bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of Severe Acute Respiratory Syndrome Pathogenesis and Innate Immunomodulation
Authors: Frieman Matthew , Baric Ralph 
Published: December 2008

SUMMARY
The modulation of the immune response is a common practice of many highly pathogenic viruses. The emergence of the highly pathogenic coronavirus severe acute respiratory virus (SARS-CoV) serves as a robust model system to elucidate the virus-host interactions that mediate severe end-stage lung disease in humans and animals. Coronaviruses encode the largest positive-sense RNA genome of ∼30 kb, encode a variety of replicase and accessory open reading frames that are structurally unique, and encode novel enzymatic functions among RNA viruses. These viruses have broad or specific host ranges, suggesting the possibility of novel strategies for targeting and regulating host innate immune responses following virus infection. Using SARS-CoV as a model, we review the current literature on the ability of coronaviruses to interact with and modify the host intracellular environment during infection. These studies are revealing a rich set of novel viral proteins that engage, modify, and/or disrupt host cell signaling and nuclear import machinery for the benefit of virus replication.
CONSTRAINING THE SYMMETRY ENERGY: A JOURNEY IN THE ISOSPIN PHYSICS FROM COULOMB BARRIER TO DECONFINEMENT
Authors: DI TORO M. , COLONNA M. , GRECO V. , FERINI G. , RIZZO C. , RIZZO J. , BARAN V. , GAITANOS T. , PRASSA V. , WOLTER H. H. , ZIELINSKA-PFABE M. 
Published: December 2008

Heavy Ion Collisions (HIC) represent a unique tool to probe the in-medium nuclear interaction in regions away from saturation. In this work we present a selection of reaction observables in dissipative collisions particularly sensitive to the isovector part of the interaction, i.e.to the symmetry term of the nuclear Equation of State (EoS). At low energies the behavior of the symmetry energy around saturation influences dissipation and fragment production mechanisms. We will first discuss the recently observed Dynamical Dipole Radiation, due to a collective neutron-proton oscillation during the charge equilibration in fusion and deep-inelastic collisions. Important Iso - EOS are stressed. Reactions induced by unstable132Sn beams appear to be very promising tools to test the sub-saturation Isovector EoS. New Isospin sensitive observables are also presented for deep-inelastic, fragmentation collisions and Isospin equilibration measurements (Imbalance Ratios).The high density symmetry term can be derived from isospin effects on heavy ion reactions at relativistic energies (few AGeV range), that can even allow a "direct" study of the covariant structure of the isovector interaction in the hadron medium. Rather sensitive observables are proposed from collective flows and from pion/kaon production. The possibility of the transition to a mixed hadron-quark phase, at high baryon and isospin density, is finally suggested. Some signatures could come from an expected "neutron trapping" effect. The importance of studying violent collisions with radioactive beams from low to relativistic energies is finally stressed.
Real-time KD-tree construction on graphics hardware
Authors: Zhou Kun , Hou Qiming , Wang Rui , Guo Baining 
Published: December 2008

We present an algorithm for constructing kd-trees on GPUs. This algorithm achieves real-time performance by exploiting the GPU's streaming architecture at all stages of kd-tree construction. Unlike previous parallel kd-tree algorithms, our method builds tree nodes completely in BFS (breadth-first search) order. We also develop a special strategy for large nodes at upper tree levels so as to further exploit the fine-grained parallelism of GPUs. For these nodes, we parallelize the computation over all geometric primitives instead of nodes at each level. Finally, in order to maintain kd-tree quality, we introduce novel schemes for fast evaluation of node split costs.
As far as we know, ours is the first real-time kd-tree algorithm on the GPU. The kd-trees built by our algorithm are of comparable quality as those constructed by off-line CPU algorithms. In terms of speed, our algorithm is significantly faster than well-optimized single-core CPU algorithms and competitive with multi-core CPU algorithms. Our algorithm provides a general way for handling dynamic scenes on the GPU. We demonstrate the potential of our algorithm in applications involving dynamic scenes, including GPU ray tracing, interactive photon mapping, and point cloud modeling.
Estimation of certainty for responses to multiple-choice questionnaires using eye movements
Authors: Nakayama Minoru , Takahasi Yosiyuki 
Published: December 2008

