bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Interior Circulation in a High-Resolution Global Ocean Model. Part I: Deep and Bottom Waters
Authors: Sen Gupta Alexander , England Matthew H. 
Published: January 2005

Abstract
Global watermass ventilation pathways and time scales are investigated using an “eddy permitting” (¼°) offline tracer model. Unlike previous Lagrangian trajectory studies, here an offline model based on a complete tracer equation that includes three-dimensional advection and mixing is employed. In doing so, the authors are able to meaningfully simulate chlorofluorocarbon (CFC) uptake and assess model skill against observation. This is the first time an eddy-permitting model has been subjected to such an assessment of interior ocean ventilation. The offline model is forced by seasonally varying prescribed velocity, temperature, and salinity fields of a state-of-the-art ocean general circulation model. A seasonally varying mixed layer parameterization is incorporated to account for the degradation of surface convection processes resulting from the temporal averaging. A series of CFC simulations are assessed against observations to investigate interdecadal-time-scale ventilation using a variety of mixed layer criteria. Simulated tracer inventories and penetration depths are in good agreement with observations, especially for thermocline, mode, and surface waters. Deep water from the Labrador Sea is well represented, forming a distinct deep western boundary current that branches at the equator, although concentrations are lower than observed. The formation of bottom water, which occurs around the Antarctic margin, is also generally too weak, although there is excellent qualitative agreement with observations in the region of the Ross and Weddell Seas. Multicentury ventilation of the outflow of North Atlantic Deep Water and bottom water from the Antarctic Margin are investigated using 1000-yr passive tracer experiments with specified interior source regions. The model captures many of the detailed pathways evident from observations, with much of the discrepancy accounted for by differences between actual and modeled topography. A comparison between model-derived “tracer age” and Δ14C “advection age” provides a semiquantitative assessment of model skill at these longer time scales.
A Simple Criterion to Determine the Transition from a Localized Convection to a Distributed Convection Regime*
Authors: Legg Sonya 
Published: January 2005

Abstract
A recent numerical study by Noh et al. of open-ocean deep convection in the presence of a single geostrophic eddy showed that two possible regimes exist: 1) the localized convection regime in which baroclinic instability of the eddy dominates, with slantwise fluxes and restratification, and 2) the distributed convection regime in which vertical mixing dominates. Noh et al. found that localized convection dominates for relatively small buoyancy forcing, strong eddies, and strong surface ambient stratification. Here it is shown that this regime transition can be expressed in terms of a ratio of time scales: the localized convection regime appears when the time scale for lateral fluxes from eddy interior to exterior tL is short in comparison with the time scale for convective erosion of the exterior stratification tc. Scaling arguments give this ratio of time scales as tL/tc ∼ f β2R2B/(A2γ) where f is the Coriolis parameter, R is the radius of the eddy, B is the buoyancy forcing, 1/β is the depth scale of the exponentially decaying surface-intensified stratification, γ is the relative amplitude of the eddy, and Aβ is the value of the surface stratification N20. Comparison with the numerical simulations of Noh et al. shows that this parameter does indeed separate the localized and distributed convection regimes, with the transition occurring at tL/tc ≈ 0.05–0.1.
Identification of the Mechanism of Interdecadal Variability in the North Atlantic Ocean
Authors: te Raa Lianke , Gerrits Jeroen , Dijkstra Henk A. 
Published: January 2005

Abstract
The aim of this paper is to identify the physical mechanism of interdecadal variability in simulations of the North Atlantic Ocean circulation with the Modular Ocean Model of the Geophysical Fluid Dynamics Laboratory. To that end, a hierarchy of increasingly complex model configurations is used. The variability in the simplest case, that of viscous, purely thermally driven flows in a flat-bottom ocean basin with a box-shaped geometry, is shown to be caused by an internal interdecadal mode. The westward propagation of temperature anomalies and the phase difference between the anomalous zonal and meridional overturning that characterize the interdecadal mode are used as “fingerprints” of the physical mechanism of the variability. In this way, the variability can be followed toward a less viscous regime in which the effects of continental geometry and bottom topography are also included. It is shown that, although quantitative aspects of the variability like period and spatial pattern are changing, the physical mechanism of the interdecadal variability in the more complex simulations can be attributed to the same processes as in the simplest model configuration.
The Eddy-Driven Thermocline
Authors: Cessi Paola , Fantini Maurizio 
Published: January 2005

