Marine biodiversity survey in the Northern Red Sea: a large-scale monitoring carried out in collaboration with volunteer divers

Concerns over global change and its effect on coral reef survivorship have highlighted the need for long-term datasets and proxy records, to interpret environmental trends and inform policymakers. Citizen science programs have showed to be a valid method for collecting data, reducing financial and time costs for institutions. This study is based on the elaboration of data collected by recreational divers and its main purpose is to evaluate changes in the state of coral reef biodiversity in the Red Sea over a long term period and validate the volunteer-based monitoring method. Volunteers recreational divers completed a questionnaire after each dive, recording the presence of 72 animal taxa and negative reef conditions. Comparisons were made between records from volunteers and independent records from a marine biologist who performed the same dive at the same time. A total of 500 volunteers were tested in 78 validation trials. Relative values of accuracy, reliability and similarity seem to be comparable to those performed by volunteer divers on precise transects in other projects, or in community-based terrestrial monitoring. 9301 recreational divers participated in the monitoring program, completing 23,059 survey questionnaires in a 5-year period. The volunteer-sightings-based index showed significant differences between the geographical areas. The area of Hurghada is distinguished by a medium-low biodiversity index, heavily damaged by a not controlled anthropic exploitation. Coral reefs along the Ras Mohammed National Park at Sharm el Sheikh, conversely showed high biodiversity index. The detected pattern seems to be correlated with the conservation measures adopted. In our experience and that of other research institutes, citizen science can integrate conventional methods and significantly reduce costs and time. Involving recreational divers we were able to build a large data set, covering a wide geographic area. The main limitation remains the difficulty of obtaining an homogeneous spatial sampling distribution.

Technologies for Ambient intelligence: from Smart Objects to Sensor Networks

n the last few years, the vision of our connected and intelligent information society has evolved to embrace novel technological and research trends. The diffusion of ubiquitous mobile connectivity and advanced handheld portable devices, amplified the importance of the Internet as the communication backbone for the fruition of services and data. The diffusion of mobile and pervasive computing devices, featuring advanced sensing technologies and processing capabilities, triggered the adoption of innovative interaction paradigms: touch responsive surfaces, tangible interfaces and gesture or voice recognition are finally entering our homes and workplaces. We are experiencing the proliferation of smart objects and sensor networks, embedded in our daily living and interconnected through the Internet. This ubiquitous network of always available interconnected devices is enabling new applications and services, ranging from enhancements to home and office environments, to remote healthcare assistance and the birth of a smart environment. This work will present some evolutions in the hardware and software development of embedded systems and sensor networks. Different hardware solutions will be introduced, ranging from smart objects for interaction to advanced inertial sensor nodes for motion tracking, focusing on system-level design. They will be accompanied by the study of innovative data processing algorithms developed and optimized to run on-board of the embedded devices. Gesture recognition, orientation estimation and data reconstruction techniques for sensor networks will be introduced and implemented, with the goal to maximize the tradeoff between performance and energy efficiency. Experimental results will provide an evaluation of the accuracy of the presented methods and validate the efficiency of the proposed embedded systems.

Quality of Service in Distributed Stream Processing for large scale Smart Pervasive Environments

The wide diffusion of cheap, small, and portable sensors integrated in an unprecedented large variety of devices and the availability of almost ubiquitous Internet connectivity make it possible to collect an unprecedented amount of real time information about the environment we live in. These data streams, if properly and timely analyzed, can be exploited to build new intelligent and pervasive services that have the potential of improving people's quality of life in a variety of cross concerning domains such as entertainment, health-care, or energy management. The large heterogeneity of application domains, however, calls for a middleware-level infrastructure that can effectively support their different quality requirements. In this thesis we study the challenges related to the provisioning of differentiated quality-of-service (QoS) during the processing of data streams produced in pervasive environments. We analyze the trade-offs between guaranteed quality, cost, and scalability in streams distribution and processing by surveying existing state-of-the-art solutions and identifying and exploring their weaknesses. We propose an original model for QoS-centric distributed stream processing in data centers and we present Quasit, its prototype implementation offering a scalable and extensible platform that can be used by researchers to implement and validate novel QoS-enforcement mechanisms. To support our study, we also explore an original class of weaker quality guarantees that can reduce costs when application semantics do not require strict quality enforcement. We validate the effectiveness of this idea in a practical use-case scenario that investigates partial fault-tolerance policies in stream processing by performing a large experimental study on the prototype of our novel LAAR dynamic replication technique. Our modeling, prototyping, and experimental work demonstrates that, by providing data distribution and processing middleware with application-level knowledge of the different quality requirements associated to different pervasive data flows, it is possible to improve system scalability while reducing costs.

