BlaSTorage: a fast package to parse, manage and store BLAST results

Background: Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them. Findings: We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components. Conclusions: BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.Pubblicat

Progettare con l'energia. Il Mediterraneo fra tradizione e innovazione

Starting from the premise that the contemporary transformations in the Mediterranean landscape have produced non places and architectures that are not recognisable by the collectivity, the research considers the environmental issue as the key to critically review the architectural solutions accrued during the man’s history in which the technique, becoming a prerequisite for progress, has taken over the nature. The sustainability, as it has been investigated in this thesis, is not only a value in time and space, but it is the way for the reform of the project of Mediterranean architecture that is ecologically sound and culturally recognisable. The key used in order to investigate the sense of Mediterranean architecture and to understand its evolution and the possible future developments in respect of sustainability is the tradition. The concept of tradition is understood as selection of the repertoire of knowledge inherited from the past through which the material culture is actualised in compliance with the invariants that constitute its identity in respect with the continuity with the present. The goal is the definition of the principles that allow to an architecture to act sustainably to the habitat, that changes the environment respecting its balance and its resources and the needs of man. In this sense in this thesis is marked the importance of the minor architectures, that result from a spontaneous process of adaptation, repetition and assimilation of models in which are tested the principles of natural ventilation, the selection of sunlight, the use of water in order to optimise the environmental comfort. The intent is to build a reflection about the architecture of today, linking it with terms such as "sustainability", "tradition" and "climate" and inserting these arguments within a geographical and cultural context, at the same time relevant but also complex, that is the Mediterranean area. It is described not only as an expression of a condition of geographical location, but also through the translation of this condition in an architectural language, which consciously prefers some principles in respect to others. Idea of architecture, with precise formal features and space, recognisable only if fully associated to its own context and cultural climate. Through the description of several design experiences located in the Mediterranean basin the thesis highlights some cases in which the project, the climate and the tradition closely coexist. The projects presented describes the compositional and formal quality, simplicity and rigour, the research for a balance between tradition and innovation. This research, in fact, while dealing with the bioclimatic architecture, explores one of the unresolved issues of the sustainable architecture, which is the difficult conciliation of the eco-compatibility requirements with the needs of the architectural composition and with the construction of the form. On the one hand the scientific horizon, on the other the figurative one, are trying to find a balance through the definition of their components: climate, architecture and man

α_S1-casein genetic variants in Sarda goat breed

Sardinia plays an important role in Italian goat breeding; this is due not only to the high extent of its patrimony and production, but also to the fact that the main breed, the Sarda goat, represents an interesting biodiversity source. As regards the morphologic variability, marked differences between subjects reared in the coast and mountain areas were found (Macciotta et al., 2002). These differences are due to the genetic selection on the autochthonous patrimony, set up by breeders and based on coat colour, horn presence and/or on functional criteria (udder shape). The need to improve milk yields also induced various breeders, mainly in those areas with better pasture conditions, to crossbreed the Sarda goats with more productive breeds. The present situation (Pazzola et al., 2002) shows how in the East coastal region (Sarrabus, Ogliastra and Baronia) and in the central mountain areas of Sardinia (Barbagia), subjects with more rural traits are reared (smaller size, small ears, presence of horns, etc.); while in the South and West areas (Sulcis and Guspinese) the influence of the Maltese breed is more evident. Both the productive traits variability (Brandano et al., 1978), and the morphologic aspect, is of great interest. Genetic variability can influence the survival of a sector hindered by the opening of the markets and by the strong competitiveness of zootechnical areas technologically more advanced. According to this point of view, considering that casein fractions are closely related to milk technological characteristics (Grosclaude et al., 1994), and to its possible productive differentiation (Remeuf, 1993), a study on αS1-casein allelic frequency was carried out, related also to the breeding region. The aim of the study is to acquire useful information in order to suggest an appropriate utilization of milk, to detect possible new alleles and to test the correlation between casein phenotype and morphology of the animals

Multiphysics Analysis of a Thermo Acoustic MHD Inductive Generator

This paper fits in the multi-physics analysis of an innovative conceptual design of Magneto-Hydrodynamic (MHD) inductive generator, coupled with a Thermo-Acoustic (TA) resonator. The thermo-acoustic effect occurs when an intense gradient of temperature is present along the axial direction of a duct containing a gas. Such effect allows the heat to be statically converted into mechanical energy of vibration. If the gas is ionized and the charges of opposite sign are separated into two clouds, an alternate electric current is associated to the thermo-acoustic vibration. That current, in its turn, can induce an electromotive force into a magnetically coupled coil. In this way, a thermo-electric conversion is performed, without solid moving parts or matter transport. A FEM analysis has been performed to assess the suitability of the complete energy transformation chain. In particular, the possibility that the charge carriers are involved in the vibration motion is investigated. An acoustic analysis has been done, in a glass tube containing a ionized gas, in order to study the velocity profiles within the duct in presence of viscous and thermal effects. Then, a multiphysics simulation has been performed by using the same geometry, by coupling the acoustic module with the electrostatic module, and the particle tracing module, in order to study the behavior of the unbalanced charge carriers when they are subject to a vibration and to an electric force, for a given set of design parameters

