Showing papers by "University of Warwick published in 2000"

The PSIPRED protein structure prediction server.

Abstract: The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.

Being Human: The Problem of Agency

Abstract: Humanity and the very notion of the human subject are under threat from postmodernist thinking which has declared not only the 'Death of God' but also the 'Death of Man'. This book is a revindication of the concept of humanity, rejecting contemporary social theory that seeks to diminish human properties and powers. Archer argues that being human depends on an interaction with the real world in which practice takes primacy over language in the emergence of human self-consciousness, thought, emotionality and personal identity - all of which are prior to, and more basic than, our acquisition of a social identity. This original and provocative new book from leading social theorist Margaret S. Archer builds on the themes explored in her previous books Culture and Agency (CUP 1988) and Realist Social Theory (CUP 1995). It will be required reading for academics and students of social theory, cultural theory, political theory, philosophy and theology.

Stable-isotope probing as a tool in microbial ecology

Abstract: Microorganisms are responsible for driving the biogeochemical cycling of elements on Earth Despite their importance and vast diversity1, the taxonomic identity of the microorganisms involved in any specific process has usually been confined to that small fraction of the microbiota that has been isolated and cultivated The recent coupling of molecular biological methods with stable-isotope abundance in biomarkers has provided a cultivation-independent means of linking the identity of bacteria with their function in the environment2,3 Here we show that 13C-DNA, produced during the growth of metabolically distinct microbial groups on a 13C-enriched carbon source, can be resolved from 12C-DNA by density-gradient centrifugation DNA isolated from the target group of microorganisms can be characterized taxonomically and functionally by gene probing and sequence analysis Application of this technique to investigate methanol-utilizing microorganisms in soil demonstrated the involvement of members of two phylogenetically distinct groups of eubacteria; the α-proteobacterial and Acidobacterium lineages Stable-isotope probing thus offers a powerful new technique for identifying microorganisms that are actively involved in specific metabolic processes under conditions which approach those occurring in situ

Factors affecting teachers' use of information and communications technology: a review of the literature

Abstract: This article reports on the literature associated with practising teachers' uptake of information and communications technology (ICT). Studies reveal a number of factors which influence teachers' decisions to use ICT in the classroom: access to resources, quality of software and hardware, ease of use, incentives to change, support and collegiality in their school, school and national polices, commitment to professional learning and background in formal computer training. The review highlights the role of pedagogy and suggests that teachers' beliefs about teaching and learning with ICT are central to integration. It is suggested that successful implementation of ICT needs to address three interlocking frameworks for change: the teacher, the school and policy makers.

Inequality and crime

Abstract: This paper considers the relationship between inequality and crime using data from urban counties. The behavior of property and violent crime are quite different. Inequality has no effect on property crime but a strong and robust impact on violent crime, with an elasticity above 0.5. By contrast, poverty and police activity have significant effects on property crime, but little on violent crime. Property crime is well explained by the economic theory of crime, while violent crime is better explained by strain and social disorganization theories.

Predators and people: using human densities to interpret declines of large carnivores

Abstract: The current extinction crisis is caused primarily by human impacts upon wild populations Large carnivores are especially sensitive to human activity; because their requirements often conflict with those of local people, predators have been actively persecuted in most regions of the world In this paper, the impact of people upon predators is analysed by relating local carnivore extinctions to past and projected human population densities There are strong associations between high human density and the loss of carnivore populations from a region Interspecific variation in ability to survive at high human densities probably reflects species' ability to adapt to human-modified habitats However, regional and temporal variation in individual species' sensitivity to human density is more likely to reflect the activities of local people than the phenotypes of local carnivores Local culture, government policy and international trade all influence human attitudes to predators and, therefore, the impact of people upon carnivore populations The importance of these factors may mean that extinction risks for carnivores will continue to increase, even though human population growth is projected to deccelerate during the new millennium This points to an urgent need for techniques to resolve conflicts between people and predators at either the local or landscape level

Chronic illness as biographical disruption or biographical disruption as chronic illness? Reflections on a core concept

Abstract: Taking as its point of departure Bury’s (1982) concept of chronic illness as biographical disruption, this paper provides a critical assessment of its fortunes since that time. Having ‘rescued’ the concept from recent postmodern and disability critiques, the paper provides a series of further reflections on its strengths and weaknesses, including the notion of ‘normal illness’; the importance of timing and context; the significance of continuity as well as loss; and the role of biographical disruption itself in the aetiology of illness. This, in turn, provides the basis for a broader set of reflections on the vicissitudes of the biographically embodied self in conditions of late modernity: a situation of chronic reflexivity in which our bodies/selves are continually problematised if not pathologised. The paper concludes, given this ‘balance sheet’, with a discussion of some potentially fruitful lines of future research, including links with the life-events and inequalities literature.