Exploring host-pathogen interactions through protein microarray. Large-scale protein microarray analysis revealed novel human receptors for the staphylococcal immune evasion protein FLIPr and for the neisserial adhesin NadA

Adhesion, immune evasion and invasion are key determinants during bacterial pathogenesis. Pathogenic bacteria possess a wide variety of surface exposed and secreted proteins which allow them to adhere to tissues, escape the immune system and spread throughout the human body. Therefore, extensive contacts between the human and the bacterial extracellular proteomes take place at the host-pathogen interface at the protein level. Recent researches emphasized the importance of a global and deeper understanding of the molecular mechanisms which underlie bacterial immune evasion and pathogenesis. Through the use of a large-scale, unbiased, protein microarray-based approach and of wide libraries of human and bacterial purified proteins, novel host-pathogen interactions were identified. This approach was first applied to Staphylococcus aureus, cause of a wide variety of diseases ranging from skin infections to endocarditis and sepsis. The screening led to the identification of several novel interactions between the human and the S. aureus extracellular proteomes. The interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting, was characterized using label-free techniques and functional assays. The same approach was also applied to Neisseria meningitidis, major cause of bacterial meningitis and fulminant sepsis worldwide. The screening led to the identification of several potential human receptors for the neisserial adhesin A (NadA), an important adhesion protein and key determinant of meningococcal interactions with the human host at various stages. The interaction between NadA and human LOX-1 (low-density oxidized lipoprotein receptor) was confirmed using label-free technologies and cell binding experiments in vitro. Taken together, these two examples provided concrete insights into S. aureus and N. meningitidis pathogenesis, and identified protein microarray coupled with appropriate validation methodologies as a powerful large scale tool for host-pathogen interactions studies.

Energy-efficient Communication and Estimation in Wireless Sensor Networks

This thesis focuses on the energy efficiency in wireless networks under the transmission and information diffusion points of view. In particular, on one hand, the communication efficiency is investigated, attempting to reduce the consumption during transmissions, while on the other hand the energy efficiency of the procedures required to distribute the information among wireless nodes in complex networks is taken into account. For what concerns energy efficient communications, an innovative transmission scheme reusing source of opportunity signals is introduced. This kind of signals has never been previously studied in literature for communication purposes. The scope is to provide a way for transmitting information with energy consumption close to zero. On the theoretical side, starting from a general communication channel model subject to a limited input amplitude, the theme of low power transmission signals is tackled under the perspective of stating sufficient conditions for the capacity achieving input distribution to be discrete. Finally, the focus is shifted towards the design of energy efficient algorithms for the diffusion of information. In particular, the endeavours are aimed at solving an estimation problem distributed over a wireless sensor network. The proposed solutions are deeply analyzed both to ensure their energy efficiency and to guarantee their robustness against losses during the diffusion of information (against information diffusion truncation more in general).

