Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Skeletal muscle mass and body fat in relation to successful ageing of older adults: The multi-national MEDIS study

BACKGROUND: The determinants that promote successful ageing still remain unknown. The aim of the present work was to evaluate the role of skeletal muscle mass and body fat percentage (BF%), in the level of successful ageing. METHODS: during 2005-2011, 2663 older (aged 65-100 years) from 21 Mediterranean islands and the rural Mani region (Peloponnesus) of Greece were voluntarily enrolled in the study. Appendicular skeletal muscle mass (ASM), skeletal muscle mass index (SMI) and BF% were calculated using population formulas. Dietary habits, energy intake, expenditure and energy balance were derived throughout standard procedures. A successful ageing index ranging from 0 to 10 was used. RESULTS: The mean ASM mass was 24±6.0kg, the SMI was 0.84±0.21 and the BF% was 44%. Females had lower SMI and higher BF% in comparison with males, respectively [(SMI: 0.66±0.09 vs. 1.03±0.11; BF%: 51% vs. 34%, (p<0.001)]. High successful agers had better rates in ASM (p=0.01), SMI (p<0.001) and BF% (p<0.001), compared with the medium and low successful ones. Changes in SMI [b-coefficient (95% CI):2.14 (1.57 to 2.71)] were positively associated with successful ageing, while changes in BF% [b-coefficient (95% CI): -0.04 (-0.05 to -0.03)] were inversely associated with successful ageing. Results from sensitivity analysis showed that the effects of variations on body composition were consistent, less pronounced in the positive energy balance group and more pronounced among the oldest old. CONCLUSIONS: Body composition changes seem to be associated with lower quality of life in the older adults, as measured through successful ageing

Stroke genetics: prospects for personalized medicine.

Epidemiologic evidence supports a genetic predisposition to stroke. Recent advances, primarily using the genome-wide association study approach, are transforming what we know about the genetics of multifactorial stroke, and are identifying novel stroke genes. The current findings are consistent with different stroke subtypes having different genetic architecture. These discoveries may identify novel pathways involved in stroke pathogenesis, and suggest new treatment approaches. However, the already identified genetic variants explain only a small proportion of overall stroke risk, and therefore are not currently useful in predicting risk for the individual patient. Such risk prediction may become a reality as identification of a greater number of stroke risk variants that explain the majority of genetic risk proceeds, and perhaps when information on rare variants, identified by whole-genome sequencing, is also incorporated into risk algorithms. Pharmacogenomics may offer the potential for earlier implementation of 'personalized genetic' medicine. Genetic variants affecting clopidogrel and warfarin metabolism may identify non-responders and reduce side-effects, but these approaches have not yet been widely adopted in clinical practice

Adherence to Mediterranean diet ; not olive oil consumption alone predicts hypercholesterolemia in elderly : the MEDIS study

Background/Aims: This analysis aimed to compare the role of olive oil consumption with that of Mediterranean diet on their diagnostic value for the presence of hypercholesterolemia. Methods: Mediterranean islands study (MEDIS) recruited 2749 older (over 65 years of age) individuals between 2005-2015. Recruitment occurred from 21 Mediterranean islands and the rural Mani region (Peloponnesus) of Greece. Dietary habits, energy intake, physical activity status, sociodemographic characteristics (altitude in residing area, lifestyle parameters) and clinical profile aspects (including blood lipids) were measured. The level of adherence to Mediterranean diet was assessed using the a-priori index MedDietScore and olive oil consumption was assessed with a validated FFQ. The diagnostic value of the food data was assessed using the AUC for the presence of hypercholesterolemia. The p value for the comparison of AUC with 0.5 was performed with Likelihood Ratio test. [Excerpt]peer-reviewe

Cooking of meat and fish in Europe—results from the European Prospective Investigation into Cancer and Nutrition (EPIC)

