Analysis and modeling techniques for ultrasonic tissue characterization

This thesis introduces new processing techniques for computer-aided interpretation of ultrasound images with the purpose of supporting medical diagnostic. In terms of practical application, the goal of this work is the improvement of current prostate biopsy protocols by providing physicians with a visual map overlaid over ultrasound images marking regions potentially affected by disease. As far as analysis techniques are concerned, the main contributions of this work to the state-of-the-art is the introduction of deconvolution as a pre-processing step in the standard ultrasonic tissue characterization procedure to improve the diagnostic significance of ultrasonic features. This thesis also includes some innovations in ultrasound modeling, in particular the employment of a continuous-time autoregressive moving-average (CARMA) model for ultrasound signals, a new maximum-likelihood CARMA estimator based on exponential splines and the definition of CARMA parameters as new ultrasonic features able to capture scatterers concentration. Finally, concerning the clinical usefulness of the developed techniques, the main contribution of this research is showing, through a study based on medical ground truth, that a reduction in the number of sampled cores in standard prostate biopsy is possible, preserving the same diagnostic power of the current clinical protocol.

Many-Core Architectures: Hardware-Software Optimization and Modeling Techniques

During the last few decades an unprecedented technological growth has been at the center of the embedded systems design paramount, with Moore’s Law being the leading factor of this trend. Today in fact an ever increasing number of cores can be integrated on the same die, marking the transition from state-of-the-art multi-core chips to the new many-core design paradigm. Despite the extraordinarily high computing power, the complexity of many-core chips opens the door to several challenges. As a result of the increased silicon density of modern Systems-on-a-Chip (SoC), the design space exploration needed to find the best design has exploded and hardware designers are in fact facing the problem of a huge design space. Virtual Platforms have always been used to enable hardware-software co-design, but today they are facing with the huge complexity of both hardware and software systems. In this thesis two different research works on Virtual Platforms are presented: the first one is intended for the hardware developer, to easily allow complex cycle accurate simulations of many-core SoCs. The second work exploits the parallel computing power of off-the-shelf General Purpose Graphics Processing Units (GPGPUs), with the goal of an increased simulation speed. The term Virtualization can be used in the context of many-core systems not only to refer to the aforementioned hardware emulation tools (Virtual Platforms), but also for two other main purposes: 1) to help the programmer to achieve the maximum possible performance of an application, by hiding the complexity of the underlying hardware. 2) to efficiently exploit the high parallel hardware of many-core chips in environments with multiple active Virtual Machines. This thesis is focused on virtualization techniques with the goal to mitigate, and overtake when possible, some of the challenges introduced by the many-core design paradigm.

The assessment of change in rural landscape and the analysis of the driving forces. Proposal of a spatial model for the rural built environment

