Classical Mobility of Highly Mobile Crystal Defects

International audienc

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

A comparative study of Tam3 and Ac transposition in transgenic tobacco and petunia plants

Transposition of the Anthirrinum majus Tam3 element and the Zea mays Ac element has been monitored in petunia and tobacco plants. Plant vectors were constructed with the transposable elements cloned into the leader sequence of a marker gene. Agrobacterium tumefaciens-mediated leaf disc transformation was used to introduce the transposable element constructs into plant cells. In transgenic plants, excision of the transposable element restores gene expression and results in a clearly distinguishable phenotype. Based on restored expression of the hygromycin phosphotransferase II (HPTII) gene, we established that Tam3 excises in 30% of the transformed petunia plants and in 60% of the transformed tobacco plants. Ac excises from the HPTII gene with comparable frequencies (30%) in both plant species. When the β-glucuronidase (GUS) gene was used to detect transposition of Tam3, a significantly lower excision frequency (13%) was found in both plant species. It could be shown that deletion of parts of the transposable elements Tam3 and Ac, removing either one of the terminal inverted repeats (TIR) or part of the presumptive transposase coding region, abolished the excision from the marker genes. This demonstrates that excision of the transposable element Tam3 in heterologous plant species, as documented for the autonomous element Ac, also depends on both properties. Southern blot hybridization shows the expected excision pattern and the reintegration of Tam3 and Ac elements into the genome of tobacco plants.

Unintended Consequences of Incentive Provision for Behaviour Change and Maintenance around Childbirth

Financial (positive or negative) and non-financial incentives or rewards are increasingly used in attempts to influence health behaviours. While unintended consequences of incentive provision are discussed in the literature, evidence syntheses did not identify any primary research with the aim of investigating unintended consequences of incentive interventions for lifestyle behaviour change. Our objective was to investigate perceived positive and negative unintended consequences of incentive provision for a shortlist of seven promising incentive strategies for smoking cessation in pregnancy and breastfeeding. A multi-disciplinary, mixed-methods approach included involving two service-user mother and baby groups from disadvantaged areas with experience of the target behaviours as study co-investigators. Systematic reviews informed the shortlist of incentive strategies. Qualitative semi-structured interviews and a web-based survey of health professionals asked open questions on positive and negative consequences of incentives. The participants from three UK regions were a diverse sample with and without direct experience of incentive interventions: 88 pregnant women/recent mothers/partners/family members; 53 service providers; 24 experts/decision makers and interactive discussions with 63 conference attendees. Maternity and early years health professionals (n = 497) including doctors, midwives, health visitors, public health and related staff participated in the survey. Qualitative analysis identified ethical, political, cultural, social and psychological implications of incentive delivery at population and individual levels. Four key themes emerged: how incentives can address or create inequalities; enhance or diminish intrinsic motivation and wellbeing; have a positive or negative effect on relationships with others within personal networks or health providers; and can impact on health systems and resources by raising awareness and directing service delivery, but may be detrimental to other health care areas. Financial incentives are controversial and generated emotive and oppositional responses. The planning, design and delivery of future incentive interventions should evaluate unexpected consequences to inform the evidence for effectiveness, cost-effectiveness and future implementation

The International-Trade Network: Gravity Equations and Topological Properties

This paper begins to explore the determinants of the topological properties of the international - trade network (ITN). We fit bilateral-trade flows using a standard gravity equation to build a "residual" ITN where trade-link weights are depurated from geographical distance, size, border effects, trade agreements, and so on. We then compare the topological properties of the original and residual ITNs. We find that the residual ITN displays, unlike the original one, marked signatures of a complex system, and is characterized by a very different topological architecture. Whereas the original ITN is geographically clustered and organized around a few large-sized hubs, the residual ITN displays many small-sized but trade-oriented countries that, independently of their geographical position, either play the role of local hubs or attract large and rich countries in relatively complex trade-interaction patterns

Need-based resource allocation: different need indicators, different results?

<p>Abstract</p> <p>Background</p> <p>A key policy objective in most publicly financed health care systems is to allocate resources according to need. Many jurisdictions implement this policy objective through need-based allocation models. To date, no gold standard exists for selecting need indicators. In the absence of a gold standard, sensitivity of the choice of need indicators is of concern. The primary objective of this study was to assess the consistency and plausibility of estimates of per capita relative need for health services across Canadian provinces based on different need indicators.</p> <p>Methods</p> <p>Using the 2000/2001 Canadian Community Health Survey, we estimated relative per capita need for general practitioner, specialist, and hospital services by province using two approaches that incorporated a different set of need indicators: (1) demographics (age and sex), and (2) demographics, socioeconomic status, and health status. For both approaches, we first fitted regression models to estimate standard utilization of each of three types of health services by indicators of need. We defined the standard as average levels of utilization by needs indicators in the national sample. Subsequently, we estimated expected per capita utilization of each type of health services in each province. We compared these estimates of per capita relative need with premature mortality in each province to check their face validity.</p> <p>Results</p> <p>Both approaches suggested that expected relative per capita need for three services vary across provinces. Different approaches, however, yielded different and inconsistent results. Moreover, provincial per capita relative need for the three health services did not always indicate the same direction of need suggested by premature mortality in each province. In particular, the two approaches suggested Newfoundland had less need than the Canadian average for all three services, but it had the highest premature mortality in Canada.</p> <p>Conclusion</p> <p>Substantial differences in need for health care may exist across Canadian provinces, but the direction and magnitude of differences depend on the need indicators used. Allocations from models using survey data lacked face validity for some provinces. These results call for the need to better understand the biases that may result from the use of survey data for resource allocation.</p