To examine the feasibility of estimating the degree of strength of belief (SOB) of responses using eye movements, the scan paths of eye movements were analyzed while subjects reviewed their own responses to multiple choice tasks. All fixation points of eye movements were classified into visual areas, or cells, which corresponded with the positions of answers. Two estimation procedures are proposed using eye-movement data. The first one is identifying SOB using scan-path transitions. By comparing subject's reports of high and low SOB and eye-movement estimations, a significant correct rate of discrimination of SOB was observed. When the threshold of discrimination was controlled, a high rate of correct responses was obtained if it was set at a low level.
The second procedure is conducting SOB discrimination using support vector machines (SVM) trained with features of fixations. Subject's gazing features were analyzed while they reviewed their own responses. A discrimination model for SOB was trained with several combinations of features to see whether performance of a significant level could be obtained. As a result, a trained model with 3 features (which consist of interval time, vertical difference, and length between fixations) can provide significant discrimination performance for SOB.
These results provide evidence that strength of belief can be estimated using eye movements
Effect of Turbulence Models and Spatial Resolution on Resolved Velocity Structure and Momentum Fluxes in Large-Eddy Simulations of Neutral Boundary Layer Flow
Authors: Ludwig Francis L. , Chow Fotini Katopodes , Street Robert L. 
Published: December 2008

Abstract
This paper demonstrates the importance of high-quality subfilter-scale turbulence models in large-eddy simulations by evaluating the resolved-scale flow features that result from various closure models. The Advanced Regional Prediction System (ARPS) model was used to simulate neutral flow over a 1.2-km square, flat, rough surface with seven subfilter turbulence models [Smagorinsky, turbulent kinetic energy (TKE)-1.5, and five dynamic reconstruction combinations]. These turbulence models were previously compared with similarity theory. Here, the differences are evaluated using mean velocity statistics and the spatial structure of the flow field. Streamwise velocity averages generally differ among models by less than 0.5 m s−1, but those differences are often significant at a 95% confidence level. Flow features vary considerably among models. As measured by spatial correlation, resolved flow features grow larger and less elongated with height for a given model and resolution. The largest differences are between dynamic models that allow energy backscatter from small to large scales and the simple eddy-viscosity closures. At low altitudes, the linear extent of Smagorinsky and TKE-1.5 structures exceeds those of dynamic models, but the relationship reverses at higher altitudes. Ejection, sweep, and upward momentum flux features differ among models and from observed neutral atmospheric flows, especially for Smagorinsky and TKE-1.5 coarse-grid simulations. Near-surface isopleths separating upward fluxes from downward are shortest for the Smagorinsky and TKE-1.5 coarse-grid simulations, indicating less convoluted turbulent interfaces; at higher altitudes they are longest. Large-eddy simulation (LES) is a powerful simulation tool, but choices of grid resolution and subfilter model can affect results significantly. Physically realistic dynamic mixed models, such as those presented here, are essential when using LES to study atmospheric processes such as transport and dispersion—in particular at coarse resolutions.
Assessing the Relative Performance of Microwave-Based Satellite Rain-Rate Retrievals Using TRMM Ground Validation Data
Authors: Wolff David B. , Fisher Brad L. 
Published: December 2008

Abstract
Spaceborne microwave sensors provide critical rain information used in several global multisatellite rain products, which in turn are used for a variety of important studies, including landslide forecasting, flash flood warning, data assimilation, climate studies, and validation of model forecasts of precipitation. This study employs 4 yr (2003–06) of satellite data to assess the relative performance and skill of the Special Sensor Microwave Imager [SSM/I (F13, F14, and F15], Advanced Microwave Sounding Unit [AMSU-B (N15, N16, and N17)], Advanced Microwave Scanning Radiometer for Earth Observing System [AMSR-E (Aqua)], and the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) in estimating surface rainfall based on direct instantaneous comparisons with ground-based rain estimates from the TRMM Ground Validation (GV) sites at Kwajalein, Republic of the Marshall Islands (KWAJ), and Melbourne, Florida (MELB). The relative performance of each of these satellite estimates is examined via comparisons with space- and time-coincident GV radar-based rain-rate estimates. Because underlying surface terrain is known to affect the relative performance of the satellite algorithms, the data for MELB were further stratified into ocean, land, and coast categories using a 0.25° terrain mask. Of all the satellite estimates compared in this study, TMI and AMSR-E exhibited considerably higher correlations and skills in estimating–observing surface precipitation. While SSM/I and AMSU-B exhibited lower correlations and skills for each of the different terrain categories, the SSM/I absolute biases trended slightly lower than AMSR-E over ocean, where the observations from both emission and scattering channels were used in the retrievals. AMSU-B exhibited the least skill relative to GV in all of the relevant statistical categories, and an anomalous spike was observed in the probability distribution functions near 1.0 mm h−1. This statistical artifact appears to be related to attempts by algorithm developers to include some lighter rain rates, not easily detectable by its scatter-only frequencies. AMSU-B, however, agreed well with GV when the matching data were analyzed on monthly scales. These results signal to developers of global rainfall products, such as the TRMM Multisatellite Precipitation Analysis (TMPA) and the Climate Data Center’s Morphing (CMORPH) technique, that care must be taken when incorporating data from these input satellite estimates to provide the highest-quality estimates in their products.
Mechanisms for Quasi-Stationary Behavior in Simulated Heavy-Rain-Producing Convective Systems
Authors: Schumacher Russ S. 
Published: December 2008

