PowerNap: an efficient power management scheme for mobile devices

We present PowerNap, an OS power management scheme, which can significantly improve the battery life of mobile devices. The key feature of PowerNap is the skipping of the periodic system timer ticks associated with the operating system. On an idle device, this modification increases the time between successive timer interrupts and enables us to put the processor/system into a more efficient low power state. This saves the energy consumed by workless timer interrupts and the excess energy consumed by the processor in less efficient low power states. PowerNap is tightly integrated with the kernel and is designed for optimal control of the latency and energy associated with transitioning in and out of the low power states. We describe an implementation of PowerNap and its impact on system software. Experiments with IBM's WatchPad verify the ability of PowerNap to extend battery life. An analytical model that quantifies the ability of the scheme to reduce power is also presented. The model is in good agreement with experimental results. We apply the model to small form-factor devices which use processors that have a PowerDown state. In such devices, PowerNap may extend battery life by more than 42 percent for small processor workloads and for background power levels below 10 mW.     

Impact on the photothermal emission from single wall nanotubes by some alkali halide salts

We demonstrate that alkali-halide salts, particularly potassium bromide, can reduce the photothermal emission (PTE) from single walled carbon nanotubes (SWNT). PTE is a prominent spectral feature in Raman spectroscopy when a near infrared laser is used to analyze a dark colored sample. We subsequently show that trapping salts inside SWNT and coating SWNT with the salt has a more pronounced impact on not only reducing PTE, but also enhancing the intensity of the Raman spectral features. The effect, which we have called nanotube enhanced Raman spectroscopy (NERS), has differences and similarities to the widely studied surface enhanced Raman spectroscopy (SERS).     

Effects of the glucocorticoid agonist, RU28362, and the antagonist RU486 on lung phosphatidylcholine and antioxidant enzyme development in the genetically obese Zucker rat

The biochemical maturation of the lung in late gestation and in the young animal is regulated by glucocorticoids. The present study was aimed at dissociating the different glucocorticoid receptor sites involved in these regulatory functions. The obese Zucker rat was selected as a model for this study as it exhibits hypersensitivity to glucocorticoid hormone action by virtue of its elevated receptor numbers and activity. Two synthetic steroid analogues were administered to obese animals; RU28362, a specific type II receptor agonist, and the type II antagonist RU486. RU28362 promoted a strong catabolic effect, which was associated with reduced food intake and the abolition of growth in the rats. The agonist, RU28362, attenuated developmental increases in antioxidant enzyme activities, and altered the growth of the tissue. At the age studied, development of the lung phosphatidylcholine (PC) system was almost complete, but RU28362 increased disaturated PC 16:0/16:0 concentrations by almost 2-fold, and altered the molecular composition of total pulmonary PC. RU486 attenuated the growth of the rats and reduced their food intake. Treatment with the type II antagonist attenuated lung growth and increased the activities of pulmonary copper zinc (Cu/Zn) and manganese (Mn) superoxide dismutases. RU486 had no effect on lung PC concentrations and molecular composition. The data suggest a role for type I glucocorticoid receptors in the regulation of the antioxidant enzyme system in the lung, as type II antagonism will channel endogenous glucocorticoid binding to the type I site. Type II receptor binding would appear to play a role in regulating the lung PC content.     

Cell cycle-dependent tumor necrosis factor apoptosis

To determine if tumor necrosis factor (TNF)-mediated apoptosis affects cells at defined stages of the cell cycle, WEHI-164/2F (WEHI) cells were synchronized at G0-G1 after 3-day cultures in medium containing RPMI 1640 and 0.5% FCS (RPMI-0.5% FCS). The arrested WEHI cells (60-75% in G0-G1) showed increased sensitivity to TNF killing, measured as 48-h 3-(5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide assays, and 15-h apoptosis by propidium iodide staining and flow cytometry analysis. The TNF killing kinetics of G0-G1-arrested cells was similar to controls, and TNF did not accelerate or retard cell cycle progression of the arrested cells after feeding with fresh RPMI-0.5% FCS. However, TNF inhibited WEHI DNA synthesis as early as 1 h after treatment, and inhibition was proportionate to sensitivity to TNF-induced apoptosis. WEHI cells treated with TNF showed a higher percentage of cells in S phase with concomitant decrease in G0-G1 and G2-M. When cultured for 3-18 h in fresh RPMI-0.5% FCS to allow progression of the G0-G1-arrested cells toward the G1-S boundary, WEHI cells became more sensitive to TNF killing, especially at the 3-9 h time points. Moreover, TNF did not degrade [125I]5-iodo-2'-deoxyuridine-labeled WEHI DNA if the labeled cells were precultured for 9 h in fresh RPMI-0.5% FCS to allow them to pass S phase before the addition of TNF. These results show that TNF-induced apoptosis of WEHI cells is connected to cell cycle events; WEHI targets receive the TNF cytotoxic signal mainly at the G1-S boundary and begin to die by apoptosis as they exit from S phase.     

