Showing papers by "University of York published in 2006"

Parallel Declines in Pollinators and Insect-Pollinated Plants in Britain and the Netherlands

Abstract: Despite widespread concern about declines in pollination services, little is known about the patterns of change in most pollinator assemblages. By studying bee and hoverfly assemblages in Britain and the Netherlands, we found evidence of declines (pre-versus post-1980) in local bee diversity in both countries; however, divergent trends were observed in hoverflies. Depending on the assemblage and location, pollinator declines were most frequent in habitat and flower specialists, in univoltine species, and/or in nonmigrants. In conjunction with this evidence, outcrossing plant species that are reliant on the declining pollinators have themselves declined relative to other plant species. Taken together, these findings strongly suggest a causal connection between local extinctions of functionally linked plant and pollinator species.

Quantifying the evidence for biodiversity effects on ecosystem functioning and services.

Abstract: Concern is growing about the consequences of biodiversity loss for ecosystem functioning, for the provision of ecosystem services, and for human well being. Experimental evidence for a relationship between biodiversity and ecosystem process rates is compelling, but the issue remains contentious. Here, we present the first rigorous quantitative assessment of this relationship through meta-analysis of experimental work spanning 50 years to June 2004. We analysed 446 measures of biodiversity effects (252 in grasslands), 319 of which involved primary producer manipulations or measurements. Our analyses show that: biodiversity effects are weaker if biodiversity manipulations are less well controlled; effects of biodiversity change on processes are weaker at the ecosystem compared with the community level and are negative at the population level; productivity-related effects decline with increasing number of trophic links between those elements manipulated and those measured; biodiversity effects on stability measures ('insurance' effects) are not stronger than biodiversity effects on performance measures. For those ecosystem services which could be assessed here, there is clear evidence that biodiversity has positive effects on most. Whilst such patterns should be further confirmed, a precautionary approach to biodiversity management would seem prudent in the meantime.

The Buccaneer software for automated model building. 1. Tracing protein chains.

Abstract: A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely Cα positions. This function is applied both in the location of a few promising `seed' positions in the map and to grow those initial Cα positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.

The distributions of a wide range of taxonomic groups are expanding polewards

Abstract: Evidence is accumulating of shifts in species' distributions during recent climate warming. However, most of this information comes predominantly from studies of a relatively small selection of taxa (i.e., plants, birds and butterflies), which may not be representative of biodiversity as a whole. Using data from less well-studied groups, we show that a wide variety of vertebrate and invertebrate species have moved northwards and uphill in Britain over approximately 25 years, mirroring, and in some cases exceeding, the responses of better-known groups.

Guidance on the conduct of narrative synthesis in sytematic reviews

Abstract: Titles & abstract s Titles & abstracts Include N=54 Include N=121 Include N=89 Exclude N = 0 Exclude N = 1,024 Exclude N = 21

Bio3d: an R package for the comparative analysis of protein structures

Abstract: Summary: An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data. Availability: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/ Contact: bgrant@mccammon.ucsd.edu

The sociology of expectations in science and technology

Abstract: In recent years a growing number of social science studies have pointed out the significance of expectations in science and technology innovation. This special issue of Technology Analysis and Stra...

Collaborative care for depression: a cumulative meta-analysis and review of longer-term outcomes.