Contesting global governance : multilateral economic institutions and global social movements

Abstract: This book argues that increasing engagement between international institutions and sectors of civil society is producing a new form of global governance. The authors investigate 'complex multilateralism' by studying the relationship between three multilateral economic institutions (the IMF, World Bank, and World Trade Organization), and three global social movements (environmental, labour and women's movements). They provide a rich comparative analysis of the institutional response to social movement pressure, tracing institutional change, policy modification and social movement tactics as they struggle to influence the rules and practices governing trade, finance and development regimes. The contest to shape global governance is increasingly being conducted upon a number of levels and amongst a diverse set of actors. Analysing a unique breadth of institutions and movements, this book charts an important part of that contest.

Kondo physics in carbon nanotubes

Abstract: The connection of electrical leads to wire-like molecules is a logical step in the development of molecular electronics, but also allows studies of fundamental physics. For example, metallic carbon nanotubes1 are quantum wires that have been found to act as one-dimensional quantum dots2,3, Luttinger liquids4,5, proximity-induced superconductors6,7 and ballistic8 and diffusive9 one-dimensional metals. Here we report that electrically contacted single-walled carbon nanotubes can serve as powerful probes of Kondo physics, demonstrating the universality of the Kondo effect. Arising in the prototypical case from the interaction between a localized impurity magnetic moment and delocalized electrons in a metallic host, the Kondo effect has been used to explain10 enhanced low-temperature scattering from magnetic impurities in metals, and also occurs in transport through semiconductor quantum dots11,12,13,14,15,16,17,18. The far greater tunability of dots (in our case, nanotubes) compared with atomic impurities renders new classes of Kondo-like effects19,20 accessible. Our nanotube devices differ from previous systems in which Kondo effects have been observed, in that they are one-dimensional quantum dots with three-dimensional metal (gold) reservoirs. This allows us to observe Kondo resonances for very large electron numbers (N) in the dot, and approaching the unitary limit (where the transmission reaches its maximum possible value). Moreover, we detect a previously unobserved Kondo effect, occurring for even values of N in a magnetic field.

Lean production and sustainable competitive advantage

Abstract: Today, “lean” may no longer be fashionable but its core principles (flow, value, pull, minimizing waste etc.) have become the paradigm for many manufacturing (and service) operations. Given this pre‐eminence, the paper seeks to establish what impact it has had on the overall competitive positions of adopter firms. Combining normative and critical theory (from lean production and resource‐based view of the firm literature) with empirical material drawn from three case studies, the paper argues that lean production can underpin competitive advantage if the firm is able to appropriate the productivity savings it creates. Similarly, the ambiguity of lean production in practice means that the implementation process can create strategic resources to underpin sustainable competitive advantage. Problematically, however, the paper also suggests that being “lean” can curtail the firm’s ability to achieve long‐term flexibility. It concludes with suggestions for further work.

Prospective and retrospective memory in normal ageing and dementia: A questionnaire study

Abstract: Frequency of prospective memory and retrospective memory failures was rated on a 16-item questionnaire by 862 volunteers, from five groups: patients with Alzheimer Disease (rated by carers), carers of Alzheimer Disease patients, elderly, young, and a group of married couples. Reported memory failures were highest for Alzheimer Disease patients, and lowest for carers, with elderly and young controls in between. More prospective memory than retrospective memory failures were reported in all groups, although the difference was small for Alzheimer Disease patients who were rated near ceiling for both. Prospective memory failures of Alzheimer Disease patients were reported as more frustrating for carers than retrospective memory failures; prospective memory and retrospective memory failures frustrated Alzheimer Disease patients equally. Data from the couples indicated that there were no biases resulting from rating on behalf of someone else. These results suggest that: (1) normal ageing has no greater effect on self-reported retrospective memory than prospective memory failures, (2) the relatively small number of memory failures reported by carers may result from comparing themselves with the Alzheimer Disease patients in their care, and (3) prospective memory failures have a greater impact on the lives of the carers and are therefore more likely to be reported as early indicants of the disease.

