An analysis of the accuracy of magnetopause reconnection rate variations deduced from cusp ion dispersion characteristics

We present an analysis of the accuracy of the method introduced by Lockwood et al. (1994) for the determination of the magnetopause reconnection rate from the dispersion of precipitating ions in the ionospheric cusp region. Tests are made by applying the method to synthesised data. The simulated cusp ion precipitation data are produced by an analytic model of the evolution of newly-opened field lines, along which magnetosheath ions are firstly injected across the magnetopause and then dispersed as they propagate into the ionosphere. The rate at which these newly opened field lines are generated by reconnection can be varied. The derived reconnection rate estimates are then compared with the input variation to the model and the accuracy of the method assessed. Results are presented for steady-state reconnection, for continuous reconnection showing a sine-wave variation in rate and for reconnection which only occurs in square wave pulses. It is found that the method always yields the total flux reconnected (per unit length of the open-closed field-line boundary) to within an accuracy of better than 5%, but that pulses tend to be smoothed so that the peak reconnection rate within the pulse is underestimated and the pulse length is overestimated. This smoothing is reduced if the separation between energy channels of the instrument is reduced; however this also acts to increase the experimental uncertainty in the estimates, an effect which can be countered by improving the time resolution of the observations. The limited time resolution of the data is shown to set a minimum reconnection rate below which the method gives spurious short-period oscillations about the true value. Various examples of reconnection rate variations derived from cusp observations are discussed in the light of this analysis.

Global analysis of radiative forcing from fire-induced shortwave albedo change

Land surface albedo, a key parameter to derive Earth's surface energy balance, is used in the parameterization of numerical weather prediction, climate monitoring and climate change impact assessments. Changes in albedo due to fire have not been fully investigated on a continental and global scale. The main goal of this study, therefore, is to quantify the changes in instantaneous shortwave albedo produced by biomass burning activities and their associated radiative forcing. The study relies on the MODerate-resolution Imaging Spectroradiometer (MODIS) MCD64A1 burned-area product to create an annual composite of areas affected by fire and the MCD43C2 bidirectional reflectance distribution function (BRDF) albedo snow-free product to compute a bihemispherical reflectance time series. The approximate day of burning is used to calculate the instantaneous change in shortwave albedo. Using the corresponding National Centers for Environmental Prediction (NCEP) monthly mean downward solar radiation flux at the surface, the global radiative forcing associated with fire was computed. The analysis reveals a mean decrease in shortwave albedo of −0.014 (1σ = 0.017), causing a mean positive radiative forcing of 3.99 Wm−2 (1σ = 4.89) over the 2002–20012 time period in areas affected by fire. The greatest drop in mean shortwave albedo change occurs in 2002, which corresponds to the highest total area burned (378 Mha) observed in the same year and produces the highest mean radiative forcing (4.5 Wm−2). Africa is the main contributor in terms of burned area, but forests globally give the highest radiative forcing per unit area and thus give detectable changes in shortwave albedo. The global mean radiative forcing for the whole period studied (~0.0275 Wm−2) shows that the contribution of fires to the Earth system is not insignificant.

Metabolic theory predicts whole-ecosystem properties

Understanding the effects of individual organisms on material cycles and energy fluxes within ecosystems is central to predicting the impacts of human-caused changes on climate, land use, and biodiversity. Here we present a theory that integrates metabolic (organism-based bottom-up) and systems (ecosystem-based top-down) approaches to characterize how the metabolism of individuals affects the flows and stores of materials and energy in ecosystems. The theory predicts how the average residence time of carbon molecules, total system throughflow (TST), and amount of recycling vary with the body size and temperature of the organisms and with trophic organization. We evaluate the theory by comparing theoretical predictions with outputs of numerical models designed to simulate diverse ecosystem types and with empirical data for real ecosystems. Although residence times within different ecosystems vary by orders of magnitude—from weeks in warm pelagic oceans with minute phytoplankton producers to centuries in cold forests with large tree producers—as predicted, all ecosystems fall along a single line: residence time increases linearly with slope = 1.0 with the ratio of whole-ecosystem biomass to primary productivity (B/P). TST was affected predominantly by primary productivity and recycling by the transfer of energy from microbial decomposers to animal consumers. The theory provides a robust basis for estimating the flux and storage of energy, carbon, and other materials in terrestrial, marine, and freshwater ecosystems and for quantifying the roles of different kinds of organisms and environments at scales from local ecosystems to the biosphere.

