bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gap-Leaping Western Boundary Current in a Circular Tank Model
Authors: Sheremet Vitalii A. , Kuehl Joseph 
Published: June 2007

Abstract
An oceanographically generic problem of the interaction of a boundary current with bathymetric features such as a gap in the ridge or a strait between two islands is considered. Multiple flow patterns (penetrating or leaping the gap) and hysteresis (dependence on prior evolution) may exist in such systems. Examples include the Gulf Stream leaping from the Yucatan to Florida and the Kuroshio leaping from Luzon to Taiwan. Using numerical analysis, Sheremet earlier found that multiple steady states can be explained by variation in the balance between the inertia (which promotes leaping state) and the β effect (which promotes penetrating state). In the present work a verification of the multiple states and hysteresis in a laboratory model are offered. To set up a gap-leaping current, a circular tank with a sloping bottom (simulating the β effect) is used, and the flow is driven using a new method of pumping fluid through sponges (thus generating a Sverdrup flow in the interior). A semicircular ridge with a gap is inserted into the western part of the tank. Using a dye release flow visualization method, the existence of multiple flow patterns over varying boundary current transport values differing by a factor of more than 2 are dramatically shown. An associated numerical model in bipolar curvilinear coordinates, which allows for the matching of all the boundaries, reproduces the laboratory results very well. This idealized problem offers a very useful geophysical test case for numerical models involving flow separation and reattachment.
The Importance of Tidal and Lateral Asymmetries in Stratification to Residual Circulation in Partially Mixed Estuaries*
Authors: Scully Malcolm E. , Friedrichs Carl T. 
Published: June 2007

Abstract
Measurements collected in the York River estuary, Virginia, demonstrate the important impact that tidal and lateral asymmetries in turbulent mixing have on the tidally averaged residual circulation. A reduction in turbulent mixing during the ebb phase of the tide caused by tidal straining of the axial density gradient results in increased vertical velocity shear throughout the water column during the ebb tide. In the absence of significant lateral differences in turbulent mixing, the enhanced ebb-directed transport caused by tidal straining is balanced by a reduction in the net seaward-directed barotropic pressure gradient, resulting in laterally uniform two-layer residual flow. However, the channel–shoal morphology of many drowned river valley estuaries often leads to lateral gradients in turbulent mixing. Tidal straining may then lead to tidal asymmetries in turbulent mixing near the deeper channel while the neighboring shoals remain relatively well mixed. As a result, the largest lateral asymmetries in turbulent mixing occur at the end of the ebb tide when the channel is significantly more stratified than the shoals. The reduced friction at the end of ebb delays the onset of the flood tide, increasing the duration of ebb in the channel. Conversely, over the shoal regions where stratification is more inhibited by tidal mixing, there is greater friction and the transition from ebb to flood occurs more rapidly. The resulting residual circulation is seaward over the channel and landward over the shoal. The shoal–channel segregation of this barotropically induced estuarine residual flow is opposite to that typically associated with baroclinic estuarine circulation over channel–shoal bathymetry.
Internal Tides in the Southwestern Atlantic off Brazil: Observations and Numerical Modeling
Authors: Pereira Adriene F. , Castro Belmiro M. 
Published: June 2007

Abstract
Data collected from moored instruments, deployed over the southeastern Brazilian continental shelf during the summer and winter months of 2001, show internal tide activity near the shelf break. To help to elucidate the observations, a fully three-dimensional nonlinear primitive equation model is applied to simulate the regional barotropic and baroclinic tides. Two semidiurnal (M2 and S2) and two diurnal (K1 and O1) tidal frequencies are considered. Tidal surface elevations are relatively small over the whole modeled area, reaching maximum values of about 0.40 m for M2 and 0.11 m for O1. Comparison between observed and computed tide elevation and Greenwich phase shows reasonable agreement. When the baroclinic response of the model is investigated, stratification is prescribed using summer and winter climatology data of potential density. In this case, the model response to summer and winter stratifications is very similar and internal tides are generated over the shelf break and slope, with vertical displacements up to 25 m, and seaward propagation. Modeled semidiurnal tidal ellipses agree well with winter and summer observations. Observed diurnal tidal ellipses in the middle of the continental shelf and close to the shelf break during summer show an intensification through the water column that could not be represented by the model. Estimates of the total baroclinic M2 offshore energy flux are about 3.5 and 0.5 MW considering winter and summer stratifications, respectively. Although these quantities are three orders of magnitude less than that estimated for regions known for intense internal tides, they refer to offshore fluxes computed for a very small section of the southeastern Brazilian shelf. This is the first published investigation into internal tides in the southwestern Atlantic Ocean off Brazil.
Distribution of Energy Spectra, Reynolds Stresses, Turbulence Production, and Dissipation in a Tidally Driven Bottom Boundary Layer
Authors: Luznik L. , Zhu W. , Gurka R. , Katz J. , Nimmo Smith W. A. M. , Osborn T. R. 
Published: June 2007

