Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy

Genome-wide association studies have been used successfully to detect associations between common genetic variants and complex diseases, but common single-nucleotide polymorphisms (SNPs) detected by these studies explain only 5–10% of disease heritability. Alternatively, the common disease/rare variants hypothesis suggests that complex diseases are often caused by multiple rare variants with moderate to high effects. Under this hypothesis, the analysis of the cumulative effect of rare variants may thus help us discover the missing genetic variations. Collapsing all rare variants across a functional region is currently a popular method to find rare variants that may have a causal effect on certain diseases. However, the power of tests based on collapsing methods is often impaired by misclassification of functional variants. We develop a data-adaptive forward selection procedure that selectively chooses only variants that improve the association signal between functional regions and the disease risk. We apply our strategy to the Genetic Analysis Workshop 17 unrelated individuals data with quantitative traits. The type I error rate and the power of different collapsing functions are evaluated. The substantially higher power of the proposed strategy was demonstrated. The new method provides a useful strategy for the association study of sequencing data by taking advantage of the selection of rare variants

An assessment of road-verge grass as a feedstock for farm-fed anaerobic digestion plants

Cuttings from road-verge grass could provide biomass for energy generation, but currently this potential is not exploited. This research assessed the technical, practical and financial feasibility of using grass harvested from road verges as a feedstock in farm-fed anaerobic digestion (AD) plants. The methane potential (191 mL CH4 gDM−1) and digestion characteristics of verge grass were similar to those of current farm feedstocks; indicating suitability for AD. Ensiling had no significant impact on the biomethane generated. Testing co-digestions of verge grass with current farm feedstocks showed enhanced methane yields, suggesting that verge grass could be a valuable addition to AD feedstock mixes. In a case study of the UK county of Lincolnshire, potential volumes and locations of verge grass biomass were estimated, with capacities and locations of existing AD plants, to assess the potential to supply practical grass volumes. Grass harvesting costs were modelled and compared with other feedstock costs. Finally, the attitudes of AD operators to using verge grass were investigated to understand whether a market for verge grass exists. In a small survey all operators were willing to use it as a feedstock and most were prepared to pay over the estimated harvesting cost. If verge grass was legally recognised as a waste product it could be attractive to AD operators especially where financial incentives to use waste feedstocks are in place. In rural areas, verge grass could be harvested and co-digested by existing farm-fed AD plants, potentially reducing the cost of road verge maintenance and increasing biodiversity

Ongoing challenges in the management of malaria

This article gives an overview of some of the ongoing challenges that are faced in the prevention, diagnosis and treatment of malaria

What is macroecology?

The symposium 'What is Macroecology?' was held in London on 20 June 2012. The event was the inaugural meeting of the Macroecology Special Interest Group of the British Ecological Society and was attended by nearly 100 scientists from 11 countries. The meeting reviewed the recent development of the macroecological agenda. The key themes that emerged were a shift towards more explicit modelling of ecological processes, a growing synthesis across systems and scales, and new opportunities to apply macroecological concepts in other research fields

Oxygen dependency of mitochondrial metabolism indicates outcome of newborn brain injury

There is a need for a method of real-time assessment of brain metabolism during neonatal hypoxic-ischaemic encephalopathy (HIE). We have used broadband near-infrared spectroscopy (NIRS) to monitor cerebral oxygenation and metabolic changes in 50 neonates with HIE undergoing therapeutic hypothermia treatment. In 24 neonates, 54 episodes of spontaneous decreases in peripheral oxygen saturation (desaturations) were recorded between 6 and 81 h after birth. We observed differences in the cerebral metabolic responses to these episodes that were related to the predicted outcome of the injury, as determined by subsequent magnetic resonance spectroscopy derived lactate/N-acetyl-aspartate. We demonstrated that a strong relationship between cerebral metabolism (broadband NIRS-measured cytochrome-c-oxidase (CCO)) and cerebral oxygenation was associated with unfavourable outcome; this is likely to be due to a lower cerebral metabolic rate and mitochondrial dysfunction in severe encephalopathy. Specifically, a decrease in the brain tissue oxidation state of CCO greater than 0.06 µM per 1 µM brain haemoglobin oxygenation drop was able to predict the outcome with 64% sensitivity and 79% specificity (receiver operating characteristic area under the curve = 0.73). With further work on the implementation of this methodology, broadband NIRS has the potential to provide an early, cotside, non-invasive, clinically relevant metabolic marker of perinatal hypoxic-ischaemic injury

Lithium and boron in calcified tissues of vicuna and its relation to the chronic exposure by water ingestion in the Andean lithium triangle

Vicuna is a wild, endangered species of Andean camelid living in the hyperarid Andean plateau. In the central part of the plateau, the Lithium Triangle defines a zone with lithium‐rich salt pans. Brine pools naturally form within the salt pans, and the adaptation strategy of vicuna consists of drinking from brine pools. Together with reporting the first chemical data on vicuna bones and teeth, we analyzed lithium, boron, and arsenic in water and brines, with the aim of assessing their relation to chronic exposure by water ingestion. We collected and analyzed bones of vicuna specimens lying in an Andean salt pan, together with brine and water samples. Brine and water samples are highly saline and contain large amounts of lithium, boron, and arsenic. Lithium (13.50–40 mg kg–1 ) and boron (40–46.80 mg kg–1 ), but not arsenic, were found in the vicuna bones and teeth. Based on our results and on previously reported data on human tissues in the Andes, we conducted statistical assessments of the relationships between lithium and boron in body tissues and water samples, and discuss their environmental significance in the context of the Lithium Triangle.Fil: López Steinmetz, Romina Lucrecia. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; Argentina. Universidad Nacional de Jujuy. Instituto de Geología Minera; ArgentinaFil: Fong, Shao Bing. University of Melbourne; AustraliaFil: Boyer, Emile. Universite de Rennes I; FranciaFil: López Steinmetz, Lorena Cecilia. Universidad Nacional de Córdoba. Instituto de Investigaciones Psicológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Psicológicas; ArgentinaFil: Tejerina, Norberto Elio. Universidad Nacional de Jujuy. Instituto de Geología Minera; ArgentinaFil: Meuric, Vincent. Universite de Rennes I; Franci

