24 h Accelerometry: impact of sleep-screening methods on estimates of sedentary behaviour and physical activity while awake.

Although accelerometers can assess sleep and activity over 24 h, sleep data must be removed before physical activity and sedentary time can be examined appropriately. We compared the effect of 6 different sleep-scoring rules on physical activity and sedentary time. Activity and sleep were obtained by accelerometry (ActiGraph GT3X) over 7 days in 291 children (51.3% overweight or obese) aged 4-8.9 years. Three methods removed sleep using individualised time filters and two methods applied standard time filters to remove sleep each day (9 pm-6 am, 12 am-6 am). The final method did not remove sleep but simply defined non-wear as at least 60 min of consecutive zeros over the 24-h period. Different methods of removing sleep from 24-h data markedly affect estimates of sedentary time, yielding values ranging from 556 to 1145 min/day. Estimates of non-wear time (33-193 min), wear time (736-1337 min) and counts per minute (384-658) also showed considerable variation. By contrast, estimates of moderate-to-vigorous activity (MVPA) were similar, varying by less than 1 min/day. Different scoring methods to remove sleep from 24-h accelerometry data do not affect measures of MVPA, whereas estimates of counts per minute and sedentary time depend considerably on which technique is used.

Sources of geogenic arsenic in well water associated with granitic bedrock from Nova Scotia, Canada.

Arsenic toxicity in drinking water is a global issue, with chronic exposure causing cancer and other health concerns. Groundwater from geochemically similar granites from mainland Nova Scotia, Canada, can have high and low levels of arsenic. The origin of this variation is uncertain, but different mineral hosts for arsenic could explain the disparity. The lability of arsenic from different minerals was assessed using laser ablation inductively coupled plasma mass spectrometry combined with calculations based upon well water data. Pyrite has the highest arsenic concentration (mean: 2300 µg/g, n = 9), is unstable in the groundwater system, and can release arsenic during oxidation. However, oxidation products replacing pyrite can adsorb arsenic, modifying the amount released. Cordierite has low arsenic concentrations (mean: 7.3 µg/g, n = 5) but is abundant and relatively soluble. Thus, cordierite could be a previously unrecognized source of arsenic in metapelitic rocks from metamorphic terranes. Pyrite from one of the granites studied was not oxidized, which in addition to the absence of cordierite in these same granites could account for the lower arsenic levels observed in associated well water. The results of this study can be used to identify potential geogenic sources of arsenic in other granitic terranes and reduce the risk of exposure through drinking water.

Genes induced during the early developmental stages of the Cane Toad, Bufo (Chaunus) marinus.

Metamorphosis, a critical stage in the development of toads and frogs, involves rapid levels of morphological change. In the current study, we have used microarray analysis to identify shifts in gene expression between tadpole and toadlet stages of the cane toad, Bufo (Chaunus) marinus. Here, we report on nine genes that show the greatest induction during metamorphosis; the gut-associated gastrokine and trefoil factor, blood components haemoglobins alpha/beta, apolipoprotein and serum albumin, a nasal gene olfactomedin, a lens gene gamma-crystallin, and a novel gene with low homology to frog harderin. We present both temporal and spatial expression patterns of these genes identified in developing and adult cane toads. This study extends our knowledge of the molecular basis of toad metamorphosis, and not only offers insights to the genes induced during the general remodelling that occurs but also reveals possible targets for control and manipulation of amphibian pest species, for example, the cane toad in Australia.

Prevention of post-operative complications by using a HMG-CoA reductase inhibitor in patients undergoing one-lung ventilation for non-cardiac surgery: study protocol for a randomised controlled trial.

