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European Union (EU) general farm animal directive applicability in Africa and bovine welfare assessment in Italy
Get PDFThe was conducted with objectives focusing on the EU farm animal directive and applicability in Africa focusing in Ethiopia, the welfare assessment and the effect of different bovine respiratory disease (BRD) treatment protocols in beef cattle fattening unit and the calves navel healing and fitness for transport. Different methodology was applied: relevant literates, international organization, regional organization, countries legislations, standards were assessed and reviewed, for assessing beef welfare and biosecurity a modified version of the Italian protocol for assessing beef cattle was adopted which is part of the ClassyFarm monitoring scheme, 264 Limousine bulls with an average age of 11 months at the entrance to fattening unit were considered. Mycoplasma bovis was tested using RT-PCR at arrival and with culture at after 15 days of arrival to the fattening unit. For studying the navel healing and effect on transport the navels of 299 dairy calves (55 males, 244 females) aged 0–90 days were examined. As a conclusion, the European Union (EU) farm directive, could not be completely implement in African countries like Ethiopia, but it could serve as a good starting point, so as after successful identification of the farm animal welfare critical points may help as a starting point with modification to the local situation in the ground. In beef welfare assessment, integration of different assessment parameters could be of useful, when assessing beef welfare, and further continues detail physiological parameters of welfare assessment for integration with other assessment protocols should be studied, our finding indicate that also BRD was a major welfare and health concern in the studied population and evidence the difficulties of antimicrobial treatment of M. bovis associated BRD. In transporting calves with a completely healed navel should be considered best practice because it ensures that calves that are too young are not transported
Deep learning and embeddings for problems of computational biology
Get PDFThe development of Next Generation Sequencing promotes Biology in the Big Data era. The ever-increasing gap between proteins with known sequences and those with a complete functional annotation requires computational methods for automatic structure and functional annotation. My research has been focusing on proteins and led so far to the development of three novel tools, DeepREx, E-SNPs&GO and ISPRED-SEQ, based on Machine and Deep Learning approaches.
DeepREx computes the solvent exposure of residues in a protein chain. This problem is relevant for the definition of structural constraints regarding the possible folding of the protein. DeepREx exploits Long Short-Term Memory layers to capture residue-level interactions between positions distant in the sequence, achieving state-of-the-art performances. With DeepRex, I conducted a large-scale analysis investigating the relationship between solvent exposure of a residue and its probability to be pathogenic upon mutation.
E-SNPs&GO predicts the pathogenicity of a Single Residue Variation. Variations occurring on a protein sequence can have different effects, possibly leading to the onset of diseases. E-SNPs&GO exploits protein embeddings generated by two novel Protein Language Models (PLMs), as well as a new way of representing functional information coming from the Gene Ontology. The method achieves state-of-the-art performances and is extremely time-efficient when compared to traditional approaches.
ISPRED-SEQ predicts the presence of Protein-Protein Interaction sites in a protein sequence. Knowing how a protein interacts with other molecules is crucial for accurate functional characterization. ISPRED-SEQ exploits a convolutional layer to parse local context after embedding the protein sequence with two novel PLMs, greatly surpassing the current state-of-the-art.
All methods are published in international journals and are available as user-friendly web servers. They have been developed keeping in mind standard guidelines for FAIRness (FAIR: Findable, Accessible, Interoperable, Reusable) and are integrated into the public collection of tools provided by ELIXIR, the European infrastructure for Bioinformatics
Enhancing the reliability of electric transportation motors through insulation coordination and improved qualification
Get PDFThe ambitious goals of increasing the efficiency, performance and power densities of transportation drives cannot be met with compromises in the motor reliability. For the insulation specialists the challenge will be critical as the use of wide-bandgap converters (WBG, based on SiC and GaN switches) and the higher operating voltages expected for the next generation drives will enhance the electrical stresses to unprecedented levels. It is expected for the DC bus in aircrafts to reach 800 V (split +/-400 V) and beyond, driven by the urban air mobility sector and the need for electrification of electro-mechanical/electro-hydraulic actuators (an essential part of the "More Electric Aircraft" concept). Simultaneously the DC bus in electric vehicles (EV) traction motors is anticipated to increase up to 1200 V very soon.
The electrical insulation system is one of the most delicate part of the machine in terms of failure probability. In particular, the appearance of partial discharges (PD) is disruptive on the reliability of the drive, especially under fast repetitive transients. Extensive experimental activity has been performed to extend the body of knowledge on PD inception, endurance under PD activity, and explore and identify new phenomena undermining the reliability. The focus has been concentrated on the impact of the WGB-converter produced waveforms and the environmental conditions typical of the aeronautical sector on insulation models. Particular effort was put in the analysis at the reduced pressures typical of aircraft cruise altitude operation.
The results obtained, after a critical discussion, have been used to suggest a coordination between the insulation PD inception voltage with the converter stresses and to propose an improved qualification procedure based on the existing IEC 60034-18-41 standard.Gli obiettivi ambiziosi di aumentare l'efficienza, le prestazioni e le densità di potenza degli azionamenti per il trasporto non possono essere raggiunti con compromessi sulla affidabilità dei motori. Per gli specialisti dell'isolamento la sfida sarà cruciale, poiché sia l'uso di convertitori a wide-bandgap (WBG) basati su semiconduttori SiC e GaN, sia le tensioni operative più elevate previste per i prossimi azionamenti, aumenteranno gli stress elettrici a livelli senza precedenti. Si prevede che il bus DC negli aeromobili raggiunga gli 800 V (split +/-400 V) e oltre, sotto la spinta del settore della mobilità aerea urbana e dalla necessità di elettrificare gli attuatori elettromeccanici/elettroidraulici (parte essenziale del concetto di "More Electric Aircraft"). Contemporaneamente, si stima che presto nei motori per trazione di veicoli elettrici il DC bus aumenterà fino a 1200 V.
