Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines

Background: Gene fusions derive from chromosomal rearrangements and the resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. So far, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive Next Generation Sequencing dataset for all the existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events. Results: In our work, we have extensively reanalyzed 935 paired-end RNA-seq experiments downloaded from "The Cancer Cell Line Encyclopedia" repository, aiming at addressing novel putative cell-line specific gene fusion events in human malignancies. The bioinformatics analysis has been performed by the execution of four different gene fusion detection algorithms. The results have been further prioritized by running a bayesian classifier which makes an in silico validation. The collection of fusion events supported by all of the predictive softwares results in a robust set of ∼ 1,700 in-silico predicted novel candidates suitable for downstream analyses. Given the huge amount of data and information produced, computational results have been systematized in a database named LiGeA. The database can be browsed through a dynamical and interactive web portal, further integrated with validated data from other well known repositories. Taking advantage of the intuitive query forms, the users can easily access, navigate, filter and select the putative gene fusions for further validations and studies. They can also find suitable experimental models for a given fusion of interest. Conclusions: We believe that the LiGeA resource can represent not only the first compendium of both known and putative novel gene fusion events in the catalog of all of the human malignant cell lines, but it can also become a handy starting point for wet-lab biologists who wish to investigate novel cancer biomarkers and specific drug targets

The Homeless and Public Space: Urban Policy and Exclusion in Bologna

L’article porte sur le rapport des personnes sans domicile à l’espace urbain. Axée sur le contexte italien et notamment sur la ville de Bologna, l’analyse focalise l’attention sur les stratégies de politique urbaine visant à exclure ces sujets des espaces publics, ou à discipliner l’usage qu’ils font de ces mêmes espaces. Les réflexions des auteurs se développent sur trois axes: le premier concerne le rôle de l’espace public dans la vie quotidienne des sans domicile; le deuxième porte sur les changements des espaces publics provoqués par les processus de régénération urbaine; le dernier explore les mécanismes de contrôle de l’espace public qui, sous forme d’interventions urbanistiques ou d’arrêtés municipaux, produisent l’exclusion spatiale des sans domicile.This article addresses the relationship between homeless people and urban public space. The analysis, focusing on the Italian context and, in particular, on the city of Bologna, centres on urban policy strategies which tend to exclude the homeless from public spaces and to regulate their use of such spaces. Our considerations encompass three dimensions: the role of public space in the daily life of the homeless; the changes in public space following urban renewal processes; public space control mechanisms, in the form of urban design and local by-laws, which translate into a spatial exclusion of the homeless

parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants.

BACKGROUND: Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data. RESULTS: To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version. CONCLUSIONS: parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF

Missense mutations of NCPAG gene affect calving ease in Piedmontese cattle: preliminary evidences

A previous genome scan on 323 Piedmontese individuals identified a cluster of 13 SNPs significantly associated with direct calving ease and centred on the three genes LAP3, LCORL and NCAPG in chromosome 6. We investigated missense mutations affecting calving ease in Piedmontese cattle in the identified region using sequences from the whole exome in eight Piedmontese individuals chosen from the extremes of the direct calving ease estimated breeding values distribution for this trait. The present study has not found missense variants in LAP3 and LCORL, while two were identified on NCAPG by three different variant calling methods. Other gene candidates in the same region harbour missense mutations, such as PPM1K, PKD2, SPP1 and MEPE, but both SIFT analysis and chi-square test on frequency of alleles make us hypothesise that NCAPG is the single gene responsible for the trait variation. The two SNPs on NCAPG are in complete linkage disequilibrium in our samples; therefore, further investigations are needed in order to discriminate their role

La discontinuità lavorativa dei laureati in servizio sociale triennale.

La ricerca si focalizza sull’inserimento nel mercato del lavoro dei laureati in Servizio Sociale in Italia. Ne emerge una situazione di insicurezza lavorativa; un quadro che richiede una riflessione approfondita non più solo sugli sbocchi occupazionali dei laureati in Servizio Sociale, ma su tutta la filiera formativa e di accreditamento della figura professionale di assistente sociale.The research focuses on the insertion in the labor market of Italian graduates in Social Work. What emerges is a picture that requires a thorough review of the entire supply chain training an

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html

Non-functioning pituitary adenoma database: a useful resource to improve the clinical management of pituitary tumors

Objective: The long-term outcome of non-functioning pituitary adenoma (NFPA) patients is not clearly established, probably due to the low annual incidence and prolonged natural history of these rare tumors. The aim of this study was to evaluate clinical data at presentation and long-term post-surgery and radiotherapy outcome in a cohort of patients with NFPA. Design and methods: A computerized database was developed using Access 2000 software (Microsoft Corporation, 1999). Retrospective registration of 295 NFPA patients was performed in seven Endocrinological Centers of North West Italy. Data were analyzed by STATA software. Results: The main presenting symptoms were visual defects (67.8%) and headache (41.4%) and the most frequent pituitary deficit was hypogonadism (43.3%), since almost all tumors were macroadenomas (96.5%). Surgery was the first choice treatment (98% of patients) and total debulking was achieved in 35.5%. Radiotherapy was performed as adjuvant therapy after surgery in 41% of patients. At the follow-up, recurrence occurred in 19.2% of patients without post-surgical residual tumor after 7.5 ± 2.6 years, regrowth in 58.4% of patients with post-surgical remnant after 5.3 ± 4.0 years and residue enlargement in 18.4% of patients post-surgically treated with radiotherapy after 8.1 ± 7.3 years. Conclusions: Our database indicates that the goal of a definitive surgical cure has been achieved during the last decade in a low percentage of patients with NFPA. This tumor database may help to reduce the delay between symptom onset and diagnosis, to assess prognostic parameters for the follow-up of patients with different risk of recurrence and to define the efficacy and safety of different treatments and their association with mortality/morbidity

All in the Game. The Wire: un campo di ricerca sociologica

Analyzing with an ethnographic approach The Wire, one of the most important TV series on American ghettos, to understand and question the sociological perspective that emerges from the series, positioning it into the broader scientific debate. This is, in a nutshell, the work presented in the book It's all in the Game, the outcome of a laboratorial research activity carried out in 2020 by students and teachers of the Sociology of Communities and Urban Neighborhoods class, at the University of Bologna. The text is structured into four chapters, resulting from the four topics used to analysis the TV series: forms of social capital, the relationship between structural forces- culture of poverty and individual agency, neighborhood effects mechanism and the relationship between statistics and political action. Four subjects that are the core of many neighborhood- studies related researches and on which the TV series makes a clear stand. We analyzed those topics through a critical perspective, not considering them as a truth about ghettos, but as a very precise way of thinking about life in the American suburbs