Empowering precision medicine through high performance computing clusters

The role of High Performance Computing (HPC) in Medicine is greatly increase in these last years, moving from basic research to the clinics. With the advent of Next Generation Sequencing (NGS) technologies, diverse areas of human health have been investigated through different omics techniques. The extensive use of these NGS platforms to high throughput profile human health issues in a cost-efficient manner, is generating huge amount of sequencing data pushing " (https://www.facebook.com/pages/Oatext/1439466783004774) # $ % (https://www.youtube.com/user/users/oatext) ○ ○ ○ Article Article Info Author Info Figures & Data bioinformatic research in the big-data field. Speed, accuracy and reproducibility of massively sequencing analysis have allowed to transfer molecular biology knowledge into precision medicine. Furthermore, Molecular Dynamics (MD) earned a great importance in aiding genome research. Sequencing studies of cancer have allowed to detect and characterize mutated genes that drive tumorigenesis. As a complementary approach, from a biophysical perspective, MD simulations, executed on HPC architectures, have permitted to investigate the role played by pathological mutations on the molecular mechanism of activation

Community sewage sensors towards evaluation of drug use trends: detection of cocaine in wastewater with DNA-directed immobilization aptamer sensors

Illicit drug use has a global concern and effective monitoring and interventions are highly required to combat drug abuse. Wastewater-based epidemiology (WBE) is an innovative and cost-effective approach to evaluate community-wide drug use trends, compared to traditional population surveys. Here we report for the first time, a novel quantitative community sewage sensor (namely DNA-directed immobilization of aptamer sensors, DDIAS) for rapid and cost-effective estimation of cocaine use trends via WBE. Thiolated single-stranded DNA (ssDNA) probe was hybridized with aptamer ssDNA in solution, followed by co-immobilization with 6-mercapto-hexane onto the gold electrodes to control the surface density to effectively bind with cocaine. DDIAS was optimized to detect cocaine at as low as 10 nM with a dynamic range from 10 nM to 5 μM, which were further employed for the quantification of cocaine in wastewater samples collected from a wastewater treatment plant in seven consecutive days. The concentration pattern of the sampling week is comparable with that from mass spectrometry. Our results demonstrate that the developed DDIAS can be used as community sewage sensors for rapid and cost-effective evaluation of drug use trends, and potentially implemented as a powerful tool for on-site and real-time monitoring of wastewater by un-skilled personnel

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

Delineation of Management Zones in Precision Agriculture by Integration of Proximal Sensing with Multivariate Geostatistics. Examples of Sensor Data Fusion

Fundamental to the philosophy of Precision Agriculture (PA) is the concept of matching inputs to needs. Recent research in PA has focused on use of Management Zones (MZ) that are field areas characterised by homogeneous attributes in landscape and soil conditions. Proximal sensing (such as Electromagnetic Induction (EMI), Ground Penetrating Radar (GPR) and X-ray fluorescence) can complement direct sampling and a multisensory platform can enable us to map soil features unambiguously. Several methods of multi-sensor data analysis have been developed to determine the location of subfield areas. Modern geostatistical techniques, treating variables as continua in a joint attribute and geographic space, offer the potential to analyse such data effectively. The objective of the paper is to show the potential of multivariate geostatistics to create MZ in the perspective of PA by integrating field data from different types of sensors, describing two study cases. In particular, in the first case study, cokriging and factorial cokriging were employed to produce thematic maps of soil trace elements and to delineate homogenous zones, respectively. In the second case, a multivariate geostatistical data-fusion technique (multi collocated cokriging) was applied to different geophysical sensor data (GPR and EMI), for stationary estimation of soil water content and for delineating within-field zone with different wetting degree. The results have shown that linking sensors of different type improves the overall assessment of soil and sensor data fusion could be effectively applied to delineate MZs in Precision Agriculture. However, techniques of data integration are urgently required as a result of the proliferation of data from different sources

Delineation of Management Zones in Precision Agriculture by Integration of Proximal Sensing with Multivariate Geostatistics. Examples of Sensor Data Fusion

