Showing papers by "University of York published in 2008"

Measuring and defining the experience of immersion in games

Abstract: Despite the word's common usage by gamers and reviewers alike, it is still not clear what immersion means. This paper explores immersion further by investigating whether immersion can be defined quantitatively, describing three experiments in total. The first experiment investigated participants' abilities to switch from an immersive to a non-immersive task. The second experiment investigated whether there were changes in participants' eye movements during an immersive task. The third experiment investigated the effect of an externally imposed pace of interaction on immersion and affective measures (state anxiety, positive affect, negative affect). Overall the findings suggest that immersion can be measured subjectively (through questionnaires) as well as objectively (task completion time, eye movements). Furthermore, immersion is not only viewed as a positive experience: negative emotions and uneasiness (i.e. anxiety) also run high.

A bias‐adjusted LM test of error cross‐section independence

Abstract: This paper proposes bias-adjusted normal approximation versions of Lagrange multiplier (NLM) test of error cross section independence of Breusch and Pagan (1980) in the case of panel models with strictly exogenous regressors and normal errors. The exact mean and variance of the Lagrange multiplier (LM) test statistic are provided for the purpose of the bias-adjustments, and it is shown that the proposed tests have a standard normal distribution for the fixed time series dimension (T) as the cross section dimension (N) tends to infinity. Importantly, the proposed bias-adjusted NLM tests are consistent even when the Pesaran’s (2004) CD test is inconsistent. Also alternative bias-adjusted NLM tests, which are consistent under local error cross section independence of any fixed order p, are proposed. The finite sample behavior of the proposed tests are investigated and compared to the LM, NLM, and CD tests. It is shown that the bias-adjusted NLM tests successfully control the size, maintaining satisfactory power in panel with exogenous regressors and normal errors, even when cross section mean of the factor loadings is close to zero, where the CD test has little power. However, it is also shown that the bias-adjusted NLM tests are not as robust as the CD test to non-normal errors and/or in the presence of weakly exogenous regressors.

High-tech applications of self-assembling supramolecular nanostructured gel-phase materials: from regenerative medicine to electronic devices.

Abstract: It is likely that nanofabrication will underpin many technologies in the 21st century. Synthetic chemistry is a powerful approach to generate molecular structures that are capable of assembling into functional nanoscale architectures. There has been intense interest in self-assembling low-molecular-weight gelators, which has led to a general understanding of gelation based on the self-assembly of molecular-scale building blocks in terms of non-covalent interactions and packing parameters. The gelator molecules generate hierarchical, supramolecular structures that are macroscopically expressed in gel formation. Molecular modification can therefore control nanoscale assembly, a process that ultimately endows specific material function. The combination of supramolecular chemistry, materials science, and biomedicine allows application-based materials to be developed. Regenerative medicine and tissue engineering using molecular gels as nanostructured scaffolds for the regrowth of nerve cells has been demonstrated in vivo, and the prospect of using self-assembled fibers as one-dimensional conductors in gel materials has captured much interest in the field of nanoelectronics.

Applications and implications of nanotechnologies for the food sector

Abstract: A review of current and projected nanotechnology-derived food ingredients, food additives and food contact materials is presented in relation to potential implications for consumer safety and regulatory controls Nanotechnology applications are expected to bring a range of benefits to the food sector, including new tastes, textures and sensations, less use of fat, enhanced absorption of nutrients, improved packaging, traceability and security of food products The review has shown that nanotechnology-derived food and health food products are set to grow worldwide and, moreover, a variety of food ingredients, additives, carriers for nutrients/supplements and food contact materials is already available in some countries The current level of applications in the European food sector is at an elementary stage; however, it is widely expected that more and more products will be available in the EU over the coming years The toxicological nature of hazard, likelihood of exposure and risk to consumers from nanotechnology-derived food/food packaging are largely unknown and this review highlights major gaps in knowledge that require further research A number of uncertainties and gaps in relevant regulatory frameworks have also been identified and ways of addressing them proposed

The minimum information about a genome sequence (MIGS) specification.

Abstract: With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Assisted colonization and rapid climate change.

Abstract: Moving species outside their historic ranges may mitigate loss of biodiversity in the face of global climate change.

