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

Lifestyle and health determinants of cardiovascular disease among Greek older adults living in Eastern Aegean Islands: An adventure within the MEDIS study.

OBJECTIVE: The aim of the present study was to evaluate lifestyle and health determinants of cardiovascular disease (CVD) risk among Greek elderly residents living in Eastern Aegean islands, in both Greece and Turkey. METHODS: Under the context of the MEDIS study, 724 older adults (aged 65 to 100 years) from 8 Eastern Aegean Sea Greek islands (n=100 living in Samothrace, 142 in Lesvos, 150 in Limnos, 76 in Ikaria, 52 in Kassos, 149 in Rhodes and Karpathos) and from Turkey (n=55older adults of Greek origin living on Gökçeada Island) were voluntarily recruited. Overall cardiometabolic risk was measured as the sum (range 0-4) of four common CVD risk factors (hypertension, diabetes, dyslipidemia and obesity). RESULTS: Greek islanders had higher CVD scores compared to Greeks of Gökçeada (1.9±1.1 vs 1.4±1.0 risk factors / participant, p<0.001). Further analysis revealed that the diet of Greek islanders was similar to the traditional Mediterranean diet; however, these individuals demonstrated 2-times higher odds (95% CI, 1.04-3.87) for having hypertension, 1.53-times higher odds (95% CI, 0.66-3.54) for having diabetes, 3.29-times higher odds (95% CI, 1.58-6.81) for having hypercholesterolemia; whereas they had 0.78-times lower odds (95% CI, 0.40-1.52) for being obese, compared to elderly Greek adults living on Gökçeada. CONCLUSIONS: Overall, CVD risk seems to be low among Eastern Aegean Islanders; certain differences in CVD risk factors exist between Greek islanders and their counterparts living in Gökçeada, and those differences may be attributed to various environmental, cultural and lifestyle factors

A modified model for the Lobula Giant Movement Detector and its FPGA implementation

The Lobula Giant Movement Detector (LGMD) is a wide-field visual neuron located in the Lobula layer of the Locust nervous system. The LGMD increases its firing rate in response to both the velocity of an approaching object and the proximity of this object. It has been found that it can respond to looming stimuli very quickly and trigger avoidance reactions. It has been successfully applied in visual collision avoidance systems for vehicles and robots. This paper introduces a modified neural model for LGMD that provides additional depth direction information for the movement. The proposed model retains the simplicity of the previous model by adding only a few new cells. It has been simplified and implemented on a Field Programmable Gate Array (FPGA), taking advantage of the inherent parallelism exhibited by the LGMD, and tested on real-time video streams. Experimental results demonstrate the effectiveness as a fast motion detector

Early Diagnosis of Pulmonary Embolism: Review and Cost-Effectiveness Analysis

Pulmonary embolism (PE) is a serious, life-threatening thrombotic disease, which results in considerable health and economic consequences each year for the United States. These consequences include a toll of 83,000 deaths and an economic impact between 1,5 and 5 billion. Approaches to strategy selection by physicians and other health-care specialists are based mainly upon cost, technology availability, and cultural tolerance regarding radiation exposure. The purpose of this study was to determine the most cost-effective diagnostic strategy with patients suspected of PE among several strategies currently used by examining their detection failure rates. This objective was met by (a) assessing parameter estimates and their uncertainty using triangular and 7 distributions, (b) conducting a cost-effectiveness analysis, and (c) testing the model for errors using sensitivity analysis. Cost-effectiveness analysis based upon a decision tree model revealed that among the investigated strategies for patients with suspected PE the most cost-effective strategy appears to be strategy 3, composed of a clinical decision rule (CDR), a D-dimer test (DD), a compression ultrasonography test (CUS), and a computed tomography pulmonary angiography (CT). Strategy 5, composed by a CDR, DD, a CT, a CUS, and an invasive pulmonary angiography (PA) appeared to be a cost-effective method, but it was more expensive than strategy 3 and included an invasive pulmonary angiography (PA). The results of a Monte Carlo simulation sensitivity analysis were robust over a number of distributions regarding the PE diagnostic test costs, sensitivities, specificities, and strategy effectiveness. Additionally, the results of this investigation were valid over an extensive range of one-way, two-way, and three-way sensitivity analyses regarding PE diagnostic test costs. Overall, the proposed analyses identified uncertainty and eliminated error; thus, it provides a practical approach to help medical professionals estimate uncertainty in the diagnosis of PE. Although this research has broadened the ability to identify uncertainty and eliminate error, further research is needed to validate these findings in a prospective clinical trial before the delivery of a clinical recommendation

