Transposable elements: structure and dynamic of the autonomous retrotransposon R2 in Arthropoda with non-canonical reproduction

Eukaryotic ribosomal DNA constitutes a multi gene family organized in a cluster called nucleolar organizer region (NOR); this region is composed usually by hundreds to thousands of tandemly repeated units. Ribosomal genes, being repeated sequences, evolve following the typical pattern of concerted evolution. The autonomous retroelement R2 inserts in the ribosomal gene 28S, leading to defective 28S rDNA genes. R2 element, being a retrotransposon, performs its activity in the genome multiplying its copy number through a “copy and paste” mechanism called target primed reverse transcription. It consists in the retrotranscription of the element’s mRNA into DNA, then the DNA is integrated in the target site. Since the retrotranscription can be interrupted, but the integration will be carried out anyway, truncated copies of the element will also be present in the genome. The study of these truncated variants is a tool to examine the activity of the element. R2 phylogeny appears, in general, not consistent with that of its hosts, except some cases (e.g. Drosophila spp. and Reticulitermes spp.); moreover R2 is absent in some species (Fugu rubripes, human, mouse, etc.), while other species have more R2 lineages in their genome (the turtle Mauremys reevesii, the Japanese beetle Popilia japonica, etc). R2 elements here presented are isolated in 4 species of notostracan branchiopods and in two species of stick insects, whose reproductive strategies range from strict gonochorism to unisexuality. From sequencing data emerges that in Triops cancriformis (Spanish gonochoric population), in Lepidurus arcticus (two putatively unisexual populations from Iceland) and in Bacillus rossius (gonochoric population from Capalbio) the R2 elements are complete and encode functional proteins, reflecting the general features of this family of transposable elements. On the other hand, R2 from Italian and Austrian populations of T. cancriformis (respectively unisexual and hermaphroditic), Lepidurus lubbocki (two elements within the same Italian population, gonochoric but with unfunctional males) and Bacillus grandii grandii (gonochoric population from Ponte Manghisi) have sequences that encode incomplete or non-functional proteins in which it is possible to recognize only part of the characteristic domains. In Lepidurus couesii (Italian gonochoric populations) different elements were found as in L. lubbocki, and the sequencing is still in progress. Two hypothesis are given to explain the inconsistency of R2/host phylogeny: vertical inheritance of the element followed by extinction/diversification or horizontal transmission. My data support previous study that state the vertical transmission as the most likely explanation; nevertheless horizontal transfer events can’t be excluded. I also studied the element’s activity in Spanish populations of T. cancriformis, in L. lubbocki, in L. arcticus and in gonochoric and parthenogenetic populations of B. rossius. In gonochoric populations of T. cancriformis and B. rossius I found that each individual has its own private set of truncated variants. The situation is the opposite for the remaining hermaphroditic/parthenogenetic species and populations, all individuals sharing – in the so far analyzed samples - the majority of variants. This situation is very interesting, because it isn’t concordant with the Muller’s ratchet theory that hypothesizes the parthenogenetic populations being either devoided of transposable elements or TEs overloaded. My data suggest a possible epigenetic mechanism that can block the retrotransposon activity, and in this way deleterious mutations don’t accumulate.

Definition, realization and evaluation of a software reference architecture for use in space applications

A recent initiative of the European Space Agency (ESA) aims at the definition and adoption of a software reference architecture for use in on-board software of future space missions. Our PhD project placed in the context of that effort. At the outset of our work we gathered all the industrial needs relevant to ESA and all the main European space stakeholders and we were able to consolidate a set of technical high-level requirements for the fulfillment of them. The conclusion we reached from that phase confirmed that the adoption of a software reference architecture was indeed the best solution for the fulfillment of the high-level requirements. The software reference architecture we set on building rests on four constituents: (i) a component model, to design the software as a composition of individually verifiable and reusable software units; (ii) a computational model, to ensure that the architectural description of the software is statically analyzable; (iii) a programming model, to ensure that the implementation of the design entities conforms with the semantics, the assumptions and the constraints of the computational model; (iv) a conforming execution platform, to actively preserve at run time the properties asserted by static analysis. The nature, feasibility and fitness of constituents (ii), (iii) and (iv), were already proved by the author in an international project that preceded the commencement of the PhD work. The core of the PhD project was therefore centered on the design and prototype implementation of constituent (i), a component model. Our proposed component model is centered on: (i) rigorous separation of concerns, achieved with the support for design views and by careful allocation of concerns to the dedicated software entities; (ii) the support for specification and model-based analysis of extra-functional properties; (iii) the inclusion space-specific concerns.

