Showing papers by "University of Leeds published in 2008"

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Living with difference: reflections on geographies of encounter:

Abstract: In this Progress in Human Geography annual lecture I reflect on geographical contributions to academic and policy debates about how we might forge civic culture out of difference. In doing so I begin by tracing a set of disparate geographical writings — about the micro-publics of everyday life, cosmopolitanism hospitality, and new urban citizenship — that have sought to understand the role of shared space in providing the opportunity for encounter between `strangers'. This literature is considered in the light of an older tradition of work about `the contact hypothesis' from psychology. Then, employing original empirical material, I critically reflect on the notion of `meaningful contact' to explore the paradoxical gap that emerges in geographies of encounter between values and practices. In the conclusion I argue for the need for geographers to pay more attention to sociospatial inequalities and the insecurities they breed, and to unpacking the complex and intersecting ways in which power operates.

IL-6 receptor inhibition with tocilizumab improves treatment outcomes in patients with rheumatoid arthritis refractory to anti-tumour necrosis factor biologicals: results from a 24-week multicentre randomised placebo-controlled trial

Abstract: Objectives: The phase III RADIATE study examined the efficacy and safety of tocilizumab, an anti-IL-6 receptor monoclonal antibody in patients with rheumatoid arthritis (RA) refractory to tumour necrosis factor (TNF) antagonist therapy. Methods: 499 patients with inadequate response to one or more TNF antagonists were randomly assigned to receive 8 mg/kg or 4 mg/kg tocilizumab or placebo (control) intravenously every 4 weeks with stable methotrexate for 24 weeks. ACR20 responses, secondary efficacy and safety endpoints were assessed. Results: ACR20 was achieved at 24 weeks by 50.0%, 30.4% and 10.1% of patients in the 8 mg/kg, 4 mg/kg and control groups, respectively (less than p Conclusion: Tocilizumab plus methotrexate is effective in achieving rapid and sustained improvements in signs and symptoms of RA in patients with inadequate response to TNF antagonists and has a manageable safety profile. Trial registration number: NCT00106522.

Peatlands and the carbon cycle: from local processes to global implications - a synthesis

Abstract: Although peatlands cover only 3% of the Earth's land surface, boreal and subarctic peatlands store about 15?30% of the world's soil carbon as peat. Despite their potential for large positive feedbacks to the climate system through sequestration and emission of greenhouse gases, peatlands are not explicitly included in global climate models and therefore in predictions of future climate change. In April 2007 a symposium was held in Wageningen, the Netherlands, to advance our understanding of peatland C cycling through integration across disciplines and research approaches and to develop a more synthetic picture of the present and future role of peatlands in the global C cycle and their interactions with the climate system. This paper aims to synthesize the main findings of the symposium, focusing on (i) small-scale processes, (ii) C fluxes at the landscape scale, and (iii) peatlands and climate. The paper concludes with a summary of the main drivers of the C balance of peatlands, and proposes directions for new research to reduce key uncertainties in our knowledge of C cycling in peatlands in order to facilitate the explicit inclusion of these ecosystems in a new generation of earth system models.

Genome-wide association analysis identifies 20 loci that influence adult height

Abstract: Adult height is a model polygenic trait, but there has been limited success in identifying the genes underlying its normal variation. To identify genetic variants influencing adult human height, we used genome-wide association data from 13,665 individuals and genotyped 39 variants in an additional 16,482 samples. We identified 20 variants associated with adult height (P < 5 x 10(-7), with 10 reaching P < 1 x 10(-10)). Combined, the 20 SNPs explain approximately 3% of height variation, with a approximately 5 cm difference between the 6.2% of people with 17 or fewer 'tall' alleles compared to the 5.5% with 27 or more 'tall' alleles. The loci we identified implicate genes in Hedgehog signaling (IHH, HHIP, PTCH1), extracellular matrix (EFEMP1, ADAMTSL3, ACAN) and cancer (CDK6, HMGA2, DLEU7) pathways, and provide new insights into human growth and developmental processes. Finally, our results provide insights into the genetic architecture of a classic quantitative trait.

