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

Combined aptamer and transcriptome sequencing of single cells.

The transcriptome and proteome encode distinct information that is important for characterizing heterogeneous biological systems. We demonstrate a method to simultaneously characterize the transcriptomes and proteomes of single cells at high throughput using aptamer probes and droplet-based single cell sequencing. With our method, we differentiate distinct cell types based on aptamer surface binding and gene expression patterns. Aptamers provide advantages over antibodies for single cell protein characterization, including rapid, in vitro, and high-purity generation via SELEX, and the ability to amplify and detect them with PCR and sequencing

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

Efficient photosynthesis of carbon monoxide from CO2 using perovskite photovoltaics

Artificial photosynthesis, mimicking nature in its efforts to store solar energy, has received considerable attention from the research community. Most of these attempts target the production of H2 as a fuel and our group recently demonstrated solar-to-hydrogen conversion at 12.3% efficiency. Here, in an effort to take this approach closer to real photosynthesis, which is based on the conversion of CO2, we demonstrate the efficient reduction of CO2 to carbon monoxide driven solely by simulated sunlight using water as the electron source. Employing series-connected perovskite photovoltaics and high-performance catalyst electrodes, we reach a solar-to-CO efficiency exceeding 6.5%, which represents a new benchmark in sunlight-driven CO2 conversion. Considering hydrogen as a secondary product, an efficiency exceeding 7% is observed. Furthermore, this study represents one of the first demonstrations of extended, stable operation of perovskite photovoltaics, whose large open-circuit voltage is shown to be particularly suited for this process

How to Test for Diagonalizability: The Discretized PT-Invariant Square-Well Potential

Given a non-hermitean matrix M, the structure of its minimal polynomial encodes whether M is diagonalizable or not. This note will explain how to determine the minimal polynomial of a matrix without going through its characteristic polynomial. The approach is applied to a quantum mechanical particle moving in a square well under the influence of a piece-wise constant PT-symmetric potential. Upon discretizing the configuration space, the system is decribed by a matrix of dimension three. It turns out not to be diagonalizable for a critical strength of the interaction, also indicated by the transition of two real into a pair of complex energy eigenvalues. The systems develops a three-fold degenerate eigenvalue, and two of the three eigenfunctions disappear at this exceptional point, giving a difference between the algebraic and geometric multiplicity of the eigenvalue equal to two.Comment: 5 page

Human Dynamics: The Correspondence Patterns of Darwin and Einstein

While living in different historical era, Charles Darwin (1809-1882) and Albert Einstein (1879-1955) were both prolific correspondents: Darwin sent (received) at least 7,591 (6,530) letters during his lifetime while Einstein sent (received) over 14,500 (16,200). Before email scientists were part of an extensive university of letters, the main venue for exchanging new ideas and results. But were the communication patterns of the pre-email times any different from the current era of instant access? Here we show that while the means have changed, the communication dynamics has not: Darwin's and Einstein's pattern of correspondence and today's electronic exchanges follow the same scaling laws. Their communication belongs, however, to a different universality class from email communication, providing evidence for a new class of phenomena capturing human dynamics.Comment: Supplementary Information available at http://www.nd.edu/~network

VANTAGGI DELL’UTILIZZO DEL SISTEMA DOSIMETRICO OSL IN CASO DI EMERGENZA

VANTAGGI DELL’UTILIZZO DEL SISTEMA DOSIMETRICO OSL IN CASO DI EMERGENZA S. Abate, F. Campi, L. Garlati, O. Tambussi Politecnico di Milano, Dipartimento di Energia, via La Masa 34, 20156 Milano [email protected] Il sistema dosimetrico per corpo intero OSL (Optically Stimulated Luminescence) è un tipo di dosimetria che si sta sempre più diffondendo in vari paesi. In Europa molti centri di ricerca si sono dotati di un proprio sistema dosimetrico, mentre commercialmente Landauer rappresenta il maggior fornitore di tale servizio dosimetrico, ma anche del sistema stesso (dosimetri e apparecchio di lettura). Il vantaggio di questo tipo di dosimetro consiste nella semplicità e velocità di lettura e azzeramento, anche se risulta meno affidabile dei film-badge. Inoltre, rispetto ai dosimetri a TL, risultano essere più stabili nel tempo, non dovendo subire cicli termici che ne alterano la struttura cristallina e di conseguenza le loro performance. Questo permette di utilizzare, leggere e azzerare anche il singolo dosimetro e non l’intero lotto di appartenenza. Questa caratteristica permette di utilizzare il dosimetro a OSL come un dosimetro passivo, ma col vantaggio della lettura indiretta al termine delle operazioni, proprio come per un dosimetro elettronico viene effettuata la lettura diretta su display. In questo lavoro si vogliono paragonare i vantaggi e gli svantaggi dei sistemi dosimetrici tradizionali (film-badge e TLD) con il sistema OSL. Si presentano i risultati sperimentali delle performance (dipendenza energetica, dosimetrica e angolare) del sistema dosimetrico OSL Inlight con sistema di lettura MicroStar. Infine si presentano i risultati degli irraggiamenti condotti in parallelo presso un centro LAT tra il sistema OSL e i dosimetri elettronici DMC 2000 (Mirion Technologies). Le caratteristiche di questo dosimetro permettono di concludere che questo tipo di sistema dosimetrico ha degli aspetti positivi per il suo utilizzo in caso di emergenza radiologica senza i costi di una dosimetria con strumentazione attiva