Showing papers by "University of Sheffield published in 2011"

TRY - a global database of plant traits

Abstract: Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Indication of Electron Neutrino Appearance from an Accelerator-produced Off-axis Muon Neutrino Beam

Abstract: The T2K experiment observes indications of nu(mu) -> nu(mu) e appearance in data accumulated with 1.43 x 10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Delta m(23)(2)| = 2.4 x 10(-3) eV(2), sin(2)2 theta(23) = 1 and sin(2)2 theta(13) = 0, the expected number of such events is 1.5 +/- 0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7 x 10(-3), equivalent to 2.5 sigma significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2 theta(13) < 0.28(0.34) for delta(CP) = 0 and a normal (inverted) hierarchy.

The health benefits of urban green spaces: a review of the evidence

Abstract: Background Urban development projects can be costly and have health impacts. An evidence-based approach to urban planning is therefore essential. However, the evidence for physical and non-physical health benefits of urban green space is unclear. Methods A literature search of academic and grey literature was conducted for studies and reviews of the health effects of green space. Articles found were appraised for their relevance, critically reviewed and graded accordingly. Their findings were then thematically categorized. Results There is weak evidence for the links between physical, mental health and well-being, and urban green space. Environmental factors such as the quality and accessibility of green space affects its use for physical activity. User determinants, such as age, gender, ethnicity and the perception of safety, are also important. However, many studies were limited by poor study design, failure to exclude confounding, bias or reverse causality and weak statistical associations. Conclusion Most studies reported findings that generally supported the view that green space have a beneficial health effect. Establishing a causal relationship is difficult, as the relationship is complex. Simplistic urban interventions may therefore fail to address the underlying determinants of urban health that are not remediable by landscape redesign.

Applications of next generation sequencing in molecular ecology of non-model organisms

Abstract: As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

Design concepts for the Cherenkov Telescope Array CTA: An advanced facility for ground-based high-energy gamma-ray astronomy

Abstract: Ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes. Ground-based gamma-ray astronomy has a huge potential in astrophysics, particle physics and cosmology. CTA is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100 GeV and above 100 TeV. CTA will consist of two arrays (one in the north, one in the south) for full sky coverage and will be operated as open observatory. The design of CTA is based on currently available technology. This document reports on the status and presents the major design concepts of CTA.

The 2010 Amazon Drought

Abstract: In 2010, dry-season rainfall was low across Amazonia, with apparent similarities to the major 2005 drought. We analyzed a decade of satellite-derived rainfall data to compare both events. Standardized anomalies of dry-season rainfall showed that 57% of Amazonia had low rainfall in 2010 as compared with 37% in 2005 (≤-1 standard deviation from long-term mean). By using relationships between drying and forest biomass responses measured for 2005, we predict the impact of the 2010 drought as 2.2 × 10(15) grams of carbon [95% confidence intervals (CIs) are 1.2 and 3.4], largely longer-term committed emissions from drought-induced tree deaths, compared with 1.6 × 10(15) grams of carbon (CIs 0.8 and 2.6) for the 2005 event.

Enhanced intercell interference coordination challenges in heterogeneous networks

Abstract: 3GPP LTE-Advanced has recently been investigating heterogeneous network (HetNet) deployments as a cost effective way to deal with the unrelenting traffic demand. HetNets consist of a mix of macrocells, remote radio heads, and low-power nodes such as picocells, femtocells, and relays. Leveraging network topology, increasing the proximity between the access network and the end users, has the potential to provide the next significant performance leap in wireless networks, improving spatial spectrum reuse and enhancing indoor coverage. Nevertheless, deployment of a large number of small cells overlaying the macrocells is not without new technical challenges. In this article, we present the concept of heterogeneous networks and also describe the major technical challenges associated with such network architecture. We focus in particular on the standardization activities within the 3GPP related to enhanced intercell interference coordination.