Scaling laws of marine predator search behaviour

Abstract: Many free-ranging predators have to make foraging decisions with little, if any, knowledge of present resource distribution and availability. The optimal search strategy they should use to maximize encounter rates with prey in heterogeneous natural environments remains a largely unresolved issue in ecology. Levy walks are specialized random walks giving rise to fractal movement trajectories that may represent an optimal solution for searching complex landscapes. However, the adaptive significance of this putative strategy in response to natural prey distributions remains untested. Here we analyse over a million movement displacements recorded from animal-attached electronic tags to show that diverse marine predators-sharks, bony fishes, sea turtles and penguins-exhibit Levy-walk-like behaviour close to a theoretical optimum. Prey density distributions also display Levy-like fractal patterns, suggesting response movements by predators to prey distributions. Simulations show that predators have higher encounter rates when adopting Levy-type foraging in natural-like prey fields compared with purely random landscapes. This is consistent with the hypothesis that observed search patterns are adapted to observed statistical patterns of the landscape. This may explain why Levy-like behaviour seems to be widespread among diverse organisms, from microbes to humans, as a 'rule' that evolved in response to patchy resource distributions.

The Unruh effect and its applications

Abstract: It has been $30\phantom{\rule{0.3em}{0ex}}\text{years}$ since the discovery of the Unruh effect. It has played a crucial role in our understanding that the particle content of a field theory is observer dependent. This effect is important in its own right and as a way to understand the phenomenon of particle emission from black holes and cosmological horizons. The Unruh effect is reviewed here with particular emphasis on its applications. A number of recent developments are also commented on and some controversies are discussed. Effort is also made to clarify what seem to be common misconceptions.

BALBES: a molecular-replacement pipeline

Abstract: The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallo­graphy (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from the PDB with multimeric as well as domain organization. A system manager written in Python controls the workflow of the process. Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

The NICE cost-effectiveness threshold: what it is and what that means.

Abstract: The National Institute for Health and Clinical Excellence (NICE) has been using a cost-effectiveness threshold range between 20,000 pound sterling and 30,000 pound sterling for over 7 years. What the cost-effectiveness threshold represents, what the appropriate level is for NICE to use, and what the other factors are that NICE should consider have all been the subject of much discussion. In this article, we briefly review these questions, provide a critical assessment of NICE's utilization of the incremental cost-effectiveness ratio (ICER) threshold to inform its guidance, and suggest ways in which NICE's utilization of the ICER threshold could be developed to promote the efficient use of health service resources. We conclude that it is feasible and probably desirable to operate an explicit single threshold rather than the current range; the threshold should be seen as a threshold at which 'other' criteria beyond the ICER itself are taken into account; interventions with a large budgetary impact may need to be subject to a lower threshold as they are likely to displace more than the marginal activities; reimbursement at the threshold transfers the full value of an innovation to the manufacturer. Positive decisions above the threshold on the grounds of innovation reduce population health; the value of the threshold should be reconsidered regularly to ensure that it captures the impact of changes in efficiency and budget over time; the use of equity weights to sustain a positive recommendation when the ICER is above the threshold requires knowledge of the equity characteristics of those patients who bear the opportunity cost. Given the barriers to obtaining this knowledge and knowledge about the characteristics of typical beneficiaries of UK NHS care, caution is warranted before accepting claims from special pleaders; uncertainty in the evidence base should not be used to justify a positive recommendation when the ICER is above the threshold. The development of a programme of disinvestment guidance would enable NICE and the NHS to be more confident that the net health benefit of the Technology Appraisal Programme is positive.

Detection and characterization of engineered nanoparticles in food and the environment

Abstract: Nanotechnology is developing rapidly and, in the future, it is expected that increasingly more products will contain some sort of nanomaterial. However, to date, little is known about the occurrence, fate and toxicity of nanoparticles. The limitations in our knowledge are partly due to the lack of methodology for the detection and characterisation of engineered nanoparticles in complex matrices, i.e. water, soil or food. This review provides an overview of the characteristics of nanoparticles that could affect their behaviour and toxicity, as well as techniques available for their determination. Important properties include size, shape, surface properties, aggregation state, solubility, structure and chemical composition. Methods have been developed for natural or engineered nanomaterials in simple matrices, which could be optimized to provide the necessary information, including microscopy, chromatography, spectroscopy, centrifugation, as well as filtration and related techniques. A combination of these is often required. A number of challenges will arise when analysing environmental and food materials, including extraction challenges, the presence of analytical artifacts caused by sample preparation, problems of distinction between natural and engineered nanoparticles and lack of reference materials. Future work should focus on addressing these challenges.

