Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises

This is a demonstration of how electrical models can be used to characterize biological membranes. This exercise also introduces biophysical terminology used in electrophysiology. The same equipment is used in the membrane model as on live preparations. Some properties of an isolated nerve cord are investigated: nerve action potentials, recruitment of neurons, and responsiveness of the nerve cord to environmental factors

Use of Bayesian inference for parameter recovery in DC and AC voltammetry

We describe the use of Bayesian inference for quantitative comparison of voltammetric methods for investigating electrode kinetics. We illustrate the utility of the approach by comparing the information content in both DC and AC voltammetry at a planar electrode for the case of a quasi-reversible one electron reaction mechanism. Using synthetic data (i. e. simulated data based on Butler-Volmer electrode kinetics for which the true parameter values are known and to which realistic levels of simulated experimental noise have been added), we are able to show that AC voltammetry is less affected by experimental noise (so that in effect it has a greater information content then the corresponding DC measurement) and hence yields more accurate estimates of the experimental parameters for a given level of noise. Significantly, the AC approach is shown to be able to distinguish higher values of the rate constant. The results of using synthetic data are then confirmed for an illustrative case of experimental data for the [Fe(CN)6]3−/4−process

Subglacial roughness of the Greenland Ice Sheet: relationship with contemporary ice velocity and geology

The subglacial environment of the Greenland Ice Sheet (GrIS) is poorly constrained both in its bulk properties, for example geology, the presence of sediment, and the presence of water, and interfacial conditions, such as roughness and bed rheology. There is, therefore, limited understanding of how spatially heterogeneous subglacial properties relate to ice-sheet motion. Here, via analysis of 2 decades of radio-echo sounding data, we present a new systematic analysis of subglacial roughness beneath the GrIS. We use two independent methods to quantify subglacial roughness: first, the variability in along-track topography – enabling an assessment of roughness anisotropy from pairs of orthogonal transects aligned perpendicular and parallel to ice flow and, second, from bed-echo scattering – enabling assessment of fine-scale bed characteristics. We establish the spatial distribution of subglacial roughness and quantify its relationship with ice flow speed and direction. Overall, the beds of fast-flowing regions are observed to be rougher than the slow-flowing interior. Topographic roughness exhibits an exponential scaling relationship with ice surface velocity parallel, but not perpendicular, to flow direction in fast-flowing regions, and the degree of anisotropy is correlated with ice surface speed. In many slow-flowing regions both roughness methods indicate spatially coherent regions of smooth beds, which, through combination with analyses of underlying geology, we conclude is likely due to the presence of a hard flat bed. Consequently, the study provides scope for a spatially variable hard- or soft-bed boundary constraint for ice-sheet models

Ion cyclotron resonance heating with consistent finite orbit widths and anisotropic equilibria

Minority ion cyclotron resonance heating is studied using the self-consistent numerical model SCENIC. This model includes 3D geometries with full shaping and anisotropic pressure effects, warm contributions to the dielectric tensor and full orbit effects. It evolves the equilibrium, wave field and hot particle distribution function iteratively until a self-consistent solution is found. We will show applications to JET-like two-dimensional equilibria with minority heating scenarios. The effects due to different heating locations on the hot particle distribution function, the hot dielectric tensor and the equilibrium will be studied for symmetric wave injection. Finally, the RF-induced particle pinch is investigated using asymmetric wave injection

Self-affine subglacial roughness:consequences for radar scattering and basal water discrimination in northern Greenland

Subglacial roughness can be determined at a variety of length scales from radio-echo sounding (RES) data either via statistical analysis of topography or inferred from basal radar scattering. Past studies have demonstrated that subglacial terrain exhibits self-affine (power law) roughness scaling behaviour, but existing radar scattering models do not take this into account. Here, using RES data from northern Greenland, we introduce a self-affine statistical framework that enables a consistent integration of topographicscale roughness with the electromagnetic theory of radar scattering. We demonstrate that the degree of radar scattering, quantified using the waveform abruptness (pulse peakiness), is topographically controlled by the Hurst (roughness power law) exponent. Notably, specular bed reflections are associated with a lower Hurst exponent, with diffuse scattering associated with a higher Hurst exponent. Abrupt waveforms (specular reflections) have previously been used as a RES diagnostic for basal water, and to test this assumption we compare our radar scattering map with a recent prediction for the basal thermal state. We demonstrate that the majority of thawed regions (above pressure melting point) exhibit a diffuse scattering signature, which is in contradiction to the prior approach. Self-affine statistics provide a generalised model for subglacial terrain and can improve our understanding of the relationship between basal properties and ice-sheet dynamics.</p