Stochastic Route Planning in Public Transport

Journey planning is a key process in public transport, where travelers get informed how to make the best use of a given public transport system for their individual travel needs. A common trait of most available journey planners is that they assume deterministic travel times, but vehicles in public transport often deviate from their schedule. The present paper investigates the problem of finding journey plans in a stochastic environment. To fully exploit the flexibility inherent in multi-service public transport systems, we propose to use the concept of a routing policy instead of a linear journey plan. A policy is a state-dependent routing advice which specifies a set of services at each location from which the traveler is recommended to take the one that arrives first. We consider current time dependent policies, that is, when the routing advice at a given location is based solely on the current time. We propose two heuristic solutions that find routing policies that perform better than deterministic journey plans. A numerical comparison shows the achievable gains when applying the different heuristic policies based on extensive simulations on the public transport network of Budapest. The results show that the probability of arriving on time to a given destination can be significantly improved by following a policy instead of a linear travel plan

Optimal Computation of Overabundant Words

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word w in a given sequence x can be used for classifying w as avoided or overabundant. The definitions used for the expectation and deviation of w in this statistical model were described and biologically justified by Brendel et al. (J Biomol Struct Dyn 1986). We have very recently introduced a time-optimal algorithm for computing all avoided words of a given sequence over an integer alphabet (Algorithms Mol Biol 2017). In this article, we extend this study by presenting an O(n)-time and O(n)-space algorithm for computing all overabundant words in a sequence x of length n over an integer alphabet. Our main result is based on a new non-trivial combinatorial property of the suffix tree T of x: the number of distinct factors of x whose longest infix is the label of an explicit node of T is no more than 3n-4. We further show that the presented algorithm is time-optimal by proving that O(n) is a tight upper bound for the number of overabundant words. Finally, we present experimental results, using both synthetic and real data, which justify the effectiveness and efficiency of our approach in practical terms

A massive hemorrhagic pleural effusion does not exclude the diagnosis of tuberculosis: a case report

We report a case of an immunocompetent 18-year-old man with a massive hemorrhagic, exudative, lymphocytic pleural effusion. Blind transthoracic pleural biopsy showed granuloma formation, while the pleural fluid culture was positive for Mycobacterium tuberculosis, confirming the diagnosis of primary tuberculous pleuritis. A massive hemorrhagic pleural effusion is extremely rare in tuberculosis, but tuberculosis is a very protean disease and should always be included in the differential diagnosis of pleural effusion

Lessons from Studies in Middle-Aged and Older Adults Living in Mediterranean Islands: The Role of Dietary Habits and Nutrition Services

Background. Islands in the Mediterranean basin share particular habits and traditions and greater life expectancy than other European regions. In this paper, particular interest has been given to the effect of the Mediterranean diet, as well as nutritional services on CVD risk, on Mediterranean islands. Methods. Published results from observational studies were retrieved from electronic databases (Pubmed and Scopus) and summarized. Results. Prevalence of CVD risk factors is increased. Adherence to the Mediterranean diet was moderate, even among the elderly participants. Furthermore, the presence of a dietician was associated with higher adherence to the Mediterranean dietary pattern and consequently lowers CVD risk. Conclusion. Adherence to the Mediterranean diet is reduced, while the prevalence of CVD risk factors is increasing at alarming rates. Public health nutrition policy has the opportunity to improve the health and quality of life of people living in isolated insular areas of the Mediterranean basin

Understanding the Experiences of Women with Anorexia Nervosa Who Complete an Exposure Therapy Protocol in a Naturalistic Setting

Anorexia Nervosa (AN) is a serious mental health concern in the United States, with the highest mortality rate of all mental disorders. Females comprise the vast majority of people with AN, although the number of males with the condition is rising. Anorexia Nervosa has a high relapse rate and is often enduring, which makes it challenging to treat successfully; therefore, the mental health profession is in need of innovative therapeutic approaches. Exposure therapy has a growing evidence base for the treatment of eating disorders, including AN; however, there are very few studies that explore body image/mirror exposure specifically in patients with AN. Further, the existing quantitative and qualitative research studies present several methodological limitations, which prompts in depth exploration of this intervention for its specific use with anorexic patients. Using Interpretative Phenomenological Analysis (IPA), the present study explored the experiences of women diagnosed with AN who participated in a novel application of body image/mirror exposure therapy in a naturalistic setting, focusing on the meaning they attributed to the intervention as part of their recovery from AN. The findings may support enhancement of the treatment protocol and inform future outcome studies on the efficacy of using body image/mirror exposure for AN