Innovative architecture of on-board and on-ground radio systems for space communication

The radio communication system is one of the most critical system of the overall satellite platform: it often represents the only way of communication, between a spacecraft and the Ground Segment or among a constellation of satellites. This thesis focuses on specific innovative architectures for on-board and on-ground radio systems. In particular, this work is an integral part of a space program started in 2004 at the University of Bologna, Forlì campus, which led to the completion of the microsatellite ALMASat-1, successfully launched on-board the VEGA maiden flight. The success of this program led to the development of a second microsatellite, named ALMASat-EO, a three-axis stabilized microsatellite able to capture images of the Earth surface. Therefore, the first objective of this study was focused on the investigation of an innovative, efficient and low cost architecture for on-board radio communication systems. The TT&C system and the high data rate transmitter for images downlink design and realization are thoroughly described in this work, together with the development of the embedded hardware and the adopted antenna systems. Moreover, considering the increasing interest in the development of constellations of microsatellite, in particular those flying in close formations, a careful analysis has been carried out for the development of innovative communication protocols for inter-satellite links. Furthermore, in order to investigate the system aspects of space communications, a study has been carried out at ESOC having as objective the design, implementation and test of two experimental devices for the enhancement of the ESA GS. Thus, a significant portion of this thesis is dedicated to the description of the results of a method for improving the phase stability of GS radio frequency equipments by means of real-time phase compensation and a new way to perform two antennas arraying tracking using already existing ESA tracking stations facilities.

Hardware/Software Design of Dynamic Real-Time Schedulers for Embedded Multiprocessor Systems

The new generation of multicore processors opens new perspectives for the design of embedded systems. Multiprocessing, however, poses new challenges to the scheduling of real-time applications, in which the ever-increasing computational demands are constantly flanked by the need of meeting critical time constraints. Many research works have contributed to this field introducing new advanced scheduling algorithms. However, despite many of these works have solidly demonstrated their effectiveness, the actual support for multiprocessor real-time scheduling offered by current operating systems is still very limited. This dissertation deals with implementative aspects of real-time schedulers in modern embedded multiprocessor systems. The first contribution is represented by an open-source scheduling framework, which is capable of realizing complex multiprocessor scheduling policies, such as G-EDF, on conventional operating systems exploiting only their native scheduler from user-space. A set of experimental evaluations compare the proposed solution to other research projects that pursue the same goals by means of kernel modifications, highlighting comparable scheduling performances. The principles that underpin the operation of the framework, originally designed for symmetric multiprocessors, have been further extended first to asymmetric ones, which are subjected to major restrictions such as the lack of support for task migrations, and later to re-programmable hardware architectures (FPGAs). In the latter case, this work introduces a scheduling accelerator, which offloads most of the scheduling operations to the hardware and exhibits extremely low scheduling jitter. The realization of a portable scheduling framework presented many interesting software challenges. One of these has been represented by timekeeping. In this regard, a further contribution is represented by a novel data structure, called addressable binary heap (ABH). Such ABH, which is conceptually a pointer-based implementation of a binary heap, shows very interesting average and worst-case performances when addressing the problem of tick-less timekeeping of high-resolution timers.

Effect of training systems and pruning methods on fruit quality in apple

The introduction of dwarfed rootstocks in apple crop has led to a new concept of intensive planting systems with the aim of producing early high yield and with returns of the initial high investment. Although yield is an important aspect to the grower, the consumer has become demanding regards fruit quality and is generally attracted by appearance. To fulfil the consumer’s expectations the grower may need to choose a proper training system along with an ideal pruning technique, which ensure a good light distribution in different parts of the canopy and a marketable fruit quality in terms of size and skin colour. Although these aspects are important, these fruits might not reach the proper ripening stage within the canopy because they are often heterogeneous. To describe the variability present in a tree, a software (PlantToon®), was used to recreate the tree architecture in 3D in the two training systems. The ripening stage of each of the fruits was determined using a non-destructive device (DA-Meter), thus allowing to estimate the fruit ripening variability. This study deals with some of the main parameters that can influence fruit quality and ripening stage within the canopy and orchard management techniques that can ameliorate a ripening fruit homogeneity. Significant differences in fruit quality were found within the canopies due to their position, flowering time and bud wood age. Bi-axis appeared to be suitable for high density planting, even though the fruit quality traits resulted often similar to those obtained with a Slender Spindle, suggesting similar fruit light availability within the canopies. Crop load confirmed to be an important factor that influenced fruit quality as much as the interesting innovative pruning method “Click”, in intensive planting systems.