Short-course antiretroviral therapy in primary HIV infection

Background Short-course antiretroviral therapy (ART) in primary human immunodeficiency virus (HIV) infection may delay disease progression but has not been adequately evaluated. Methods We randomly assigned adults with primary HIV infection to ART for 48 weeks, ART for 12 weeks, or no ART (standard of care), with treatment initiated within 6 months after seroconversion. The primary end point was a CD4+ count of less than 350 cells per cubic millimeter or long-term ART initiation. Results A total of 366 participants (60% men) underwent randomization to 48-week ART (123 participants), 12-week ART (120), or standard care (123), with an average followup of 4.2 years. The primary end point was reached in 50% of the 48-week ART group, as compared with 61% in each of the 12-week ART and standard-care groups. The average hazard ratio was 0.63 (95% confidence interval [CI], 0.45 to 0.90; P = 0.01) for 48-week ART as compared with standard care and was 0.93 (95% CI, 0.67 to 1.29; P = 0.67) for 12-week ART as compared with standard care. The proportion of participants who had a CD4+ count of less than 350 cells per cubic millimeter was 28% in the 48-week ART group, 40% in the 12-week group, and 40% in the standard-care group. Corresponding values for long-term ART initiation were 22%, 21%, and 22%. The median time to the primary end point was 65 weeks (95% CI, 17 to 114) longer with 48-week ART than with standard care. Post hoc analysis identified a trend toward a greater interval between ART initiation and the primary end point the closer that ART was initiated to estimated seroconversion (P = 0.09), and 48-week ART conferred a reduction in the HIV RNA level of 0.44 log10 copies per milliliter (95% CI, 0.25 to 0.64) 36 weeks after the completion of short-course therapy. There were no significant between-group differences in the incidence of the acquired immunodeficiency syndrome, death, or serious adverse events. Conclusions A 48-week course of ART in patients with primary HIV infection delayed disease progression, although not significantly longer than the duration of the treatment. There was no evidence of adverse effects of ART interruption on the clinical outcome. (Funded by the Wellcome Trust; SPARTAC Controlled-Trials.com number, ISRCTN76742797, and EudraCT number, 2004-000446-20.

Methods for improving the accuracy of automated NDE systems

Automated inspection systems using twin six-axis industrial robots have been available for a number of years, including the IntACom system at TWI Wales. Utilising phased array ultrasonic probes to quickly inspect complex geometries, the IntACom system is now routinely used in various inspections of composite components. In the present work we introduce a number of methods for improving and quantifying the accuracy of an automated inspection system. The key challenges are identified and addressed through a number of methods including calibration procedures and interfacing multiple sensors with industrial robots for Non Destructive Evaluation (NDE) purposes. The authors also introduce a novel method for improving the Tool Centre Point (TCP) calibration of an industrial robot when the tool is an ultrasonic phased array probe. Experimental trials show that the average positioning error is less than 0.5mm using this new method

Self-consistent ICRF simulations in fully shaped anisotropic plasmas

For self-consistent ICRF heating simulations, four codes have been coupled: VMEC[1] provides a fully shaped, anisotropic 3D MHD equilibrium (bi- Maxwellian distribution function), transferred to Boozer coordinates by TERPSICHORE[2]. The full-wave code LEMan[3,4] provides the IC wave field, power deposition and wave numbers (new anisotropic dielectric tensor and upshifted k). Finally, VENUS[5,6] computes the evolution of the distribution function due to ICRF heating and Coulomb collisions on the background thermal plasma (using Monte Carlo operators for Coulomb collisions and ICRH)

