Development, degeneration and neural network of the bodily self

The question addressed by this dissertation is how the human brain builds a coherent representation of the body, and how this representation is used to recognize its own body. Recent approaches by neuroimaging and TMS revealed hints for a distinct brain representation of human body, as compared with other stimulus categories. Neuropsychological studies demonstrated that body-parts and self body-parts recognition are separate processes sub-served by two different, even if possibly overlapping, networks within the brain. Bodily self-recognition is one aspect of our ability to distinguish between self and others and the self/other distinction is a crucial aspect of social behaviour. This is the reason why I have conducted a series of experiment on subjects with everyday difficulties in social and emotional behaviour, such as patients with autism spectrum disorders (ASD) and patients with Parkinson’s disease (PD). More specifically, I studied the implicit self body/face recognition (Chapter 6) and the influence of emotional body postures on bodily self-processing in TD children as well as in ASD children (Chapter 7). I found that the bodily self-recognition is present in TD and in ASD children and that emotional body postures modulate self and others’ body processing. Subsequently, I compared implicit and explicit bodily self-recognition in a neuro-degenerative pathology, such as in PD patients, and I found a selective deficit in implicit but not in explicit self-recognition (Chapter 8). This finding suggests that implicit and explicit bodily self-recognition are separate processes subtended by different mechanisms that can be selectively impaired. If the bodily self is crucial for self/other distinction, the space around the body (personal space) represents the space of interaction and communication with others. When, I studied this space in autism, I found that personal space regulation is impaired in ASD children (Chapter 9).

Nanostructured piezoelectric materials for the design and development of self-sensing composite materials and energy harvesting devices

The work activities reported in this PhD thesis regard the functionalization of composite materials and the realization of energy harvesting devices by using nanostructured piezoelectric materials, which can be integrated in the composite without affecting its mechanical properties. The self-sensing composite materials were fabricated by interleaving between the plies of the laminate the piezoelectric elements. The problem of negatively impacting on the mechanical properties of the hosting structure was addressed by shaping the piezoelectric materials in appropriate ways. In the case of polymeric piezoelectric materials, the electrospinning technique allowed to produce highly-porous nanofibrous membranes which can be immerged in the hosting matrix without inducing delamination risk. The flexibility of the polymers was exploited also for the production of flexible tactile sensors. The sensing performances of the specimens were evaluated also in terms of lifetime with fatigue tests. In the case of ceramic piezo-materials, the production and the interleaving of nanometric piezoelectric powder limitedly affected the impact resistance of the laminate, which showed enhanced sensing properties. In addition to this, a model was proposed to predict the piezoelectric response of the self-sensing composite materials as function of the amount of the piezo-phase within the laminate and to adapt its sensing functionalities also for quasi-static loads. Indeed, one final application of the work was to integrate the piezoelectric nanofibers in the sole of a prosthetic foot in order to detect the walking cycle, which has a period in the order of 1 second. In the end, the energy harvesting capabilities of the piezoelectric materials were investigated, with the aim to design wearable devices able to collect energy from the environment and from the body movements. The research activities focused both on the power transfer capability to an external load and the charging of an energy storage unit, like, e.g., a supercapacitor.