A design pattern for multimodal and multidevice user interfaces

In this paper, we introduce the MVIC pattern for creating multidevice and multimodal interfaces. We discuss the advantages provided by introducing a new component to the MVC pattern for those interfaces which must adapt to different devices and modalities. The proposed solution is based on an input model defining equivalent and complementary sequence of inputs for the same interaction. In addition, we discuss Djestit, a javascript library which allows creating multidevice and multimodal input models for web applications, applying the aforementioned pattern. The library supports the integration of multiple devices (Kinect 2, Leap Motion, touchscreens) and different modalities (gestural, vocal and touch). Copyright is held by the owner/author(s)

Integrated approach for post-fire reinforced concrete structures assessment

In order to assess decay in the mechanical characteristics of re-exposed Reinforced Concrete (RC), it is crucial to recon- struct the temperature time history and the evolution of strain and stress elds. In this paper, the state of the art of assessment methods is presented and applied to a real structure damaged by re. It is a prestressed RC industrial warehouse located in the outskirts of the city of Cagliari (Italy). The collected data of several assessment methods are presented in order to produce the owchart of an integrated approach for post- re investi- gation. Among the various techniques, the authors highlight a thorough laser scanner geometric survey and destructive and non-destructive testing. In addition, the temperature distribu- tion and its time history has been reconstructed by means of optical and Scanning Electron Microscopy, X-ray diffractom- etry, Thermogravimetric Differential Thermo-Analysis and calibrated Colorimetry. Actually, refurbishment is needed, but the structure withstood the re very well. Central columns displayed the most impor- tant damage, and several beams presented important de ec- tions having lost the prestressing actions of the tendons

Influence of body weight on reproductive activity in Sarda female lambs

One way to improve reproductive performance of ewes is through extending its lifetime productivity. Breeding ewe lambs is one method of improving the reproductive performance in the sheep. In order to produce an offspring when the ewe lamb is approximately 1 yr of age, the autumn-born ewe must obtain puberty before the autumn breeding season begins. Onset of puberty is determined by integration of both internal and external factors, which then enable the neuroendocrine or hormonal event occur (Shirley et al., 2001). Age, photoperiod and body weight are the principal factors influencing puberty. The age at onset of the reproductive activity in the sheep is different among the various breeds. In the Sarda lambs the age of the onset of puberty is about 7-8 months. However the animals that have this age don’t reach the puberty if photoperiod and body weight are not suitable. Both the female lambs born in October-November and in February reach puberty in the same subsequent autumn breeding season. This reproductive behaviour evidences that photoperiod plays an important role in the onset of puberty (Papachristoforou et al., 2000).The female lambs born in later spring uneasily reach puberty within the subsequent breeding season, although photoperiod is favourable. This retard in the onset of reproductive activity is due to the attainment of the body maturity only during subsequent long day period but they reach reproductive activity only during the autumn of the subsequent year (Foster et al., 1985). In fact, some authors suggested that besides photoperiod and age, attainment of the 60% of adult weight is essential for onset of puberty (Abecia et al., 2001). Indeed the undernourished animals delay puberty, in comparison to well nourished subjects (I’Anson et al., 1997). This behaviour is linked to the different LH pulse frequency: restricted diet lambs show one pulse per 4 hours, instead fed ad libitum subjects manifest four or five pulse per 4 hours (Ebling et al., 1990). The purpose of this investigation is to determine the onset of puberty and to research its linkage with body weight in Sarda female lambs during breeding season under natural condition

Genotype at the MTNR1A locus and response to melatonin treatment in Sarda lambs

With the aim to evaluate the effect of melatonin treatment and melatonin receptor 1A (MTNR1A) genotype on advance of puberty, 423 Sarda lambs were chosen. On June 26th, they were divided into three groups, each of 141 animals (groups 0, 1, and 2), on the basis of live weight. On June 30th, animals in group 1 received a single implant (18 mg melatonin), while group 2 received two implants. Group 0 was untreated. Thirty-five days after treatment (August 4th), rams were introduced and after 40 days they were removed. From January 1st to February 10th lambing dates were recorded. Genomic DNA was extracted and subjected to PCR for the amplification of exon II and then digested with enzymes MnlI and RsaI and placed into +/+, +/−, or −/− group for MnlI and C/C, C/T, or T/T group for RsaI. Samples were cloned and sequenced. Data obtained were subjected to χ2 test in order to evaluate the difference in fertility among groups and the link between genotype and reproductive activity. Genotype +/+ and C/C showed the highest incidence. Treated groups showed a higher number of lambing at 10th February compared to control group (P<0.04). Melatonin treatment results more efficient in +/+ genotype

Inter-firm collaborations, networks and facilitators: how industrial symbiosis disseminated in Italy.

