Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

Middleware principles and design for the integration of ubiquitos mobile services

Nowadays, in Ubiquitous computing scenarios users more and more require to exploit online contents and services by means of any device at hand, no matter their physical location, and by personalizing and tailoring content and service access to their own requirements. The coordinated provisioning of content tailored to user context and preferences, and the support for mobile multimodal and multichannel interactions are of paramount importance in providing users with a truly effective Ubiquitous support. However, so far the intrinsic heterogeneity and the lack of an integrated approach led to several either too vertical, or practically unusable proposals, thus resulting in poor and non-versatile support platforms for Ubiquitous computing. This work investigates and promotes design principles to help cope with these ever-changing and inherently dynamic scenarios. By following the outlined principles, we have designed and implemented a middleware support platform to support the provisioning of Ubiquitous mobile services and contents. To prove the viability of our approach, we have realized and stressed on top of our support platform a number of different, extremely complex and heterogeneous content and service provisioning scenarios. The encouraging results obtained are pushing our research work further, in order to provide a dynamic platform that is able to not only dynamically support novel Ubiquitous applicative scenarios by tailoring extremely diverse services and contents to heterogeneous user needs, but is also able to reconfigure and adapt itself in order to provide a truly optimized and tailored support for Ubiquitous service provisioning.

Cooperative and reconfigurable telecommunication systems based on FPGA

This work has been realized by the author in his PhD course in Electronics, Computer Science and Telecommunication at the University of Bologna, Faculty of Engineering, Italy. The subject of this thesis regards important channel estimation aspects in wideband wireless communication systems, such as echo cancellation in digital video broadcasting systems and pilot aided channel estimation through an innovative pilot design in Multi-Cell Multi-User MIMO-OFDM network. All the documentation here reported is a summary of years of work, under the supervision of Prof. Oreste Andrisano, coordinator of Wireless Communication Laboratory - WiLab, in Bologna. All the instrumentation that has been used for the characterization of the telecommunication systems belongs to CNR (National Research Council), CNIT (Italian Inter-University Center), and DEIS (Dept. of Electronics, Computer Science, and Systems). From November 2009 to May 2010, the author spent his time abroad, working in collaboration with DOCOMO - Communications Laboratories Europe GmbH (DOCOMO Euro-Labs) in Munich, Germany, in the Wireless Technologies Research Group. Some important scientific papers, submitted and/or published on IEEE journals and conferences have been produced by the author.

Life Cycle Assessment of Peach Nectar: a comparative analysis between conventional and bioenergy-from-waste integrated food chains

Modern food systems are characterized by a high energy intensity as well as by the production of large amounts of waste, residuals and food losses. This inefficiency presents major consequences, in terms of GHG emissions, waste disposal, and natural resource depletion. The research hypothesis is that residual biomass material could contribute to the energetic needs of food systems, if recovered as an integrated renewable energy source (RES), leading to a sensitive reduction of the impacts of food systems, primarily in terms of fossil fuel consumption and GHG emissions. In order to assess these effects, a comparative life cycle assessment (LCA) has been conducted to compare two different food systems: a fossil fuel-based system and an integrated system with the use of residual as RES for self-consumption. The food product under analysis has been the peach nectar, from cultivation to end-of-life. The aim of this LCA is twofold. On one hand, it allows an evaluation of the energy inefficiencies related to agro-food waste. On the other hand, it illustrates how the integration of bioenergy into food systems could effectively contribute to reduce this inefficiency. Data about inputs and waste generated has been collected mainly through literature review and databases. Energy balance, GHG emissions (Global Warming Potential) and waste generation have been analyzed in order to identify the relative requirements and contribution of the different segments. An evaluation of the energy “loss” through the different categories of waste allowed to provide details about the consequences associated with its management and/or disposal. Results should provide an insight of the impacts associated with inefficiencies within food systems. The comparison provides a measure of the potential reuse of wasted biomass and the amount of energy recoverable, that could represent a first step for the formulation of specific policies on the integration of bioenergies for self-consumption.

