A wave-induced stirring mechanism in the mid-depth equatorial ocean

A wave-induced stirring and transport mechanism for the mid-depth equatorial ocean is proposed and examined using both analytic linear equatorial wave solutions and a fully nonlinear reduced-gravity model. The study of kinematic stirring using the linear solutions suggests that a superimposition of a few simple equatorial waves can lead to strong Lagrangian stirring and transport along the equator. In particular, a combination of an annual long Rossby wave and a high-frequency Yanai wave appears to be most effective in producing strong stirring in the interior equatorial region. Further investigations of stirring properties using an inverted, fully nonlinear reduced gravity shallow-water model support the results of the kinematic stirring study. By evaluating the finite-time estimates of Lyapunov exponents, we identified two regions where chaotic stirring is most active. One is the western boundary region where short Rossby waves likely play a dominant role in producing the strong chaotic stirring. The other is the equatorial waveguide where a low-frequency Rossby wave prescribes the pattern of the stirring geometry, and a high-frequency Yanai wave plays a role of stirring the fluid. The proposed stirring mechanism provides a plausible explanation of the observed chlorofluorocarbon distribution found in the mid-depth equatorial Atlantic Ocean

BxDF material acquisition, representation, and rendering for VR and design

Photorealistic and physically-based rendering of real-world environments with high fidelity materials is important to a range of applications, including special effects, architectural modelling, cultural heritage, computer games, automotive design, and virtual reality (VR). Our perception of the world depends on lighting and surface material characteristics, which determine how the light is reflected, scattered, and absorbed. In order to reproduce appearance, we must therefore understand all the ways objects interact with light, and the acquisition and representation of materials has thus been an important part of computer graphics from early days. Nevertheless, no material model nor acquisition setup is without limitations in terms of the variety of materials represented, and different approaches vary widely in terms of compatibility and ease of use. In this course, we describe the state of the art in material appearance acquisition and modelling, ranging from mathematical BSDFs to data-driven capture and representation of anisotropic materials, and volumetric/thread models for patterned fabrics. We further address the problem of material appearance constancy across different rendering platforms. We present two case studies in architectural and interior design. The first study demonstrates Yulio, a new platform for the creation, delivery, and visualization of acquired material models and reverse engineered cloth models in immersive VR experiences. The second study shows an end-to-end process of capture and data-driven BSDF representation using the physically-based Radiance system for lighting simulation and rendering

Icebergs in the North Atlantic: Modelling circulation changes and glacio-marine deposition

In order to investigate meltwater events in the North Atlantic, a simple iceberg generation, drift, and melting routine was implemented in a high-resolution OGCM. Starting from the modelled last glacial state, every 25th day cylindrical model icebergs 300 meters high were released at 32 specific points along the coasts. Icebergs launched at the Barents Shelf margin spread a light meltwater lid over the Norwegian and Greenland Seas, shutting down the deep convection and the anti-clockwise circulation in this area. Due to the constraining ocean circulation, the icebergs produce a tongue of relatively cold and fresh water extending eastward from Hudson Strait that must develop at this location, regardless of iceberg origin. From the total amount of freshwater inferred by the icebergs, the thickness of the deposited IRD could be calculated in dependance of iceberg sediment concentration. In this way, typical extent and thickness of Heinrich layers could be reproduced, running the model for 250 years of steady state with constant iceberg meltwater inflow

Campylobacter jejuni bacteremia and Helicobacter pylori in a patient with X-linked agammaglobulinemia

We describe a 15-year-old patient with X-linked agammaglobulinemia who developed malabsorption and bacteremia due to infection of Helicobacter pylori and Campylobacter jejuni. The Campylobacter bacteremia was only recognized after subculturing of blood culture bottles that failed to signal in the automated system. After 2 weeks of treatment with meropenem and erythromycin for 4 weeks, the patient developed a relapse of bacteremia 10 months later with a high level erythromycin resistant C. jejuni. Sequencing revealed an A2058C mutation in the 23 S rRNA gene associated with this resistance. Treatment with doxycycline for 4 weeks finally resulted in complete eradication. This case report illustrates the importance for physicians to use adapted culture methods and adequate prolonged therapy in patients with an immunodeficiency. A summary of published case reports and series of patients with hypogammaglobulinemia or agammaglobulinemia with Campylobacter or Helicobacter bacteremia is given

Adaptive Multidimensional Modeling with Applications in Scientific Computing

No abstract availabl

The North Atlantic subpolar gyre in four high resolution models

The authors present the first quantitative comparison between new velocity datasets and high-resolution models in the North Atlantic subpolar gyre [1/10° Parallel Ocean Program model (POPNA10), Miami Isopycnic Coordinate Ocean Model (MICOM), ° Atlantic model (ATL6), and Family of Linked Atlantic Ocean Model Experiments (FLAME)]. At the surface, the model velocities agree generally well with World Ocean Circulation Experiment (WOCE) drifter data. Two noticeable exceptions are the weakness of the East Greenland coastal current in models and the presence in the surface layers of a strong southwestward East Reykjanes Ridge Current. At depths, the most prominent feature of the circulation is the boundary current following the continental slope. In this narrow flow, it is found that gridded float datasets cannot be used for a quantitative comparison with models. The models have very different patterns of deep convection, and it is suggested that this could be related to the differences in their barotropic transport at Cape Farewell. Models show a large drift in watermass properties with a salinization of the Labrador Sea Water. The authors believe that the main cause is related to horizontal transports of salt because models with different forcing and vertical mixing share the same salinization problem. A remarkable feature of the model solutions is the large westward transport over Reykjanes Ridge [10 Sv (Sv ≡ 106 m3 s−1) or more