The presented study carried out an analysis on rural landscape changes. In particular the study focuses on the understanding of driving forces acting on the rural built environment using a statistical spatial model implemented through GIS techniques. It is well known that the study of landscape changes is essential for a conscious decision making in land planning. From a bibliography review results a general lack of studies dealing with the modeling of rural built environment and hence a theoretical modelling approach for such purpose is needed. The advancement in technology and modernity in building construction and agriculture have gradually changed the rural built environment. In addition, the phenomenon of urbanization of a determined the construction of new volumes that occurred beside abandoned or derelict rural buildings. Consequently there are two types of transformation dynamics affecting mainly the rural built environment that can be observed: the conversion of rural buildings and the increasing of building numbers. It is the specific aim of the presented study to propose a methodology for the development of a spatial model that allows the identification of driving forces that acted on the behaviours of the building allocation. In fact one of the most concerning dynamic nowadays is related to an irrational expansion of buildings sprawl across landscape. The proposed methodology is composed by some conceptual steps that cover different aspects related to the development of a spatial model: the selection of a response variable that better describe the phenomenon under study, the identification of possible driving forces, the sampling methodology concerning the collection of data, the most suitable algorithm to be adopted in relation to statistical theory and method used, the calibration process and evaluation of the model. A different combination of factors in various parts of the territory generated favourable or less favourable conditions for the building allocation and the existence of buildings represents the evidence of such optimum. Conversely the absence of buildings expresses a combination of agents which is not suitable for building allocation. Presence or absence of buildings can be adopted as indicators of such driving conditions, since they represent the expression of the action of driving forces in the land suitability sorting process. The existence of correlation between site selection and hypothetical driving forces, evaluated by means of modeling techniques, provides an evidence of which driving forces are involved in the allocation dynamic and an insight on their level of influence into the process. GIS software by means of spatial analysis tools allows to associate the concept of presence and absence with point futures generating a point process. Presence or absence of buildings at some site locations represent the expression of these driving factors interaction. In case of presences, points represent locations of real existing buildings, conversely absences represent locations were buildings are not existent and so they are generated by a stochastic mechanism. Possible driving forces are selected and the existence of a causal relationship with building allocations is assessed through a spatial model. The adoption of empirical statistical models provides a mechanism for the explanatory variable analysis and for the identification of key driving variables behind the site selection process for new building allocation. The model developed by following the methodology is applied to a case study to test the validity of the methodology. In particular the study area for the testing of the methodology is represented by the New District of Imola characterized by a prevailing agricultural production vocation and were transformation dynamic intensively occurred. The development of the model involved the identification of predictive variables (related to geomorphologic, socio-economic, structural and infrastructural systems of landscape) capable of representing the driving forces responsible for landscape changes.. The calibration of the model is carried out referring to spatial data regarding the periurban and rural area of the study area within the 1975-2005 time period by means of Generalised linear model. The resulting output from the model fit is continuous grid surface where cells assume values ranged from 0 to 1 of probability of building occurrences along the rural and periurban area of the study area. Hence the response variable assesses the changes in the rural built environment occurred in such time interval and is correlated to the selected explanatory variables by means of a generalized linear model using logistic regression. Comparing the probability map obtained from the model to the actual rural building distribution in 2005, the interpretation capability of the model can be evaluated. The proposed model can be also applied to the interpretation of trends which occurred in other study areas, and also referring to different time intervals, depending on the availability of data. The use of suitable data in terms of time, information, and spatial resolution and the costs related to data acquisition, pre-processing, and survey are among the most critical aspects of model implementation. Future in-depth studies can focus on using the proposed model to predict short/medium-range future scenarios for the rural built environment distribution in the study area. In order to predict future scenarios it is necessary to assume that the driving forces do not change and that their levels of influence within the model are not far from those assessed for the time interval used for the calibration.

Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

The effect of two-dimensional squat elements on the seismic behavior of building structures

This thesis reports a study on the seismic response of two-dimensional squat elements and their effect on the behavior of building structures. Part A is devoted to the study of unreinforced masonry infills, while part B is focused on reinforced concrete sandwich walls. Part A begins with a comprehensive review of modelling techniques and code provisions for infilled frame structures. Then state-of-the practice techniques are applied for a real case to test the ability of actual modeling techniques to reproduce observed behaviors. The first developments towards a seismic-resistant masonry infill system are presented. Preliminary design recommendations for the seismic design of the seismic-resistant masonry infill are finally provided. Part B is focused on the seismic behavior of a specific reinforced concrete sandwich panel system. First, the results of in-plane psuudostatic cyclic tests are described. Refinements to the conventional modified compression field theory are introduced in order to better simulate the monotonic envelope of the cyclic response. The refinements deal with the constitutive model for the shotcrete in tension and the embedded bars. Then the hysteretic response of the panels is studied according to a continuum damage model. Damage state limits are identified. Design recommendations for the seismic design of the studied reinforced concrete sandwich walls are finally provided.

Modeling and optimization techniques for advanced vehicular networking

This thesis deals with optimization techniques and modeling of vehicular networks. Thanks to the models realized with the integer linear programming (ILP) and the heuristic ones, it was possible to study the performances in 5G networks for the vehicular. Thanks to Software-defined networking (SDN) and Network functions virtualization (NFV) paradigms it was possible to study the performances of different classes of service, such as the Ultra Reliable Low Latency Communications (URLLC) class and enhanced Mobile BroadBand (eMBB) class, and how the functional split can have positive effects on network resource management. Two different protection techniques have been studied: Shared Path Protection (SPP) and Dedicated Path Protection (DPP). Thanks to these different protections, it is possible to achieve different network reliability requirements, according to the needs of the end user. Finally, thanks to a simulator developed in Python, it was possible to study the dynamic allocation of resources in a 5G metro network. Through different provisioning algorithms and different dynamic resource management techniques, useful results have been obtained for understanding the needs in the vehicular networks that will exploit 5G. Finally, two models are shown for reconfiguring backup resources when using shared resource protection.

