Reverse Engineering tools: development and experimentation of innovative methods for physical and geometrical data integration and post-processing

In recent years, the use of Reverse Engineering systems has got a considerable interest for a wide number of applications. Therefore, many research activities are focused on accuracy and precision of the acquired data and post processing phase improvements. In this context, this PhD Thesis deals with the definition of two novel methods for data post processing and data fusion between physical and geometrical information. In particular a technique has been defined for error definition in 3D points’ coordinates acquired by an optical triangulation laser scanner, with the aim to identify adequate correction arrays to apply under different acquisition parameters and operative conditions. Systematic error in data acquired is thus compensated, in order to increase accuracy value. Moreover, the definition of a 3D thermogram is examined. Object geometrical information and its thermal properties, coming from a thermographic inspection, are combined in order to have a temperature value for each recognizable point. Data acquired by an optical triangulation laser scanner are also used to normalize temperature values and make thermal data independent from thermal-camera point of view.

Dynamic identification of structures: experimental assessment of modal parameteres through methods in frequency domain, in time-frequency domain and model updating

Among the experimental methods commonly used to define the behaviour of a full scale system, dynamic tests are the most complete and efficient procedures. A dynamic test is an experimental process, which would define a set of characteristic parameters of the dynamic behaviour of the system, such as natural frequencies of the structure, mode shapes and the corresponding modal damping values associated. An assessment of these modal characteristics can be used both to verify the theoretical assumptions of the project, to monitor the performance of the structural system during its operational use. The thesis is structured in the following chapters: The first introductive chapter recalls some basic notions of dynamics of structure, focusing the discussion on the problem of systems with multiply degrees of freedom (MDOF), which can represent a generic real system under study, when it is excited with harmonic force or in free vibration. The second chapter is entirely centred on to the problem of dynamic identification process of a structure, if it is subjected to an experimental test in forced vibrations. It first describes the construction of FRF through classical FFT of the recorded signal. A different method, also in the frequency domain, is subsequently introduced; it allows accurately to compute the FRF using the geometric characteristics of the ellipse that represents the direct input-output comparison. The two methods are compared and then the attention is focused on some advantages of the proposed methodology. The third chapter focuses on the study of real structures when they are subjected to experimental test, where the force is not known, like in an ambient or impact test. In this analysis we decided to use the CWT, which allows a simultaneous investigation in the time and frequency domain of a generic signal x(t). The CWT is first introduced to process free oscillations, with excellent results both in terms of frequencies, dampings and vibration modes. The application in the case of ambient vibrations defines accurate modal parameters of the system, although on the damping some important observations should be made. The fourth chapter is still on the problem of post processing data acquired after a vibration test, but this time through the application of discrete wavelet transform (DWT). In the first part the results obtained by the DWT are compared with those obtained by the application of CWT. Particular attention is given to the use of DWT as a tool for filtering the recorded signal, in fact in case of ambient vibrations the signals are often affected by the presence of a significant level of noise. The fifth chapter focuses on another important aspect of the identification process: the model updating. In this chapter, starting from the modal parameters obtained from some environmental vibration tests, performed by the University of Porto in 2008 and the University of Sheffild on the Humber Bridge in England, a FE model of the bridge is defined, in order to define what type of model is able to capture more accurately the real dynamic behaviour of the bridge. The sixth chapter outlines the necessary conclusions of the presented research. They concern the application of a method in the frequency domain in order to evaluate the modal parameters of a structure and its advantages, the advantages in applying a procedure based on the use of wavelet transforms in the process of identification in tests with unknown input and finally the problem of 3D modeling of systems with many degrees of freedom and with different types of uncertainty.

