Experimental observations of rapid maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background. Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ∼10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results. We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion. These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. © 2008 Walt et al; licensee BioMed Central Ltd.

More men than women make mucosal IgA antibodies to human papillomavirus type 16 (HPV-16) and HPV-18: A study of oral HPV and oral HPV antibodies in a normal healthy population

Background: We have previously shown the high prevalence of oral anti-human papillomavirus type 16 (HPV-16) antibodies in women with HPV-associated cervical neoplasia. It was postulated that the HPV antibodies were initiated after HPV antigenic stimulation at the cervix via the common mucosal immune system. The present study aimed to further evaluate the effectiveness of oral fluid testing for detecting the mucosal humoral response to HPV infection and to advance our limited understanding of the immune response to HPV. Methods: The prevalence of oral HPV infection and oral antibodies to HPV types 16, 18 and 11 was determined in a normal, healthy population of children, adolescents and adults, both male and female, attending a dental clinic. HPV types in buccal cells were determined by DNA sequencing. Oral fluid was collected from the gingival crevice of the mouth by the OraSure method. HPV-16, HPV-18 and HPV-11 antibodies in oral fluid were detected by virus-like particle-based enzyme-linked immunosorbent assay. As a reference group 44 women with cervical neoplasia were included in the study. Results: Oral HPV infection was h ighest in children (9/114, 7.9%), followed by adolescents (4/78, 5.1%), and lowest in normal adults (4/116, 3.5%). The predominant HPV type found was HPV-13 (7/22, 31.8%) followed by HPV-32 (5/22, 22.7%). The prevalence of oral antibodies to HPV-16, HPV-18 and HPV-11 was low in children and increased substantially in adolescents and normal adults. Oral HPV-16 IgA was significantly more prevalent in women with cervical neoplasia (30/44, 68.2%) than the women from the dental clinic (18/69, 26.1% P = 0.0001). Significantly more adult men than women displayed oral HPV-16 IgA (30/47 compared with 18/69, OR 5.0, 95% CI 2.09-12.1, P < 0.001) and HPV-18 IgA (17/47 compared with 13/69, OR 2.4, 95% CI 0.97-6.2, P = 0.04). Conclusion: The increased prevalence of oral HPV antibodies in adolescent individuals compared with children was attributed to the onset of sexual activity. The increased prevalence of oral anti-HPV IgA in men compared with women was noteworthy considering reportedly fewer men than women make serum antibodies, and warrants further investigation. © 2006 Marais et al; licensee BioMed Central Ltd.

Evaluation of implementation of a healthy food and drink supply strategy throughout the whole school environment in Queensland state schools, Australia

BACKGROUND/OBJECTIVES: This paper reports on the evaluation of the Smart Choices healthy food and drink supply strategy for Queensland schools (Smart Choices) implementation across the whole school environment in state government primary and secondary schools in Queensland, Australia. SUBJECTS/METHODS: Three concurrent surveys using different methods for each group of stakeholders that targeted all 1275 school Principals, all 1258 Parent and Citizens’ Associations (P&Cs) and a random sample of 526 tuckshop convenors throughout Queensland. Nine hundred and seventy-three Principals, 598 P&Cs and 513 tuckshop convenors participated with response rates of 78%, 48% and 98%, respectively. RESULTS: Nearly all Principals (97%), P&Cs (99%) and tuckshop convenors (97%) reported that their school tuckshop had implemented Smart Choices. The majority of Principals and P&Cs reported implementation, respectively, in: school breakfast programs (98 and 92%); vending machine stock (94 and 83%); vending machine advertising (85 and 84%); school events (87 and 88%); school sporting events (81 and 80%); sponsorship and advertising (93 and 84%); fundraising events (80 and 84%); and sporting clubs (73 and 75%). Implementation in curriculum activities, classroom rewards and class parties was reported, respectively, by 97%, 86% and 75% of Principals. Respondents also reported very high levels of understanding of Smart Choices and engagement of the school community. CONCLUSIONS: The results demonstrated that food supply interventions to promote nutrition across all domains of the school environment can be implemented successfully.

