Solutions to common issues in widefield microscopy: vignetting, mosaicing and depth of focus

In this thesis we have developed solutions to common issues regarding widefield microscopes, facing the problem of the intensity inhomogeneity of an image and dealing with two strong limitations: the impossibility of acquiring either high detailed images representative of whole samples or deep 3D objects. First, we cope with the problem of the non-uniform distribution of the light signal inside a single image, named vignetting. In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any prior information. After getting flat-field corrected images, we studied how to fix the problem related to the limitation of the field of view of the camera, so to be able to acquire large areas at high magnification. To this purpose, we developed mosaicing techniques capable to work on-line. Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images. Finally, we worked to virtually extend the field of view of the camera in the third dimension, with the purpose of reconstructing a single image completely in focus, stemming from objects having a relevant depth or being displaced in different focus planes. After studying the existing approaches for extending the depth of focus of the microscope, we proposed a general method that does not require any prior information. In order to compare the outcome of existing methods, different standard metrics are commonly used in literature. However, no metric is available to compare different methods in real cases. First, we validated a metric able to rank the methods as the Universal Quality Index does, but without needing any reference ground truth. Second, we proved that the approach we developed performs better in both synthetic and real cases.

Phenotypic and molecular characterization of ethylene biosynthesis in apples

Ethylene plays an important role in apple fruit development. Its biosynthesis is catalyzed by two enzymes ACS and ACO. The first is considered to catalyzes the rate-limiting step of ethylene production and in apple two different alleles (MdACS1-1 and MdACS1-2) of this gene have been identified. The presence in the promoter region of MdACS1-2 allele of a SINE insertion is considered to be responsible for a low transcription level and a pronounced reduction in ethylene production in apple cultivar homozygous for this allele. However, the specific expression of each MdACS1 allele has never been reported as well as any in vivo analysis of its 5’-flanking region. With the present study we addressed these issues by developing a set of qPCR allele specific primers for MdACS1 and by a functional characterization of the MdACS1 promoters by transient expression analysis. qPCR analysis on different apple tissues and stages of development demonstrated that MdACS1-2 allele is never express and that MdACS1-1 allele is ripening-related and expresses predominantly but not exclusively in apple fruit. To test MdACS1 promoter in fruit the only protocol available in literature for transient transformation of apple fruit was evaluated and optimized. Twenty chimeric promoter::reporter constructs were generated and analyzed by Agrobacterium-transient transformation. The in vivo analysis allowed to identify an enhancer-like region of 261 bp in MdACS1 promoter and a region of 57 bp in MdACS1-2 responsible, also if not alone, in the inactivation of the MdACS1-2 allele. Through the assessment of ethylene production in a segregating progeny derived from the cross between Fuji and Mondial Gala (homozygous for MdACS1-2 allele) we demonstrated that at least two other genes may be involved in apple ethylene production. An hypothesis that could explain the difference between Fuji and Mondial Gala have been proposed.

Characterization of fold-related fractures in the carbonate rocks of the Cingoli anticline, northern Apennines, Italy

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different structures, such as joints, faults, pressure solution seams, and deformation bands. Defining the development of fracture systems related to the folding process is significant both for theoretical and practical purposes. Fracture systems are useful constrains in order to understand the kinematical evolution of the fold. Furthermore, understanding the relationships between folding and fracturing provides a noteworthy contribution for reconstructing the geodynamic and the structural evolution of the studied area. Moreover, as fold-related fractures influence fluid flow through rocks, fracture systems are relevant for energy production (geothermal studies, methane and CO2 , storage and hydrocarbon exploration), environmental and social issues (pollutant distribution, aquifer characterization). The PhD project shows results of a study carried out in a multilayer carbonate anticline characterized by different mechanical properties. The aim of this study is to understand the factors which influence the fracture formation and to define their temporal sequence during the folding process. The studied are is located in the Cingoli anticline (Northern Apennines), which is characterized by a pelagic multilayer characterized by sequences with different mechanical stratigraphies. A multi-scale analysis has been made in several outcrops located in different structural positions. This project shows that the conceptual sketches proposed in literature and the strain distribution models outline well the geometrical orientation of most of the set of fractures observed in the Cingoli anticline. On the other hand, the present work suggests the relevance of the mechanical stratigraphy in particular controlling the type of fractures formed (e.g. pressure solution seams, joints or shear fractures) and their subsequent evolution. Through a multi-scale analysis, and on the basis of the temporal relationship between fracture sets and their orientation respect layering, I also suggest a conceptual model for fracture systems formation.

