Packet Level Coding for Mobile Broadcasting

The thesis deals with channel coding theory applied to upper layers in the protocol stack of a communication link and it is the outcome of four year research activity. A specific aspect of this activity has been the continuous interaction between the natural curiosity related to the academic blue-sky research and the system oriented design deriving from the collaboration with European industry in the framework of European funded research projects. In this dissertation, the classical channel coding techniques, that are traditionally applied at physical layer, find their application at upper layers where the encoding units (symbols) are packets of bits and not just single bits, thus explaining why such upper layer coding techniques are usually referred to as packet layer coding. The rationale behind the adoption of packet layer techniques is in that physical layer channel coding is a suitable countermeasure to cope with small-scale fading, while it is less efficient against large-scale fading. This is mainly due to the limitation of the time diversity inherent in the necessity of adopting a physical layer interleaver of a reasonable size so as to avoid increasing the modem complexity and the latency of all services. Packet layer techniques, thanks to the longer codeword duration (each codeword is composed of several packets of bits), have an intrinsic longer protection against long fading events. Furthermore, being they are implemented at upper layer, Packet layer techniques have the indisputable advantages of simpler implementations (very close to software implementation) and of a selective applicability to different services, thus enabling a better matching with the service requirements (e.g. latency constraints). Packet coding technique improvement has been largely recognized in the recent communication standards as a viable and efficient coding solution: Digital Video Broadcasting standards, like DVB-H, DVB-SH, and DVB-RCS mobile, and 3GPP standards (MBMS) employ packet coding techniques working at layers higher than the physical one. In this framework, the aim of the research work has been the study of the state-of-the-art coding techniques working at upper layer, the performance evaluation of these techniques in realistic propagation scenario, and the design of new coding schemes for upper layer applications. After a review of the most important packet layer codes, i.e. Reed Solomon, LDPC and Fountain codes, in the thesis focus our attention on the performance evaluation of ideal codes (i.e. Maximum Distance Separable codes) working at UL. In particular, we analyze the performance of UL-FEC techniques in Land Mobile Satellite channels. We derive an analytical framework which is a useful tool for system design allowing to foresee the performance of the upper layer decoder. We also analyze a system in which upper layer and physical layer codes work together, and we derive the optimal splitting of redundancy when a frequency non-selective slowly varying fading channel is taken into account. The whole analysis is supported and validated through computer simulation. In the last part of the dissertation, we propose LDPC Convolutional Codes (LDPCCC) as possible coding scheme for future UL-FEC application. Since one of the main drawbacks related to the adoption of packet layer codes is the large decoding latency, we introduce a latency-constrained decoder for LDPCCC (called windowed erasure decoder). We analyze the performance of the state-of-the-art LDPCCC when our decoder is adopted. Finally, we propose a design rule which allows to trade-off performance and latency.

Studio Sperimentale e Modellazione della Separazione di Proteine con Membrane di Affinità

Chromatography represents one of the most important and widely used unit operation in the biotechnology industry. However this technique suffers from several limitations such as high pressure drop, slow mass transfer through the diffusive pores and strong dependence of the binding capacity on flow rate. In this work, affinity membranes with improved capacity have been considered as an alternative technology for the capturing step in antibody manufacturing. Several affinity membranes have been prepared starting from various membrane supports. Different affinity ligands have been utilized like Protein A, the natural ligand of choice for antibodies, as well as synthetic ligands that exhibit affinity for the Fc portion of antibodies. The membranes have been characterized in detail: binding and elution performance was evaluated in adsorption experiments using pure IgG solutions, while membrane selectivity was evaluated using complex solutions like a cell culture supernatant. The most promising affinity membranes were extensively tested in dynamic experiments. The effects of operating parameters like feed concentration and flow rate on separation performances like binding capacity, selectivity and process yield have been studied in detail in order to find the optimal conditions for binding and elution steps. The membranes have been used over several complete chromatographic cycles to evaluate the effects of ageing and of membrane regeneration on dynamic binding capacity. A novel mathematical model is proposed that can describe all the chromatographic steps involved in the membrane affinity chromatography process for protein purification. The mathematical description is based on the species continuity equation coupled with a proper binding kinetic equation, and suitable to describe adequately the dispersion phenomena occurring both in the micro-porous membranes as well as in the extra-column devices used in the system. The model considers specifically all the different chromatographic steps, namely adsorption, washing and elution. The few relevant fitting parameters of the model were derived from a calibration with the experimental affinity cycles performed with pure IgG solutions, then the model is used to describe experimental data obtained in chromatographic cycles carried out with complex feeds as the cell culture supernatant. Simulations reveal a good agreement with experimental data in all the chromatography steps, both in the case of pure IgG solutions and for the cell culture supernatant considered.