A phase III randomized comparison of lapatinib plus capecitabine versus capecitabine alone in women with advanced breast cancer that has progressed on trastuzumab: updated efficacy and biomarker analyses

Abstract: Purpose Lapatinib is a small molecule, dual tyrosine kinase inhibitor of epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor type 2 (HER2). Initial results of a phase III trial demonstrated that lapatinib plus capecitabine is superior to capecitabine alone in women with HER2-positive advanced breast cancer that progressed following prior therapy including trastuzumab. Updated efficacy and initial biomarker results from this trial are reported. Methods Women with HER2-positive, locally advanced or metastatic breast cancer previously treated with anthracycline-, taxane-, and trastuzumab-containing regimens were randomized to lapatinib 1,250 mg/day continuously plus capecitabine 2,000 mg/m2 days 1–14 of a 21-day cycle or capecitabine 2,500 mg/m2 on the same schedule. The primary endpoint was time to progression (TTP) as determined by an independent review panel. Relationship between progression-free survival (PFS) and tumor HER2 expression and serum levels of HER2 extracellular domain (ECD) were assessed. Results 399 women were randomized. The addition of lapatinib prolonged TTP with a hazard ratio (HR) of 0.57 (95% CI, 0.43–0.77; P < 0.001) and provided a trend toward improved overall survival (HR: 0.78, 95% CI: 0.55–1.12, P = 0.177), and fewer cases with CNS involvement at first progression (4 vs. 13, P = 0.045). Baseline serum HER2 ECD did not predict for benefit from lapatinib. Conclusion The addition of lapatinib to capecitabine provides superior efficacy for women with HER2-positive, advanced breast cancer progressing after treatment with anthracycline-, taxane-, and trastuzumab-based therapy. Biomarker studies could not identify a subgroup of patients who failed to benefit from the addition of lapatinib to capecitabine.

Recent advances in stream and river temperature research

Abstract: Research on stream and river temperatures is reviewed with particular attention being given to advances in understanding gained since 1990 and on investigations of fundamental controls on thermal behaviour, thermal heterogeneity at different spatial scales, the influence of human impacts and the nature of past and future trends. Copyright  2008 John Wiley & Sons, Ltd.

Energy Spectrum of Cosmic-Ray Electrons at TeV Energies

Abstract: The very large collection area of ground-based gamma-ray telescopes gives them a substantial advantage over balloon/satellite based instruments in the detection of very-high-energy (>600 GeV) cosmic-ray electrons. Here we present the electron spectrum derived from data taken with the H.E.S.S. system of imaging atmospheric Cherenkov telescopes. In this measurement, the first of this type, we are able to extend the measurement of the electron spectrum beyond the range accessible to direct measurements. We find evidence for a substantial steepening in the energy spectrum above 600 GeV compared to lower energies.

EULAR recommendations for the management of Behçet disease

Abstract: Objectives: To develop evidence-based European League Against Rheumatism (EULAR) recommendations for the management of Behcet disease (BD) supplemented where necessary by expert opinion. Methods: The multidisciplinary expert committee, a task force of the EULAR Standing Committee for Clinical Affairs (ESCCA), consisted of nine rheumatologists (one who was also a clinical epidemiologist and one also a Rehabilitation Medicine doctor), three ophthalmologists, one internist, one dermatologist and one neurologist, representing six European countries plus Tunisia and Korea. A patient representative was also present. Problem areas and related keywords for systematic literature research were identified. Systematic literature research was performed using Medline and the Cochrane Library databases from 1966 through to December 2006. A total of 40 initial statements were generated based on the systematic literature research. These yielded the final recommendations devel- oped from two blind Delphi rounds of voting. Results: Nine recommendations were developed for the management of different aspects of BD. The strength of each recommendation was determined by the level of evidence and the experts' opinions. The level of agreement for each recommendation was determined using a visual analogue scale for the whole committee and for each individual aspect by the subgroups, who consider themselves experts in that field of BD. There was excellent concordance between the level of agreement of the whole group and the ''experts in the field''. Conclusion: Recommendations related to the eye, skin- mucosa disease and arthritis are mainly evidence based, but recommendations on vascular disease, neurological and gastrointestinal involvement are based largely on expert opinion and uncontrolled evidence from open trials and observational studies. The need for further properly designed controlled clinical trials is apparent.

