From the sun to the Earth: The 13 May 2005 coronal mass ejection

We report the results of a multi-instrument, multi-technique, coordinated study of the solar eruptive event of 13 May 2005. We discuss the resultant Earth-directed (halo) coronal mass ejection (CME), and the effects on the terrestrial space environment and upper Earth atmosphere. The interplanetary CME (ICME) impacted the Earth’s magnetosphere and caused the most-intense geomagnetic storm of 2005 with a Disturbed Storm Time (Dst) index reaching −263 nT at its peak. The terrestrial environment responded to the storm on a global scale. We have combined observations and measurements from coronal and interplanetary remote-sensing instruments, interplanetary and near-Earth in-situ measurements, remote-sensing observations and in-situ measurements of the terrestrial magnetosphere and ionosphere, along with coronal and heliospheric modelling. These analyses are used to trace the origin, development, propagation, terrestrial impact, and subsequent consequences of this event to obtain the most comprehensive view of a geo-effective solar eruption to date. This particular event is also part of a NASA-sponsored Living With a Star (LWS) study and an on-going US NSF-sponsored Solar, Heliospheric, and INterplanetary Environment (SHINE) community investigation.

Analytical potentials for triatomic molecules from spectroscopic data VI. On choosing internal coordinates to describe triatomic potential energy surfaces with more than one minimum

Orthogonal internal coordinates are defined which have useful properties for constructing the potential energy functions of triatomic molecules with two or three minima on the surface. The coordinates are used to obtain ground state potentials of ClOO and HOF, both of which have three minima.

A covariate adjustment for zero-truncated approaches to estimating the size of hidden and elusive populations

In this paper we consider the estimation of population size from onesource capture–recapture data, that is, a list in which individuals can potentially be found repeatedly and where the question is how many individuals are missed by the list. As a typical example, we provide data from a drug user study in Bangkok from 2001 where the list consists of drug users who repeatedly contact treatment institutions. Drug users with 1, 2, 3, . . . contacts occur, but drug users with zero contacts are not present, requiring the size of this group to be estimated. Statistically, these data can be considered as stemming from a zero-truncated count distribution.We revisit an estimator for the population size suggested by Zelterman that is known to be robust under potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a locally truncated Poisson likelihood which is equivalent to a binomial likelihood. This result allows the extension of the Zelterman estimator by means of logistic regression to include observed heterogeneity in the form of covariates. We also review an estimator proposed by Chao and explain why we are not able to obtain similar results for this estimator. The Zelterman estimator is applied in two case studies, the first a drug user study from Bangkok, the second an illegal immigrant study in the Netherlands. Our results suggest the new estimator should be used, in particular, if substantial unobserved heterogeneity is present.

Forward modelling to determine the observational signatures of white-light imaging and interplanetary scintillation for the propagation of an interplanetary shock in the ecliptic plane

Recent coordinated observations of interplanetary scintillation (IPS) from the EISCAT, MERLIN, and STELab, and stereoscopic white-light imaging from the two heliospheric imagers (HIs) onboard the twin STEREO spacecraft are significant to continuously track the propagation and evolution of solar eruptions throughout interplanetary space. In order to obtain a better understanding of the observational signatures in these two remote-sensing techniques, the magnetohydrodynamics of the macro-scale interplanetary disturbance and the radio-wave scattering of the micro-scale electron-density fluctuation are coupled and investigated using a newly constructed multi-scale numerical model. This model is then applied to a case of an interplanetary shock propagation within the ecliptic plane. The shock could be nearly invisible to an HI, once entering the Thomson-scattering sphere of the HI. The asymmetry in the optical images between the western and eastern HIs suggests the shock propagation off the Sun–Earth line. Meanwhile, an IPS signal, strongly dependent on the local electron density, is insensitive to the density cavity far downstream of the shock front. When this cavity (or the shock nose) is cut through by an IPS ray-path, a single speed component at the flank (or the nose) of the shock can be recorded; when an IPS ray-path penetrates the sheath between the shock nose and this cavity, two speed components at the sheath and flank can be detected. Moreover, once a shock front touches an IPS ray-path, the derived position and speed at the irregularity source of this IPS signal, together with an assumption of a radial and constant propagation of the shock, can be used to estimate the later appearance of the shock front in the elongation of the HI field of view. The results of synthetic measurements from forward modelling are helpful in inferring the in-situ properties of coronal mass ejection from real observational data via an inverse approach.

