bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Reception of Aristotle's History of Animals in the Marginalia of Some Latin Manuscripts of Michael Scot's Arabic-Latin Translation
Authors: Van Oppenraay Aafke M.I. 
Published: December 2007

AbstractA considerable number of the thirteenth and early fourteenth-century manuscripts of Michael Scot's Arabic-Latin translation of Aristotle's De animalibus (ca. 1215) display a system of guiding marginal glosses. These glosses are usually added by a later hand with respect to the hand that had written the text. The manuscripts were not only annotated for personal use, but also so as to allow for a better use in compiling commentaries, encyclopaedias and compendia. We can say that the marginalia form the main, if not only, key to our understanding today of the use that readers made of the text. Apart from offering a mere explanation of the contents, we can see that their interest in the text was chiefly related to biblical exegesis and to scientific and medical knowledge. The approach to the text was often allegorical and moralizing in character. Some remarks reflect the reader's own experience and associations in relation to the text.
Ventilation Rates Estimated from Tracers in the Presence of Mixing
Authors: Hall Timothy M. , Haine Thomas W. N. , Waugh Darryn W. , Holzer Mark , Terenzi Francesca , LeBel Deborah A. 
Published: December 2007

Abstract
The intimate relationship among ventilation, transit-time distributions, and transient tracer budgets is analyzed. To characterize the advective–diffusive transport from the mixed layer to the interior ocean in terms of flux we employ a cumulative ventilation-rate distribution, Φ(τ), defined as the one-way mass flux of water that resides at least time τ in the interior before returning. A one-way (or gross) flux contrasts with the net advective flux, often called the subduction rate, which does not accommodate the effects of mixing, and it contrasts with the formation rate, which depends only on the net effects of advection and diffusive mixing. As τ decreases Φ(τ) increases, encompassing progressively more one-way flux. In general, Φ is a rapidly varying function of τ (it diverges at small τ), and there is no single residence time at which Φ can be evaluated to fully summarize the advective–diffusive flux. To reconcile discrepancies between estimates of formation rates in a recent GCM study, Φ(τ) is used. Then chlorofluorocarbon data are used to bound Φ(τ) for Subtropical Mode Water and Labrador Sea Water in the North Atlantic Ocean. The authors show that the neglect of diffusive mixing leads to spurious behavior, such as apparent time dependence in the formation, even when transport is steady.
Impact of Channel Geometry and Rotation on the Trapping of Internal Tides
Authors: Drijfhout Sybren , Maas Leo R. M. 
Published: December 2007

Abstract
The generation and propagation of internal tides has been studied with an isopycnic three-dimensional ocean model. The response of a uniformly stratified sea in a channel, which is forced by a barotropic tide on its open boundary, is considered. The tide progresses into the channel and forces internal tides over a continental slope at the other end. The channel has a length of 1200 km and a width of 191.25 km. The bottom profile has been varied. In a series of four experiments it is shown how the cross-channel geometry affects the propagation and trapping of internal tides, and the penetration scale of wave energy, away from the continental slope, is discussed. In particular it is found that a cross-channel bottom slope constrains the penetration of the internal tidal energy. Most internal waves refract toward a cross-channel plane where they are trapped. The exception is formed by edge waves that carry part of the energy away from the continental slope. In the case of rotation near the continental slope, the Poincaré waves that arise in the absence of a cross-channel slope no longer bear the characteristics of the wave attractor predicted by 2D theory, but are almost completely arrested, while the right-bound Kelvin wave preserves the 2D attractor in the cross-channel plane, which is present in the nonrotating case. The reflected, barotropic right-bound Kelvin wave acts as a secondary internal wave generator along the cross-channel slope.
Evaluation of Interior Circulation in a High-Resolution Global Ocean Model. Part II: Southern Hemisphere Intermediate, Mode, and Thermocline Waters
Authors: Sen Gupta Alexander , England Matthew H. 
Published: December 2007

