Metagenomic analysis through the extended Burrows-Wheeler transform

Background: The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification of metagenomic reads, i.e., identifying the microorganisms that are present in a sample collected directly from the environment. The analysis of environmental samples (metagenomes) are particularly important to figure out the microbial composition of different ecosystems and it is used in a wide variety of fields: for instance, metagenomic studies in agriculture can help understanding the interactions between plants and microbes, or in ecology, they can provide valuable insights into the functions of environmental communities. Results: In this paper, we describe a new lightweight alignment-free and assembly-free framework for metagenomic classification that compares each unknown sequence in the sample to a collection of known genomes. We take advantage of the combinatorial properties of an extension of the Burrows-Wheeler transform, and we sequentially scan the required data structures, so that we can analyze unknown sequences of large collections using little internal memory. The tool LiME (Lightweight Metagenomics via eBWT) is available at https://github.com/veronicaguerrini/LiME. Conclusions: In order to assess the reliability of our approach, we run several experiments on NGS data from two simulated metagenomes among those provided in benchmarking analysis and on a real metagenome from the Human Microbiome Project. The experiment results on the simulated data show that LiME is competitive with the widely used taxonomic classifiers. It achieves high levels of precision and specificity - e.g. 99.9% of the positive control reads are correctly assigned and the percentage of classified reads of the negative control is less than 0.01% - while keeping a high sensitivity. On the real metagenome, we show that LiME is able to deliver classification results comparable to that of MagicBlast. Overall, the experiments confirm the effectiveness of our method and its high accuracy even in negative control samples

Gsufsort: Constructing suffix arrays, LCP arrays and BWTs for string collections

Background: The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows-Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections. Result: In this paper we introduce gsufsort, an open source software for constructing the suffix array and related data indexing structures for a string collection with N symbols in O(N) time. Our tool is written in ANSI/C and is based on the algorithm gSACA-K (Louza et al. in Theor Comput Sci 678:22-39, 2017), the fastest algorithm to construct suffix arrays for string collections. The tool supports large fasta, fastq and text files with multiple strings as input. Experiments have shown very good performance on different types of strings. Conclusions: gsufsort is a fast, portable, and lightweight tool for constructing the suffix array and additional data structures for string collections

Mucopolysaccharidosis I, II, and VI: Brief review and guidelines for treatment

Mucopolysaccharidoses (MPS) are rare genetic diseases caused by the deficiency of one of the lysosomal enzymes involved in the glycosaminoglycan (GAG) breakdown pathway. This metabolic block leads to the accumulation of GAG in various organs and tissues of the affected patients, resulting in a multisystemic clinical picture, sometimes including cognitive impairment. Until the beginning of the XXI century, treatment was mainly supportive. Bone marrow transplantation improved the natural course of the disease in some types of MPS, but the morbidity and mortality restricted its use to selected cases. The identification of the genes involved, the new molecular biology tools and the availability of animal models made it possible to develop specific enzyme replacement therapies (ERT) for these diseases. At present, a great number of Brazilian medical centers from all regions of the country have experience with ERT for MPS I, II, and VI, acquired not only through patient treatment but also in clinical trials. Taking the three types of MPS together, over 200 patients have been treated with ERT in our country. This document summarizes the experience of the professionals involved, along with the data available in the international literature, bringing together and harmonizing the information available on the management of these severe and progressive diseases, thus disclosing new prospects for Brazilian patients affected by these conditions

La gestione del rischio di frana nei centri storici minori della Sicilia

La nota fornisce un contributo alla pianificazione della gestione del rischio di frana, con un esempio di approccio metodologico rivolto ai centri urbani “minori” della Sicilia caratterizzati da patrimoni architettonici, urbanistici e culturali di valenza storica meritevoli di salvaguardia. Si espone una metodologia di primo livello, condotta con i dati territoriali disponibili a scala regionale, per la valutazione della condizione di suscettibilità e di esposizione a rischio frana dei centri di rilevante valore storico-culturale. I risultati permettono di giungere ad una scala di valori di comparazione tra le diverse situazioni di suscettibilità da frana e ad una prima identificazione delle misure di gestione del rischio specifiche per i centri urbani esaminat