BACKGROUND: Postoperative pulmonary complications (PPC) and peri-operative myocardial infarction (MI) have a significant impact on the long-term mortality of surgical patients. Patients undergoing one-lung ventilation (OLV) for surgery are at a high risk of developing these complications. These complications could be associated with intensive care unit (ICU) admissions and longer hospital stay with associated resource and economic burden. Simvastatin, a HMG-CoA reductase enzyme inhibitor has been shown to have pleiotropic anti-inflammatory effects as well as being endothelial protective. The benefits of statins have been shown in various observational studies and in small proof-of-concept studies. There is an urgent need for a well-designed, large clinical trial powered to detect clinical outcomes. The Prevention HARP 2 trial will test the hypothesis 'simvastatin 80 mg when compared to placebo will reduce cardiac and pulmonary complications in patients undergoing elective oesophagectomy, lobectomy or pneumonectomy'. METHODS/DESIGN: The Prevention HARP 2 trial is a UK multi-centre, randomised, double-blind, placebo-controlled trial. Adult patients undergoing elective oesophagectomy, lobectomy or pneumonectomy will be eligible. Patients who are already on statins will be excluded from this trial. Patients will be randomised to receive simvastatin 80 mg or matched placebo for 4 days pre surgery and for up to 7 days post surgery. The primary outcome is a composite outcome of PPC and MI within 7 days post surgery. Various secondary outcome measures including clinical outcomes, safety outcomes and health economic outcomes will be collected. The study aims to recruit 452 patients in total across 12 UK sites. DISCUSSION: The results of the Prevention HARP 2 trial should add to our understanding of the benefits of peri-operative statins and influence clinical decision-making. Analysis of blood and urine samples from the patients will provide insight into the mechanism of simvastatin action. TRIAL REGISTRATION: International Standard Randomised Controlled Trials registry, ID: ISRCTN48095567 . Registered on 11 November 2016.

Gluteus medius coactivation response in field hockey players with and without low back pain.

OBJECTIVES: To examine the effect of prolonged standing on gluteus medius coactivation and to observe whether the changes in gluteus medius coactivation over time were related to the development of low back pain in elite female field hockey players. DESIGN: Prospective cohort design. METHODS: Participants were 39 elite female field hockey players (14 with a history of low back pain). Before the prolonged stand, maximal hip abduction strength, side bridge hold endurance and hip abduction range of motion were measured bilaterally. Surface electromyography was collected from the gluteus medius for coactivation analysis during a prolonged stand for 70 min. Low back pain was rated every 10 min on a visual analogue scale. RESULTS: Fourteen of 39 participants developed low back pain. The Time effect was significant for gluteus medius coactivation response (p = 0.003) and visual analogue scale score (p < 0.001). There were no significant group × time interactions. Yet athletes who developed pain had higher coactivation for the majority of the stand task. CONCLUSIONS: While female field hockey players have high agonist-antagonist coactivation patterns during prolonged standing, stand task is a useful tool to predict low back pain occurrence in players with and without history of pain.

Multi-dimensional coordination in cross-country skiing analyzed using self-organizing maps.

This study sought to ascertain how multi-dimensional coordination patterns changed with five poling speeds for 12 National Standard cross-country skiers during roller skiing on a treadmill. Self-organizing maps (SOMs), a type of artificial neural network, were used to map the multi-dimensional time series data on to a two-dimensional output grid. The trajectories of the best-matching nodes of the output were then used as a collective variable to train a second SOM to produce attractor diagrams and attractor surfaces to study coordination stability. Although four skiers had uni-modal basins of attraction that evolved gradually with changing speed, the other eight had two or three basins of attraction as poling speed changed. Two skiers showed bi-modal basins of attraction at some speeds, an example of degeneracy. What was most clearly evident was that different skiers showed different coordination dynamics for this skill as poling speed changed: inter-skier variability was the rule rather than an exception. The SOM analysis showed that coordination was much more variable in response to changing speeds compared to outcome variables such as poling frequency and cycle length.

Algorithms for using an activity-based accelerometer for identification of infant sleep-wake states during nap studies.