Abstract: Background Depression is common in primary care but is suboptimally managed. Collaborative care, that is, structured care involving a greater role of nonmedical specialists to augment primary care, has emerged as a potentially effective candidate intervention to improve quality of primary care and patient outcomes. Methods To quantify the short-term and longer-term effectiveness of collaborative care compared with standard care and to understand mechanisms of action by exploring between-study heterogeneity, we conducted a systematic review of randomized controlled trials that compared collaborative care with usual primary care in patients with depression. We searched MEDLINE (from the beginning of 1966), EMBASE (from the beginning of 1980), CINAHL (from the beginning of 1980), PsycINFO (from the beginning of 1980), the Cochrane Library (from the beginning of 1966), and DARE (Database of Abstracts of Reviews of Effectiveness) (from the beginning of 1985) databases from study inception to February 6, 2006. Results We found 37 randomized studies including 12 355 patients with depression receiving primary care. Random effects meta-analysis showed that depression outcomes were improved at 6 months (standardized mean difference, 0.25; 95% confidence interval, 0.18-0.32), and evidence of longer-term benefit was found for up to 5 years (standardized mean difference, 0.15; 95% confidence interval, 0.001-0.31). When exploring determinants of effectiveness, effect size was directly related to medication compliance and to the professional background and method of supervision of case managers. The addition of brief psychotherapy did not substantially improve outcome, nor did increased numbers of sessions. Cumulative meta-analysis showed that sufficient evidence had emerged by 2000 to demonstrate the statistically significant benefit of collaborative care. Conclusions Collaborative care is more effective than standard care in improving depression outcomes in the short and longer terms. Future research needs to address the implementation of collaborative care, particularly in settings other than the United States.

DeerAnalysis2006 - a comprehensive software package for analyzing pulsed ELDOR data

Abstract: Pulsed electron-electron double resonance techniques such as the four-pulse double electron-electron resonance experiment measure a dipolar evolution function of the sample. For a sample consisting of spin-carrying nanoobjects, this function is the product of a form factor, corresponding to the internal structure of the nanoobject, and a background factor, corresponding to the distribution of nanoobjects in space. The form factor contains information on the spin-to-spin distance distribution within the nanoobject and on the average number of spins per nanoobject, while the background factor depends on constraints, such as a confinement of the nanoobjects to a two-dimensional layer. Separation of the dipolar evolution function into these two contributions and extraction of the spin-to-spin distance distribution require numerically stable mathematical algorithms that can handle data for different classes of samples, e.g., spin-labelled biomacromolecules and synthetic materials. Furthermore, experimental imperfections such as the limited excitation bandwidth of microwave pulses need to be considered. The software package DeerAnalysis2006 provides access to a comprehensive set of tools for such data analysis within a common user interface. This interface allows for several tests of the reliability and precision of the extracted information. User-supplied models for the spin-to-spin distance distribution within a certain class of nanoobjects can be added to an existing library and be fitted with a universal algorithm.

Model-based uncertainty in species range prediction

Abstract: Aim Many attempts to predict the potential range of species rely on environmental niche (or 'bioclimate envelope') modelling, yet the effects of using different niche-based methodologies require further investigation. Here we investigate the impact that the choice of model can have on predictions, identify key reasons why model output may differ and discuss the implications that model uncertainty has for policy-guiding applications. Location The Western Cape of South Africa. Methods We applied nine of the most widely used modelling techniques to model potential distributions under current and predicted future climate for four species (including two subspecies) of Proteaceae. Each model was built using an identical set of five input variables and distribution data for 3996 sampled sites. We compare model predictions by testing agreement between observed and simulated distributions for the present day (using the area under the receiver operating characteristic curve (AUC) and kappa statistics) and by assessing consistency in predictions of range size changes under future climate (using cluster analysis). Results Our analyses show significant differences between predictions from different models, with predicted changes in range size by 2030 differing in both magnitude and direction (e.g. from 92% loss to 322% gain). We explain differences with reference to two characteristics of the modelling techniques: data input requirements (presence/absence vs. presence-only approaches) and assumptions made by each algorithm when extrapolating beyond the range of data used to build the model. The effects of these factors should be carefully considered when using this modelling approach to predict species ranges. Main Conclusions We highlight an important source of uncertainty in assessments of the impacts of climate change on biodiversity and emphasize that model predictions should be interpreted in policy-guiding applications along with a full appreciation of uncertainty.

Nonword repetition and word learning: The nature of the relationship.