Understanding the pharmacokinetics of Coartem®

Artemether and lumefantrine (AL), the active constituents of Coartem® exhibit complementary pharmacokinetic profiles. Artemether is absorbed quickly; peak concentrations of artemether and its main active metabolite, dihydroartemisinin (DHA) occur at approximately two hours post-dose, leading to a rapid reduction in asexual parasite mass and a prompt resolution of symptoms. Lumefantrine is absorbed and cleared more slowly (terminal elimination half-life 3-4 days in malaria patients), and accumulates with successive doses, acting to prevent recrudescence by destroying any residual parasites that remain after artemether and DHA have been cleared from the body. Food intake significantly enhances the bioavailability of both artemether and lumefantrine, an effect which is more apparent for the highly lipophilic lumefantrine. However, a meal with only a small amount of fat (1.6 g) is considered sufficient to achieve adequate exposure to lumefantrine. The pharmacokinetics of artemether or lumefantrine are similar in children, when dosed according to their body weight, compared with adults. No randomized study has compared the pharmacokinetics of either agent in pregnant versus non-pregnant women. Studies in healthy volunteers and in children with malaria have confirmed that the pharmacokinetic characteristics of crushed standard AL tablets and the newly-developed Coartem® Dispersible tablet formulation are similar. Studies to date in healthy volunteers have not identified any clinically relevant drug-drug interactions; data relating to concomitant administration of HIV therapies are limited. While dose-response analyses are difficult to undertake because of the low rate of treatment failures under AL, it appears that artemether and DHA exposure impact on parasite clearance time while lumefantrine exposure is associated with cure rate, consistent with their respective modes of action. In conclusion, knowledge of the pharmacokinetic profiles of artemether and lumefantrine is increasing within a range of settings, including infants and children. However, additional data would be warranted to better characterize artemether and lumefantrine pharmacokinetics in patients with hepatic impairment, in pregnant women, and in patients undergoing HIV/AIDS chemotherapy

Population pharmacokinetics of intravenous artesunate: a pooled analysis of individual data from patients with severe malaria.

There are ~660,000 deaths from severe malaria each year. Intravenous artesunate (i.v. ARS) is the first-line treatment in adults and children. To optimize the dosing regimen of i.v. ARS, the largest pooled population pharmacokinetic study to date of the active metabolite dihydroartemisinin (DHA) was performed. The pooled dataset consisted of 71 adults and 195 children with severe malaria, with a mixture of sparse and rich sampling within the first 12 h after drug administration. A one-compartment model described the population pharmacokinetics of DHA adequately. Body weight had the greatest impact on DHA pharmacokinetics, resulting in lower DHA exposure for smaller children (6-10 kg) than adults. Post hoc estimates of DHA exposure were not significantly associated with parasitological outcomes. Comparable DHA exposure in smaller children and adults after i.v. ARS was achieved under a dose modification for intramuscular ARS proposed in a separate analysis of children

Bell Correlations and the Common Future

Reichenbach's principle states that in a causal structure, correlations of classical information can stem from a common cause in the common past or a direct influence from one of the events in correlation to the other. The difficulty of explaining Bell correlations through a mechanism in that spirit can be read as questioning either the principle or even its basis: causality. In the former case, the principle can be replaced by its quantum version, accepting as a common cause an entangled state, leaving the phenomenon as mysterious as ever on the classical level (on which, after all, it occurs). If, more radically, the causal structure is questioned in principle, closed space-time curves may become possible that, as is argued in the present note, can give rise to non-local correlations if to-be-correlated pieces of classical information meet in the common future --- which they need to if the correlation is to be detected in the first place. The result is a view resembling Brassard and Raymond-Robichaud's parallel-lives variant of Hermann's and Everett's relative-state formalism, avoiding "multiple realities."Comment: 8 pages, 5 figure

Experimental Evolution of Resistance to Artemisinin Combination Therapy Results in Amplification of the mdr1 Gene in a Rodent Malaria Parasite

Background: Lacking suitable alternatives, the control of malaria increasingly depends upon Artemisinin Combination Treatments (ACT): resistance to these drugs would therefore be disastrous. For ACTs, the biology of resistance to the individual components has been investigated, but experimentally induced resistance to component drugs in combination has not been generated. Methodology/Principal Findings: We have used the rodent malaria parasite Plasmodium chabaudi to select in vivo resistance to the artesunate (ATN) + mefloquine (MF) version of ACT, through prolonged exposure of parasites to both drugs over many generations. The selection procedure was carried out over twenty-seven consecutive sub-inoculations under increasing ATN + MF doses, after which a genetically stable resistant parasite, AS-ATNMF1, was cloned. AS-ATNMF1 showed increased resistance to ATN + MF treatment and to artesunate or mefloquine administered separately. Investigation of candidate genes revealed an mdr1 duplication in the resistant parasites and increased levels of mdr1 transcripts and protein. There were no point mutations in the atpase6 or ubp1genes. Conclusion: Resistance to ACTs may evolve even when the two drugs within the combination are taken simultaneously and amplification of the mdr1 gene may contribute to this phenotype. However, we propose that other gene(s), as ye