Methodological improvement of 3D fluoroscopic analysis for the robust quantification of 3D kinematics of human joints

3D video-fluoroscopy is an accurate but cumbersome technique to estimate natural or prosthetic human joint kinematics. This dissertation proposes innovative methodologies to improve the 3D fluoroscopic analysis reliability and usability. Being based on direct radiographic imaging of the joint, and avoiding soft tissue artefact that limits the accuracy of skin marker based techniques, the fluoroscopic analysis has a potential accuracy of the order of mm/deg or better. It can provide fundamental informations for clinical and methodological applications, but, notwithstanding the number of methodological protocols proposed in the literature, time consuming user interaction is exploited to obtain consistent results. The user-dependency prevented a reliable quantification of the actual accuracy and precision of the methods, and, consequently, slowed down the translation to the clinical practice. The objective of the present work was to speed up this process introducing methodological improvements in the analysis. In the thesis, the fluoroscopic analysis was characterized in depth, in order to evaluate its pros and cons, and to provide reliable solutions to overcome its limitations. To this aim, an analytical approach was followed. The major sources of error were isolated with in-silico preliminary studies as: (a) geometric distortion and calibration errors, (b) 2D images and 3D models resolutions, (c) incorrect contour extraction, (d) bone model symmetries, (e) optimization algorithm limitations, (f) user errors. The effect of each criticality was quantified, and verified with an in-vivo preliminary study on the elbow joint. The dominant source of error was identified in the limited extent of the convergence domain for the local optimization algorithms, which forced the user to manually specify the starting pose for the estimating process. To solve this problem, two different approaches were followed: to increase the optimal pose convergence basin, the local approach used sequential alignments of the 6 degrees of freedom in order of sensitivity, or a geometrical feature-based estimation of the initial conditions for the optimization; the global approach used an unsupervised memetic algorithm to optimally explore the search domain. The performances of the technique were evaluated with a series of in-silico studies and validated in-vitro with a phantom based comparison with a radiostereometric gold-standard. The accuracy of the method is joint-dependent, and for the intact knee joint, the new unsupervised algorithm guaranteed a maximum error lower than 0.5 mm for in-plane translations, 10 mm for out-of-plane translation, and of 3 deg for rotations in a mono-planar setup; and lower than 0.5 mm for translations and 1 deg for rotations in a bi-planar setups. The bi-planar setup is best suited when accurate results are needed, such as for methodological research studies. The mono-planar analysis may be enough for clinical application when the analysis time and cost may be an issue. A further reduction of the user interaction was obtained for prosthetic joints kinematics. A mixed region-growing and level-set segmentation method was proposed and halved the analysis time, delegating the computational burden to the machine. In-silico and in-vivo studies demonstrated that the reliability of the new semiautomatic method was comparable to a user defined manual gold-standard. The improved fluoroscopic analysis was finally applied to a first in-vivo methodological study on the foot kinematics. Preliminary evaluations showed that the presented methodology represents a feasible gold-standard for the validation of skin marker based foot kinematics protocols.

Spectral-Element and Adjoint 3D Full-Wave Tomography for the Lithosphere of Central Italy

The primary objective of this thesis is to obtain a better understanding of the 3D velocity structure of the lithosphere in central Italy. To this end, I adopted the Spectral-Element Method to perform accurate numerical simulations of the complex wavefields generated by the 2009 Mw 6.3 L’Aquila event and by its foreshocks and aftershocks together with some additional events within our target region. For the mainshock, the source was represented by a finite fault and different models for central Italy, both 1D and 3D, were tested. Surface topography, attenuation and Moho discontinuity were also accounted for. Three-component synthetic waveforms were compared to the corresponding recorded data. The results of these analyses show that 3D models, including all the known structural heterogeneities in the region, are essential to accurately reproduce waveform propagation. They allow to capture features of the seismograms, mainly related to topography or to low wavespeed areas, and, combined with a finite fault model, result into a favorable match between data and synthetics for frequencies up to ~0.5 Hz. We also obtained peak ground velocity maps, that provide valuable information for seismic hazard assessment. The remaining differences between data and synthetics led us to take advantage of SEM combined with an adjoint method to iteratively improve the available 3D structure model for central Italy. A total of 63 events and 52 stations in the region were considered. We performed five iterations of the tomographic inversion, by calculating the misfit function gradient - necessary for the model update - from adjoint sensitivity kernels, constructed using only two simulations for each event. Our last updated model features a reduced traveltime misfit function and improved agreement between data and synthetics, although further iterations, as well as refined source solutions, are necessary to obtain a new reference 3D model for central Italy tomography.

