Quality and safety of oils and fats obtained as co-products or by-products of the food chain and destined to animal production

The aim of the first part of this thesis was to evaluate the effect of trans fatty acid- (TFA), contaminant, polycyclic aromatic hydrocarbon (PAH)- and oxidation productenriched diets on the content of TFA and conjugated linoleic acid (CLA) isomers in meat and liver of both poultry and rabbit. The enriched feedings were prepared with preselected fatty co-and by-products that contained low and high levels of TFA (low, palm fatty acid distillate; high, hydrogenated palm fatty acid distillate), environmental contaminants (dioxins and PCBs) (two different fish oils), PAH (olive oil acid oils and pomace olive oil from chemical refining, for low and high levels) and oxidation products (sunflower-olive oil blend before and after frying), so as to obtain single feedings with three enrichment degrees (high, medium and low) of the compound of interest. This experimental set-up is a part of a large, collaborative European project (http://www.ub.edu/feedfat/), where other chemical and health parameters are assessed. Lipids were extracted, methylated with diazomethane, then transmethylated with 2N KOH/methanol and analyzed by GC and silver-ion TLC-GC. TFA and CLA were determined in the fats, the feedings, meat and liver of both poultry and rabbit. In general, the level of TFA and CLA in meat and liver mainly varied according to those originally found in the feeding fats. It must be pointed out, though, that TFA and CLA accumulation was different for the two animal species, as well as for the two types of tissues. The TFA composition of meat and liver changes according to the composition of the oils added to the feeds with some differences between species. Chicken meat with skin shows higher TFA content (2.6–5.4 fold) than rabbit meat, except for the “PAH” trial. Chicken liver shows higher TFA content (1.2–2.1 fold) than rabbit liver, except for the “TRANS” and “PAH” trials. In both chicken and rabbit meats, the TFA content was higher for the “TRANS” trial, followed by the “DIOXIN” trial. Slight differences were found on the “OXIDATION” and “PAH” trends in both types of meats. In both chicken and rabbit livers, the TFA content was higher for the “TRANS” trial, followed by those of the “PAH”, “DIOXIN” and “OXIDATION” trials. This trend, however, was not identical to that of feeds, where the TFA content varied as follows: “TRANS” > “DIOXIN” >“PAH” > “OXIDATION”. In chicken and rabbit meat samples, C18:1 TFA were the most abundant, followed by C18:2 TFA and C18:3 TFA, except for the “DIOXIN” trial where C18:3 TFA > C18:2 TFA. In chicken and rabbit liver samples of the “TRANS” and “OXIDATION” trials, C18:1 TFA were the most abundant, followed by C18:2 TFA and C18:3 TFA, whereas C18:3 TFA > C18:2 in the “DIOXIN” trial. Slight differences were found on the “PAH” trend in livers from both species. The second part of the thesis dealt with the study of lipid oxidation in washed turkey muscle added with different antioxidants. The evaluation on the oxidative stability of muscle foods found that oxidation could be measured by headspace solid phase microestraction (SPME) of hexanal and propanal. To make this method effective, an antioxidant system was added to stored muscle to stop the oxidative processes. An increase in ionic strength of the sample was also implemented to increase the concentration of aldehydes in the headspace. This method was found to be more sensitive than the commonly used thiobarbituric acid reactive substances (TBARs) method. However, after antioxidants were added and oxidation was stopped, the concentration of aldehydes decreased. It was found that the decrease in aldehyde concentration was due to the binding of the aldehydes to muscle proteins, thus decreasing the volatility and making them less detectable.

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.

Development of new tools and devices for CMB and foreground data analysis and future experiments