Climate versus carbon dioxide controls on biomass burning: a model analysis of the glacial–interglacial contrast

Climate controls fire regimes through its influence on the amount and types of fuel present and their dryness. CO2 concentration constrains primary production by limiting photosynthetic activity in plants. However, although fuel accumulation depends on biomass production, and hence on CO2 concentration, the quantitative relationship between atmospheric CO2 concentration and biomass burning is not well understood. Here a fire-enabled dynamic global vegetation model (the Land surface Processes and eXchanges model, LPX) is used to attribute glacial–interglacial changes in biomass burning to an increase in CO2, which would be expected to increase primary production and therefore fuel loads even in the absence of climate change, vs. climate change effects. Four general circulation models provided last glacial maximum (LGM) climate anomalies – that is, differences from the pre-industrial (PI) control climate – from the Palaeoclimate Modelling Intercomparison Project Phase~2, allowing the construction of four scenarios for LGM climate. Modelled carbon fluxes from biomass burning were corrected for the model's observed prediction biases in contemporary regional average values for biomes. With LGM climate and low CO2 (185 ppm) effects included, the modelled global flux at the LGM was in the range of 1.0–1.4 Pg C year-1, about a third less than that modelled for PI time. LGM climate with pre-industrial CO2 (280 ppm) yielded unrealistic results, with global biomass burning fluxes similar to or even greater than in the pre-industrial climate. It is inferred that a substantial part of the increase in biomass burning after the LGM must be attributed to the effect of increasing CO2 concentration on primary production and fuel load. Today, by analogy, both rising CO2 and global warming must be considered as risk factors for increasing biomass burning. Both effects need to be included in models to project future fire risks.

A Posteriori analysis of discontinuous Galerkin schemes for systems of hyperbolic conservation laws

In this work we construct reliable a posteriori estimates for some semi- (spatially) discrete discontinuous Galerkin schemes applied to nonlinear systems of hyperbolic conservation laws. We make use of appropriate reconstructions of the discrete solution together with the relative entropy stability framework, which leads to error control in the case of smooth solutions. The methodology we use is quite general and allows for a posteriori control of discontinuous Galerkin schemes with standard flux choices which appear in the approximation of conservation laws. In addition to the analysis, we conduct some numerical benchmarking to test the robustness of the resultant estimator.

Using Distributed Temperature Sensing to monitor field scale dynamics of ground surface temperature and related substrate heat flux

We present one of the first studies of the use of Distributed Temperature Sensing (DTS) along fibre-optic cables to purposely monitor spatial and temporal variations in ground surface temperature (GST) and soil temperature, and provide an estimate of the heat flux at the base of the canopy layer and in the soil. Our field site was at a groundwater-fed wet meadow in the Netherlands covered by a canopy layer (between 0-0.5 m thickness) consisting of grass and sedges. At this site, we ran a single cable across the surface in parallel 40 m sections spaced by 2 m, to create a 40×40 m monitoring field for GST. We also buried a short length (≈10 m) of cable to depth of 0.1±0.02 m to measure soil temperature. We monitored the temperature along the entire cable continuously over a two-day period and captured the diurnal course of GST, and how it was affected by rainfall and canopy structure. The diurnal GST range, as observed by the DTS system, varied between 20.94 and 35.08◦C; precipitation events acted to suppress the range of GST. The spatial distribution of GST correlated with canopy vegetation height during both day and night. Using estimates of thermal inertia, combined with a harmonic analysis of GST and soil temperature, substrate and soil-heat fluxes were determined. Our observations demonstrate how the use of DTS shows great promise in better characterising area-average substrate/soil heat flux, their spatiotemporal variability, and how this variability is affected by canopy structure. The DTS system is able to provide a much richer data set than could be obtained from point temperature sensors. Furthermore, substrate heat fluxes derived from GST measurements may be able to provide improved closure of the land surface energy balance in micrometeorological field studies. This will enhance our understanding of how hydrometeorological processes interact with near-surface heat fluxes.

