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.

Interactive simulation of flexible parts

Computer simulations play an ever growing role for the development of automotive products. Assembly simulation, as well as many other processes, are used systematically even before the first physical prototype of a vehicle is built in order to check whether particular components can be assembled easily or whether another part is in the way. Usually, this kind of simulation is limited to rigid bodies. However, a vehicle contains a multitude of flexible parts of various types: cables, hoses, carpets, seat surfaces, insulations, weatherstrips... Since most of the problems using these simulations concern one-dimensional components and since an intuitive tool for cable routing is still needed, we have chosen to concentrate on this category, which includes cables, hoses and wiring harnesses. In this thesis, we present a system for simulating one dimensional flexible parts such as cables or hoses. The modeling of bending and torsion follows the Cosserat model. For this purpose we use a generalized spring-mass system and describe its configuration by a carefully chosen set of coordinates. Gravity and contact forces as well as the forces responsible for length conservation are expressed in Cartesian coordinates. But bending and torsion effects can be dealt with more effectively by using quaternions to represent the orientation of the segments joining two neighboring mass points. This augmented system allows an easy formulation of all interactions with the best appropriate coordinate type and yields a strongly banded Hessian matrix. An energy minimizing process accounts for a solution exempt from the oscillations that are typical of spring-mass systems. The use of integral forces, similar to an integral controller, allows to enforce exactly the constraints. The whole system is numerically stable and can be solved at interactive frame rates. It is integrated in the DaimlerChrysler in-house Virtual Reality Software veo for use in applications such as cable routing and assembly simulation and has been well received by users. Parts of this work have been published at the ACM Solid and Physical Modeling Conference 2006 and have been selected for the special issue of the Computer-Aided-Design Journal to the conference.

Stock boundaries of Parapenaeus longirostris (Lucas, 1846) populations in the Italian seas: Development of genomic 2b-RAD markers and biological variation analysis.

This thesis is developed in the contest of Ritmare project WP1, which main objective is the development of a sustainable fishery through the identification of populations boundaries in commercially important species in Italian Seas. Three main objectives are discussed in order to help reach the main purpose of identification of stock boundaries in Parapenaeus longirostris: 1 -Development of a representative sampling design for Italian seas; 2 -Evaluation of 2b-RAD protocol; 3 -Investigation of populations through biological data analysis. First of all we defined and accomplished a sampling design which properly represents all Italian seas. Then we used information and data about nursery areas distribution, abundance of populations and importance of P. longirostris in local fishery, to develop an experimental design that prioritize the most important areas to maximize the results with actual project funds. We introduced for the first time the use of 2b-RAD on this species, a genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Thanks to this method we were able to move from genetics to the more complex genomics. In order to proceed with 2b-RAD we performed several tests to identify the best DNA extraction kit and protocol and finally we were able to extract 192 high quality DNA extracts ready to be processed. We tested 2b-RAD with five samples and after high-throughput sequencing of libraries we used the software “Stacks” to analyze the sequences. We obtained positive results identifying a great number of SNP markers among the five samples. To guarantee a multidisciplinary approach we used the biological data associated to the collected samples to investigate differences between geographical samples. Such approach assures continuity with other project, for instance STOCKMED, which utilize a combination of molecular and biological analysis as well.

The secret life of software applications

One of the most undervalued problems by smartphone users is the security of data on their mobile devices. Today smartphones and tablets are used to send messages and photos and especially to stay connected with social networks, forums and other platforms. These devices contain a lot of private information like passwords, phone numbers, private photos, emails, etc. and an attacker may choose to steal or destroy this information. The main topic of this thesis is the security of the applications present on the most popular stores (App Store for iOS and Play Store for Android) and of their mechanisms for the management of security. The analysis is focused on how the architecture of the two systems protects users from threats and highlights the real presence of malware and spyware in their respective application stores. The work described in subsequent chapters explains the study of the behavior of 50 Android applications and 50 iOS applications performed using network analysis software. Furthermore, this thesis presents some statistics about malware and spyware present on the respective stores and the permissions they require. At the end the reader will be able to understand how to recognize malicious applications and which of the two systems is more suitable for him. This is how this thesis is structured. The first chapter introduces the security mechanisms of the Android and iOS platform architectures and the security mechanisms of their respective application stores. The Second chapter explains the work done, what, why and how we have chosen the tools needed to complete our analysis. The third chapter discusses about the execution of tests, the protocol followed and the approach to assess the “level of danger” of each application that has been checked. The fourth chapter explains the results of the tests and introduces some statistics on the presence of malicious applications on Play Store and App Store. The fifth chapter is devoted to the study of the users, what they think about and how they might avoid malicious applications. The sixth chapter seeks to establish, following our methodology, what application store is safer. In the end, the seventh chapter concludes the thesis.

Anpassung des Metamodells PerPot an den ausdauerorientierten Laufsport zur Trainings- und Wettkampfoptimierung

Schon seit einigen Jahrzehnten wird die Sportwissenschaft durch computergestützte Methoden in ihrer Arbeit unterstützt. Mit der stetigen Weiterentwicklung der Technik kann seit einigen Jahren auch zunehmend die Sportpraxis von deren Einsatz profitieren. Mathematische und informatische Modelle sowie Algorithmen werden zur Leistungsoptimierung sowohl im Mannschafts- als auch im Individualsport genutzt. In der vorliegenden Arbeit wird das von Prof. Perl im Jahr 2000 entwickelte Metamodell PerPot an den ausdauerorientierten Laufsport angepasst. Die Änderungen betreffen sowohl die interne Modellstruktur als auch die Art der Ermittlung der Modellparameter. Damit das Modell in der Sportpraxis eingesetzt werden kann, wurde ein Kalibrierungs-Test entwickelt, mit dem die spezifischen Modellparameter an den jeweiligen Sportler individuell angepasst werden. Mit dem angepassten Modell ist es möglich, aus gegebenen Geschwindigkeitsprofilen die korrespondierenden Herzfrequenzverläufe abzubilden. Mit dem auf den Athleten eingestellten Modell können anschliessend Simulationen von Läufen durch die Eingabe von Geschwindigkeitsprofilen durchgeführt werden. Die Simulationen können in der Praxis zur Optimierung des Trainings und der Wettkämpfe verwendet werden. Das Training kann durch die Ermittlung einer simulativ bestimmten individuellen anaeroben Schwellenherzfrequenz optimal gesteuert werden. Die statistische Auswertung der PerPot-Schwelle zeigt signifikante Übereinstimmungen mit den in der Sportpraxis üblichen invasiv bestimmten Laktatschwellen. Die Wettkämpfe können durch die Ermittlung eines optimalen Geschwindigkeitsprofils durch verschiedene simulationsbasierte Optimierungsverfahren unterstützt werden. Bei der neuesten Methode erhält der Athlet sogar im Laufe des Wettkampfs aktuelle Prognosen, die auf den Geschwindigkeits- und Herzfrequenzdaten basieren, die während des Wettkampfs gemessen werden. Die mit PerPot optimierten Wettkampfzielzeiten für die Athleten zeigen eine hohe Prognosegüte im Vergleich zu den tatsächlich erreichten Zielzeiten.