Individuals in the Workplatform. Exploring Implications for Work Identity and Algorithmic Reputation Management

In the new world of work, workers not only change jobs more frequently, but also perform independent work on online labor markets. As they accomplish smaller and shorter jobs at the boundaries of organizations, employment relationships become unstable and career trajectories less linear. These new working conditions question the validity of existing management theories and call for more studies explaining gig workers’ behavior. Aim of this dissertation is contributing to this emerging body of knowledge by (I) exploring how gig workers shape their work identity on online platforms, and (II) investigating how algorithmic reputation changes dynamics of quality signaling and affects gig workers’ behavior. Chapter 1 introduces the debate on gig work, detailing why existing theories and definitions cannot be applied to this emergent workforce. Chapter 2 provides a systematic review of studies on individual work in online labor markets and identifies areas for future research. Chapter 3 describes the exploratory, qualitative methodology applied to collect and analyze data. Chapter 4 presents the first empirical paper investigating how the process of work identity construction unfolds for gig workers. It explores how digital platforms, intended both as providers of technological features and online environments, affect this process. Findings reveal the online environment constrains the action of workers who are pushed to take advantage of platform’s technological features to succeed. This interplay leads workers to develop an entrepreneurial orientation. Drawing on signaling theory, Chapter 5 understands how gig workers interpret algorithmic calculated reputation and with what consequences for their experience. Results show that, after complying to platform’s rules in the first period, freelancers respond to algorithmic management through different strategies – i.e. manipulation, nurturing relationships, and living with it. Although reputation scores standardize information on freelancers’ quality, and, apparently, freelancers’ work, this study shows instead responses to algorithmic control can be diverse.

Deep learning and embeddings for problems of computational biology

The development of Next Generation Sequencing promotes Biology in the Big Data era. The ever-increasing gap between proteins with known sequences and those with a complete functional annotation requires computational methods for automatic structure and functional annotation. My research has been focusing on proteins and led so far to the development of three novel tools, DeepREx, E-SNPs&GO and ISPRED-SEQ, based on Machine and Deep Learning approaches. DeepREx computes the solvent exposure of residues in a protein chain. This problem is relevant for the definition of structural constraints regarding the possible folding of the protein. DeepREx exploits Long Short-Term Memory layers to capture residue-level interactions between positions distant in the sequence, achieving state-of-the-art performances. With DeepRex, I conducted a large-scale analysis investigating the relationship between solvent exposure of a residue and its probability to be pathogenic upon mutation. E-SNPs&GO predicts the pathogenicity of a Single Residue Variation. Variations occurring on a protein sequence can have different effects, possibly leading to the onset of diseases. E-SNPs&GO exploits protein embeddings generated by two novel Protein Language Models (PLMs), as well as a new way of representing functional information coming from the Gene Ontology. The method achieves state-of-the-art performances and is extremely time-efficient when compared to traditional approaches. ISPRED-SEQ predicts the presence of Protein-Protein Interaction sites in a protein sequence. Knowing how a protein interacts with other molecules is crucial for accurate functional characterization. ISPRED-SEQ exploits a convolutional layer to parse local context after embedding the protein sequence with two novel PLMs, greatly surpassing the current state-of-the-art. All methods are published in international journals and are available as user-friendly web servers. They have been developed keeping in mind standard guidelines for FAIRness (FAIR: Findable, Accessible, Interoperable, Reusable) and are integrated into the public collection of tools provided by ELIXIR, the European infrastructure for Bioinformatics.

