A Cloud Infrastructure for Optimization of a Massive Parallel Sequencing Workflow

Massive Parallel Sequencing is a term used to describe several revolutionary approaches to DNA sequencing, the so-called Next Generation Sequencing technologies. These technologies generate millions of short sequence fragments in a single run and can be used to measure levels of gene expression and to identify novel splice variants of genes allowing more accurate analysis. The proposed solution provides novelty on two fields, firstly an optimization of the read mapping algorithm has been designed, in order to parallelize processes, secondly an implementation of an architecture that consists of a Grid platform, composed of physical nodes, a Virtual platform, composed of virtual nodes set up on demand, and a scheduler that allows to integrate the two platform

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

On the stability of some isoperimetric inequalities for the fundamental tones of free plates

We provide a quantitative version of the isoperimetric inequality for the fundamental tone of a biharmonic Neumann problem. Such an inequality has been recently established by Chasman adapting Weinberger's argument for the corresponding second order problem. Following a scheme introduced by Brasco and Pratelli for the second order case, we prove that a similar quantitative inequality holds also for the biharmonic operator. We also prove the sharpness of both such an inequality and the corresponding one for the biharmonic Steklov problem

Comparison between adenosine triphosphate bioluminescence and aerobic colony count to assess surface sanitation in the hospital environment

Background: Adenosine triphosphate bioluminescence produced by the firefly luciferase has been successfully introduced to verify cleaning procedures in the food industry according to the Hazard Analysis Critical Control Point program. Our aim was to evaluate the reliability of bioluminescence as a tool to monitor the effectiveness of sanitation in healthcare settings, in comparison with the microbiological gold standard. Methods: 614 surfaces of various material were randomly sampled in Policlinico University Hospital units in Palermo, Italy, to detect adenosine triphosphate bioluminescence and aerobic colony count. Linear regression model and Pearson correlation coefficient were used to estimate the relationship between the two variables of the study. Results: Aerobic colony count median was 1.71 colony forming units/cm2 (interquartile range = 3.8), whereas adenosine triphosphate median was 59.9 relative light units/cm2 (interquartile range = 128.3). Pearson coefficient R2 was 0.09. Sensitivity and specificity of bioluminescence test with respect to microbiology were 46% and 71%, whereas positive predictive value and negative predictive value were 53% and 65%, respectively. Conclusion: According to our results, there seemed to be no linear correlation between aerobic colony count and adenosine triphosphate values, suggesting that current bioluminescence technology has not any proportional relationships with culturable microbes contaminating environmental surfaces in health-care settings

Strong existence and uniqueness of the stationary distribution for a stochastic inviscid dyadic model

We consider an inviscid stochastically forced dyadic model, where the additive noise acts only on the first component. We prove that a strong solution for this problem exists and is unique by means of uniform energy estimates. Moreover, we exploit these results to establish strong existence and uniqueness of the stationary distribution

Determinants associated with obesity and physical activity in the public and private schools of the city of palermo

Introduction: Obesity is a medical condition associated with premature death and it is a risk factor for many chronic diseases. In this context, performing a regular physical activity promotes a healthy lifestyle, with significant health benefits. The aim of the study was to investigate behaviors that increase the risk of obesity and the determinants that encourage physical activity among adolescents. Materials and methods: The HBSC (Health Behavior in School-aged Children) questionnaire was administered to students in Palermo's private and public schools. For the sampling of public schools the protocol of the HBSC Surveillance System was followed; for the private ones it was opportunistic. Results: Private school students are more likely to exercise more than 3 days per week (OR 1.58) and are more likely to exercise more than 2 times a week (OR 2.08). Obese students in private schools in Palermo are more likely to perform physical activity for less than 3 days a week (OR 3.52) and a higher risk of not having breakfast (OR 10.11) and a snack between main meals (OR 3.82) every day. For all the schools examined, it emerged that obese subjects are more likely not to consume fruit (OR 3.13), to stay more than 6 hours a day in front of PCs and video games (OR 3.24) and more than 2 hours a day in front of TV (OR 3.79). Male students are more likely to perform physical activity for more than 3 days per week (OR 1.48) and intense physical activity at least 2 times per week (OR 1.76) Conclusions: It is necessary to intervene early with training on school and family in order to promote correct and responsible food choices and increase the level of physical activity among students. Therefore prevention interventions must be an integral part of coherent strategies based on tests of agreed effectiveness in order to minimize the risk linked to the development of diseases

Sars-cov-2 and the risk assessment document in italian work; specific or generic risk even if aggravated?

In December 2019, several cases of atypical pneumonia were detected in Wuhan city, Hubei province, inland China. The initial outbreak was of considerable size first in China subsequently spread to the rest of the world. Immediately after the epidemic (which according to the World Health Organization had risen to pandemic status), the problem of whether or not to update the occupational risk assessment arose, also considering how the biological risk from SARS CoV-2 should be understood: specific or generic. To this end, we conducted a literature review to identify national health legislation and policies, examining how Italy has addressed the COVID-19 emergency in occupational health planning, in order to develop considerations on the need to update the Risk Assessment Document following the pandemic status. The data that emerged from the review of current legislation allowed us to conclude that the risk from SARS-CoV-2 is in most work activities to be understood as a generic or aggravated generic risk, requiring the employer to apply and control the preventive measures suggested by health authorities to contain the spread of the virus

Water extract of Cryphaea heteromalla (Hedw.) D. Mohr bryophyte as a natural powerful source of biologically active compounds

Bryophytes comprise of the mosses, liverworts, and hornworts. Cryphaea heteromalla, (Hedw.) D. Mohr, is a non-vascular lower plant belonging to mosses group. To the date, the most chemically characterized species belong to the liverworts, while only 3.2% and 8.8% of the species belonging to the mosses and hornworts, respectively, have been investigated. In this work, we present Folin–Ciocalteu and oxygen radical absorbance capacity (ORAC) data related to crude extracts of C. heteromalla obtained by three different extraction solvents: pure water (WT), methanol:water (80:20 v/v) (MET), and ethanol:water (80:20 v/v) (ETH). The water extract proved to be the best solvent showing the highest content of biophenols and the highest ORAC value. The C. heteromalla-WT extract was investigated by HPLC-TOF/MS (High Performance Liquid Chromatography-Time of Flight/Mass Spectrometry) allowing for the detection of 14 compounds, five of which were phenolic compounds, derivatives of benzoic, caffeic, and coumaric acids. Moreover, the C. heteromalla WT extract showed a protective effect against reactive oxygen species (ROS) generation induced by tert-butyl hydroperoxide (TBH) on the murine NIH-3T3 fibroblast cell line