Abstract: This article presents a theoretical framework designed to accommodate core evidence that the abilities to repeat nonwords and to learn the phonological forms of new words are closely linked. Basic findings relating nonword repetition and word learning both in typical samples of children and adults and in individuals with disorders of language learning are described. The theoretical analysis of this evidence is organized around the following claims: first, that nonword repetition and word learning both rely on phonological storage; second, that they are both multiply determined, constrained also by auditory, phonological, and speech–motor output processes; third, that a phonological storage deficit alone may not be sufficient to impair language learning to a substantial degree. It is concluded that word learning mediated by temporary phonological storage is a primitive learning mechanism that is particularly important in the early stages of acquiring a language, but remains available to support word learning across the life span.

Evaluation of QUADAS, a tool for the quality assessment of diagnostic accuracy studies

Abstract: A quality assessment tool for diagnostic accuracy studies, named QUADAS, has recently been developed. Although QUADAS has been used in several systematic reviews, it has not been formally validated. The objective was to evaluate the validity and usefulness of QUADAS. Three reviewers independently rated the quality of 30 studies using QUADAS. We assessed the proportion of agreements between each reviewer and the final consensus rating. This was done for all QUADAS items combined and for each individual item. Twenty reviewers who had used QUADAS in their reviews completed a short structured questionnaire on their experience of QUADAS. Over all items, the agreements between each reviewer and the final consensus rating were 91%, 90% and 85%. The results for individual QUADAS items varied between 50% and 100% with a median value of 90%. Items related to uninterpretable test results and withdrawals led to the most disagreements. The feedback on the content of the tool was generally positive with only small numbers of reviewers reporting problems with coverage, ease of use, clarity of instructions and validity. Major modifications to the content of QUADAS itself are not necessary. The evaluation highlighted particular difficulties in scoring the items on uninterpretable results and withdrawals. Revised guidelines for scoring these items are proposed. It is essential that reviewers tailor guidelines for scoring items to their review, and ensure that all reviewers are clear on how to score studies. Reviewers should consider whether all QUADAS items are relevant to their review, and whether additional quality items should be assessed as part of their review.

Escherichia coli K-12: a cooperatively developed annotation snapshot—2005

Abstract: The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

Dynamics of facial expression: recognition of facial actions and their temporal segments from face profile image sequences

Abstract: Automatic analysis of human facial expression is a challenging problem with many applications. Most of the existing automated systems for facial expression analysis attempt to recognize a few prototypic emotional expressions, such as anger and happiness. Instead of representing another approach to machine analysis of prototypic facial expressions of emotion, the method presented in this paper attempts to handle a large range of human facial behavior by recognizing facial muscle actions that produce expressions. Virtually all of the existing vision systems for facial muscle action detection deal only with frontal-view face images and cannot handle temporal dynamics of facial actions. In this paper, we present a system for automatic recognition of facial action units (AUs) and their temporal models from long, profile-view face image sequences. We exploit particle filtering to track 15 facial points in an input face-profile sequence, and we introduce facial-action-dynamics recognition from continuous video input using temporal rules. The algorithm performs both automatic segmentation of an input video into facial expressions pictured and recognition of temporal segments (i.e., onset, apex, offset) of 27 AUs occurring alone or in a combination in the input face-profile video. A recognition rate of 87% is achieved.

The genome of Rhizobium leguminosarum has recognizable core and accessory components

Abstract: Rhizobium leguminosarum is an α-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Phloem-sap feeding by animals: problems and solutions

Abstract: The incidence of phloem sap feeding by animals appears paradoxical. Although phloem sap is nutrient-rich compared with many other plant products and generally lacking in toxins and feeding deterrents, it is consumed as the dominant or sole diet by a very restricted range of animals, exclusively insects of the order Hemiptera. These insects display two sets of adaptations. First, linked to the high ratio of non-essential:essential amino acids in phloem sap, these insects contain symbiotic micro-organisms which provide them with essential amino acids. For example, bacteria of the genus Buchnera contribute up to 90% of the essential amino acids required by the pea aphid Acyrthosiphon pisum feeding on Vicia faba. Second, the insect tolerance of the very high sugar content and osmotic pressure of phloem sap is promoted by their possession in the gut of sucrase-transglucosidase activity, which transforms excess ingested sugar into long-chain oligosaccharides voided via honeydew. Various other animals consume phloem sap by proxy, through feeding on the honeydew of phloem-feeding hemipterans. Honeydew is physiologically less extreme than phloem sap, with a higher essential:non-essential amino acid ratio and lower osmotic pressure. Even so, ant species strongly dependent on honeydew as food may benefit from nutrients derived from their symbiotic bacteria Blochmannia.