Calcolo della posizione di reti di stazioni permanenti

Con il trascorrere del tempo, le reti di stazioni permanenti GNSS (Global Navigation Satellite System) divengono sempre più un valido supporto alle tecniche di rilevamento satellitare. Esse sono al tempo stesso un’efficace materializzazione del sistema di riferimento e un utile ausilio ad applicazioni di rilevamento topografico e di monitoraggio per il controllo di deformazioni. Alle ormai classiche applicazioni statiche in post-processamento, si affiancano le misure in tempo reale sempre più utilizzate e richieste dall’utenza professionale. In tutti i casi risulta molto importante la determinazione di coordinate precise per le stazioni permanenti, al punto che si è deciso di effettuarla tramite differenti ambienti di calcolo. Sono stati confrontati il Bernese, il Gamit (che condividono l’approccio differenziato) e il Gipsy (che utilizza l’approccio indifferenziato). L’uso di tre software ha reso indispensabile l’individuazione di una strategia di calcolo comune in grado di garantire che, i dati ancillari e i parametri fisici adottati, non costituiscano fonte di diversificazione tra le soluzioni ottenute. L’analisi di reti di dimensioni nazionali oppure di reti locali per lunghi intervalli di tempo, comporta il processamento di migliaia se non decine di migliaia di file; a ciò si aggiunge che, talora a causa di banali errori, oppure al fine di elaborare test scientifici, spesso risulta necessario reiterare le elaborazioni. Molte risorse sono quindi state investite nella messa a punto di procedure automatiche finalizzate, da un lato alla preparazione degli archivi e dall’altro all’analisi dei risultati e al loro confronto qualora si sia in possesso di più soluzioni. Dette procedure sono state sviluppate elaborando i dataset più significativi messi a disposizione del DISTART (Dipartimento di Ingegneria delle Strutture, dei Trasporti, delle Acque, del Rilevamento del Territorio - Università di Bologna). E’ stato così possibile, al tempo stesso, calcolare la posizione delle stazioni permanenti di alcune importanti reti locali e nazionali e confrontare taluni fra i più importanti codici scientifici che assolvono a tale funzione. Per quanto attiene il confronto fra i diversi software si è verificato che: • le soluzioni ottenute dal Bernese e da Gamit (i due software differenziati) sono sempre in perfetto accordo; • le soluzioni Gipsy (che utilizza il metodo indifferenziato) risultano, quasi sempre, leggermente più disperse rispetto a quelle degli altri software e mostrano talvolta delle apprezzabili differenze numeriche rispetto alle altre soluzioni, soprattutto per quanto attiene la coordinata Est; le differenze sono però contenute in pochi millimetri e le rette che descrivono i trend sono comunque praticamente parallele a quelle degli altri due codici; • il citato bias in Est tra Gipsy e le soluzioni differenziate, è più evidente in presenza di determinate combinazioni Antenna/Radome e sembra essere legato all’uso delle calibrazioni assolute da parte dei diversi software. E’ necessario altresì considerare che Gipsy è sensibilmente più veloce dei codici differenziati e soprattutto che, con la procedura indifferenziata, il file di ciascuna stazione di ciascun giorno, viene elaborato indipendentemente dagli altri, con evidente maggior elasticità di gestione: se si individua un errore strumentale su di una singola stazione o se si decide di aggiungere o togliere una stazione dalla rete, non risulta necessario il ricalcolo dell’intera rete. Insieme alle altre reti è stato possibile analizzare la Rete Dinamica Nazionale (RDN), non solo i 28 giorni che hanno dato luogo alla sua prima definizione, bensì anche ulteriori quattro intervalli temporali di 28 giorni, intercalati di sei mesi e che coprono quindi un intervallo temporale complessivo pari a due anni. Si è così potuto verificare che la RDN può essere utilizzata per l’inserimento in ITRF05 (International Terrestrial Reference Frame) di una qualsiasi rete regionale italiana nonostante l’intervallo temporale ancora limitato. Da un lato sono state stimate le velocità ITRF (puramente indicative e non ufficiali) delle stazioni RDN e, dall’altro, è stata effettuata una prova di inquadramento di una rete regionale in ITRF, tramite RDN, e si è verificato che non si hanno differenze apprezzabili rispetto all’inquadramento in ITRF, tramite un congruo numero di stazioni IGS/EUREF (International GNSS Service / European REference Frame, SubCommission for Europe dello International Association of Geodesy).

