Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n^2) clustering algorithm which computes time averages over a continously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 100,000-fold for short multistable molecules (<150 bases). We performed extensive folding statistics on random and natural RNA sequences, and found that pseudoknots are unevenly distributed amongst RNAstructures and account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/ ).Comment: 6 pages, 5 figure

"Living together with dementia": preliminary results of a training programme for family caregivers

The aim of this article was to present the preliminar results of a training programme for family caregivers of people with dementia at an early to moderate stage living at home ? ?Living Together With Dementia?. In this randomised controlled trial, 27 family caregivers who met the inclusion criteria were recruited from the neurology outpatient consultation clinic of a hospital in the north of Portugal and randomised into two groups (control and experimental) between October 2015 and March 2016. The programme ?Living Together With Dementia? was applied to the participants of the experimental group. The strategies used, overload, difficulties and satisfaction of the caregivers were assessed at three different stages (at the beginning and end of the intervention, as well as at follow-up). For the data analysis, quantitative parametric measures were applied. The Health Ethical Commission of the Hospital Centre approved the study, and its protocol and Helsinki Declaration ethical principles were considered throughout the process. In the final assessment, an improvement in the overload and difficulties was confirmed, as was an increase in the caregivers? satisfaction level and an improvement in coping/problem-solving strategies. In the follow-up stage, the results tended to revert towards those of the initial assessment. The programme ?Living Together With Dementia? appeared to be a major contribution enabling family caregivers of people with dementia, although there is a need to develop an efficacy study using a more substantial sample. The programme contributed to a reduction in the overload and difficulties borne by the family caregivers of people with dementia at an early to moderate stagB910-DDDF-6BB2 | Lu?s Carlos Carvalho da Gra?aN/

Influence of total sugar intake on metabolic blood markers at 8 years of age in the Childhood Obesity Project

PURPOSE We aimed to characterize the association of dietary sugar intake with blood lipids and glucose-related markers in childhood. METHODS Data from the multicentric European Childhood Obesity Project Trial were used. Three-day weighed dietary records were obtained at 8~years of age along with serum concentrations of triglycerides, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol (HDL-C), glucose, and insulin. Total sugar intake comprised all mono- and disaccharides; different sugar sources were defined. Linear regression models were applied to investigate the cross-sectional association of total sugar intake with blood lipids and glucose-related markers with adjustment for total energy intake using the residual method. RESULTS Data were available for 325 children. Children consumed on average 332~kcal (SD 110) and 21% (SD 6) of energy from total sugar. In an energy-adjusted model, an increase of 100~kcal from total sugar per day was significantly associated with a z score HDL-C decrease (-~0.14; 95% CI -~0.01, -~0.27; p value = 0.031). Concerning different food groups of total sugar intake, 100~kcal total sugar from sweetened beverages was negatively associated with z score HDL-C (-~1.67; 95% CI -~0.42, -~2.91; p value = 0.009), while total sugar from milk products was positively related to z score HDL-C (1.38, 95% CI 0.03, 2.72; p value = 0.045). None of the other blood lipids or glucose-related markers showed a significant relationship with total sugar intake. CONCLUSION Increasing dietary total sugar intake in children, especially from sweetened beverages, was associated with unfavorable effects on HDL-C, which might increase the long-term risk for dyslipidemia and cardiovascular disease. CLINICAL TRIAL REGISTRY ClinicalTrials.gov Identifier: NCT00338689; Registered: June 19, 2006. URL: https://clinicaltrials.gov/ct2/show/NCT00338689?term=NCT00338689&rank=1

Constitutively Active CaMKKα Stimulates Skeletal Muscle Glucose Uptake in Insulin-Resistant Mice In Vivo

In insulin-sensitive skeletal muscle, the expression of constitutively active Ca(2+)/calmodulin-dependent protein kinase kinase α (caCaMKKα) stimulates glucose uptake independent of insulin signaling (i.e., Akt and Akt-dependent TBC1D1/TBC1D4 phosphorylation). Our objectives were to determine whether caCaMKKα could stimulate glucose uptake additively with insulin in insulin-sensitive muscle, in the basal state in insulin-resistant muscle, and if so, to determine whether the effects were associated with altered TBC1D1/TBC1D4 phosphorylation. Mice were fed a control or high-fat diet (60% kcal) for 12 weeks to induce insulin resistance. Muscles were transfected with empty vector or caCaMKKα plasmids using in vivo electroporation. After 2 weeks, caCaMKKα protein was robustly expressed. In insulin-sensitive muscle, caCaMKKα increased basal in vivo [(3)H]-2-deoxyglucose uptake approximately twofold, insulin increased glucose uptake approximately twofold, and caCaMKKα plus insulin increased glucose uptake approximately fourfold. caCaMKKα did not increase basal TBC1D1 (Ser(237), Thr(590), Ser(660), pan-Thr/Ser) or TBC1D4 (Ser(588), Thr(642), pan-Thr/Ser) phosphorylation. In insulin-resistant muscle, caCaMKKα increased basal glucose uptake approximately twofold, and attenuated high-fat diet–induced basal TBC1D1 (Thr(590), pan-Thr/Ser) and TBC1D4 (Ser(588), Thr(642), pan-Thr/Ser) phosphorylation. In cell-free assays, CaMKKα increased TBC1D1 (Thr(590), pan-Thr/Ser) and TBC1D4 (Ser(588), pan-Thr/Ser) phosphorylation. Collectively, these results demonstrate that caCaMKKα stimulates glucose uptake additively with insulin, and in insulin-resistant muscle, and alters the phosphorylation of TBC1D1/TBC1D4