Markers of bone turnover for the prediction of fracture risk and monitoring of osteoporosis treatment: a need for international reference standards

Abstract: The International Osteoporosis Foundation (IOF) and the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) recommend that a marker of bone formation (serum procollagen type I N propeptide, s-PINP) and a marker of bone resorption (serum C-terminal telopeptide of type I collagen, s-CTX) are used as reference analytes for bone turnover markers in clinical studies. Bone turnover markers (BTM) predict fracture risk, and treatment-induced changes in specific markers account for a substantial proportion of fracture risk reduction. The aims of this report were to determine their clinical potential in the prediction of fracture risk and for monitoring the treatment of osteoporosis and to set an appropriate research agenda. Evidence from prospective studies was gathered through literature review of the PUBMED database between the years 2000 and 2010 and the systematic review of the Agency for Healthcare Research and Quality up to 2001. High levels of BTMs may predict fracture risk independently from bone mineral density in postmenopausal women. They have been used for this purpose in clinical practice for many years, but there is still a need for stronger evidence on which to base practice. BTMs provide pharmacodynamic information on the response to osteoporosis treatment, and as a result, they are widely used for monitoring treatment in the individual. However, their clinical value for monitoring is limited by inadequate appreciation of the sources of variability, by limited data for comparison of treatments using the same BTM and by inadequate quality control. IOF/IFCC recommend one bone formation marker (s-PINP) and one bone resorption marker (s-CTX) to be used as reference markers and measured by standardised assays in observational and intervention studies in order to compare the performance of alternatives and to enlarge the international experience of the application of markers to clinical medicine. BTM hold promise in fracture risk prediction and for monitoring treatment. Uncertainties over their clinical use can be in part resolved by adopting international reference standards.

The interdependence of mechanisms underlying climate-driven vegetation mortality

Abstract: Climate-driven vegetation mortality is occurring globally and is predicted to increase in the near future. The expected climate feedbacks of regional-scale mortality events have intensified the need to improve the simple mortality algorithms used for future predictions, but uncertainty regarding mortality processes precludes mechanistic modeling. By integrating new evidence from a wide range of fields, we conclude that hydraulic function and carbohydrate and defense metabolism have numerous potential failure points, and that these processes are strongly interdependent, both with each other and with destructive pathogen and insect populations. Crucially, most of these mechanisms and their interdependencies are likely to become amplified under a warmer, drier climate. Here, we outline the observations and experiments needed to test this interdependence and to improve simulations of this emergent global phenomenon.

Growth of Candida albicans hyphae

Abstract: The fungus Candida albicans is often a benign member of the mucosal flora; however, it commonly causes mucosal disease with substantial morbidity and in vulnerable patients it causes life-threatening bloodstream infections. A striking feature of its biology is its ability to grow in yeast, pseudohyphal and hyphal forms. The hyphal form has an important role in causing disease by invading epithelial cells and causing tissue damage. This Review describes our current understanding of the network of signal transduction pathways that monitors environmental cues to activate a programme of hypha-specific gene transcription, and the molecular processes that drive the highly polarized growth of hyphae.

Don't judge species on their origins

Abstract: Conservationists should assess organisms on environmental impact rather than on whether they are natives, argue Mark Davis and 18 other ecologists.

A gravitational wave observatory operating beyond the quantum shot-noise limit

Abstract: Around the globe several observatories are seeking the first direct detection of gravitational waves (GWs). These waves are predicted by Einstein’s general theory of relativity1 and are generated, for example, by black-hole binary systems2. Present GW detectors are Michelson-type kilometre-scale laser interferometers measuring the distance changes between mirrors suspended in vacuum. The sensitivity of these detectors at frequencies above several hundred hertz is limited by the vacuum (zero-point) fluctuations of the electromagnetic field. A quantum technology—the injection of squeezed light3—offers a solution to this problem. Here we demonstrate the squeezed-light enhancement of GEO 600, which will be the GW observatory operated by the LIGO Scientific Collaboration in its search for GWs for the next 3–4 years. GEO 600 now operates with its best ever sensitivity, which proves the usefulness of quantum entanglement and the qualification of squeezed light as a key technology for future GW astronomy4.

