Statistical methods for analysis and processing of medical ultrasound: applications to segmentation and restoration

In this thesis two major topics inherent with medical ultrasound images are addressed: deconvolution and segmentation. In the first case a deconvolution algorithm is described allowing statistically consistent maximum a posteriori estimates of the tissue reflectivity to be restored. These estimates are proven to provide a reliable source of information for achieving an accurate characterization of biological tissues through the ultrasound echo. The second topic involves the definition of a semi automatic algorithm for myocardium segmentation in 2D echocardiographic images. The results show that the proposed method can reduce inter- and intra observer variability in myocardial contours delineation and is feasible and accurate even on clinical data.

Development of an X-ray spectrometric system and feasibility tests of Silicon Drift Detector for medical and space applications

The thesis work concerns X-ray spectrometry for both medical and space applications and is divided into two sections. The first section addresses an X-ray spectrometric system designed to study radiological beams and is devoted to the optimization of diagnostic procedures in medicine. A parametric semi-empirical model capable of efficiently reconstructing diagnostic X-ray spectra in 'middle power' computers was developed and tested. In addition, different silicon diode detectors were tested as real-time detectors in order to provide a real-time evaluation of the spectrum during diagnostic procedures. This project contributes to the field by presenting an improved simulation of a realistic X-ray beam emerging from a common X-ray tube with a complete and detailed spectrum that lends itself to further studies of added filtration, thus providing an optimized beam for different diagnostic applications in medicine. The second section describes the preliminary tests that have been carried out on the first version of an Application Specific Integrated Circuit (ASIC), integrated with large area position-sensitive Silicon Drift Detector (SDD) to be used on board future space missions. This technology has been developed for the ESA project: LOFT (Large Observatory for X-ray Timing), a new medium-class space mission that the European Space Agency has been assessing since February of 2011. The LOFT project was proposed as part of the Cosmic Vision Program (2015-2025).

An experimental and theoretical approach to correct for the scattered radiation in an X-ray computer tomography system for industrial applications

The main problem connected to cone beam computed tomography (CT) systems for industrial applications employing 450 kV X-ray tubes is the high amount of scattered radiation which is added to the primary radiation (signal). This stray radiation leads to a significant degradation of the image quality. A better understanding of the scattering and methods to reduce its effects are therefore necessary to improve the image quality. Several studies have been carried out in the medical field at lower energies, whereas studies in industrial CT, especially for energies up to 450 kV, are lacking. Moreover, the studies reported in literature do not consider the scattered radiation generated by the CT system structure and the walls of the X-ray room (environmental scatter). In order to investigate the scattering on CT projections a GEANT4-based Monte Carlo (MC) model was developed. The model, which has been validated against experimental data, has enabled the calculation of the scattering including the environmental scatter, the optimization of an anti-scatter grid suitable for the CT system, and the optimization of the hardware components of the CT system. The investigation of multiple scattering in the CT projections showed that its contribution is 2.3 times the one of primary radiation for certain objects. The results of the environmental scatter showed that it is the major component of the scattering for aluminum box objects of front size 70 x 70 mm2 and that it strongly depends on the thickness of the object and therefore on the projection. For that reason, its correction is one of the key factors for achieving high quality images. The anti-scatter grid optimized by means of the developed MC model was found to reduce the scatter-toprimary ratio in the reconstructed images by 20 %. The object and environmental scatter calculated by means of the simulation were used to improve the scatter correction algorithm which could be patented by Empa. The results showed that the cupping effect in the corrected image is strongly reduced. The developed CT simulation is a powerful tool to optimize the design of the CT system and to evaluate the contribution of the scattered radiation to the image. Besides, it has offered a basis for a new scatter correction approach by which it has been possible to achieve images with the same spatial resolution as state-of-the-art well collimated fan-beam CT with a gain in the reconstruction time of a factor 10. This result has a high economic impact in non-destructive testing and evaluation, and reverse engineering.