La Ricostruzione 3D di Bologna nel XVI Secolo

Il lavoro presentato ha come oggetto la ricostruzione tridimensionale della città di Bologna nella sua fase rinascimentale. Tale lavoro vuole fornire un modello 3D delle architetture e degli spazi urbani utilizzabile sia per scopi di ricerca nell’ambito della storia delle città sia per un uso didattico-divulgativo nel settore del turismo culturale. La base del lavoro è una fonte iconografica di grande importanza: l’affresco raffigurante Bologna risalente al 1575 e situato in Vaticano; questa è una veduta a volo d’uccello di grandi dimensioni dell’intero tessuto urbano bolognese all’interno della terza cerchia di mura. In esso sono rappresentate in maniera particolareggiata le architetture civili e ecclesiastiche, gli spazi ortivi e cortilivi interni agli isolati e alcune importanti strutture urbane presenti in città alla fine del Cinquecento, come l’area portuale e i canali interni alla città, oggi non più visibili. La ricostruzione tridimensionale è stata realizzata tramite Blender, software per la modellazione 3D opensource, attraverso le fasi di modellazione, texturing e creazione materiali (mediante campionamento delle principali cromie presenti nell’affresco), illuminazione e animazione. Una parte della modellazione è stata poi testata all’interno di un GIS per verificare l’utilizzo delle geometrie 3D come elementi collegabili ad altre fonti storiche relative allo sviluppo urbano e quindi sfruttabili per la ricerca storica. Grande attenzione infine è stata data all’uso dei modelli virtuali a scopo didattico-divulgativo e per il turismo culturale. La modellazione è stata utilizzata all’interno di un motore grafico 3D per costruire un ambiente virtuale interattivo nel quale un utente anche non esperto possa muoversi per esplorare gli spazi urbani della Bologna del Cinquecento. In ultimo è stato impostato lo sviluppo di un’applicazione per sistemi mobile (Iphone e Ipad) al fine di fornire uno strumento per la conoscenza della città storica in mobilità, attraverso la comparazione dello stato attuale con quello ricostruito virtualmente.

L'area dei Lungarni di Pisa nel tardo Medioevo (XIV-XV secolo). un tentativo di ricostruzione in 3D.

Lo scopo di questa ricerca è la ricostruzione dei Lungarni di Pisa nel Tardo Medioevo (XIV-XV secolo); lo studio intende sottolineare le trasformazioni urbanistiche che hanno cambiato il volto di Pisa nel corso del tempo e ricordare che l’area fluviale ebbe un ruolo di primo piano come baricentro commerciale ed economico della città, vocazione che si è in gran parte persa con l’età moderna e contemporanea. La metodologia seguita, affinata e perfezionata durante la partecipazione al progetto Nu.M.E. (Nuovo Museo Elettronico della Città di Bologna), si basa sull’analisi e il confronto di fonti eterogenee ma complementari, che includono precedenti studi di storia dell’urbanistica, un corpus di documentazione di epoca medievale (provvedimenti amministrativi come gli Statuti del Comune di Pisa, ma anche descrizioni di cronisti e viaggiatori), fonti iconografiche, tra cui vedute e mappe cinquecentesche o successive, e fonti materiali, come le persistenze medievali ancora osservabili all’interno degli edifici ed i reperti rinvenuti durante alcune campagne di scavo archeologiche. Il modello 3D non è concepito come statico e “chiuso”, ma è liberamente esplorabile all’interno di un engine tridimensionale; tale prodotto può essere destinato a livelli di utenza diversi, che includono sia studiosi e specialisti interessati a conoscere un maggior numero di informazioni e ad approfondire la ricerca, sia semplici cittadini appassionati di storia o utenti più giovani, come studenti di scuole medie superiori e inferiori.