OBJECTIVE: To determine the accuracy of using different algorithms on the output from an Actical accelerometer, a device normally used to measure physical activity, to distinguish sleep from wake states. METHODS: Thirty-one infants aged 10-22 weeks wore the accelerometer on the shin for a daytime nap recording in tandem with polysomnography. Sleep-wake epochs were identified using four computations/algorithms: the zero-threshold computation, two common algorithms used for wrist-based devices (Sadeh and Cole), and a new algorithm developed for this study (count-scaled). Accuracy was examined in direct epoch comparison with polysomnography using 15-, 30- and 60-s sampling epochs. RESULTS: Overall agreements (accuracy) for sleep-wake states were >80% for all computations. The count-scaled algorithm sampling 15-s epochs gave the highest accuracy, with sensitivity (sleep agreement) at 86% and specificity (awake agreement) at 85%. Other computations yielded higher sensitivity at the expense of specificity. Another way to assess the accuracy of identification of sleep-wake states was to compare sleep parameter outputs. All computations and sampling epochs were significantly correlated with total sleep time (r=0.76-0.88), sleep latency (r=0.70-0.93), sleep efficiency (r=0.76-0.87), and wake time after sleep onset (r=0.41-0.53). The number of awakenings after sleep onset was overestimated by accelerometry. CONCLUSIONS: The Actical accelerometer, designed to measure physical activity, can reliably identify sleep in infants during napping, with the count-scaled algorithm showing some advantages over other methods for accurate identification of sleep-wake epochs.

Effects of prior heavy exercise on energy supply and 4000-m cycling performance.

PURPOSE: This study was designed to determine the effects of prior exercise on energy supply and performance in a laboratory-based 4000-m time trial. METHODS: After one familiarization trial, eight well-trained cyclists (mean +/- SD; age = 30 +/- 8 yr, body mass = 78.7 +/- 8.6 kg, stature = 181 +/- 5 cm, .VO2 peak = 63.7 +/- 6.7 mL.kg.(-1)min(-1), peak power output (PPO) = 366 +/- 39 W) performed three 4000-m laboratory-based cycling time trials each preceded by one of three prior exercise regimens in randomized order: no prior exercise (control), prior heavy exercise, and self-selected prior exercise. RESULTS: Cyclists adopted a wide range of self-selected prior exercise regimens: duration ranged = 11-80 min, intensity = 48-120% PPO, and recovery = 2-11 min. Relative to control, pre-time-trial blood lactate was raised by 2.5 +/- 1.9 and 1.4 +/- 1.5 mmol.L(-1) after prior heavy and self-selected exercise, respectively. The 4000 m was completed 2.0 +/- 2.3% and 2.2 +/- 1.9% faster after prior heavy and self-selected exercise regimens, respectively, and mean power output was 5.4 +/- 3.6% and 6.0 +/- 5.8% higher, respectively. The overall aerobic contribution (.VO2) and oxygen deficit were not different between conditions (approximately 323 +/- 23 and approximately 64 +/- 22 mL.kg,(-1) respectively), although .VO2 was higher (P < 0.05) in the prior heavy (by 2.1-5.8 mL.kg(-1).min(-1)) and self-selected (2.5-4.3 mL.kg(-1).min(-1)) regimens compared with the control throughout the first half of the time trial. CONCLUSION: Very high intensity cycling performance was improved after both self-selected and prior heavy exercise. Such priming increased the early aerobic contribution but did not change overall aerobic contribution or oxygen deficit. Thus, athletes seem to manage their energy potential to exploit the available anaerobic capacity, independent of the aerobic contribution. Athletes are advised to perform a bout of heavy exercise as part of their prior exercise regimen.

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.

Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of approximately 5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.

Large scale transcriptome analysis of the effects of nitrogen nutrition on accumulation of stem carbohydrate reserves in reproductive stage wheat.