Evaluation of Human Exposure to Magnetic Fields Generated by Electric Power Systems in Complex Configurations

The international growing concern for the human exposure to magnetic fields generated by electric power lines has unavoidably led to imposing legal limits. Respecting these limits, implies being able to calculate easily and accurately the generated magnetic field also in complex configurations. Twisting of phase conductors is such a case. The consolidated exact and approximated theory regarding a single-circuit twisted three-phase power cable line has been reported along with the proposal of an innovative simplified formula obtained by means of an heuristic procedure. This formula, although being dramatically simpler, is proven to be a good approximation of the analytical formula and at the same time much more accurate than the approximated formula found in literature. The double-circuit twisted three-phase power cable line case has been studied following different approaches of increasing complexity and accuracy. In this framework, the effectiveness of the above-mentioned innovative formula is also examined. The experimental verification of the correctness of the twisted double-circuit theoretical analysis has permitted its extension to multiple-circuit twisted three-phase power cable lines. In addition, appropriate 2D and, in particularly, 3D numerical codes for simulating real existing overhead power lines for the calculation of the magnetic field in their vicinity have been created. Finally, an innovative ‘smart’ measurement and evaluation system of the magnetic field is being proposed, described and validated, which deals with the experimentally-based evaluation of the total magnetic field B generated by multiple sources in complex three-dimensional arrangements, carried out on the basis of the measurement of the three Cartesian field components and their correlation with the field currents via multilinear regression techniques. The ultimate goal is verifying that magnetic induction intensity is within the prescribed limits.

Diversity of the proximal femur in humans: morphological variations of the head-neck junction

The proximal femur is a high-diversity region of the human skeleton, especially at the anterior junction between head and neck, where various bony morphologies have been recognized since mid nineteenth century. Classical literature on this topic is chaotic and contradictory, making almost impossible the comparison of data from different researches. Starting from an extensive bibliographic review, the first standardized method to score these traits has been created. This method allows representing both the anatomical diversity of the region already described in literature and a part of variability not considered before, giving few and univocal definitions and allowing to collect comparable data. The method has been applied to three identified and five archaeological European skeletal collections, with the aim of investigating the distribution of these features by sex, age and side, in different places and time periods. It has also been applied to 3D digital reconstructions of femurs from CT scan files of coxo-femoral joints from fresh cadavers. In addition to the osseous traits described in the standardized method, the presence and frequency of some features known as herniation pits have been scored both on bones and on CT scans. The various osseous traits of the proximal femur are present at similar frequencies in skeletal samples from different countries and different historical periods, even if with clear local differentiation. Some of the features examined show significant trends related to their distribution by gender and age. Some hypotheses are proposed about the etiology of these morphologies and their possible implication with the acquisition of bipedalism in Humans. It is therefore highlighted the possible relation of some of these traits with the development of disorders of the hip joint. Moreover, it is not recommended the use of any of these features as a specific activity-related marker.

Effect of different management intensities on natural and human-induced carbon fluxes in a golf course in northern Italy