Comparison of affinity chromatography supports for separation of protein

Chromatography is the most widely used technique for high-resolution separation and analysis of proteins. This technique is very useful for the purification of delicate compounds, e.g. pharmaceuticals, because it is usually performed at milder conditions than separation processes typically used by chemical industry. This thesis focuses on affinity chromatography. Chromatographic processes are traditionally performed using columns packed with porous resin. However, these supports have several limitations, including the dependence on intra-particle diffusion, a slow mass transfer mechanism, for the transport of solute molecules to the binding sites within the pores and high pressure drop through the packed bed. These limitations can be overcome by using chromatographic supports like membranes or monoliths. Dye-ligands are considered important alternatives to natural ligands. Several reactive dyes, particularly Cibacron Blue F3GA, are used as affinity ligand for protein purification. Cibacron Blue F3GA is a triazine dye that interacts specifically and reversibly with albumin. The aim of this study is to prepare dye-affinity membranes and monoliths for efficient removal of albumin and to compare the three different affinity supports: membranes and monoliths and a commercial column HiTrapTM Blue HP, produced by GE Healthcare. A comparison among the three supports was performed in terms of binding capacity at saturation (DBC100%) and dynamic binding capacity at 10% breakthrough (DBC10%) using solutions of pure BSA. The results obtained show that the CB-RC membranes and CB-Epoxy monoliths can be compared to commercial support, column HiTrapTM Blue HP, for the separation of albumin. These results encourage a further characterization of the new supports examined.

Malattie immunomediate del cane e del gatto: aspetti diagnostici e terapeutici

La presente tesi di dottorato affronta alcune delle più comuni malattie immunomediate del cane e del gatto. Il manoscritto è incentrato sugli aspetti diagnostici e terapeutici in corso di: anemia emolitica immunomediata (Immune-mediated hemolytic anemia, IMHA), trombocitopenia immunomediata (Immune-mediated thrombocytopenia, ITP) e poliartrite immunomediata (Immune-mediated polyarthritis, IMP). Il capitolo 1 costituisce un’introduzione all’argomento delle malattie immunologiche; vengono sottolineati alcuni aspetti patogenetici delle singole malattie immunomediate e riassunte le difficoltà diagnostiche e terapeutiche. Il capitolo 2 riporta uno studio riguardante una popolazione di gatti con diagnosi, o sospetto diagnostico, di IMHA che evidenziava una discrepanza tra i test diagnostici per il virus della leucemia felina (Feline Leukemia Virus, FeLV). La positività FeLV al test point of care, non confermata dalla PCR del DNA provirale, lascia spazio a diverse interpretazioni. Il capitolo 3 mostra i dati relativi al confronto tra tre diversi protocolli immunosoppressivi (glucocorticoidi, glucocorticoidi+ciclosporina, glucocorticoidi+micofenolato mofetile) in una popolazione di cani con IMHA non associativa. Il confronto verteva, principalmente, sulla risposta ematologica dei pazienti, che non si è dimostrata differente tra i tre gruppi terapeutici. Il capitolo 4 riporta una revisione della letteratura riguardante l’ITP del cane e del gatto. Si tratta di una malattia eterogenea in cui le manifestazioni cliniche appaiono variabili: alcuni pazienti sono asintomatici, altri presentano dei sanguinamenti spontanei. La mancanza di criteri diagnostici standardizzati, porta il clinico a considerare l’ITP una diagnosi “ad esclusione”. Le strategie terapeutiche non si basano purtroppo su linee guida condivise, pertanto il target della terapia rimane, ad oggi, sconosciuto. Nel capitolo 5 viene posta l’attenzione su alcuni interrogativi diagnostici e terapeutici che riguardano l’IMP del cane e del gatto. La sintomatologia clinica, caratterizzata da zoppia, febbre e riluttanza al movimento, talvolta può essere subdola. Anche in questa malattia, non vi sono evidenze scientifiche circa il regime immunosoppressivo più corretto ed indicato.