The effect of environmental change on human migration

Abstract: The influence of the environment and environmental change is largely unrepresented in standard theories of migration, whilst recent debates on climate change and migration focus almost entirely on displacement and perceive migration to be a problem. Drawing on an increasing evidence base that has assessed elements of the influence of the environment on migration, this paper presents a new framework for understanding the effect of environmental change on migration. The framework identifies five families of drivers which affect migration decisions: economic, political, social, demographic and environmental drivers. The environment drives migration through mechanisms characterised as the availability and reliability of ecosystem services and exposure to hazard. Individual migration decisions and flows are affected by these drivers operating in combination, and the effect of the environment is therefore highly dependent on economic, political, social and demographic context. Environmental change has the potential to affect directly the hazardousness of place. Environmental change also affects migration indirectly, in particular through economic drivers, by changing livelihoods for example, and political drivers, through affecting conflicts over resources, for example. The proposed framework, applicable to both international and internal migration, emphasises the role of human agency in migration decisions, in particular the linked role of family and household characteristics on the one hand, and barriers and facilitators to movement on the other in translating drivers into actions. The framework can be used to guide new research, assist with the evaluation of policy options, and provide a context for the development of scenarios representing a range of plausible migration futures.

Climate change and plant regeneration from seed

Abstract: At the core of plant regeneration, temperature and water supply are critical drivers for seed dormancy (initiation, break) and germination. Hence, global climate change is altering these environmental cues and will preclude, delay, or enhance regeneration from seeds, as already documented in some cases. Along with compromised seedling emergence and vigour, shifts in germination phenology will influence population dynamics, and thus, species composition and diversity of communities. Altered seed maturation (including consequences for dispersal) and seed mass will have ramifications on life history traits of plants. Predicted changes in temperature and precipitation, and thus in soil moisture, will affect many components of seed persistence in soil, e.g. seed longevity, dormancy release and germination, and soil pathogen activity. More/less equitable climate will alter geographic distribution for species, but restricted migratory capacity in some will greatly limit their response. Seed traits for weedy species could evolve relatively quickly to keep pace with climate change enhancing their negative environmental and economic impact. Thus, increased research in understudied ecosystems, on key issues related to seed ecology, and on evolution of seed traits in nonweedy species is needed to more fully comprehend and plan for plant responses to global warming.

Secular trends in the incidence of hip and other osteoporotic fractures

Abstract: Osteoporosis constitutes a major public health problem through its association with age-related fractures, most notably those of the proximal femur. Substantial geographic variation has been noted in the incidence of hip fracture throughout the world, and estimates of recent incidence trends have varied widely. Studies in the published literature have reported an increase, plateau, and decrease in age-adjusted incidence rates for hip fracture among both men and women. Accurate characterisation of these temporal trends is important in predicting the health care burden attributable to hip fracture in future decades. We therefore conducted a review of studies worldwide, addressing secular trends in the incidence of hip and other fractures. Studies in western populations, whether in North America, Europe or Oceania, have generally reported increases in hip fracture incidence through the second half of the last century, but those continuing to follow trends over the last two decades have found that rates stabilise with age-adjusted decreases being observed in certain centres. In contrast, some studies suggest that the rate is rising in Asia. This synthesis of temporal trends in the published literature will provide an important resource for preventing fractures. Understanding the reasons for the recent declines in rates of hip fracture may help understand ways to reduce rates of hip fracture worldwide.

