Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.

The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture

Background: Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other. Methods and Findings: We have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas. Conclusions/Significance: Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.1561024 nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation.

A tan in a test tube -in vitro models for investigating ultraviolet radiation-induced damage in skin

Presently, global rates of skin cancers induced by ultraviolet radiation (UVR) exposure are on the rise. In view of this, current knowledge gaps in the biology of photocarcinogenesis and skin cancer progression urgently need to be addressed. One factor that has limited skin cancer research has been the need for a reproducible and physiologically-relevant model able to represent the complexity of human skin. This review outlines the main currently-used in vitro models of UVR-induced skin damage. This includes the use of conventional two-dimensional cell culture techniques and the major animal models that have been employed in photobiology and photocarcinogenesis research. Additionally, the progression towards the use of cultured skin explants and tissue-engineered skin constructs, and their utility as models of native skin's responses to UVR are described. The inherent advantages and disadvantages of these in vitro systems are also discussed.

The national specificity of horror sources in Asian horror cinema

This dissertation explores the relationship between horror films and the national contexts in which they are produced by analyzing several Asian horror movies – Ringu (Japan), The Eye (Hong Kong) and Shutter (Thailand). Utilizing these films as case studies, the dissertation examines the degree to which genre cinemas are nationally-specific, and the degree to which it is possible to make genre films that can enter international markets and be comprehensible in various national markets as well. The dissertation also makes the following claims on the national specificity of genre cinema: i) The sources of frightening elements in horror films are nationally-specific. ii) There is a regional "Asian" horror because of the intertwining national histories and shared cultural elements across several Asian countries.

Re-examining the evidence in radiation dermatitis management literature : an overview and a critical appraisal of systematic reviews

Purpose: To provide an overview and a critical appraisal of systematic reviews (SRs) of published interventions for the prevention/management of radiation dermatitis. Methods and Materials: We searched Medline, CINAHL, Embase, and the Cochrane Library. We also manually searched through individual reference lists of potentially eligible articles and a number of key journals in the topic area. Two authors screened all potential articles and included eligible SRs. Two authors critically appraised and extracted key findings from the included reviews using AMSTAR (the measurement tool for “assessment of multiple systematic reviews”). Results: Of 1837 potential titles, 6 SRs were included. A number of interventions have been reported to be potentially beneficial for managing radiation dermatitis. Interventions evaluated in these reviews included skin care advice, steroidal/nonsteroidal topical agents, systemic therapies, modes of radiation delivery, and dressings. However, all the included SRs reported that there is insufficient evidence supporting any single effective intervention. The methodological quality of the included studies varied, and methodological shortfalls in these reviews might create biases to the overall results or recommendations for clinical practice. Conclusions: An up-to-date high-quality SR in the prevention/management of radiation dermatitis is needed to guide practice and direction for future research. We recommend that clinicians or guideline developers critically evaluate the information of SRs in their decision making.

A double-blind randomised controlled trial of a natural oil-based emulsion containing allantoin versus aqueous cream for managing radiation-induced skin reactions in patients with cancer

Background: Radiation-induced skin reaction (RISR) is one of the most common and distressing side effects of radiotherapy in patients with cancer. It is featured with swelling, redness, itching, pain, breaks in skin, discomfort, and a burning sensation. There is a lack of convincing evidence supporting any single practice in the prevention or management of RISR. Methods/Designs: This double-blinded randomised controlled trial aims to investigate the effects of a natural oil-based emulsion containing allantoin (as known as Moogoo Udder Cream®) versus aqueous cream in reducing RISR, improving pain, itching and quality of life in this patient group. One group will receive Moogoo Udder Cream®. Another group will receive aqueous cream. Outcome measures will be collected using patient self-administered questionnaire, interviewer administered questionnaire and clinician assessment at commencement of radiotherapy, weekly during radiotherapy, and four weeks after the completion of radiotherapy. Discussion: Despite advances of radiologic advances and supportive care, RISR are still not well managed. There is a lack of efficacious interventions in managing RISR. While anecdotal evidence suggests that Moogoo Udder Cream® may be effective in managing RISR, research is needed to substantiate this claim. This paper presents the design of a double blind randomised controlled trial that will evaluate the effects of Moogoo Udder Cream® versus aqueous cream for managing in RISR in patients with cancer. Trial registration: ACTRN 12612000568819

Folate degradation due to ultraviolet radiation : possible implications for human health and nutrition

Folate is essential for human health in the prevention of megaloblastic anaemia and neural tube birth defects as well as roles in cardiovascular disease and cancer. Therefore research into environmental factors that may impact folate status, such as solar ultraviolet radiation, is of great health significance. In vitro studies have shown that ultraviolet (UV) radiation can degrade folate and folic acid in human blood and this has been confirmed in several human studies. Despite these findings, there is a dearth of epidemiological research into investigating the relationship between folate status and the links to solar UV exposure.