Abstract
The role of baroclinic eddies in transferring thermal gradients laterally, and thus determining the stratification of the ocean, is examined. The hypothesis is that the density differences imposed at the surface by differential heating are a source of available potential energy that can be partially released by mesocale eddies with horizontal scales on the order of 100 km. Eddy fluxes balance the diapycnal mixing of heat and thus determine the vertical scale of penetration of horizontal thermal gradients (i.e., the depth of the thermocline). This conjecture is in contrast with the current thinking that the deep stratification is determined by a balance between diapycnal mixing and the large-scale thermohaline circulation. Eddy processes are analyzed in the context of a rapidly rotating primitive equation flow driven by specified surface temperature, with isotropic diffusion and viscosity. The barotropic component of the eddies is found to be responsible for most of the heat flux, and so the eddy transport is horizontal rather than isopycnal. This eddy transport takes place in the shallow surface layer where eddies, as well as the mean temperature, undergo diabatic, irreversible mixing. Scaling laws for the depth of the thermocline as a function of the external parameters are proposed. In the classical thermocline theory, the depth of the thermocline depends on the diffusivity, the rotation rate, and the imposed temperature gradient. In this study the authors find an additional dependence on the viscosity and on the domain width.
The Motion of a Point Vortex near Large-Amplitude Topography in a Two-Layer Fluid
Authors: White Andrew J. , McDonald N. Robb 
Published: January 2005

Abstract
This work examines the dynamics of point vortices in a two-layer fluid near large-amplitude, sharply varying topography like that which occurs in continental shelf regions. Topography takes the form of an infinitely long step change in depth, and the two-layer stratification is chosen such that the height of topography in the upper layer is a small fraction of the overall depth, enabling quasigeostrophic theory to be used in both layers. An analytic expression for the dispersion relation of free topographic waves in this system is found. Weak vortices are studied using linear theory and, if located in the lower layer, propagate mainly because of their image in the topography. Depending on their sign, they are able to produce significant topographic wave radiation in their wakes. Upper-layer vortices propagate much slower and produce relatively small amplitude topographic wave radiation. Contour dynamics results are used to investigate the nonlinear regions of parameter space. For lower-layer vortices, linear theory is a good approximation, but for upper-layer vortices complicated features evolve and linear theory is only valid for weak vortices.
Mass Flux and Vertical Distribution of Currents Caused by Strong Winds in a Wave Tank
Authors: Ogasawara Toshinori , Yasuda Takashi 
Published: January 2005

Abstract
The velocity fields of wind-driven currents under strong winds were measured in a wind-wave tank with a double bottom. The tank has the characteristics to satisfy partially the continuity of the mass flux and to reduce return-flow effects on the currents. The lower part of the double-bottom tank functions as a duct to circulate the currents, allowing the measurement of the return-flow velocity. The velocity measurements were made on the currents just below the mean water level by using a high-resolution particle image velocimetry (PIV) system and tracking floats and on the currents inside of the duct by using a normal PIV system. Thus, accurate data of the vertical distribution and mass flux of the currents driven by strong winds were obtained from the PIV data. As a result, it is found that the flux in the surface layer with the thickness of 2 times the significant wave height amounts to about 30% of the total mass flux of the currents driven by strong winds with a reference wind speed of 12.0 m s−1.
On the Linear Parameterization of Drag Coefficient over Sea Surface
Authors: Guan Changlong , Xie Lian 
Published: January 2005

Abstract
Combining the logarithmic law with the Charnock relation yields a drag coefficient that is a function of wind speed with the Charnock coefficient as a parameter. It is found that the function is nearly linear within the typically measured range of the drag coefficient. The slope of the linear function is dominated by the Charnock coefficient. When the Charnock relation is extended to a wave age–dependent function, the drag coefficient remains a near-linear function of wind speed after invoking the 3/2 power law. The slope of the linear function is dominated by wave steepness.
Influence of the Surface Heating on Langmuir Circulation
Authors: Min Hong Sik , Noh Yign 
Published: January 2005

Abstract
Large-eddy simulation of the oceanic mixed layer showed that Langmuir circulation (LC) is weakened under the surface heating and is ultimately broken down if the intensity of the surface heating becomes sufficiently strong. The critical condition for the breakdown of LC was mainly determined by the Hoenikker number Ho, and the transition occurs in the range Ho ∼ 1–2. The breakdown of LC leads to a drastic change in the characteristics of the oceanic mixed layer, such as the variation of the rms horizontal velocities with time, the ratio of the horizontal spectra of vertical velocity field, and the pitch. The stability condition for LC suggested by Leibovich was still observed in this simulation. Furthermore, it was found that LC is largely responsible for the formation of a thermocline and the maintenance of a well-mixed layer above it, and the depth of a thermocline was estimated in that case.
A comparison of biologically variable ventilation to recruitment manoeuvres in a porcine model of acute lung injury
Authors: Funk Duane J , Graham M Ruth , Girling Linda G , Thliveris James A , McManus Bruce M , Walker Elizabeth KY , Rector Edward S , Hillier Craig , Scott J Elliott , Mutch W Alan C 
Published: January 2005

Abstract
Background
Biologically variable ventilation (return of physiological variability in rate and tidal volume using a computer-controller) was compared to control mode ventilation with and without a recruitment manoeuvre – 40 cm H2O for 40 sec performed hourly; in a porcine oleic acid acute lung injury model.