The T2K Experiment

Abstract: The T2K experiment is a long-baseline neutrino oscillation experiment Its main goal is to measure the last unknown lepton sector mixing angle {\theta}_{13} by observing { u}_e appearance in a { u}_{\mu} beam It also aims to make a precision measurement of the known oscillation parameters, {\Delta}m^{2}_{23} and sin^{2} 2{\theta}_{23}, via { u}_{\mu} disappearance studies Other goals of the experiment include various neutrino cross section measurements and sterile neutrino searches The experiment uses an intense proton beam generated by the J-PARC accelerator in Tokai, Japan, and is composed of a neutrino beamline, a near detector complex (ND280), and a far detector (Super-Kamiokande) located 295 km away from J-PARC This paper provides a comprehensive review of the instrumentation aspect of the T2K experiment and a summary of the vital information for each subsystem

Mechanistic Insights for Block Copolymer Morphologies: How Do Worms Form Vesicles?

Abstract: Amphiphilic diblock copolymers composed of two covalently linked, chemically distinct chains can be considered to be biological mimics of cell membrane-forming lipid molecules, but with typically more than an order of magnitude increase in molecular weight. These macromolecular amphiphiles are known to form a wide range of nanostructures (spheres, worms, vesicles, etc.) in solvents that are selective for one of the blocks. However, such self-assembly is usually limited to dilute copolymer solutions (<1%), which is a significant disadvantage for potential commercial applications such as drug delivery and coatings. In principle, this problem can be circumvented by polymerization-induced block copolymer self-assembly. Here we detail the synthesis and subsequent in situ self-assembly of amphiphilic AB diblock copolymers in a one pot concentrated aqueous dispersion polymerization formulation. We show that spherical micelles, wormlike micelles, and vesicles can be predictably and efficiently obtained (within 2 ...

Review of statistical methods for analysing healthcare resources and costs.

Abstract: We review statistical methods for analysing healthcare resource use and costs, their ability to address skewness, excess zeros, multimodality and heavy right tails, and their ease for general use. We aim to provide guidance on analysing resource use and costs focusing on randomised trials, although methods often have wider applicability. Twelve broad categories of methods were identified: (I) methods based on the normal distribution, (II) methods following transformation of data, (III) single-distribution generalized linear models (GLMs), (IV) parametric models based on skewed distributions outside the GLM family, (V) models based on mixtures of parametric distributions, (VI) two (or multi)-part and Tobit models, (VII) survival methods, (VIII) non-parametric methods, (IX) methods based on truncation or trimming of data, (X) data components models, (XI) methods based on averaging across models, and (XII) Markov chain methods. Based on this review, our recommendations are that, first, simple methods are preferred in large samples where the near-normality of sample means is assured. Second, in somewhat smaller samples, relatively simple methods, able to deal with one or two of above data characteristics, may be preferable but checking sensitivity to assumptions is necessary. Finally, some more complex methods hold promise, but are relatively untried; their implementation requires substantial expertise and they are not currently recommended for wider applied work.

Associations of Breast Cancer Risk Factors With Tumor Subtypes: A Pooled Analysis From the Breast Cancer Association Consortium Studies