Turfgrasses are ubiquitous in urban landscape and their role on carbon (C) cycle is increasing important also due to the considerable footprint related to their management practices. It is crucial to understand the mechanisms driving the C assimilation potential of these terrestrial ecosystems Several approaches have been proposed to assess C dynamics: micro-meteorological methods, small-chamber enclosure system (SC), chrono-sequence approach and various models. Natural and human-induced variables influence turfgrasses C fluxes. Species composition, environmental conditions, site characteristics, former land use and agronomic management are the most important factors considered in literature driving C sequestration potential. At the same time different approaches seem to influence C budget estimates. In order to study the effect of different management intensities on turfgrass, we estimated net ecosystem exchange (NEE) through a SC approach in a hole of a golf course in the province of Verona (Italy) for one year. The SC approach presented several advantages but also limits related to the measurement frequency, timing and duration overtime, and to the methodological errors connected to the measuring system. Daily CO2 fluxes changed according to the intensity of maintenance, likely due to different inputs and disturbances affecting biogeochemical cycles, combined also to the different leaf area index (LAI). The annual cumulative NEE decreased with the increase of the intensity of management. NEE was related to the seasonality of turfgrass, following temperatures and physiological activity. Generally on the growing season CO2 fluxes towards atmosphere exceeded C sequestered. The cumulative NEE showed a system near to a steady state for C dynamics. In the final part greenhouse gases (GHGs) emissions due to fossil fuel consumption for turfgrass upkeep were estimated, pinpointing that turfgrass may result a considerable C source. The C potential of trees and shrubs needs to be considered to obtain a complete budget.

Topics in Local Economic Development

This thesis contributes to the current debate in literature about local economic development by considering two different topics: quality of institutions, and the role of clusters in innovation and productivity growth. The research is built upon three papers. The first paper deals with the analysis of the effect of administrative continuity on administrative efficiency. The analysis underlines the importance of different typologies of social capital. Findings reveal a positive impact on administrative efficiency (AE) by administrative continuity (AC) when it is coupled by bridging and linking social capital. On the contrary, bonding social capital influences negatively the effect by AC on AE. The second paper investigates the spatial interaction in levels of quality of government (QoG) among European regions. Notwithstanding the largely recognised role by institutions in the design of regional policies, no study has been conducted about the mechanisms of interaction and diffusion of QoG at regional level. This research wants to overcome this knowledge gap in literature. Findings reveal a heterogeneity in spatial interaction among groups of regions, i.e. ‘leader regions’ (Northern regions) and ‘lagging regions’ (Southern regions), when considering different mechanisms of interaction (learning / imitating competition and pure competition). Moreover, the effect of wealth on the levels of QoG is nonlinear. Finally, the third paper analyses the relation among specialization and productivity within the agricultural sector. In literature, the study of clusters dynamics has long neglected agriculture. The analysis describes the changes in sectorial specialization for eight main crop groups in Italian regions (NUTS 3), assessing the existence of spatial autocorrelations by using an exploratory data analysis. Furthermore, the effect of specialization on productivity is analysed within the main crop groups using a spatial panel data model. Findings reveal a marked tendency to specialization in the Italian agriculture, and a heterogeneous effect by specialization on productivity.

Guidelines of Special Care Dentistry in Patients with Chromosomal and Genetic syndromes

Chromosomal and genetic syndromes are frequently associated with dental and cranio-facial alterations. The aim of our study is to identify and describe the dental and craniofacial alterations typical of six genetic and chromosomal syndromes examined. Materials and Methods- A dental visit was performed to 195 patients referred from Sant’Orsola Hospital of Bologna, University of Bologna, to Service of Special Need Dentistry, Dental Clinic, Department of Biomedical and Neuromotor Science, University of Bologna. The patients recruited were 137 females and 58 males, in an age range of 3-49 years (mean age of 13.8±7.4). The total sample consisted of subjects affected with Down Syndrome (n=133), Familiar Hypophosphatemic Ricket (n=10), Muscular Dystrophies (n=12), Noonan Syndrome (n=13), Turner Syndrome (n=17), Williams Syndrome(n=10). A questionnaire regarding detailed medical and dental history, oral health and dietary habits, was filled by parents/caregivers, or patients themselves when possible. The intra-oral and extra-oral examination valued the presence of facial asymmetries, oral habits, dental and skeletal malocclusions, dental formula, dental anomalies, Plaque Index (Silness&LÖe Index), caries prevalence (dmft/DMFT index), gingivitis and periodontal disease, and mucosal lesions. Radiographic examinations (Intraoral radiographies, Orthopanoramic, Skull teleradiography) were executed according to patient’s age and treatment planning. A review of literature about each syndrome and its dental and cranio-facial characteristics and about caries, hygiene status and malocclusion prevalence on syndromic and non-syndromic population was performed. Results - The data of all the patients were collected in the “Data Collection Tables” created for each syndrome. General anamnesis information, oral hygiene habits and dmft/DMFT, PI, malocclusion prevalence were calculated and compared to syndromic and non-syndromic population results found in literature. Discussions and conclusions - Guidelines of Special Care dentistry were indicated for each syndrome, in relation to each syndrome features and individual patient characteristics.