Constraining mass and shape of galaxy clusters through large scale structures

The mass estimation of galaxy clusters is a crucial point for modern cosmology, and can be obtained by several different techniques. In this work we discuss a new method to measure the mass of galaxy clusters connecting the gravitational potential of the cluster with the kinematical properties of its surroundings. We explore the dynamics of the structures located in the region outside virialized cluster, We identify groups of galaxies, as sheets or filaments, in the cluster outer region, and model how the cluster gravitational potential perturbs the motion of these structures from the Hubble fow. This identification is done in the redshift space where we look for overdensities with a filamentary shape. Then we use a radial mean velocity profile that has been found as a quite universal trend in simulations, and we fit the radial infall velocity profile of the overdensities found. The method has been tested on several cluster-size haloes from cosmological N-body simulations giving results in very good agreement with the true values of virial masses of the haloes and orientation of the sheets. We then applied the method to the Coma cluster and even in this case we found a good correspondence with previous. It is possible to notice a mass discrepancy between sheets with different alignments respect to the center of the cluster. This difference can be used to reproduce the shape of the cluster, and to demonstrate that the spherical symmetry is not always a valid assumption. In fact, if the cluster is not spherical, sheets oriented along different axes should feel a slightly different gravitational potential, and so give different masses as result of the analysis described before. Even this estimation has been tested on cosmological simulations and then applied to Coma, showing the actual non-sphericity of this cluster.

Integrating wireless sensor networks and internet of things: A coap-based approach

L'obiettivo su cui è stata basata questa Tesi di Laurea è stato quello di integrare la tecnologia delle Wireless Sensor Networks (WSN) al contesto dell'Internet delle cose (IoT). Per poter raggiungere questo obiettivo, il primo passo è stato quello di approfondire il concetto dell'Internet delle cose, in modo tale da comprendere se effettivamente fosse stato possibile applicarlo anche alle WSNs. Quindi è stata analizzata l'architettura delle WSNs e successivamente è stata fatta una ricerca per capire quali fossero stati i vari tipi di sistemi operativi e protocolli di comunicazione supportati da queste reti. Infine sono state studiate alcune IoT software platforms. Il secondo passo è stato quindi di implementare uno stack software che abilitasse la comunicazione tra WSNs e una IoT platform. Come protocollo applicativo da utilizzare per la comunicazione con le WSNs è stato usato CoAP. Lo sviluppo di questo stack ha consentito di estendere la piattaforma SensibleThings e il linguaggio di programmazione utilizzato è stato Java. Come terzo passo è stata effettuata una ricerca per comprendere a quale scenario di applicazione reale, lo stack software progettato potesse essere applicato. Successivamente, al fine di testare il corretto funzionamento dello stack CoAP, è stata sviluppata una proof of concept application che simulasse un sistema per la rilevazione di incendi. Questo scenario era caratterizzato da due WSNs che inviavano la temperatura rilevata da sensori termici ad un terzo nodo che fungeva da control center, il cui compito era quello di capire se i valori ricevuti erano al di sopra di una certa soglia e quindi attivare un allarme. Infine, l'ultimo passo di questo lavoro di tesi è stato quello di valutare le performance del sistema sviluppato. I parametri usati per effettuare queste valutazioni sono stati: tempi di durata delle richieste CoAP, overhead introdotto dallo stack CoAP alla piattaforma Sensible Things e la scalabilità di un particolare componente dello stack. I risultati di questi test hanno mostrato che la soluzione sviluppata in questa tesi ha introdotto un overheadmolto limitato alla piattaforma preesistente e inoltre che non tutte le richieste hanno la stessa durata, in quanto essa dipende dal tipo della richiesta inviata verso una WSN. Tuttavia, le performance del sistema potrebbero essere ulteriormente migliorate, ad esempio sviluppando un algoritmo che consenta la gestione concorrente di richieste CoAP multiple inviate da uno stesso nodo. Inoltre, poichè in questo lavoro di tesi non è stato considerato il problema della sicurezza, una possibile estensione al lavoro svolto potrebbe essere quello di implementare delle politiche per una comunicazione sicura tra Sensible Things e le WSNs.