Circulating Amino Acids and Risk of Peripheral Artery Disease in the PREDIMED Trial

Effective prevention and risk prediction are important for peripheral artery disease (PAD) due to its poor prognosis and the huge disease burden it produces. Circulating amino acids (AA) and their metabolites may serve as biomarkers of PAD risk, but they have been scarcely investigated. The objective was to prospectively analyze the associations of baseline levels of plasma AA (and their pathways) with subsequent risk of PAD and the potential effect modification by a nutritional intervention with the Mediterranean diet (MedDiet). A matched case-control study was nested in the PREDIMED trial, in which participants were randomized to three arms: MedDiet with tree nut supplementation group, MedDiet with extra-virgin olive oil (EVOO) supplementation group or control group (low-fat diet). One hundred and sixty-seven PAD cases were matched with 250 controls. Plasma AA was measured with liquid chromatography/mass spectrometry at the Broad Institute. Baseline tryptophan, serine and threonine were inversely associated with PAD (ORfor 1 SD increase = 0.78 (0.61–0.99); 0.67 (0.51–0.86) and 0.75 (0.59–0.95), respectively) in a multivariable-adjusted conditional logistic regression model. The kynurenine/tryptophan ratio was directly associated with PAD (ORfor 1 SD increase = 1.50 (1.14–1.98)). The nutritional intervention with the MedDiet+nuts modified the association between threonine and PAD (p-value interaction = 0.018) compared with the control group. However, subjects allocated to the MedDiet+EVOO group were protected against PAD independently of baseline threonine. Plasma tryptophan, kynurenine/tryptophan ratio, serine and threonine might serve as early biomarkers of future PAD in subjects at a high risk of cardiovascular disease. The MedDiet supplemented with EVOO exerted a protective effect, regardless of baseline levels of threonine

Expression analysis of the BFN1 nuclease gene promoter during senescence, abscission, and programmed cell death-related processes

Little is known about the biological role of nucleases induced during plant senescence and programmed cell death (PCD). Arabidopsis BFN1 has been identified as a senescence-associated type I nuclease, whose protein sequence shares high homology with some other senescence- or PCD-associated plant nucleases. To learn about BFN1 regulation, its expression pattern was analysed. A 2.3 kb portion of the 5′ promoter sequence of BFN1 was cloned and its ability to activate the GUS reporter gene was examined. Transgenic Arabidopsis and tomato plants harbouring this chimeric construct were analysed for GUS expression. In both, the BFN1 promoter was able specifically to direct GUS expression in senescent leaves, differentiating xylem and the abscission zone of flowers. Thus, at least part of the regulation of BFN1 is mediated at the transcriptional level, and the regulatory elements are recognized in the two different plants. In tomato, specific expression was observed in the leaf and the fruit abscission zones. The BFN1 promoter was also active in other tissues, including developing anthers and seeds, and in floral organs after fertilization. PCD has been implicated in all of these processes, suggesting that in addition to senescence, BFN1 is involved in PCD associated with different development processes in Arabidopsis

A historical perspective on the discovery of statins

Cholesterol is essential for the functioning of all human organs, but it is nevertheless the cause of coronary heart disease. Over the course of nearly a century of investigation, scientists have developed several lines of evidence that establish the causal connection between blood cholesterol, atherosclerosis, and coronary heart disease. Building on that knowledge, scientists and the pharmaceutical industry have successfully developed a remarkably effective class of drugs—the statins—that lower cholesterol levels in blood and reduce the frequency of heart attacks

Larger is Better: The Scale Effects of the Italian Local Healthcare Authorities Amalgamation Program

Consolidation is often considered as a means to lower service delivery costs and enhance accountability. This paper uses a prospective evaluation design to derive estimates of the potential cost savings that may arise from Local Healthcare Authorities (LHAs) amalgamation process, which is concerning the Itali an National Health System. We focus specifically on cost savings due to scale economies with reference to a particular subset of the production costs of the LHAs, i.e. the administrative costs together with the purchasing costs of both goods as well as non-healthcare related services. Our results demonstrate the existence of economies of scale linked to the size of the LHA population. Hence, the decision to reduce the number of LHAs may result in larger local health authorities that are more cost efficient, especially when the consolidation process concerns merging a large number of LHA