An Integrated Transmission-Media Noise Calibration Software For Deep-Space Radio Science Experiments

The thesis describes the implementation of a calibration, format-translation and data conditioning software for radiometric tracking data of deep-space spacecraft. All of the available propagation-media noise rejection techniques available as features in the code are covered in their mathematical formulations, performance and software implementations. Some techniques are retrieved from literature and current state of the art, while other algorithms have been conceived ex novo. All of the three typical deep-space refractive environments (solar plasma, ionosphere, troposphere) are dealt with by employing specific subroutines. Specific attention has been reserved to the GNSS-based tropospheric path delay calibration subroutine, since it is the most bulky module of the software suite, in terms of both the sheer number of lines of code, and development time. The software is currently in its final stage of development and once completed will serve as a pre-processing stage for orbit determination codes. Calibration of transmission-media noise sources in radiometric observables proved to be an essential operation to be performed of radiometric data in order to meet the more and more demanding error budget requirements of modern deep-space missions. A completely autonomous and all-around propagation-media calibration software is a novelty in orbit determination, although standalone codes are currently employed by ESA and NASA. The described S/W is planned to be compatible with the current standards for tropospheric noise calibration used by both these agencies like the AMC, TSAC and ESA IFMS weather data, and it natively works with the Tracking Data Message file format (TDM) adopted by CCSDS as standard aimed to promote and simplify inter-agency collaboration.

Operating System Contribution to Composable Timing Behaviour in High-Integrity Real-Time Systems

The development of High-Integrity Real-Time Systems has a high footprint in terms of human, material and schedule costs. Factoring functional, reusable logic in the application favors incremental development and contains costs. Yet, achieving incrementality in the timing behavior is a much harder problem. Complex features at all levels of the execution stack, aimed to boost average-case performance, exhibit timing behavior highly dependent on execution history, which wrecks time composability and incrementaility with it. Our goal here is to restitute time composability to the execution stack, working bottom up across it. We first characterize time composability without making assumptions on the system architecture or the software deployment to it. Later, we focus on the role played by the real-time operating system in our pursuit. Initially we consider single-core processors and, becoming less permissive on the admissible hardware features, we devise solutions that restore a convincing degree of time composability. To show what can be done for real, we developed TiCOS, an ARINC-compliant kernel, and re-designed ORK+, a kernel for Ada Ravenscar runtimes. In that work, we added support for limited-preemption to ORK+, an absolute premiere in the landscape of real-word kernels. Our implementation allows resource sharing to co-exist with limited-preemptive scheduling, which extends state of the art. We then turn our attention to multicore architectures, first considering partitioned systems, for which we achieve results close to those obtained for single-core processors. Subsequently, we shy away from the over-provision of those systems and consider less restrictive uses of homogeneous multiprocessors, where the scheduling algorithm is key to high schedulable utilization. To that end we single out RUN, a promising baseline, and extend it to SPRINT, which supports sporadic task sets, hence matches real-world industrial needs better. To corroborate our results we present findings from real-world case studies from avionic industry.

Software zur automatischen Tumordiagnose in der funktionalen MRT der weiblichen Brust

In den westlichen Industrieländern ist das Mammakarzinom der häufigste bösartige Tumor der Frau. Sein weltweiter Anteil an allen Krebserkrankungen der Frau beläuft sich auf etwa 21 %. Inzwischen ist jede neunte Frau bedroht, während ihres Lebens an Brustkrebs zu erkranken. Die alterstandardisierte Mortalitätrate liegt derzeit bei knapp 27 %.rnrnDas Mammakarzinom hat eine relative geringe Wachstumsrate. Die Existenz eines diagnostischen Verfahrens, mit dem alle Mammakarzinome unter 10 mm Durchmesser erkannt und entfernt werden, würden den Tod durch Brustkrebs praktisch beseitigen. Denn die 20-Jahres-Überlebungsrate bei Erkrankung durch initiale Karzinome der Größe 5 bis 10 mm liegt mit über 95 % sehr hoch.rnrnMit der Kontrastmittel gestützten Bildgebung durch die MRT steht eine relativ junge Untersuchungsmethode zur Verfügung, die sensitiv genug zur Erkennung von Karzinomen ab einer Größe von 3 mm Durchmesser ist. Die diagnostische Methodik ist jedoch komplex, fehleranfällig, erfordert eine lange Einarbeitungszeit und somit viel Erfahrung des Radiologen.rnrnEine Computer unterstützte Diagnosesoftware kann die Qualität einer solch komplexen Diagnose erhöhen oder zumindest den Prozess beschleunigen. Das Ziel dieser Arbeit ist die Entwicklung einer vollautomatischen Diagnose Software, die als Zweitmeinungssystem eingesetzt werden kann. Meines Wissens existiert eine solche komplette Software bis heute nicht.rnrnDie Software führt eine Kette von verschiedenen Bildverarbeitungsschritten aus, die dem Vorgehen des Radiologen nachgeahmt wurden. Als Ergebnis wird eine selbstständige Diagnose für jede gefundene Läsion erstellt: Zuerst eleminiert eine 3d Bildregistrierung Bewegungsartefakte als Vorverarbeitungsschritt, um die Bildqualität der nachfolgenden Verarbeitungsschritte zu verbessern. Jedes kontrastanreichernde Objekt wird durch eine regelbasierte Segmentierung mit adaptiven Schwellwerten detektiert. Durch die Berechnung kinetischer und morphologischer Merkmale werden die Eigenschaften der Kontrastmittelaufnahme, Form-, Rand- und Textureeigenschaften für jedes Objekt beschrieben. Abschließend werden basierend auf den erhobenen Featurevektor durch zwei trainierte neuronale Netze jedes Objekt in zusätzliche Funde oder in gut- oder bösartige Läsionen klassifiziert.rnrnDie Leistungsfähigkeit der Software wurde auf Bilddaten von 101 weiblichen Patientinnen getested, die 141 histologisch gesicherte Läsionen enthielten. Die Vorhersage der Gesundheit dieser Läsionen ergab eine Sensitivität von 88 % bei einer Spezifität von 72 %. Diese Werte sind den in der Literatur bekannten Vorhersagen von Expertenradiologen ähnlich. Die Vorhersagen enthielten durchschnittlich 2,5 zusätzliche bösartige Funde pro Patientin, die sich als falsch klassifizierte Artefakte herausstellten.rn