A modeling study of the seasonal oxygen budget of the global ocean

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): C05017, doi:10.1029/2006JC003731.An ecosystem model embedded in a global ocean general circulation model is used to quantify roles of biological and physical processes on seasonal oxygen variations. We find that the thermally induced seasonal net outgassing (SNO) of oxygen is overestimated by about 30% if gas phase equilibrium is assumed, and we find that seasonal variations in thermocline oxygen due to biology are approximated well using the oxygen anomaly. Outside the tropics and the north Indian Ocean, biological SNO is, on average, 56% of net community production (defined as net oxygen production above 76 m) during the outgassing period and 35% of annual net community production. In the same region the seasonal drawdown of the oxygen anomaly within the upper thermocline (76–500 m) is 76% of the remineralization during the drawdown and 48% of annual remineralization. Applying model-derived relationships to observed O2 climatologies and using independent estimates for tropical and monsoonal systems, we estimate global net community production to be 14.9 ± 2.5 Pg C yr−1.R.N., X.J., and F.L. were supported from the following grants: NOAA NA16GP2987, NASA NAG5-6451, and NSF OCE-9711937

Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting

This manuscript provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward

Major Depletion of Plasmacytoid Dendritic Cells in HIV-2 Infection, an Attenuated Form of HIV Disease

Plasmacytoid dendritic cells (pDC) provide an important link between innate and acquired immunity, mediating their action mainly through IFN-α production. pDC suppress HIV-1 replication, but there is increasing evidence suggesting they may also contribute to the increased levels of cell apoptosis and pan-immune activation associated with disease progression. Although having the same clinical spectrum, HIV-2 infection is characterized by a strikingly lower viremia and a much slower rate of CD4 decline and AIDS progression than HIV-1, irrespective of disease stage. We report here a similar marked reduction in circulating pDC levels in untreated HIV-1 and HIV-2 infections in association with CD4 depletion and T cell activation, in spite of the undetectable viremia found in the majority of HIV-2 patients. Moreover, the same overexpression of CD86 and PD-L1 on circulating pDC was found in both infections irrespective of disease stage or viremia status. Our observation that pDC depletion occurs in HIV-2 infected patients with undetectable viremia indicates that mechanisms other than direct viral infection determine the pDC depletion during persistent infections. However, viremia was associated with an impairment of IFN-α production on a per pDC basis upon TLR9 stimulation. These data support the possibility that diminished function in vitro may relate to prior activation by HIV virions in vivo, in agreement with our finding of higher expression levels of the IFN-α inducible gene, MxA, in HIV-1 than in HIV-2 individuals. Importantly, serum IFN-α levels were not elevated in HIV-2 infected individuals. In conclusion, our data in this unique natural model of “attenuated” HIV immunodeficiency contribute to the understanding of pDC biology in HIV/AIDS pathogenesis, showing that in the absence of detectable viremia a major depletion of circulating pDC in association with a relatively preserved IFN-α production does occur

Fibrotic Myofibroblasts Manifest Genome-Wide Derangements of Translational Control

Background: As a group, fibroproliferative disorders of the lung, liver, kidney, heart, vasculature and integument are common, progressive and refractory to therapy. They can emerge following toxic insults, but are frequently idiopathic. Their enigmatic propensity to resist therapy and progress to organ failure has focused attention on the myofibroblast–the primary effector of the fibroproliferative response. We have recently shown that aberrant beta 1 integrin signaling in fibrotic fibroblasts results in defective PTEN function, unrestrained Akt signaling and subsequent activation of the translation initiation machinery. How this pathological integrin signaling alters the gene expression pathway has not been elucidated. Results: Using a systems approach to study this question in a prototype fibrotic disease, Idiopathic Pulmonary Fibrosis (IPF); here we show organized changes in the gene expression pathway of primary lung myofibroblasts that persist for up to 9 sub-cultivations in vitro. When comparing IPF and control myofibroblasts in a 3-dimensional type I collagen matrix, more genes differed at the level of ribosome recruitment than at the level of transcript abundance, indicating pathological translational control as a major characteristic of IPF myofibroblasts. To determine the effect of matrix state on translational control, myofibroblasts were permitted to contract the matrix. Ribosome recruitment in control myofibroblasts was relatively stable. In contrast, IPF cells manifested large alterations in the ribosome recruitment pattern. Pathological studies suggest an epithelial origin for IPF myofibroblasts through the epithelial to mesenchymal transition (EMT). In accord wit