Prediction of global and local model quality in CASP8 using the ModFOLD server

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0-an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/.

Assessing and understanding the impact of stratospheric dynamics and variability on the earth system

Advances in weather and climate research have demonstrated the role of the stratosphere in the Earth system across a wide range of temporal and spatial scales. Stratospheric ozone loss has been identified as a key driver of Southern Hemisphere tropospheric circulation trends, affecting ocean currents and carbon uptake, sea ice, and possibly even the Antarctic ice sheets. Stratospheric variability has also been shown to affect short term and seasonal forecasts, connecting the tropics and midlatitudes and guiding storm track dynamics. The two-way interactions between the stratosphere and the Earth system have motivated the World Climate Research Programme's (WCRP) Stratospheric Processes and Their Role in Climate (SPARC) DynVar activity to investigate the impact of stratospheric dynamics and variability on climate. This assessment will be made possible by two new multi-model datasets. First, roughly 10 models with a well resolved stratosphere are participating in the Coupled Model Intercomparison Project 5 (CMIP5), providing the first multi-model ensemble of climate simulations coupled from the stratopause to the sea floor. Second, the Stratosphere Historical Forecasting Project (SHFP) of WCRP's Climate Variability and predictability (CLIVAR) program is forming a multi-model set of seasonal hindcasts with stratosphere resolving models, revealing the impact of both stratospheric initial conditions and dynamics on intraseasonal prediction. The CMIP5 and SHFP model-data sets will offer an unprecedented opportunity to understand the role of the stratosphere in the natural and forced variability of the Earth system and to determine whether incorporating knowledge of the middle atmosphere improves seasonal forecasts and climate projections. Capsule New modeling efforts will provide unprecedented opportunities to harness our knowledge of the stratosphere to improve weather and climate prediction.

The prevalence and nature of prescribing and monitoring errors in English general practice – a retrospective case note review

Objective To determine the prevalence and nature of prescribing and monitoring errors in general practices in England. Design Retrospective case note review of unique medication items prescribed over a 12 month period to a 2% random sample of patients. Mixed effects logistic regression was used to analyse the data. Setting Fifteen general practices across three primary care trusts in England. Data sources Examination of 6048 unique prescription items prescribed over the previous 12 months for 1777 patients. Main outcome measures Prevalence of prescribing and monitoring errors, and severity of errors, using validated definitions. Results Prescribing and/or monitoring errors were detected in 4.9% (296/6048) of all prescription items (95% confidence interval 4.4 - 5.5%). The vast majority of errors were of mild to moderate severity, with 0.2% (11/6048) of items having a severe error. After adjusting for covariates, patient-related factors associated with an increased risk of prescribing and/or monitoring errors were: age less than 15 (Odds Ratio (OR) 1.87, 1.19 to 2.94, p=0.006) or greater than 64 years (OR 1.68, 1.04 to 2.73, p=0.035), and higher numbers of unique medication items prescribed (OR 1.16, 1.12 to 1.19, p<0.001). Conclusion Prescribing and monitoring errors are common in English general practice, although severe errors are unusual. Many factors increase the risk of error. Having identified the most common and important errors, and the factors associated with these, strategies to prevent future errors should be developed based on the study findings.

The effects of dairy management and processing on quality characteristics of milk and dairy products

Studies within the QLIF project reviewed in this article suggest that organic or low-input management is more likely to result in milk with fatty acid profiles that are higher in α-linolenic acid and/or beneficial isomers of conjugated linoleic acid and antioxidants with up to a 2.5-fold increase in some cases, relative to milk from conventional production. These advantages are preserved during processing, resulting in elevated contents or concentrations of these constituents in processed dairy products of organic or low input origin. Much of the literature suggests that these benefits are very likely to be a result of a greater reliance on forages in the dairy diets (especially grazed grass). Since the adoption of alternative breeds or crosses is often an integral part sustaining these low-input systems, it is not possible to rule out an interaction with genotype in these monitored herds. The results suggest that milk fat composition with respect to human health can be optimized by exploiting grazing in the diet of dairy cows. However, in many European regions this may not be possible due to extremes in temperature, soil moisture levels or both. In such cases milk quality can be maintained by the inclusion of oil seeds in the dairy diets.

Does milk consumption contribute to cardiometabolic health and overall diet quality?

