A dynamic model of neurovascular coupling: Implications for blood vessel dilation and constriction

Neurovascular coupling in response to stimulation of the rat barrel cortex was investigated using concurrent multichannel electrophysiology and laser Doppler flowmetry. The data were used to build a linear dynamic model relating neural activity to blood flow. Local field potential time series were subject to current source density analysis, and the time series of a layer IV sink of the barrel cortex was used as the input to the model. The model output was the time series of the changes in regional cerebral blood flow (CBF). We show that this model can provide excellent fit of the CBF responses for stimulus durations of up to 16 s. The structure of the model consisted of two coupled components representing vascular dilation and constriction. The complex temporal characteristics of the CBF time series were reproduced by the relatively simple balance of these two components. We show that the impulse response obtained under the 16-s duration stimulation condition generalised to provide a good prediction to the data from the shorter duration stimulation conditions. Furthermore, by optimising three out of the total of nine model parameters, the variability in the data can be well accounted for over a wide range of stimulus conditions. By establishing linearity, classic system analysis methods can be used to generate and explore a range of equivalent model structures (e.g., feed-forward or feedback) to guide the experimental investigation of the control of vascular dilation and constriction following stimulation.

Controls on inorganic nitrogen leaching from Finnish catchments assessed using a sensitivity and uncertainty analysis of the INCA-N model

The semi-distributed, dynamic INCA-N model was used to simulate the behaviour of dissolved inorganic nitrogen (DIN) in two Finnish research catchments. Parameter sensitivity and model structural uncertainty were analysed using generalized sensitivity analysis. The Mustajoki catchment is a forested upstream catchment, while the Savijoki catchment represents intensively cultivated lowlands. In general, there were more influential parameters in Savijoki than Mustajoki. Model results were sensitive to N-transformation rates, vegetation dynamics, and soil and river hydrology. Values of the sensitive parameters were based on long-term measurements covering both warm and cold years. The highest measured DIN concentrations fell between minimum and maximum values estimated during the uncertainty analysis. The lowest measured concentrations fell outside these bounds, suggesting that some retention processes may be missing from the current model structure. The lowest concentrations occurred mainly during low flow periods; so effects on total loads were small.

Dynamic group communication for large-scale parallel data mining

Exascale systems are the next frontier in high-performance computing and are expected to deliver a performance of the order of 10^18 operations per second using massive multicore processors. Very large- and extreme-scale parallel systems pose critical algorithmic challenges, especially related to concurrency, locality and the need to avoid global communication patterns. This work investigates a novel protocol for dynamic group communication that can be used to remove the global communication requirement and to reduce the communication cost in parallel formulations of iterative data mining algorithms. The protocol is used to provide a communication-efficient parallel formulation of the k-means algorithm for cluster analysis. The approach is based on a collective communication operation for dynamic groups of processes and exploits non-uniform data distributions. Non-uniform data distributions can be either found in real-world distributed applications or induced by means of multidimensional binary search trees. The analysis of the proposed dynamic group communication protocol has shown that it does not introduce significant communication overhead. The parallel clustering algorithm has also been extended to accommodate an approximation error, which allows a further reduction of the communication costs. The effectiveness of the exact and approximate methods has been tested in a parallel computing system with 64 processors and in simulations with 1024 processing elements.

Dynamic hydrological modeling in drylands with TRMM based rainfall

This paper introduces and evaluates DryMOD, a dynamic water balance model of the key hydrological process in drylands that is based on free, public-domain datasets. The rainfall model of DryMOD makes optimal use of spatially disaggregated Tropical Rainfall Measuring Mission (TRMM) datasets to simulate hourly rainfall intensities at a spatial resolution of 1-km. Regional-scale applications of the model in seasonal catchments in Tunisia and Senegal characterize runoff and soil moisture distribution and dynamics in response to varying rainfall data inputs and soil properties. The results highlight the need for hourly-based rainfall simulation and for correcting TRMM 3B42 rainfall intensities for the fractional cover of rainfall (FCR). Without FCR correction and disaggregation to 1 km, TRMM 3B42 based rainfall intensities are too low to generate surface runoff and to induce substantial changes to soil moisture storage. The outcomes from the sensitivity analysis show that topsoil porosity is the most important soil property for simulation of runoff and soil moisture. Thus, we demonstrate the benefit of hydrological investigations at a scale, for which reliable information on soil profile characteristics exists and which is sufficiently fine to account for the heterogeneities of these. Where such information is available, application of DryMOD can assist in the spatial and temporal planning of water harvesting according to runoff-generating areas and the runoff ratio, as well as in the optimization of agricultural activities based on realistic representation of soil moisture conditions.

