Human papillomavirus (HPV) and associated diseases: between applied diagnostic and basic research

Human Papillomavirus (HPV) is the cause of cervical cancers (among these, adenocarcinoma, AdCa) and is associated to a subgroup of oropharyngeal carcinomas (OPSCCs). Even if the risk for cancer development is linked to the infection by some viral genotypes, mainly HPV16 and 18, viral DNA alone seems not to be sufficient for diagnosis. Moreover, the role of the virus in OPSCCs has not been totally clarified yet. In the first part of the thesis, the performances concerning viral genotyping in clinical cervical samples of a new pyrosequencing-based test and a well-known hybridization-based assay have been compared. Similar results between the methods have been obtained. However, the former showed advantages in detecting intratype variants, higher specificity and a broader spectrum of detectable HPV types. The second part deals with the evaluation of virological markers (genotyping, viral oncoproteins expression, viral load, physical state and CpG methylation of HPV16 genome) in the diagnosis/prognosis of cervical AdCa and HPV-associated OPSCCs. HPV16 has been confirmed the most prevalent genotype in both the populations. Interestingly, the mean methylation frequency of viral DNA at the early promoter showed the tendency to be associated to invasion for cervical AdCa and to a worse prognosis for OPSCCs, suggesting a promising role as diagnostic/prognostic biomarker. The experiments of the third part were performed at the DKFZ in Heidelberg (Germany) and dealt with the analysis of the response to IFN-k transfection in HPV16-positive cervical cancer and head&neck carcinoma cell lines to evaluate its potential role as new treatment. After 24h, we observed increased IFN-b expression which lead to the up-regulation of genes involved in the antigens presentation pathway (MHC class I and immunoproteasome) and antiviral response as well, in particular in cervical cancer cell lines. This fact suggested also the presence of different HPV-mediated carcinogenic pathways between the two anatomical districts.

Sustainable pavements for rural scenarios: laboratory and in-situ characterization of recycled materials and innovative construction solutions

Growing need for infrastructure has led to expanding research on advances in road pavement materials. Finding solutions that are sustainable, environmentally friendly and cost-efficient is a priority. Focusing such efforts on low-traffic and rural roads can contribute with a significant progress in the vital circulatory system of transport for rural and agricultural areas. An important alternative material for pavement construction is recycled aggregates from solid wastes, including waste from civil engineering activities, mainly construction and demolition. A literature review on studies is made; it is performed a planned set of laboratory testing procedures aimed to fully characterize and assess the potential in-situ mechanical performance and chemical impact. Furthermore, monitoring the full-scale response of the selected materials in a real field construction site, including the production, laying and compaction operations. Moreover, a novel single-phase solution for the construction of semi-flexible paving layers to be used as alternative material to common concrete and bituminous layers is experimented and introduced, aiming the production and laying of a single-phase laid material instead of a traditional two phases grouted macadam. Finally, on a parallel research work for farming pavements, the possible use of common geotechnical anti-erosive products for the improvement of soil bearing capacity of paddock areas in cattle husbandries of bio-farms is evaluated. this thesis has clearly demonstrated the feasibility of using the sustainable recycled aggregates for low-traffic rural roads and the pavements of farming and agriculture areas. The pavement layers constructed with recycled aggregates provided satisfying performance under heavy traffic conditions in experimental pavements. This, together with the fact that these aggregates can be available in most areas and in large quantities, provides great impetus towards shifting from traditional materials to more sustainable alternatives. The chemical and environmental stability of these materials proves their soundness to be utilized in farming environments.

The bursting behavior of gas slugs: laboratory and analytical insights into Strombolian volcanic eruptions.

The aim of this thesis is to study how explosive behavior and geophysical signals in a volcanic conduit are related to the development of overpressure in slug-driven eruptions. A first suite of laboratory experiments of gas slugs ascending in analogue conduits was performed. Slugs ascended into a range of analogue liquids and conduit diameters to allow proper scaling to the natural volcanoes. The geometrical variation of the slug in response to the explored variables was parameterised. Volume of gas slug and rheology of the liquid phase revealed the key parameters in controlling slug overpressure at bursting. Founded on these results, a theoretical model to calculate burst overpressure for slug-driven eruptions was developed. The dimensionless approach adopted allowed to apply the model to predict bursting pressure of slugs at Stromboli. Comparison of predicted values with measured data from Stromboli volcano showed that the model can explain the entire spectrum of observed eruptive styles at Stromboli – from low-energy puffing, through normal Strombolian eruptions, up to paroxysmal explosions – as manifestations of a single underlying physical process. Finally, another suite of laboratory experiments was performed to observe oscillatory pressure and forces variations generated during the expansion and bursting of gas slugs ascending in a conduit. Two end-member boundary conditions were imposed at the base of the pipe, simulating slug ascent in closed base (zero magma flux) and open base (constant flux) conduit. At the top of the pipe, a range of boundary conditions that are relevant at a volcanic vent were imposed, going from open to plugged vent. The results obtained illustrate that a change in boundary conditions in the conduit concur to affect the dynamic of slug expansion and burst: an upward flux at the base of the conduit attenuates the magnitude of the pressure transients, while a rheological stiffening in the top-most region of conduit changes dramatically the magnitude of the observed pressure transients, favoring a sudden, and more energetic pressure release into the overlying atmosphere. Finally, a discussion on the implication of changing boundary on the oscillatory processes generated at the volcanic scale is also given.