A weak turbulence theory for incompressible magnetohydrodynamics

Abstract: We derive a weak turbulence formalism for incompressible magnetohy- drodynamics. Three-wave interactions lead to a system of kinetic equations for the spectral densities of energy and helicity. The kinetic equations conserve energy in all wavevector planes normal to the applied magnetic eld B0 ^k. Numerically and analytically, we nd energy spectra E k n ? , such that n+ +n = 4, where E are the spectra of the Elsvariables z = v b in the two-dimensional case (kk = 0). The constants of the spectra are computed exactly and found to depend on the amount of correlation between the velocity and the magnetic eld. Comparison with several numerical simulations and models is also made.

Salicylic acid has a role in regulating gene expression during leaf senescence

Abstract: Leaf senescence is a complex process that is controlled by multiple developmental and environmental signals and is manifested by induced expression of a large number of different genes. In this paper we describe experiments that show, for the first time, that the salicylic acid (SA)-signalling pathway has a role in the control of gene expression during developmental senescence. Arabidopsis plants defective in the SA-signalling pathway (npr1 and pad4 mutants and NahG transgenic plants) were used to investigate senescence-enhanced gene expression, and a number of genes showed altered expression patterns. Senescence-induced expression of the cysteine protease gene SAG12, for example, was conditional on the presence of SA, together with another unidentified senescence-specific factor. Changes in gene expression patterns were accompanied by a delayed yellowing and reduced necrosis in the mutant plants defective in SA-signalling, suggesting a role for SA in the cell death that occurs at the final stage of senescence. We propose the presence of a minimum of three senescence-enhanced signalling factors in senescing leaves, one of which is SA. We also suggest that a combination of signalling factors is required for the optimum expression of many genes during senescence.

Host‐plant selection by insects – a theory based on ‘appropriate/inappropriate landings’ by pest insects of cruciferous plants

Abstract: Seven hypotheses, including the ‘Resource Concentration Hypothesis’ and the ‘Enemies Hypothesis’, have been put forward to explain why fewer specialist insects are found on host plants growing in diverse backgrounds than on similar plants growing in bare soil. All seven hypotheses are discussed and discounted, primarily because no one has used any of them to produce a general theory of host plant selection, they still remain as hypotheses. However, we have developed a general theory based on detailed observations of insect behaviour. Our theory is based on the fact that during host plant finding the searching insects land indiscriminately on green objects such as the leaves of host plants (appropriate landings) and non-host plants (inappropriate landings), but avoid landing on brown surfaces, such as soil. The complete system of host plant selection involves a three-link chain of events in which the first link is governed by cues from volatile plant chemicals, the central link by visual stimuli, and the final link by cues from non-volatile plant chemicals. The previously ‘missing’ central link, which is based on what we have described as ‘appropriate/inappropriate landings’, is governed by visual stimuli. Our theory explains why attempts to show that olfaction is the crucial component in the central link of host plant selection proved intractable. The ‘appropriate/inappropriate landings’ theory is discussed to indicate the type of work needed in future studies to improve our understanding of how intercropping, undersowing and companion planting can be used to optimum effect in crop protection. The new theory is used also to suggest how insect biotypes could develop and to describe why pest insects do not decimate wild host plants growing in ‘natural’ situations.

Dogs as catalysts for social interactions : Robustness of the effect

Abstract: It is known that pet dogs can act as catalysts for human social interactions, and it has been suggested that this may enhance feelings of well-being. Two studies were carried out to establish the robustness of this effect. In Study 1, a highly trained dog was used to ensure that the dog itself did not solicit attention from passers-by, and data were collected across a range of normal daily activities in which a dog could be included, not confined to conventional dog walking areas as in previous studies. Being accompanied by a dog increased the frequency of social interactions, especially interactions with strangers. In Study 2, also using a trained dog, a different (male) participant observer was dressed either smartly or scruffily. Although there were significantly more interactions when he was smartly dressed, the greatest effect was between the Dog present and No Dog conditions irrespective of the handler's dress. It is concluded that the social catalysis effect is very robust, which opens the way for investigating possible consequences of the effect for well-being and health.

