bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Amino Acid Residues in BK Virus VP1 That Are Critical for Viability and Growth
Authors: Dugan Aisling S. , Gasparovic Megan L. , Tsomaia Natia , Mierke Dale F. , O'Hara Bethany A. , Manley Kate , Atwood Walter J. 
Published: August 2007

ABSTRACT
BK virus (BKV) is a ubiquitous pathogen that establishes a persistent infection in the urinary tract of 80% of the human population. Like other polyomaviruses, the major capsid protein of BKV, virion protein 1 (VP1), is critical for host cell receptor recognition and for proper virion assembly. BKV uses a carbohydrate complex containing α(2,3)-linked sialic acid attached to glycoprotein and glycolipid motifs as a cellular receptor. To determine the amino acids important for BKV binding to the sialic acid portion of the complex, we generated a series of 17 point mutations in VP1 and scored them for viral growth. The first set of mutants behaved identically to wild-type virus, suggesting that these amino acids were not critical for virus propagation. Another group of VP1 mutants rendered the virus nonviable. These mutations failed to protect viral DNA from DNase I digestion, indicating a role for these domains in capsid assembly and/or packaging of DNA. A third group of VP1 mutations packaged DNA similarly to the wild type but failed to propagate. The initial burst size of these mutations was similar to that of the wild type, indicating that there is no defect in the lytic release of the mutated virions. Binding experiments revealed that a subset of the BKV mutants were unable to attach to their host cells. These motifs are likely important for sialic acid recognition. We next mapped these mutations onto a model of BKV VP1 to provide atomic insight into the role of these sites in the binding of sialic acid to VP1.
Novel Adeno-Associated Virus Serotypes Efficiently Transduce Murine Photoreceptors
Authors: Allocca Mariacarmela , Mussolino Claudio , Garcia-Hoyos Maria , Sanges Daniela , Iodice Carolina , Petrillo Marco , Vandenberghe Luk H. , Wilson James M. , Marigo Valeria , Surace Enrico M. , Auricchio Alberto 
Published: August 2007

ABSTRACT
Severe inherited retinal diseases, such as retinitis pigmentosa and Leber congenital amaurosis, are caused by mutations in genes preferentially expressed in photoreceptors. While adeno-associated virus (AAV)-mediated gene transfer can correct retinal pigment epithelium (RPE) defects in animal models, approaches for the correction of photoreceptor-specific diseases are less efficient. We evaluated the ability of novel AAV serotypes (AAV2/7, AAV2/8, AAV2/9, AAV2rh.43, AAV2rh.64R1, and AAV2hu.29R) in combination with constitutive or photoreceptor-specific promoters to improve photoreceptor transduction, a limiting step in photoreceptor rescue. Based on a qualitative analysis, all AAV serotypes tested efficiently transduce the RPE as well as rod and cone photoreceptors after subretinal administration in mice. Interestingly, AAV2/9 efficiently transduces Müller cells. To compare photoreceptor transduction from different AAVs and promoters in both a qualitative and quantitative manner, we designed a strategy based on the use of a bicistronic construct expressing both enhanced green fluorescent protein and luciferase. We found that AAV2/8 and AAV2/7 mediate six- to eightfold higher levels of in vivo photoreceptor transduction than AAV2/5, considered so far the most efficient AAV serotype for photoreceptor targeting. In addition, following subretinal administration of AAV, the rhodopsin promoter allows significantly higher levels of photoreceptor expression than the other ubiquitous or photoreceptor-specific promoters tested. Finally, we show that AAV2/7, AAV2/8, and AAV2/9 outperform AAV2/5 following ex vivo transduction of retinal progenitor cells differentiated into photoreceptors. We conclude that AAV2/7 or AAV2/8 and the rhodopsin promoter provide the highest levels of photoreceptor transduction both in and ex vivo and that this may overcome the limitation to therapeutic success observed so far in models of inherited severe photoreceptor diseases.
Inhalable β(1→3)glucans as a non-allergenic exposure factor in Dutch bakeries
Authors: Stuurman B , Meijster T , Heederik D , Doekes G 
Published: August 2007