Modeling the cosmological co-evolution of supermassive black holes and galaxies

In this Thesis, we investigate the cosmological co-evolution of supermassive black holes (BHs), Active Galactic Nuclei (AGN) and their hosting dark matter (DM) halos and galaxies, within the standard CDM scenario. We analyze both analytic, semi-analytic and hybrid techniques and use the most recent observational data available to constrain the assumptions underlying our models. First, we focus on very simple analytic models where the assembly of BHs is directly related to the merger history of DM haloes. For this purpose, we implement the two original analytic models of Wyithe & Loeb 2002 and Wyithe & Loeb 2003, compare their predictions to the AGN luminosity function and clustering data, and discuss possible modifications to the models that improve the match to the observation. Then we study more sophisticated semi-analytic models in which however the baryonic physics is neglected as well. Finally we improve the hybrid simulation of De Lucia & Blaizot 2007, adding new semi-analytical prescriptions to describe the BH mass accretion rate during each merger event and its conversion into radiation, and compare the derived BH scaling relations, fundamental plane and mass function, and the AGN luminosity function with observations. All our results support the following scenario: • The cosmological co-evolution of BHs, AGN and galaxies can be well described within the CDM model. • At redshifts z & 1, the evolution history of DM halo fully determines the overall properties of the BH and AGN populations. The AGN emission is triggered mainly by DM halo major mergers and, on average, AGN shine at their Eddington luminosity. • At redshifts z . 1, BH growth decouples from halo growth. Galaxy major mergers cannot constitute the only trigger to accretion episodes in this phase. • When a static hot halo has formed around a galaxy, a fraction of the hot gas continuously accretes onto the central BH, causing a low-energy “radio” activity at the galactic centre, which prevents significant gas cooling and thus limiting the mass of the central galaxies and quenching the star formation at late time. • The cold gas fraction accreted by BHs at high redshifts seems to be larger than at low redshifts.

Parallel modeling of the electric field distribution in the brain

The term "Brain Imaging" identi�es a set of techniques to analyze the structure and/or functional behavior of the brain in normal and/or pathological situations. These techniques are largely used in the study of brain activity. In addition to clinical usage, analysis of brain activity is gaining popularity in others recent �fields, i.e. Brain Computer Interfaces (BCI) and the study of cognitive processes. In this context, usage of classical solutions (e.g. f MRI, PET-CT) could be unfeasible, due to their low temporal resolution, high cost and limited portability. For these reasons alternative low cost techniques are object of research, typically based on simple recording hardware and on intensive data elaboration process. Typical examples are ElectroEncephaloGraphy (EEG) and Electrical Impedance Tomography (EIT), where electric potential at the patient's scalp is recorded by high impedance electrodes. In EEG potentials are directly generated from neuronal activity, while in EIT by the injection of small currents at the scalp. To retrieve meaningful insights on brain activity from measurements, EIT and EEG relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of the electric �field distribution therein. The inhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeo�ff between physical accuracy and technical feasibility, which currently severely limits the capabilities of these techniques. Moreover elaboration of data recorded requires usage of regularization techniques computationally intensive, which influences the application with heavy temporal constraints (such as BCI). This work focuses on the parallel implementation of a work-flow for EEG and EIT data processing. The resulting software is accelerated using multi-core GPUs, in order to provide solution in reasonable times and address requirements of real-time BCI systems, without over-simplifying the complexity and accuracy of the head models.

Modeling, design and experimental characterization of Micro-Electro-Mechanical-Systems for gas chromatographic applications