Newly identified genetic risk variants for celiac disease related to the immune response

Abstract: Our genome-wide association study of celiac disease previously identified risk variants in the IL2-IL21 region. To identify additional risk variants, we genotyped 1,020 of the most strongly associated non-HLA markers in an additional 1,643 cases and 3,406 controls. Through joint analysis including the genome-wide association study data (767 cases, 1,422 controls), we identified seven previously unknown risk regions (P < 5 x 10(-7)). Six regions harbor genes controlling immune responses, including CCR3, IL12A, IL18RAP, RGS1, SH2B3 (nsSNP rs3184504) and TAGAP. Whole-blood IL18RAP mRNA expression correlated with IL18RAP genotype. Type 1 diabetes and celiac disease share HLA-DQ, IL2-IL21, CCR3 and SH2B3 risk regions. Thus, this extensive genome-wide association follow-up study has identified additional celiac disease risk variants in relevant biological pathways.

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.

Estimating animal density using camera traps without the need for individual recognition

Abstract: Summary 1Density estimation is of fundamental importance in wildlife management. The use of camera traps to estimate animal density has so far been restricted to capture–recapture analysis of species with individually identifiable markings. This study developed a method that eliminates the requirement for individual recognition of animals by modelling the underlying process of contact between animals and cameras. 2The model provides a factor that linearly scales trapping rate with density, depending on two key biological variables (average animal group size and day range) and two characteristics of the camera sensor (distance and angle within which it detects animals). 3We tested the approach in an enclosed animal park with known abundances of four species, obtaining accurate estimates in three out of four cases. Inaccuracy in the fourth species was because of biased placement of cameras with respect to the distribution of this species. 4Synthesis and applications. Subject to unbiased camera placement and accurate measurement of model parameters, this method opens the possibility of reduced labour costs for estimating wildlife density and may make estimation possible where it has not been previously. We provide guidelines on the trapping effort required to obtain reasonably precise estimates.

Observation of the suppression of the flux of cosmic rays above 4x10(19) eV

Abstract: The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.

Measuring bee diversity in different european habitats and biogeographical regions

Abstract: Bee pollinators are currently recorded with many different sampling methods. However, the relative performances of these methods have not been systematically evaluated and compared. In response to the strong need to record ongoing shifts in pollinator diversity and abundance, global and regional pollinator initiatives must adopt standardized sampling protocols when developing large-scale and long-term monitoring schemes. We systematically evaluated the performance of six sampling methods (observation plots, pan traps, standardized and variable transect walks, trap nests with reed internodes or paper tubes) that are commonly used across a wide range of geographical regions in Europe and in two habitat types (agricultural and seminatural). We focused on bees since they represent the most important pollinator group worldwide. Several characteristics of the methods were considered in order to evaluate their performance in assessing bee diversity: sample coverage, observed species richness, species richness estimators, collector biases (identified by subunit-based rarefaction curves), species composition of the samples, and the indication of overall bee species richness (estimated from combined total samples). The most efficient method in all geographical regions, in both the agricultural and seminatural habitats, was the pan trap method. It had the highest sample coverage, collected the highest number of species, showed negligible collector bias, detected similar species as the transect methods, and was the best indicator of overall bee species richness. The transect methods were also relatively efficient, but they had a significant collector bias. The observation plots showed poor performance. As trap nests are restricted to cavity-nesting bee species, they had a naturally low sample coverage. However, both trap nest types detected additional species that were not recorded by any of the other methods. For large-scale and long-term monitoring schemes with surveyors with different experience levels, we recommend pan traps as the most efficient, unbiased, and cost-effective method for sampling bee diversity. Trap nests with reed internodes could be used as a complementary sampling method to maximize the numbers of collected species. Transect walks are the principal method for detailed studies focusing on plant-pollinator associations. Moreover, they can be used in monitoring schemes after training the surveyors to standardize their collection skills.