AbstractSeven sets of 2D particle image velocimetry data obtained in the bottom boundary layer of the coastal ocean along the South Carolina and Georgia coast [at the South Atlantic Bight Synoptic Offshore Observational Network (SABSOON) site] are examined, covering the accelerating and decelerating phases of a single tidal cycle at several heights above the seabed. Additional datasets from a previous deployment are also included in the analysis. The mean velocity profiles are logarithmic, and the vertical distribution of Reynolds stresses normalized by the square of the free stream velocity collapse well for data obtained at the same elevation but at different phases of the tidal cycle. The magnitudes of 〈u′u′〉, 〈w′w′〉, and −〈u′w′〉 decrease with height above bottom in the 25–160-cm elevation range and are consistent with the magnitudes and trends observed in laboratory turbulent boundary layers. If a constant stress layer exists, it is located below 25-cm elevation. Two methods for estimating dissipation rate are compared. The first, a direct estimate, is based on the measured in-plane instantaneous velocity gradients. The second method is based on fitting the resolved part of the dissipation spectrum to the universal dissipation spectrum available in Gargett et al. Being undervalued, the direct estimates are a factor of 2–2.5 smaller than the spectrum-based estimates. Taylor microscale Reynolds numbers for the present analysis range from 24 to 665. Anisotropy is present at all resolved scales. At the transition between inertial and dissipation range the longitudinal spectra exhibit a flatter than −5/3 slope and form spectral bumps. Second-order statistics of the velocity gradients show a tendency toward isotropy with increasing Reynolds number. Dissipation exceeds production at all measurement heights, but the difference varies with elevation. Close to the bottom, the production is 40%–70% of the dissipation, but it decreases to 10%–30% for elevations greater than 80 cm.
Vortex Dipole Formation by Baroclinic Instability of Boundary Currents
Authors: Chérubin L. , Carton X. , Dritschel D. G. 
Published: June 2007

Abstract
In situ data of the Mediterranean Water undercurrents and eddies south of Portugal indicate that the undercurrents have a tubelike structure in potential vorticity and that dipole formation can occur when the lower undercurrent extends seaward below an offshore upper countercurrent. A two-layer quasigeostrophic model is used to determine the dynamical conditions under which dipole formation is possible. With piecewise-constant potential vorticity, the flow exhibits two linear modes of instability comparable to those found in the Phillips model with topography. Weakly nonlinear analysis and fully nonlinear simulations of the flow evolution agree on the regimes of either finite-amplitude perturbation saturation, corresponding to filamentation, or amplification, corresponding to vortex or dipole formation. This latter regime is more specifically studied: vortex dipole formation and ejection from the coast is obtained for long waves, with opposite-signed but similar amplitude layer potential vorticities. A simple point vortex model reproduces this phenomenon under the same conditions. It is then shown that dipole formation occurs for minimal wave dispersion, and hence for weak horizontal velocity shears. As observed at sea, dipoles are formed when the lower potential vorticity core extends seaward below a countercurrent.
Dynamical Tropical Cyclone 96- and 120-h Track Forecast Errors in the Western North Pacific
Authors: Kehoe Ryan M. , Boothe Mark A. , Elsberry Russell L. 
Published: June 2007

