Synthetic data generation for the assessment of antimicrobial resistance through machine learning

As a consequence of the diffusion of next generation sequencing techniques, metagenomics databases have become one of the most promising repositories of information about features and behavior of microorganisms. One of the subjects that can be studied from those data are bacteria populations. Next generation sequencing techniques allow to study the bacteria population within an environment by sampling genetic material directly from it, without the needing of culturing a similar population in vitro and observing its behavior. As a drawback, it is quite complex to extract information from those data and usually there is more than one way to do that; AMR is no exception. In this study we will discuss how the quantified AMR, which regards the genotype of the bacteria, can be related to the bacteria phenotype and its actual level of resistance against the specific substance. In order to have a quantitative information about bacteria genotype, we will evaluate the resistome from the read libraries, aligning them against CARD database. With those data, we will test various machine learning algorithms for predicting the bacteria phenotype. The samples that we exploit should resemble those that could be obtained from a natural context, but are actually produced by a read libraries simulation tool. In this way we are able to design the populations with bacteria of known genotype, so that we can relay on a secure ground truth for training and testing our algorithms.

Waste management in Forlì-Cesena province: Life Cycle Assessment (LCA) of Forlì incinerator

This work assesses the environmental impact of a municipal solid waste incinerator with energy recovery in Forlì-Cesena province (Emilia-Romagna region, Italy). The methodology used is Life Cycle Assessment (LCA). As the plant already applies the best technologies available in waste treatment, this study focuses on the fate of the residues (bottom and fly ash) produced during combustion. Nine scenarios are made, based on different ash treatment disposing/recycling techniques. The functional unit is the amount of waste incinerated in 2011. Boundaries are set from waste arrival in the plant to the disposal/recovery of the residues produced, with energy recovery. Only the operative period is considered. Software used is GaBi 4 and the LCIA method used is CML2001. The impact categories analyzed are: abiotic depletion, acidification, eutrophication, freshwater aquatic ecotoxicity, global warming, human toxicity, ozone layer depletion, photochemical oxidant formation, terrestrial ecotoxicity and primary energy demand. Most of the data are taken from Herambiente. When primary data are not available, data from Ecoinvent and GaBi databases or literature data are used. The whole incineration process is sustainable, due to the relevant avoided impact given by co-generator. As far as regards bottom ash treatment, the most influential process is the impact savings from iron recovery. Bottom ash recycling in road construction or as building material are both valid alternatives, even if the first option faces legislative limits in Italy. Regarding fly ash inertization, the adding of cement and Ferrox treatment results the most feasible alternatives. However, this inertized fly ash can maintain its hazardous nature. The only method to ensure the stability of an inertized fly ash is to couple two different stabilization treatments. Ash stabilization technologies shall improve with the same rate of the flexibility of the national legislation about incineration residues recycling.

Life cycle assessment in construction field: A life cycle cost analysis of reinforcement concrete bridge

The present work is included in the context of the assessment of sustainability in the construction field and is aimed at estimating and analyzing life cycle cost of the existing reinforced concrete bridge “Viadotto delle Capre” during its entire life. This was accomplished by a comprehensive data collection and results evaluation. In detail, the economic analysis of the project is performed. The work has investigated possible design alternatives for maintenance/rehabilitation and end-of-life operations, when structural, functional, economic and also environmental requirements have to be fulfilled. In detail, the economic impact of different design options for the given reinforced concrete bridge have been assessed, whereupon the most economically, structurally and environmentally efficient scenario was chosen. The Integrated Life-Cycle Analysis procedure and Environmental Impact Assessment were also discussed in this work. The scope of this thesis is to illustrate that Life Cycle Cost analysis as part of Life Cycle Assessment approach could be effectively used to drive the design and management strategy of new and existing structures. The final objective of this contribution is to show how an economic analysis can influence decision-making in the definition of the most sustainable design alternatives. The designers can monitor the economic impact of different design strategies in order to identify the most appropriate option.

