Computational methods for genome screening

Motivation An actual issue of great interest, both under a theoretical and an applicative perspective, is the analysis of biological sequences for disclosing the information that they encode. The development of new technologies for genome sequencing in the last years, opened new fundamental problems since huge amounts of biological data still deserve an interpretation. Indeed, the sequencing is only the first step of the genome annotation process that consists in the assignment of biological information to each sequence. Hence given the large amount of available data, in silico methods became useful and necessary in order to extract relevant information from sequences. The availability of data from Genome Projects gave rise to new strategies for tackling the basic problems of computational biology such as the determination of the tridimensional structures of proteins, their biological function and their reciprocal interactions. Results The aim of this work has been the implementation of predictive methods that allow the extraction of information on the properties of genomes and proteins starting from the nucleotide and aminoacidic sequences, by taking advantage of the information provided by the comparison of the genome sequences from different species. In the first part of the work a comprehensive large scale genome comparison of 599 organisms is described. 2,6 million of sequences coming from 551 prokaryotic and 48 eukaryotic genomes were aligned and clustered on the basis of their sequence identity. This procedure led to the identification of classes of proteins that are peculiar to the different groups of organisms. Moreover the adopted similarity threshold produced clusters that are homogeneous on the structural point of view and that can be used for structural annotation of uncharacterized sequences. The second part of the work focuses on the characterization of thermostable proteins and on the development of tools able to predict the thermostability of a protein starting from its sequence. By means of Principal Component Analysis the codon composition of a non redundant database comprising 116 prokaryotic genomes has been analyzed and it has been showed that a cross genomic approach can allow the extraction of common determinants of thermostability at the genome level, leading to an overall accuracy in discriminating thermophilic coding sequences equal to 95%. This result outperform those obtained in previous studies. Moreover, we investigated the effect of multiple mutations on protein thermostability. This issue is of great importance in the field of protein engineering, since thermostable proteins are generally more suitable than their mesostable counterparts in technological applications. A Support Vector Machine based method has been trained to predict if a set of mutations can enhance the thermostability of a given protein sequence. The developed predictor achieves 88% accuracy.

Multidimensional Measures of Firm Competitiveness: a Model-Based Approach

The concept of competitiveness, for a long time considered as strictly connected to economic and financial performances, evolved, above all in recent years, toward new, wider interpretations disclosing its multidimensional nature. The shift to a multidimensional view of the phenomenon has excited an intense debate involving theoretical reflections on the features characterizing it, as well as methodological considerations on its assessment and measurement. The present research has a twofold objective: going in depth with the study of tangible and intangible aspect characterizing multidimensional competitive phenomena by assuming a micro-level point of view, and measuring competitiveness through a model-based approach. Specifically, we propose a non-parametric approach to Structural Equation Models techniques for the computation of multidimensional composite measures. Structural Equation Models tools will be used for the development of the empirical application on the italian case: a model based micro-level competitiveness indicator for the measurement of the phenomenon on a large sample of Italian small and medium enterprises will be constructed.

Il geografo riluttante. R.K. Narayan e il mondo di Malgudi

Il presente lavoro è dedicato allo studio della geografia immaginaria creata dallo scrittore indiano di lingua inglese R.K. Narayan (1906-2001), allo scopo non solo di indagare la relazione che si stabilisce tra spazio, personaggi e racconto, ma anche di rilevare l’interazione tra il mondo narrativo e le rappresentazioni dominanti dello spazio indiano elaborate nel contesto coloniale e postcoloniale. Dopo un primo capitolo di carattere teorico-metodologico (che interroga le principali riflessioni seguite allo "spatial turn" che ha interessato le scienze umane nel corso del Novecento, i concetti fondamentali formulati nell’ambito della teoria dei "fictional worlds", e i più recenti approcci al rapporto tra spazio e letteratura), la ricerca si articola in due ulteriori sezioni, che si rivolgono ai quattordici romanzi dell’autore attraverso una pratica interpretativa di ispirazione geocritica e “spazializzata”. Nel secondo capitolo, che concerne la dimensione “verticale” che si estende dal cronotopo dei romanzi a quello dell’autore e dei lettori, si procede al rilevamento, all’interno del mondo narrativo, di tre macro-paesaggi, successivamente messi a confronto con le rappresentazioni endogene e esogene dello spazio extratestuale; da questo confronto, la cittadina di Malgudi emerge come proposta autoriale di riorganizzazione sociale e urbana dal carattere innovativo e dallo statuto eterotopico, sia in rapporto alla tradizione letteraria dalla quale origina, sia rispetto alle circostanze ambientali dell’India meridionale in cui essa è finzionalmente collocata. Seguendo una dinamica “orizzontale”, il terzo capitolo esamina infine il rapporto tra lo spazio frazionato di Malgudi, i luoghi praticati dai suoi abitanti e la relazione che questi instaurano con il territorio transfrontaliero e con la figura del forestiero; inoltre, al fine di stabilire la misura in cui la natura dello spazio narrativo influisce sulla forma del racconto, si osservano le coincidenze tra il tema dell’incompiutezza che pervade le vicende dei personaggi e la forma aperta dei finali romanzeschi.