Objectives: There is epidemiologic evidence that the consumption of fried, grilled or barbecued meat and fish that are well-done or browned may be associated with an increased cancer risk. These high-temperature cooking methods are thought to be surrogates for mutagens and carcinogens produced in meat and fish, eg heterocyclic amines or polycyclic hydrocarbons. Since data on food cooking methods are scarce, the aim of this study was to describe the variation in meat and fish cooking methods in different parts of Europe. Design: Using a standardized 24 h recall from a sub-sample of the EPIC cohort (35 644 persons, 35-75 y old), mean daily intake of meat and fish prepared by different cooking methods and the relative contribution of the cooking methods to the overall cooking of meat and fish was calculated. Results: Whereas frying was more often noted in northern Europe, roasting and stir frying were more often used in the south. Concerning high-temperature cooking methods, their frequency of application varies between 15% in the EPIC cohort of North-Italy and 49% in the cohort of The Netherlands. Average consumption of fried, grilled and barbecued meat and fish ranges from a low of 12 g/day in the centres in southern Spain to a high of 91 g/day in northern Spain. Conclusion: High variation in both the kind of meat/fish consumed as well as its cooking methods is observed within EPIC. In order to use this variation for the evaluation of the impact of cooking methods on cancer risk, a questionnaire on meat and fish cooking methods is being developed and could be applied in the whole EPIC cohort

Is Parental Longevity Associated With the Cardiovascular Risk and the Successful Aging of Their Offspring? Results From the Multinational MEDIS Study

The aim of the present study was to evaluate the role of parental longevity and parental cardiovascular disease (CVD) history in CVD risk and successful aging of a random sample of older adults living in the Mediterranean basin and who participated in the MEDiterranean Islands (MEDIS) study. During 2005 to 2011, 2663 elders were voluntarily enrolled. A multidimensional successful aging index consisting of 10 components was used. Paternal and maternal longevity was defined as those older participants of whom both parents lived above the age of 90. The burden of CVD-related factors (CVD-RFs) was calculated as the total score of 4 major CVD-RFs (range 0-4). After adjustment, parental longevity was inversely associated with the burden of CVD-RFs (P= .04). Moreover, parental longevity was positively associated with the older adults' successful aging score (β-coefficient [95% confidence interval]: .38 [0.06-0.71]). Parent's long living was revealed as an important factor for successful aging and for reduced CVD risk, suggesting that further research is needed in the genetic predisposition of longevity

The association between sleeping time and metabolic syndrome features among older adults living in Mediterranean region. The MEDIS study.

Background: Metabolic Syndrome (MetS) as a combination of features has been known to significantly increase Cardiovascular Disease (CVD) risk, whilst MetS presence is linked to lifestyle parameters including physical activity and dietary habits; recently, the potential impact of sleeping habits has also become an issue under consideration. The aim of this study was to investigate the role of sleep quantity in several MetS components. Methods: Design:Cross-sectional observational study. Setting: 26 Mediterranean islands and the rural Mani region (Peloponnesus) of Greece. Participants: during 2005-2017, 3130 older (aged 65-100 years) Mediterranean residents were voluntarily enrolled. Measurements: Dietary habits (including MedDietScore assessment), physical activity status, socio-demographic characteristics, lifestyle parameters (sleeping and smoking habits) and clinical profile aspects including Metabolic Syndrome (MetS) components (i.e., waist circumference, systolic and diastolic blood pressure, fasting glucose, triglycerides, LDL and HDL-cholesterol) were derived through standard procedures. Results: The number of daily hours of sleep was independently associated with greater waist circumference (b coefficient per 1 hour=0.91, 95% Confidence Interval (CI); 0.34, 1.49), higher LDL-cholesterol levels (b per 1 hour=3.84, 95%CI; 0.63, 7.05) and lower diastolic blood pressure levels (b per 1 hour=-0.98, 95%CI; - 1.57, -0.39) after adjusting for participants’ age, gender, body mass index, daily walking time, level of adherence to Mediterranean diet and smoking status. No association was revealed between hours of sleep per day and fasting glucose, triglycerides, HDL-cholesterol and systolic blood pressure. Conclusions: Increased hours of sleep is an indicator of metabolic disorders among elderly inviduals, and further research is needed to identify the paths through which sleep quantity is linked to MetS features in different age-groups

Association between siesta (daytime sleep), dietary patterns and the presence of metabolic syndrome in elderly living in Mediterranean area (MEDIS study):The moderating effect of gender