Objectives:To obtain an overview of inhalable β(1→3)glucans levels in Dutch industrial bakeries and explore possible associations with reported respiratory health effects in bakery workers.Methods:β(1→3)glucan levels were analysed in 186 personal inhalable dust measurements obtained from a random population of bakery workers. Association between respiratory health effects and exposure to β(1→3)glucan was explored in a population of industrial bakery workers participating in a Health Surveillance System for flour processing sectors. Based on their job, bakery workers were assigned to low or high exposure categories given the average job exposure estimates obtained from the measurement study.Results:Bread bakers and dough makers had the highest exposures to β(1→3)glucans (GM 1.48 μg/m3 and 1.37 μg/m3 respectively). Strong correlations were found between airborne levels of inhalable dust and β(1→3)glucans, and between β(1→3)glucans and wheat allergens (Pearson correlation coefficients were 0.74 and 0.68 respectively). No significant associations could be identified between β(1→3)glucan exposure and work-related respiratory symptoms.Conclusion:This study has shown that bakery workers are exposed to inhalable β(1→3)glucan levels comparable with exposure levels found in other occupational settings. More refined exposure assessment is necessary to fully understand the role of β(1→3)glucan exposure on respiratory health in bakery workers.
What Controls the Strength of Snow-Albedo Feedback?
Authors: Qu Xin , Hall Alex 
Published: August 2007

Abstract
The strength of snow-albedo feedback (SAF) in transient climate change simulations of the Fourth Assessment of the Intergovernmental Panel on Climate Change is generally determined by the surface-albedo decrease associated with a loss of snow cover rather than the reduction in snow albedo due to snow metamorphosis in a warming climate. The large intermodel spread in SAF strength is likewise attributable mostly to the snow cover component. The spread in the strength of this component is in turn mostly attributable to a correspondingly large spread in mean effective snow albedo. Models with large effective snow albedos have a large surface-albedo contrast between snow-covered and snow-free regions and exhibit a correspondingly large surface-albedo decrease when snow cover decreases. Models without explicit treatment of the vegetation canopy in their surface-albedo calculations typically have high effective snow albedos and strong SAF, often stronger than observed. In models with explicit canopy treatment, completely snow-covered surfaces typically have lower albedos and the simulations have weaker SAF, generally weaker than observed. The authors speculate that in these models either snow albedos or canopy albedos when snow is present are too low, or vegetation shields snow-covered surfaces excessively. Detailed observations of surface albedo in a representative sampling of snow-covered surfaces would therefore be extremely useful in constraining these parameterizations and reducing SAF spread in the next generation of models.
Simulation of the Stable Water Isotopes in Precipitation over South America: Comparing Regional to Global Circulation Models
Authors: Sturm Christophe , Hoffmann Georg , Langmann Bärbel 
Published: August 2007

Abstract
A simulation of the stable water isotope cycle over South America by the regional circulation model REMOiso is discussed. The performance of the regional model, with a resolution of 0.5° (∼55 km), is compared to simulations by the global circulation model ECHAMiso at two coarser resolutions and evaluated against observations of precipitation and δ18O.
Here REMOiso is demonstrated to reproduce reasonably well climatic and isotopic features across South America. This paper explores further insights of δ18O as a climate proxy, based on REMOiso’s improvements as compared to ECHAMiso. In particular, the authors focus on the seasonal variation of the amount effect (δ18O decrease with precipitation amounts) and the anomalous δ18O continental gradient across the Amazon basin, as inferred from the REMOiso, ECHAMiso, and GNIP datasets. The finer resolution of topography in REMOiso enables a detailed analysis of the altitude effect: not only the first, but also the second derivative of δ18O with altitude is considered. It appears that high-altitude grid cells show an isotopic signature similar to Rayleigh distillation, in accordance with experimental studies. Finally, a Lagrangian reference frame is adopted to describe the evolution of δ18O in precipitation along its trajectory, in order to relate the simulation analysis to the fractionation mechanisms. This confirms that the amount effect, via Rayleigh distillation processes, is dominant during the wet season. During the dry season, the δ18O in precipitation is controlled by isotopic reequilibration of rain droplets with surrounding vapor, reflecting the impact of nonfractionating transpiration by the vegetation.
Comparison of Spectrally Resolved Outgoing Longwave Radiation over the Tropical Pacific between 1970 and 2003 Using IRIS, IMG, and AIRS
Authors: Griggs J. A. , Harries J. E. 
Published: August 2007