Design parameters, process flows, electro-thermal-fluidic simulations and experimental characterizations of Micro-Electro-Mechanical-Systems (MEMS) suited for gas-chromatographic (GC) applications are presented and thoroughly described in this thesis, whose topic belongs to the research activities the Institute for Microelectronics and Microsystems (IMM)-Bologna is involved since several years, i.e. the development of micro-systems for chemical analysis, based on silicon micro-machining techniques and able to perform analysis of complex gaseous mixtures, especially in the field of environmental monitoring. In this regard, attention has been focused on the development of micro-fabricated devices to be employed in a portable mini-GC system for the analysis of aromatic Volatile Organic Compounds (VOC) like Benzene, Toluene, Ethyl-benzene and Xylene (BTEX), i.e. chemical compounds which can significantly affect environment and human health because of their demonstrated carcinogenicity (benzene) or toxicity (toluene, xylene) even at parts per billion (ppb) concentrations. The most significant results achieved through the laboratory functional characterization of the mini-GC system have been reported, together with in-field analysis results carried out in a station of the Bologna air monitoring network and compared with those provided by a commercial GC system. The development of more advanced prototypes of micro-fabricated devices specifically suited for FAST-GC have been also presented (silicon capillary columns, Ultra-Low-Power (ULP) Metal OXide (MOX) sensor, Thermal Conductivity Detector (TCD)), together with the technological processes for their fabrication. The experimentally demonstrated very high sensitivity of ULP-MOX sensors to VOCs, coupled with the extremely low power consumption, makes the developed ULP-MOX sensor the most performing metal oxide sensor reported up to now in literature, while preliminary test results proved that the developed silicon capillary columns are capable of performances comparable to those of the best fused silica capillary columns. Finally, the development and the validation of a coupled electro-thermal Finite Element Model suited for both steady-state and transient analysis of the micro-devices has been described, and subsequently implemented with a fluidic part to investigate devices behaviour in presence of a gas flowing with certain volumetric flow rates.

Statistical analysis and simulation techniques in wall-bounded turbulence

The present work is devoted to the assessment of the energy fluxes physics in the space of scales and physical space of wall-turbulent flows. The generalized Kolmogorov equation will be applied to DNS data of a turbulent channel flow in order to describe the energy fluxes paths from production to dissipation in the augmented space of wall-turbulent flows. This multidimensional description will be shown to be crucial to understand the formation and sustainment of the turbulent fluctuations fed by the energy fluxes coming from the near-wall production region. An unexpected behavior of the energy fluxes comes out from this analysis consisting of spiral-like paths in the combined physical/scale space where the controversial reverse energy cascade plays a central role. The observed behavior conflicts with the classical notion of the Richardson/Kolmogorov energy cascade and may have strong repercussions on both theoretical and modeling approaches to wall-turbulence. To this aim a new relation stating the leading physical processes governing the energy transfer in wall-turbulence is suggested and shown able to capture most of the rich dynamics of the shear dominated region of the flow. Two dynamical processes are identified as driving mechanisms for the fluxes, one in the near wall region and a second one further away from the wall. The former, stronger one is related to the dynamics involved in the near-wall turbulence regeneration cycle. The second suggests an outer self-sustaining mechanism which is asymptotically expected to take place in the log-layer and could explain the debated mixed inner/outer scaling of the near-wall statistics. The same approach is applied for the first time to a filtered velocity field. A generalized Kolmogorov equation specialized for filtered velocity field is derived and discussed. The results will show what effects the subgrid scales have on the resolved motion in both physical and scale space, singling out the prominent role of the filter length compared to the cross-over scale between production dominated scales and inertial range, lc, and the reverse energy cascade region lb. The systematic characterization of the resolved and subgrid physics as function of the filter scale and of the wall-distance will be shown instrumental for a correct use of LES models in the simulation of wall turbulent flows. Taking inspiration from the new relation for the energy transfer in wall turbulence, a new class of LES models will be also proposed. Finally, the generalized Kolmogorov equation specialized for filtered velocity fields will be shown to be an helpful statistical tool for the assessment of LES models and for the development of new ones. As example, some classical purely dissipative eddy viscosity models are analyzed via an a priori procedure.

Modeling systems and vis/NIR device to improve peach and nectarine pre and post-harvest fruit maturity management