New functionalized ligands for luminescent metal complexes: from design to applications

The synthesis of luminescent metal complexes is a very challenging task since they can be regarded as the starting point for a lot of different areas. Luminescent complexes, in fact, can be used for technological, industrial, medical and biological applications. During my PhD I worked with different metals having distinguishing intrinsic properties that make them different from each other and, in particular, more or less suitable for the different possible uses. Iridium complexes show the best photophysical properties: they have high quantum yields, very long lifetimes and possess easily tunable emissions throughout the visible range. On the other hand, Iridium is very expensive and scarcely available. The aim of my work concerning this metal was, therefore, to synthesize ligands able not only to form luminescent complexes, but also able to add functionalities to the final complex, increasing its properties, and therefore its possible practical uses. Since Re(I) derivatives have been reported to be suitable as probes in biological system, and the use of Re(I) reduces the costs, the synthesized bifunctional ligands containing a pyridine-triazole and a biotin unit were employed to obtain new Re(I) luminescent probes. Part of my work involved the design and synthesis of new ligands able to form stable complexes with Eu(III) and Ce(III) salts, in order to obtain an emission in the range of visible light: these two metals are quite cheap and relatively non-toxic compared to other heavy metals. Finally, I plan to synthesize organic derivatives that already possessed an emission thanks to the presence of other many chromophoric groups and can be able to link the Zinc (II), a low cost and especially non-toxic “green” metal. Zinc has not its own emission, but when it sticks to ligands, it increases their photophysical properties.

Advanced aspects of radiation protection in the use of particle accelerators in the medical field

In this work, the well-known MC code FLUKA was used to simulate the GE PETrace cyclotron (16.5 MeV) installed at “S. Orsola-Malpighi” University Hospital (Bologna, IT) and routinely used in the production of positron emitting radionuclides. Simulations yielded estimates of various quantities of interest, including: the effective dose distribution around the equipment; the effective number of neutron produced per incident proton and their spectral distribution; the activation of the structure of the cyclotron and the vault walls; the activation of the ambient air, in particular the production of 41Ar, the assessment of the saturation yield of radionuclides used in nuclear medicine. The simulations were validated against experimental measurements in terms of physical and transport parameters to be used at the energy range of interest in the medical field. The validated model was also extensively used in several practical applications uncluding the direct cyclotron production of non-standard radionuclides such as 99mTc, the production of medical radionuclides at TRIUMF (Vancouver, CA) TR13 cyclotron (13 MeV), the complete design of the new PET facility of “Sacro Cuore – Don Calabria” Hospital (Negrar, IT), including the ACSI TR19 (19 MeV) cyclotron, the dose field around the energy selection system (degrader) of a proton therapy cyclotron, the design of plug-doors for a new cyclotron facility, in which a 70 MeV cyclotron will be installed, and the partial decommissioning of a PET facility, including the replacement of a Scanditronix MC17 cyclotron with a new TR19 cyclotron.

Development and optimization of techniques and design parameters for the engineering of atmospheric pressure plasma devices for biomedical applications and plasma medicine

In the last decades, the possibility to generate plasma at atmospheric pressure gave rise to a new emerging field called plasma medicine; it deals with the application of cold atmospheric pressure plasmas (CAPs) or plasma-activated solutions on or in the human body for therapeutic effects. Thanks to a blend of synergic biologically active agents and biocompatible temperatures, different CAP sources were successfully employed in many different biomedical applications such as dentistry, dermatology, wound healing, cancer treatment, blood coagulation, etc.… Despite their effectiveness has been verified in the above-mentioned biomedical applications, over the years, researchers throughout the world described numerous CAP sources which are still laboratory devices not optimized for the specific application. In this perspective, the aim of this dissertation was the development and the optimization of techniques and design parameters for the engineering of CAP sources for different biomedical applications and plasma medicine among which cancer treatment, dentistry and bioaerosol decontamination. In the first section, the discharge electrical parameters, the behavior of the plasma streamers and the liquid and the gas phase chemistry of a multiwire device for the treatment of liquids were performed. Moreover, two different plasma-activated liquids were used for the treatment of Epithelial Ovarian Cancer cells and fibroblasts to assess their selectivity. In the second section, in accordance with the most important standard regulations for medical devices, were reported the realization steps of a Plasma Gun device easy to handle and expected to be mounted on a tabletop device that could be used for dental clinical applications. In the third section, in relation to the current COVID-19 pandemic, were reported the first steps for the design, realization, and optimization of a dielectric barrier discharge source suitable for the treatment of different types of bioaerosol.