Abstract
The Joint Typhoon Warning Center has been issuing 96- and 120-h track forecasts since May 2003. It uses four dynamical models that provide guidance at these forecast intervals and relies heavily on a consensus of these four models in producing the official forecast. Whereas each of the models has skill, each occasionally has large errors. The objective of this study is to provide a characterization of these errors in the western North Pacific during 2004 for two of the four models: the Navy Operational Global Atmospheric Prediction System (NOGAPS) and the U.S. Navy’s version of the Geophysical Fluid Dynamics Laboratory model (GFDN). All 96- and 120-h track errors greater than 400 and 500 n mi, respectively, are examined following the approach developed recently by Carr and Elsberry. All of these large-error cases can be attributed to the models not properly representing the physical processes known to control tropical cyclone motion, which were classified in a series of conceptual models by Carr and Elsberry for either tropical-related or midlatitude-related mechanisms. For those large-error cases where an error mechanism could be established, midlatitude influences caused 83% (85%) of the NOGAPS (GFDN) errors. The most common tropical influence is an excessive direct cyclone interaction in which the tropical cyclone track is erroneously affected by an adjacent cyclone. The most common midlatitude-related errors in the NOGAPS tracks arise from an erroneous prediction of the environmental flow dominated by a ridge in the midlatitudes. Errors in the GFDN tracks are caused by both ridge-dominated and trough-dominated environmental flows in the midlatitudes. Case studies illustrating the key error mechanisms are provided. An ability to confidently identify these error mechanisms and thereby eliminate likely erroneous tracks from the consensus would improve the accuracy of 96- and 120-h track forecasts.
The New French Operational Radar Rainfall Product. Part II: Validation
Authors: Tabary P. , Desplats J. , Do Khac K. , Eideliman F. , Gueguen C. , Heinrich J-C. 
Published: June 2007

Abstract
A new operational radar-based rainfall product has been developed at Météo-France and is currently being deployed within the French operational network. The new quantitative precipitation estimation (QPE) product is based entirely on radar data and includes a series of modules aimed at correcting for ground clutter, partial beam blocking, and vertical profile of reflectivity (VPR) effects, as well as the nonsimultaneity of radar measurements. The surface rainfall estimation is computed as a weighted mean of the corrected tilts. In addition to the final QPE, a map of quality indexes is systematically generated. This paper is devoted to the validation of the new radar QPE. The VPR identification module has been specifically validated by analyzing 489 precipitation events observed over 1 yr by a representative eight-radar subset of the network. The conceptual model of VPR used in the QPE processing chain is shown to be relevant. A climatology of the three shape parameters of the conceptual VPR (brightband peak, brightband thickness, and upper-level decreasing rate) is established and the radar-derived freezing-level heights are shown to be in good agreement with radiosonde data. A total of 27 precipitation events observed by three S-band radars of the network during the winter of 2005 and the autumns of 2002 and 2003 are used to compare the new radar QPE to the old one. Results are stratified according to the distance to the radar and according to the height of the freezing level. The Nash criterion is increased from 0.23 to 0.62 at close range (below 50 km) and from 0.35 to 0.42 at long range (between 100 and 150 km). The relevance of the proposed quality indexes is assessed by examining their statistical relationship with long-term radar–rain gauge statistics. Mosaics of QPE and quality indexes are also illustrated.
Forecasting the Maintenance of Quasi-Linear Mesoscale Convective Systems
Authors: Coniglio Michael C. , Brooks Harold E. , Weiss Steven J. , Corfidi Stephen F. 
Published: June 2007

Abstract
The problem of forecasting the maintenance of mesoscale convective systems (MCSs) is investigated through an examination of observed proximity soundings. Furthermore, environmental variables that are statistically different between mature and weakening MCSs are input into a logistic regression procedure to develop probabilistic guidance on MCS maintenance, focusing on warm-season quasi-linear systems that persist for several hours. Between the mature and weakening MCSs, shear vector magnitudes over very deep layers are the best discriminators among hundreds of kinematic and thermodynamic variables. An analysis of the shear profiles reveals that the shear component perpendicular to MCS motion (usually parallel to the leading line) accounts for much of this difference in low levels and the shear component parallel to MCS motion accounts for much of this difference in mid- to upper levels. The lapse rates over a significant portion of the convective cloud layer, the convective available potential energy, and the deep-layer mean wind speed are also very good discriminators and collectively provide a high level of discrimination between the mature and dissipation soundings as revealed by linear discriminant analysis. Probabilistic equations developed from these variables used with short-term numerical model output show utility in forecasting the transition of an MCS with a solid line of 50+ dBZ echoes to a more disorganized system with unsteady changes in structure and propagation. This study shows that empirical forecast tools based on environmental relationships still have the potential to provide forecasters with improved information on the qualitative characteristics of MCS structure and longevity. This is especially important since the current and near-term value added by explicit numerical forecasts of convection is still uncertain.
The Use of a Vortex Insertion Technique to Simulate the Extratropical Transition of Hurricane Michael (2000)
Authors: Fogarty Christopher T. , Greatbatch Richard J. , Ritchie Harold 
Published: June 2007