3D nanostructured microcarriers for cell therapy in regenerative medicine

Supercritical Emulsion Extraction technology (SEE-C) was proposed for the production of poly-lactic-co-glycolic acid microcarriers. SEE-C operating parameters as pressure, temperature and flow rate ratios were analyzed and the process performance was optimized in terms of size distribution and encapsulation efficiency. Microdevices loaded with bovine serum insulin were produced with different sizes (2 and 3 µm) or insulin charges (3 and 6 mg/g) and with an encapsulation efficiency of 60%. The microcarriers were characterized in terms of insulin release profile in two different media (PBS and DMEM) and the diffusion and degradation constants were also estimated by using a mathematical model. PLGA microdevices were also used in a cultivation of embryonic ventricular myoblasts (cell line H9c2 obtained from rat) in a FBS serum free medium to monitor cell viability and growth in dependence of insulin released. Good cell viability and growth were observed on 3 µm microdevices loaded with 3 mg/g of insulin. PLGA microspheres loaded with growth factors (GFs) were charged into alginate scaffold with human Mesenchimal Steam Cells (hMSC) for bone tissue engineering with the aim of monitoring the effect of the local release of these signals on cells differentiation. These “living” 3D scaffolds were incubated in a direct perfusion tubular bioreactor to enhance nutrient transport and exposing the cells to a given shear stress. Different GFs such as, h-VEGF, h-BMP2 and a mix of two (ratio 1:1) were loaded and alginate beads were recovered from dynamic (tubular perfusion system bioreactor) and static culture at different time points (1st, 7th, 21st days) for the analytical assays such as, live/dead; alkaline phosphatase; osteocalcin; osteopontin and Van Kossa Immunoassay. The immunoassay confirmed always a better cells differentiation in the bioreactor with respect to the static culture and revealed a great influence of the BMP-2 released in the scaffold on cell differentiation.

Toward a 3D in vitro model based on decellularized thymus to maintain adult thymic ephitelial cells functionality

During my PhD,I have been develop an innovative technique to reproduce in vitro the 3D thymic microenvironment, to be used for growth and differentiation of thymocytes, and possible transplantation replacement in conditions of depressed thymic immune regulation. The work has been developed in the laboratory of Tissue Engineering at the University Hospital in Basel, Switzerland, under the tutorship of Prof.Ivan Martin. Since a number of studies have suggested that the 3D structure of the thymic microenvironment might play a key role in regulating the survival and functional competence of thymocytes, I’ve focused my effort on the isolation and purification of the extracellular matrix of the mouse thymus. Specifically, based on the assumption that TEC can favour the differentiation of pre-T lymphocytes, I’ve developed a specific decellularization protocol to obtain the intact, DNA-free extracellular matrix of the adult mouse thymus. Two different protocols satisfied the main characteristics of a decellularized matrix, according to qualitative and quantitative assays. In particular, the quantity of DNA was less than 10% in absolute value, no positive staining for cells was found and the 3D structure and composition of the ECM were maintained. In addition, I was able to prove that the decellularized matrixes were not cytotoxic for the cells themselves, and were able to increase expression of MHC II antigens compared to control cells grown in standard conditions. I was able to prove that TECs grow and proliferate up to ten days on top the decellularized matrix. After a complete characterization of the culture system, these innovative natural scaffolds could be used to improve the standard culture conditions of TEC, to study in vitro the action of different factors on their differentiation genes, and to test the ability of TECs to induce in vitro maturation of seeded T lymphocytes.

Effetto dell'analgesia epidurale sulla progressione della testa fetale valutata mediante ecografia 3D

Introduzione: L'analgesia epidurale è stata messa in correlazione con l'aumento della durata del secondo stadio del travaglio e del tasso di utilizzo della ventosa ostetrica. Diversi meccanismi sono stati ipotizzati, tra cui la riduzione di percezione della discesa fetale, della forza di spinta e dei riflessi che promuovono la progressione e rotazione della testa fetale nel canale del parto. Tali parametri sono solitamente valutati mediante esame clinico digitale, costantemente riportato essere poco accurato e riproducibile. Su queste basi l'uso dell'ecografia in travaglio, con introduzione di diversi parametri ecografici di valutazione della discesa della testa fetale, sono stati proposti per supportare la diagnosi clinica nel secondo stadio del travaglio. Scopi dello studio: studiare effetto dell’analgesia epidurale sulla progressione della testa fetale durante il II stadio del travaglio valutata mediante ecografia intrapartum. Materiali e metodi: una serie di pazienti nullipare a basso rischio a termine (37+0-42+0) sono state reclutate in modo prospettico nella sala parto del nostro Policlinico Universitario. In ciascuna di esse abbiamo acquisito un volume ecografico ogni 20 minuti dall’inizio della fase attiva del secondo stadio fino al parto ed una serie di parametri ecografici sono stati ricavati in un secondo tempo (angolo di progressione, distanza di progressione distanza testa sinfisi pubica e midline angle). Tutti questi parametri sono stati confrontati ad ogni intervallo di tempo nei due gruppi. Risultati: 71 pazienti totali, di cui 41 (57.7%) con analgesia epidurale. In 58 (81.7%) casi il parto è stato spontaneo, mentre in 8 (11.3%) e 5 (7.0%) casi rispettivamente si è ricorsi a ventosa ostetrica o taglio cesareo. I valori di tutti i parametri ecografici misurati sono risultati sovrapponibili nei due gruppi in tutti gli intervalli di misurazione. Conclusioni: la progressione della testa fetale valutata longitudinalmente mediante ecografia 3D non sembra differire significativamente nelle pazienti con o senza analgesia epidurale.