Weighted geometric mean of large-scale matrices: numerical analysis and algorithms

Computing the weighted geometric mean of large sparse matrices is an operation that tends to become rapidly intractable, when the size of the matrices involved grows. However, if we are not interested in the computation of the matrix function itself, but just in that of its product times a vector, the problem turns simpler and there is a chance to solve it even when the matrix mean would actually be impossible to compute. Our interest is motivated by the fact that this calculation has some practical applications, related to the preconditioning of some operators arising in domain decomposition of elliptic problems. In this thesis, we explore how such a computation can be efficiently performed. First, we exploit the properties of the weighted geometric mean and find several equivalent ways to express it through real powers of a matrix. Hence, we focus our attention on matrix powers and examine how well-known techniques can be adapted to the solution of the problem at hand. In particular, we consider two broad families of approaches for the computation of f(A) v, namely quadrature formulae and Krylov subspace methods, and generalize them to the pencil case f(A\B) v. Finally, we provide an extensive experimental evaluation of the proposed algorithms and also try to assess how convergence speed and execution time are influenced by some characteristics of the input matrices. Our results suggest that a few elements have some bearing on the performance and that, although there is no best choice in general, knowing the conditioning and the sparsity of the arguments beforehand can considerably help in choosing the best strategy to tackle the problem.

UWB radar sensor networks: Detection algorithms design and experimental analysis

In the last years radar sensor networks for localization and tracking in indoor environment have generated more and more interest, especially for anti-intrusion security systems. These networks often use Ultra Wide Band (UWB) technology, which consists in sending very short (few nanoseconds) impulse signals. This approach guarantees high resolution and accuracy and also other advantages such as low price, low power consumption and narrow-band interference (jamming) robustness. In this thesis the overall data processing (done in MATLAB environment) is discussed, starting from experimental measures from sensor devices, ending with the 2D visualization of targets movements over time and focusing mainly on detection and localization algorithms. Moreover, two different scenarios and both single and multiple target tracking are analyzed.

MaxMAC: a Maximally Traffic-Adaptive MAC Protocol for Wireless Sensor Networks

Energy efficiency is a major concern in the design of Wireless Sensor Networks (WSNs) and their communication protocols. As the radio transceiver typically accounts for a major portion of a WSN node’s power consumption, researchers have proposed Energy-Efficient Medium Access (E2-MAC) protocols that switch the radio transceiver off for a major part of the time. Such protocols typically trade off energy-efficiency versus classical quality of service parameters (throughput, latency, reliability). Today’s E2-MAC protocols are able to deliver little amounts of data with a low energy footprint, but introduce severe restrictions with respect to throughput and latency. Regrettably, they yet fail to adapt to varying traffic load at run-time. This paper presents MaxMAC, an E2-MAC protocol that targets at achieving maximal adaptivity with respect to throughput and latency. By adaptively tuning essential parameters at run-time, the protocol reaches the throughput and latency of energy-unconstrained CSMA in high-traffic phases, while still exhibiting a high energy-efficiency in periods of sparse traffic. The paper compares the protocol against a selection of today’s E2-MAC protocols and evaluates its advantages and drawbacks.

Phenology for tropoclimatological surveys and large-scale mapping

Biotic and abiotic phenological observations can be collected from continental to local spatial scale. Plant phenological observations may only be recorded wherever there is vegetation. Fog, snow and ice are available as phenological para-meters wherever they appear. The singularity of phenological observations is the possibility of spatial intensification to a microclimatic scale where the equipment of meteorological measurements is too expensive for intensive campaigning. The omnipresence of region-specific phenological parameters allows monitoring for a spatially much more detailed assessment of climate change than with weather data. We demonstrate this concept with phenological observations with the use of a special network in the Canton of Berne, Switzerland, with up to 600 observations sites (more than 1 to 10 km² of the inhabited area). Classic cartography, gridding, the integration into a Geographic Information System GIS and large-scale analysis are the steps to a detailed knowledge of topoclimatic conditions of a mountainous area. Examples of urban phenology provide other types of spatially detailed applications. Large potential in phenological mapping in future analyses lies in combining traditionally observed species-specific phenology with remotely sensed and modelled phenology that provide strong spatial information. This is a long history from cartographic intuition to algorithm-based representations of phenology.