Proper evaluation of the external convective heat transfer for the thermal analysis of cool roofs

Cool materials are characterized by high solar reflectance and high thermal emittance; when applied to the external surface of a roof, they make it possible to limit the amount of solar irradiance absorbed by the roof, and to increase the rate of heat flux emitted by irradiation to the environment, especially during nighttime. However, a roof also releases heat by convection on its external surface; this mechanism is not negligible, and an incorrect evaluation of its entity might introduce significant inaccuracy in the assessment of the thermal performance of a cool roof, in terms of surface temperature and rate of heat flux transferred to the indoors. This issue is particularly relevant in numerical simulations, which are essential in the design stage, therefore it deserves adequate attention. In the present paper, a review of the most common algorithms used for the calculation of the convective heat transfer coefficient due to wind on horizontal building surfaces is presented. Then, with reference to a case study in Italy, the simulated results are compared to the outcomes of a measurement campaign. Hence, the most appropriate algorithms for the convective coefficient are identified, and the errors deriving by an incorrect selection of this coefficient are discussed.

Improvement and sensitivity analysis of thermal thin-ice thickness retrievals

Considering the sea ice decline in the Arctic during the last decades, polynyas are of high research interest since these features are core areas of new ice formation. The determination of ice formation requires accurate retrieval of polynya area and thin-ice thickness (TIT) distribution within the polynya.We use an established energy balance model to derive TITs with MODIS ice surface temperatures (Ts) and NCEP/DOE Reanalysis II in the Laptev Sea for two winter seasons. Improvements of the algorithm mainly concern the implementation of an iterative approach to calculate the atmospheric flux components taking the atmospheric stratification into account. Furthermore, a sensitivity study is performed to analyze the errors of the ice thickness. The results are the following: 1) 2-m air temperatures (Ta) and Ts have the highest impact on the retrieved ice thickness; 2) an overestimation of Ta yields smaller ice thickness errors as an underestimation of Ta; 3) NCEP Ta shows often a warm bias; and 4) the mean absolute error for ice thicknesses up to 20 cm is ±4.7 cm. Based on these results, we conclude that, despite the shortcomings of the NCEP data (coarse spatial resolution and no polynyas), this data set is appropriate in combination with MODIS Ts for the retrieval of TITs up to 20 cm in the Laptev Sea region. The TIT algorithm can be applied to other polynya regions and to past and future time periods. Our TIT product is a valuable data set for verification of other model and remote sensing ice thickness data.

An analysis of the environmental energetics associated with the transition of the first South Atlantic hurricane

This study presents the first analysis of the energetics associated with a hybrid cyclone`s transition in the Southern Hemisphere, Hurricane Catarina ( March 2004). Catarina has earned a place in history as the first documented South Atlantic hurricane, but its unusual tropical transition is still poorly understood. Here we show that Catarina`s transition was preceded by marked environmental changes in the Lorenz energy cycle, with an abrupt shift from a baroclinic to a predominantly barotropic state. Such changes help to explain the unusual vortex`s growth until its transition was completed. Although the vortex`s energy flux is not explicitly calculated, a likely mechanism linking the environmental energetics with Catarina is the extraction of eddy kinetic energy from horizontal momentum and heat transfers within the through component of the blocking. The results advance the understanding of this rare event and suggest that the technique has a great potential to study transitioning systems in general.

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.