Patterns of reading ability in children with autism spectrum disorder.

Abstract: This study investigated reading skills in 41 children with autism spectrum disorder. Four components of reading skill were assessed: word recognition, nonword decoding, text reading accuracy and text comprehension. Overall, levels of word and nonword reading and text reading accuracy fell within average range although reading comprehension was impaired. However, there was considerable variability across the sample with performance on most tests ranging from floor to ceiling levels. Some children read accurately but showed very poor comprehension, consistent with a hyperlexia reading profile; some children were poor at reading words and nonwords whereas others were unable to decode nonwords, despite a reasonable level of word reading skill. These findings demonstrate the heterogeneous nature of reading skills in children with ASD.

How to identify randomized controlled trials in MEDLINE: ten years on

Abstract: PMCID: PMC1435857 This article has been corrected. See J Med Libr Assoc. 2006 July; 94(3): 354. http://europepmc.org/articles/PMC1525311/

Alternative explanations for rising dissolved organic carbon export from organic soils

Abstract: Since 1988, there has been, on average, a 91% increase in dissolved organic carbon (DOC) concentrations of UK lakes and streams in the Acid Waters Monitoring Network (AWMN). Similar DOC increases have been observed in surface waters across much of Europe and North America. Much of the debate about the causes of rising DOC has, as in other studies relating to the carbon cycle, focused on factors related to climate change. Data from our peat-core experiments support an influence of climate on DOC, notably an increase in production with temperature under aerobic, and to a lesser extent anaerobic, conditions. However, we argue that climatic factors may not be the dominant drivers of DOC change. DOC solubility is suppressed by high soil water acidity and ionic strength, both of which have decreased as a result of declining sulphur deposition since the 1980s, augmented during the 1990s in the United Kingdom by a cyclical decline in sea-salt deposition. Our observational and experimental data demonstrate a clear, inverse and quantitatively important link between DOC and sulphate concentrations in soil solution. Statistical analysis of 11 AWMN lakes suggests that rising temperature, declining sulphur deposition and changing sea-salt loading can account for the majority of the observed DOC trend. This combination of evidence points to the changing chemical composition of atmospheric deposition, particularly the substantial reduction in anthropogenic sulphur emissions during the last 20 years, as a key cause of rising DOC. The implications of rising DOC export for the carbon cycle will be very different if linked primarily to decreasing acid deposition, rather than to changes in climate, suggesting that these systems may be recovering rather than destabilising.

The identification of 100 ecological questions of high policy relevance in the UK

Abstract: 1. Evidence-based policy requires researchers to provide the answers to ecological questions that are of interest to policy makers. To find out what those questions are in the UK, representatives from 28 organizations involved in policy, together with scientists from 10 academic institutions, were asked to generate a list of questions from their organizations. 2. During a 2-day workshop the initial list of 1003 questions generated from consulting at least 654 policy makers and academics was used as a basis for generating a short list of 100 questions of significant policy relevance. Short-listing was decided on the basis of the preferences of the representatives from the policy-led organizations. 3. The areas covered included most major issues of environmental concern in the UK, including agriculture, marine fisheries, climate change, ecosystem function and land management. 4. The most striking outcome was the preference for general questions rather than narrow ones. The reason is that policy is driven by broad issues rather than specific ones. In contrast, scientists are frequently best equipped to answer specific questions. This means that it may be necessary to extract the underpinning specific question before researchers can proceed. 5. Synthesis and applications. Greater communication between policy makers and scientists is required in order to ensure that applied ecologists are dealing with issues in a way that can feed into policy. It is particularly important that applied ecologists emphasize the generic value of their work wherever possible.