Evolutionary methods for self-organizing cooperation in peer-to-peer networks

The Peer-to-Peer network paradigm is drawing the attention of both final users and researchers for its features. P2P networks shift from the classic client-server approach to a high level of decentralization where there is no central control and all the nodes should be able not only to require services, but to provide them to other peers as well. While on one hand such high level of decentralization might lead to interesting properties like scalability and fault tolerance, on the other hand it implies many new problems to deal with. A key feature of many P2P systems is openness, meaning that everybody is potentially able to join a network with no need for subscription or payment systems. The combination of openness and lack of central control makes it feasible for a user to free-ride, that is to increase its own benefit by using services without allocating resources to satisfy other peers’ requests. One of the main goals when designing a P2P system is therefore to achieve cooperation between users. Given the nature of P2P systems based on simple local interactions of many peers having partial knowledge of the whole system, an interesting way to achieve desired properties on a system scale might consist in obtaining them as emergent properties of the many interactions occurring at local node level. Two methods are typically used to face the problem of cooperation in P2P networks: 1) engineering emergent properties when designing the protocol; 2) study the system as a game and apply Game Theory techniques, especially to find Nash Equilibria in the game and to reach them making the system stable against possible deviant behaviors. In this work we present an evolutionary framework to enforce cooperative behaviour in P2P networks that is alternative to both the methods mentioned above. Our approach is based on an evolutionary algorithm inspired by computational sociology and evolutionary game theory, consisting in having each peer periodically trying to copy another peer which is performing better. The proposed algorithms, called SLAC and SLACER, draw inspiration from tag systems originated in computational sociology, the main idea behind the algorithm consists in having low performance nodes copying high performance ones. The algorithm is run locally by every node and leads to an evolution of the network both from the topology and from the nodes’ strategy point of view. Initial tests with a simple Prisoners’ Dilemma application show how SLAC is able to bring the network to a state of high cooperation independently from the initial network conditions. Interesting results are obtained when studying the effect of cheating nodes on SLAC algorithm. In fact in some cases selfish nodes rationally exploiting the system for their own benefit can actually improve system performance from the cooperation formation point of view. The final step is to apply our results to more realistic scenarios. We put our efforts in studying and improving the BitTorrent protocol. BitTorrent was chosen not only for its popularity but because it has many points in common with SLAC and SLACER algorithms, ranging from the game theoretical inspiration (tit-for-tat-like mechanism) to the swarms topology. We discovered fairness, meant as ratio between uploaded and downloaded data, to be a weakness of the original BitTorrent protocol and we drew inspiration from the knowledge of cooperation formation and maintenance mechanism derived from the development and analysis of SLAC and SLACER, to improve fairness and tackle freeriding and cheating in BitTorrent. We produced an extension of BitTorrent called BitFair that has been evaluated through simulation and has shown the abilities of enforcing fairness and tackling free-riding and cheating nodes.

Self-organising coordination systems

Many research fields are pushing the engineering of large-scale, mobile, and open systems towards the adoption of techniques inspired by self-organisation: pervasive computing, but also distributed artificial intelligence, multi-agent systems, social networks, peer-topeer and grid architectures exploit adaptive techniques to make global system properties emerge in spite of the unpredictability of interactions and behaviour. Such a trend is visible also in coordination models and languages, whenever a coordination infrastructure needs to cope with managing interactions in highly dynamic and unpredictable environments. As a consequence, self-organisation can be regarded as a feasible metaphor to define a radically new conceptual coordination framework. The resulting framework defines a novel coordination paradigm, called self-organising coordination, based on the idea of spreading coordination media over the network, and charge them with services to manage interactions based on local criteria, resulting in the emergence of desired and fruitful global coordination properties of the system. Features like topology, locality, time-reactiveness, and stochastic behaviour play a key role in both the definition of such a conceptual framework and the consequent development of self-organising coordination services. According to this framework, the thesis presents several self-organising coordination techniques developed during the PhD course, mainly concerning data distribution in tuplespace-based coordination systems. Some of these techniques have been also implemented in ReSpecT, a coordination language for tuple spaces, based on logic tuples and reactions to events occurring in a tuple space. In addition, the key role played by simulation and formal verification has been investigated, leading to analysing how automatic verification techniques like probabilistic model checking can be exploited in order to formally prove the emergence of desired behaviours when dealing with coordination approaches based on self-organisation. To this end, a concrete case study is presented and discussed.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Development of newly conceived biomimetic nano-structured biomaterials as scaffolds for bone and osteochondral regeneration

The present research thesis was focused on the development of new biomaterials and devices for application in regenerative medicine, particularly in the repair/regeneration of bone and osteochondral regions affected by degenerative diseases such as Osteoarthritis and Osteoporosis or serious traumas. More specifically, the work was focused on the synthesis and physico-chemical-morphological characterization of: i) a new superparamagnetic apatite phase; ii) new biomimetic superparamagnetic bone and osteochondral scaffolds; iii) new bioactive bone cements for regenerative vertebroplasty. The new bio-devices were designed to exhibit high biomimicry with hard human tissues and with functionality promoting faster tissue repair and improved texturing. In particular, recent trends in tissue regeneration indicate magnetism as a new tool to stimulate cells towards tissue formation and organization; in this perspective a new superparamagnetic apatite was synthesized by doping apatite lattice with di-and trivalent iron ions during synthesis. This finding was the pin to synthesize newly conceived superparamagnetic bone and osteochondral scaffolds by reproducing in laboratory the biological processes yielding the formation of new bone, i.e. the self-assembly/organization of collagen fibrils and heterogeneous nucleation of nanosized, ionically substituted apatite mimicking the mineral part of bone. The new scaffolds can be magnetically switched on/off and function as workstations guiding fast tissue regeneration by minimally invasive and more efficient approaches. Moreover, in the view of specific treatments for patients affected by osteoporosis or traumas involving vertebrae weakening or fracture, the present work was also dedicated to the development of new self-setting injectable pastes based on strontium-substituted calcium phosphates, able to harden in vivo and transform into strontium-substituted hydroxyapatite. The addition of strontium may provide an anti-osteoporotic effect, aiding to restore the physiologic bone turnover. The ceramic-based paste was also added with bio-polymers, able to be progressively resorbed thus creating additional porosity in the cement body that favour cell colonization and osseointegration.