To swim or not to swim: an interpretation of farmed mink's motivation for a water bath

How an animal’s behavioural (ethological) needs can be met is a pivotal issue in the assessment of welfare for captive animals. The value of swimming water for farmed mink is an example how scientific and societal questions relating to animal welfare can be answered. A number of studies have addressed the issue of the indispensability of swimming water for mink; however, so far with inconclusive evidence. In this paper, the results of these studies and related literature are reviewed. First, the biological definition of need is discussed. Subsequently, attention is paid to the effects of the presence, absence and the removal of swimming water on behavioural and physiological correlates of well-being including stereotypic and anticipatory behaviour and urinary cortisol. Thereafter we discuss individual differences in the use of swimming water, the price animals pay for access to a water bath, and the effect of access to swimming water on juvenile play. The main conclusions of the literature review are that 1) the use of a water bath for mink is most likely related to foraging behaviour (foraging areas: land and water); 2) absence of swimming water, without prior experience, does not lead to consistent changes in level of stereotypic behaviour, or anticipatory responses; 3) removal of a previously experienced water bath may induce short-term stress as indicated by behavioural parameters and elevated cortisol responses; 4) mink work hard for access to a swimming bath and running wheel in consumer demand studies. Other cage modifications such as tunnels and biting objects, may also provide environmental enrichment, if they are added to otherwise impoverished conditions; 5) There are individual differences in the use of swimming water: these are related in part to variation in prior experience of aquatic resources.; 6) As prior experience is important both with respect to individual use of swimming water and the response to deprivation, swimming water can not be described as biological need in the sense of a fixed requirement for survival. As swimming water appears to act as an incentive that induces its own motivation a more accurate term may be an “incentive induced or environmentally facilitated need”. Given the available evidence, it is not possible to conclude whether mink that have never experienced swimming water, suffer as a consequence of its absence. However, it is possible to predict that mink with access to water have improved quality of life, due to increased behavioural opportunities, in comparison to farmed mink without access to swimming water. In practical terms, it is still open to debate whether mink should be provided with swimming water, or if alternative, less valued, but easier to install and maintain forms of environmental enrichment, should be provided in mink housing. To clarify these issues a number of future studies would be valuable. These include; 1) whether specific environmental cues affect motivation to swim, such as the form of drinking water delivery systems ; 2) whether prior experience of swimming water affects its incentive value; in other words “can you miss what you never experienced?”; 3) do behavioural parameters such as stereotypic behaviour; rebound effects and vacuum activity have any general utility in assessing the value of absent resources; 4) what are preferences for and the value of alternative resources which may act as substitutes for swimming water. In addition we would recommend further work investigating: relationship between access to swimming water and positive indicators of welfare such as play and/or anticipatory behaviour; the effects of preventing the performance of rewarding behaviours and deprivation of a previous experienced resource; and health and hygeine issues related to provision of a water bath. In future work, it would be desirable to present be the actual percentages of animals using a water bath during the experiment and the use of power analyses, to aid their interpretation

Quantemol Electron Collisions (QEC): An Enhanced Expert System for Performing Electron Molecule Collision Calculations Using the R-Matrix Method

Collisions of low energy electrons with molecules are important for understanding many aspects of the environment and technologies. Understanding the processes that occur in these types of collisions can give insights into plasma etching processes, edge effects in fusion plasmas, radiation damage to biological tissues and more. A radical update of the previous expert system for computing observables relevant to these processes, Quantemol-N, is presented. The new Quantemol Electron Collision (QEC) expert system simplifyies the user experience, improving reliability and implements new features. The QEC graphical user interface (GUI) interfaces the Molpro quantum chemistry package for molecular target setups, and the sophisticated UKRmol+ codes to generate accurate and reliable cross-sections. These include elastic cross-sections, super elastic cross-sections between excited states, electron impact dissociation, scattering reaction rates, dissociative electron attachment, differential cross-sections, momentum transfer cross-sections, ionization cross sections, and high energy electron scattering cross-sections. With this new interface we will be implementing dissociative recombination estimations, vibrational excitations for neutrals and ions, and effective core potentials in the near future