Study of two novel streptococcus pneumoniae operons: pilus islet 2 and the lantibiotic operon

Analysis of publicly available genomes of Streptococcus pneumoniae has led to the identification of a new genomic element resembling gram-positive pilus islets (PIs). Here, we demonstrate that this genomic region, herein referred to as PI-2 (containing the genes pitA, sipA, pitB, srtG1, and srtG2) codes for a novel functional pilus in pneumococcus. Therefore, there are two pilus islets identified so far in this pathogen (PI-1 and PI-2). Polymerization of the PI-2 pilus requires the backbone protein PitB as well as the sortase SrtG1 and the signal peptidase-like protein SipA. PI-2 is associated with serotypes 1, 2, 7F, 19A, and 19F, considered to be emerging in both industrialized and developing countries. Interestingly, strains belonging to clonal complex 271 (CC271) contain both PI-1 and PI-2, as revealed by genome analyses. In these strains both pili are surface exposed and independently assembled. Furthermore, in vitro experiments provide evidence that the pilus encoded by PI-2 of S. pneumoniae is involved in adherence. Thus, pneumococci encode at least two types of pili that may play a role in the initial host cell contact to the respiratory tract. In addition, the pilus proteins are potential antigens for inclusion in a new generation of pneumococcal vaccines. Adherence by pili could represent important factor in bacterial community formation, since it has been demonstrated that bacterial community formation plays an important role in pneumococcal otitis media. In vitro quantification of bacterial community formation by S. pneumoniae was performed in order to investigate the possible role of pneumococcal pili to form communities. By using different growth media we were not able to see clear association between pili and community formation. But our findings revealed that strains belonging to MLST clonal complex CC15 efficiently form bacterial communities in vitro in a glucose dependent manner. We compared the genome of forty-four pneumococcal isolates discovering four open reading frames specifically associated with CC15. These four genes are annotated as members of an operon responsible for the biosynthesis of a putative lanctibiotic peptide, described to be involved in bacterial community formation. Our experiments show that the lanctibiotic operon deletion affects glucose mediated community formation in CC 15 strain INV200. Moreover, since glucose consumption during bacterial growth produce an acidic environment, we tested bacterial community formation at different pH and we showed that the lanctibiotic operon deletion affected pH mediated community formation in CC 15 strain INV200. In conclusion, these data demonstrate that the putative lanctibiotic operon is associated with pneumococcal CC 15 strains in vitro bacterial community formation.

Percorsi di gender performance: fotografia tra arte e moda dagli anni Novanta ad oggi