An enhanced model for small-signal analysis of the phase-shifted full-bridge converter

This paper presents an in-depth critical discussion and derivation of a detailed small-signal analysis of the Phase-Shifted Full-Bridge (PSFB) converter. Circuit parasitics, resonant inductance and transformer turns ratio have all been taken into account in the evaluation of this topology’s open-loop control-to-output, line-to-output and load-to-output transfer functions. Accordingly, the significant impact of losses and resonant inductance on the converter’s transfer functions is highlighted. The enhanced dynamic model proposed in this paper enables the correct design of the converter compensator, including the effect of parasitics on the dynamic behavior of the PSFB converter. Detailed experimental results for a real-life 36V-to-14V/10A PSFB industrial application show excellent agreement with the predictions from the model proposed herein.1

A model analysis of climate and CO2 controls on tree growth in a semi-arid woodland

We used a light-use efficiency model of photosynthesis coupled with a dynamic carbon allocation and tree-growth model to simulate annual growth of the gymnosperm Callitris columellaris in the semi-arid Great Western Woodlands, Western Australia, over the past 100 years. Parameter values were derived from independent observations except for sapwood specific respiration rate, fine-root turnover time, fine-root specific respiration rate and the ratio of fine-root mass to foliage area, which were estimated by Bayesian optimization. The model reproduced the general pattern of interannual variability in radial growth (tree-ring width), including the response to the shift in precipitation regimes that occurred in the 1960s. Simulated and observed responses to climate were consistent. Both showed a significant positive response of tree-ring width to total photosynthetically active radiation received and to the ratio of modeled actual to equilibrium evapotranspiration, and a significant negative response to vapour pressure deficit. However, the simulations showed an enhancement of radial growth in response to increasing atmospheric CO2 concentration (ppm) ([CO2]) during recent decades that is not present in the observations. The discrepancy disappeared when the model was recalibrated on successive 30-year windows. Then the ratio of fine-root mass to foliage area increases by 14% (from 0.127 to 0.144 kg C m-2) as [CO2] increased while the other three estimated parameters remained constant. The absence of a signal of increasing [CO2] has been noted in many tree-ring records, despite the enhancement of photosynthetic rates and water-use efficiency resulting from increasing [CO2]. Our simulations suggest that this behaviour could be explained as a consequence of a shift towards below-ground carbon allocation.

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.

Modelling spectral reflectance of open cork oak woodland: a simulation analysis of the effects of vegetation structure and background

This study analyses the influence of vegetation structure (i.e. leaf area index and canopy cover) and seasonal background changes on moderate-resolution imaging spectrometer (MODIS)-simulated reflectance data in open woodland. Approximately monthly spectral reflectance and transmittance field measurements (May 2011 to October 2013) of cork oak tree leaves (Quercus suber) and of the herbaceous understorey were recorded in the region of Ribatejo, Portugal. The geometric-optical and radiative transfer (GORT) model was used to simulate MODIS response (red, near-infrared) and to calculate vegetation indices, investigating their response to changes in the structure of the overstorey vegetation and to seasonal changes in the understorey using scenarios corresponding to contrasting phenological status (dry season vs. wet season). The performance of normalized difference vegetation index (NDVI), soil-adjusted vegetation index (SAVI), and enhanced vegetation index (EVI) is discussed. Results showed that SAVI and EVI were very sensitive to the emergence of background vegetation in the wet season compared to NDVI and that shading effects lead to an opposing trend in the vegetation indices. The information provided by this research can be useful to improve our understanding of the temporal dynamic of vegetation, monitored by vegetation indices.

The role of CO2 and dynamic vegetation on the impact of temperate land use change in the HadCM3 coupled climate model

Human induced land-use change (LUC) alters the biogeophysical characteristics of the land surface influencing the surface energy balance. The level of atmospheric CO2 is expected to increase in the coming century and beyond, modifying temperature and precipitation patterns and altering the distribution and physiology of natural vegetation. It is important to constrain how CO2-induced climate and vegetation change may influence the regional extent to which LUC alters climate. This sensitivity study uses the HadCM3 coupled climate model under a range of equilibrium forcings to show that the impact of LUC declines under increasing atmospheric CO2, specifically in temperate and boreal regions. A surface energy balance analysis is used to diagnose how these changes occur. In Northern Hemisphere winter this pattern is attributed in part to the decline in winter snow cover and in the summer due to a reduction in latent cooling with higher levels of CO2. The CO2-induced change in natural vegetation distribution is also shown to play a significant role. Simulations run at elevated CO2 yet present day vegetation show a significantly increased sensitivity to LUC, driven in part by an increase in latent cooling. This study shows that modelling the impact of LUC needs to accurately simulate CO2 driven changes in precipitation and snowfall, and incorporate accurate, dynamic vegetation distribution.