Fingerprint Recognition: Enhancement, Feature Extraction and Automatic Evaluation of Algorithms

The identification of people by measuring some traits of individual anatomy or physiology has led to a specific research area called biometric recognition. This thesis is focused on improving fingerprint recognition systems considering three important problems: fingerprint enhancement, fingerprint orientation extraction and automatic evaluation of fingerprint algorithms. An effective extraction of salient fingerprint features depends on the quality of the input fingerprint. If the fingerprint is very noisy, we are not able to detect a reliable set of features. A new fingerprint enhancement method, which is both iterative and contextual, is proposed. This approach detects high-quality regions in fingerprints, selectively applies contextual filtering and iteratively expands like wildfire toward low-quality ones. A precise estimation of the orientation field would greatly simplify the estimation of other fingerprint features (singular points, minutiae) and improve the performance of a fingerprint recognition system. The fingerprint orientation extraction is improved following two directions. First, after the introduction of a new taxonomy of fingerprint orientation extraction methods, several variants of baseline methods are implemented and, pointing out the role of pre- and post- processing, we show how to improve the extraction. Second, the introduction of a new hybrid orientation extraction method, which follows an adaptive scheme, allows to improve significantly the orientation extraction in noisy fingerprints. Scientific papers typically propose recognition systems that integrate many modules and therefore an automatic evaluation of fingerprint algorithms is needed to isolate the contributions that determine an actual progress in the state-of-the-art. The lack of a publicly available framework to compare fingerprint orientation extraction algorithms, motivates the introduction of a new benchmark area called FOE (including fingerprints and manually-marked orientation ground-truth) along with fingerprint matching benchmarks in the FVC-onGoing framework. The success of such framework is discussed by providing relevant statistics: more than 1450 algorithms submitted and two international competitions.

Valutazione della risposta sismica di edifici mediante modelli anelastici equivalenti

Nella presente tesi è proposta una metodologia per lo studio e la valutazione del comportamento sismico di edifici a telaio. Il metodo prevede la realizzazione di analisi non-lineari su modelli equivalenti MDOF tipo stick, in accordo alla classificazione data nel report FEMA 440. Gli step per l’applicazione del metodo sono descritti nella tesi. Per la validazione della metodologia si sono utilizzati confronti con analisi time-history condotte su modelli tridimensionali dettagliati delle strutture studiate (detailed model). I parametri ingegneristici considerati nel confronto, nell’ottica di utilizzare il metodo proposto in un approccio del tipo Displacement-Based Design sono lo spostamento globale in sommità, gli spostamenti di interpiano, le forze di piano e la forza totale alla base. I risultati delle analisi condotte sui modelli stick equivalenti, mostrano una buona corrispondenza, ottima in certi casi, con quelli delle analisi condotte sui modelli tridimensionali dettagliati. Le time-history realizzate sugli stick model permettono però, un consistente risparmio in termini di onere computazionale e di tempo per il post-processing dei risultati ottenuti.

Pyrolysis-Gas Chromatography-Mass Spectometry and Chemometric Analysis for the Characterization of Complex Matrices

The present PhD thesis was focused on the development and application of chemical methodology (Py-GC-MS) and data-processing method by multivariate data analysis (chemometrics). The chromatographic and mass spectrometric data obtained with this technique are particularly suitable to be interpreted by chemometric methods such as PCA (Principal Component Analysis) as regards data exploration and SIMCA (Soft Independent Models of Class Analogy) for the classification. As a first approach, some issues related to the field of cultural heritage were discussed with a particular attention to the differentiation of binders used in pictorial field. A marker of egg tempera the phosphoric acid esterified, a pyrolysis product of lecithin, was determined using HMDS (hexamethyldisilazane) rather than the TMAH (tetramethylammonium hydroxide) as a derivatizing reagent. The validity of analytical pyrolysis as tool to characterize and classify different types of bacteria was verified. The FAMEs chromatographic profiles represent an important tool for the bacterial identification. Because of the complexity of the chromatograms, it was possible to characterize the bacteria only according to their genus, while the differentiation at the species level has been achieved by means of chemometric analysis. To perform this study, normalized areas peaks relevant to fatty acids were taken into account. Chemometric methods were applied to experimental datasets. The obtained results demonstrate the effectiveness of analytical pyrolysis and chemometric analysis for the rapid characterization of bacterial species. Application to a samples of bacterial (Pseudomonas Mendocina), fungal (Pleorotus ostreatus) and mixed- biofilms was also performed. A comparison with the chromatographic profiles established the possibility to: • Differentiate the bacterial and fungal biofilms according to the (FAMEs) profile. • Characterize the fungal biofilm by means the typical pattern of pyrolytic fragments derived from saccharides present in the cell wall. • Individuate the markers of bacterial and fungal biofilm in the same mixed-biofilm sample.

