bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Surface Flux Formulations and Geostrophic Forcing on Large-Eddy Simulations of Diurnal Atmospheric Boundary Layer Flow
Authors: Kumar Vijayant , Svensson Gunilla , Holtslag A. A. M. , Meneveau Charles , Parlange Marc B. 
Published: January 2010

Abstract
The impact of surface flux boundary conditions and geostrophic forcing on multiday evolution of flow in the atmospheric boundary layer (ABL) was assessed using large-eddy simulations (LES). The LES investigations included several combinations of surface boundary conditions (temperature and heat flux) and geostrophic forcing (constant, time varying, time and height varying). The setup was based on ABL characteristics observed during a selected period of the Cooperative Atmosphere–Surface Exchange Study—1999 (CASES-99) campaign. The LES cases driven by a constant geostrophic wind achieved the best agreement with the CASES-99 observations specifically in terms of daytime surface fluxes and daytime and nighttime profiles. However, the nighttime fluxes were significantly overestimated. The LES cases with the surface temperature boundary condition and driven by a time- and height-varying geostrophic forcing showed improved agreement with the observed nighttime fluxes, but there was less agreement with other observations (e.g., daytime profiles). In terms of the surface boundary condition, the LES cases driven by either surface temperature or heat fluxes produced similar trends in terms of the daytime profiles and comparisons with data from soundings. However, in reproducing the fluxes and nighttime profiles, the agreement was better with imposed temperature because of its ability to interact dynamically with the air temperature field. Therefore, it is concluded that surface temperature boundary condition is better suited for simulations of temporally evolving ABL flow as in the diurnal evolution of the ABL.
Partially Coherent Backscatter in Radar Observations of Precipitation
Authors: Jameson A. R. , Kostinski A. B. 
Published: January 2010

Abstract
Classical radar theory only considers incoherent backscatter from precipitation. Can precipitation generate coherent scatter as well? Until now, the accepted answer has been no, because hydrometeors are distributed sparsely in space (relative to radar wavelength) so that the continuum assumption used to explain coherent scatter in clear air and clouds does not hold.
In this work, a theory for a different mechanism is presented. The apparent existence of the proposed mechanism is then illustrated in both rain and snow. A new power spectrum Z( f ), the Fourier transform of the time series of the radar backscattered reflectivities, reveals statistically significant frequencies f of periodic components that cannot be ascribed to incoherent scatter. It is shown that removing those significant fs from Z( f ) at lower frequencies greatly reduces the temporal coherency. These lower frequencies, then, are associated with the increased temporal coherency. It is also shown that these fs are also directly linked to the Doppler spectral peaks through integer multiples of one-half the radar wavelength, characteristic of Bragg scatter. Thus, the enhanced temporal coherency is directly related to the presence of coherent scatter in agreement with theory.
Moreover, the normalized backscattered power spectrum Z( f ) permits the estimation of the fractional coherent power contribution to the total power, even for an incoherent radar. Analyses of approximately 26 000 one-second Z( f ) in both rain and snow reveal that the coherent scatter is pervasive in these data. These findings present a challenge to the usual assumption that the scatter of radar waves from precipitation is always incoherent and to interpretations of backscattered power based on this assumption.
Using Different Formulations of the Transformed Eulerian Mean Equations and Eliassen–Palm Diagnostics in General Circulation Models
Authors: Hardiman Steven C. , Andrews David G. , White Andy A. , Butchart Neal , Edmond Ian 
Published: January 2010

Abstract
Transformed Eulerian mean (TEM) equations and Eliassen–Palm (EP) flux diagnostics are presented for the general nonhydrostatic, fully compressible, deep atmosphere formulation of the primitive equations in spherical geometric coordinates. The TEM equations are applied to a general circulation model (GCM) based on these general primitive equations. It is demonstrated that a naive application in this model of the widely used approximations to the EP diagnostics, valid for the hydrostatic primitive equations using log-pressure as a vertical coordinate and presented, for example, by Andrews et al. in 1987 can lead to misleading features in these diagnostics. These features can be of the same order of magnitude as the diagnostics themselves throughout the winter stratosphere. Similar conclusions are found to hold for “downward control” calculations. The reasons are traced to the change of vertical coordinate from geometric height to log-pressure. Implications for the modeling community, including comparison of model output with that from reanalysis products available only on pressure surfaces, are discussed.
Modal and Nonmodal Growths of Symmetric Perturbations in Unbounded Domain
Authors: Xu Qin 
Published: January 2010