A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo.

Abstract: A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo

Nanoparticle analysis and characterization methodologies in environmental risk assessment of engineered nanoparticles

Abstract: Environmental risk assessments of engineered nanoparticles require thorough characterization of nanoparticles and their aggregates. Furthermore, quantitative analytical methods are required to determine environmental concentrations and enable both effect and exposure assessments. Many methods still need optimization and development, especially for new types of nanoparticles in water, but extensive experience can be gained from the fields of environmental chemistry of natural nanomaterials and from fundamental colloid chemistry. This review briefly describes most methods that are being exploited in nanoecotoxicology for analysis and characterization of nanomaterials. Methodological aspects are discussed in relation to the fields of nanometrology, particle size analysis and analytical chemistry. Differences in both the type of size measures (length, radius, aspect ratio, etc.), and the type of average or distributions afforded by the specific measures are compared. The strengths of single particle methods, such as electron microscopy and atomic force microscopy, with respect to imaging, shape determinations and application to particle process studies are discussed, together with their limitations in terms of counting statistics and sample preparation. Methods based on the measurement of particle populations are discussed in terms of their quantitative analyses, but the necessity of knowing their limitations in size range and concentration range is also considered. The advantage of combining complementary methods is highlighted.

Physical interventions to interrupt or reduce the spread of respiratory viruses: systematic review

Abstract: Objective To systematically review evidence for the effectiveness of physical interventions to interrupt or reduce the spread of respiratory viruses. Data extraction Search strategy of the Cochrane Library, Medline, OldMedline, Embase, and CINAHL, without language restriction, for any intervention to prevent transmissionofrespiratoryviruses(isolation,quarantine, social distancing, barriers, personal protection, and hygiene). Study designs were randomised trials, cohort studies, case-control studies, and controlled before and after studies. Data synthesis Of 2300 titles scanned 138 full papers were retrieved, including 49 papers of 51 studies. Study qualitywaspoorforthethreerandomisedcontrolledtrials and most of the cluster randomised controlled trials; the observational studies were of mixed quality. Heterogeneity precluded meta-analysis of most data except that from six case-control studies. The highest quality cluster randomised trials suggest that the spread of respiratory viruses into the community can be prevented by intervening with hygienic measures aimed at younger children. Meta-analysis of six case-control studies suggests that physical measures are highly effective in preventing the spread of SARS: handwashing more than 10 times daily (odds ratio 0.45, 95% confidence interval 0.36 to 0.57; number needed to treat =4, 95% confidence interval 3.65 to 5.52); wearing masks (0.32, 0.25 to 0.40; NNT=6, 4.54 to 8.03); wearing N95 masks (0.09, 0.03 to 0.30; NNT=3, 2.37 to 4.06); wearing gloves (0.43, 0.29 to 0.65; NNT=5, 4.15 to 15.41); wearing gowns (0.23, 0.14 to 0.37; NNT=5, 3.37 to 7.12); and handwashing, masks, gloves, and gowns combined (0.09, 0.02 to 0.35; NNT=3, 2.66 to 4.97). The incremental effect of adding virucidals or antiseptics to normal handwashing to decrease the spread of respiratory disease remains uncertain. The lack of proper evaluation of global measures such as screening at entry ports and social distancing prevent firm conclusions being drawn. Conclusion Routine long term implementation of some physical measures to interrupt or reduce the spread of

Biofuels: a technological perspective

Abstract: Environmental issues, the growing demand for energy, political concerns and the medium-term depletion of petroleum has created the need for development of sustainable technologies based on renewable raw materials. Biofuels might help to meet the future energy supply demands as well as contributing to a reduction of green house gas emissions. Although this topic is highly controversial and many investigations are currently ongoing, this review is intended to give a brief overview about certain aspects of the complex biofuel issue, providing the latest update of the production and potential of biofuels in the transport sector including types of biofuel, feedstocks and technologies and some of the possible socio-economic, environmental and political implications of the widespread use of biofuels in our society.