Conglobation in the Pill Bug, Armadillidium vulgare, as a Water Conservation Mechanism

Water balance of the terrestrial isopod, Armadillidium vulgare, was investigated during conglobation (rolling-up behavior). Water loss and metabolic rates were measured at 18 ± 1°C in dry air using flow-through respirometry. Water-loss rates decreased 34.8% when specimens were in their conglobated form, while CO2 release decreased by 37.1%. Water loss was also measured gravimetrically at humidities ranging from 6 to 75 %RH. Conglobation was associated with a decrease in water-loss rates up to 53 %RH, but no significant differences were observed at higher humidities. Our findings suggest that conglobation behavior may help to conserve water, in addition to its demonstrated role in protection from predation

The relationship between general practice characteristics and quality of care: a national survey of quality indicators used in the UK Quality and Outcomes Framework, 2004–5

BACKGROUND: The descriptive information now available for primary care in the UK is unique in international terms. Under the 'Quality and Outcomes Framework' (QOF), data for 147 performance indicators are available for each general practice. We aimed to determine the relationship between the quality of primary care, as judged by the total QOF score, social deprivation and practice characteristics. METHODS: We obtained QOF data for each practice in England and linked these with census derived data (deprivation indices and proportion of patients born in a developing country). Characteristics of practices were also obtained. QOF and census data were available for 8480 practices. RESULTS: The median QOF score was 999.7 out of a possible maximum of 1050 points. Three characteristics were independently associated with higher QOF scores: training practices, group practices and practices in less socially deprived areas. In a regression model, these three factors explained 14.6% of the variation in QOF score. Higher list sizes per GP, turnover of registered patients, chronic disease prevalence, proportions of elderly patients or patients born in a developing country did not contribute to lower QOF scores in the final model. CONCLUSION: Socially deprived areas experience a lower quality of primary care, as judged by QOF scores. Social deprivation itself is an independent predictor of lower quality. Training and group practices are independent predictors of higher quality but these types of practices are less well represented in socially deprived areas

Parents’ perspectives on their children’s music therapy: A synthesis of qualitative literature

There is no existing qualitative synthesis of the music therapy literature on parents’ perspectives on their children’s music therapy. This study seeks to fill this gap, motivated by the first author’s experiences as a clinician/researcher. A systematic search of health databases, hand searches of key journals and searches of doctoral theses were undertaken to identify relevant studies. Thirteen studies which met inclusion criteria, including a total of 102 participants, were identified. Relevant data were extracted from these studies for comparison and analysis, with quality of studies assessed using the CASP appraisal tool. Findings were analysed following procedures of thematic synthesis. Six descriptive themes were grouped into three analytic themes: Parents perceived positive impacts of music therapy on their children; parents experienced music therapy as a nurturing environment for themselves and their children; and some parents experienced challenges to their engagement with music therapy. Most studies (12/13) explored parents’ perceptions of music therapy where they were included in sessions. The findings identify positive perceptions of family-centred models of music therapy for children and parents. Parents’ perceptions of children were altered positively through experiencing them in new ways in music therapy. Parents also perceived positive outcomes for their children. These findings identify an emphasis in the qualitative literature on parents’ perceptions on research into music therapy which includes parents in sessions. Only one study explored perceptions of a model where parents were not present during their child’s sessions. More research is needed into parents’ perceptions of music therapy where parents are not present during sessions. Further intervention studies into family-centred models of music therapy with children are also recommended

Differences in the quality of primary medical care for CVD and diabetes across the NHS: evidence from the quality and outcomes framework

Background: Health policy in the UK has rapidly diverged since devolution in 1999. However, there is relatively little comparative data available to examine the impact of this natural experiment in the four UK countries. The Quality and Outcomes Framework of the 2004 General Medical Services Contract provides a new and potentially rich source of comparable clinical quality data through which we compare quality of primary medical care for coronary heart disease (CHD), stroke, hypertension and diabetes across the four UK countries. &lt;p/&gt;Methods: A cross-sectional analysis was undertaken involving 10,064 general practices in England, Scotland, Wales and Northern Ireland. The main outcome measures were prevalence rates for CHD, stroke, hypertension and diabetes. Achievement on 14 simple process, 3 complex process, 9 intermediate outcome and 5 treatment indicators for the four clinical areas. &lt;p/&gt;Results: Prevalence varies by up to 28% between the four UK countries, which is not reflected in resource distribution between countries, and penalises practices in the high prevalence countries (Wales and Scotland). Differences in simple process measures across countries are small. Larger differences are found for complex process, intermediate outcome and treatment measures, most notably for Wales, which has consistently lower quality of care. Scotland has generally higher quality than England and Northern Ireland is most consistently the highest quality. &lt;p/&gt;Conclusion: Previously identified weaknesses in Wales related to waiting times appear to reflect a more general quality problem within NHS Wales. Identifying explanations for the observed differences is limited by the lack of comparable data on practice resources and organisation. Maximising the value of cross-jurisdictional comparisons of the ongoing natural experiment of health policy divergence within the UK requires more detailed examination of resource and organisational differences