poleward displacement of warmer water and a local higher-than-normal temperature. Near the surface, alongshore advection dominates vertical advection but both contribute comparably near the thermocline and below. The correlation of observed temperature and dynamic height anomalies from the California Cooperative Oceanic Fisheries Investigation (CalCOFI) data is positive, which is consistent with the theory. The correlation is highest (r ≈ 0.8) near 100-m depth in the thermocline. Although the correlation falls toward the surface, it is still between 0.5 and 0.6, suggesting that the advection mechanism is a major contributor to the temperature anomalies there.
The anomalous Rossby wave currents, acting on the mean background salinity gradient, also induce salinity anomalies. At halocline depths of 100–200 m, consistent with the theory, the correlation of observed CalCOFI salinity and dynamic height anomalies is negative and large in magnitude (r ≈ −0.8). However, the surface salinity anomaly is not due to Rossby wave dynamics; instead, much of it is driven by the alongshore wind stress, which it lags by 4 months.
Marginal Instability?
Authors: Thorpe S. A. , Liu Zhiyu 
Published: April 2009

Abstract
Some naturally occurring, continually forced, turbulent, stably stratified, mean shear flows are in a state close to that in which their stability changes, usually from being dynamically unstable to being stable: the time-averaged flows that are observed are in a state of marginal instability. By “marginal instability” the authors mean that a small fractional increase in the gradient Richardson number Ri of the mean flow produced by reducing the velocity and, hence, shear is sufficient to stabilize the flow: the increase makes Rimin, the minimum Ri in the flow, equal to Ric, the critical value of this minimum Richardson number. The value of Ric is determined by solving the Taylor–Goldstein equation using the observed buoyancy frequency and the modified velocity. Stability is quantified in terms of a factor, Φ, such that multiplying the flow speed by (1 + Φ) is just sufficient to stabilize it, or that Ric = Rimin/(1 + Φ)2.
The hypothesis that stably stratified boundary layer flows are in a marginal state with Φ &lt; 0 and with |Φ| small compared to unity is examined. Some dense water cascades are marginally unstable with small and negative Φ and with Ric substantially less than ¼. The mean flow in a mixed layer driven by wind stress on the water surface is, however, found to be relatively unstable, providing a counterexample that refutes the hypothesis. In several naturally occurring flows, the time for exponential growth of disturbances (the inverse of the maximum growth rate) is approximately equal to the average buoyancy period observed in the turbulent region.
Measuring Storm Surge with an Airborne Wide-Swath Radar Altimeter
Authors: Wright C. W. , Walsh E. J. , Krabill W. B. , Shaffer W. A. , Baig S. R. , Peng M. , Pietrafesa L. J. , Garcia A. W. , Marks F. D. , Black P. G. , Sonntag J. , Beckley B. D. 
Published: April 2009

Abstract
Over the years, hurricane track forecasts and storm surge models, as well the digital terrain and bathymetry data they depend on, have improved significantly. Strides have also been made in the knowledge of the detailed variation of the surface wind field driving the surge. The area of least improvement has been in obtaining data on the temporal/spatial evolution of the mound of water that the hurricane wind and waves push against the shore to evaluate the performance of the numerical models. Tide gauges in the vicinity of the landfall are frequently destroyed by the surge. Survey crews dispatched after the event provide no temporal information and only indirect indications of the maximum water level over land. The landfall of Hurricane Bonnie on 26 August 1998, with a surge less than 2 m, provided an excellent opportunity to demonstrate the potential benefits of direct airborne measurement of the temporal/spatial evolution of the water level over a large area. Despite a 160-m variation in aircraft altitude, an 11.5-m variation in the elevation of the mean sea surface relative to the ellipsoid over the flight track, and the tidal variation over the 5-h data acquisition interval, a survey-quality global positioning system (GPS) aircraft trajectory allowed the NASA scanning radar altimeter carried by a NOAA hurricane research aircraft to demonstrate that an airborne wide-swath radar altimeter could produce targeted measurements of storm surge that would provide an absolute standard for assessing the accuracy of numerical storm surge models.
Initial Condition Sensitivity of Western Pacific Extratropical Transitions Determined Using Ensemble-Based Sensitivity Analysis
Authors: Torn Ryan D. , Hakim Gregory J. 
Published: April 2009

Abstract
An ensemble Kalman filter based on the Weather Research and Forecasting (WRF) model is used to generate ensemble analyses and forecasts for the extratropical transition (ET) events associated with Typhoons Tokage (2004) and Nabi (2005). Ensemble sensitivity analysis is then used to evaluate the relationship between forecast errors and initial condition errors at the onset of transition, and to objectively determine the observations having the largest impact on forecasts of these storms. Observations from rawinsondes, surface stations, aircraft, cloud winds, and cyclone best-track position are assimilated every 6 h for a period before, during, and after transition. Ensemble forecasts initialized at the onset of transition exhibit skill similar to the operational Global Forecast System (GFS) forecast and to a WRF forecast initialized from the GFS analysis. WRF ensemble forecasts of Tokage (Nabi) are characterized by relatively large (small) ensemble variance and greater (smaller) sensitivity to the initial conditions. In both cases, the 48-h forecast of cyclone minimum SLP and the RMS forecast error in SLP are most sensitive to the tropical cyclone position and to midlatitude troughs that interact with the tropical cyclone during ET. Diagnostic perturbations added to the initial conditions based on ensemble sensitivity reduce the error in the storm minimum SLP forecast by 50%. Observation impact calculations indicate that assimilating approximately 40 observations in regions of greatest initial condition sensitivity produces a large, statistically significant impact on the 48-h cyclone minimum SLP forecast. For the Tokage forecast, assimilating the single highest impact observation, an upper-tropospheric zonal wind observation from a Mongolian rawinsonde, yields 48-h forecast perturbations in excess of 10 hPa and 60 m in SLP and 500-hPa height, respectively.