AbstractThe observation of changes in the earth’s spectrally resolved outgoing longwave radiation (OLR) provides a direct method of determining changes in the radiative forcing of the climate system. An earlier study showed that satellite-observed changes in the clear-sky outgoing longwave spectrum between 1997 and 1970 from the Infrared Interferometer Spectrometer (IRIS) and Interferometic Monitor of Greenhouse Gases (IMG) instruments could be related to changes in greenhouse gas composition. The authors present a new study that extends this to 2003, through the first use of a new, independent source of global atmospheric infrared spectra, from the Atmospheric Infrared Sounder (AIRS) experiment. AIRS is a dispersion grating spectrometer, while the other two were Fourier transform spectrometers, and this is taken into account in the analysis. The observed difference spectrum between the years 2003 and 1970 generally shows the signatures of greenhouse gas forcing, and also shows the sensitivity of the signatures to interannual variations in temperature. The new 2003 data support the conclusions found in the earlier work, though, interestingly, the methane (CH4) Q branch centered at 1304 cm−1 exhibits more complex behavior, showing a decrease in intensity in the difference spectrum between 1997 and 2003. Sensitivity analysis indicates that this is due to changes in temperature structure, superposed on an underlying increase in CH4. Radiative transfer calculations based on reanalysis data are used to simulate the changes in the OLR spectrum; limitations in such data and possible variations that could account for several observed effects are discussed.
Variability of Tibetan Spring Snow and Its Associations with the Hemispheric Extratropical Circulation and East Asian Summer Monsoon Rainfall: An Observational Investigation
Authors: Zhao Ping , Zhou Zijiang , Liu Jiping 
Published: August 2007

Abstract
Using station observations of the number of days covered by snow (SCD) and snowfall over the Tibetan Plateau (TP), the National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP–NCAR) reanalysis, and precipitation from rain gauge stations in China for the period of 1973–2001, temporal/spatial variations of SCD over the TP and its associations with the hemispheric extratropical atmospheric circulation and East Asian summer monsoon rainfall are investigated.
An increase of spring (April–May) SCD over the TP is associated with decreases of local tropospheric temperature and geopotential height in the spring and early summer (June). The anomalies in the tropospheric temperature and geopotential height show a westward propagation from the TP to western Asia as a result of the westward propagation of the anomalous wave energy. These tropospheric anomalies over the TP are connected with changes in the hemispheric extratropical atmospheric circulation along the westerly jet stream that acts as a waveguide.
The increase of the spring SCD is also associated with the variation of the East Asian summer monsoon rainfall. Soil moisture in May–June might act as a bridge linking the spring snow anomaly and the subsequent summer monsoon. Corresponding to the increase of SCD, there is a significant decrease of the June 500-mb geopotential height from the TP to the western North Pacific. Meanwhile, the anomalous northeasterlies extend from Japan, through the east coast of China, to central-eastern China, which weaken the East Asian summer monsoon, leading to a decrease of surface air temperature and rainfall in the Yangtze and Hwai Rivers and an increase of rainfall in southeastern China.
Additionally, the spring SCD anomaly is likely due to a variation of local synchronous snowfall, rather than previous winter SCD conditions. The spring SCD is not related to previous winter El Niño/La Niña events, but is associated with the equatorial central and eastern Pacific sea surface temperature from the subsequent summer through winter. The climatic implications for this relationship are not clear.
Investigation of the Summer Climate of the Contiguous United States and Mexico Using the Regional Atmospheric Modeling System (RAMS). Part I: Model Climatology (1950–2002)
Authors: Castro Christopher L. , Pielke Roger A. , Adegoke Jimmy O. 
Published: August 2007