Abstract
A high-resolution, offline ocean general circulation model, incorporating a realistic parameterization of mixed layer convection, is used to diagnose pathways and time scales of Southern Hemisphere intermediate, mode, and lower thermocline water ventilation. The use of such an offline methodology represents the only feasible way of simulating the long time scales required to validate the internal pathways of a high-resolution ocean model. Simulated and observed chlorofluorocarbon-11 (CFC-11) are in reasonably good agreement, demonstrating the model’s skill in representing realistic ventilation. Regional passive dye and age tracer experiments aid in the identification of pathways originating from different Southern Hemisphere locations. Northern Hemisphere penetration of intermediate, mode, and thermocline waters is most extensive and rapid into the North Atlantic Ocean because these waters are involved in closing the Atlantic meridional overturning cell. However, less than 8% of this ventilation is derived from subduction within the South Atlantic in the simulation. Instead, this water enters the Atlantic just to the south of South Africa, having originally subducted primarily in the east Indian Ocean, but also in the west Indian Ocean and the west Pacific region where a pathway advects water westward to the south of Australia. This pathway also plays a large part, together with water overturned in the east Indian Ocean, in ventilating the northern reaches of the Indian basin. Northward propagation in the Pacific Ocean is limited to the low latitudes of the Northern Hemisphere and is almost exclusively accomplished by water subducted in the South Pacific. A small contribution is made from the other basins from water that spreads northward, fed by a circumpolar pathway associated with the Antarctic Circumpolar Current that forms a conduit for intermediate and mode water exchange between all three basins. Intermediate water is injected into and branches off this pathway in all basins, but most vigorously in the southeastern Pacific.
Interannual Variations in Upper-Ocean Heat Content and Heat Transport Convergence in the Western North Atlantic
Authors: Dong Shenfu , Hautala Susan L. , Kelly Kathryn A. 
Published: December 2007

Abstract
Subsurface temperature data in the western North Atlantic Ocean are analyzed to study the variations in the heat content above a fixed isotherm and contributions from surface heat fluxes and oceanic processes. The study region is chosen based on the data density; its northern boundary shifts with the Gulf Stream position and its southern boundary shifts to contain constant volume. The temperature profiles are objectively mapped to a uniform grid (0.5° latitude and longitude, 10 m in depth, and 3 months in time). The interannual variations in upper-ocean heat content show good agreement with the changes in the sea surface height from the Ocean Topography Experiment (TOPEX)/Poseidon altimeter; both indicate positive anomalies in 1994 and 1998–99 and negative anomalies in 1996–97. The interannual variations in surface heat fluxes cannot explain the changes in upper-ocean heat storage rate. On the contrary, a positive anomaly in heat released to the atmosphere corresponds to a positive upper-ocean heat content anomaly. The oceanic heat transport, mainly owing to the geostrophic advection, controls the interannual variations in heat storage rate, which suggests that geostrophic advection plays an important role in the air–sea heat exchange. The 18°C isotherm depth and layer thickness also show good correspondence to the upper-ocean heat content; a deep and thin 18°C layer corresponds to a positive heat content anomaly. The oceanic transport in each isotherm layer shows an annual cycle, converging heat in winter, and diverging in summer in a warm layer; it also shows interannual variations with the largest heat convergence occurring in even warmer layers during the period of large ocean-to-atmosphere flux.
The Role of Wind Stress Curl in Jet Separation at a Cape
Authors: Castelao Renato M. , Barth John A. 
Published: December 2007

Abstract
A high-resolution numerical model is used to study the importance of spatial variability in the wind forcing to the separation of a coastal upwelling jet at a cape. An idealized topography and wind field based on observations from the Cape Blanco (Oregon) region are used. Several simulations are investigated, with both the intensity and the spatial structure of the wind forcing varied to isolate the importance of the observed intensification in the wind stress and wind stress curl magnitudes to the separation process. A simulation using a straight coast confirms that the presence of the cape is crucial for separation. Wind stress intensification by itself, with zero curl, does not aid separation. The wind stress curl intensification south of the cape, on the other hand, is important for controlling details of the process. Because the positive wind stress curl drives upwelling, isotherms in the offshore region tilt upward, creating a pressure gradient that sustains an intensification of the southward velocities via the thermal wind balance. This aids jet separation via continuity and by creating potential vorticity contours that track far offshore of the cape. The timing of the separation is dependent on the intensity of the wind stress curl (stronger curl leads to earlier separation), while how far offshore the jet is deflected depends on the offshore extent of the region of positive curl close to the coast (increasing the extent increases the deflection).
The Coastal Bottom Boundary Layer: A Note on the Model of Chapman and Lentz
Authors: Pedlosky Joseph 
Published: December 2007