Abstract
Modal and nonmodal growths of nonhydrostatic symmetric perturbations in an unbounded domain are examined in comparison with their hydrostatic counterparts. It is shown that the modal growth rate is a function of a single internal parameter s, the slope of the cross-band wave pattern. The maximum nonmodal growth of total perturbation energy norm is produced, also as a function of s, by an optimal combination of one geostrophic neutral mode and two paired nongeostrophic growing and decaying (or propagating) modes in the unstable (or stable) region. The hydrostatic approximation inflates the maximum modal growth rate significantly (or boundlessly) as the basic-state Richardson number Ri is small (or → 0) and inflates the maximum nonmodal growth rate significantly (or boundlessly) as |s| is large (or → ∞).
Inside the unstable region, the maximum nonmodal growth scaled by the modal growth is a bounded increasing function of growth time τ but reduces to 1 at (Ri, s) = (¼, −2) where the three modes become orthogonal to each other. Outside the unstable region, the maximum nonmodal growth is a periodic function of τ and the maximum growth time τm is bounded between ¼ and ½ of the period of the paired propagating modes. The scaled maximum nonmodal growth reaches the global maximum at s = −Ri−1 ± Ri−1(1 − Ri)1/2 (the marginal-stability boundary) for any τ if Ri ≤ 1, or at s = −1 ± (1 − Ri−1)1/2 for τ = τm if Ri &gt; 1. When the neutral mode is filtered, the nonmodal growth becomes nongeostrophic and smaller than its counterpart growth constructed by the three modes but still significantly larger than the modal growth in general. The scaled maximum nongeostrophic nonmodal growth reaches the global maximum at s = −Ri−1 ± Ri−1(1 − Ri)1/2 for any τ if Ri ≤ 1, or at s = −Ri−1/2 for τ = τm if Ri &gt; 1. Normalized inner products between the modes are introduced to measure their nonorthogonality and interpret their constructed nonmodal growths physically.
The Surface Expression of Semidiurnal Internal Tides near a Strong Source at Hawaii. Part I: Observations and Numerical Predictions*
Authors: Chavanne C. , Flament P. , Carter G. , Merrifield M. , Luther D. , Zaron E. , Gurgel K-W. 
Published: January 2010

Abstract
Observations of semidiurnal currents from high-frequency radio Doppler current meters and moored acoustic Doppler current profilers (ADCPs) in the Kauai Channel, Hawaii, are described and compared with two primitive equation numerical models of the tides. The Kauai Channel, separating the islands of Oahu and Kauai, is a site of strong internal tide generation by the barotropic tides flowing over Kaena Ridge, the subsurface extension of Oahu. The nature and impacts of internal tide generation in the Kauai Channel were intensively studied during the 2002–03 near-field component of the Hawaii Ocean Mixing Experiment.
Comparisons of observed coherent (i.e., phase locked to the astronomical forcing) M2 and S2 surface currents with model predictions show good agreement for the phases, indicating propagation of internal tides away from the ridge. Although the predicted M2 and S2 surface currents are similar (except for their magnitudes), as expected for internal waves at periods closer to each other (12.4 and 12 h, respectively) than to the inertial period (33 h), the observed M2 and S2 surface currents differ significantly. The S2 kinetic energy pattern resembles the predicted pattern. In contrast, the observed structure and magnitude of the more important M2 kinetic energy pattern differs significantly from the model predictions. The models predict a band of enhanced M2 surface kinetic energy 30–40 km from the ridge axis, corresponding to the first surface reflection of internal tide beams generated on the ridge flanks. The beams are clearly observed by the moored ADCPs, albeit with weaker amplitudes than predicted. Observations at the surface show an area of enhanced kinetic energy that is 10–20 km farther away from the ridge than predicted, with weaker magnitude. Observed M2 surface currents also exhibit apparent seasonal variability, with magnitudes weaker in spring 2003 than in fall 2002.
Complex-demodulated semidiurnal currents exhibit significant temporal variability in amplitude and phase, not only because of the interference between semidiurnal constituents (e.g., the spring–neap cycle) but also on shorter and irregular time scales. The result is that ∼20% of semidiurnal energy is incoherent with astronomical forcing. Furthermore, the temporal variability is not spatially coherent; the spatial patterns of semidiurnal kinetic energy resemble those predicted by the numerical models during the strongest spring tides but differ from them at other times. As a result, M2 and S2 kinetic energy patterns phase locked to the astronomical forcing differ from each other. Some features of the observed spatial pattern and amplitude modulations can be qualitatively reproduced by a simple analytical model of the effects of homogeneous barotropic background currents on internal tide beams.
Modeling Wind-Driven Circulation and Landfast Ice-Edge Processes during Polynya Events in Northern Baffin Bay
Authors: Dumont Dany , Gratton Yves , Arbetter Todd E. 
Published: January 2010