Pre-clinical and clinical development of leukemia stem cell inhibitors in acute leukemias

In Leukemias, recent developments have demonstrated that the Hedgehog pathway plays a key-role in the peculiar ability of self renewal of leukemia stem cells. The aim of this research activity was to investigate, through a first in man, Phase I, open label, clinical trial, the role and the impact, mainly in terms of safety profile, adverse events and pharmacokinetics, of a Sonic Hedgehog inhibitor compound on a population of heavely pretreated patients affected by AML, CML, MF, or MDS, resistant or refractory to standard chemotherapy. Thirty-five patients have been enrolled. The drug was administered orally, in 28 days cycles, without rest periods. The compound showed a good safety profile. The half life was of 17-35 hours, justifying the daily administration. Significant signs of activity, in terms of reduction of bone marrow blast cell amount were seen in most of the patients enrolled. Interestingly, correlative biological studies demonstrated that, comparing the gene expression profyiling signature of separated CD34+ cells before and after one cycle of treatment, the most variably expressed genes were involved in the Hh pathway. Moreover, we observed that many genes involved in MDR (multidrug resistance)were significantly down regulated after treatment. These data might lead to future clinical trials based on combinatory approaches, including, for instance, Hh inhibitors and conventional chemotherapy.

Development and characterization of micromachined devices for separation techniques

Nowadays microfluidic is becoming an important technology in many chemical and biological processes and analysis applications. The potential to replace large-scale conventional laboratory instrumentation with miniaturized and self-contained systems, (called lab-on-a-chip (LOC) or point-of-care-testing (POCT)), offers a variety of advantages such as low reagent consumption, faster analysis speeds, and the capability of operating in a massively parallel scale in order to achieve high-throughput. Micro-electro-mechanical-systems (MEMS) technologies enable both the fabrication of miniaturized system and the possibility of developing compact and portable systems. The work described in this dissertation is towards the development of micromachined separation devices for both high-speed gas chromatography (HSGC) and gravitational field-flow fractionation (GrFFF) using MEMS technologies. Concerning the HSGC, a complete platform of three MEMS-based GC core components (injector, separation column and detector) is designed, fabricated and characterized. The microinjector consists of a set of pneumatically driven microvalves, based on a polymeric actuating membrane. Experimental results demonstrate that the microinjector is able to guarantee low dead volumes, fast actuation time, a wide operating temperature range and high chemical inertness. The microcolumn consists of an all-silicon microcolumn having a nearly circular cross-section channel. The extensive characterization has produced separation performances very close to the theoretical ideal expectations. A thermal conductivity detector (TCD) is chosen as most proper detector to be miniaturized since the volume reduction of the detector chamber results in increased mass and reduced dead volumes. The microTDC shows a good sensitivity and a very wide dynamic range. Finally a feasibility study for miniaturizing a channel suited for GrFFF is performed. The proposed GrFFF microchannel is at early stage of development, but represents a first step for the realization of a highly portable and potentially low-cost POCT device for biomedical applications.