Energy-efficient Communication and Estimation in Wireless Sensor Networks

This thesis focuses on the energy efficiency in wireless networks under the transmission and information diffusion points of view. In particular, on one hand, the communication efficiency is investigated, attempting to reduce the consumption during transmissions, while on the other hand the energy efficiency of the procedures required to distribute the information among wireless nodes in complex networks is taken into account. For what concerns energy efficient communications, an innovative transmission scheme reusing source of opportunity signals is introduced. This kind of signals has never been previously studied in literature for communication purposes. The scope is to provide a way for transmitting information with energy consumption close to zero. On the theoretical side, starting from a general communication channel model subject to a limited input amplitude, the theme of low power transmission signals is tackled under the perspective of stating sufficient conditions for the capacity achieving input distribution to be discrete. Finally, the focus is shifted towards the design of energy efficient algorithms for the diffusion of information. In particular, the endeavours are aimed at solving an estimation problem distributed over a wireless sensor network. The proposed solutions are deeply analyzed both to ensure their energy efficiency and to guarantee their robustness against losses during the diffusion of information (against information diffusion truncation more in general).

Experimental Project on the Safety and the Optimization of the Use of Glyphosate-Based Herbicides in the Grain Sector.

INTRODUCTION: Glyphosate is the most widely applied pesticide worldwide and it is an active ingredient of all glyphosate-based herbicides (GBHs), including in the formulation “Roundup” . It is unclear if the glyphosate present in ground water can be absorbed and translocated in different parts of the pants, particularly wheat plants. This indeed represents an important aspect for productivity (being this a powerful herbicide) and organic certification of the products (the use of glyphosate is not admitted in organic farming and the ubiquitous contamination of glyphosate in water might in theory affect the level of glyphosate in the plants). Overall, epidemiological, in vivo and in vitro studies available in literature present conflicting findings on the safety of glyphosate. METHODS: The work performed for this PhD thesis aimed to experimentally test the root absorption and the eventual translocation of the glyphosate herbicide in the different parts of the wheat plant (Triticum durum) starting from ground water. Furthermore we aimed to experimentally test the effects of the exposure to GBHs at doses of glyphosate considered to be “safe”, the US ADI of 1.75 mg/kg bw/day, defined as the chronic Reference Dose (cRfD) determined by the US EPA, in in vivo models (Sprague-Dawley rats) and in vitro models (Caco2 and L929). RESULTS: All the experimental absorption studies on wheat plants performed have given negative results in terms of the presence of glyphosate or AMPA in the grain of durum wheat. On the other hand the experimental safety studies on in vitro and in vivo models highlighted different effects at doses currently considered safe for humans and with no effects in animals. CONCLUSION: Overall the integration of the findings from absorption in plants and safety studies will serve as solid evidence-base for risk assessment and productive strategies for agriculture.

Sleep disorders in Multiple System Atrophy: a longitudinal study

Introduction: A higher frequency of sleep and breathing disorders in Multiple System Atrophy (MSA) populations is documented in literature. The analysis of disease progression and prognosis in patients with sleep and breathing disorders could shed light on specific neuropathology and pathophysiology of MSA. Objective: To characterize sleep disorders and their longitudinal modifications during disease course in MSA patients, and to determine their prognostic value. Methods: This is a retrospective and prospective cohort study including 182 MSA patients (58.8% males). Type of onset was defined by the first reported motor or autonomic symptom/sign related to MSA. The occurrence of symptoms/signs and milestones of disease progression and their latency were collected. REM sleep behaviour disorder (RBD) and stridor were video-polysomnography (VPSG)-confirmed. VPSG recordings were analysed in a standardized fashion during the disease course. Survival data were based on time to death from the first symptom of disease. Results: Isolated RBD represented the first MSA symptom in 30% of patients, preceding disease onset according to international criteria with a median of 3(1–5) years. Patients developing early stridor or presenting with RBD at disease onset showed a more rapid and severe disease progression. These features had independent negative prognostic value for survival. Sleep architecture was characterized by peculiar features which could represent negative markers in MSA prognosis. Patients with stridor treated with tracheostomy showed a reduced risk of death. Conclusions: This is one of the first studies focusing on longitudinal progression of sleep in MSA. Sleep disorders are key features of disease, playing a role in presentation, prognosis and progression. In our MSA cohort, RBD represented the most frequent mode of disease presentation. Moreover, some specific clinical and instrumental sleep features could represent a hallmark of MSA and could be involved in prognosis and, in particular, in sudden death and death during sleep.