Do thermal agents affect range of movement and mechanical properties in soft tissues? A systematic review

OBJECTIVES: To examine the effect of thermal agents on the range of movement (ROM) and mechanical properties in soft tissue and to discuss their clinical relevance. DATA SOURCES: Electronic databases (Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE) were searched from their earliest available record up to May 2011 using Medical Subjects Headings and key words. We also undertook related articles searches and read reference lists of all incoming articles. STUDY SELECTION: Studies involving human participants describing the effects of thermal interventions on ROM and/or mechanical properties in soft tissue. Two reviewers independently screened studies against eligibility criteria. DATA EXTRACTION: Data were extracted independently by 2 review authors using a customized form. Methodologic quality was also assessed by 2 authors independently, using the Cochrane risk of bias tool. DATA SYNTHESIS: Thirty-six studies, comprising a total of 1301 healthy participants, satisfied the inclusion criteria. There was a high risk of bias across all studies. Meta-analyses were not undertaken because of clinical heterogeneity; however, effect sizes were calculated. There were conflicting data on the effect of cold on joint ROM, accessory joint movement, and passive stiffness. There was limited evidence to determine whether acute cold applications enhance the effects of stretching, and further evidence is required. There was evidence that heat increases ROM, and a combination of heat and stretching is more effective than stretching alone. CONCLUSIONS: Heat is an effective adjunct to developmental and therapeutic stretching techniques and should be the treatment of choice for enhancing ROM in a clinical or sporting setting. The effects of heat or ice on other important mechanical properties (eg, passive stiffness) remain equivocal and should be the focus of future study.

Assessing Cardiovascular Risk in Regional Areas: The Healthy Hearts – Beyond City Limits Program

Background: Cardiovascular disease (CVD) is more prevalent in regional and remote Australia compared to metropolitan areas. The aim of Healthy Hearts was to determine age and sex specific CVD risk factor levels and the potential value of national risk clinics. Methods: Healthy Hearts was an observational research study conducted in four purposefully selected higher risk communities in regional Victoria, Australia. The main outcome measures were the proportion of participants with CVD risk factors with group comparisons to determine the adjusted likelihood of elevated risk factor levels. Trained personnel used a standardized protocol over four weeks per community to measure CVD risk factor levels, estimate absolute CVD risk and provide feedback and advice. Results: A total of 2125 self-selected participants were assessed (mean age 58 ± 15 years, 57% women). Overall, CVD risk factors were highly prevalent. More men than women had ≥ 2 modifiable CVD risk factors (76% vs. 68%, p < .001), pre-existing CVD (20 vs. 15%, p < .01) and a major ECG abnormality requiring follow-up (15% vs. 7%, p < .001) . Less men reported depressive symptoms compared to women (28% vs. 22%, p < .01). A higher proportion of women were obese (adjusted OR 1.36, 95% CI 1.13 to 1.63), and physically inactive (adjusted OR 1.32, 95% CI 1.07 to 1.63). Conclusions: High CVD risk factor levels were confirmed for regional Victoria. Close engagement with individuals and communities provides scope for the application of regional risk management clinics to reduce the burden of CVD risk in regional Australia.

Ambulance use is associated with higher self-rated illness seriousness : user attitudes and perceptions

Objectives The objective was to study the role and effect of patients' perceptions on reasons for using ambulance services in Queensland, Australia. Methods A cross-sectional survey was conducted of patients (n = 911) presenting via ambulance or self-transport at eight public hospital emergency departments (EDs). The survey included perceived illness severity, attitudes toward ambulance, and reasons for using ambulance. A theoretical framework was developed to inform this study. Results Ambulance users had significantly higher self-rated perceived seriousness, urgency, and pain than self-transports. They were also more likely to agree that ambulance services are for everyone to use, regardless of the severity of their conditions. In compared to self-transports, likelihood of using an ambulance increased by 26% for every unit increase in perceived seriousness; and patients who had not used an ambulance in the 6 months prior to the survey were 66% less likely to arrive by ambulance. Patients who had presented via ambulance stated they considered the urgency (87%) or severity (84%) of their conditions as reasons for calling the ambulance. Other reasons included requiring special care (76%), getting higher priority at the ED (34%), not having a car (34%), and financial concerns (17%). Conclusions Understanding patients' perceptions is essential in explaining their actions and developing safe and effective health promotion programs. Individuals use ambulances for various reasons and justifications according to their beliefs, attitudes, and sociodemographic conditions. Policies to reduce and manage demand for such services need to address both general opinions and specific attitudes toward emergency health services to be effective.

