Electrostatic shock dynamics in superthermal plasmas

The propagation of ion acoustic shocks in nonthermal plasmas is investigated, both analytically and numerically. An unmagnetized collisionless electron-ion plasma is considered, featuring a superthermal (non-Maxwellian) electron distribution, which is modeled by a ?-(kappa) distribution function. Adopting a multiscale approach, it is shown that the dynamics of low-amplitude shocks is modeled by a hybrid Korteweg-de Vries-Burgers (KdVB) equation, in which the nonlinear and dispersion coefficients are functions of the ? parameter, while the dissipative coefficient is a linear function of the ion viscosity. All relevant shock parameters are shown to depend on ?: higher deviations from a pure Maxwellian behavior induce shocks which are narrower, faster, and of larger amplitude. The stability profile of the kink-shaped solutions of the KdVB equation against external perturbations is investigated. The spatial profile of the shocks is found to depend upon the dispersion and the dissipation term, and the role of the interplay between dispersion and dissipation is elucidated.

Nonlinear Modulated Envelope Electrostatic Wavepacket Propagation in Plasmas

A brief review of the occurrence of amplitude modulated structures in space and laboratory plasmas is provided, followed by a theoretical analysis of the mechanism of carrier wave (self-) interaction, with respect to electrostatic plasma modes. A generic collisionless unmagnetized fluid model is employed. Both cold-(zero-temperature) and warm-(finite temperature) fluid descriptions are considered and compared. The weakly nonlinear oscillation regime is investigated by applying a multiple scale (reductive perturbation) technique and a Nonlinear Schrödinger Equation (NLSE) is obtained, describing the evolution of the slowly varying wave amplitude in time and space. The amplitude’s stability profile reveals the possibility of modulational instability to occur under the influence of external perturbations. The NLSE admits exact localized envelope (solitary wave) solutions of bright (pulses) or dark (holes, voids) type, whose characteristics depend on intrinsic plasma parameters. The role of perturbation obliqueness (with respect to the propagation direction), finite temperature and — possibly — defect (dust) concentration is explicitly considered. The relevance of this description with respect to known electron-ion (e-i) as well as dusty (complex) plasma modes is briefly discussed. © 2004 American Institute of Physics

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Proteomic analysis of colorectal cancer metastasis:stathmin-1 revealed as a player in cancer cell migration and prognostic marker

Metastasis accounts largely for the high mortality rate of colorectal cancer (CRC) patients. In this study, we performed comparative proteome analysis of primary CRC cell lines HCT-116 and its metastatic derivative E1 using 2-D DIGE. We identified 74 differentially expressed proteins, many of which function in transcription, translation, angiogenesis signal transduction, or cytoskeletal remodeling pathways, which are indispensable cellular processes involved in the metastatic cascade. Among these proteins, stathmin-1 (STMN1) was found to be highly up-regulated in E1 as compared to HCT-116 and was thus selected for further functional studies. Our results showed that perturbations in STMN1 levels resulted in significant changes in cell migration, invasion, adhesion, and colony formation. We further showed that the differential expression of STMN1 correlated with the cells' metastatic potential in other paradigms of CRC models. Using immunohistochemistry, we also showed that STMN1 was highly expressed in colorectal primary tumors and metastatic tissues as compared to the adjacent normal colorectal tissues. Furthermore, we also showed via tissue microarray analyses of 324 CRC tissues and Kaplan-Meier survival plot that CRC patients with higher expression of STMN1 have poorer prognosis.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

Antioxidants and diabetic retinopathy

The biochemical perturbations in diabetes mellitus (DM) create the conditions for the production of free radicals, the consequence of which is increased oxidative stress. Evidence has accrued over the past 2 decades that suggests that oxidative stress is an important pathogenetic factor in the development of diabetic retinopathy (DR). Experimental data show that the use of strategies that ameliorate oxidative stress can prevent and retard the development of DR in the animal model. Clinical observations also suggest that reducing oxidative stress may help to reverse pathological manifestations of DR. The present article constitutes an examination of the role of antioxidants in the management of DR and the current state of clinically relevant knowledge. © 2013 Springer Science+Business Media New York.