Abstract
The bottom boundary layer of a stratified flow on a coastal continental shelf is examined using the model of Chapman and Lentz. The flow is driven by a surface stress, uniform in the alongshore coordinate, in a downwelling-favorable direction. The stress diminishes in the offshore direction and produces an Ekman pumping, as well as an onshore Ekman flux. The model yields an interior flow, sandwiched between an upper Ekman layer and a bottom boundary layer. The interior has a horizontal density gradient produced by a balance between horizontal diffusion of density and vertical advection of a background vertical density gradient. The interior flow is vertically sheared and in thermal wind balance. Whereas the original model of Chapman and Lentz considered an alongshore flow that is freely evolving, the present note focuses on the equilibrium structure of a flow driven by stress and discusses the vertical and lateral structure of the flow and, in particular, the boundary layer thickness. The vertical diffusivity of density in the bottom boundary layer is considered so strong, locally, as to render the bottom boundary layer’s density a function of only offshore position. Boundary layer budgets of mass, momentum, and buoyancy determine the barotropic component of the interior flow as well as the boundary layer thickness, which is a function of the offshore coordinate. The alongshore flow has enhanced vertical shear in the boundary layer that reduces the alongshore flow in the boundary layer; however, the velocity at the bottom is generally not zero but produces a stress that locally balances the applied surface stress. The offshore transport in the bottom boundary layer therefore balances the onshore surface Ekman flux. The model predicts the thickness of the bottom boundary layer, which is a complicated function of several parameters, including the strength of the forcing stress, the vertical and horizontal diffusion coefficients in the interior, and the horizontal diffusion in the boundary layer. The model yields a boundary layer over only a finite portion of the bottom slope if the interior diffusion coefficients are too large; otherwise, the layer extends over the full lateral extent of the domain.
Wave-Follower Field Measurements of the Wind-Input Spectral Function. Part III: Parameterization of the Wind-Input Enhancement due to Wave Breaking
Authors: Babanin Alexander V. , Banner Michael L. , Young Ian R. , Donelan Mark A. 
Published: December 2007

AbstractThis is the third in a series of papers describing wave-follower observations of the aerodynamic coupling between wind and waves on a large shallow lake during the Australian Shallow Water Experiment (AUSWEX). It focuses on the long-standing problem of the aerodynamic consequences of wave breaking on the wind–wave coupling. Direct field measurements are reported of the influence of wave breaking on the wave-induced pressure in the airflow over water waves, and hence the energy flux to the waves. The level of forcing, measured by the ratio of wind speed to the speed of the dominant (spectral peak) waves, covered the range of 3–7. The propagation speeds of the dominant waves were limited by the water depth and the waves were correspondingly steep. These measurements allowed an assessment of the magnitude of any breaking-induced enhancement operative for these field conditions and provided a basis for parameterizing the effect. Overall, appreciable levels of wave breaking occurred for the strong wind forcing conditions that prevailed during the observational period. Associated with these breaking wave events, a significant phase shift is observed in the local wave-coherent surface pressure. This produced an enhanced wave-coherent energy flux from the wind to the waves with a mean value of 2 times the corresponding energy flux to the nonbreaking waves. It is proposed that the breaking-induced enhancement of the wind input to the waves can be parameterized by the sum of the nonbreaking input and the contribution due to the breaking probability.
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
Authors: Ye Jingjing , Liu Hao , Kirmiz Crystal , Lebrilla Carlito B , Rocke David M 
Published: December 2007

AbstractBackgroundNovel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechnologies that are highly promising to improve health outcome. Previous literatures have identified some proteomics biomarkers that can distinguish healthy patients from cancer patients using MS data. In this paper, an MS study is demonstrated which uses glycomics to identify ovarian cancer. Glycomics is the study of glycans and glycoproteins. The glycans on the proteins may deviate between a cancer cell and a normal cell and may be visible in the blood. High-resolution MS has been applied to measure relative abundances of potential glycan biomarkers in human serum. Multiple potential glycan biomarkers are measured in MS spectra. With the objection of maximizing the empirical area under the ROC curve (AUC), an analysis method was considered which combines potential glycan biomarkers for the diagnosis of cancer.ResultsMaximizing the empirical AUC of glycomics MS data is a large-dimensional optimization problem. The technical difficulty is that the empirical AUC function is not continuous. Instead, it is in fact an empirical 0–1 loss function with a large number of linear predictors. An approach was investigated that regularizes the area under the ROC curve while replacing the 0–1 loss function with a smooth surrogate function. The constrained threshold gradient descent regularization algorithm was applied, where the regularization parameters were chosen by the cross-validation method, and the confidence intervals of the regression parameters were estimated by the bootstrap method. The method is called TGDR-AUC algorithm. The properties of the approach were studied through a numerical simulation study, which incorporates the positive values of mass spectrometry data with the correlations between measurements within person. The simulation proved asymptotic properties that estimated AUC approaches the true AUC. Finally, mass spectrometry data of serum glycan for ovarian cancer diagnosis was analyzed. The optimal combination based on TGDR-AUC algorithm yields plausible result and the detected biomarkers are confirmed based on biological evidence.ConclusionThe TGDR-AUC algorithm relaxes the normality and independence assumptions from previous literatures. In addition to its flexibility and easy interpretability, the algorithm yields good performance in combining potential biomarkers and is computationally feasible. Thus, the approach of TGDR-AUC is a plausible algorithm to classify disease status on the basis of multiple biomarkers.
Unravelling the molecular control of calvarial suture fusion in children with craniosynostosis
Authors: Coussens Anna K , Wilkinson Christopher R , Hughes Ian P , Morris C Phillip , van Daal Angela , Anderson Peter J , Powell Barry C 
Published: December 2007