Learning personalized tag ontology from user tagging information

The cross-sections of the Social Web and the Semantic Web has put folksonomy in the spot light for its potential in overcoming knowledge acquisition bottleneck and providing insight for "wisdom of the crowds". Folksonomy which comes as the results of collaborative tagging activities has provided insight into user's understanding about Web resources which might be useful for searching and organizing purposes. However, collaborative tagging vocabulary poses some challenges since tags are freely chosen by users and may exhibit synonymy and polysemy problem. In order to overcome these challenges and boost the potential of folksonomy as emergence semantics we propose to consolidate the diverse vocabulary into a consolidated entities and concepts. We propose to extract a tag ontology by ontology learning process to represent the semantics of a tagging community. This paper presents a novel approach to learn the ontology based on the widely used lexical database WordNet. We present personalization strategies to disambiguate the semantics of tags by combining the opinion of WordNet lexicographers and users’ tagging behavior together. We provide empirical evaluations by using the semantic information contained in the ontology in a tag recommendation experiment. The results show that by using the semantic relationships on the ontology the accuracy of the tag recommender has been improved.

Gender bias in schooling : the case for Bhutan

Differing parental considerations for girls and boys in households are a primary cause of the gender gap in school enrolment and educational attainment in developing countries, particularly in Sub-Saharan Africa and South Asia. While a number of studies have focused on the inequality of educational opportunities in South Asia, little is known about Bhutan. This study uses recent household expenditure data from the Bhutan Living Standard Survey to evaluate the gender gap in the allocation of resources for schooling. The findings, based on cross-sectional as well as household fixed-effect approaches, suggest that girls are less likely to enrol in school but are not allocated fewer resources once they are enrolled.

Fatalism, superstition, religion, and culture : road user beliefs and behaviour in Pakistan

