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

Epidemiology of interstitial lung diseases in Greece

SummaryIntroductionFew data are available on the epidemiology of interstitial lung diseases (ILDs), especially after the current classification of idiopathic interstitial pneumonias. The aim of this study is to provide data on the epidemiology of ILDs in Greece, under the ATS/ERS international consensus.MethodsDepartments of Pneumonology were contacted and asked to complete a questionnaire for every case of ILD that was alive on 2004 as well as for every new case from 1st January 2004 to 31st December 2004. Questions on the patients' demographic data, the exact diagnosis and the procedures used to establish the diagnosis were included. Centers covering about 60% of the Greek population have been analyzed.ResultsA total of 967 cases have been registered. The estimated prevalence of ILDs is 17.3 cases per 100,000 inhabitants. The estimated annual incidence of ILDs is 4.63 new cases per 100,000 inhabitants. The most frequent disease is sarcoidosis (34.1%), followed in decreasing order by idiopathic pulmonary fibrosis (19.5%), ILD associated with collagen vascular diseases (12.4%), cryptogenic organizing pneumonia (5.3%), histiocytosis (3.8%), and hypersensitivity pneumonitis (2.6%). Unclassified ILD or not otherwise specified accounted for the 8.5% of prevalent cases.ConclusionsThese data suggest that sarcoidosis and idiopathic pulmonary fibrosis are the most frequent ILDs in our population. In comparison with the few previous reports, interesting dissimilarities have been observed

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

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

Add-on topiramate in the treatment of refractory partial-onset epilepsy: Clinical experience of outpatient epilepsy clinics from 11 general hospitals

SummaryAn open, prospective, observational study was performed to assess efficacy and adverse-event profile of topiramate as add-on therapy in epilepsy. Outpatient neurology clinics from 11 general hospitals in Greece participated in the study. In total, 211 patients with treatment resistant partial-onset seizures who met the inclusion criteria, were studied. After baseline evaluation, topiramate was given at a target dose of 200mg/day over a 1-month titration period. In the subsequent maintenance period, the topiramate dose could be varied according to the clinical results. Patients were followed for in total 6 months, with monthly visits and regular physical, neurological and laboratory examinations. Seizure frequencies decreased to 35–40% of baseline values following 3 months of treatment and remained relatively constant thereafter. The average monthly seizure frequency over the 6-month study period was 4.61, compared to 9.21 at baseline. The number of responders (patients with at least 50% reduction in seizure frequency) followed a similar pattern, i.e., increase during the first 3 months levelling off at a final 80–85% response rate. Of those completing the study, 30% had been seizure-free for at least 3 months and 12% for 5 months. Topiramate was well tolerated, no deviations in laboratory values were found. Adverse events appeared to occur less frequently, and antiepileptic effects were more pronounced in this prospective open-label study than in earlier reports from randomised controlled trials. The nature of the patient population and the application of individualised dose optimisation are proposed as contributing factors to explain the favourable results of this study

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

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