Fundamental to the philosophy of Precision Agriculture (PA) is the concept of matching inputs to needs. Recent research in PA has focused on use of Management Zones (MZ) that are field areas characterised by homogeneous attributes in landscape and soil conditions. Proximal sensing (such as Electromagnetic Induction (EMI), Ground Penetrating Radar (GPR) and X-ray fluorescence) can complement direct sampling and a multisensory platform can enable us to map soil features unambiguously. Several methods of multi-sensor data analysis have been developed to determine the location of subfield areas. Modern geostatistical techniques, treating variables as continua in a joint attribute and geographic space, offer the potential to analyse such data effectively. The objective of the paper is to show the potential of multivariate geostatistics to create MZ in the perspective of PA by integrating field data from different types of sensors, describing two study cases. In particular, in the first case study, cokriging and factorial cokriging were employed to produce thematic maps of soil trace elements and to delineate homogenous zones, respectively. In the second case, a multivariate geostatistical data-fusion technique (multi collocated cokriging) was applied to different geophysical sensor data (GPR and EMI), for stationary estimation of soil water content and for delineating within-field zone with different wetting degree. The results have shown that linking sensors of different type improves the overall assessment of soil and sensor data fusion could be effectively applied to delineate MZs in Precision Agriculture. However, techniques of data integration are urgently required as a result of the proliferation of data from different sources

Mario Marti e la storia linguistica del Salento (bilanci e prospettive)

EnDuring his long and prestigious career, Mario Marti has always cultivated the current of Salento literature with care and dedication, with the intention of renewing the local culture in a supra-regional perspective. These pages retrace Marti's bibliography to highlight the contribution he gave to the linguistic history of Salento. At the same time, some possible research paths for the future are identified. The titles reviewed are grouped into three areas: studies on texts in the Salento vernacular, articles (and books) dedicated to reflected dialectal literature, writings on Italian literature by Salento authors. In the end, the story of the "Biblioteca di Scrittori Salentini" is reconstructed, a work strongly desired by Mario Marti and not yet completed.ItNel corso della sua lunga e prestigiosa carriera, Mario Marti ha sempre coltivato con cura e dedizione il filone della letteratura salentina, con l'intento di rifondare la cultura locale in un'ottica sovraregionale. Queste pagine ripercorrono la bibliografia di Marti allo scopo di evidenziare il contributo da lui dato alla storia linguistica del Salento. Allo stesso tempo, vengono individuati alcuni possibili percorsi di ricerca per il futuro. I titoli passati in rassegna sono raggruppati in tre aree: studi sui testi in volgare salentino, articoli (e libri) dedicati alla letteratura dialettale riflessa, scritti sulla letteratura italiana di autori salentini. Nel finale viene ricostruita la storia della "Biblioteca di Scrittori Salentini", opera fortemente voluta da Mario Marti e non ancora compiuta

Un poeta di retroguardia negli anni dell'avanguardia futurista

EnThe purpose of this study is to demonstrate, through the restoration of an unknown collection of verses by the poet Vincenzo Modoni (1883-1945), the rearguard position (or refusal of the avant-garde) of certain regional literature in the years between the two wars. The article intends first of all to document the rejection of Futurism by the author in question and the persistence in his texts of nineteenth-century positions (in the manner of Leopardi and Pascoli). Each text, verified philologically, is subjected to historical and stylistic analysis (with appropriate references to the sources).ItObiettivo del presente studio è dimostrare, attraverso la riproposizione di una sconosciuta raccolta di versi del poeta carpignanese Vincenzo Modoni (1883-1945), la posizione di retroguardia (o di rifiuto dell'avanguardia) di certa letteratura salentina negli anni dell'avvento del fascismo. L'articolo intende documentare anzitutto il rifiuto del futurismo da parte dell'autore in questione e il permanere nelle sue liriche di posizioni ottocentesche (alla maniera di Leopardi e Pascoli). Ogni testo, filologicamente accertato, è sottoposto ad analisi storica e stilistica (con gli opportuni rinvii alle fonti)

The effect of mycorrhizal symbiosis on the development of micropropagated artichokes

In this work, microrosettes of Cynara cardunculus L. var. scolymus Fiori of the "catanese" type were subcultured in a medium supplemented with 6-benzylaminopurine (BAP) (0.05 mg l-1). For root induction, indoleacetic acid (IAA), α-naphthalene acetic acid (NAA) and indole-3-butyrric acid (IBA) were used at three concentrations: 2, 5 and 10 mg l-1. The highest percentage of rooted shoots was aided by the presence of 10 mg l-1IAA. Once transplanted in pots, the plantlets were inoculated with 10 g Glomus viscosum strain A6 (AM fungus). Acclimatisation was clearly facilitated by the addition of the AM fungus. Indeed, the mycorrhizal plantlets registered a survival of between 90 and 95% for the rooting shoots and 60% for the non-rooting shoots. The botanical characterization of the material produced was carried out in field and was based on several morphological and productive parameters. Data collected confirm the characteristics of the original cultivar, the efficiency of the in vitro propagation material and the possibility of using this technique in early types of artichoke. © 2005 Elsevier B.V. All rights reserved