Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

New insights into methodology and interpretation of osteoarthritis. The study of Frassetto identified skeletal collection.

Osteoarthritis (OA) or degenerative joint disease (DJD) is a pathology which affects the synovial joints and characterised by a focal loss of articular cartilage and subsequent bony reaction of the subcondral and marginal bone. Its etiology is best explained by a multifactorial model including: age, sex, genetic and systemic factors, other predisposing diseases and functional stress. In this study the results of the investigation of a modern identified skeletal collection will be presented. In particular, we will focus on the relationship between the presence of OA at various joints. The joint modifications have been analysed using a new methodology that allows the scoring of different degrees of expression of the features considered. Materials and Methods The sample examined comes from the Sassari identified skeletal collection (part of “Frassetto collections”). The individuals were born between 1828 and 1916 and died between 1918 and 1932. Information about sex and age is known for all the individuals. The occupation is known for 173 males and 125 females. Data concerning the occupation of the individuals indicate a preindustrial and rural society. OA has been diagnosed when eburnation (EB) or loss of morphology (LM) were present, or when at least two of the following: marginal lipping (ML), esostosis (EX) or erosion (ER), were present. For each articular surface affected a “mean score” was calculated, reflecting the “severity” of the alterations. A further “score” was calculated for each joint. In the analysis sexes and age classes were always kept separate. For the statistical analyses non parametric test were used. Results The results show there is an increase of OA with age in all the joints analyzed and in particular around 50 years and 60 years. The shoulder, the hip and the knee are the joints mainly affected with ageing while the ankle is the less affected; the correlation values confirm this result. The lesion which show the major correlation with age is the ML. In our sample males are more frequently and more severely affected by OA than females, particularly at the superior limbs, while hip and knee are similarly affected in the two sexes. Lateralization shows some positive results in particular in the right shoulder of males and in various articular surfaces especially of the superior limb of both males and females; articular surfaces and joints are quite always lateralized to the right. Occupational analyses did not show remarkable results probably because of the homogeneity of the sample; males although performing different activities are quite all employed in stressful works. No highest prevalence of knee and hip OA was found in farm-workers respect to the other males. Discussion and Conclusion In this work we propose a methodology to score the different features, necessary to diagnose OA, that allows the investigation of the severity of joint degeneration. This method is easier than the one proposed by Buikstra and Ubelaker (1994), but in the same time allows a quite detailed recording of the features. Epidemiological results can be interpreted quite simply and they are in accordance with other studies; more difficult is the interpretation of the occupational results because many questions concerning the activities performed by the individuals of the collection during their lifespan cannot be solved. Because of this, caution is suggested in the interpretation of bioarcheological specimens. With this work we hope to contribute to the discussion on the puzzling problem of the etiology of OA. The possibility of studying identified skeletons will add important data to the description of osseous features of OA, enriching the medical documentation, based on different criteria. Even if we are aware that the clinical diagnosis is different from the palaeopathological one we think our work will be useful in clarifying some epidemiological as well as pathological aspects of OA.

Nanocrystalline Silicon Based Films for Renewable Energy Applications

The present thesis is focused on the study of innovative Si-based materials for third generation photovoltaics. In particular, silicon oxi-nitride (SiOxNy) thin films and multilayer of Silicon Rich Carbide (SRC)/Si have been characterized in view of their application in photovoltaics. SiOxNy is a promising material for applications in thin-film solar cells as well as for wafer based silicon solar cells, like silicon heterojunction solar cells. However, many issues relevant to the material properties have not been studied yet, such as the role of the deposition condition and precursor gas concentrations on the optical and electronic properties of the films, the composition and structure of the nanocrystals. The results presented in the thesis aim to clarify the effects of annealing and oxygen incorporation within nc-SiOxNy films on its properties in view of the photovoltaic applications. Silicon nano-crystals (Si NCs) embedded in a dielectric matrix were proposed as absorbers in all-Si multi-junction solar cells due to the quantum confinement capability of Si NCs, that allows a better match to the solar spectrum thanks to the size induced tunability of the band gap. Despite the efficient solar radiation absorption capability of this structure, its charge collection and transport properties has still to be fully demonstrated. The results presented in the thesis aim to the understanding of the transport mechanisms at macroscopic and microscopic scale. Experimental results on SiOxNy thin films and SRC/Si multilayers have been obtained at macroscopical and microscopical level using different characterizations techniques, such as Atomic Force Microscopy, Reflection and Transmission measurements, High Resolution Transmission Electron Microscopy, Energy-Dispersive X-ray spectroscopy and Fourier Transform Infrared Spectroscopy. The deep knowledge and improved understanding of the basic physical properties of these quite complex, multi-phase and multi-component systems, made by nanocrystals and amorphous phases, will contribute to improve the efficiency of Si based solar cells.