Citizen science as a tool for the environmental quality assessment of the Mediterranean coastal habitats

The growing need to assess the environmental status of the Mediterranean coastal marine habitats and the large availability of data collected by Reef Check Italia onlus (RCI) volunteers suggest the possibility to develop innovative and reliable indices that may support decision makers in applying conservation strategies. The aims of this study were to check the reliability of data collected by RCI volunteers, analyse the spatial and temporal distribution of RCI available data, resume the knowledge on the biology and ecology of the monitored species, and develop innovative indices to asses the ecological quality of Mediterranean subtidal rocky shores and coralligenous habitats. Subtidal rocky shores and coralligenous were chosen because these are the habitats more attractive for divers; therefore mlst data are referring to them, moreover subtidal rocky bottom are strongly affected by coastal urbanisation, land use, fishing and tourist activities, that increase pollution, turbidity and sedimentation. Non-indigenous species (NIS) have been recognized as a major threat to the integrity of Mediterranean native communities because of their proliferation, spread and impact on resident communities. Monitoring of NIS’ spreading dynamics at the basin spatial scale is difficult but urgent. According to a field test, the training provided by RCI appears adequate to obtain reliable data by volunteers. Based on data collected by RCI volunteers, three main categories of indices were developed: indices based on species diversity, indices on the occurrence non-indigenous species, and indices on species sensitive toward physical, chemical and biological disturbances. As case studies, indices were applied to stretches of coastline defined according to management criteria (province territories and marine protected areas). The assessments of ecological quality in the Tavolara Marine Protected Area using the species sensitivities index were consisten with those previously obtained with traditional methods.

First assessment on genetic structure and phylogeography of Mediterranean blue shark (prionace glauca, L. 1758) population using mitochondrial gene variation: a comparison with the Atlantic.

The blue shark, Prionace glauca, is one of the most vagile shark species worldwide distributed. The particular body shape allows blue sharks make transoceanic movements, leading to a circumglobal distribution. Due to its reproductive cycle, an extraordinarily high number of specimens is globally registered but, even if it is still a major bycatch of longline fishery rather than a commercial target, it is characterized by a high vulnerability. In this perspective it is important to increase the amount of informations regarding its population extent in the different worldwide areas, evaluating the possible phylogeographic patterns between different locations. This study, included in the "MedBlueSGen" European project, aims exactly at filling a gap in knowledges regarding the genetic population structure of the Mediterranean blue sharks, which has never been investigated before, with a comparison with the North-Eastern Atlantic blue shark population. To reach this objective, we used a dataset of samples from different Mediterranean areas implementing it with some samples from North-Eastern Atlantic. Analyzing the variability of the two mitochondrial markers control region and cytochrome b, with the design of new species-specific primer pairs, we assessed the mitochondrial genetic structure of Mediterranean and North-Eastern Atlantic samples, focusing on the analysis of their possible connectivity, and we tried to reconstruct their demographic history and population size. Data analyses highlighted the absence of a genetic structuring within the Mediterranean and among it and North-Eastern Atlantic, suggesting that the Strait of Gibraltar doesn't represent a phylogeographic barrier. These results are coherent to what has been found in similar investigations on other worldwide blue shark populations. Analysis of the historical demographic trend revealed a general stable pattern for the cytochrome-b and a slightly population expansion for the control region marker.

Assessment of marine litter in the Western Adriatic Sea and its impact on marine biota

Due to its environmental, safety, health and socio-economic impacts, marine litter has been recognized as a 21st century global challenge, so that it has been included in Descriptor 10 of the EU MSFD. For its morphological features and anthropogenic pressures, the Adriatic Sea is very sensitive to the accumulation of debris, but data are inconsistent and fragmented. This thesis, in the framework of DeFishGear project, intents to assess marine litter on beaches and on seafloor in the Western Adriatic sea, and test if debris ingestion by fish occurs. Three beaches were sampled during two surveys in 2015. Benthic litter monitoring was carried out in the FAO GSA17 during fall 2014, using a rapido trawl. Litter ingestion was investigated through gut contents analysis of 260 fish belonging to 8 commercial species collected in Western Gulf of Venice. Average litter density on beaches was 1.5 items/m2 during spring, and decreased to 0.8 items/m2 in summer. Litter composition was heterogeneous and varied among sites, even if no significant differences were found. Most of debris consisted of plastic sheets, fragments, polystyrene pieces, mussels nets and cottons bud sticks, showing that sources are many and include aquaculture, land-based activities and local users of beaches. Average density of benthic litter was 913 items/Km2 (82 Kg/Km2). Plastic dominated in terms of numbers and weight, and consisted mainly of bags, sheets and mussel nets. The highest density was found close to the coast, and sources driving the major differences in litter distribution were mussel farms and shipping lanes. Litter ingestion occurred in 47% of examined fish, mainly consisting of fibers. Among species, S. pilchardus swallowed almost all debris categories. Findinds may provide a baseline to set the necessary measures to manage and minimize marine litter in the Western Adriatic region and to protect aquatic life from plastic pollution, even accounting the possible implications on human health.