Methods
We compared gas exchange, respiratory mechanics, and measured bronchoalveolar fluid for inflammatory cytokines, cell counts and surfactant function. Lung injury was scored by light microscopy. Pigs received mechanical ventilation (FIO2 = 0.3; PEEP 5 cm H2O) in control mode until PaO2 decreased to 60 mm Hg with oleic acid infusion (PaO2/FIO2 <200 mm Hg). Additional PEEP to 10 cm H2O was added after injury. Animals were randomized to one of the 3 modes of ventilation and followed for 5 hr after injury.

Results
PaO2 and respiratory system compliance was significantly greater with biologically variable ventilation compared to the other 2 groups. Mean and mean peak airway pressures were also lower. There were no differences in cell counts in bronchoalveolar fluid by flow cytometry, or interleukin-8 and -10 levels between groups. Lung injury scoring revealed no difference between groups in the regions examined. No differences in surfactant function were seen between groups by capillary surfactometry.

Conclusions
In this porcine model of acute lung injury, various indices to measure injury or inflammation did not differ between the 3 approaches to ventilation. However, when using a low tidal volume strategy with moderate levels of PEEP, sustained improvements in arterial oxygen tension and respiratory system compliance were only seen with BVV when compared to CMV or CMV with a recruitment manoeuvre.
Constraint Logic Programming approach to protein structure prediction
Authors: Dal Palù Alessandro , Dovier Agostino , Fogolari Federico 
Published: January 2005

Abstract
Background
The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems.

Results
Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics.

Conclusions
The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.
prot4EST: Translating Expressed Sequence Tags from neglected genomes
Authors: Wasmuth James D , Blaxter Mark L 
Published: January 2005

Abstract
Background
The genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects.

Results
As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We show that this integrated approach goes a long way to overcoming the deficit in training data.

Conclusions
prot4EST provides a portable EST translation solution and can be usefully applied to >95% of EST projects to improve downstream annotation. It is freely available from http://www.nematodes.org/PartiGene.
A two-way interface between limited Systems Biology Markup Language and R
Authors: Radivoyevitch Tomas 
Published: January 2005

Abstract
Background
Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R.

Results
A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML.

Conclusions
List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.
ABC: software for interactive browsing of genomic multiple sequence alignment data
Authors: Cooper Gregory M , Singaravelu Senthil AG , Sidow Arend 
Published: January 2005

Abstract
Background
Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task.

Results
The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics.

Conclusions
The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available http://mendel.stanford.edu/sidowlab/downloads.html.
Analysis of superfamily specific profile-profile recognition accuracy
Authors: Casbon James A , Saqi Mansoor AS 
Published: January 2005

Abstract
Background
Annotation of sequences that share little similarity to sequences of known function remains a major obstacle in genome annotation. Some of the best methods of detecting remote relationships between protein sequences are based on matching sequence profiles. We analyse the superfamily specific performance of sequence profile-profile matching. Our benchmark consists of a set of 16 protein superfamilies that are highly diverse at the sequence level. We relate the performance to the number of sequences in the profiles, the profile diversity and the extent of structural conservation in the superfamily.

Results
The performance varies greatly between superfamilies with the truncated receiver operating characteristic, ROC10, varying from 0.95 down to 0.01. These large differences persist even when the profiles are trimmed to approximately the same level of diversity.

Conclusions
Although the number of sequences in the profile (profile width) and degree of sequence variation within positions in the profile (profile diversity) contribute to accurate detection there are other superfamily specific factors.
4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin – poor tracks
Authors: Bacher Christian P , Reichenzeller Michaela , Athale Chaitanya , Herrmann Harald , Eils Roland 
Published: January 2005

Abstract
Background
The dynamics of nuclear organization, nuclear bodies and RNPs in particular has been the focus of many studies. To understand their function, knowledge of their spatial nuclear position and temporal translocation is essential. Typically, such studies generate a wealth of data that require novel methods in image analysis and computational tools to quantitatively track particle movement on the background of moving cells and shape changing nuclei.

Results
We developed a novel 4-D image processing platform (TIKAL) for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software. With this new tool, we studied the dynamics of two different types of nuclear particles, namely nuclear bodies made from GFP-NLS-vimentin and microinjected 0.1 μm – wide polystyrene beads, by live cell time-lapse microscopy combined with single particle tracking and mobility analysis. We now provide a tool for the automatic 3-D analysis of particle movement in parallel with the acquisition of chromatin density data.

Conclusions
Kinetic analysis revealed 4 modes of movement: confined obstructed, normal diffusion and directed motion. Particle tracking on the background of stained chromatin revealed that particle movement is directly related to local reorganization of chromatin. Further a direct comparison of particle movement in the nucleoplasm and the cytoplasm exhibited an entirely different kinetic behaviour of vimentin particles in both compartments.
The kinetics of nuclear particles were slightly affected by depletion of ATP and significantly disturbed by disruption of actin and microtubule networks. Moreover, the hydration state of the nucleus had a strong impact on the mobility of nuclear bodies since both normal diffusion and directed motion were entirely abolished when cells were challenged with 0.6 M sorbitol. This effect correlated with the compaction of chromatin. We conclude that alteration in chromatin density directly influences the mobility of protein assemblies within the nucleus.