Volunteer-based coral reef monitoring: reliability of data, environmental education and implications for conservation

Coral reefs are the most biodiverse ecosystems of the ocean and they provide notable ecosystem services. Nowadays, they are facing a number of local anthropogenic threats and environmental change is threatening their survivorship on a global scale. Large-scale monitoring is necessary to understand environmental changes and to perform useful conservation measurements. Governmental agencies are often underfunded and are not able of sustain the necessary spatial and temporal large-scale monitoring. To overcome the economic constrains, in some cases scientists can engage volunteers in environmental monitoring. Citizen Science enables the collection and analysis of scientific data at larger spatial and temporal scales than otherwise possible, addressing issues that are otherwise logistically or financially unfeasible. “STE: Scuba Tourism for the Environment” was a volunteer-based Red Sea coral reef biodiversity monitoring program. SCUBA divers and snorkelers were involved in the collection of data for 72 taxa, by completing survey questionnaires after their dives. In my thesis, I evaluated the reliability of the data collected by volunteers, comparing their questionnaires with those completed by professional scientists. Validation trials showed a sufficient level of reliability, indicating that non-specialists performed similarly to conservation volunteer divers on accurate transects. Using the data collected by volunteers, I developed a biodiversity index that revealed spatial trends across surveyed areas. The project results provided important feedbacks to the local authorities on the current health status of Red Sea coral reefs and on the effectiveness of the environmental management. I also analysed the spatial and temporal distribution of each surveyed taxa, identifying abundance trends related with anthropogenic impacts. Finally, I evaluated the effectiveness of the project to increase the environmental education of volunteers and showed that the participation in STEproject significantly increased both the knowledge on coral reef biology and ecology and the awareness of human behavioural impacts on the environment.

Investigating interpreter-mediated interaction in the Chinese bilingual courtroom: Analysis based on a multimodal corpus

This research project is based on the Multimodal Corpus of Chinese Court Interpreting (MUCCCI [mutʃɪ]), a small-scale multimodal corpus on the basis of eight authentic court hearings with Chinese-English interpreting in Mainland China. The corpus has approximately 92,500 word tokens in total. Besides the transcription of linguistic and para-linguistic features, utilizing the facial expression classification rules suggested by Black and Yacoob (1995), MUCCCI also includes approximately 1,200 annotations of facial expressions linked to the six basic types of human emotions, namely, anger, disgust, happiness, surprise, sadness, and fear (Black & Yacoob, 1995). This thesis is an example of conducting qualitative analysis on interpreter-mediated courtroom interactions through a multimodal corpus. In particular, miscommunication events (MEs) and the reasons behind them were investigated in detail. During the analysis, although queries were conducted based on non-verbal annotations when searching for MEs, both verbal and non-verbal features were considered indispensable parts contributing to the entire context. This thesis also includes a detailed description of the compilation process of MUCCCI utilizing ELAN, from data collection to transcription, POS tagging and non-verbal annotation. The research aims at assessing the possibility and feasibility of conducting qualitative analysis through a multimodal corpus of court interpreting. The concept of integrating both verbal and non-verbal features to contribute to the entire context is emphasized. The qualitative analysis focusing on MEs can provide an inspiration for improving court interpreters’ performances. All the constraints and difficulties presented can be regarded as a reference for similar research in the future.