AbstractBackgroundCraniosynostosis, the premature fusion of calvarial sutures, is a common craniofacial abnormality. Causative mutations in more than 10 genes have been identified, involving fibroblast growth factor, transforming growth factor beta, and Eph/ephrin signalling pathways. Mutations affect each human calvarial suture (coronal, sagittal, metopic, and lambdoid) differently, suggesting different gene expression patterns exist in each human suture. To better understand the molecular control of human suture morphogenesis we used microarray analysis to identify genes differentially expressed during suture fusion in children with craniosynostosis. Expression differences were also analysed between each unfused suture type, between sutures from syndromic and non-syndromic craniosynostosis patients, and between unfused sutures from individuals with and without craniosynostosis.ResultsWe identified genes with increased expression in unfused sutures compared to fusing/fused sutures that may be pivotal to the maintenance of suture patency or in controlling early osteoblast differentiation (i.e.RBP4,GPC3,C1QTNF3,IL11RA,PTN,POSTN). In addition, we have identified genes with increased expression in fusing/fused suture tissue that we suggest could have a role in premature suture fusion (i.e.WIF1,ANXA3,CYFIP2). Proteins of two of these genes, glypican 3 and retinol binding protein 4, were investigated by immunohistochemistry and localised to the suture mesenchyme and osteogenic fronts of developing human calvaria, respectively, suggesting novel roles for these proteins in the maintenance of suture patency or in controlling early osteoblast differentiation. We show that there is limited difference in whole genome expression between sutures isolated from patients with syndromic and non-syndromic craniosynostosis and confirmed this by quantitative RT-PCR. Furthermore, distinct expression profiles for each unfused suture type were noted, with the metopic suture being most disparate. Finally, although calvarial bones are generally thought to grow without a cartilage precursor, we show histologically and by identification of cartilage-specific gene expression that cartilage may be involved in the morphogenesis of lambdoid and posterior sagittal sutures.ConclusionThis study has provided further insight into the complex signalling network which controls human calvarial suture morphogenesis and craniosynostosis. Identified genes are candidates for targeted therapeutic development and to screen for craniosynostosis-causing mutations.
Imparting carrier status results detected by universal newborn screening for sickle cell and cystic fibrosis in England: a qualitative study of current practice and policy challenges
Authors: Parker Hilda , Qureshi Nadeem , Ulph Fiona , Kai Joe 
Published: December 2007

Abstract
Background
Universal newborn screening for early detection of children affected by sickle cell disorders and cystic fibrosis is currently being implemented across England. Parents of infants identified as carriers of these disorders must also be informed of their baby's result. However there is a lack of evidence for most effective practice internationally when doing so. This study describes current or proposed models for imparting this information in practice and explores associated challenges for policy.

Methods
Thematic analysis of semi-structured interviews with Child Health Coordinators from all English Health Regions.

Results
Diverse methods for imparting carrier results, both within and between regions, and within and between conditions, were being implemented or planned. Models ranged from result by letter to in-person communication during a home visit. Non-specialists were considered the best placed professionals to give results and a similar approach for both conditions was emphasised. While national guidance has influenced choice of models, other factors contributed such as existing service structures and lack of funding. Challenges included uncertainty about guidance specifying face to face notification; how best to balance allaying parental anxiety by using familiar non-specialist health professionals with concerns about practitioner competence; and extent of information parents should be given. Inadequate consideration of resource and service workload was seen as the main policy obstacle. Clarification of existing guidance; more specific protocols to ensure consistent countrywide practice; integration of the two programmes; and 'normalising' carrier status were suggested as improvements.

Conclusion
Differing models for communicating carrier results raise concerns about equity and clinical governance. However, this variation provides opportunity for evaluation. Timely and more detailed guidance on protocols with clarification of existing recommendations is needed.