Results from a set of three-dimensional numerical experiments of a hot Jupiter atmosphere

We present highlights from a large set of simulations of a hot Jupiter atmosphere, nominally based on HD 209458b, aimed at exploring both the evolution of the deep atmosphere, and the acceleration of the zonal flow or jet. We find the occurrence of a super-rotating equatorial jet is robust to changes in various parameters, and over long timescales, even in the absence of strong inner or bottom boundary drag. This jet is diminished in one simulation only, where we strongly force the deep atmosphere equator-to-pole temperature gradient over long timescales. Finally, although the eddy momentum fluxes in our atmosphere show similarities with the proposed mechanism for accelerating jets on tidally-locked planets, the picture appears more complex. We present tentative evidence for a jet driven by a combination of eddy momentum transport and mean flow.Comment: 26 pages, 22 Figures. Accepted for publication in Astronomy and Astrophysic

Natural resources of Lake Earl and Smith River Delta

The Lake Earl/Smith River Delta area is a key coastal wetland situated in northern California. The Lake and Delta have retained much of their value to wildlife and serve as an important link in a chain of such wetlands that extend southward along the Pacific Ocean from Alaska to South America. Millions of water-associated birds of the Pacific Flyway utilize these areas as feeding and resting stops along their migration paths. In California, these wetlands also serve as a significant portion of the available wintering grounds for a major share of the birds within the flyway. The Smith River is also one of the State's most productive salmon and steelhead streams. Anadromous fish produced here provide thousands of angler use days to sport fishermen and contribute substantially to the commercial fishing catch off the northern coast. Because of the importance of coastal wetlands to the fish and wildlife of California, the Department of Fish and Game has initiated a high priority statewide inventory and assessment of these wetlands. This publication is an integral part of that program. This report identifies specific resources and uses; directs attention to problems; and recommends courses of action needed to insure resource protection. It is intended as a guide for citizens, planners, administrators and other interested in the use and development of California's coastal land and waters. (132pp.

Transcription factor distribution in Escherichia coli: studies with FNR protein

Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli chromosome in exponentially growing cells. Sixty-three binding targets, each located at the 5′ end of a gene, were identified. Some targets are adjacent to poorly transcribed genes where FNR has little impact on transcription. In stationary phase, the distribution of FNR was largely unchanged. Control experiments showed that, like FNR, the distribution of the nucleoid-associated protein, IHF, is little altered when cells enter stationary phase, whilst RNA polymerase undergoes a complete redistribution

Heme b distributions through the Atlantic Ocean: evidence for "anemic" phytoplankton populations

Heme b is an iron-containing cofactor in hemoproteins that participates in the fundamental processes of photosynthesis and respiration in phytoplankton. Heme b concentrations typically decline in waters with low iron concentrations but due to lack of field data, the distribution of heme b in particulate material in the ocean is poorly constrained. Here we report particulate heme b distributions across the Atlantic Ocean (59.9°N to 34.6°S). Heme b concentrations in surface waters ranged from 0.10 to 33.7 pmol L−1 (median = 1.47 pmol L−1, n = 974) and were highest in regions with a high biomass. The ratio of heme b to particulate organic carbon (POC) exhibited a mean value of 0.44 μmol heme b mol−1 POC. We identified the ratio of 0.10 µmol heme b mol−1 POC as the cut-off between heme b replete and heme b deficient (anemic) phytoplankton. By this definition, we observed anemic phytoplankton populations in the Subtropical South Atlantic and Irminger Basin. Comparison of observed and modelled heme b suggested that heme b could account for between 0.17–9.1% of biogenic iron. Our large scale observations of heme b relative to organic matter provide further evidence of the impact of changes in iron supply on phytoplankton iron status across the Atlantic Ocean

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions.

The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure the binding of RutR across the chromosome of exponentially growing E. coli cells. Twenty RutR-binding targets were identified and analysis of these targets generated a DNA consensus logo for RutR binding. Complementary in vitro binding assays showed high-affinity RutR binding to 16 of the 20 targets, with the four low-affinity RutR targets lacking predicted key binding determinants. Surprisingly, most of the DNA targets for RutR are located within coding segments of the genome and appear to have little or no effect on transcript levels in the conditions tested. This contrasts sharply with other E. coli transcription factors whose binding sites are primarily located in intergenic regions. We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness

Acute corticospinal tract diffusion tensor imaging predicts 6-month functional outcome after intracerebral haemorrhage

INTRODUCTION: Diffusion tensor imaging (DTI) can assess the structural integrity of the corticospinal tract (CST) in vivo. We aimed to investigate whether CST DTI metrics after intracerebral haemorrhage (ICH) are associated with 6-month functional outcome and can improve the predictive performance of the existing ICH score. METHODS: We retrospectively included 42 patients with DTI performed within 5 days after deep supratentorial spontaneous ICH. Ipsilesional-to-contralesional ratios were calculated for fractional anisotropy (rFA) and mean diffusivity (rMD) in the pontine segment (PS) of the CST. We determined the most predictive variables for poor 6-month functional outcome [modified Rankin Scale (mRS) > 2] using the least absolute shrinkage and selection operator (LASSO) method. We calculated discrimination using optimism-adjusted estimation of the area under the curve (AUC). RESULTS: Patients with 6-month mRS > 2 had lower rFA (0.945 [± 0.139] vs 1.045 [± 0.130]; OR 0.004 [95% CI 0.00-0.77]; p =  0.04) and higher rMD (1.233 [± 0.418] vs 0.963 [± 0.211]; OR 22.5 [95% CI 1.46-519.68]; p = 0.02). Discrimination (AUC) values were: 0.76 (95% CI 0.61-0.91) for the ICH score, 0.71 (95% CI 0.54-0.89) for rFA, and 0.72 (95% CI 0.61-0.91) for rMD. Combined models with DTI and non-DTI variables offer an improvement in discrimination: for the best model, the AUC was 0.82 ([95% CI 0.68-0.95]; p = 0.15). CONCLUSION: In our exploratory study, PS-CST rFA and rMD had comparable predictive ability to the ICH score for 6-month functional outcome. Adding DTI metrics to clinical-radiological scores might improve discrimination, but this needs to be investigated in larger studies

Why Some Interfaces Cannot be Sharp

A central goal of modern materials physics and nanoscience is control of materials and their interfaces to atomic dimensions. For interfaces between polar and non-polar layers, this goal is thwarted by a polar catastrophe that forces an interfacial reconstruction. In traditional semiconductors this reconstruction is achieved by an atomic disordering and stoichiometry change at the interface, but in multivalent oxides a new option is available: if the electrons can move, the atoms don`t have to. Using atomic-scale electron energy loss spectroscopy we find that there is a fundamental asymmetry between ionically and electronically compensated interfaces, both in interfacial sharpness and carrier density. This suggests a general strategy to design sharp interfaces, remove interfacial screening charges, control the band offset, and hence dramatically improving the performance of oxide devices.Comment: 12 pages of text, 6 figure