Applied deep learning and data science with a human-centric and data-centric approach

The term Artificial intelligence acquired a lot of baggage since its introduction and in its current incarnation is synonymous with Deep Learning. The sudden availability of data and computing resources has opened the gates to myriads of applications. Not all are created equal though, and problems might arise especially for fields not closely related to the tasks that pertain tech companies that spearheaded DL. The perspective of practitioners seems to be changing, however. Human-Centric AI emerged in the last few years as a new way of thinking DL and AI applications from the ground up, with a special attention at their relationship with humans. The goal is designing a system that can gracefully integrate in already established workflows, as in many real-world scenarios AI may not be good enough to completely replace its humans. Often this replacement may even be unneeded or undesirable. Another important perspective comes from, Andrew Ng, a DL pioneer, who recently started shifting the focus of development from “better models” towards better, and smaller, data. He defined his approach Data-Centric AI. Without downplaying the importance of pushing the state of the art in DL, we must recognize that if the goal is creating a tool for humans to use, more raw performance may not align with more utility for the final user. A Human-Centric approach is compatible with a Data-Centric one, and we find that the two overlap nicely when human expertise is used as the driving force behind data quality. This thesis documents a series of case-studies where these approaches were employed, to different extents, to guide the design and implementation of intelligent systems. We found human expertise proved crucial in improving datasets and models. The last chapter includes a slight deviation, with studies on the pandemic, still preserving the human and data centric perspective.

New senthesis and derivatizations of peptidomimetics and peptide-conjugates for theranostic applications

In the contest of a modern green chemistry approach, we firstly tried to substituent the classic peptide synthesis approach with the use of N-carboxyanhydrides in the presence of Hydroxyapatite, a high biocompatible inorganic base. Despite the great results, further developments are necessary for a daily use in laboratory and for our research, we decided to proceed with solid phase or liquid phase synthesis. In the first chapter, the treatment of pain with the use of opioids is introduced. The abuse and misuse of these kind of potent analgesics, led to the necessity of developing new drugs with less side effects. Starting from a previous study, where the introduction of a lactam-like structure in the place of the proline of Endomorphine1, switched the selectivity from MOR to KOR, we designed and synthetized three different libraries by placing a different trans inducer element to gain the desired selectivity and activity forcing the structure to adopt a linear rather than folded position. In the second chapter, we focused on lactate dehydrogenase, an enzyme overexpressed when the cells in hypoxia conditions, like in a tumour mass, need to produce energy through the transformation of pyruvate into lactate. We synthetized different cyclic peptidomimetics, designed to be inhibitors, as powerful tool to contrast cancer cells growing. Biological assays produced satisfactory preliminary results, but further studies are necessary for a definitive output. Finally in the last chapter, the cancer treatment problem is also approached through the design of nanoparticles, able to deliver drugs with efficacy and selectivity. We firstly synthetized silica core nanoparticles, built with toxic peptide sequences conjugated through click chemistry with Pluronic acid and then, in collaboration with Miriam Royo’s research group, we synthetized multivalent platforms for used drugs for the treatment of advanced colorectal cancer.

Novel biomaterials for regeneration of periapical bone defects in endodontic and implant therapy

Endodontic-related periapical bone defects are a common occurrence in the global populations. Considering the number of root canal treatments performed annually, new strategies and new biomaterials for the management of these bone defects will be important and highlight the need for continued research and development in endodontic field. The present PhD thesis have several objectives and is divided into two main sections: one focused on in vitro and laboratory research and the other on clinical in vivo investigations. The first part, focused on laboratory and in vitro research, investigated 2 main topics: • the microbial communities of apical periodontitis to evaluate the predominant bacterial using 16sr DNA-targeted Nanopore sequencing; • the physical-chemical properties of innovative premixed calcium-silicate based bioceramic sealers for endodontic therapy; The second part, focused on in vivo clinical studies, investigated 2 main topics: • the clinical application of premixed calcium-silicate-based sealers. Ethical committee approval was obtained in 2 separate in vivo studies. The first one is a prospective cohort study with a two-year follow-up where the test group was compared with a control group (considered the gold standard). The second is a pilot prospective cohort study with a 12-month follow-up which set the foundation for a subsequent randomized investigation. Thanks to these investigations, we validated a new technique that innovatively associates a warm obturation technique with calcium-silicate-based sealers. Historically, these sealers were only used with cold techniques. This investigation highlights the possibility for wider utilization and improvements in endodontic techniques. • The outcome of 2 different types of implants characterized by different surface treatments and placed with different techniques. The marginal bone level and periodontal parameters were evaluated with a follow-up of 4 and 10 years. This Ph.D thesis is based on a compilation of published papers I have done during my three-year PhD program.