Novel hydroxystearoyl-, heterocyclic and carbocyclic derivatives: synthesis and applications in biological field

This PhD project has been mainly focused on the synthesis of novel organic compounds containing heterocyclic and/or carbocyclic scaffold and on the study of stearic acid derivatives and their applications in biological field. The synthesis of novel derivatives of 9-hydroxystearic acid (9-HSA) evidenced how the presence of substituents on C9, able to make hydrogen bonds is of crucial importance for the biological activity. Also the position of the hydroxy group along the chain of hydroxystearic acids was investigated: regioisomers with the hydroxy group bound to odd carbons resulted more active than those bearing the hydroxy group on even carbons. Further, the insertion of (R)-9-HSA in magnetic nanoparticles gave a novel material which characterization remarked its suitability for drug delivery. Structural hybrids between amino aza-heterocycles and azelaic acid have been synthesized and some of them showed a selective activity towards osteosarcoma cell line U2OS. Several Apcin analogues bearing indole, benzothiazole, benzofurazan moieties connected to tryptaminyl-, amino pyridinyl-, pyrimidinyl- and pyrazinyl ring through a 1,1,1-trichloroethyl group were synthesized. Biological tests showed the importance of both the tryptaminyl and the pyrimidinyl moieties, confirming the effectiveness against acute leukemia models. The SNAr between 2-aminothiazole derivatives and 7-chlorodinitrobenzofuroxan revealed different behaviour depending from amino substituent of the thiazole. The reaction with 2-N-piperidinyl-, 2-N-morpholinyl-, or 2-N-pyrrolidinyl thiazole gave two isomeric species derived from the attack on C-5 of thiazole ring. Thiazoles substituted with primary- or not-cyclic secondary amines reacted with the exocyclic amino nitrogen atom giving a series of compounds whose biological activity have highlighted as they might be promising candidates for further development of antitumor agents. A series of 9-fluorenylidene derivatives, of interest in medical and optoelectronic field as organic scintillators, was synthesized through Wittig or Suzuky reaction and will be analyzed to test their potential scintillatory properties.

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.

Nanostructured smart materials as functional components of medical devices

The field of medical devices has experienced, more than others, technological advances, developments and innovations, thanks to the rapidly expanding scientific knowledge and collaboration between different disciplines such as biology, engineering and materials science. The design of functional components can be achieved by exploiting composite materials based on nanostructured smart materials, that due to the inherent characteristics of single constituents develop unique properties that make them suitable for different applications preserving excellent mechanical proprieties. For instance, recent developments have focused on the fabrication of piezoelectric devices with multiple biomedical functions, as actuation and sensing functions in one component for monitoring pressure signals. The present Ph.D. Thesis aims at investigating nanostructured smart materials embedded into a polymeric matrix to obtain a composite material that can be used as a functional component for medical devices. (i) Nanostructured piezoelectric material with self-sensing capability was successfully manufactured by using ceramic (i.e. lead zirconate titanate (PZT)) and (ii) polymeric (i.e. poly(vinylidene fluoride-trifluoro ethylene (PVDF-TRFE)) piezoelectric materials. PZT nanofibers were obtained by sol-gel electrospinning starting from synthetized PZT precursor solution. Synthesis, sol-gel electrospinning process, and thermal treatment were accurately controlled to obtain PZT nanofibers dimensionally stable with densely packed grains in the perovskite phase. To guarantee the impact resistance of the laminate, the morphology and size of the hosting filler were accurately designed by increasing the surface area to volume ratio. Moreover, to solve the issue relative to the mechanical discrepancy between rigid electronic materials/soft human tissues/different material of the device (iii) a nanostructured flexible composite material based on a network of Poly-L-lactic acid (PLLA) made of curled nanofibers that present a tuneable mechanical response as a function of the applied stress was successful fabricated.