The discovery of the Cosmic Microwave Background (CMB) radiation in 1965 is one of the fundamental milestones supporting the Big Bang theory. The CMB is one of the most important source of information in cosmology. The excellent accuracy of the recent CMB data of WMAP and Planck satellites confirmed the validity of the standard cosmological model and set a new challenge for the data analysis processes and their interpretation. In this thesis we deal with several aspects and useful tools of the data analysis. We focus on their optimization in order to have a complete exploitation of the Planck data and contribute to the final published results. The issues investigated are: the change of coordinates of CMB maps using the HEALPix package, the problem of the aliasing effect in the generation of low resolution maps, the comparison of the Angular Power Spectrum (APS) extraction performances of the optimal QML method, implemented in the code called BolPol, and the pseudo-Cl method, implemented in Cromaster. The QML method has been then applied to the Planck data at large angular scales to extract the CMB APS. The same method has been applied also to analyze the TT parity and the Low Variance anomalies in the Planck maps, showing a consistent deviation from the standard cosmological model, the possible origins for this results have been discussed. The Cromaster code instead has been applied to the 408 MHz and 1.42 GHz surveys focusing on the analysis of the APS of selected regions of the synchrotron emission. The new generation of CMB experiments will be dedicated to polarization measurements, for which are necessary high accuracy devices for separating the polarizations. Here a new technology, called Photonic Crystals, is exploited to develop a new polarization splitter device and its performances are compared to the devices used nowadays.

Application Platforms for the Internet of Things: Theory, Architecture, Protocols, Data Formats, and Privacy

The Internet of Things (IoT) is the next industrial revolution: we will interact naturally with real and virtual devices as a key part of our daily life. This technology shift is expected to be greater than the Web and Mobile combined. As extremely different technologies are needed to build connected devices, the Internet of Things field is a junction between electronics, telecommunications and software engineering. Internet of Things application development happens in silos, often using proprietary and closed communication protocols. There is the common belief that only if we can solve the interoperability problem we can have a real Internet of Things. After a deep analysis of the IoT protocols, we identified a set of primitives for IoT applications. We argue that each IoT protocol can be expressed in term of those primitives, thus solving the interoperability problem at the application protocol level. Moreover, the primitives are network and transport independent and make no assumption in that regard. This dissertation presents our implementation of an IoT platform: the Ponte project. Privacy issues follows the rise of the Internet of Things: it is clear that the IoT must ensure resilience to attacks, data authentication, access control and client privacy. We argue that it is not possible to solve the privacy issue without solving the interoperability problem: enforcing privacy rules implies the need to limit and filter the data delivery process. However, filtering data require knowledge of how the format and the semantics of the data: after an analysis of the possible data formats and representations for the IoT, we identify JSON-LD and the Semantic Web as the best solution for IoT applications. Then, this dissertation present our approach to increase the throughput of filtering semantic data by a factor of ten.

Opportunistic Data Gathering and Dissemination in Urban Scenarios

In the era of the Internet of Everything, a user with a handheld or wearable device equipped with sensing capability has become a producer as well as a consumer of information and services. The more powerful these devices get, the more likely it is that they will generate and share content locally, leading to the presence of distributed information sources and the diminishing role of centralized servers. As of current practice, we rely on infrastructure acting as an intermediary, providing access to the data. However, infrastructure-based connectivity might not always be available or the best alternative. Moreover, it is often the case where the data and the processes acting upon them are of local scopus. Answers to a query about a nearby object, an information source, a process, an experience, an ability, etc. could be answered locally without reliance on infrastructure-based platforms. The data might have temporal validity limited to or bounded to a geographical area and/or the social context where the user is immersed in. In this envisioned scenario users could interact locally without the need for a central authority, hence, the claim of an infrastructure-less, provider-less platform. The data is owned by the users and consulted locally as opposed to the current approach of making them available globally and stay on forever. From a technical viewpoint, this network resembles a Delay/Disruption Tolerant Network where consumers and producers might be spatially and temporally decoupled exchanging information with each other in an adhoc fashion. To this end, we propose some novel data gathering and dissemination strategies for use in urban-wide environments which do not rely on strict infrastructure mediation. While preserving the general aspects of our study and without loss of generality, we focus our attention toward practical applicative scenarios which help us capture the characteristics of opportunistic communication networks.

Learning with Kernels on Graphs: DAG-based kernels, data streams and RNA function prediction.