Ancestral Monogamy Shows Kin Selection Is Key to the Evolution of Eusociality

Abstract: Close relatedness has long been considered crucial to the evolution of eusociality. However, it has recently been suggested that close relatedness may be a consequence, rather than a cause, of eusociality. We tested this idea with a comparative analysis of female mating frequencies in 267 species of eusocial bees, wasps, and ants. We found that mating with a single male, which maximizes relatedness, is ancestral for all eight independent eusocial lineages that we investigated. Mating with multiple males is always derived. Furthermore, we found that high polyandry (>2 effective mates) occurs only in lineages whose workers have lost reproductive totipotency. These results provide the first evidence that monogamy was critical in the evolution of eusociality, strongly supporting the prediction of inclusive fitness theory.

A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3

Abstract: To identify colorectal cancer (CRC) susceptibility alleles, we conducted a genome-wide association study. In phase 1, we genotyped 550,163 tagSNPs in 940 familial colorectal tumor cases (627 CRC, 313 high-risk adenoma) and 965 controls. In phase 2, we genotyped 42,708 selected SNPs in 2,873 CRC cases and 2,871 controls. In phase 3, we evaluated 11 SNPs showing association at P < 10(-4) in a joint analysis of phases 1 and 2 in 4,287 CRC cases and 3,743 controls. Two SNPs were taken forward to phase 4 genotyping (10,731 CRC cases and 10,961 controls from eight centers). In addition to the previously reported 8q24, 15q13 and 18q21 CRC risk loci, we identified two previously unreported associations: rs10795668, located at 10p14 (P = 2.5 x 10(-13) overall; P = 6.9 x 10(-12) replication), and rs16892766, at 8q23.3 (P = 3.3 x 10(-18) overall; P = 9.6 x 10(-17) replication), which tags a plausible causative gene, EIF3H. These data provide further evidence for the 'common-disease common-variant' model of CRC predisposition.

Certolizumab pegol plus methotrexate is significantly more effective than placebo plus methotrexate in active rheumatoid arthritis: findings of a fifty-two-week, phase III, multicenter, randomized, double-blind, placebo-controlled, parallel-group study.

Abstract: Objective To evaluate the efficacy and safety of 2 dosage regimens of lyophilized certolizumab pegol (a novel PEGylated anti–tumor necrosis factor agent) as adjunctive therapy to methotrexate (MTX) in patients with active rheumatoid arthritis (RA) with an inadequate response to MTX therapy alone. Methods In this 52-week, phase III, multicenter, randomized, double-blind, placebo-controlled, parallel-group trial, 982 patients were randomized 2:2:1 to receive treatment with subcutaneous certolizumab pegol at an initial dosage of 400 mg given at weeks 0, 2, and 4, with a subsequent dosage of 200 mg or 400 mg given every 2 weeks, plus MTX, or placebo plus MTX. Co-primary end points were the response rate at week 24 according to the American College of Rheumatology 20% criteria for improvement (ACR20) and the mean change from baseline in the modified total Sharp score at week 52. Results At week 24, ACR20 response rates using nonresponder imputation for the certolizumab pegol 200-mg and 400-mg groups were 58.8% and 60.8%, respectively, as compared with 13.6% for the placebo group. Differences in ACR20 response rates versus placebo were significant at week 1 and were sustained to week 52 (P < 0.001). At week 52, mean radiographic progression from baseline was reduced in patients treated with certolizumab pegol 200 mg (0.4 Sharp units) or 400 mg (0.2 Sharp units) as compared with that in placebo-treated patients (2.8 Sharp units) (P < 0.001 by rank analysis). Improvements in all ACR core set of disease activity measures, including physical function, were observed by week 1 with both certolizumab pegol dosage regimens. Most adverse events were mild or moderate. Conclusion Treatment with certolizumab pegol 200 or 400 mg plus MTX resulted in a rapid and sustained reduction in RA signs and symptoms, inhibited the progression of structural joint damage, and improved physical function as compared with placebo plus MTX treatment in RA patients with an incomplete response to MTX.