My project explores and compares different forms of gender performance in contemporary art and visual culture according to a perspective centered on photography. Thanks to its attesting power this medium can work as a ready-made. In fact during the 20th century it played a key role in the cultural emancipation of the body which (using a Michel Foucault’s expression) has now become «the zero point of the world». Through performance the body proves to be a living material of expression and communication while photography ensures the recording of any ephemeral event that happens in time and space. My questioning approach considers the gender constructed imagery from the 1990s to the present in order to investigate how photography’s strong aura of realism promotes and allows fantasies of transformation. The contemporary fascination with gender (especially for art and fashion) represents a crucial issue in the global context of postmodernity and is manifested in a variety of visual media, from photography to video and film. Moreover the internet along with its digital transmission of images has deeply affected our world (from culture to everyday life) leading to a postmodern preference for performativity over the more traditional and linear forms of narrativity. As a consequence individual borders get redefined by the skin itself which (dissected through instant vision) turns into a ductile material of mutation and hybridation in the service of identity. My critical assumptions are taken from the most relevant changes occurred in philosophy during the last two decades as a result of the contributions by Jacques Lacan, Michel Foucault, Jacques Derrida, Gilles Deleuze who developed a cross-disciplinary and comparative approach to interpret the crisis of modernity. They have profoundly influenced feminist studies so that the category of gender has been reassessed in contrast with sex (as a biological connotation) and in relation to history, culture, society. The ideal starting point of my research is the year 1990. I chose it as the approximate historical moment when the intersection of race, class and gender were placed at the forefront of international artistic production concerned with identity, diversity and globalization. Such issues had been explored throughout the 1970s but it was only from the mid-1980s onward that they began to be articulated more consistently. Published in 1990, the book "Gender trouble: feminism and the subversion of identity" by Judith Butler marked an important breakthrough by linking gender to performance as well as investigating the intricate connections between theory and practice, embodiment and representation. It inspired subsequent research in a variety of disciplines, art history included. In the same year Teresa de Lauretis launched the definition of queer theory to challenge the academic perspective in gay and lesbian studies. In the meantime the rise of Third Wave Feminism in the US introduced a racially and sexually inclusive vision over the global situation in order to reflect on subjectivity, new technologies and popular culture in connection with gender representation. These conceptual tools have enabled prolific readings of contemporary cultural production whether fine arts or mass media. After discussing the appropriate framework of my project and taking into account the postmodern globalization of the visual, I have turned to photography to map gender representation both in art and in fashion. Therefore I have been creating an archive of images around specific topics. I decided to include fashion photography because in the 1990s this genre moved away from the paradigm of an idealized and classical beauty toward a new vernacular allied with lifestyles, art practices, pop and youth culture; as one might expect the dominant narrative modes in fashion photography are now mainly influenced by cinema and snapshot. These strategies originate story lines and interrupted narratives using models’ performance to convey a particular imagery where identity issues emerge as an essential part of fashion spectacle. Focusing on the intersections of gender identities with socially and culturally produced identities, my approach intends to underline how the fashion world has turned to current trends in art photography and in some case turned to the artists themselves. The growing fluidity of the categories that distinguish art from fashion photography represents a particularly fruitful moment of visual exchange. Varying over time the dialogue between these two fields has always been vital; nowadays it can be studied as a result of this close relationship between contemporary art world and consumer culture. Due to the saturation of postmodern imagery the feedback between art and fashion has become much more immediate and then increasingly significant for anyone who wants to investigate the construction of gender identity through performance. In addition to that a lot of magazines founded in the 1990s bridged the worlds of art and fashion because some of their designers and even editors were art-school graduates encouraging innovation. The inclusion of art within such magazines aimed at validating them as a form of art in themselves supporting a dynamic intersection for music, fashion, design and youth culture: an intersection that also contributed to create and spread different gender stereotypes. This general interest in fashion produced many exhibitions of and about fashion itself at major international venues such as the Victoria and Albert Museum in London, the Metropolitan Museum of Art and the Solomon R. Guggenheim Museum in New York. Since then this celebrated success of fashion has been regarded as a typical element of postmodern culture. Owing to that I have also based my analysis on some important exhibitions dealing with gender performance like "Féminin-Masculin" at the Centre Pompidou of Paris (1995), "Rrose is a Rrose is a Rrose. Gender performance in photography" at the Solomon R. Guggenheim Museum of New York (1997), "Global Feminisms" at the Brooklyn Museum (2007), "Female Trouble" at the Pinakothek der Moderne in München together with the workshops dedicated to "Performance: gender and identity" in June 2005 at the Tate Modern of London. Since 2003 in Italy we have had Gender Bender - an international festival held annually in Bologna - to explore the gender imagery stemming from contemporary culture. In few days this festival offers a series of events ranging from visual arts, performance, cinema, literature to conferences and music. Being aware that any method of research is neither race nor gender neutral I have traced these critical paths to question gender identity in a multicultural perspective taking account of the political implications too. In fact, if visibility may be equated with exposure, we can also read these images as points of intersection of visibility with social power. Since gender assignations rely so heavily on the visual, the postmodern dismantling of gender certainty through performance has wide-ranging effects that need to be analyzed. In some sense this practice can even contest the dominance of visual within postmodernism. My visual map in contemporary art and fashion photography includes artists like Nan Goldin, Cindy Sherman, Hellen van Meene, Rineke Dijkstra, Ed Templeton, Ryan McGinley, Anne Daems, Miwa Yanagi, Tracey Moffat, Catherine Opie, Tomoko Sawada, Vanessa Beecroft, Yasumasa Morimura, Collier Schorr among others.