Italian higher education students’ perspectives on internationalization at home and their identity as English as lingua franca users

This study aims to explore the Italian students’ perspectives on using English in English-medium instruction (EMI) programs in light of the practices of internationalization at home (IaH) at the University of Bologna (UNIBO) in Italy and further investigates whether these attitudes affect their language identity as English as lingua franca (ELF) users. To serve this aim, a mixed-method approach was adopted to collect quantitative and in-depth qualitative data in two phases through an online survey and a semi-structured interview. A total number of 78 Italian students participated in the survey, out of which 14 participants were interviewed. The findings of the online survey indicated that most participants (92%) held a positive perspective toward the use of English in EMI programs and the findings from the interviews were in line with the results of the survey. However, the purpose of the interviews was to explore the participants’ views on their language identity as ELF users. Thematic analysis of the interviews revealed that students experience emotional, cognitive, and social transitions in EMI programs in response to their shift from a non-EMI to an EMI academic setting. Overall, all the above-mentioned transitions were positive and could lead to personal development. However, it can be concluded that the EMI context provides few opportunities for the emergence of significant new subject positions mediated by English in this study. The focus on students’ perspectives on the use of English in EMI programs can contribute to the improvement in language policy planning and internationalized curriculum design by policymakers and alleviate tensions over the controversial issue of the Englishization of higher education by considering how EMI students perceive their use of English as ELF users not superior standard English users.

Exact and heuristic algorithms for the integrated planning of multi-energy systems

The aim of this thesis is to present exact and heuristic algorithms for the integrated planning of multi-energy systems. The idea is to disaggregate the energy system, starting first with its core the Central Energy System, and then to proceed towards the Decentral part. Therefore, a mathematical model for the generation expansion operations to optimize the performance of a Central Energy System system is first proposed. To ensure that the proposed generation operations are compatible with the network, some extensions of the existing network are considered as well. All these decisions are evaluated both from an economic viewpoint and from an environmental perspective, as specific constraints related to greenhouse gases emissions are imposed in the formulation. Then, the thesis presents an optimization model for solar organic Rankine cycle in the context of transactive energy trading. In this study, the impact that this technology can have on the peer-to-peer trading application in renewable based community microgrids is inspected. Here the consumer becomes a prosumer and engages actively in virtual trading with other prosumers at the distribution system level. Moreover, there is an investigation of how different technological parameters of the solar Organic Rankine Cycle may affect the final solution. Finally, the thesis introduces a tactical optimization model for the maintenance operations’ scheduling phase of a Combined Heat and Power plant. Specifically, two types of cleaning operations are considered, i.e., online cleaning and offline cleaning. Furthermore, a piecewise linear representation of the electric efficiency variation curve is included. Given the challenge of solving the tactical management model, a heuristic algorithm is proposed. The heuristic works by solving the daily operational production scheduling problem, based on the final consumer’s demand and on the electricity prices. The aggregate information from the operational problem is used to derive maintenance decisions at a tactical level.

Video transmission over wireless channel

This work has been realized by the author in his PhD course in Electrical, Computer Science and Telecommunication at the University of Bologna, Faculty of Engineering, Italy. All the documentation here reported is a summary of years of work, under the supervision of Prof. Oreste Andrisano, coordinator of Wireless Communication Laboratory - WiLab, in Bologna. The subject of this thesis is the transmission of video in a context of heterogeneous network, and in particular, using a wireless channel. All the instrumentation that has been used for the characterization of the telecommunication systems belongs to CNR (National Research Council), CNIT (Italian Inter- University Center), and DEIS (Dept. of Electrical, Computer Science, and Systems). From November 2009 to July 2010, the author spent his time abroad, working in collaboration with DLR - German Aerospace Center in Munich, Germany, on channel coding area, developing a general purpose decoder machine to decode a huge family of iterative codes. A patent concerning Doubly Generalized-Low Density Parity Check codes has been produced by the author as well as some important scientic papers, published on IEEE journals and conferences.

Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

L'altro eccezionalismo: William Appleman Williams tra storia, storiografia e impegno civile

La storiografia statunitense, a partire dagli anni Cinquanta, vide l’affermarsi di una nuova interpretazione della politica estera americana. Archiviata la storia diplomatica come storia dei trattati o storia delle interazioni delle élites dominanti, abbandonata una visione incentrata sull’equilibrio di potenza, il dibattito storiografico si arricchì della cosiddetta interpretazione «revisionista», antitetica rispetto a quella che, fino a quel momento, aveva predominato. Soggetto di analisi storica restava sempre lo Stato ma l’enfasi maggiore era posta sui fattori economici che ne influenzavano l’azione: si metteva in rilievo l’interazione tra l’interesse privato e il soggetto statale. Capofila di questa nuova scuola fu William Appleman Williams. Questa ricerca si pone l’obiettivo di delineare il contesto storiografico dal quale emersero gli studi di Williams e di cui egli ne roviesciò alcuni assunti fondamentali. Si intende tracciare il suo percorso intellettuale – storiografico e pubblico – al fine di restituire la complessità di un personaggio che divenne un vero e proprio «intellettuale pubblico». I quesiti, a cui questa ricerca vuole dar risposta riguardano l’evoluzione del percorso intellettuale di Williams tanto in ambito storiografico quanto, più in generale, in quello pubblico; il contributo alla ridefinizione dell’identità statunitense e del suo ruolo internazionale; il lascito della sua riflessione nella storiografia. Prendendo le mosse dall’idea di frontiera proposta da Turner, Williams sostenne che la fine dell’espansione territoriale «interna» aveva obbligato gli Stati Uniti a cercare nuovi mercati per il proprio surplus. Era stata tale necessità a catalizzare la Open Door Diplomacy, guidata da ragioni economiche, che presto identificarono l’interesse nazionale per trasformarsi in una vera e propria ideologia nel XX secolo.L’esito di tale politica estera fu la creazione di un impero non più territoriale ma frutto dell’espansione economica. E proprio questa riflessione sull’impero influenzò, negli anni Sessanta, la protesta studentesca che chiese un ripensamento del ruolo internazionale degli Stati Uniti.

Comunicazione d'impresa in Alto Adige: Indagine sulle strategie di gestione del multilinguismo nelle PMI insediate in un territorio di contatto linguistico

La ricerca sulla comunicazione e gestione multilingue della conoscenza in azienda si è sinora concentrata sulle multinazionali o PMI in fase di globalizzazione. La presente ricerca riguarda invece le PMI in zone storicamente multilingui al fine di studiare se l’abitudine all’uso di lingue diverse sul mercato locale possa rappresentare un vantaggio competitivo. La tesi illustra una ricerca multimetodo condotta nel 2012-2013 in Alto Adige/Südtirol. Il dataset consiste in 443 risposte valide a un questionario online e 23 interviste con manager e imprenditori locali. Le domande miravano a capire come le aziende altoatesine affrontino la sfida del multilinguismo, con particolare attenzione ai seguenti ambiti: comunicazione multilingue, documentazione, traduzione e terminologia. I risultati delineano un quadro generale delle strategie di multilinguismo applicate in Alto Adige, sottolineandone punti di forza e punti deboli. Nonostante la presenza di personale multilingue infatti il potenziale vantaggio competitivo che ne deriva non è sfruttato appieno: le aziende si rivolgono ai mercati in cui si parla la loro stessa lingua (le imprese a conduzione italiana al mercato nazionale, quelle di lingua tedesca ad Austria e Germania). La comunicazione interna è multilingue solo nei casi in sia imprescindibile. Le “traduzioni fai-da-te” offrono l’illusione di gestire lingue diverse, ma il livello qualitativo rimane limitato. I testi sono sovente tradotti da personale interno privo di competenze specifiche. Anche nella cooperazione con i traduttori esterni si evidenza la mancata capacità di ottenere il massimo profitto dagli investimenti. La tesi propone delle raccomandazioni pratiche volte a ottimizzare i processi attuali e massimizzare la resa delle risorse disponibili per superare la sfida della gestione e comunicazione multilingue. Le raccomandazioni non richiedono investimenti economici di rilievo e sono facilmente trasferibili anche ad altre regioni multilingui/di confine, come ad altre PMI che impiegano personale plurilingue. Possono dunque risultare utili per un elevato numero di imprese.