A cost-benefit analysis of culling badgers to control bovine tuberculosis

Bovine tuberculosis (TB) is an important economic problem. The incidence of TB in cattle herds has steadily risen in the UK, and badgers are strongly implicated in spreading disease. Since the mid-1970s the UK government has adopted a number of badger culling strategies to attempt to reduce infection in cattle. In this report, an established model has been used to simulate TB in badgers, transmission to cattle, and control by badger culling. Costs were supplied by the UK Government's Department for Environment Food and Rural Affairs (Defra) for badger trapping and gassing. Regardless of culling intensity or area simulated, an overall reduction in the herd breakdown rate was seen. With a high culling efficacy and no social perturbation, the mean Net Present Value of a few simulated culling strategies in an "ideal world" was positive, meaning the economic benefits outweighed the costs. Further work is required before these results could be considered definitive, as it is necessary to evaluate uncertainties and simulate less than perfect conditions. (c) 2005 Elsevier Ltd. All rights reserved.

Use of airborne remote sensing to detect riverside Brassica rapa to aid in risk assessment of transgenic crops

High resolution descriptions of plant distribution have utility for many ecological applications but are especially useful for predictive modeling of gene flow from transgenic crops. Difficulty lies in the extrapolation errors that occur when limited ground survey data are scaled up to the landscape or national level. This problem is epitomized by the wide confidence limits generated in a previous attempt to describe the national abundance of riverside Brassica rapa (a wild relative of cultivated rapeseed) across the United Kingdom. Here, we assess the value of airborne remote sensing to locate B. rapa over large areas and so reduce the need for extrapolation. We describe results from flights over the river Nene in England acquired using Airborne Thematic Mapper (ATM) and Compact Airborne Spectrographic Imager (CASI) imagery, together with ground truth data. It proved possible to detect 97% of flowering B. rapa on the basis of spectral profiles. This included all stands of plants that occupied >2m square (>5 plants), which were detected using single-pixel classification. It also included very small populations (<5 flowering plants, 1-2m square) that generated mixed pixels, which were detected using spectral unmixing. The high detection accuracy for flowering B. rapa was coupled with a rather large false positive rate (43%). The latter could be reduced by using the image detections to target fieldwork to confirm species identity, or by acquiring additional remote sensing data such as laser altimetry or multitemporal imagery.

Aligning sequences to structures

Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target sequences to a set of representative template structures within a fold library. In this chapter, I discuss the development of template-based approaches to fold prediction, from the traditional techniques to the recent state-of-the-art methods. I also discuss the recent development of structural annotation databases, which contain models built by aligning the sequences from entire proteomes against known structures. Finally, I run through a practical step-by-step guide for aligning target sequences to known structures and contemplate the future direction of template-based structure prediction.

Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations

We review the application of mathematical modeling to understanding the behavior of populations of chemotactic bacteria. The application of continuum mathematical models, in particular generalized Keller-Segel models, is discussed along with attempts to incorporate the microscale (individual) behavior on the macroscale, modeling the interaction between different species of bacteria, the interaction of bacteria with their environment, and methods used to obtain experimentally verified parameter values. We allude briefly to the role of modeling pattern formation in understanding collective behavior within bacterial populations. Various aspects of each model are discussed and areas for possible future research are postulated.

Regulated deficit irrigation - a means to control growth in woody ornamentals

Improving plant quality and the uniformity of a crop are major objectives for growers of ornamental nursery stock. The potential to control excess vigour and to improve quality through regulated deficit irrigation (RDI) was investigated using a range of woody ornamental species. RDI regimes reduced vegetative growth consistently across different species and growing seasons. Plants adapted to reduced water supplies primarily via stomatal control, but also by osmotic adjustment when grown under the most severe RDI regimes. Only plants exposed to <= 25% of potential evapo-transpiration demonstrated any evidence of leaf injury, and the extent was slight. Growth inhibition increased as the severity of RDI increased. Improvements in quality were attained through a combination of shorter internodes and final shoot lengths, yet the number of 'formative' primary shoots remained unaffected. Compact, well-branched plants could be formed without a requirement for mid-season pruning. In addition to severity, the timing of RDI also influenced growth responses. Applying 50% ETp for 8 weeks during July-August resulted in the formation of good quality plants, which retained their shape until the following Spring. Re-positioning irrigation drippers within the pots of well-watered plants, in an attempt to induce a partial root drying (PRD) treatment, reduced growth, but not significantly. The adoption of irrigation scheduling, based on 50-100% ETp, has the potential to improve commercial crop quality across a range of ornamental species.

The determination of molecular properties from MULTIMODE with an application to the calculation of Franck-Condon factors for photoionization of CF3 to CF3+

Extensions to the code MULTIMODE to obtain rovibrational wave functions and properties are described. An application of these new capabilities is made to a calculation of the Franck-Condon factors for photoionization of CF3 to CF3+. These calculations make use of a new, full-dimensional ab initio potential energy surface, which is also described here.