A 3D biomimetic in vitro model: a novel strategy to investigate glioma biology

Gliomas are one of the most frequent primary malignant brain tumors. Acquisition of stem-like features likely contributes to the malignant nature of high-grade gliomas and may be responsible for the initiation, growth, and recurrence of these tumors. In this regard, although the traditional 2D cell culture system has been widely used in cancer research, it shows limitations in maintaining the stemness properties of cancer and in mimicking the in vivo microenvironment. In order to overcome these limitations, different three-dimensional (3D) culture systems have been developed to mimic better the tumor microenvironment. Cancer cells cultured in 3D structures may represent a more reliable in vitro model due to increased cell-cell and cell-extracellular matrix (ECM) interaction. Several attempts to recreate brain cancer tissue in vitro are described in literature. However, to date, it is still unclear which main characteristics the ideal model should reproduce. The overall goal of this project was the development of a 3D in vitro model able to reproduce the brain ECM microenvironment and to recapitulate pathological condition for the study of tumor stroma interactions, tumor invasion ability, and molecular phenotype of glioma cells. We performed an in silico bioinformatic analysis using GEPIA2 Software to compare the expression level of seven matrix protein in the LGG tumors with healthy tissues. Then, we carried out a FFPE retrospective study in order to evaluate the percentage of expression of selected proteins. Thus, we developed a 3D scaffold composed by Hyaluronic Acid and Collagen IV in a ratio of 50:50. We used two astrocytoma cell lines, HTB-12 and HTB-13. In conclusion, we developed an in vitro 3D model able to reproduce the composition of brain tumor ECM, demonstrating that it is a feasible platform to investigate the interaction between tumor cells and the matrix.

Fluorogenic hyaluronan-based probe: characterization and use in advanced microscopy

Among all, the application of nanomaterials in biomedical research and most recently in the environmental one has opened the fields of nanomedicine and nanoremediation. Sensing methods based on fluorescence optical probe are generally requested for their selectivity, sensitivity. However, most imaging methods in literature rely on a fluorescent covalent labelling of the system. Therefore, the main aim of this project was to synthetise a biocompatible fluorogenic hyaluronan probe (HA) polymer functionalised with a rhomadine B (RB) moieties and study its behaviour as an optical probe with different materials with microscopy techniques. A derivatization of HA with RB (HA-RB) was successfully obtained providing a photophysical characterization showing a particular fluorescence mechanism of the probe. Firstly, we tested the interaction with different lab-grade micro and nanoplastics in water. Thanks to the peculiar photophysical behaviour of the probe nanoplastics can be detected with confocal microscopy and more interestingly their nature can be discriminated based on the fluorescence lifetime decay with FLIM microscopy. After, the interaction of a model plant derived metabolic enzyme GAPC1 undergoing oxidative-triggered aggregation was explored with the HA-RB. We highlighted the probe interaction with the protein even at early stage of the kinetic. Moreover, nanoparticle tracking analysis (NTA) experiment demonstrates that the probe is in fact able to interact with the small pre-aggregates in the early stage of the aggregation kinetic. Ultimately, we focused on the possibility to apply the probe in a super resolution microscopy technique, PALM, exploiting its aspecific interaction to characterize the surface topography of PTFE polydisperse microplastics. Optimal conditions were reached at high concentration of the probe (70 nM) where 0.5-5 nM is always advisable for this technique. Thanks to the polymeric nature and fluorescence mechanism of the probe, this technique was able to reveal features of PTFE surface under the diffraction limit (< 250 nm).