We investigated the molecular basis of the long-term adaptation to nitrogen (N) limitation of wheat plants grown in a simulated crop canopy, with a focus on the stage when carbon (C) reserves are accumulated in stems for later remobilization to grain. A cDNA microarray representing approximately 36,000 unique sequences was used to compare gene expression in a number of above-ground organs at anthesis. Fructan accumulation in stems was accompanied by elevated transcripts for a suite of fructosyltransferases (FTs) and for a fructan 6-exohydrolase (6-FEH) in the low N compared to high N stems. Clustering analysis identified a grouping that included several FTs and a number of genes thought to be involved in regulation of storage C metabolism or senescence in other systems. Transcripts for three FTs and for 6-FEH increased, while transcripts for 1-FEH decreased, in sucrose-fed wheat stems compared to controls. The opposite trends were seen for these transcripts in wheat stems fed ABA. Of the putative regulators, only transcripts for the WPK4 kinase increased in response to sucrose, suggesting a role for this kinase in C storage metabolism in the reproductive wheat stems grown in low N. This work represents the first large-scale transcriptome study of responses to the most common nutrient limitation in one of the world's most economically important crops.

A mutation in a chromosome condensin II subunit, kleisin beta, specifically disrupts T cell development.

Condensins are ubiquitously expressed multiprotein complexes that are important for chromosome condensation and epigenetic regulation of gene transcription, but whose specific roles in vertebrates are poorly understood. We describe a mouse strain, nessy, isolated during an ethylnitrosourea screen for recessive immunological mutations. The nessy mouse has a defect in T lymphocyte development that decreases circulating T cell numbers, increases their expression of the activation/memory marker CD44, and dramatically decreases the numbers of CD4(+)CD8(+) thymocytes and their immediate DN4 precursors. A missense mutation in an unusual alternatively spliced first exon of the kleisin beta gene, a member of the condensin II complex, was shown to be responsible and act in a T cell-autonomous manner. Despite the ubiquitous expression and role of condensins, kleisin beta(nes/nes) mice were viable, fertile, and showed no defects even in the parallel pathway of B cell lymphocyte differentiation. These data define a unique lineage-specific requirement for kleisin beta in mammalian T cell differentiation.

Microarray analysis reveals vegetative molecular phenotypes of Arabidopsis flowering-time mutants.

The transition to flowering occurs at the shoot apex; however, most of the characterized genes that affect the timing of floral induction are expressed throughout the plant. To further our understanding of these genes and the flowering process, the vegetative molecular phenotypes of 16 Arabidopsis mutants associated with the major flowering initiation pathways were assayed using a 13,000 clone microarray under two different conditions that affect flowering. All mutants showed at least one change in gene expression other than the mutant flowering gene. Metabolism- and defence-related pathways were the areas with the most frequent gene expression changes detected in the mutants. Several genes such as EARLI1 were differentially expressed in a number of flowering mutants from different flowering pathways. Analysis of the promoter regions of genes differentially expressed identified common promoter elements, indicating some form of common regulation.

Plant functional genomics: opportunities in microarray databases and data mining.

High-throughput gene expression profiling using microarrays has given plant biologists a powerful new technology to discover gene function and understand cellular processes. Bioinformatics has rapidly developed to deliver the tools necessary to interpret this gene expression data, but opportunities to further exploit the mass of data from hundreds of experiments are becoming dependent upon the use of sophisticated database repositories. Data mining of these resources will allow plant biologists to compare and link expression profiles and experimental factors to uncover functions and processes that would not normally be visible from analysing a small set of microarray experiments. This in-silico analysis will become critical when designing new experiments and interpreting new results. Consequently microarray databases and their ongoing development are now as important to plant functional genomics as the initial microarray data capture and analysis tools. In order for plant biologists to grasp these new opportunities, an appreciation of microarray database technology and future developments in biological data integration is required. The challenge for plant functional genomics is to embrace these new technologies lest the opportunities for significant discoveries be lost.