Towards the 3D attenuation imaging of active volcanoes: methods and tests on real and simulated data

The purpose of my PhD thesis has been to face the issue of retrieving a three dimensional attenuation model in volcanic areas. To this purpose, I first elaborated a robust strategy for the analysis of seismic data. This was done by performing several synthetic tests to assess the applicability of spectral ratio method to our purposes. The results of the tests allowed us to conclude that: 1) spectral ratio method gives reliable differential attenuation (dt*) measurements in smooth velocity models; 2) short signal time window has to be chosen to perform spectral analysis; 3) the frequency range over which to compute spectral ratios greatly affects dt* measurements. Furthermore, a refined approach for the application of spectral ratio method has been developed and tested. Through this procedure, the effects caused by heterogeneities of propagation medium on the seismic signals may be removed. The tested data analysis technique was applied to the real active seismic SERAPIS database. It provided a dataset of dt* measurements which was used to obtain a three dimensional attenuation model of the shallowest part of Campi Flegrei caldera. Then, a linearized, iterative, damped attenuation tomography technique has been tested and applied to the selected dataset. The tomography, with a resolution of 0.5 km in the horizontal directions and 0.25 km in the vertical direction, allowed to image important features in the off-shore part of Campi Flegrei caldera. High QP bodies are immersed in a high attenuation body (Qp=30). The latter is well correlated with low Vp and high Vp/Vs values and it is interpreted as a saturated marine and volcanic sediments layer. High Qp anomalies, instead, are interpreted as the effects either of cooled lava bodies or of a CO2 reservoir. A pseudo-circular high Qp anomaly was detected and interpreted as the buried rim of NYT caldera.

Soil-structure interaction during tunnelling in urban area: observations and 3D numerical modelling

This work illustrates a soil-tunnel-structure interaction study performed by an integrated,geotechnical and structural,approach based on 3D finite element analyses and validated against experimental observations.The study aims at analysing the response of reinforced concrete framed buildings on discrete foundations in interaction with metro lines.It refers to the case of the twin tunnels of the Milan (Italy) metro line 5,recently built in coarse grained materials using EPB machines,for which subsidence measurements collected along ground and building sections during tunnelling were available.Settlements measured under freefield conditions are firstly back interpreted using Gaussian empirical predictions. Then,the in situ measurements’ analysis is extended to include the evolving response of a 9 storey reinforced concrete building while being undercrossed by the metro line.In the finite element study,the soil mechanical behaviour is described using an advanced constitutive model. This latter,when combined with a proper simulation of the excavation process, proves to realistically reproduce the subsidence profiles under free field conditions and to capture the interaction phenomena occurring between the twin tunnels during the excavation. Furthermore, when the numerical model is extended to include the building, schematised in a detailed manner, the results are in good agreement with the monitoring data for different stages of the twin tunnelling. Thus, they indirectly confirm the satisfactory performance of the adopted numerical approach which also allows a direct evaluation of the structural response as an outcome of the analysis. Further analyses are also carried out modelling the building with different levels of detail. The results highlight that, in this case, the simplified approach based on the equivalent plate schematisation is inadequate to capture the real tunnelling induced displacement field. The overall behaviour of the system proves to be mainly influenced by the buried portion of the building which plays an essential role in the interaction mechanism, due to its high stiffness.