Abstract
Fifty-three years of the NCEP–NCAR Reanalysis I are dynamically downscaled using the Regional Atmospheric Modeling System (RAMS) to generate a regional climate model (RCM) climatology of the contiguous United States and Mexico. Data from the RAMS simulations are compared to the recently released North American Regional Reanalysis (NARR), as well as observed precipitation and temperature data. The RAMS simulations show the value added by using a RCM in a process study framework to represent North American summer climate beyond the driving global atmospheric reanalysis. Because of its enhanced representation of the land surface topography, the diurnal cycle of convective rainfall is present. This diurnal cycle largely governs the transitions associated with the evolution of the North American monsoon with regards to rainfall, the surface energy budget, and surface temperature. The lower frequency modes of convective rainfall, though weaker, account for rainfall variability at a remote distance from elevated terrain. As in previous studies with other RCMs, RAMS precipitation is overestimated compared to observations. The Great Plains low-level jet (LLJ) is also well represented in both RAMS and NARR, but the Baja LLJ and associated gulf surges are not.
A Bayesian Regression Approach for Predicting Seasonal Tropical Cyclone Activity over the Central North Pacific
Authors: Chu Pao-Shin , Zhao Xin 
Published: August 2007

Abstract
In this study, a Poisson generalized linear regression model cast in the Bayesian framework is applied to forecast the tropical cyclone (TC) activity in the central North Pacific (CNP) in the peak hurricane season (July–September) using large-scale environmental variables available up to the antecedent May and June. Specifically, five predictor variables are considered: sea surface temperatures, sea level pressures, vertical wind shear, relative vorticity, and precipitable water. The Pearson correlation between the seasonal TC frequency and each of the five potential predictors over the eastern and central North Pacific is computed. The critical region for which the local correlation is statistically significant at the 99% confidence level is determined. To keep the predictor selection process robust, a simple average of the predictor variable over the critical region is then computed. With a noninformative prior assumption for the model parameters, a Bayesian inference for this model is derived in detail. A Gibbs sampler based on the Markov chain Monte Carlo (MCMC) method is designed to integrate the desired posterior predictive distribution. The proposed hierarchical model is physically based and yields a probabilistic prediction for seasonal TC frequency, which would better facilitate decision making. A cross-validation procedure was applied to predict the seasonal TC counts within the period of 1966–2003 and satisfactory results were obtained.
A New Methodology for Estimating the Unpredictable Component of Seasonal Atmospheric Variability
Authors: Kumar Arun , Jha Bhaskar , Zhang Qin , Bounoua Lahouari 
Published: August 2007

Abstract
Predictability limits for seasonal atmospheric climate variability depend on the fraction of variability that is due to factors external to the atmosphere (e.g., boundary conditions) and the fraction that is internal. From the analysis of observed data alone, however, separation of the total seasonal atmospheric variance into its external and internal components remains a difficult and controversial issue. In this paper a simple procedure for estimating atmospheric internal variability is outlined. This procedure is based on the expected value of the mean square error between the observed and the general circulation model simulated (or predicted) seasonal mean anomaly. The end result is a spatial map for the estimate of the observed seasonal atmospheric internal (or unpredictable) variability. As improved general circulation models become available, mean square error estimated from the new generation of general circulation models can be easily included in the procedure proposed herein, bringing the estimate for the internal variability closer to its true estimate.
Characterization of the Diurnal Cycle of the West African Monsoon around the Monsoon Onset
Authors: Sultan Benjamin , Janicot Serge , Drobinski Philippe 
Published: August 2007