From inverted pendulum to N-link chain: inertial sensors-based assessment of movement kinematics and dynamics for functional evaluation and rehabilitation

Despite several clinical tests that have been developed to qualitatively describe complex motor tasks by functional testing, these methods often depend on clinicians' interpretation, experience and training, which make the assessment results inconsistent, without the precision required to objectively assess the effect of the rehabilitative intervention. A more detailed characterization is required to fully capture the various aspects of motor control and performance during complex movements of lower and upper limbs. The need for cost-effective and clinically applicable instrumented tests would enable quantitative assessment of performance on a subject-specific basis, overcoming the limitations due to the lack of objectiveness related to individual judgment, and possibly disclosing subtle alterations that are not clearly visible to the observer. Postural motion measurements at additional locations, such as lower and upper limbs and trunk, may be necessary in order to obtain information about the inter-segmental coordination during different functional tests involved in clinical practice. With these considerations in mind, this Thesis aims: i) to suggest a novel quantitative assessment tool for the kinematics and dynamics evaluation of a multi-link kinematic chain during several functional motor tasks (i.e. squat, sit-to-stand, postural sway), using one single-axis accelerometer per segment, ii) to present a novel quantitative technique for the upper limb joint kinematics estimation, considering a 3-link kinematic chain during the Fugl-Meyer Motor Assessment and using one inertial measurement unit per segment. The suggested methods could have several positive feedbacks from clinical practice. The use of objective biomechanical measurements, provided by inertial sensor-based technique, may help clinicians to: i) objectively track changes in motor ability, ii) provide timely feedback about the effectiveness of administered rehabilitation interventions, iii) enable intervention strategies to be modified or changed if found to be ineffective, and iv) speed up the experimental sessions when several subjects are asked to perform different functional tests.

Graphene and Semicondutor or Metallic Nanoparticles for Energy Conversion

The purpose of the present PhD thesis is to investigate the properties of innovative nano- materials with respect to the conversion of renewable energies to electrical and chemical energy. The materials have been synthesized and characterized by means of a wide spectrum of morphological, compositional and photophysical techniques, in order to get an insight into the correlation between the properties of each material and the activity towards different energy conversion applications. Two main topics are addressed: in the first part of the thesis the light harvesting in pyrene functionalized silicon nanocrystals has been discussed, suggesting an original approach to suc- cessfully increase the absorption properties of these nanocrystals. The interaction of these nanocrystals was then studied, in order to give a deeper insight on the charge and energy extraction, preparing the way to implement SiNCs as active material in optoelectronic devices and photovoltaic cells. In addition to this, the luminescence of SiNCs has been exploited to increase the efficiency of conventional photovoltaic cells by means of two innovative architectures. Specifically, SiNCs has been used as luminescent downshifting layer in dye sensitized solar cells, and they were shown to be very promising light emitters in luminescent solar concentrators. The second part of the thesis was concerned on the production of hydrogen by platinum nanoparticles coupled to either electro-active or photo-active materials. Within this context, the electrocatalytic activity of platinum nanoparticles supported on exfoliated graphene has been studied, preparing an high-efficiency catalyst and disclosing the role of the exfoliation technique towards the catalytic activity. Furthermore, platinum nanoparticles have been synthesized within photoactive dendrimers, providing the first proof of concept of a dendrimer-based photocatalytic system for the hydrogen production where both sensitizer and catalyst are anchored to a single scaffold.