Determination of Power System Response during Small Load Fluctuations

This paper proposes a calculation method to determine power system response during small load perturbations or minor disturbances. The method establishes the initial value of active power transient using traditional reduction technique on admittance matrix, which incorporates voltage variations in the determination. The method examines active power distribution among generators when several loads simultaneously change, and verifies that the superposition principle is applicable for this scenario. The theoretical derivation provided in the paper is validated by numerical simulations using a 3-generator 9-bus benchmark model. The results indicate that the inclusion of voltage variation renders an independent and precise measure of active power response during transient conditions.

Habitat Isolation Reduces the Temporal Stability of Island Ecosystems in the Face of Flood Disturbance

Natural ecosystems are increasingly exposed to multiple anthropogenic stressors, including land-use change, deforestation, agricultural intensification, and urbanisation, all of which have led to widespread habitat fragmentation, which is also likely to be amplified further by predicted climate change. The potential interactive effects of these different stressors cannot be determined by studying each in isolation, although such synergies have been largely ignored in ecological field studies to date. Here, we use a model system of naturally fragmented islands in a braided river network, which is exposed to periodic inundation, to investigate the interactive effects of habitat isolation and flood disturbance. Food web structure was similar across the islands during periods of hydrological stability, but several key properties were altered in the aftermath of flood disturbance, based on distance of the islands from the regional source pool of species: taxon richness and mean food chain length declined with habitat isolation after flooding, while the proportion of basal species increased. Greater species turnover through time reflected the slower process of re-colonisation on the more distant islands following disturbance. Increased variability of several food web properties over a 1-year period highlighted the reduced temporal stability of isolated habitat fragments. Many of these effects reflected the differential successes of predator and prey species at re-colonising the islands: even though larger, more mobile consumers may reach the more distant islands first, they cannot establish populations until the lower trophic levels have successfully reassembled. These results highlight the susceptibility of fragmented ecosystems to environmental perturbations. © 2013 Elsevier Ltd.

Consensus in organizations:Hunting for the social choice conundrum in APA elections

According to the axiomatic literature on consensus methods, the best collective choice by one method of preference aggregation can easily be the worst by another. Are award committees, electorates, managers, online retailers, and web-based recommender systems stuck with an impossibility of rational preference aggregation? We investigate this social choice conundrum for seven social choice methods: Condorcet, Borda, Plurality, Antiplurality, the Single Transferable Vote, Coombs, and Plurality Runoff. We rely on Monte Carlo simulations for theoretical results and on twelve ballot datasets from American Psychological Association (APA) presidential elections for empirical results. Each of these elections provides partial rankings of five candidates from about 13,000 to about 20,000 voters. APA preferences are neither domain-restricted nor generated by an Impartial Culture. We find virtually no trace of a Condorcet paradox. In direct contrast with the classical social choice conundrum, competing consensus methods agree remarkably well, especially on the overall best and worst options. The agreement is also robust under perturbations of the preference prole via resampling, even in relatively small pseudosamples. We also explore prescriptive implications of our findings.

Spatial and Temporal Changes in Soil Organic Carbon Assessment using an Integrated Geostatistical and Compositional Data Analysis Approach