Road traffic crashes have emerged as a major health problem around the world. Road crash fatalities and injuries have been reduced significantly in developed countries, but they are still an issue in low and middle-income countries. The World Health Organization (WHO, 2009) estimates that the death toll from road crashes in low- and middle-income nations is more than 1 million people per year, or about 90% of the global road toll, even though these countries only account for 48% of the world's vehicles. Furthermore, it is estimated that approximately 265,000 people die every year in road crashes in South Asian countries and Pakistan stands out with 41,494 approximately deaths per year. Pakistan has the highest rate of fatalities per 100,000 population in the region and its road crash fatality rate of 25.3 per 100,000 population is more than three times that of Australia's. High numbers of road crashes not only cause pain and suffering to the population at large, but are also a serious drain on the country's economy, which Pakistan can ill-afford. Most studies identify human factors as the main set of contributing factors to road crashes, well ahead of road environment and vehicle factors. In developing countries especially, attention and resources are required in order to improve things such as vehicle roadworthiness and poor road infrastructure. However, attention to human factors is also critical. Human factors which contribute to crashes include high risk behaviours like speeding and drink driving, and neglect of protective behaviours such as helmet wearing and seat belt wearing. Much research has been devoted to the attitudes, beliefs and perceptions which contribute to these behaviours and omissions, in order to develop interventions aimed at increasing safer road use behaviours and thereby reducing crashes. However, less progress has been made in addressing human factors contributing to crashes in developing countries as compared to the many improvements in road environments and vehicle standards, and this is especially true of fatalistic beliefs and behaviours. This is a significant omission, since in different cultures in developing countries there are strong worldviews in which predestination persists as a central idea, i.e. that one's life (and death) and other events have been mapped out and are predetermined. Fatalism refers to a particular way in which people regard the events that occur in their lives, usually expressed as a belief that an individual does not have personal control over circumstances and that their lives are determined through a divine or powerful external agency (Hazen & Ehiri, 2006). These views are at odds with the dominant themes of modern health promotion movements, and present significant challenges for health advocates who aim to avert road crashes and diminish their consequences. The limited literature on fatalism reveals that it is not a simple concept, with religion, culture, superstition, experience, education and degree of perceived control of one's life all being implicated in accounts of fatalism. One distinction in the literature that seems promising is the distinction between empirical and theological fatalism, although there are areas of uncertainty about how well-defined the distinction between these types of fatalism is. Research into road safety in Pakistan is scarce, as is the case for other South Asian countries. From the review of the literature conducted, it is clear that the descriptions given of the different belief systems in developing countries including Pakistan are not entirely helpful for health promotion purposes and that further research is warranted on the influence of fatalism, superstition and other related beliefs in road safety. Based on the information available, a conceptual framework is developed as a means of structuring and focusing the research and analysis. The framework is focused on the influence of fatalism, superstition, religion and culture on beliefs about crashes and road user behaviour. Accordingly, this research aims to provide an understanding of the operation of fatalism and related beliefs in Pakistan to assist in the development and implementation of effective and culturally appropriate interventions. The research examines the influence of fatalism, superstition, religious and cultural beliefs on risky road use in Pakistan and is guided by three research questions: 1. What are the perceptions of road crash causation in Pakistan, in particular the role of fatalism, superstition, religious and cultural beliefs? 2. How does fatalism, superstition, and religious and cultural beliefs influence road user behaviour in Pakistan? 3. Do fatalism, superstition, and religious and cultural beliefs work as obstacles to road safety interventions in Pakistan? To address these questions, a qualitative research methodology was developed. The research focused on gathering data through individual in-depth interviewing using a semi-structured interview format. A sample of 30 participants was interviewed in Pakistan in the cities of Lahore, Rawalpindi and Islamabad. The participants included policy makers (with responsibility for traffic law), experienced police officers, religious orators, professional drivers (truck, bus and taxi) and general drivers selected through a combination of purposive, criterion and snowball sampling. The transcripts were translated from Urdu and analysed using a thematic analysis approach guided by the conceptual framework. The findings were divided into four areas: attribution of crash causation to fatalism; attribution of road crashes to beliefs about superstition and malicious acts; beliefs about road crash causation linked to popular concepts of religion; and implications for behaviour, safety and enforcement. Fatalism was almost universally evident, and expressed in a number of ways. Fate was used to rationalise fatal crashes using the argument that the people killed were destined to die that day, one way or another. Related to this was the sense of either not being fully in control of the vehicle, or not needing to take safety precautions, because crashes were predestined anyway. A variety of superstitious-based crash attributions and coping methods to deal with road crashes were also found, such as belief in the role of the evil eye in contributing to road crashes and the use of black magic by rivals or enemies as a crash cause. There were also beliefs related to popular conceptions of religion, such as the role of crashes as a test of life or a source of martyrdom. However, superstitions did not appear to be an alternative to religious beliefs. Fate appeared as the 'default attribution' for a crash when all other explanations failed to account for the incident. This pervasive belief was utilised to justify risky road use behaviour and to resist messages about preventive measures. There was a strong religious underpinning to the statement of fatalistic beliefs (this reflects popular conceptions of Islam rather than scholarly interpretations), but also an overlap with superstitious and other culturally and religious-based beliefs which have longer-standing roots in Pakistani culture. A particular issue which is explored in more detail is the way in which these beliefs and their interpretation within Pakistani society contributed to poor police reporting of crashes. The pervasive nature of fatalistic beliefs in Pakistan affects road user behaviour by supporting continued risk taking behaviour on the road, and by interfering with public health messages about behaviours which would reduce the risk of traffic crashes. The widespread influence of these beliefs on the ways that people respond to traffic crashes and the death of family members contribute to low crash reporting rates and to a system which appears difficult to change. Fate also appeared to be a major contributing factor to non-reporting of road crashes. There also appeared to be a relationship between police enforcement and (lack of) awareness of road rules. It also appears likely that beliefs can influence police work, especially in the case of road crash investigation and the development of strategies. It is anticipated that the findings could be used as a blueprint for the design of interventions aimed at influencing broad-spectrum health attitudes and practices among the communities where fatalism is prevalent. The findings have also identified aspects of beliefs that have complex social implications when designing and piloting driver intervention strategies. By understanding attitudes and behaviours related to fatalism, superstition and other related concepts, it should be possible to improve the education of general road users, such that they are less likely to attribute road crashes to chance, fate, or superstition. This study also underscores the understanding of this issue in high echelons of society (e.g., policy makers, senior police officers) as their role is vital in dispelling road users' misconceptions about the risks of road crashes. The promotion of an evidence or scientifically-based approach to road user behaviour and road safety is recommended, along with improved professional education for police and policy makers.