The drivers of Chinese CO2 emissions from 1980 to 2030

Abstract: China's energy consumption doubled within the first 25 years of economic reforms initiated at the end of the 1970s, and doubled again in the past 5 years. It has resulted of a threefold CO2 emissions increase since early of 1980s. China's heavy reliance on coal will make it the largest emitter of CO2 in the world. By combining structural decomposition and input–output analysis we seek to assess the driving forces of China's CO2 emissions from 1980 to 2030. In our reference scenario, production-related CO2 emissions will increase another three times by 2030. Household consumption, capital investment and growth in exports will largely drive the increase in CO2 emissions. Efficiency gains will be partially offset the projected increases in consumption, but our scenarios show that this will not be sufficient if China's consumption patterns converge to current US levels. Relying on efficiency improvements alone will not stabilize China's future emissions. Our scenarios show that even extremely optimistic assumptions of widespread installation of carbon dioxide capture and storage will only slow the increase in CO2 emissions.

Woody cover in African savannas: the role of resources, fire and herbivory

Abstract: Aim To determine the functional relationships between, and the relative importance of, different driver variables (mean annual precipitation, soil properties, fire and herbivory) in regulating woody plant cover across broad environmental gradients in African savannas. Location Savanna grasslands of East, West and Southern Africa. Methods The dependence of woody cover on mean annual precipitation (MAP), soil properties (texture, nitrogen mineralization potential and total phosphorus), fire regimes, and herbivory (grazer, browser + mixed feeder, and elephant biomass) was determined for 161 savanna sites across Africa using stochastic gradient boosting, a refinement of the regression tree analysis technique. Results All variables were significant predictors of woody cover, collectively explaining 71% of the variance in our data set. However, their relative importance as regulators of woody cover varied. MAP was the most important predictor, followed by fire return periods, soil characteristics and herbivory regimes. Woody cover showed a strong positive dependence on MAP between 200 and 700 mm, but no dependence on MAP above this threshold when the effects of other predictors were accounted for. Fires served to reduce woody cover below rainfall-determined levels. Woody cover showed a complex, non-linear relationship with total soil phosphorus, and was negatively correlated with clay content. There was a strong negative dependence of woody cover on soil nitrogen (N) availability, suggesting that increased N-deposition may cause shifts in savannas towards more grassy states. Elephants, mixed feeders and browsers had negative effects on woody cover. Grazers, on the other hand, depressed woody cover at low biomass, but favoured woody vegetation when their biomass exceeded a certain threshold. Main conclusions Our results indicate complex and contrasting relationships between woody cover, rainfall, soil properties and disturbance regimes in savannas, and suggest that future environmental changes such as altered precipitation regimes, N-enrichment and elevated levels of CO2 are likely to have opposing, and potentially interacting, influences on the tree–grass balance in savannas.

The UKIDSS galactic plane survey

Abstract: 'The definitive version is available at www.blackwell-synergy.com .' Copyright Blackwell Publishing DOI: 10.1111/j.1365-2966.2008.13924.x

Ecosystem services and economic theory: integration for policy-relevant research.

Abstract: It has become essential in policy and decision-making circles to think about the economic benefits (in addition to moral and scientific motivations) humans derive from well-functioning ecosystems. The concept of ecosystem services has been developed to address this link between ecosystems and human welfare. Since policy decisions are often evaluated through cost–benefit assessments, an economic analysis can help make ecosystem service research operational. In this paper we provide some simple economic analyses to discuss key concepts involved in formalizing ecosystem service research. These include the distinction between services and benefits, understanding the importance of marginal ecosystem changes, formalizing the idea of a safe minimum standard for ecosystem service provision, and discussing how to capture the public benefits of ecosystem services. We discuss how the integration of economic concepts and ecosystem services can provide policy and decision makers with a fuller spectrum of information for making conservation–conversion trade-offs. We include the results from a survey of the literature and a questionnaire of researchers regarding how ecosystem service research can be integrated into the policy process. We feel this discussion of economic concepts will be a practical aid for ecosystem service research to become more immediately policy relevant.