Abstract
In this study, idealized numerical simulations are used to identify the processes responsible for initiating, organizing, and maintaining quasi-stationary convective systems that produce locally extreme rainfall amounts. Of particular interest are those convective systems that have been observed to occur near mesoscale convective vortices (MCVs) and other midlevel circulations. To simulate the lifting associated with such circulations, a low-level momentum forcing is applied to an initial state that is representative of observed extreme rain events. The initial vertical wind profile includes a sharp reversal of the vertical wind shear with height, indicative of observed low-level jets.
Deep moist convection initiates within the region of mesoscale lifting, and the resulting convective system replicates many of the features of observed systems. The low-level thermodynamic environment is nearly saturated, which is not conducive to the production of a strong surface cold pool; yet the convection quickly organizes into a back-building line. It is shown that a nearly stationary convectively generated low-level gravity wave is responsible for the linear organization, which continues for several hours. New convective cells repeatedly form on the southwest end of the line and move to the northeast, resulting in large local rainfall amounts. In the later stages of the simulated convective system, a cold pool does develop, but its interaction with the strong reverse shear at low levels is not optimized for the maintenance of deep convection along its edge. A series of sensitivity experiments shows some of the effects of hydrometeor evaporation and melting, planetary rotation, and the imposed mesoscale forcing.
Attribution of the Seasonality and Regionality in Climate Trends over the United States during 1950–2000
Authors: Wang Hailan , Schubert Siegfried , Suarez Max , Chen Junye , Hoerling Martin , Kumar Arun , Pegion Philip 
Published: December 2008

Abstract
The observed climate trends over the United States during 1950–2000 exhibit distinct seasonality and regionality. The surface air temperature exhibits a warming trend during winter, spring, and early summer and a modest countrywide cooling trend in late summer and fall, with the strongest warming occurring over the northern United States in spring. Precipitation trends are positive in all seasons, with the largest trend occurring over the central and southern United States in fall. This study investigates the causes of the seasonality and regionality of those trends, with a focus on the cooling and wetting trends in the central United States during late summer and fall. In particular, the authors examine the link between the seasonality and regionality of the climate trends over the United States and the leading patterns of sea surface temperature (SST) variability, including a global warming (GW) pattern and a Pacific decadal variability (PDV) pattern.
A series of idealized atmospheric general circulation model (AGCM) experiments were performed forced by SST trends associated with these leading SST patterns, as well as the residual trend pattern (obtained by removing the GW and PDV contributions). The results show that the observed seasonal and spatial variations of the climate trends over the United States are to a large extent explained by changes in SST. Among the leading patterns of SST variability, the PDV pattern plays a prominent role in producing both the seasonality and regionality of the climate trends over the United States. In particular, it is the main contributor to the apparent cooling and wetting trends over the central United States. The residual SST trend, a manifestation of phase changes of the Atlantic multidecadal SST variation during 1950–2000, also exerts influences that show strong seasonality with important contributions to the central U.S. temperature and precipitation during the summer and fall seasons. In contrast, the response over the United States to the GW SST pattern is an overall warming with little seasonality or regional variation. These results highlight the important contributions of decadal and multidecadal variability in the Pacific and Atlantic in explaining the observed seasonality and regionality of the climate trends over the United States during the period of 1950–2000.
Understanding Recent Stratospheric Climate Change
Authors: Thompson David W. J. , Solomon Susan 
Published: December 2008

Abstract
The long-term, global-mean cooling of the lower stratosphere stems from two downward steps in temperature, both of which are coincident with the cessation of transient warming after the volcanic eruptions of El Chichón and Mount Pinatubo. Previous attribution studies reveal that the long-term cooling is linked to ozone trends, and modeling studies driven by a range of known forcings suggest that the steps reflect the superposition of the long-term cooling with transient variability in upwelling longwave radiation from the troposphere. However, the long-term cooling of the lower stratosphere is evident at all latitudes despite the fact that chemical ozone losses are thought to be greatest at middle and polar latitudes. Further, the ozone concentrations used in such studies are based on either 1) smooth mathematical functions fit to sparsely sampled observations that are unavailable during postvolcanic periods or 2) calculations by a coupled chemistry–climate model.
Here the authors provide observational analyses that yield new insight into three key aspects of recent stratospheric climate change. First, evidence is provided that shows the unusual steplike behavior of global-mean stratospheric temperatures is dependent not only upon the trend but also on the temporal variability in global-mean ozone immediately following volcanic eruptions. Second, the authors argue that the warming/cooling pattern in global-mean temperatures following major volcanic eruptions is consistent with the competing radiative and chemical effects of volcanic eruptions on stratospheric temperature and ozone. Third, it is revealed that the contrasting latitudinal structures of recent stratospheric temperature and ozone trends are consistent with large-scale increases in the stratospheric overturning Brewer–Dobson circulation.
“Modes of Variability” and Climate Change
Authors: Branstator Grant , Selten Frank 
Published: December 2008