In many application domains data can be naturally represented as graphs. When the application of analytical solutions for a given problem is unfeasible, machine learning techniques could be a viable way to solve the problem. Classical machine learning techniques are defined for data represented in a vectorial form. Recently some of them have been extended to deal directly with structured data. Among those techniques, kernel methods have shown promising results both from the computational complexity and the predictive performance point of view. Kernel methods allow to avoid an explicit mapping in a vectorial form relying on kernel functions, which informally are functions calculating a similarity measure between two entities. However, the definition of good kernels for graphs is a challenging problem because of the difficulty to find a good tradeoff between computational complexity and expressiveness. Another problem we face is learning on data streams, where a potentially unbounded sequence of data is generated by some sources. There are three main contributions in this thesis. The first contribution is the definition of a new family of kernels for graphs based on Directed Acyclic Graphs (DAGs). We analyzed two kernels from this family, achieving state-of-the-art results from both the computational and the classification point of view on real-world datasets. The second contribution consists in making the application of learning algorithms for streams of graphs feasible. Moreover,we defined a principled way for the memory management. The third contribution is the application of machine learning techniques for structured data to non-coding RNA function prediction. In this setting, the secondary structure is thought to carry relevant information. However, existing methods considering the secondary structure have prohibitively high computational complexity. We propose to apply kernel methods on this domain, obtaining state-of-the-art results.

Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA.

The use of Ground Penetrating Radar and alternative geophysical techniques for assessing embankments and dykes safety

The research is part of a survey for the detection of the hydraulic and geotechnical conditions of river embankments funded by the Reno River Basin Regional Technical Service of the Region Emilia-Romagna. The hydraulic safety of the Reno River, one of the main rivers in North-Eastern Italy, is indeed of primary importance to the Emilia-Romagna regional administration. The large longitudinal extent of the banks (several hundreds of kilometres) has placed great interest in non-destructive geophysical methods, which, compared to other methods such as drilling, allow for the faster and often less expensive acquisition of high-resolution data. The present work aims to experience the Ground Penetrating Radar (GPR) for the detection of local non-homogeneities (mainly stratigraphic contacts, cavities and conduits) inside the Reno River and its tributaries embankments, taking into account supplementary data collected with traditional destructive tests (boreholes, cone penetration tests etc.). A comparison with non-destructive methodologies likewise electric resistivity tomography (ERT), Multi-channels Analysis of Surface Waves (MASW), FDEM induction, was also carried out in order to verify the usability of GPR and to provide integration of various geophysical methods in the process of regular maintenance and check of the embankments condition. The first part of this thesis is dedicated to the explanation of the state of art concerning the geographic, geomorphologic and geotechnical characteristics of Reno River and its tributaries embankments, as well as the description of some geophysical applications provided on embankments belonging to European and North-American Rivers, which were used as bibliographic basis for this thesis realisation. The second part is an overview of the geophysical methods that were employed for this research, (with a particular attention to the GPR), reporting also their theoretical basis and a deepening of some techniques of the geophysical data analysis and representation, when applied to river embankments. The successive chapters, following the main scope of this research that is to highlight advantages and drawbacks in the use of Ground Penetrating Radar applied to Reno River and its tributaries embankments, show the results obtained analyzing different cases that could yield the formation of weakness zones, which successively lead to the embankment failure. As advantages, a considerable velocity of acquisition and a spatial resolution of the obtained data, incomparable with respect to other methodologies, were recorded. With regard to the drawbacks, some factors, related to the attenuation losses of wave propagation, due to different content in clay, silt, and sand, as well as surface effects have significantly limited the correlation between GPR profiles and geotechnical information and therefore compromised the embankment safety assessment. Recapitulating, the Ground Penetrating Radar could represent a suitable tool for checking up river dike conditions, but its use has significantly limited by geometric and geotechnical characteristics of the Reno River and its tributaries levees. As a matter of facts, only the shallower part of the embankment was investigate, achieving also information just related to changes in electrical properties, without any numerical measurement. Furthermore, GPR application is ineffective for a preliminary assessment of embankment safety conditions, while for detailed campaigns at shallow depth, which aims to achieve immediate results with optimal precision, its usage is totally recommended. The cases where multidisciplinary approach was tested, reveal an optimal interconnection of the various geophysical methodologies employed, producing qualitative results concerning the preliminary phase (FDEM), assuring quantitative and high confidential description of the subsoil (ERT) and finally, providing fast and highly detailed analysis (GPR). Trying to furnish some recommendations for future researches, the simultaneous exploitation of many geophysical devices to assess safety conditions of river embankments is absolutely suggested, especially to face reliable flood event, when the entire extension of the embankments themselves must be investigated.