AbstractA high-resolution sea ice–ocean numerical model of the North Water polynya has been developed to study the wind-driven circulation during polynya events. An idealized three-layer stratified ocean is used to initialize the model to characterize the baroclinic response to realistic wind and ice conditions. The model general circulation pattern is mainly forced by an along-channel sea level gradient between the Arctic Ocean and Baffin Bay, which determines the magnitude of the southward Baffin Current, and by an across-channel sea level gradient in Baffin Bay, which drives the northward West Greenland Current (WGC). These two currents are found to be anticorrelated to each other in the Smith Sound area. During strong northerly wind events, occurring quite frequently in the winter–spring period in the polynya, nutrient-rich Baffin Bay waters transported by the WGC are forced toward the Greenland shelf, coinciding with upwelling events along the Greenland coast. Whenever an ice bridge is present (i.e., the polynya exists and is substantially open), upwelling also occurs at the landfast ice edge. In such cases, the total upwelling area is increased by an amount that depends on the form of the ice bridge but could easily double during certain years. The baroclinic circulation associated with the upwelling response includes the formation of a cyclonic eddy attached to the ice edge that is generated during strong northerly wind events. Primary production estimations reveal that upwelling during polynya events plays a significant role in the early spring phytoplankton bloom, suggesting that the disappearance of the polynya as a result of climate change may have profound implications for the entire ecosystem.
Two-Layer Tidal Circulation in a Frictional, Rotating Basin
Authors: Winant Clinton D. 
Published: January 2010

Abstract
The three-dimensional tidal circulation in an elongated basin of arbitrary depth is described with a coupled barotropic and baroclinic two-layer model on the f plane. As long as friction is not dominant, near-standing waves are present on the interface as well as on the surface. The surface pattern is principally determined by the product of the tidal barotropic wavenumber by the basin length. The interface deformation is determined by a baroclinic equivalent, usually a much larger number. As a result, the shape of the interface is characterized by horizontally smaller features than the surface. If the product of the tidal baroclinic wavenumber by the basin width is greater than one, both lateral and axial modes can be excited at the interface. If these modes are near resonant, large internal tides can be forced directly by the co-oscillating surface tide at the basin entrance. The amplitude and phase of the baroclinic component are sensitive functions of the density anomaly and the interface depth. As a result, the phase and amplitude of the interface vary by large amounts with comparatively small changes in those parameters. The model behavior is qualitatively consistent with observations in fjords and straits.
An Examination of the Pressure–Wind Relationship for Intense Tropical Cyclones
Authors: Kieu Chanh Q. , Chen Hua , Zhang Da-Lin 
Published: January 2010

Abstract
In this study, the dynamical constraints underlining the pressure–wind relationship (PWR) for intense tropical cyclones (TCs) are examined with the particular focus on the physical connections between the maximum surface wind (VMAX) and the minimum sea level pressure (PMIN). Use of the Rankine vortex demonstrates that the frictional forcing in the planetary boundary layer (PBL) could explain a sizeable portion of the linear contributions of VMAX to pressure drops. This contribution becomes increasingly important for intense TCs with small eye sizes, in which the radial inflows in the PBL could no longer be neglected. Furthermore, the inclusion of the tangential wind tendency can make an additional contribution to the pressure drops when coupled with the surface friction.
An examination of the double-eyewall configuration reveals that the formation of an outer eyewall or well-organized spiral rainbands complicates the PWR. An analysis of a cloud-resolving simulation of Hurricane Wilma (2005) shows that the outer eyewall could result in the continuous deepening of PMIN even with a constant VMAX. The results presented here suggest that (i) the TC size should be coupled with VMAX rather than being treated as an independent predictor as in the current PWRs, (ii) the TC intensity change should be at least coupled linearly with the radius of VMAX, and (iii) the radial wind in the PBL is of equal importance to the linear contribution of VMAX and its impact should be included in the PWR.
Environment Associated with Deep Moist Convection under SALLJ Conditions: A Case Study
Authors: Borque Paloma , Salio Paola , Nicolini Matilde , García Skabar Yanina 
Published: January 2010