A weak turbulence theory for incompressible MHD

Abstract: We derive a weak turbulence formalism for incompressible MHD. Three-wave interactions lead to a system of kinetic equations for the spectral densities of energy and helicity. We find energy spectra solution of the kinetic equations. The constants of the spectra are computed exactly and found to depend on the amount of correlation between the velocity and the magnetic field. Comparison with several numerical simulations and models is also made.

Does Maintaining Green Leaf Area in Sorghum Improve Yield under Drought? II. Dry Matter Production and Yield

Abstract: Retention of green leaf area at maturity (GLAM), known as stay-green, is used as an indicator of postanthesis drought resistance in sorghum [Sorghum bicolor (L.) Moench] breeding programs in the USA and Australia. The critical issue is whether maintaining green leaves under postanthesis drought increases grain yield in stay-green compared with senescent hybrids. Field studies were undertaken in northeastern Australia on a cracking and self-mulching gay clay. Nine closely related hybrids varying in rate of leaf senescence were grown under two water-limiting regimes, post-flowering water deficit and terminal (pre- and postflowering) water deficit, and a fully irrigated control. Under terminal water deficit, grain yield tvas correlated positively with GLAM (r = 0.75**) and negatively with rate of leaf senescence (r = -0.74**). Grain yield also increased by approximate to 0.35 Mg ha(-1) for every day that onset of leaf senescence was delayed beyond 76 DAE in the water-limited treatments. Stay-green hybrids produced 47% more postanthesis biomass than their senescent counterparts (920 vs. 624 g m(-2)) under the terminal water deficit regime. No differences in grain yield were found among eight of the nine hybrids under fully irrigated conditions, suggesting that the stay-green trait did not constrain yield in the well-watered control. The results indicate that sorghum hybrids possessing the stay-green trait have a significant yield advantage under postanthesis drought compared with hybrids not possessing this trait.

Universal Aging Features in the Restructuring of Fractal Colloidal Gels

Abstract: We use multispeckle dynamic light scattering to measure the dynamic structure factor, f(q,tau), of gels formed by aggregation of colloids. Although the gel is an elastic solid, f(q,tau) nearly completely decays on long time scales, with an unusual form, f(q, tau) approximately exp{-(tau/tau(f))(mu)}, with mu approximately 1.5 and with tau(f) proportional variant q(-1). A model for restructuring of the gel with aging correctly accounts for this behavior. Aging leads to a dramatic increase in tau(f); however, all data can be scaled on a single master curve, with tau(f) asymptotically growing linearly with age. This behavior is strikingly similar to that predicted for aging in disordered glassy systems, offering convincing proof of the universality of these concepts.

Crime and Economic Incentives

Abstract: In economic models of crime, changing economic incentives alter the participation of individuals in criminal activities. We critically appraise the work in this area. After a brief overview of the workhorse economics of crime model for organizing our discussion on crime and economic incentives, we first document the significant rise of the economics of crime as a research field and then go on to review the evidence on the relationship between crime and economic incentives. We divide this discussion into incentives operating through legal wages in the formal labor market and the economic returns to illegal activities. Evidence that economic incentives matter for crime emerges from both.

Suprathreshold stochastic resonance in multilevel threshold systems

Abstract: A new form of stochastic resonance (SR) that occurs in multilevel threshold signal detectors is reported. In contrast to classical SR, which extends the dynamic range of threshold detectors to subthreshold signal levels, this new form of SR extends the dynamic range to suprathreshold signal strengths. The effect is most dominant, and can outperform networks based on standard engineering design, when all thresholds adapt to the dc level of the signal. This has an interesting analogy to dc adaptation in neurons. The possible connection between these two effects is discussed.

Psychometric evaluation of Horowitz's Impact of Event Scale: a review.