Abstract
A 62-member ensemble of coupled general circulation model (GCM) simulations of the years 1940–2080, including the effects of projected greenhouse gas increases, is examined. The focus is on the interplay between the trend in the Northern Hemisphere December–February (DJF) mean state and the intrinsic modes of variability of the model atmosphere as given by the upper-tropospheric meridional wind. The structure of the leading modes and the trend are similar. Two commonly proposed explanations for this similarity are considered.
Several results suggest that this similarity in most respects is consistent with an explanation involving patterns that result from the model dynamics being well approximated by a linear system. Specifically, the leading intrinsic modes are similar to the leading modes of a stochastic model linearized about the mean state of the GCM atmosphere, trends in GCM tropical precipitation appear to excite the leading linear pattern, and the probability density functions (PDFs) of prominent circulation patterns are quasi-Gaussian.
There are, on the other hand, some subtle indications that an explanation for the similarity involving preferred states (which necessarily result from nonlinear influences) has some relevance. For example, though unimodal, PDFs of prominent patterns have departures from Gaussianity that are suggestive of a mixture of two Gaussian components. And there is some evidence of a shift in probability between the two components as the climate changes. Interestingly, contrary to the most prominent theory of the influence of nonlinearly produced preferred states on climate change, the centroids of the components also change as the climate changes. This modification of the system’s preferred states corresponds to a change in the structure of its dominant patterns. The change in pattern structure is reproduced by the linear stochastic model when its basic state is modified to correspond to the trend in the general circulation model’s mean atmospheric state. Thus, there is a two-way interaction between the trend and the modes of variability.
Impact of Resolution on the Tropical Pacific Circulation in a Matrix of Coupled Models
Authors: Roberts Malcolm J. , Clayton A. , Demory M.-E. , Donners J. , Vidale P. L. , Norton W. , Shaffrey L. , Stevens D. P. , Stevens I. , Wood R. A. , Slingo J. 
Published: December 2008

Abstract
Results are presented from a matrix of coupled model integrations, using atmosphere resolutions of 135 and 90 km, and ocean resolutions of 1° and 1/3°, to study the impact of resolution on simulated climate. The mean state of the tropical Pacific is found to be improved in the models with a higher ocean resolution. Such an improved mean state arises from the development of tropical instability waves, which are poorly resolved at low resolution; these waves reduce the equatorial cold tongue bias. The improved ocean state also allows for a better simulation of the atmospheric Walker circulation.
Several sensitivity studies have been performed to further understand the processes involved in the different component models. Significantly decreasing the horizontal momentum dissipation in the coupled model with the lower-resolution ocean has benefits for the mean tropical Pacific climate, but decreases model stability. Increasing the momentum dissipation in the coupled model with the higher-resolution ocean degrades the simulation toward that of the lower-resolution ocean.
These results suggest that enhanced ocean model resolution can have important benefits for the climatology of both the atmosphere and ocean components of the coupled model, and that some of these benefits may be achievable at lower ocean resolution, if the model formulation allows.
Equilibrium Climate Sensitivity: Is It Accurate to Use a Slab Ocean Model?
Authors: Danabasoglu Gokhan , Gent Peter R. 
Published: December 2008

Abstract
The equilibrium climate sensitivity of a climate model is usually defined as the globally averaged equilibrium surface temperature response to a doubling of carbon dioxide. This is virtually always estimated in a version with a slab model for the upper ocean. The question is whether this estimate is accurate for the full climate model version, which includes a full-depth ocean component. This question has been answered for the low-resolution version of the Community Climate System Model, version 3 (CCSM3). The answer is that the equilibrium climate sensitivity using the full-depth ocean model is 0.14°C higher than that using the slab ocean model, which is a small increase. In addition, these sensitivity estimates have a standard deviation of nearly 0.1°C because of interannual variability. These results indicate that the standard practice of using a slab ocean model does give a good estimate of the equilibrium climate sensitivity of the full CCSM3. Another question addressed is whether the effective climate sensitivity is an accurate estimate of the equilibrium climate sensitivity. Again the answer is yes, provided that at least 150 yr of data from the doubled carbon dioxide run are used.