Chemiluminescence – based bioanalytical devices for astrobiological, food safety and clinical applications

At the intersection of biology, chemistry, and engineering, biosensors are a multidisciplinary innovation that provide a cost-effective alternative to traditional laboratory techniques. Due to their advantages, biosensors are used in medical diagnostics, environmental monitoring, food safety and many other fields. The first part of the thesis is concerned with learning the state of the art of paper-based immunosensors with bioluminescent (BL) and chemiluminescent (CL) detection. The use of biospecific assays combined with CL detection and paper-based technology offers an optimal approach to creating analytical tools for on-site applications and we have focused on the specific areas that need to be considered more in order to ensure a future practical implementation of these methods in routine analyses. The subsequent part of the thesis addresses the development of an autonomous lab-on-chip platform for performing chemiluminescent-based bioassays in space environment, exploiting a CubeSat platform for astrobiological investigations. An origami-inspired microfluidic paper-based analytical device has been developed with the purpose of assesses its performance in space and to evaluate its functionality and the resilience of the (bio)molecules when exposed to a radiation-rich environment. Subsequently, we designed a paper-based assay to detect traces of ovalbumin in food samples, creating a user-friendly immunosensing platform. To this purpose, we developed an origami device that exploits a competitive immunoassay coupled with chemiluminescence detection and magnetic microbeads used to immobilize ovalbumin on paper. Finally, with the aim of exploring the use of biomimetic materials, an hydrogel-based chemiluminescence biosensor for the detection of H2O2 and glucose was developed. A guanosine hydrogel was prepared and loaded with luminol and hemin, miming a DNAzyme activity. Subsequently, the hydrogel was modified by incorporating glucose oxidase enzyme to enable glucose biosensing. The emitted photons were detected using a portable device equipped with a smartphone's CMOS (complementary metal oxide semiconductor) camera for CL emission detection.

Regularization meets GreenAI: a new framework for image reconstruction in life sciences applications

Ill-conditioned inverse problems frequently arise in life sciences, particularly in the context of image deblurring and medical image reconstruction. These problems have been addressed through iterative variational algorithms, which regularize the reconstruction by adding prior knowledge about the problem's solution. Despite the theoretical reliability of these methods, their practical utility is constrained by the time required to converge. Recently, the advent of neural networks allowed the development of reconstruction algorithms that can compute highly accurate solutions with minimal time demands. Regrettably, it is well-known that neural networks are sensitive to unexpected noise, and the quality of their reconstructions quickly deteriorates when the input is slightly perturbed. Modern efforts to address this challenge have led to the creation of massive neural network architectures, but this approach is unsustainable from both ecological and economic standpoints. The recently introduced GreenAI paradigm argues that developing sustainable neural network models is essential for practical applications. In this thesis, we aim to bridge the gap between theory and practice by introducing a novel framework that combines the reliability of model-based iterative algorithms with the speed and accuracy of end-to-end neural networks. Additionally, we demonstrate that our framework yields results comparable to state-of-the-art methods while using relatively small, sustainable models. In the first part of this thesis, we discuss the proposed framework from a theoretical perspective. We provide an extension of classical regularization theory, applicable in scenarios where neural networks are employed to solve inverse problems, and we show there exists a trade-off between accuracy and stability. Furthermore, we demonstrate the effectiveness of our methods in common life science-related scenarios. In the second part of the thesis, we initiate an exploration extending the proposed method into the probabilistic domain. We analyze some properties of deep generative models, revealing their potential applicability in addressing ill-posed inverse problems.