The Irish and UK governments, along with other countries, have made a commitment to limit the concentrations of greenhouse gases in the atmosphere by reducing emissions from the burning of fossil fuels. This can be achieved (in part) through increasing the sequestration of CO2 from the atmosphere including monitoring the amount stored in vegetation and soils. A large proportion of soil carbon is held within peat due to the relatively high carbon density of peat and organic-rich soils. This is particularly important for a country such as Ireland, where some 16% of the land surface is covered by peat. For Northern Ireland, it has been estimated that the total amount of carbon stored in vegetation is 4.4Mt compared to 386Mt stored within peat and soils. As a result it has become increasingly important to measure and monitor changes in stores of carbon in soils. The conservation and restoration of peat covered areas, although ongoing for many years, has become increasingly important. This is summed up in current EU policy outlined by the European Commission (2012) which seeks to assess the relative contributions of the different inputs and outputs of organic carbon and organic matter to and from soil. Results are presented from the EU-funded Tellus Border Soil Carbon Project (2011 to 2013) which aimed to improve current estimates of carbon in soil and peat across Northern Ireland and the bordering counties of the Republic of Ireland.
Historical reports and previous surveys provide baseline data. To monitor change in peat depth and soil organic carbon, these historical data are integrated with more recently acquired airborne geophysical (radiometric) data and ground-based geochemical data generated by two surveys, the Tellus Project (2004-2007: covering Northern Ireland) and the EU-funded Tellus Border project (2011-2013) covering the six bordering counties of the Republic of Ireland, Donegal, Sligo, Leitrim, Cavan, Monaghan and Louth. The concept being applied is that saturated organic-rich soil and peat attenuate gamma-radiation from underlying soils and rocks. This research uses the degree of spatial correlation (coregionalization) between peat depth, soil organic carbon (SOC) and the attenuation of the radiometric signal to update a limited sampling regime of ground-based measurements with remotely acquired data. To comply with the compositional nature of the SOC data (perturbations of loss on ignition [LOI] data), a compositional data analysis approach is investigated. Contemporaneous ground-based measurements allow corroboration for the updated mapped outputs. This provides a methodology that can be used to improve estimates of soil carbon with minimal impact to sensitive habitats (like peat bogs), but with maximum output of data and knowledge.

Impact of geometric variations on delivered dose in highly focused single vocal cord IMRT

Purpose. To investigate the robustness of single vocal cord intensity modulated radiation therapy (IMRT) treatment plans for set-up errors, respiration, and deformation. Material and methods. Four-dimensional computed tomography (4D-CT) scans of 10 early glottic carcinoma patients, previously treated with conventional techniques, were used in this simulation study. For each patient a pre-treatment 4D-CT was used for IMRT planning, generating a reference dose distribution. Prescribed PTV dose was 66 Gy. The impact of systematic set-up errors was simulated by applying shifts of ± 2 mm to the planning CT scans, followed by dose re-calculation with original beam segments, MUs, etc. Effects of respiration and deformation were determined utilizing extreme inhale and exhale CT scans, and repeat scans acquired after 22 Gy, 44 Gy, and 66 Gy, respectively. All doses were calculated using Monte Carlo dose simulations. Results. Considering all investigated geometrical perturbations, reductions in the clinical target volume (CTV) V95%, D98%, D2%, and generalized equivalent uniform dose (gEUD) were limited to 1.2 ± 2.2%, 2.4 ± 2.9%, 0.2 ± 1.8%, and 0.6 ± 1.1 Gy, respectively. The near minimum dose, D98%, was always higher than 89%, and gEUD always remained higher than 66 Gy. Planned contra-lateral (CL) vocal cord DMean, gEUD, and V40 Gy were 38.2 ± 6.0 Gy, 43.4 ± 5.6 Gy, and 42.7 ± 14.9%. With perturbations these values changed by -0.1 ± 4.3 Gy, 0.1 ± 4.0 Gy, and -1.0 ± 9.6%, respectively. Conclusions. On average, CTV dose reductions due to geometrical perturbations were very low, and sparing of the CL vocal cord was maintained. In a few observations (6 of 103 simulated situations), the near-minimum CTV-dose was around 90%, requiring attention in deciding on a future clinical protocol. 

Global Sensitivity Analysis for MAP Inference in Graphical Models

We study the sensitivity of a MAP configuration of a discrete probabilistic graphical model with respect to perturbations of its parameters. These perturbations are global, in the sense that simultaneous perturbations of all the parameters (or any chosen subset of them) are allowed. Our main contribution is an exact algorithm that can check whether the MAP configuration is robust with respect to given perturbations. Its complexity is essentially the same as that of obtaining the MAP configuration itself, so it can be promptly used with minimal effort. We use our algorithm to identify the largest global perturbation that does not induce a change in the MAP configuration, and we successfully apply this robustness measure in two practical scenarios: the prediction of facial action units with posed images and the classification of multiple real public data sets. A strong correlation between the proposed robustness measure and accuracy is verified in both scenarios.