Abstract
This study investigates the diurnal cycle of the West African monsoon and its seasonal modulation with particular focus on the monsoon onset period. A composite analysis around the monsoon onset date is applied to the 1979–2000 NCEP–DOE reanalysis and 40-yr ECMWF Re-Analysis (ERA-40) at 0000, 0600, 1200, and 1800 UTC. This study points out two independent modes describing the space–time variability of the diurnal cycle of low-level wind and temperature. While the first mode appears to belong to a gradual and seasonal pattern linked with the northward migration of the whole monsoon system, the second mode is characterized by more rapid time variations with a peak of both temperature and wind anomalies around the monsoon onset date. This latter mode is connected with the time pattern of a nocturnal jet reaching its highest values around the onset date.
The diurnal cycle of dry and deep convection is also investigated through the same method. A distinct diurnal cycle of deep convection in the ITCZ is evidenced with a peak at 1200 UTC before the monsoon onset, and at 1800 UTC after the monsoon onset. Strong ascending motions associated with deep convection may generate a gravity wave that propagates northward and reaches the Saharan heat low region 12 h later. The diurnal cycle of the dry convection in the Saharan heat low is similar during the preonset and the postonset periods with a peak at night (0000 UTC) consistent with the nocturnal jet intensification. This convection is localized at 15° and 20°N before and after the monsoon onset, respectively. Both during the first rainy season in spring and the monsoon season in summer, the nocturnal jet brings moisture in the boundary layer north of the ITCZ favoring humidification and initiation of new convective cells, helping the northward progression of the ITCZ. At the end of the summer the southward return of the ITCZ is associated with the disappearance of the core of the monsoon jet.
Despite a lot of similarities between the results obtained using NCEP–DOE and ERA-40 reanalyses, giving confidence in the significance of these results, some differences are identified, especially in the diurnal cycle of deep convection, which limit the interpretation of some of these results and highlight discrepancies in the reanalyses.
Intraseasonal Teleconnection between the Summer Eurasian Wave Train and the Indian Monsoon*
Authors: Ding Qinghua , Wang Bin 
Published: August 2007

AbstractThis study investigated the most recurrent coupled pattern of intraseasonal variability between midlatitude circulation and the Indian summer monsoon (ISM). The leading singular vector decomposition (SVD) pattern reveals a significant, coupled intraseasonal variation between a Rossby wave train across the Eurasian continent and the summer monsoon convection in northwestern India and Pakistan (hereafter referred to as NISM). The wave train associated with an active phase of NISM rainfall displays two high pressure anomalies, one located over central Asia and the other over northeastern Asia. They are accompanied by increased rainfall over the western Siberia plain and northern China and decreased rainfall over the eastern Mediterranean Sea and southern Japan. The circulation of the wave train shows a barotropic structure everywhere except the anomalous central Asian high, located to the northwest of India, where a heat-induced baroclinic circulation structure dominates. The time-lagged SVD analysis shows that the midlatitude wave train originates from the northeastern Atlantic and traverses Europe to central Asia. The wave train enhances the upper-level high pressure and reinforces the convection over the NISM region; meanwhile, it propagates farther toward East Asia along the waveguide provided by the westerly jet. After an outbreak of NISM convection, the anomalous central Asian high retreats westward. Composite analysis suggests a coupling between the central Asian high and the convective fluctuation in the NISM. The significance of the midlatitude–ISM interaction is also revealed by the close resemblance between the individual empirical orthogonal functions and the coupled (SVD) modes of the midlatitude circulation and the ISM.It is hypothesized that the eastward and southward propagation of the wave train originating from the northeastern Atlantic contributes to the intraseasonal variability in the NISM by changing the intensity of the monsoonal easterly vertical shear and its associated moist dynamic instability. On the other hand, the rainfall variations over the NISM reinforce the variations of the central Asian high through the “monsoon–desert” mechanism, thus reenergizing the downstream propagation of the wave train. The coupling between the Eurasian wave train and NISM may be instrumental for understanding their interaction and can provide a way to predict the intraseasonal variations of the Indian summer monsoon and East Asian summer monsoon.