The ethnographer as community manager : language translation and user negotiation

This article investigates the ethnographic methodological question of how the researcher observes objectively while being part of the problem they are observing. It uses a case study of ABC Pool to argue a cooperative approach that combines the roles of the ethnographer with that of a community manager who assists in constructing a true representation of the researched environment. By using reflexivity as a research tool, the ethnographer engages in a process to self-check their personal presumptions and prejudices, and to strengthen the constructed representation of the researched environment. This article also suggests combining management and expertise research from the social sciences with ethnography, to understand and engage with the research field participants more intimately - which, ultimately, assists in gathering and analysing richer qualitative data.

Assessment bias : physical activity questionnaire assessment inadvertently influences patients’ desire to be ‘more physically active’

Evaluating physical activity is important for public health population research and evaluating lifestyle interventions among targeted groups. Self-reported questionnaires are frequently used to evaluate physical activity in a variety of contexts where resource or pragmatic limitations prohibit the use of more sophisticated approaches. However, prior research in the use of other patient reported outcomes in healthcare settings has highlighted that simply completing a questionnaire may change a patients’ behaviour or responses to subsequent questions. This methodology study aimed to examine whether completing a standard physical activity questionnaire altered patients responses to two related questions a) whether they are ‘sufficiently physically active’ and b) whether they desire ‘to be more physically active.’

Recruiting and engaging new mothers in nutrition research studies : lessons from the Australian NOURISH randomised controlled trial

Background: Despite important implications for the budgets, statistical power and generalisability of research findings, detailed reports of recruitment and retention in randomised controlled trials (RCTs) are rare. The NOURISH RCT evaluated a community-based intervention for first-time mothers that promoted protective infant feeding practices as a primary prevention strategy for childhood obesity. The aim of this paper is to provide a detailed description and evaluation of the recruitment and retention strategies used. Methods: A two stage recruitment process designed to provide a consecutive sampling framework was used. First time mothers delivering healthy term infants were initially approached in postnatal wards of the major maternity services in two Australian cities for consent to later contact (Stage 1). When infants were about four months old mothers were re-contacted by mail for enrolment (Stage 2), baseline measurements (Time 1) and subsequent random allocation to the intervention or control condition. Outcomes were assessed at infant ages 14 months (Time 2) and 24 months (Time 3). Results: At Stage 1, 86% of eligible mothers were approached and of these women, 76% consented to later contact. At Stage 2, 3% had become ineligible and 76% could be recontacted. Of the latter, 44% consented to full enrolment and were allocated. This represented 21% of mothers screened as eligible at Stage 1. Retention at Time 3 was 78%. Mothers who did not consent or discontinued the study were younger and less likely to have a university education. Conclusions: The consent and retention rates of our sample of first time mothers are comparable with or better than other similar studies. The recruitment strategy used allowed for detailed information from non-consenters to be collected; thus selection bias could be estimated. Recommendations for future studies include being able to contact participants via mobile phone (particular text messaging), offering home visits to reduce participant burden and considering the use of financial incentives to support participant retention.