Advanced modelling of time domain electromagnetic data with updated hydrogeological interpretations

Several countries have acquired, over the past decades, large amounts of area covering Airborne Electromagnetic data. Contribution of airborne geophysics has dramatically increased for both groundwater resource mapping and management proving how those systems are appropriate for large-scale and efficient groundwater surveying. We start with processing and inversion of two AEM dataset from two different systems collected over the Spiritwood Valley Aquifer area, Manitoba, Canada respectively, the AeroTEM III (commissioned by the Geological Survey of Canada in 2010) and the “Full waveform VTEM” dataset, collected and tested over the same survey area, during the fall 2011. We demonstrate that in the presence of multiple datasets, either AEM and ground data, due processing, inversion, post-processing, data integration and data calibration is the proper approach capable of providing reliable and consistent resistivity models. Our approach can be of interest to many end users, ranging from Geological Surveys, Universities to Private Companies, which are often proprietary of large geophysical databases to be interpreted for geological and\or hydrogeological purposes. In this study we deeply investigate the role of integration of several complimentary types of geophysical data collected over the same survey area. We show that data integration can improve inversions, reduce ambiguity and deliver high resolution results. We further attempt to use the final, most reliable output resistivity models as a solid basis for building a knowledge-driven 3D geological voxel-based model. A voxel approach allows a quantitative understanding of the hydrogeological setting of the area, and it can be further used to estimate the aquifers volumes (i.e. potential amount of groundwater resources) as well as hydrogeological flow model prediction. In addition, we investigated the impact of an AEM dataset towards hydrogeological mapping and 3D hydrogeological modeling, comparing it to having only a ground based TEM dataset and\or to having only boreholes data.

Anatomical biomarkers of body composition in oncological population: application and development of artificial intelligences

In the Era of precision medicine and big medical data sharing, it is necessary to solve the work-flow of digital radiological big data in a productive and effective way. In particular, nowadays, it is possible to extract information “hidden” in digital images, in order to create diagnostic algorithms helping clinicians to set up more personalized therapies, which are in particular targets of modern oncological medicine. Digital images generated by the patient have a “texture” structure that is not visible but encrypted; it is “hidden” because it cannot be recognized by sight alone. Thanks to artificial intelligence, pre- and post-processing software and generation of mathematical calculation algorithms, we could perform a classification based on non-visible data contained in radiological images. Being able to calculate the volume of tissue body composition could lead to creating clasterized classes of patients inserted in standard morphological reference tables, based on human anatomy distinguished by gender and age, and maybe in future also by race. Furthermore, the branch of “morpho-radiology" is a useful modality to solve problems regarding personalized therapies, which is particularly needed in the oncological field. Actually oncological therapies are no longer based on generic drugs but on target personalized therapy. The lack of gender and age therapies table could be filled thanks to morpho-radiology data analysis application.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

Le scelte di investimento delle aziende agricole e la PAC post-2013: valutazione di scenari mediante un modello real options

Negli ultimi decenni la Politica Agricola Comune (PAC) è stata sottoposta a diverse revisioni, più o meno programmate, che ne hanno modificato gli obiettivi operativi e gli strumenti per perseguirli. In letteratura economica agraria sono state eseguite diverse ricerche che affrontano analisi ex-ante sui possibili impatti delle riforme politiche, in particolare al disaccoppiamento, riguardo all’allocazione dei terreni alle diverse colture e all’adozione di tecniche di coltivazione più efficienti. Ma tale argomento, nonostante sia di grande importanza, non è stato finora affrontato come altri temi del mondo agricolo. Le principali lacune si riscontrano infatti nella carenza di analisi ex-ante, di modelli che includano le preferenze e le aspettative degli agricoltori. Questo studio valuta le scelte di investimento in terreno di un’azienda agricola di fronte a possibili scenari PAC post-2013, in condizioni di incertezza circa le specifiche condizioni in cui ciascuno scenario verrebbe a verificarsi. L’obiettivo è di ottenere indicazioni utili in termini di comprensione delle scelte di investimento dell’agricoltore in presenza di incertezza sul futuro. L’elemento maggiormente innovativo della ricerca consiste nell’applicazione di un approccio real options e nell’interazione tra la presenza di diversi scenari sul futuro del settore agricolo post-2013, e la componente di incertezza che incide e gravita su di essi. La metodologia adottata nel seguente lavoro si basa sulla modellizzazione di un’azienda agricola, in cui viene simulato il comportamento dell’azienda agricola in reazione alle riforme della PAC e alla variazione dei prezzi dei prodotti in presenza di incertezza. Mediante un modello di Real Option viene valutata la scelta della tempistica ottimale per investire nell’acquisto di terreno (caratterizzato da incertezza e irreversibilità). Dai risultati emerge come in presenza di incertezza all’agricoltore convenga rimandare la decisione a dopo il 2013 e in base alle maggiori informazioni disponibili eseguire l’investimento solo in presenza di condizioni favorevoli. La variazione dei prezzi dei prodotti influenza le scelte più dell’incertezza dei contributi PAC. Il Real Option sembra interpretare meglio il comportamento dell’agricoltore rispetto all’approccio classico del Net Present Value.