Seed Storage Oil Mobilization

Abstract: Storage oil mobilization starts with the onset of seed germination. Oil bodies packed with triacylglycerol (TAG) exist in close proximity with glyoxysomes, the single membrane-bound organelles that house most of the biochemical machinery required to convert fatty acids derived from TAG to 4-carbon compounds. The 4-carbon compounds in turn are converted to soluble sugars that are used to fuel seedling growth. Biochemical analysis over the last 50 years has identified the main pathways involved in this process, including beta-oxidation, the glyoxylate cycle, and gluconeogenesis. In the last few years molecular genetic dissection of the overall process in the model oilseed species Arabidopsis has provided new insight into its complexity, particularly with respect to the specific role played by individual enzymatic steps and the subcellular compartmentalization of the glyoxylate cycle. Both abscisic acid (ABA) and sugars inhibit storage oil mobilization and a substantial degree of the control appears to operate at the transcriptional level.

Children as ‘Being and Becomings’: Children, Childhood and Temporality

Abstract: Notions of ‘being’ and ‘becoming’ are intrinsic to childhood research. Whilst the ‘being’ child is seen as a social actor actively constructing ‘childhood’, the ‘becoming’ child is seen as an ‘adult in the making’, lacking competencies of the ‘adult’ that he or she will ‘become’. However, I argue that both approaches are in themselves problematic. Instead, theorising children as ‘being and becomings’ not only addresses the temporality of childhood that children themselves voice, but presents a conceptually realistic construction suitable to both childhood researchers and practitioners.

Contingency and Action: A Comparison of Two Forms of Requesting

Abstract: In this article, we explore the syntactic forms speakers use when making requests. An initial investigation of ordinary telephone calls between family and friends and out-of-hours calls to the doctor showed a difference in the distribution of modal verbs (e.g., Can you …), and requests prefaced by I wonder if. Modals are most common in ordinary conversation, whereas I wonder if … is most frequent in requests made to the doctor. This distributional difference seemed to be supported by calls from private homes to service organizations in which speakers also formatted requests as I wonder if. Further investigation of these and other corpora suggests that this distributional pattern is related not so much with the sociolinguistic speech setting but rather with speakers' orientations to known or anticipated contingencies associated with their request. The request forms speakers select embody, or display, their understandings of the contingencies associated with the recipient's ability to grant the request.

Does Practical Work Really Work? A study of the effectiveness of practical work as a teaching and learning method in school science

Abstract: Many within the science education community and beyond see practical work carried out by students as an essential feature of science education Questions have, however, been raised by some science educators about its effectiveness as a teaching and learning strategy This study explored the effectiveness of practical work by analysing a sample of 25 ‘typical’ science lessons involving practical work in English secondary schools Data took the form of observational field notes and tape‐recorded interviews with teachers and students The analysis used a model of effectiveness based on the work of Millar et al and Tiberghien The teachers’ focus in these lessons was predominantly on developing students’ substantive scientific knowledge, rather than on developing understanding of scientific enquiry procedures Practical work was generally effective in getting students to do what is intended with physical objects, but much less effective in getting them to use the intended scientific ideas to guide their acti

An architectural approach to the comparative ecology of plant root systems

Abstract: Summary Although plants devote a large proportion of their resources to roots, we have a poor understanding of the constraints under which root systems function. Roots are much less variable morphologically than leaves and it is likely that root systems rather than individual roots are the focus of natural selection. In other words, architecture is more important than morphology. Existing classifications of root systems, based on the developmental model, have failed to provide much insight into their functioning and an alternative, topological model is outlined, in which the link is the basic unit of classification. Other components of the architecture of root systems, including link lengths, branching angles and diameters, are considered and the ecological implications of variation in each is discussed. Simulation models of transport and space exploration are discussed and it is shown that resource cost, transport efficiency and exploration efficiency cannot be simultaneously minimized and that optimum form may vary with the mobility of the resource. In general, a ‘herringbone’ structure seems to be the most efficient at exploration of space but the least transport-efficient and the most expensive.

Aligning Conservation Priorities Across Taxa in Madagascar with High-Resolution Planning Tools

Abstract: Globally, priority areas for biodiversity are relatively well known, yet few detailed plans exist to direct conservation action within them, despite urgent need. Madagascar, like other globally recognized biodiversity hot spots, has complex spatial patterns of endemism that differ among taxonomic groups, creating challenges for the selection of within-country priorities. We show, in an analysis of wide taxonomic and geographic breadth and high spatial resolution, that multitaxonomic rather than single-taxon approaches are critical for identifying areas likely to promote the persistence of most species. Our conservation prioritization, facilitated by newly available techniques, identifies optimal expansion sites for the Madagascar government's current goal of tripling the land area under protection. Our findings further suggest that high-resolution multitaxonomic approaches to prioritization may be necessary to ensure protection for biodiversity in other global hot spots.

