A comprehensive review of the sequential extraction schemes for metal fractionation in environmental samples (ie., sediment, soil, sewage sludge, fly ash, etc.) is presented. The review contains more than 400 references and covers principally the literature published over the last decade. The use of each reagent involved in these schemes is looked at critically, and guidelines for their selectivity and extraction capacity are given. The operational character of these schemes is emphasised. Topics such as comparability between sequential extraction schemes of widespread use, harmonisation, acceleration, validation, etc. are addressed and future developments outlined.
Abstract We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem.
Abstract Motivation Advances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The phylogenomic analysis of next-generation sequencing (NGS) data requires a complex computational pipeline where multiple technical and methodological decisions are necessary that can influence the final tree obtained, like those related to coverage, assembly, mapping, variant calling and/or phasing. Results To assess the influence of these variables we introduce NGSphy, an open-source tool for the simulation of Illumina reads/read counts obtained from haploid/diploid individual genomes with thousands of independent gene families evolving under a common species tree. In order to resemble real NGS experiments, NGSphy includes multiple options to model sequencing coverage (depth) heterogeneity across species, individuals and loci, including off-target or uncaptured loci. For comprehensive simulations covering multiple evolutionary scenarios, parameter values for the different replicates can be sampled from user-defined statistical distributions. Availability and implementation Source code, full documentation and tutorials including a ‘Getting started’ guide are available at http://github.com/merlyescalona/ngsphy Supplementary information Supplementary data are available at Bioinformatics online.
In resistant hypertension, ingesting one or more blood pressure (BP)-lowering medications at bedtime is associated with significant reduction of sleep-time BP, a sensitive prognostic marker of cardiovascular disease (CVD) risk. This randomized trial investigated if bedtime therapy with at least one hypertension medication exerts better BP control and CVD risk reduction than conventional, morning-time therapy with all medications. We conducted a prospective, open-label, blinded-endpoint trial on 776 patients (387 men/389 women) with resistant hypertension, 61.6 ± 11.2 (mean ± SD) yrs of age. Patients were randomized to ingest all their prescribed hypertension medications upon awakening or ≥1 of them at bedtime. BP was measured by ambulatory monitoring for 48 h at baseline, and again annually or more frequently (quarterly) if treatment adjustment was required. After a median follow-up of 5.4 yrs (range, .5-8.5 yrs), participants ingesting ≥1 hypertension medications at bedtime showed a significantly lower hazard ratio (HR) of total CVD events (adjusted by age, sex, and diabetes) than those ingesting all medications upon awakening (.38 [95% CI: .27-.55]; number of events 102 vs. 41; p < .001). The difference between groups in the adjusted HR of major CVD events (a composite of CVD death, myocardial infarction, ischemic stroke, and hemorrhagic stroke) was also statistically significant (.35 [95% CI: .18-.68]; number of events 32 vs. 12; p = .002). At the last evaluation, patients treated with the bedtime versus awakening-time-treatment regimen showed significantly lower sleep-time systolic/diastolic BP mean values (121.6/65.4 vs. 113.0/61.1 mm Hg; p < .001) and higher prevalence of controlled ambulatory BP (61% vs. 46%; p < .001). The progressive decrease in the sleep-time systolic BP mean during follow-up was the most significant predictor of event-free survival (15% risk reduction per 5 mm Hg decreased asleep systolic BP mean). Among patients with resistant hypertension, ingestion of at least one hypertension medication at bedtime, compared with all medications upon waking, resulted in improved ambulatory BP control and fewer hard and soft CVD events.
Torasemide is a high-ceiling loop diuretic frequently used in the treatment of congestive heart failure, renal failure, and hypertension. Low doses of torasemide (2.5 to 5 mg/day) do not elevate 24 h natriuresis, and they constitute effective monotherapy for mild-to-moderate uncomplicated essential hypertension according to results based on clinic blood pressure (BP). However, there has yet to be a proper evaluation of its 24 h efficacy or potential dependency of effects according to the circadian time of treatment. Accordingly, this trial investigated the administration time-dependent efficacy of torasemide in uncomplicated essential hypertensive patients. We studied a total of 113 grade 1 and 2 hypertensive patients, 51.7+/-10.6 yrs of age, randomly assigned to receive torasemide (5 mg/day) as a monotherapy either upon awakening or at bedtime. BP was measured by ambulatory monitoring for 48 consecutive hours before and after six weeks of treatment. The efficacy of torasemide was significantly greater with bedtime dosing (i.e., 14.8 and 9.5 mmHg reduction in the 24 h mean systolic and diastolic BP, respectively) as compared with morning dosing upon awakening (i.e., 6.4 and 3.4 mmHg reduction in mean systolic and diastolic BP; p<0.001 between the two treatment-time groups). The percentage of patients with controlled ambulatory BP after treatment was also higher after bedtime treatment (64 vs. 23%; p<0.001). Safety and tolerability were comparable between the two treatment-time groups. A dose of 5 mg/day torasemide is more effective for BP reduction for uncomplicated essential hypertensive patients when ingested at bedtime than in the morning upon arising. The difference in antihypertensive efficacy as a function of the circadian dosing-time of torasemide here documented should be taken into account when prescribing this loop diuretic to treat essential hypertensive patients.
Significant evidence suggests that polyphenol-rich diets have the ability to protect against diabetes. Since several previous reviews focused on the nutrition and health effects including type 2 diabetes of polyphenols in 2007-2008, a number of related original publications have been pulished in this field. This review summarizes important advances related to influence of dietary polyphenols and polyphenol-rich diets on preventing and managing type 2 diabetes, as well as diabetes-mediated changes in bioactivities of dietary polyphenols. It appears that anthocyanins or anthocyanin-rich food intake is related to the risk of type 2 diabetes, but there is no association for other polyphenol subclasses. It is discussed that procyanidins are more active when administered individually than when mixed with food. The benefits of dietary polyphenols for type 2 diabetes can be summarized as: protection of pancreatic β-cells against glucose toxicity, anti-inflammatory and antioxidant effects, inhibition of α-amylases or α- glucosidases and thus decrease of starch digestion, and inhibition of advanced glycation end products formation. Moreover, type 2 diabetes also significantly influences the benefits of dietary polyphenols, although there are very limited studies have been conducted so far. How type 2 diabetes impacts the pharmacology of dietary polyphenols is not well understood. Comprehension of type 2 diabetes-mediated changes in pharmacokinetics and bioactivity of dietary polyphenols might lead to improve the benefits of these phytochemicals and subsequent clinical outcomes for type 2 diabetics.
Chromatographers rightly regard Mass Spectrometry (MS) as more than just a detection method. It is, in fact, another separation technique, and it is orthogonal to high performance liquid chromatography (HPLC), that is, it relies on a different physical property of the analyte to effect separation. Although HPLC relies on the analyte affinity for a stationary phase, MS relies on the mass-to-charge ratio (m/z) of ions derived from the compounds of interest. Liquid chromatography coupled to mass spectrometry (LC-MS) has become an indispensable tool for problem solving in virtually all analytical fields requiring "information-rich" chemical analysis. In the next decade, the LC-MS instrument market is expected to grow at more than twice the rate of the broader instrument market and will probably surpass gas chromatography–mass spectrometry (GC-MS) as the leader of the so-called hyphenated techniques. The aim of this review is to facilitate the growth, efficiency, and discussion of the use of LC-MS in studies of chemical migration from food packaging materials and other materials intended to come into contact with food.