Computational investigations of ion conduction mechanisms using enhanced sampling methods

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

Exact Algorithms for Different Classes of Vehicle Routing Problems

We deal with five problems arising in the field of logistics: the Asymmetric TSP (ATSP), the TSP with Time Windows (TSPTW), the VRP with Time Windows (VRPTW), the Multi-Trip VRP (MTVRP), and the Two-Echelon Capacitated VRP (2E-CVRP). The ATSP requires finding a lest-cost Hamiltonian tour in a digraph. We survey models and classical relaxations, and describe the most effective exact algorithms from the literature. A survey and analysis of the polynomial formulations is provided. The considered algorithms and formulations are experimentally compared on benchmark instances. The TSPTW requires finding, in a weighted digraph, a least-cost Hamiltonian tour visiting each vertex within a given time window. We propose a new exact method, based on new tour relaxations and dynamic programming. Computational results on benchmark instances show that the proposed algorithm outperforms the state-of-the-art exact methods. In the VRPTW, a fleet of identical capacitated vehicles located at a depot must be optimally routed to supply customers with known demands and time window constraints. Different column generation bounding procedures and an exact algorithm are developed. The new exact method closed four of the five open Solomon instances. The MTVRP is the problem of optimally routing capacitated vehicles located at a depot to supply customers without exceeding maximum driving time constraints. Two set-partitioning-like formulations of the problem are introduced. Lower bounds are derived and embedded into an exact solution method, that can solve benchmark instances with up to 120 customers. The 2E-CVRP requires designing the optimal routing plan to deliver goods from a depot to customers by using intermediate depots. The objective is to minimize the sum of routing and handling costs. A new mathematical formulation is introduced. Valid lower bounds and an exact method are derived. Computational results on benchmark instances show that the new exact algorithm outperforms the state-of-the-art exact methods.

Coordination and Control of Autonomous Mobile Robots Swarms by using Particle Swarm Optimization Algorithm and Consensus Theory

This thesis presents some different techniques designed to drive a swarm of robots in an a-priori unknown environment in order to move the group from a starting area to a final one avoiding obstacles. The presented techniques are based on two different theories used alone or in combination: Swarm Intelligence (SI) and Graph Theory. Both theories are based on the study of interactions between different entities (also called agents or units) in Multi- Agent Systems (MAS). The first one belongs to the Artificial Intelligence context and the second one to the Distributed Systems context. These theories, each one from its own point of view, exploit the emergent behaviour that comes from the interactive work of the entities, in order to achieve a common goal. The features of flexibility and adaptability of the swarm have been exploited with the aim to overcome and to minimize difficulties and problems that can affect one or more units of the group, having minimal impact to the whole group and to the common main target. Another aim of this work is to show the importance of the information shared between the units of the group, such as the communication topology, because it helps to maintain the environmental information, detected by each single agent, updated among the swarm. Swarm Intelligence has been applied to the presented technique, through the Particle Swarm Optimization algorithm (PSO), taking advantage of its features as a navigation system. The Graph Theory has been applied by exploiting Consensus and the application of the agreement protocol with the aim to maintain the units in a desired and controlled formation. This approach has been followed in order to conserve the power of PSO and to control part of its random behaviour with a distributed control algorithm like Consensus.