Dynamic simulations of the molecular conformations of wild type and mutant xanthan polymers suggest that conformational differences may contribute to observed differences in viscosity

Xanthan gum is an exopolysaccharide secreted by the bacterium Xanthamonas campestris whose ability to make solutions viscous at low concentrations and over a pH and temperature range have generated much interest in both academic and industrial environments. Mutant Xanthamonas strains have been derived that produce xanthan gums with an altered or variant subunit chemical structure and different measured viscosities when compared with the wild type (wt) form of the polymer. Two variant gums were targeted as potentially interesting in this study, these being the nonacetylated tetramer (natet) and the acetylated tetramer (atet), which both lack a side-chain terminal mannose residue and in one case (natet) lacks an acetate group on an internal mannose residue. Solutions of these tetrameric gums possess viscosities higher (natet) and lower (atet) than the wt gum, and therefore we have attempted to determine whether these molecules possess unique conformational preferences when compared with the wt and with each other. In this manner we can initiate an understanding of how a polysaccharide's conformation contributes to its solution properties. The GEGOP software permits a sampling of the static and dynamic equilibrium states of carbohydrate molecules, and this software was employed to calculate equilibrium states of representative oligosaccharides with chemical structures representative of xanthan-like molecules. Energy minimization techniques revealed similar local minima for all three molecules. Some of these minima are comprised of elongate backbone conformations (A type) in which side chains fold onto backbone surfaces. Other minima with A backbones possessed side chains in less intimate backbone contact especially when calculations were performed with a low dielectric constant. This phenomenon was particularly pronounced in the wt molecule where an increased number of negatively charged side-chain residues experience charge repulsion resulting in reduced side-chain-backbone contact. Metropolis Monte Carlo (MMC) dynamic simulations performed with an elevated temperature factor (1000 K) allowed a better qualitative representation of conformational space than 300 K simulations. Employing a nonhierarchical cluster analysis method (population density profile: PDP) coupled with a classification scheme, it was possible to partition resulting MMC data sets into conformational families. This analysis revealed that in simulations performed with different dielectric constant values (10, 25, and infinity) all molecules possessed primarily A-type backbones. Less elongate, more open helical backbone forms (B, C, D, J, and Flat-a) did occur during the simulations but were populated to a lesser extent. In the natet molecule significantly open helical backbones existed (E, F, G, H, and I) that did not occur in the lower viscosity wt and atet molecules. PDP clustering methods and subsequent conformational classification applied to the first residue (mannose) of the side chain permitted a determination of side-chain orientation. Comparison of all three molecules indicated a larger population of side-chain conformational families in less direct backbone contact for the wt molecule than either of the variant molecules (natet/atet) suggesting that the side chains in the wt are more flexible. Thus, a major conformational difference between the high viscosity natet and the lower viscosities of the wt/atet is the increased amount of open helical backbone in the natet. In addition, the significant difference between the higher viscosity wt and the lower viscosity atet is the increase side-chain flexibility in the wt. We hypothesize that conformational differences of this kind could form a partial explanation of the observed differences in viscosity between these xanthan-like polymers.     

Evaluating hyperspectral imaging of wetland vegetation as a tool for detecting estuarine nutrient enrichment