Although milk consumption is recommended in most dietary guidelines around the world, its contribution to overall diet quality remains a matter of debate in the scientific community as well as in the public. This paper summarizes the discussion among experts in the field on the place of milk in a balanced, healthy diet. The evidence to date suggests at least a neutral effect of milk intake on health outcomes. The possibility that milk intake is simply a marker of higher nutritional quality diets cannot be ruled out. This review also identifies a number of key research gaps pertaining to the impact of milk consumption on health. These need to be addressed to better inform future dietary guidelines.

Development of site-specific sediment quality guidelines for North and South Atlantic littoral zones: Comparison against national and international sediment quality benchmarks

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Impact of atmosphere, organic acids, and calcium on quality of fresh-cut 'Kensington' mango

Fresh-cut slices from ripe 'Kensington' mango (Mangifera indica L.) were prepared aseptically and stored under various treatments at 3 degrees C. Treatments included reduced oxygen (2.5%), enhanced carbon dioxide (5-40%), organic acid application, calcium chloride application, and combinations of the above. Symptoms limiting shelf-life were characterised by tissue darkening, development of a 'glassy' appearance, surface desiccation, and loss of firmness. Reduced oxygen (2.5%) was effective at controlling tissue darkening and the development of a 'glassy' appearance, while calcium application (3%) was partly effective at controlling darkening. Calcium chloride however significantly slowed (but did not stop) loss of tissue firmness. Carbon dioxide (5-40%) and citric acid had little positive effect on shelf-life, with both treatments appearing to promote tissue softening. A combination of low oxygen and calcium allowed 'Kensington' slices to be held for at least 15 days at 3 degrees C. (C) 2006 Elsevier B.V All rights reserved.

Factors affecting fertilisation and early embryo quality in single- and superovulated dairy cattle

Data on fertilisation and embryo quality in dairy cattle are presented and the main factors responsible for the low fertility of single-ovulating lactating cows and embryo yield in superovulated dairy cattle are highlighted. During the past 50 years, the fertility in high-producing lactating dairy cattle has decreased as milk production increased. Recent data show conception rates to first service to be approximately 32% in lactating cows, whereas in heifers it has remained above 50%. Fertilisation does not seem to be the principal factor responsible for the low fertility in single-ovulating cows, because it has remained above 80%. Conversely, early embryonic development is impaired in high-producing dairy cows, as observed by most embryonic losses occurring during the first week after fertilisation. However, in superovulated dairy cattle, although fertilisation failure is more pronounced, averaging approximately 45%, the percentage of fertilised embryos viable at 1 week is quite high (>70%). Among the multifactorial causes of low fertility in lactating dairy cows, high feed intake associated with low concentrations of circulating steroids may contribute substantially to reduced embryo quality. Fertilisation failure in superovulated cattle may be a consequence of inappropriate gamete transport due to hormonal imbalances.

Effects of Short-term Hyper- and Hypoprolactinaemia on Hormones of the Pituitary, Gonad and -Thyroid Axis and on Semen Quality in Male Beagles

Effects of a short-term hyper- and hypoprolactinaemia on serum concentrations of LH, testosterone and semen quality in six male Beagles were investigated. Blood samples were collected at 3-day intervals for 12 weeks. The time span was divided into five 3-week periods: pre-treatment, metoclopramide (MCP) treatment (0.2 mg/kg orally three times daily), cabergoline (CAB) treatment (5 mu g/kg orally once daily), post-treatment 1 and post-treatment 2. In the latter, only semen characteristics were evaluated. Semen parameters were analyzed once per week during the whole 15-week investigation time. At the end of each period, the effects of a single intravenous injection of thyrotropin-releasing hormone (TRH; 10 mu g/kg) on the secretion of prolactin (PRL), LH, testosterone, thyroid-stimulating hormone and thyroxine (T4) were investigated. Pre-treatment serum PRL concentration increased under MCP (p < 0.05), followed by a decrease under CAB administration (p < 0.05). Luteinizing hormone and testosterone concentrations were not affected. Except for straight-line sperm velocity, semen quality did not differ between collection periods. A single iv TRH injection induced a significant PRL increase at 20 min in all experimental periods except during CAB treatment. Luteinizing hormone and testosterone did not show clear TRH-related changes. Basic T4 levels were significantly reduced after CAB treatment ( p < 0.05). The results of the present study demonstrate that MCP-induced short-term hyperprolactinaemia in male beagles does not seriously affect the hypothalamo-pituitary axis and semen quality.