Hyperphosphorylation of microtubule-associated protein tau: a promising therapeutic target for Alzheimer disease.

Abstract: Alzheimer disease (AD) is the most common cause of dementia in adults. The current therapy for AD has only moderate efficacy in controlling symptoms, and it does not cure the disease. Recent studies have suggested that abnormal hyperphosphorylation of tau in the brain plays a vital role in the molecular pathogenesis of AD and in neurodegeneration. This article reviews the current advances in understanding of tau protein, regulation of tau phosphorylation, and the role of its abnormal hyperphosphorylation in neurofibrillary degeneration. Furthermore, several therapeutic strategies for treating AD on the basis of the important role of tau hyperphosphorylation in the pathogenesis of the disease are described. These strategies include (1) inhibition of glycogen synthase kinase-3beta (GSK-3beta), cyclin-dependent kinase 5 (cdk5), and other tau kinases; (2) restoration of PP2A activity; and (3) targeting tau O-GlcNAcylation. Development of drugs on the basis of these strategies is likely to lead to disease-modifying therapies for AD.

Economic deprivation, maternal depression, parenting and children's cognitive and emotional development in early childhood.

Abstract: This study uses data from the UK Millennium Cohort Study to examine the extent to which economic circumstances in infancy and mother's mental well-being are associated with children's cognitive development and behaviour problems at age 3 years, and what part parenting behaviours and attitudes play in mediating these factors. The analyses derived from Structural Equation Modelling show that economic deprivation and maternal depression separately and collectively diminish the cognitive and emotional well-being of children, and part of this diminution emanates from less nurturing and engaged parenting by those with less economic and emotional resources.

Sugar Absorption in the Intestine: The Role of GLUT2

Abstract: Intestinal glucose absorption comprises two components. One is classical active absorption mediated by the Na+/glucose cotransporter. The other is a diffusive component, formerly attributed to paracellular flow. Recent evidence, however, indicates that the diffusive component is mediated by the transient insertion of glucose transporter type 2 (GLUT2) into the apical membrane. This apical GLUT2 pathway of intestinal sugar absorption is present in species from insect to human, providing a major route at high sugar concentrations. The pathway is regulated by rapid trafficking of GLUT2 to the apical membrane induced by glucose during assimilation of a meal. Apical GLUT2 is therefore a target for multiple short-term and long-term nutrient-sensing mechanisms. These include regulation by a newly recognized pathway of calcium absorption through the nonclassical neuroendocrine l-type channel Cav1.3 operating during digestion, activation of intestinal sweet taste receptors by natural sugars and artificial sweeteners, paracrine and endocrine hormones, especially insulin and GLP-2, and stress. Permanent apical GLUT2, resulting in increased sugar absorption, is a characteristic of experimental diabetes and of insulin-resistant states induced by fructose and fat. The nutritional consequences of apical and basolateral GLUT2 regulation are discussed in the context of Western diet, processed foods containing artificial sweeteners, obesity, and diabetes.

Sustainable liquid biofuels from biomass: the writing's on the walls

Abstract: Domination of the global biosphere by human beings is unprecedented in the history of the planet, and our impact is such that substantive changes in ecosystems, and the global environment as a whole, are now becoming apparent. Our activity drives the steady increase in global temperature observed in recent decades. The realization of the adverse effects of greenhouse gas emissions on the environment, together with declining petroleum reserves, has ensured that the quest for sustainable and environmentally benign sources of energy for our industrial economies and consumer societies has become urgent in recent years. Consequently, there is renewed interest in the production and use of fuels from plants. The 'first-generation' biofuels made from starch and sugar appear unsustainable because of the potential stress that their production places on food commodities. Second-generation biofuels, produced from cheap and abundant plant biomass, are seen as the most attractive solution to this problem, but a number of technical hurdles must be overcome before their potential is realized. This review will focus on the underpinning research necessary to enable the cost-effective production of liquid fuels from plant biomass, with a particular focus on aspects related to plant cell walls and their bioconversion.