Design, implementation and evaluation of a virtual laboratory for Computer Engineering Education

Broad consensus has been reached within the Education and Cognitive Psychology research communities on the need to center the learning process on experimentation and concrete application of knowledge, rather than on a bare transfer of notions. Several advantages arise from this educational approach, ranging from the reinforce of students learning, to the increased opportunity for a student to gain greater insight into the studied topics, up to the possibility for learners to acquire practical skills and long-lasting proficiency. This is especially true in Engineering education, where integrating conceptual knowledge and practical skills assumes a strategic importance. In this scenario, learners are called to play a primary role. They are actively involved in the construction of their own knowledge, instead of passively receiving it. As a result, traditional, teacher-centered learning environments should be replaced by novel learner-centered solutions. Information and Communication Technologies enable the development of innovative solutions that provide suitable answers to the need for the availability of experimentation supports in educational context. Virtual Laboratories, Adaptive Web-Based Educational Systems and Computer-Supported Collaborative Learning environments can significantly foster different learner-centered instructional strategies, offering the opportunity to enhance personalization, individualization and cooperation. More specifically, they allow students to explore different kinds of materials, to access and compare several information sources, to face real or realistic problems and to work on authentic and multi-facet case studies. In addition, they encourage cooperation among peers and provide support through coached and scaffolded activities aimed at fostering reflection and meta-cognitive reasoning. This dissertation will guide readers within this research field, presenting both the theoretical and applicative results of a research aimed at designing an open, flexible, learner-centered virtual lab for supporting students in learning Information Security.

"Making Sense of Figures": Statistics, Computing and Information Technologies in Agriculture and Biology in Britain, 1920s-1960s

Throughout the twentieth century statistical methods have increasingly become part of experimental research. In particular, statistics has made quantification processes meaningful in the soft sciences, which had traditionally relied on activities such as collecting and describing diversity rather than timing variation. The thesis explores this change in relation to agriculture and biology, focusing on analysis of variance and experimental design, the statistical methods developed by the mathematician and geneticist Ronald Aylmer Fisher during the 1920s. The role that Fisher’s methods acquired as tools of scientific research, side by side with the laboratory equipment and the field practices adopted by research workers, is here investigated bottom-up, beginning with the computing instruments and the information technologies that were the tools of the trade for statisticians. Four case studies show under several perspectives the interaction of statistics, computing and information technologies, giving on the one hand an overview of the main tools – mechanical calculators, statistical tables, punched and index cards, standardised forms, digital computers – adopted in the period, and on the other pointing out how these tools complemented each other and were instrumental for the development and dissemination of analysis of variance and experimental design. The period considered is the half-century from the early 1920s to the late 1960s, the institutions investigated are Rothamsted Experimental Station and the Galton Laboratory, and the statisticians examined are Ronald Fisher and Frank Yates.

When the Practice of Theorizing Meets the Theorizing of Practice. Social Knowledge Making in Organization Science Academia and Managerial Communities

The aim of the present work is to contribute to a better understanding of the relation between organization theory and management practice. It is organized as a collection of two papers, a theoretical and conceptual contribution and an ethnographic study. The first paper is concerned with systematizing different literatures inside and outside the field of organization studies that deal with the theory-practice relation. After identifying a series of positions to the theory-practice debate and unfolding some of their implicit assumptions and limitations, a new position called entwinement is developed in order to overcome status quo through reconciliation and integration. Accordingly, the paper proposes to reconceptualize theory and practice as a circular iterative process of action and cognition, science and common-sense enacted in the real world both by organization scholars and practitioners according to purposes at hand. The second paper is the ethnographic study of an encounter between two groups of expert academics and practitioners occasioned by a one-year executive business master in an international business school. The research articulates a process view of the knowledge exchange between management academics and practitioners in particular and between individuals belonging to different communities of practice, in general, and emphasizes its dynamic, relational and transformative mechanisms. Findings show that when they are given the chance to interact, academics and practitioners set up local provisional relations that enable them to act as change intermediaries vis-a-vis each other’s worlds, without tying themselves irremediably to each other and to the scenarios they conjointly projected during the master’s experience. Finally, the study shows that provisional relations were accompanied by a recursive shift in knowledge modes. While interacting, academics passed from theory to practical theorizing, practitioners passed from an involved practical mode to a reflexive and quasi-theoretical one, and then, as exchanges proceeded, the other way around.