Multifarious tumor-oriented small molecules: development of synthetic methodologies and application for diagnostic platforms

Cancer represents one of the most relevant and widespread diseases in the modern age. In this context, integrin receptors are important for the interactions of cells with extracellular matrix and for the development of both inflammation and carcinogenic phenomena. There are many tricks to improve the bioactivity and receptor selectivity of exogenous ligands; one of these is to integrate the amino acid sequence into a cyclic peptide to restrict its conformational space. Another approach is to develop small peptidomimetic molecules in order to enhance the molecular stability and open the way to versatile synthetic strategies. Starting from isoxazoline-based peptidomimetic molecules we recently reported, in this thesis we are going to present the synthesis of new integrin ligands obtained by modifying or introducing appendages on already reported structures. Initially, we are going to introduce the synthesis of linear and cyclic α-dehydro-β-amino acids as scaffolds for the preparation of bioactive peptidomimetics. Subsequently, we are going to present the construction of small molecule ligands (SMLs) based delivery systems performed starting from a polyfunctionalised isoxazoline scaffold, whose potency towards αVβ3 and α5β1 integrins has already been established by our research group. In the light of these results and due to the necessity to understand the behaviour of a single enantiomer of the isoxazoline-based compounds, the research group decided to synthesise the enantiopure heterocycle using a 1,3-dipolar cycloaddiction approach. Subsequently, we are going to introduce the synthesis of a Reporting Drug Delivery System composed by a carrier, a first spacer, a linker, a self-immolative system, a second spacer and a latent fluorophore. The last part of this work will describe the results obtained during the internship abroad in Prof. Aggarwal’s laboratory at the University of Bristol. The project was focused on the Mycapolyol A synthesis.

Development and Implementation of the Plasma Focus Technology for Radiation Therapy Applications

A Plasma Focus device can confine in a small region a plasma generated during the pinch phase. When the plasma is in the pinch condition it creates an environment that produces several kinds of radiations. When the filling gas is nitrogen, a self-collimated backwardly emitted electron beam, slightly spread by the coulomb repulsion, can be considered one of the most interesting outputs. That beam can be converted into X-ray pulses able to transfer energy at an Ultra-High Dose-Rate (UH-DR), up to 1 Gy pulse-1, for clinical applications, research, or industrial purposes. The radiation fields have been studied with the PFMA-3 hosted at the University of Bologna, finding the radiation behavior at different operating conditions and working parameters for a proper tuning of this class of devices in clinical applications. The experimental outcomes have been compared with available analytical formalisms as benchmark and the scaling laws have been proposed. A set of Monte Carlo models have been built with direct and adjoint techniques for an accurate X-ray source characterization and for setting fast and reliable irradiation planning for patients. By coupling deterministic and Monte Carlo codes, a focusing lens for the charged particles has been designed for obtaining a beam suitable for applications as external radiotherapy or intra-operative radiation therapy. The radiobiological effectiveness of the UH PF DR, a FLASH source, has been evaluated by coupling different Monte Carlo codes estimating the overall level of DNA damage at the multi-cellular and tissue levels by considering the spatial variation effects as well as the radiation field characteristics. The numerical results have been correlated to the experimental outcomes. Finally, ambient dose measurements have been performed for tuning the numerical models and obtaining doses for radiation protection purposes. The PFMA-3 technology has been fully characterized toward clinical implementation and installation in a medical facility.

Development of numerical tools for the simulation, design and optimization of a Helicon Plasma Thruster

This work thesis focuses on the Helicon Plasma Thruster (HPT) as a candidate for generating thrust for small satellites and CubeSats. Two main topics are addressed: the development of a Global Model (GM) and a 3D self-consistent numerical tool. The GM is suitable for preliminary analysis of HPTs with noble gases such as argon, neon, krypton, and xenon, and alternative propellants such as air and iodine. A lumping methodology is developed to reduce the computational cost when modelling the excited species in the plasma chemistry. A 3D self-consistent numerical tool is also developed that can treat discharges with a generic 3D geometry and model the actual plasma-antenna coupling. The tool consists of two main modules, an EM module and a FLUID module, which run iteratively until a steady state solution is converged. A third module is available for solving the plume with a simplified semi-analytical approach, a PIC code, or directly by integration of the fluid equations. Results obtained from both the numerical tools are benchmarked against experimental measures of HPTs or Helicon reactors, obtaining very good qualitative agreement with the experimental trend for what concerns the GM, and an excellent agreement of the physical trends predicted against the measured data for the 3D numerical strategy.