Abstract: BACKGROUND: Previous studies have suggested that breast cancer risk factors are associated with estrogen receptor (ER) and progesterone receptor (PR) expression status of the tumors. METHODS: We pooled tumor marker and epidemiological risk factor data from 35,568 invasive breast cancer case patients from 34 studies participating in the Breast Cancer Association Consortium. Logistic regression models were used in case-case analyses to estimate associations between epidemiological risk factors and tumor subtypes, and case-control analyses to estimate associations between epidemiological risk factors and the risk of developing specific tumor subtypes in 12 population-based studies. All statistical tests were two-sided. RESULTS: In case-case analyses, of the epidemiological risk factors examined, early age at menarche (≤12 years) was less frequent in case patients with PR(-) than PR(+) tumors (P = .001). Nulliparity (P = 3 × 10(-6)) and increasing age at first birth (P = 2 × 10(-9)) were less frequent in ER(-) than in ER(+) tumors. Obesity (body mass index [BMI] ≥ 30 kg/m(2)) in younger women (≤50 years) was more frequent in ER(-)/PR(-) than in ER(+)/PR(+) tumors (P = 1 × 10(-7)), whereas obesity in older women (>50 years) was less frequent in PR(-) than in PR(+) tumors (P = 6 × 10(-4)). The triple-negative (ER(-)/PR(-)/HER2(-)) or core basal phenotype (CBP; triple-negative and cytokeratins [CK]5/6(+) and/or epidermal growth factor receptor [EGFR](+)) accounted for much of the heterogeneity in parity-related variables and BMI in younger women. Case-control analyses showed that nulliparity, increasing age at first birth, and obesity in younger women showed the expected associations with the risk of ER(+) or PR(+) tumors but not triple-negative (nulliparity vs parity, odds ratio [OR] = 0.94, 95% confidence interval [CI] = 0.75 to 1.19, P = .61; 5-year increase in age at first full-term birth, OR = 0.95, 95% CI = 0.86 to 1.05, P = .34; obesity in younger women, OR = 1.36, 95% CI = 0.95 to 1.94, P = .09) or CBP tumors. CONCLUSIONS: This study shows that reproductive factors and BMI are most clearly associated with hormone receptor-positive tumors and suggest that triple-negative or CBP tumors may have distinct etiology.

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

Abstract: The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis

Abstract: Amyotrophic lateral sclerosis (ALS) is a genetically diverse disease. At least 15 ALS-associated gene loci have so far been identified, and the causative gene is known in approximately 30% of familial ALS cases. Less is known about the factors underlying the sporadic form of the disease. The molecular mechanisms of motor neuron degeneration are best understood in the subtype of disease caused by mutations in superoxide dismutase 1, with a current consensus that motor neuron injury is caused by a complex interplay between multiple pathogenic processes. A key recent finding is that mutated TAR DNA-binding protein 43 is a major constituent of the ubiquitinated protein inclusions in ALS, providing a possible link between the genetic mutation and the cellular pathology. New insights have also indicated the importance of dysregulated glial cell-motor neuron crosstalk, and have highlighted the vulnerability of the distal axonal compartment early in the disease course. In addition, recent studies have suggested that disordered RNA processing is likely to represent a major contributing factor to motor neuron disease. Ongoing research on the cellular pathways highlighted in this Review is predicted to open the door to new therapeutic interventions to slow disease progression in ALS.

Convergent Cenozoic CO2 history

Abstract: Reconstructions of atmospheric carbon dioxide concentrations over the past 65 million years are heading towards consensus. It is time for systematic testing of the proxies, against measurements and against each other.

Principles of planar polarity in animal development.

Abstract: Planar polarity describes the coordinated polarisation of cells or structures in the plane of a tissue. The patterning mechanisms that underlie planar polarity are well characterised in Drosophila, where many events are regulated by two pathways: the 'core' planar polarity complex and the Fat/Dachsous system. Components of both pathways also function in vertebrates and are implicated in diverse morphogenetic processes, some of which self-evidently involve planar polarisation and some of which do not. Here, we review the molecular mechanisms and cellular consequences of planar polarisation in diverse contexts, seeking to identify the common principles across the animal kingdom.

Models of cardiac tissue electrophysiology: progress, challenges and open questions.

Abstract: Models of cardiac tissue electrophysiology are an important component of the Cardiac Physiome Project, which is an international effort to build biophysically based multi-scale mathematical models of the heart. Models of tissue electrophysiology can provide a bridge between electrophysiological cell models at smaller scales, and tissue mechanics, metabolism and blood flow at larger scales. This paper is a critical review of cardiac tissue electrophysiology models, focussing on the micro-structure of cardiac tissue, generic behaviours of action potential propagation, different models of cardiac tissue electrophysiology, the choice of parameter values and tissue geometry, emergent properties in tissue models, numerical techniques and computational issues. We propose a tentative list of information that could be included in published descriptions of tissue electrophysiology models, and used to support interpretation and evaluation of simulation results. We conclude with a discussion of challenges and open questions.