Safeguarding historic towns on hilltops threatened by land sliding: The case of San Fratello in Sicily

The paper presents the case history of San Fratello, a small town in the Nebrodi Mountains in Sicily rich in history and having very peculiar environmental and cultural characteristics. Both slopes of the narrow ridge where San Fratello lies were affected in 1754, 1922, 1986 and 2010 by very large landslides. The landslide of February 2010 is largely the reactivation of that of 1754. It destroyed many infrastructures and seriously damaged more than 200 buildings and caused the evacuation of 25% of the population. Emergency actions to block regression of uphill movements and secure the buildings and their inhabitants as quickly as possible, were carried out. The sliding slope down to the town was left to its natural evolution. The paper presents the results of the geomorphological and geotechnical analyses recently carried out to understand the whole landslide reactivation mechanisms. It is felt necessary to define an advanced geotechnical model of the landslide for quantitative evaluation of hazard and rational landslide risk management in the area

Evaluation of the In-Situ Behaviour of a Lime-Treated Clay in a Real-Scale Experimental Embankment

The international commitment to achieve carbon neutrality in the next few decades has oriented infrastructure construction towards the preservation of natural and non-renewable resources. In this context, lime treatment of clayey soils involved in earthworks can be considered among the main sustainable options in the field of infrastructure construction. Lime stabilization technique has been extensively tested and validated through laboratory tests, however, the literature is lacking in full-scale tests, where the volumes of soils treated are large and many variables are involved in the execution process. This paper discusses the mechanical response of clayey soil after lime treatment in a trial embankment specifically designed and built for the full-scale evaluation of the stabilisation technique to be used in road construction works for widening an existing roadway to four lanes in Sicily. To this aim, in-situ tests, including plate load tests, in-place density via cone-sand tests, dynamic penetrometer tests and pressure meter tests, were conducted on the different layers of the embankment. The experimental results are useful not only for evaluating the lime stabilisation technique used, but also for understanding how and to what extent the execution processes for embankment construction with large volumes of treated clayey soils can affect the expected mechanical behaviour

ESPLORAZIONE ULTRASONOGRAFICA dello SCROTO. Ruolo Diagnostico ed Implicazioni Terapeutiche in Et\ue0 Pediatrica

Ultrasonography of the scrotal contents was used to identify 41 patients with testicular disease

Modulo resiliente di un’argilla a scaglie trattata con calce come parametro meccanico per l’impiego in strati di sottofondazione stradale

La nota presenta i risultati di un programma sperimentale mirato alla valutazione della possibilità di utilizzare le argille a scaglie trattate con calce come materiale di sottofondo per opere di Ingegneria Civile. Tali risultati evidenziano che le caratteristiche di tale materiale migliorano rapidamente nel tempo e che esso diventa, dopo 28 giorni dal trattamento, molto stabile nei riguardi delle sollecitazioni dinamiche indotte dal traffico veicolare, simulate in laboratorio attraverso l’esecuzione di prove di compressione triassiale cicliche mirate alla misura del modulo resiliente

L'EMATOMA SURRENALICO DEL NEONATO

gLI aUTORI POMGONO IN RISALTO L'IMPORTANZA DELLA ULTRASONOGRAFIA NELLA DIAGNOSI E NEL MONITORAGGIO DELL'EMATOMA SURRENALICO DEL NEONAT

UNA RARA CAUSA DI ADDOME ACUTO NELL'INFANZIA. L'Epiploite acuta segmentaria

L'Epiploite acuta segmentaria è fra le cause più rare di addome acuto nell'infanzia. Gli Autori ne riportano tre casi