During the last decade peach and nectarine fruit have lost considerable market share, due to increased consumer dissatisfaction with quality at retail markets. This is mainly due to harvesting of too immature fruit and high ripening heterogeneity. The main problem is that the traditional used maturity indexes are not able to objectively detect fruit maturity stage, neither the variability present in the field, leading to a difficult post-harvest management of the product and to high fruit losses. To assess more precisely the fruit ripening other techniques and devices can be used. Recently, a new non-destructive maturity index, based on the vis-NIR technology, the Index of Absorbance Difference (IAD), that correlates with fruit degreening and ethylene production, was introduced and the IAD was used to study peach and nectarine fruit ripening from the “field to the fork”. In order to choose the best techniques to improve fruit quality, a detailed description of the tree structure, of fruit distribution and ripening evolution on the tree was faced. More in details, an architectural model (PlantToon®) was used to design the tree structure and the IAD was applied to characterize the maturity stage of each fruit. Their combined use provided an objective and precise evaluation of the fruit ripening variability, related to different training systems, crop load, fruit exposure and internal temperature. Based on simple field assessment of fruit maturity (as IAD) and growth, a model for an early prediction of harvest date and yield, was developed and validated. The relationship between the non-destructive maturity IAD, and the fruit shelf-life, was also confirmed. Finally the obtained results were validated by consumer test: the fruit sorted in different maturity classes obtained a different consumer acceptance. The improved knowledge, leaded to an innovative management of peach and nectarine fruit, from “field to market”.

Nanomechanical characterization of soft bioelectronic interfaces via modeling-informed atomic force microscopy

The field of bioelectronics involves the use of electrodes to exchange electrical signals with biological systems for diagnostic and therapeutic purposes in biomedical devices and healthcare applications. However, the mechanical compatibility of implantable devices with the human body has been a challenge, particularly with long-term implantation into target organs. Current rigid bioelectronics can trigger inflammatory responses and cause unstable device functions due to the mechanical mismatch with the surrounding soft tissue. Recent advances in flexible and stretchable electronics have shown promise in making bioelectronic interfaces more biocompatible. To fully achieve this goal, material science and engineering of soft electronic devices must be combined with quantitative characterization and modeling tools to understand the mechanical issues at the interface between electronic technology and biological tissue. Local mechanical characterization is crucial to understand the activation of failure mechanisms and optimizing the devices. Experimental techniques for testing mechanical properties at the nanoscale are emerging, and the Atomic Force Microscope (AFM) is a good candidate for in situ local mechanical characterization of soft bioelectronic interfaces. In this work, in situ experimental techniques with solely AFM supported by interpretive models for the characterization of planar and three-dimensional devices suitable for in vivo and in vitro biomedical experimentations are reported. The combination of the proposed models and experimental techniques provides access to the local mechanical properties of soft bioelectronic interfaces. The study investigates the nanomechanics of hard thin gold films on soft polymeric substrates (Poly(dimethylsiloxane) PDMS) and 3D inkjet-printed micropillars under different deformation states. The proposed characterization methods provide a rapid and precise determination of mechanical properties, thus giving the possibility to parametrize the microfabrication steps and investigate their impact on the final device.

Assessing brain connectivity through electroencephalographic signal processing and modeling analysis

Brain functioning relies on the interaction of several neural populations connected through complex connectivity networks, enabling the transmission and integration of information. Recent advances in neuroimaging techniques, such as electroencephalography (EEG), have deepened our understanding of the reciprocal roles played by brain regions during cognitive processes. The underlying idea of this PhD research is that EEG-related functional connectivity (FC) changes in the brain may incorporate important neuromarkers of behavior and cognition, as well as brain disorders, even at subclinical levels. However, a complete understanding of the reliability of the wide range of existing connectivity estimation techniques is still lacking. The first part of this work addresses this limitation by employing Neural Mass Models (NMMs), which simulate EEG activity and offer a unique tool to study interconnected networks of brain regions in controlled conditions. NMMs were employed to test FC estimators like Transfer Entropy and Granger Causality in linear and nonlinear conditions. Results revealed that connectivity estimates reflect information transmission between brain regions, a quantity that can be significantly different from the connectivity strength, and that Granger causality outperforms the other estimators. A second objective of this thesis was to assess brain connectivity and network changes on EEG data reconstructed at the cortical level. Functional brain connectivity has been estimated through Granger Causality, in both temporal and spectral domains, with the following goals: a) detect task-dependent functional connectivity network changes, focusing on internal-external attention competition and fear conditioning and reversal; b) identify resting-state network alterations in a subclinical population with high autistic traits. Connectivity-based neuromarkers, compared to the canonical EEG analysis, can provide deeper insights into brain mechanisms and may drive future diagnostic methods and therapeutic interventions. However, further methodological studies are required to fully understand the accuracy and information captured by FC estimates, especially concerning nonlinear phenomena.