Evaluation of 3D cell culture systems for host-pathogen interaction studies

Traditional cell culture models have limitations in extrapolating functional mechanisms that underlie strategies of microbial virulence. Indeed during the infection the pathogens adapt to different tissue-specific environmental factors. The development of in vitro models resembling human tissue physiology might allow the replacement of inaccurate or aberrant animal models. Three-dimensional (3D) cell culture systems are more reliable and more predictive models that can be used for the meaningful dissection of host–pathogen interactions. The lung and gut mucosae often represent the first site of exposure to pathogens and provide a physical barrier against their entry. Within this context, the tracheobronchial and small intestine tract were modelled by tissue engineering approach. The main work was focused on the development and the extensive characterization of a human organotypic airway model, based on a mechanically supported co-culture of normal primary cells. The regained morphological features, the retrieved environmental factors and the presence of specific epithelial subsets resembled the native tissue organization. In addition, the respiratory model enabled the modular insertion of interesting cell types, such as innate immune cells or multipotent stromal cells, showing a functional ability to release pertinent cytokines differentially. Furthermore this model responded imitating known events occurring during the infection by Non-typeable H. influenzae. Epithelial organoid models, mimicking the small intestine tract, were used for a different explorative analysis of tissue-toxicity. Further experiments led to detection of a cell population targeted by C. difficile Toxin A and suggested a role in the impairment of the epithelial homeostasis by the bacterial virulence machinery. The described cell-centered strategy can afford critical insights in the evaluation of the host defence and pathogenic mechanisms. The application of these two models may provide an informing step that more coherently defines relevant molecular interactions happening during the infection.

A new 3D modelling paradigm for discrete model

Until few years ago, 3D modelling was a topic confined into a professional environment. Nowadays technological innovations, the 3D printer among all, have attracted novice users to this application field. This sudden breakthrough was not supported by adequate software solutions. The 3D editing tools currently available do not assist the non-expert user during the various stages of generation, interaction and manipulation of 3D virtual models. This is mainly due to the current paradigm that is largely supported by two-dimensional input/output devices and strongly affected by obvious geometrical constraints. We have identified three main phases that characterize the creation and management of 3D virtual models. We investigated these directions evaluating and simplifying the classic editing techniques in order to propose more natural and intuitive tools in a pure 3D modelling environment. In particular, we focused on freehand sketch-based modelling to create 3D virtual models, interaction and navigation in a 3D modelling environment and advanced editing tools for free-form deformation and objects composition. To pursuing these goals we wondered how new gesture-based interaction technologies can be successfully employed in a 3D modelling environments, how we could improve the depth perception and the interaction in 3D environments and which operations could be developed to simplify the classical virtual models editing paradigm. Our main aims were to propose a set of solutions with which a common user can realize an idea in a 3D virtual model, drawing in the air just as he would on paper. Moreover, we tried to use gestures and mid-air movements to explore and interact in 3D virtual environment, and we studied simple and effective 3D form transformations. The work was carried out adopting the discrete representation of the models, thanks to its intuitiveness, but especially because it is full of open challenges.

Kinematics of local and high-z galaxies through 3D modeling of emission-line datacubes

The kinematics is a fundamental tool to infer the dynamical structure of galaxies and to understand their formation and evolution. Spectroscopic observations of gas emission lines are often used to derive rotation curves and velocity dispersions. It is however difficult to disentangle these two quantities in low spatial-resolution data because of beam smearing. In this thesis, we present 3D-Barolo, a new software to derive the gas kinematics of disk galaxies from emission-line data-cubes. The code builds tilted-ring models in the 3D observational space and compares them with the actual data-cubes. 3D-Barolo works with data at a wide range of spatial resolutions without being affected by instrumental biases. We use 3D-Barolo to derive rotation curves and velocity dispersions of several galaxies in both the local and the high-redshift Universe. We run our code on HI observations of nearby galaxies and we compare our results with 2D traditional approaches. We show that a 3D approach to the derivation of the gas kinematics has to be preferred to a 2D approach whenever a galaxy is resolved with less than about 20 elements across the disk. We moreover analyze a sample of galaxies at z~1, observed in the H-alpha line with the KMOS/VLT spectrograph. Our 3D modeling reveals that the kinematics of these high-z systems is comparable to that of local disk galaxies, with steeply-rising rotation curves followed by a flat part and H-alpha velocity dispersions of 15-40 km/s over the whole disks. This evidence suggests that disk galaxies were already fully settled about 7-8 billion years ago. In summary, 3D-Barolo is a powerful and robust tool to separate physical and instrumental effects and to derive a reliable kinematics. The analysis of large samples of galaxies at different redshifts with 3D-Barolo will provide new insights on how galaxies assemble and evolve throughout cosmic time.