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.

Performance evaluation of low environmental impact asphalt concretes using the mechanistic empirical design method based on laboratory fatigue and permanent deformation models

The "sustainability" concept relates to the prolonging of human economic systems with as little detrimental impact on ecological systems as possible. Construction that exhibits good environmental stewardship and practices that conserve resources in a manner that allow growth and development to be sustained for the long-term without degrading the environment are indispensable in a developed society. Past, current and future advancements in asphalt as an environmentally sustainable paving material are especially important because the quantities of asphalt used annually in Europe as well as in the U.S. are large. The asphalt industry is still developing technological improvements that will reduce the environmental impact without affecting the final mechanical performance. Warm mix asphalt (WMA) is a type of asphalt mix requiring lower production temperatures compared to hot mix asphalt (HMA), while aiming to maintain the desired post construction properties of traditional HMA. Lowering the production temperature reduce the fuel usage and the production of emissions therefore and that improve conditions for workers and supports the sustainable development. Even the crumb-rubber modifier (CRM), with shredded automobile tires and used in the United States since the mid 1980s, has proven to be an environmentally friendly alternative to conventional asphalt pavement. Furthermore, the use of waste tires is not only relevant in an environmental aspect but also for the engineering properties of asphalt [Pennisi E., 1992]. This research project is aimed to demonstrate the dual value of these Asphalt Mixes in regards to the environmental and mechanical performance and to suggest a low environmental impact design procedure. In fact, the use of eco-friendly materials is the first phase towards an eco-compatible design but it cannot be the only step. The eco-compatible approach should be extended also to the design method and material characterization because only with these phases is it possible to exploit the maximum potential properties of the used materials. Appropriate asphalt concrete characterization is essential and vital for realistic performance prediction of asphalt concrete pavements. Volumetric (Mix design) and mechanical (Permanent deformation and Fatigue performance) properties are important factors to consider. Moreover, an advanced and efficient design method is necessary in order to correctly use the material. A design method such as a Mechanistic-Empirical approach, consisting of a structural model capable of predicting the state of stresses and strains within the pavement structure under the different traffic and environmental conditions, was the application of choice. In particular this study focus on the CalME and its Incremental-Recursive (I-R) procedure, based on damage models for fatigue and permanent shear strain related to the surface cracking and to the rutting respectively. It works in increments of time and, using the output from one increment, recursively, as input to the next increment, predicts the pavement conditions in terms of layer moduli, fatigue cracking, rutting and roughness. This software procedure was adopted in order to verify the mechanical properties of the study mixes and the reciprocal relationship between surface layer and pavement structure in terms of fatigue and permanent deformation with defined traffic and environmental conditions. The asphalt mixes studied were used in a pavement structure as surface layer of 60 mm thickness. The performance of the pavement was compared to the performance of the same pavement structure where different kinds of asphalt concrete were used as surface layer. In comparison to a conventional asphalt concrete, three eco-friendly materials, two warm mix asphalt and a rubberized asphalt concrete, were analyzed. The First Two Chapters summarize the necessary steps aimed to satisfy the sustainable pavement design procedure. In Chapter I the problem of asphalt pavement eco-compatible design was introduced. The low environmental impact materials such as the Warm Mix Asphalt and the Rubberized Asphalt Concrete were described in detail. In addition the value of a rational asphalt pavement design method was discussed. Chapter II underlines the importance of a deep laboratory characterization based on appropriate materials selection and performance evaluation. In Chapter III, CalME is introduced trough a specific explanation of the different equipped design approaches and specifically explaining the I-R procedure. In Chapter IV, the experimental program is presented with a explanation of test laboratory devices adopted. The Fatigue and Rutting performances of the study mixes are shown respectively in Chapter V and VI. Through these laboratory test data the CalME I-R models parameters for Master Curve, fatigue damage and permanent shear strain were evaluated. Lastly, in Chapter VII, the results of the asphalt pavement structures simulations with different surface layers were reported. For each pavement structure, the total surface cracking, the total rutting, the fatigue damage and the rutting depth in each bound layer were analyzed.