Abstract: Despite being developed before the formal introduction of posttraumatic stress disorder (PTSD) within the diagnostic literature, the Impact of Event Scale (Horowitz, Wilner, & Alvarez, 1979) remains one of the most widely used self-report measures of posttraumatic stress. This paper presents an overview of research using the IES in an attempt to assess its psychometric status. It is concluded that the psychometric properties of the IES are satisfactory (although not as a PTSD diagnostic measure) and that continued use of the IES as a measure of intrusive and avoidant processes is warranted.

Ectopic expression of a tomato 9-cis-epoxycarotenoid dioxygenase gene causes over-production of abscisic acid.

Abstract: Summary The tomato mutant notabilis has a wilty phenotype as a result of abscisic acid (ABA) deficiency. The wild-type allele of notabilis, LeNCED1, encodes a putative 9-cis-epoxycarotenoid dioxygenase (NCED) with a potential regulatory role in ABA biosynthesis. We have created transgenic tobacco plants in which expression of the LeNCED1 coding region is under tetracycline-inducible control. When leaf explants from these plants were treated with tetracycline, NCED mRNA was induced and bulk leaf ABA content increased by up to 10-fold. Transgenic tomato plants were also produced containing the LeNCED1 coding region under the control of one of two strong constitutive promoters, either the doubly enhanced CaMV 35S promoter or the chimaeric ‘Super-Promoter’. Many of these plants were wilty, suggesting co-suppression of endogenous gene activity; however three transformants displayed a common, heritable phenotype that could be due to enhanced ABA biosynthesis, showing increased guttation and seed dormancy. Progeny from two of these transformants were further characterized, and it was shown that they also exhibited reduced stomatal conductance, increased NCED mRNA and elevated seed ABA content. Progeny of one transformant had significantly higher bulk leaf ABA content compared to the wild type. The increased seed dormancy was reversed by addition of the carotenoid biosynthesis inhibitor norflurazon. These data provide strong evidence that NCED is indeed a key regulatory enzyme in ABA biosynthesis in leaves, and demonstrate for the first time that plant ABA content can be increased through manipulating NCED.

Combined Scanning Electrochemical−Atomic Force Microscopy

Abstract: A combined scanning electrochemical microscope (SECM)−atomic force microscope (AFM) is described. The instrument permits the first simultaneous topographical and electrochemical measurements at surfaces, under fluid, with high spatial resolution. Simple probe tips suitable for SECM−AFM, have been fabricated by coating flattened and etched Pt microwires with insulating, electrophoretically deposited paint. The flattened portion of the probe provides a flexible cantilever (force sensor), while the coating insulates the probe such that only the tip end (electrode) is exposed to the solution. The SECM−AFM technique is illustrated with simultaneous electrochemical-probe deflection approach curves, simultaneous topographical and electrochemical imaging studies of track-etched polycarbonate ultrafiltration membranes, and etching studies of crystal surfaces.

Thinking Feminism with and against Bourdieu

Abstract: This article argues that a positive engagement between Bourdieu’s sociology of practice and contemporary feminist theory would be mutually profitable. It compares Bourdieu’s account of the social c...

Meta-analysis, funnel plots and sensitivity analysis

Abstract: Publication bias is a major problem, perhaps the major problem, in meta-analysis (or systematic reviews). Small studies are more likely to be published if their results are 'significant' than if their results are negative or inconclusive, and so the studies available for review are biased in favour of those with positive outcomes. Correcting for this bias is not possible without making untestable assumptions. In this paper, a sensitivity analysis is suggested which is based on fitting a model to the funnel plot. Some examples are discussed.

Universal Aging Features in the Restructuring of Fractal Colloidal Gels

Abstract: We use multispeckle dynamic light scattering to measure the dynamic structure factor, f(q,tau), of gels formed by aggregation of colloids. Although the gel is an elastic solid, f(q,tau) nearly completely decays on long time scales, with an unusual form, f(q, tau) approximately exp{-(tau/tau(f))(mu)}, with mu approximately 1.5 and with tau(f) proportional variant q(-1). A model for restructuring of the gel with aging correctly accounts for this behavior. Aging leads to a dramatic increase in tau(f); however, all data can be scaled on a single master curve, with tau(f) asymptotically growing linearly with age. This behavior is strikingly similar to that predicted for aging in disordered glassy systems, offering convincing proof of the universality of these concepts.