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.

Software tools and efficient algorithms for the feature detection, feature tracking, event localization, and visualization of large sets of atmospheric data

Data sets describing the state of the earth's atmosphere are of great importance in the atmospheric sciences. Over the last decades, the quality and sheer amount of the available data increased significantly, resulting in a rising demand for new tools capable of handling and analysing these large, multidimensional sets of atmospheric data. The interdisciplinary work presented in this thesis covers the development and the application of practical software tools and efficient algorithms from the field of computer science, aiming at the goal of enabling atmospheric scientists to analyse and to gain new insights from these large data sets. For this purpose, our tools combine novel techniques with well-established methods from different areas such as scientific visualization and data segmentation. In this thesis, three practical tools are presented. Two of these tools are software systems (Insight and IWAL) for different types of processing and interactive visualization of data, the third tool is an efficient algorithm for data segmentation implemented as part of Insight.Insight is a toolkit for the interactive, three-dimensional visualization and processing of large sets of atmospheric data, originally developed as a testing environment for the novel segmentation algorithm. It provides a dynamic system for combining at runtime data from different sources, a variety of different data processing algorithms, and several visualization techniques. Its modular architecture and flexible scripting support led to additional applications of the software, from which two examples are presented: the usage of Insight as a WMS (web map service) server, and the automatic production of a sequence of images for the visualization of cyclone simulations. The core application of Insight is the provision of the novel segmentation algorithm for the efficient detection and tracking of 3D features in large sets of atmospheric data, as well as for the precise localization of the occurring genesis, lysis, merging and splitting events. Data segmentation usually leads to a significant reduction of the size of the considered data. This enables a practical visualization of the data, statistical analyses of the features and their events, and the manual or automatic detection of interesting situations for subsequent detailed investigation. The concepts of the novel algorithm, its technical realization, and several extensions for avoiding under- and over-segmentation are discussed. As example applications, this thesis covers the setup and the results of the segmentation of upper-tropospheric jet streams and cyclones as full 3D objects. Finally, IWAL is presented, which is a web application for providing an easy interactive access to meteorological data visualizations, primarily aimed at students. As a web application, the needs to retrieve all input data sets and to install and handle complex visualization tools on a local machine are avoided. The main challenge in the provision of customizable visualizations to large numbers of simultaneous users was to find an acceptable trade-off between the available visualization options and the performance of the application. Besides the implementational details, benchmarks and the results of a user survey are presented.

Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Autonomous Vehicle and Internet on Vehicles

In questa tesi mi occupo di spiegare come si comportano i veicoli autonomi per prendere tutte le decisioni e come i dati dei sensori di ogni auto vengono condivisi con la flotta di veicoli

The Small Project Observatory: Visualizing Software Ecosystems

Software evolution research has focused mostly on analyzing the evolution of single software systems. However, it is rarely the case that a project exists as standalone, independent of others. Rather, projects exist in parallel within larger contexts in companies, research groups or even the open-source communities. We call these contexts software ecosystems, and on this paper we present The Small Project Observatory, a prototype tool which aims to support the analysis of project ecosystems through interactive visualization and exploration. We present a case-study of exploring an ecosystem using our tool, we describe about the architecture of the tool, and we distill the lessons learned during the tool-building experience.