Abstract
On 19 October 2000, Hurricane Michael merged with an approaching baroclinic trough over the western North Atlantic Ocean south of Nova Scotia. As the hurricane moved over cooler sea surface temperatures (SSTs; less than 25°C), it intensified to category-2 intensity on the Saffir–Simpson hurricane scale [maximum sustained wind speeds of 44 m s−1 (85 kt)] while tapping energy from the baroclinic environment. The large “hybrid” storm made landfall on the south coast of Newfoundland with maximum sustained winds of 39 m s−1 (75 kt) causing moderate damage to coastal communities east of landfall. Hurricane Michael presented significant challenges to weather forecasters. The fundamental issue was determining which of two cyclones (a newly formed baroclinic low south of Nova Scotia or the hurricane) would become the dominant circulation center during the early stages of the extratropical transition (ET) process. Second, it was difficult to predict the intensity of the storm at landfall owing to competing factors: 1) decreasing SSTs conducive to weakening and 2) the approaching negatively tilted upper-level trough, favoring intensification. Numerical hindcast simulations using the limited-area Mesoscale Compressible Community model with synthetic vortex insertion (cyclone bogus) prior to the ET of Hurricane Michael led to a more realistic evolution of wind and pressure compared to running the model without vortex insertion. Specifically, the mesoscale model correctly simulates the hurricane as the dominant circulation center early in the transition process, versus the baroclinic low to its north, which was the favored development in the runs not employing vortex insertion. A suite of experiments is conducted to establish the sensitivity of the ET to various initial conditions, lateral driving fields, domain sizes, and model parameters. The resulting storm tracks and intensities fall within the range of the operational guidance, lending support to the possibility of improving numerical forecasts using synthetic vortex insertion prior to ET in such a model.
Operational Evaluation of a Selective Consensus in the Western North Pacific Basin
Authors: Sampson Charles R. , Knaff John A. , Fukada Edward M. 
Published: June 2007

Abstract
The Systematic Approach Forecast Aid (SAFA) has been in use at the Joint Typhoon Warning Center since the 2000 western North Pacific season. SAFA is a system designed for determination of erroneous 72-h track forecasts through identification of predefined error mechanisms associated with numerical weather prediction models. A metric for the process is a selective consensus in which model guidance suspected to have 72-h error greater than 300 n mi (1 n mi = 1.85 km) is first eliminated prior to calculating the average of the remaining model tracks. The resultant selective consensus should then provide improved forecasts over the nonselective consensus. In the 5 yr since its introduction into JTWC operations, forecasters have been unable to produce a selective consensus that provides consistent improved guidance over the nonselective consensus. Also, the rate at which forecasters exercised the selective consensus option dropped from approximately 45% of all forecasts in 2000 to 3% in 2004.
Increasing the Reliability of Reliability Diagrams
Authors: Bröcker Jochen , Smith Leonard A. 
Published: June 2007

Abstract
The reliability diagram is a common diagnostic graph used to summarize and evaluate probabilistic forecasts. Its strengths lie in the ease with which it is produced and the transparency of its definition. While visually appealing, major long-noted shortcomings lie in the difficulty of interpreting the graph visually; for the most part, ambiguities arise from variations in the distributions of forecast probabilities and from various binning procedures. A resampling method for assigning consistency bars to the observed frequencies is introduced that allows for immediate visual evaluation as to just how likely the observed relative frequencies are under the assumption that the predicted probabilities are reliable. Further, an alternative presentation of the same information on probability paper eases quantitative evaluation and comparison. Both presentations can easily be employed for any method of binning.
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites
Authors: Hummel Jan , Niemann Michaela , Wienkoop Stefanie , Schulze Waltraud , Steinhauser Dirk , Selbig Joachim , Walther Dirk , Weckwerth Wolfram 
Published: June 2007

Abstract

Background
In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system [1]. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology.

Results
A mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry (LC-IT-MS). Protein samples derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula, and Sinorhizobium meliloti were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting [2] and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included in vivo phosphorylation sites of Arabidopsis thaliana proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by ProMEX is linked to other levels of biological organization such as metabolite, pathway, and transcript data. The database is further connected to annotation and classification services via BioMoby.

Conclusion
The ProMEX protein/peptide database represents a mass spectral reference library with the capability of matching unknown samples for protein identification. The database allows text searches based on metadata such as experimental information of the samples, mass spectrometric instrument parameters or unique protein identifier like AGI codes. ProMEX integrates proteomics data with other levels of molecular organization including metabolite, pathway, and transcript information and may thus become a useful resource for plant systems biology studies. The ProMEX mass spectral library is available at http://promex.mpimp-golm.mpg.de/.