Nutrient enrichment and eutrophication are major concerns in many estuarine and wetland ecosystems, and the need is urgent for fast, efficient, and synoptic ways to detect and monitor nutrients in wetlands and other coastal systems across multiple spatial and temporal scales. We integrated three approaches in a multi-disciplinary evaluation of the potential for using hyperspectral imaging as a tool to assess nutrient enrichment and vegetation responses in tidal wetlands. For hyperspectral imaging to be an effective tool, spectral signatures must vary in ways correlated with water nutrient content either directly, or indirectly via such proxies as vegetation responses to elevated nitrogen. Working in Elkhorn Slough, central California, where intensive farming practices generate considerable runoff of fertilizers and pesticides, we looked first for long- and short-term trends among temporally ephemeral point data for nutrients and other water quality characters collected monthly at 18 water sampling stations since 1988. Second, we assessed responses of the dominant wetland plant, Salicornia virginica (common pickleweed) to two fertilizer regimes in 0.25 m² experimental plots, and measured changes in tissue composition (C, H, N), biomass, and spectral responses at leaf and at canopy scales. Third, we used HyMap hyperspectral imagery (126 bands; 15–19 nm spectral resolution; 2.5 m spatial resolution) for a synoptic assessment of the entire wetland ecosystem of Elkhorn Slough. We mapped monospecific Salicornia patches (～ 56–500 m²) on the ground adjacent to the 18 regular water sampling sites, and then located these patches in the hyperspectral imagery to correlate long-term responses of larger patches to water nutrient regimes. These were used as standards for correlating plant canopy spectral responses with nitrogen variation described by the water sampling program. There were consistent positive relationships between nitrogen levels and plant responses in both the field experiment and the landscape analyses. Two spectral indices, the Photochemical Reflectance Index (PRI) and Derivative Chlorophyll Index (DCI), were correlated significantly with water nutrients. We conclude that hyperspectral imagery can be used to detect nutrient enrichment across three spatial and at least two temporal scales, and suggest that more quantitative information could be extracted with further research and a greater understanding of physiological and physical mechanisms linking water chemistry, plant properties and spectral imaging characteristics.     

Sea-air flux of CO2 in the Caribbean Sea estimated using in situ and remote sensing data

Empirical relationships between sea surface carbon dioxide fugacity (fCO₂^sw) and sea surface temperature (SST) were applied to datasets of remotely sensed SST to create fCO₂^sw fields in the Caribbean Sea. SST datasets from different sensors were used, as well as the SST fields created by optimum interpolation of bias corrected AVHRR data. Empirical relationships were derived using shipboard fCO₂^sw data, in situ SST data, and SST data from the remote sensing platforms. The results show that the application of a relationship based on shipboard SST data, on fields of remotely sensed SST yields biased fCO₂^sw values. This bias is reduced if the fCO₂^sw-SST relationships are derived using the same SST data that are used to create the SST fields. The fCO₂^sw fields found to best reproduce observed fCO₂^sw are used in combination with wind speed data from QuikSCAT to create weekly maps of the sea-air CO₂ flux in the Caribbean Sea in 2002. The region to the SW of Cuba was a source of CO₂ to the atmosphere throughout 2002, and the region to the NE was a sink during winter and spring and a source during summer and fall. The net uptake of CO₂ in the region was doubled when potential skin layer effects on fCO₂^sw were taken into account.     

Solution structure of the superactive monomeric des-[Phe(B25)] human insulin mutant: elucidation of the structural basis for the monomerization of des-[Phe(B25)] insulin and the dimerization of native insulin

The three-dimensional solution structure of des-[Phe(B25)] human insulin has been determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics calculations. Thirty-five structures were calculated by distance geometry from 581 nuclear Overhauser enhancement-derived distance constraints, ten phi torsional angle restraints, the restraints from 16 helical hydrogen bonds, and three disulfide bridges. The distance geometry structures were optimized using simulated annealing and restrained energy minimization. The average root-mean-square (r.m.s.) deviation for the best 20 refined structures is 1.07 angstroms for the backbone and 1.92 angstroms for all atoms if the less well-defined N and C-terminal residues are excluded. The helical regions are more well defined, with r.m.s. deviations of 0.64 angstroms for the backbone and 1.51 angstroms for all atoms. It is found that the des-[Phe(B25)] insulin is a monomer under the applied conditions (4.6 to 4.7 mM, pH 3.0, 310 K), that the overall secondary and tertiary structures of the monomers in the 2Zn crystal hexamer of native insulin are preserved, and that the conformation-averaged NMR solution structure is close to the structure of molecule 1 in the hexamer. The structure reveals that the lost ability of des-[Phe(B25)] insulin to self-associate is caused by a conformational change of the C-terminal region of the B-chain, which results in an intra-molecular hydrophobic interaction between Pro(B28) and the hydrophobic region Leu(B11)-Leu(B15) of the B-chain alpha-helix. This interaction interferes with the inter-molecular hydrophobic interactions responsible for the dimerization of native insulin, depriving the mutant of the ability to dimerize. Further, the structure displays a series of features that may explain the high potency of the mutant on the basis of the current model for the insulin-receptor interaction. These features are: a change in conformation of the C-terminal region of the B-chain, the absence of strong hydrogen bonds between this region and the rest of the molecule, and a relatively easy accessibility to the Val(A3) residue.