Charitable grants and donations from maching gaming sources : Does it all work out in the wash up?

Material for this paper comes partly from a report commissioned by the Department of Family Services, Aboriginal and Islander Affairs. The report is the result of a multi-strategy research project designed to assess the impact of gaming machines on the fundraising capacity of charitable and community organisations in Queensland. The first Queensland gaming machine was commissioned on 11 February 1992. By 30 November 1994 there were: · 636 clubs operating 13,162 gaming machines · 436 hotels/taverns operating 3,468 gaming machines.1 It was anticipated that the introduction of gaming machines would impact on charities and community organisations. The adverse impacts would be through competition with charity gaming and disposable income that might otherwise be directed towards donations. Some also expressed concern that charities would be relied on to finance social services for problem gamblers. This paper seeks to describe the donations and grants derived by charities from Gaming Machine revenues. Such revenues primarily come from either government distributions from its gaming machine taxes and levies or gaming machine club donations. A final comment is made on the opinions of charitable fundraising professionals about the impact of gaming machine levies on club donations.

Evaluation of coronary angiographic projections to balance the clinical yield with the radiation risk

Objective: Radiation safety principles dictate that imaging procedures should minimise the radiation risks involved, without compromising diagnostic performance. This study aims to define a core set of views that maximises clinical information yield for minimum radiation risk. Angiographers would supplement these views as clinically indicated. Methods: An algorithm was developed to combine published data detailing the quality of information derived for the major coronary artery segments through the use of a common set of views in angiography with data relating to the dose–area product and scatter radiation associated with these views. Results: The optimum view set for the left coronary system comprised four views: left anterior oblique (LAO) with cranial (Cr) tilt, shallow right anterior oblique (AP-RAO) with caudal (Ca) tilt, RAO with Ca tilt and AP-RAO with Cr tilt. For the right coronary system three views were identified: LAO with Cr tilt, RAO and AP-RAO with Cr tilt. An alternative left coronary view set including a left lateral achieved minimally superior efficiency (,5%), but with an ,8% higher radiation dose to the patient and 40% higher cardiologist dose. Conclusion: This algorithm identifies a core set of angiographic views that optimises the information yield and minimises radiation risk. This basic data set would be supplemented by additional clinically determined views selected by the angiographer for each case. The decision to use additional views for diagnostic angiography and interventions would be assisted by referencing a table of relative radiation doses for the views being considered.

Sustainable water provision : challenges, alternative strategies and sources in the ERA of climate change

As a result of rapid urbanisation, population growth, changes in lifestyle, pollution and the impacts of climate change, water provision has become a critical challenge for planners and policy-makers. In the wake of increasingly difficult water provision and drought, the notion that freshwater is a finite and vulnerable resource is increasingly being realised. Many city administrations around the world are struggling to provide water security for their residents to maintain lifestyle and economic growth. This chapter reviews the global challenge of providing freshwater to sustain lifestyles and economic growth, and the contributing challenges of climate change, urbanisation, population growth and problems in rainfall distribution. The chapter proceeds to evaluate major alternatives to current water sources such as conservation, recycling and reclamation, and desalination. Integrated water resource management is briefly looked at to explore its role in complementing water provision. A comparative study on alternative resources is undertaken to evaluate their strengths, weaknesses, opportunities and constraints, and the results are discussed.

Training program impact on thermoplastic immobilization for head and neck radiation therapy

Purpose: To determine whether uniform guidelines and training in the stabilization and formation of thermoplastic shells can improve the reproducibility of set-up for Head and Neck cancer patients. Methods and materials: Image based measurements of the planning and treatment positions for 35 head and neck cancer patients undergoing radical radiotherapy were analysed to provide a baseline of the reproducibility of thermoplastic immobilization. Radiation therapists (RT) were surveyed to establish a perception of their confidence in thermoplastic procedures. An evidence based staff training program was created and implemented. Set-up reproduction and staff perception were reviewed to measure the impact of the training program. Results: The mean (SD) 3D vectors of anatomical displacement, measured on the patient images, improved from 4.64 (2.03) for the baseline group compared to 3.02 (1.65) following training (p < 0.01). The proportion of 3D displacements of patient data exceeding 5 mm 3D vector was decreased from 37.1% to 5.7% (p < 0.001) and the 3 mm vector from 85.7% to 42.9% (p < 0.001). The post-training survey scores demonstrated improved confidence in reproducibility of set-up for head and neck patients. Conclusion: The Thermoplastic Shells Training Program has been found to improve the treatment reproducibility for head and neck radiation therapy patients. Uniform guidelines have increased RT confidence in thermoplastic procedures.