Profiling allergic asthma volatile metabolic patterns using a headspace-solid phase microextraction/gas chromatography based methodology

Allergicasthmarepresentsanimportantpublichealthissuewithsignificantgrowthovertheyears,especially in the paediatric population. Exhaled breath is a non-invasive, easily performed and rapid method forobtainingsamplesfromthelowerrespiratorytract.Inthepresentmanuscript,themetabolicvolatile profiles of allergic asthma and control children were evaluated by headspace solid-phase microextraction combined with gas chromatography–quadrupole mass spectrometry (HS-SPME/GC–qMS). The lack ofstudiesinbreathofallergicasthmaticchildrenbyHS-SPMEledtothedevelopmentofanexperimental design to optimize SPME parameters. To fulfil this objective, three important HS-SPME experimental parameters that influence the extraction efficiency, namely fibre coating, temperature and time extractions were considered. The selected conditions that promoted higher extraction efficiency corresponding to the higher GC peak areas and number of compounds were: DVB/CAR/PDMS coating fibre, 22◦C and 60min as the extraction temperature and time, respectively. The suitability of two containers, 1L Tedlar® bags and BIOVOC®, for breath collection and intra-individual variability were also investigated. The developed methodology was then applied to the analysis of children exhaled breath with allergicasthma(35),fromwhich13hadalsoallergicrhinitis,andhealthycontrolchildren(15),allowing to identify 44 volatiles distributed over the chemical families of alkanes (linear and ramified) ketones, aromatic hydrocarbons, aldehydes, acids, among others. Multivariate studies were performed by Partial LeastSquares–DiscriminantAnalysis(PLS–DA)usingasetof28selectedmetabolitesanddiscrimination between allergic asthma and control children was attained with a classification rate of 88%. The allergic asthma paediatric population was characterized mainly by the compounds linked to oxidative stress, such as alkanes and aldehydes. Furthermore, more detailed information was achieved combining the volatile metabolic data, suggested by PLS–DA model, and clinical data.

Analysis of the Priestley-Taylor alpha parameter for a bean crop

This work deals with the Priestley-Taylor model for evapotranspiration in different grown stages of a bean crop. Priestley and Taylor derived a practical Formulation for energy partitioning between the sensible and latent heat fluxes through the a parameter. Bowen ratio energy balance (BREB) was carried out for daily sensible and latent heat flux estimations in three different crop stages. Mean daily values of Priestley-Taylor a parameter were determined for eleven days during the crop cycle. Diurnal variation patterns of a are presented for the growing, flowering and graining periods. The mean values of 1.13 +/- 0.33, 1.26 +/- 0.74, 1.22 +/- 0.55 were obtained for a day in the growing, in the flowering and for graining periods, respectively. Eleven days values of a are shown and gave a mean value of 1.23 +/- 0.10 which agree on the reported literature.

Organic and inorganic sources of zinc, copper and selenium in diets for dairy cows: intake, blood metabolic profile, milk yield and composition

The present study was carried out with the objective of evaluating the effects of feeding dairy cows with organic or inorganic sources of zinc (Zn), copper (Cu) and selenium (Se) on blood concentrations of these minerals, blood metabolic profiles, nutrient intake and milk yield and composition. Nineteen Holstein cows were selected and randomly assigned to two groups for receiving organic (n = 9) or inorganic (n = 10) sources of Zn, Cu and Se from 60 days before the expected date of calving to 80 days of lactation. Samples of feed, orts and milk were collected for analysis. Body condition score (BCS) was determined and blood samples were collected for analysis of Zn, Cu and Se concentrations, as well as for metabolic profile. Supplying organic or inorganic sources of Zn, Cu, and Se did not affect dry matter and nutrient intake, blood metabolic profile, milk yield and composition, plasma concentration of these minerals, and BCS or change the BCS in cows from 60 days before the expected date of calving to 80 days of lactation. An effect of time was observed on all feed intake variables, plasma concentrations of Zn and Se, milk yield, milk protein content, BCS and change in BCS.

Xylella fastidiosa gene expression analysis by DNA microarrays

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Differential gene expression analysis of Paracoccidioides brasiliensis during keratinocyte infection

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)