Development of new collagen cross-linkers for adhesive bonding stabilization

Aims: This thesis aimed to investigate the influence of different collagen cross-linkers, as separate primers or contained within desensitizing agents, on the longevity of dental restorations and on the dentinal enzymatic activity immediately, or after aging in vitro. Methods: A series of studies was conducted using several different cross-linking molecules and several adhesive systems. Four studies investigated the longevity of the hybrid layer by means of microtensile bond strength test, and the enzymatic activity using gelatin and in situ zymography, immediately or after 1 year of aging in the artificial saliva. The first study tested samples bonded with or without a cross-linking agent, that were previously aged for 5 years. The degradation of the hybrid layer was observed using transmission electron microscopy, the enzymatic activity in the hybrid layer using in situ zymography. Raman spectroscopy was used to investigate whether the active substance was still within the hybrid layer after 5 years. Results: The results of the studies showed that collagen cross-linkers were efficient in preserving bond strength after aging in vitro when used as separate primers on demineralized or partially demineralized dentin. In the cases when the cross-linker was utilized on mineralized dentin, bond strength results were higher than in the control groups immediately and after aging, however, no difference in enzymatic activity was detected after aging. Conclusions: The tested cross-linker molecules used as separate primers in etch-and-rinse and self-etch adhesives seem to be clinically applicable, since the procedure is not overly time-consuming and seems to preserve the hybrid layer over time. As for the cross-linkers contained in the desensitizing agent, when utilized before the adhesive procedures, it has shown to increase the bond strength of self-etch adhesives, but further studies are needed to better understand its effect on the enzymatic activity and crosslinking effects on mineralized dentin.

Oto-Bio-Graphies: auditory perception in twentieth-century self-narratives

Throughout the twentieth century, the study of auditory perception emerged as a significant area of inquiry across various disciplines, particularly within the fields of poststructuralism and psychoanalysis. These theories converge in their understanding of hearing as a fundamental aspect of the development of the subject, leading to a decentering and reformulation of the autobiographical subject, suggesting that the rhythmic is a state of being outside of and prior to the social, verbal, thinking subject. This research aims to examine the connection between auditory perception and the formation of subjectivity in twentieth-century self-narratives. Drawing both from psychoanalysis and poststructuralism, this research proposes a reading of three autobiographical works, namely Elias Canetti’s Die gerettete Zunge, Nathalie Ginzburg’s Lessico famigliare and Nathalie Sarraute’s Enfance. By highlighting the importance of the voice and of the sonorous envelope of childhood, these works artistically anticipate what would be theorised only a few decades later and create the conditions for a pre-verbal apprehension of the world, raising questions about the ineffable source of writing and the writing process itself.

Development and testing of methodologies for the control and diagnosis of innovative combustion systems

In pursuit of aligning with the European Union's ambitious target of achieving a carbon-neutral economy by 2050, researchers, vehicle manufacturers, and original equipment manufacturers have been at the forefront of exploring cutting-edge technologies for internal combustion engines. The introduction of these technologies has significantly increased the effort required to calibrate the models implemented in the engine control units. Consequently the development of tools that reduce costs and the time required during the experimental phases, has become imperative. Additionally, to comply with ever-stricter limits on 〖"CO" 〗_"2" emissions, it is crucial to develop advanced control systems that enhance traditional engine management systems in order to reduce fuel consumption. Furthermore, the introduction of new homologation cycles, such as the real driving emissions cycle, compels manufacturers to bridge the gap between engine operation in laboratory tests and real-world conditions. Within this context, this thesis showcases the performance and cost benefits achievable through the implementation of an auto-adaptive closed-loop control system, leveraging in-cylinder pressure sensors in a heavy-duty diesel engine designed for mining applications. Additionally, the thesis explores the promising prospect of real-time self-adaptive machine learning models, particularly neural networks, to develop an automatic system, using in-cylinder pressure sensors for the precise calibration of the target combustion phase and optimal spark advance in a spark-ignition engines. To facilitate the application of these combustion process feedback-based algorithms in production applications, the thesis discusses the results obtained from the development of a cost-effective sensor for indirect cylinder pressure measurement. Finally, to ensure the quality control of the proposed affordable sensor, the thesis provides a comprehensive account of the design and validation process for a piezoelectric washer test system.

Development of molecular-level switches and implementation into novel nanostructures and smart materials

The work presented in this thesis deals with the design, synthesis and investigation of (supra)molecular switches, and their implementation into novel nanostructures and smart devices. Part A deals with investigation of fundamental properties of Donor Acceptor Stenhouse Adducts (DASAs) as well as their implementation into polymer matrices in order to construct novel smart materials. Part B deals with the implementation of azobenzene photoswitches into pseudorotaxanes and the investigation of the effect of light-driven isomerization on the self-assembly and disassembly processes.