Analysis of human body kinematics using a hybrid markerless video acquisition and processing

A main objective of the human movement analysis is the quantitative description of joint kinematics and kinetics. This information may have great possibility to address clinical problems both in orthopaedics and motor rehabilitation. Previous studies have shown that the assessment of kinematics and kinetics from stereophotogrammetric data necessitates a setup phase, special equipment and expertise to operate. Besides, this procedure may cause feeling of uneasiness on the subjects and may hinder with their walking. The general aim of this thesis is the implementation and evaluation of new 2D markerless techniques, in order to contribute to the development of an alternative technique to the traditional stereophotogrammetric techniques. At first, the focus of the study has been the estimation of the ankle-foot complex kinematics during stance phase of the gait. Two particular cases were considered: subjects barefoot and subjects wearing ankle socks. The use of socks was investigated in view of the development of the hybrid method proposed in this work. Different algorithms were analyzed, evaluated and implemented in order to have a 2D markerless solution to estimate the kinematics for both cases. The validation of the proposed technique was done with a traditional stereophotogrammetric system. The implementation of the technique leads towards an easy to configure (and more comfortable for the subject) alternative to the traditional stereophotogrammetric system. Then, the abovementioned technique has been improved so that the measurement of knee flexion/extension could be done with a 2D markerless technique. The main changes on the implementation were on occlusion handling and background segmentation. With the additional constraints, the proposed technique was applied to the estimation of knee flexion/extension and compared with a traditional stereophotogrammetric system. Results showed that the knee flexion/extension estimation from traditional stereophotogrammetric system and the proposed markerless system were highly comparable, making the latter a potential alternative for clinical use. A contribution has also been given in the estimation of lower limb kinematics of the children with cerebral palsy (CP). For this purpose, a hybrid technique, which uses high-cut underwear and ankle socks as “segmental markers” in combination with a markerless methodology, was proposed. The proposed hybrid technique is different than the abovementioned markerless technique in terms of the algorithm chosen. Results showed that the proposed hybrid technique can become a simple and low-cost alternative to the traditional stereophotogrammetric systems.

CT perfusion image processing: analysis of liver tumors

Perfusion CT imaging of the liver has potential to improve evaluation of tumour angiogenesis. Quantitative parameters can be obtained applying mathematical models to Time Attenuation Curve (TAC). However, there are still some difficulties for an accurate quantification of perfusion parameters due, for example, to algorithms employed, to mathematical model, to patient’s weight and cardiac output and to the acquisition system. In this thesis, new parameters and alternative methodologies about liver perfusion CT are presented in order to investigate the cause of variability of this technique. Firstly analysis were made to assess the variability related to the mathematical model used to compute arterial Blood Flow (BFa) values. Results were obtained implementing algorithms based on “ maximum slope method” and “Dual input one compartment model” . Statistical analysis on simulated data demonstrated that the two methods are not interchangeable. Anyway slope method is always applicable in clinical context. Then variability related to TAC processing in the application of slope method is analyzed. Results compared with manual selection allow to identify the best automatic algorithm to compute BFa. The consistency of a Standardized Perfusion Index (SPV) was evaluated and a simplified calibration procedure was proposed. At the end the quantitative value of perfusion map was analyzed. ROI approach and map approach provide related values of BFa and this means that pixel by pixel algorithm give reliable quantitative results. Also in pixel by pixel approach slope method give better results. In conclusion the development of new automatic algorithms for a consistent computation of BFa and the analysis and definition of simplified technique to compute SPV parameter, represent an improvement in the field of liver perfusion CT analysis.