Objectives: Several lifestyle parameters including diet, physical activity and sleep were associated in isolation with the presence of Metabolic Syndrome (MetS) in adults, to date there is a paucity of studies which evaluated their combined role aging populations and especially with respect to gender. Therefore, the aim of the present study was to provide a global consideration of the lifestyle factors associated with MetS among elderly individuals. Design: Cross-sectional observational study. Setting: 21 Mediterranean islands and the rural Mani region (Peloponnesus) of Greece. Participants: during 2005-2015, 2749 older (aged 65-100 years) from were voluntarily enrolled in the study. Measurements: Dietary habits, energy intake, physical activity status, sociodemographic characteristics, lifestyle parameters (sleeping and smoking habits) and clinical profile aspects were derived through standard procedures. The presence of MetS was defined using the definition provided by NCEP ATP III (revised) and cluster analysis was used to identify overall dietary habit patterns. Results: The overall prevalence of MetS in the study sample was 36.2%, but occurred more frequently in females (40.0% vs. 31.8%, respectively, p=0.03). Individuals with MetS were more likely to sleep during the day (89.4% vs. 76.8% respectively, p=0.039) and frequent ‘siesta’ was positively linked to the odds of MetS presence in females (Odds Ratio (OR) =3.43, 95% Confidence Intervals (CI): 1.08-10.9), but not for men (p=0.999). The lower carbohydrate (i.e., 45.2% of total daily energy, 120±16gr/day) dietary cluster was inversely associated with the odds for MetS presence, but only for men (OR=0.094, 95%CI: 0.010-0.883). Conclusions: Lifestyle parameters including sleep and diet quality are strongly associated with the presence of MetS in elderly cohort, but different their level of influence appears to be different, depending on gender. Further research is needed to better consider the role of lifestyle characteristics in the management of MetS in clinical practice

Anti-Inflammatory Nutrition and Successful Ageing in Elderly Individuals: The Multinational MEDIS Study

BACKGROUND: The role of diet and inflammation in successful ageing is not transparent, and as such, is still being investigated. The aim of the present work was to evaluate the inflammatory potential of dietary habits in the successful ageing of a random sample of older adults living in the Mediterranean basin and who participated in the MEDIS (MEDiterranean ISlands) study. METHODS: During 2005-2016, 3,128 older adults (aged 65-100 years) from 24 Mediterranean islands and the rural Mani region (Peloponnesus) of Greece were enrolled in the study. A multidimensional successful ageing index consisting of 10 components was employed. A validated and reproducible Food Frequency Questionnaire (FFQ) was used to evaluate the dietary habits of the older adults. A nutrition anti-inflammatory (NAI) score based on the participants' specific dietary habits was assessed. RESULTS: Participants with high NAI scores (proinflammatory nutrition) had a higher prevalence of hypercholesterolemia and lower levels of successful ageing. After adjusting for several confounders, the NAI score was associated with successful ageing (-0.03, 95% CI -0.5 to -0.006). Stratified analysis by gender and advanced age revealed heterogeneity in the NAI score, predicting successful ageing. CONCLUSIONS: The inflammatory potential of nutrition was reported as an important factor for successful ageing, suggesting that further research is needed on the role of anti- and proinflammatory dietary habits in healthy and successful ageing

Identification of 4 novel human ocular coloboma genes ANK3, BMPR1B, PDGFRA, and CDH4 through evolutionary conserved vertebrate gene analysis

Purpose: Ocular coloboma arises from genetic or environmental perturbations that inhibit optic fissure (OF) fusion during early eye development. Despite high genetic heterogeneity, 70% to 85% of patients remain molecularly undiagnosed. In this study, we have identified new potential causative genes using cross-species comparative meta-analysis. Methods: Evolutionarily conserved differentially expressed genes were identified through in silico analysis, with in situ hybridization, gene knockdown, and rescue performed to confirm spatiotemporal gene expression and phenotype. Interrogation of the 100,000 Genomes Project for putative pathogenic variants was performed. Results: Nine conserved differentially expressed genes between zebrafish and mouse were identified. Expression of zebrafish ank3a, bmpr1ba/b, cdh4, and pdgfaa was localized to the OF, periocular mesenchyme cells, or ciliary marginal zone, regions traversed by the OF. Knockdown of ank3, bmpr1b, and pdgfaa revealed a coloboma and/or microphthalmia phenotype. Novel pathogenic variants in ANK3, BMPR1B, PDGFRA, and CDH4 were identified in 8 unrelated coloboma families. We showed BMPR1B rescued the knockdown phenotype but variant messenger RNAs failed, providing evidence of pathogenicity. Conclusion: We show the utility of cross-species meta-analysis to identify several novel coloboma disease-causing genes. There is a potential to increase the diagnostic yield for new and unsolved patients while adding to our understanding of the genetic basis of OF morphogenesis