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

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

I tumori del rene

non presente (capitolo di libro

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

Considerations on the Update of the Risk Assessment Document During the Pandemic State by COVID-19 in Italy

Immediately after the outbreak of the SARS-CoV-2 epidemic (which had risen to the level of a pandemic according to the World Health Organization), the question arose whether or not to update the risk assessment, which, as required by Legislative Decree 81/2008, with the consequent updating of the prevention measures. In light of these forecasts, we asked ourselves whether the risk of coronavirus infection should be taken into account by the employer by updating the risk assessment or not. An in-depth analysis of current legislation has led to the conclusion that the biological risk from SARS-CoV-2 is to be considered specific only in health-related activities, in other activities it can be considered exclusively generic or generic aggravated. The Risk Assessment Document can therefore only be integrated

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 environment

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

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