LAUREA MAGISTRALELa simbiosi industriale (IS), una delle strategie per applicare l’economia circolare, è emersa dal campo dell'ecologia industriale negli anni '70 ed è diventata sempre più importante dagli anni 2000. Questa tesi si concentra sullo studio del contesto italiano indagando come questa strategia viene sviluppata e implementata nei vari settori, quali sono le relazioni e gli scambi tra gli attori che vi partecipano e il ruolo delle tecnologie digitali in questa strategia. Inoltre è stata condotta un'analisi del ruolo dell'ENEA come facilitatore. La ricerca si avvale sia di metodologie quantitative che qualitative. In primo luogo, un database di casi italiani di IS è stato creato utilizzando la letteratura accademica e grigia come fonti. Dall'analisi quantitativa di questo database sono emersi 50 casi di simbiosi in diverse fasi di sviluppo, settori produttivi e regioni geografiche. Come risultato della revisione della letteratura e dell'analisi del database è stata definita una linea guida per le intervista. Sono state condotte interviste strutturate con 10 aziende per approfondire 5 casi studio e il ruolo dell'ENEA nella diffusione della IS in Italia. Si presentano cinque casi concentrandosi sul loro sviluppo, le relazioni tra le parti interessate e le tecnologie impiegate. Due casi si concentrano sugli scambi simbiotici tra i produttori di acciaio e il recupero di calore, uno descrive la simbiosi nella valle di Fiemme che recupera i sottoprodotti forestali e delle segherie per il recupero energetico, e un altro presenta i casi della conceria toscana di San Miniato e la relativa produzione di gelatina e collagene, concludendo con un piccolo caso in cui gli scarti vegetali della GDO vengono recuperati per l'allevamento di chiocciole. L'analisi della banca dati e delle interviste hanno portato alla realizzazione di una panoramica della situazione italiana dello sviluppo delle simbiosi industriali. Mostrando che le relazioni tra stakeholders più comuni nei casi sono accordi contrattuali e meccanismi di partecipazione degli azionisti, e che i sistemi di comunicazione e di informazione sono le tecnologie più impiegate nelle IS. A proposito di ENEA è emerso che l'ente pubblico sostiene le imprese nella ricerca e pianificazione della simbiosi ma non nell'esecuzione degli scambi, le sue attività sono concentrate nella divulgazione del concetto di simbiosi e nella raccolta di storie di successo.Industrial symbiosis (IS), one of the strategies to achieve a circular economy, emerged from the field of industrial ecology in the ‘70s and has become increasingly important since the 2000s. In this work, the spotlight is on the Italian field researching how this strategy is applied in various sectors, which are the relationships and exchanges among the actors that partake in an IS and the role of digital technologies in this strategy. In addition an analysis of the role of ENEA as IS facilitator was conducted. The research employs both quantitative and qualitative methodologies. First, a detailed literature review was performed to understand the state of the art and the gaps in the literature. Then a database of Italian cases of IS was created using academic and grey literature as sources; from the quantitative analysis of this database emerged 50 cases of in different developing stages, productive sectors and geographic regions. As result of the literature review and the database analysis, an interview guideline and a list of cases to deepen with interviews were defined. Structured interviews were conducted with 10 companies to further investigate 5 case studies and the role of ENEA in disseminating IS in Italy. Five case studies are presented showing how they developed, the relationships among the stakeholders and the employed digital technologies. Two cases focus on the symbiotic exchanges among steelmakers and heat recovery, one describes the symbiosis in the Fiemme Valley that recovers forestry and sawmill by-products for energy recovery, another presents the cases of the tannery district of San Miniato and the related gelatine and collagen production, concluding with a small case where organic by-products from grocery stores are recovered for snail farm. The analysis of the database and interviews provided insight into the Italian working field of IS, uncovering that contractual agreements and shareholder mechanisms are the most common inter-firm relationships and that communication and information systems are the most employed technologies in IS. About ENEA it emerged that the public agency supports companies in the research and planning of symbiosis but not in the execution of the exchanges, its activities are to disseminate the strategy