A molecular T-matrix approach to calculating low-energy electron diffusion intensities for ordered molecular adsorbates

We present a novel approach to calculating Low-Energy Electron Diffraction (LEED) intensities for ordered molecular adsorbates. First, the intra-molecular multiple scattering is computed to obtain a non-diagonal molecular T-matrix. This is then used to represent the entire molecule as a single scattering object in a conventional LEED calculation, where the Layer Doubling technique is applied to assemble the different layers, including the molecular ones. A detailed comparison with conventional layer-type LEED calculations is provided to ascertain the accuracy of this scheme of calculation. Advantages of this scheme for problems involving ordered arrays of molecules adsorbed on surfaces are discussed.

Photochromic switches incorporated in bridging ligands: a new tool to modulate energy-transfer processes

The thoughtful construction of molecular switches has led to a gamut of supramolecular systems that can be used in molecular electronics. These include molecules based on thienylethenes, spiropyrans, fulgides, dithienylphenanthrolines, and diazafluorenes. This article reviews the recent developments made in the synthesis and characterization of all these systems, thereby allowing a comparative study to validate the viability of these switchable molecules on a nanoscale. Also, the drawbacks of each class are demonstrated and, at the same time, the remedies for further improvisation are prescribed. We have made an honest attempt to present at? exhaustive account of all the different photochromic switches developed by us hitherto.

Theory of mind and attentional bias to facial emotional expressions: A preliminary study

Theory of mind ability has been associated with performance in interpersonal interactions and has been found to influence aspects such as emotion recognition, social competence, and social anxiety. Being able to attribute mental states to others requires attention to subtle communication cues such as facial emotional expressions. Decoding and interpreting emotions expressed by the face, especially those with negative valence, are essential skills to successful social interaction. The current study explored the association between theory of mind skills and attentional bias to facial emotional expressions. According to the study hypothesis, individuals with poor theory of mind skills showed preferential attention to negative faces over both non-negative faces and neutral objects. Tentative explanations for the findings are offered emphasizing the potential adaptive role of vigilance for threat as a way of allocating a limited capacity to interpret others’ mental states to obtain as much information as possible about potential danger in the social environment.

Local versus organic: a turn in consumer preferences and willingness-to-pay

Demand for local food in the United States has significantly increased over the last decade. In an attempt to understand the drivers of this demand and how they have changed over time, we investigate the literature on organic and local foods over the last few decades. We focus our review on studies that allow comparison of characteristics now associated with both local and organic food. We summarize the major findings of these studies and their implications for understanding drivers of local food demand. Prior to the late 1990s, most studies failed to consider factors now associated with local food, and the few that included these factors found very little support for them. In many cases, the lines between local and organic were blurred. Coincident with the development of federal organic food standards, studies began to find comparatively more support for local food as distinct and separate from organic food. Our review uncovers a distinct turn in the demand for local and organic food. Before the federal organic standards, organic food was linked to small farms, animal welfare, deep sustainability, community support, and many other factors that are not associated with most organic foods today. Based on our review, we argue that demand for local food arose largely in response to corporate cooptation of the organic food market and the arrival of “organic lite.” This important shift in consumer preferences away from organic and toward local food has broad implications for the environment and society. If these patterns of consumer preferences prove to be sustainable, producers, activists, and others should be aware of the implications that these trends have for the food system at large.

On the response of the Antarctic Circumpolar Current transport to climate change in coupled climate models

The CMIP3 (IPCC AR4) models show a consistent intensification and poleward shift of the westerly winds over the Southern Ocean during the 21st century. However, the responses of the Antarctic Circumpolar Currents (ACC) show great diversity in these models, with many even showing reductions in transport. To obtain some understanding of diverse responses in the ACC transport, we investigate both external atmospheric and internal oceanic processes that control the ACC transport responses in these models. While the strengthened westerlies act to increase the tilt of isopycnal surfaces and hence the ACC transport through Ekman pumping effects, the associated changes in buoyancy forcing generally tend to reduce the surface meridional density gradient. The steepening of isopycnal surfaces induced by increased wind forcing leads to enhanced (parameterized) eddy-induced transports that act to reduce the isopycnal slopes. There is also considerable narrowing of the ACC that tends to reduce the ACC transport, caused mainly by the poleward shifts of the subtropical gyres and to a lesser extent by the equatorward expansions of the subpolar gyres in some models. If the combined effect of these retarding processes is larger than that of enhanced Ekman pumping, the ACC transport will be reduced. In addition, the effect of Ekman pumping on the ACC is reduced in weakly stratified models. These findings give insight into the reliability of IPCC-class model predictions of the Southern Ocean circulation, and into the observed decadal-scale steady ACC transport.