Modeling relativistic soliton interactions in overdense plasmas: A perturbed nonlinear Schrodinger equation framework

We investigate the dynamics of localized solutions of the relativistic cold-fluid plasma model in the small but finite amplitude limit, for slightly overcritical plasma density. Adopting a multiple scale analysis, we derive a perturbed nonlinear Schrodinger equation that describes the evolution of the envelope of circularly polarized electromagnetic field. Retaining terms up to fifth order in the small perturbation parameter, we derive a self-consistent framework for the description of the plasma response in the presence of localized electromagnetic field. The formalism is applied to standing electromagnetic soliton interactions and the results are validated by simulations of the full cold-fluid model. To lowest order, a cubic nonlinear Schrodinger equation with a focusing nonlinearity is recovered. Classical quasiparticle theory is used to obtain analytical estimates for the collision time and minimum distance of approach between solitons. For larger soliton amplitudes the inclusion of the fifth-order terms is essential for a qualitatively correct description of soliton interactions. The defocusing quintic nonlinearity leads to inelastic soliton collisions, while bound states of solitons do not persist under perturbations in the initial phase or amplitude

Pressure anisotropy effects on nonlinear electrostatic excitations in magnetized electron-positron-ion plasmas

The propagation of linear and nonlinear electrostatic waves is investigated in a magnetized anisotropic electron-positron-ion (e-p-i) plasma with superthermal electrons and positrons. A two-dimensional plasma geometry is assumed. The ions are assumed to be warm and anisotropic due to an external magnetic field. The anisotropic ion pressure is defined using the double adiabatic Chew-Golberger-Low (CGL) theory. In the linear regime, two normal modes are predicted, whose characteristics are investigated parametrically, focusing on the effect of superthermality of electrons and positrons, ion pressure anisotropy, positron concentration and magnetic field strength. A Zakharov-Kuznetsov (ZK) type equation is derived for the electrostatic potential (disturbance) via a reductive perturbation method. The parametric role of superthermality, positron content, ion pressure anisotropy and magnetic field strength on the characteristics of solitary wave structures is investigated. Following Allen and Rowlands [J. Plasma Phys. 53, 63 (1995)], we have shown that the pulse soliton solution of the ZK equation is unstable to oblique perturbations, and have analytically traced the dependence of the instability growth rate on superthermality and ion pressure anisotropy.

Grazing under experimental hypercapnia and elevated temperature does not affect the radula of a chiton (Mollusca, Polyplacophora, Lepidopleurida)

Chitons (class Polyplacophora) are benthic grazing molluscs with an eight-part aragonitic shell armature. The radula, a serial tooth ribbon that extends internally more than half the length of the body, is mineralised on the active feeding teeth with iron magnetite apparently as an adaptation to constant grazing on rocky substrates. As the anterior feeding teeth are eroded they are shed and replaced with a new row. The efficient mineralisation and function of the radula could hypothetically be affected by changing oceans in two ways: changes in seawater chemistry (pH and pCO(2)) may impact the biomineralisation pathway, potentially leading to a weaker or altered density of the feeding teeth; rising temperatures could increase activity levels in these ectothermic animals, and higher feeding rates could increase wear on the feeding teeth beyond the animals' ability to synthesise, mineralise, and replace radular rows. We therefore examined the effects of pH and temperature on growth and integrity in the radula of the chiton Leptochiton asellus. Our experiment implemented three temperature (similar to 10, 15, 20 degrees C) and two pCO(2) treatments (similar to 400 mu atm, pH 8.0; similar to 2000 mu atm, pH 7.5) for six treatment groups. Animals (n = 50) were acclimated to the treatment conditions for a period of 4 weeks. This is sufficient time for growth of ca. 7-9 new tooth rows or 20% turnover of the mineralised portion. There was no significant difference in the number of new (non-mineralised) teeth or total tooth row count in any treatment. Examination of the radulae via SEM revealed no differences in microwear or breakage on the feeding cusps correlating to treatment groups. The shell valves also showed no signs of dissolution. As a lineage, chitons have survived repeated shifts in Earth's climate through geological time, and at least their radulae may be robust to future perturbations.