Microglial involvement in brain physiopathology: in vitro studies using rat primary cultures

Microglial involvement in neurological disorders is well-established, being microglial activation not only associated with neurotoxic consequences, but also with neuroprotective effects. The studies presented here, based on microglia rat primary cell cultures and mainly on microglial conditioned medium (MCM), show insights into the mechanism of Superoxide dismutase 1 (SOD1) and Apolipoprotein E (ApoE) secretion by microglia as well as their neuroprotective effect towards primary cerebellar granule neurons (CGNs) exposed to the dopaminergic toxin 6-hydroxydopamine (6-OHDA). SOD1 and ApoE are released respectively through non-classical lysosomal or the classical ER/Golgi-mediated secretion pathway. Microglial conditioned medium, in which SOD1 and ApoE accumulated, protected CGNs from degeneration and these effects were replicated when exogenous SOD1 or ApoE was added to a non-conditioned medium. SOD1 neuroprotective action was mediated by increased cell calcium from an external source. ApoE release is negatively affected by microglia activation, both with lipopolysaccharide (LPS) and Benzoylbenzoyl-ATP (Bz-ATP) but is stimulated by neuronal-conditioned medium as well as in microglia-neurons co-culture conditions. This neuronal-stimulated microglial ApoE release is differently regulated by activation states (i.e. LPS vs ATP) and by 6-hydroxydopamine-induced neurodegeneration. In co-culture conditions, microglial ApoE release is essential for neuroprotection, since microglial ApoE silencing through siRNA abrogated protection of cerebellar granule neurons against 6-OHDA toxicity. Therefore, these molecules could represent a target for manipulation aimed at promoting neuroprotection in brain diseases. Considering a pathological context, and the microglial ability to adopt a neuroprotective or neurotoxic profile, we characterize the microglial M1/M2 phenotype in transgenic rats (McGill-R-Thy1-APP) which reproduce extensively the Alzheimer’s-like amyloid pathology. Here, for the first time, cortical, hippocampal and cerebellar microglia of wild type and transgenic adult rats were compared, at both early and advanced stages of the pathology. In view of possible therapeutic translations, these findings are relevant to test microglial neuroprotection, in animal models of neurodegenerative diseases.

Constraints on neutrino mass fraction using Redshift Space Distortions

Redshift Space Distortions (RSD) are an apparent anisotropy in the distribution of galaxies due to their peculiar motion. These features are imprinted in the correlation function of galaxies, which describes how these structures distribute around each other. RSD can be represented by a distortions parameter $\beta$, which is strictly related to the growth of cosmic structures. For this reason, measurements of RSD can be exploited to give constraints on the cosmological parameters, such us for example the neutrino mass. Neutrinos are neutral subatomic particles that come with three flavours, the electron, the muon and the tau neutrino. Their mass differences can be measured in the oscillation experiments. Information on the absolute scale of neutrino mass can come from cosmology, since neutrinos leave a characteristic imprint on the large scale structure of the universe. The aim of this thesis is to provide constraints on the accuracy with which neutrino mass can be estimated when expoiting measurements of RSD. In particular we want to describe how the error on the neutrino mass estimate depends on three fundamental parameters of a galaxy redshift survey: the density of the catalogue, the bias of the sample considered and the volume observed. In doing this we make use of the BASICC Simulation from which we extract a series of dark matter halo catalogues, characterized by different value of bias, density and volume. This mock data are analysed via a Markov Chain Monte Carlo procedure, in order to estimate the neutrino mass fraction, using the software package CosmoMC, which has been conveniently modified. In this way we are able to extract a fitting formula describing our measurements, which can be used to forecast the precision reachable in future surveys like Euclid, using this kind of observations.