Abstract
The present work focuses on the study of the environmental conditions preceding the development of a group of subtropical mesoscale convective systems over central and northern Argentina on 6–7 February 2003 during the South American Low Level Jet Experiment. This period was characterized by an extreme northerly low-level flow along the eastern Andes foothills [South American low-level jet (SALLJ)]. The entire studied episode was dominated by the presence of a very unstable air mass over northern Argentina and a frontal zone near 40°S. The SALLJ generated an important destabilization of the atmosphere due to the strong humidity and differential temperature advection. Orography provided an extra lifting motion to the configuration of the regional wind field, which was efficient in forcing the initiation of convection. Once convection developed, it moved and regenerated in regions where the convective instability was horizontally homogeneous and stronger.
Mast cells enhance proliferation of B lymphocytes and drive their differentiation toward IgA-secreting plasma cells
Authors: Merluzzi Sonia , Frossi Barbara , Gri Giorgia , Parusso Serena , Tripodo Claudio , Pucillo Carlo 
Published: January 2010

AbstractThe evidence of a tight spatial interaction between mast cells (MCs) and B lymphocytes in secondary lymphoid organs, along with the data regarding the abundance of MCs in several B-cell lymphoproliferative disorders prompted us to investigate whether MCs could affect the proliferation and differentiation of B cells. To this aim, we performed coculture assays using mouse splenic B cells and bone marrow–derived MCs. Both nonsensitized and activated MCs proved able to induce a significant inhibition of cell death and an increase in proliferation of naive B cells. Such proliferation was further enhanced in activated B cells. This effect relied on cell-cell contact and MC-derived interleukin-6 (IL-6). Activated MCs could regulate CD40 surface expression on unstimulated B cells and the interaction between CD40 with CD40 ligand (CD40L) on MCs, together with MC-derived cytokines, was involved in the differentiation of B cells into CD138+ plasma cells and in selective immunoglobulin A (IgA) secretion. These data were corroborated by in vivo evidence of infiltrating MCs in close contact with IgA-expressing plasma cells within inflamed tissues. In conclusion, we reported here a novel role for MCs in sustaining B-cell expansion and driving the development of IgA-oriented humoral immune responses.
Power and sample size estimation in microarray studies
Authors: Lin Wei-Jiun , Hsueh Huey-Miin , Chen James J 
Published: January 2010

AbstractBackgroundBefore conducting a microarray experiment, one important issue that needs to be determined is the number of arrays required in order to have adequate power to identify differentially expressed genes. This paper discusses some crucial issues in the problem formulation, parameter specifications, and approaches that are commonly proposed for sample size estimation in microarray experiments. Common methods for sample size estimation are formulated as the minimum sample size necessary to achieve a specified sensitivity (proportion of detected truly differentially expressed genes)on averageat a specified false discovery rate (FDR) level and specified expected proportion (π1) of the true differentially expression genes in the array. Unfortunately, the probability of detecting the specified sensitivity in such a formulation can be low. We formulate the sample size problem as the number of arrays needed to achieve a specified sensitivity with95% probabilityat the specified significance level. A permutation method using a small pilot dataset to estimate sample size is proposed. This method accounts for correlation and effect size heterogeneity among genes.ResultsA sample size estimate based on the common formulation, to achieve the desired sensitivity on average, can be calculated using a univariate method without taking the correlation among genes into consideration. This formulation of sample size problem is inadequate because the probability of detecting the specified sensitivity can be lower than 50%. On the other hand, the needed sample size calculated by the proposed permutation method will ensure detecting at least the desired sensitivity with 95% probability. The method is shown to perform well for a real example dataset using a small pilot dataset with 4-6 samples per group.ConclusionsWe recommend that the sample size problem should be formulated to detect a specified proportion of differentially expressed genes with 95% probability. This formulation ensures finding the desired proportion of true positives with high probability. The proposed permutation method takes the correlation structure and effect size heterogeneity into consideration and works well using only a small pilot dataset.
FiGS: a filter-based gene selection workbench for microarray data
Authors: Hwang Taeho , Sun Choong-Hyun , Yun Taegyun , Yi Gwan-Su 
Published: January 2010

Abstract

Background
The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset.

Results
FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs.

Conclusion
FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
Authors: Krzeminski Mickaël , Loth Karine , Boelens Rolf , Bonvin Alexandre MJJ 
Published: January 2010

Abstract

Background
The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.

Results
We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.

Conclusions
The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces. The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.