Good Practice Guidelines for Decision-Analytic Modelling in Health Technology Assessment: A Review and Consolidation of Quality Assessment

Abstract: The use of decision-analytic modelling for the purpose of health technology assessment (HTA) has increased dramatically in recent years. Several guidelines for best practice have emerged in the literature; however, there is no agreed standard for what constitutes a 'good model' or how models should be formally assessed. The objective of this paper is to identify, review and consolidate existing guidelines on the use of decision-analytic modelling for the purpose of HTA and to develop a consistent framework against which the quality of models may be assessed. The review and resultant framework are summarised under the three key themes of Structure, Data and Consistency. 'Structural' aspects relate to the scope and mathematical structure of the model including the strategies under evaluation. Issues covered under the general heading of 'Data' include data identification methods and how uncertainty should be addressed. 'Consistency' relates to the overall quality of the model. The review of existing guidelines showed that although authors may provide a consistent message regarding some aspects of modelling, such as the need for transparency, they are contradictory in other areas. Particular areas of disagreement are how data should be incorporated into models and how uncertainty should be assessed. For the purpose of evaluation, the resultant framework is applied to a decision-analytic model developed as part of an appraisal for the National Institute for Health and Clinical Excellence (NICE) in the UK. As a further assessment, the review based on the framework is compared with an assessment provided by an independent experienced modeller not using the framework. It is hoped that the framework developed here may form part of the appraisals process for assessment bodies such as NICE and decision models submitted to peer review journals. However, given the speed with which decision-modelling methodology advances, there is a need for its continual update.

Interchanges: Gender, sexuality and heterosexuality: The complexity (and limits) of heteronormativity

Abstract: According to Steven Seidman, analysts of institutionalized heterosexuality have ‘focused exclusively on its role in regulating homosexuality’ and, while queer approaches theorize how ‘homosexuality gains its coherence in relation to heterosexuality, the impact of regimes of normative heterosexuality on heterosexuality has largely been ignored’ (2005: 40). Over the last decade and more, however, feminists have been analysing how normative heterosexuality affects the lives of heterosexuals (see Wilkinson and Kitzinger, 1993; Richardson, 1996; Jackson, 1999; Ingraham, 1996, 1999). In so doing they have drawn on earlier feminists, such as Charlotte Bunch (1975), Adrienne Rich (1980) and Monique Wittig (1992), who related heterosexuality to the perpetuation of gendered divisions of labour and male appropriation of women’s productive and reproductive capacities. Indeed, Rich’s concept of ‘compulsory heterosexuality’ could be seen as a forerunner of ‘heteronormativity’ and I would like to preserve an often neglected legacy of the former concept: that institutionalized, normative heterosexuality regulates those kept within its boundaries as well as marginalizing and sanctioning those outside them. The term ‘heteronormativity’ has not always captured this double-sided social regulation. Feminists have a vested interest in what goes on within heterosexual relations because we are concerned with the ways in which heterosexuality depends upon and guarantees gender division. Heterosexuality, however, is not a singular, monolithic entity – it exists in many variants. As Seidman points out there are hierarchies of respectability and good citizenship among heterosexuals, and what tends to be valorized as ‘normative’ is a very particular form founded on traditional gender arrangements and lifelong monogamy (see Seidman, 2005: 59–60; see also Seidman, 2002). Thus the analysis of heteronormativity needs to be rethought in terms of what is subject to regulation on both sides of the normatively prescribed boundaries of heterosexuality: both sexuality and gender. With this in mind, this article re-examines the intersections between gender, sexuality in general and heterosexuality in particular. How these terms are defined is clearly consequential for any analysis of linkages between them. There is no consensus on the question of definition, in large

Range retractions and extinction in the face of climate warming.

Abstract: Until recently, published evidence for the responses of species to climate change had revealed more examples of species expanding than retracting their distributions. However, recent papers on butterflies and frogs now show that population-level and species-level extinctions are occurring. The relative lack of previous information about range retractions and extinctions appears to stem, at least partly, from a failure to survey the distributions of species at sufficiently fine resolution to detect declines, and from a failure to attribute such declines to climate change. The new evidence suggests that climate-driven extinctions and range retractions are already widespread.