Dynamic picture of the inner asteroid belt: implications for the density, size and taxonomic distributions of real objects

In this paper, we construct a dynamic portrait of the inner asteroidal belt. We use information about the distribution of test particles, which were initially placed on a perfectly rectangular grid of initial conditions, after 4.2 Myr of gravitational interactions with the Sun and five planets, from Mars to Neptune. Using the spectral analysis method introduced by Michtchenko et al., the asteroidal behaviour is illustrated in detail on the dynamical, averaged and frequency maps. On the averaged and frequency maps, we superpose information on the proper elements and proper frequencies of real objects, extracted from the data base, AstDyS, constructed by Milani and Knezevic. A comparison of the maps with the distribution of real objects allows us to detect possible dynamical mechanisms acting in the domain under study; these mechanisms are related to mean-motion and secular resonances. We note that the two- and three-body mean-motion resonances and the secular resonances (strong linear and weaker non-linear) have an important role in the diffusive transportation of the objects. Their long-lasting action, overlaid with the Yarkovsky effect, may explain many observed features of the density, size and taxonomic distributions of the asteroids.

Dynamic portrait of the planetary 2/1 mean-motion resonance - II. Systems with a more massive inner planet

This paper presents the second part in our study of the global structure of the planar phase space of the planetary three-body problem, when both planets lie in the vicinity of a 2/1 mean-motion resonance. While Paper I was devoted to cases where the outer planet is the more massive body, the present work is devoted to the cases where the more massive body is the inner planet. As before, outside the well-known Apsidal Corotation Resonances (ACR), the phase space shows a complex picture marked by the presence of several distinct regimes of resonant and non-resonant motion, crossed by families of periodic orbits and separated by chaotic zones. When the chosen values of the integrals of motion lead to symmetric ACR, the global dynamics are generally similar to the structure presented in Paper I. However, for asymmetric ACR the resonant phase space is strikingly different and shows a galore of distinct dynamical states. This structure is shown with the help of dynamical maps constructed on two different representative planes, one centred on the unstable symmetric ACR and the other on the stable asymmetric equilibrium solution. Although the study described in the work may be applied to any mass ratio, we present a detailed analysis for mass values similar to the Jupiter-Saturn case. Results give a global view of the different dynamical states available to resonant planets with these characteristics. Some of these dynamical paths could have marked the evolution of the giant planets of our Solar system, assuming they suffered a temporary capture in the 2/1 resonance during the latest stages of the formation of our Solar system.

The R2 mobile element of Rhynchosciara americana: Molecular, cytological and dynamic aspects

Ribosomal RNA genes are encoded by large units clustered (18S, 5S, and 28S) in the nucleolar organizer region in several organisms. Sometimes additional insertions are present in the coding region for the 28S rDNA. These insertions are specific non-long terminal repeat retrotransposons that have very restricted integration targets within the genome. The retrotransposon present in the genome of Rhynchosciara americana, RaR2, was isolated by the screening of a genomic library. Sequence analysis showed the presence of conserved regions, such as a reverse transcriptase domain and a zinc finger motif in the amino terminal region. The insertion site was highly conserved in R. americana and a phylogenetic analysis showed that this element belongs to the R2 clade. The chromosomal localization confirmed that the RaR2 mobile element was inserted into a specific site in the rDNA gene. The expression level of RaR2 in salivary glands during larval development was determined by quantitative RT-PCR, and the increase of relative expression in the 3P of the fourth instar larval could be related to intense gene activity characteristic of this stage. 5`-Truncated elements were identified in different DNA samples. Additionally, in three other Rhynchosciara species, the R2 element was present as a full-length element.

A complex network-based approach for boundary shape analysis

This paper introduces a novel methodology to shape boundary characterization, where a shape is modeled into a small-world complex network. It uses degree and joint degree measurements in a dynamic evolution network to compose a set of shape descriptors. The proposed shape characterization method has all efficient power of shape characterization, it is robust, noise tolerant, scale invariant and rotation invariant. A leaf plant classification experiment is presented on three image databases in order to evaluate the method and compare it with other descriptors in the literature (Fourier descriptors, Curvature, Zernike moments and multiscale fractal dimension). (C) 2008 Elsevier Ltd. All rights reserved.

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Useful Strategies for Algal Volatile Analysis

The production of volatile organic compounds (VOC) by plants is well known. However, few scientific groups have studied VOC produced by green, brown and red algae. Headspace collection of volatiles and solid phase microextraction, as well as the traditional extraction by hydrodistillation combined with analytical chromatographic techniques (i.e., GC-MS), have significantly improved the investigation of VOC from plants and algae. The major volatile compounds found in seaweeds are hydrocarbons, terpenes, phenols, alcohols, aldehydes, ketones, esters, fatty acids and halogen or sulfur-containing compounds. This article presents an overview of VOC isolated from and identified in marine macro-algae. Focus is given to non-halogenated and non-sulfur volatile compounds, as well as strategies to analyze and identify algal VOC by GC-MS.