Il sistema di isolamento elettrico è una delle parti più delicate di una macchina elettrica in termini di probabilità di guasto. In particolare, la comparsa di scariche parziali (PD) è deleteria per l'affidabilità dell'azionamento, soprattutto in presenza di transitori veloci e ripetitivi. In questa tesi è stata condotta un'ampia attività sperimentale per ampliare le conoscenze sull'innesco di PD, sulla resistenza dei materiali in loro presenza e per identificare nuovi fenomeni che compromettono l'affidabilità dell'isolante. L'attenzione si è concentrata sull'impatto che hanno le forme d'onda prodotte da convertitori WGB e le condizioni ambientali tipiche del settore trasporti su modelli di isolamento. Particolare impegno è stato profuso nell'analisi alle pressioni ridotte tipiche del funzionamento alle quote di crociera degli aerei di linea.
I risultati ottenuti, dopo una discussione critica, sono stati utilizzati per suggerire un coordinamento tra le tensione di innesco di scarica e gli stress del convertitore, al fine di proporre una procedura di qualificazione migliorata basata sulla già esistente norma IEC 60034-18-41
Essays in development and political economy
Get PDFThis thesis includes three papers studying diverse questions in development, economic history and political economy. The first two chapters, that fall under development and economic history, use novel forms of text data and analysis to answer the questions at hand. The first chapter studies the possible impact of a historically matrilineal and matrilocal caste group on present day outcomes of gender equality. It introduces a novel surname strategy using electoral data to deduce caste from the surnames of electors and overcomes the unavailability of caste data. It shows proof of persistence of caste in space. And finally, following a matching exercise it concludes that the effect of the matrilineal and matrilocal caste on present day gender outcomes might not be as strong as previously believed. The second paper studies how discriminatory fake news arises and spatially diffuses. It focuses on India at the onset of the COVID-19 pandemic: on March 30, a Muslim convention (the Tablighi Jamaat) in New Delhi became publicly recognized as a COVID hotspot, and the next day, fake news on Muslims intentionally spreading the virus spiked. Using Twitter data, it finds, in cross-sectional and difference-in-difference settings, that discriminatory fake news became much more widespread after March 30 (1) in New Delhi, (2) in districts closer to New Delhi, and (3) in districts with higher social media interactions with New Delhi. Further, it shows that, after March 30, discriminatory fake news was more common in districts historically exposed to attacks by Muslim groups. The final paper is a political economy paper that studies the short term and long term effect of earlier eligibility on voting in the context of a large North Italian municipality setting with little institutional barriers to voting. It also studies the differing mobilisation of members in the same household by newly eligible voters
Catchability and survival of the resources during fishing operation
Get PDFThe present Ph.D. thesis aims to test and evaluate by-catch reduction devices (BRDs) that minimize the retention of undersized fish and do not penalize revenues of the fishing industry. Considering that a fraction of fish that escape from fishing gear or that are rejected at the sea probably does not survive (unaccounted mortality), it is a major concern for sustainable fisheries management, as unaccounted mortality may lead to biased stock assessment since they will tend to underestimate fishing mortality and overestimate stock size. In this context, in the present Ph.D. thesis, the escape survival (i.e. survival of the fish escaped through the trawl net codend) of the Mullus barbatus Linnaeus 1758 and the discard survival (survival of fish rejected at the sea after being hauled on deck) of Trachurus trachurus were evaluated for the first time in the central Mediterranean Sea. In conclusion, the use of underwater lights in Mediterranean trawl fisheries should be carefully regulated through ad hoc measures that are currently lacking, to minimize the potential impacts of artificial light on some already overexploited stocks. Even if further works should be carried out in the future to test BRDs performances in different areas and seasons, the T90 50 mm codend and the Grid-T45 40 mm seem promising tools to reduce the catch of undersized individuals and contribute to mitigating the current overfishing of Parapenaeus longirostris and Merluccius merluccius. The escape survival of M. barbatus was high and thanks to an improved methodology the bias in the sampling was minimized. However, for improved stock assessment of M. barbatus, the experiment should be repeated to provide accurate escape mortality estimates. While the discard survival of T. trachurus was very low and according to the landing obligation (Reg. EU 1380/2013) all the juveniles of the species should be landed
Study and characterization of polymorphs of BTBT derivatives and their application in organic electronics
Get PDFThe perquisites of organic semiconductors (OSCs) in the field of organic electronics have attracted much attention due to the advantages like cost-effectiveness, solution processibility, etc. A key property in OSCs is charge carrier mobility, which depends on molecular packing, as even the slightest changes in the packing of OSC can significantly impact the mobility. Organic molecules are constructed by weak interactions, which makes the OSCs prone to adopt multiple packing arrangements, thus giving rise to polymorphism. Therefore, polymorph screening in bulk and thin films is crucial for material development.
This thesis aims to present a systematic study of polymorphism of [1]benzothieno[3,2-b]benzothiophene (BTBT) derivatives functionalized with different side chains. The role of peripheral side chains has been studied since they can promote different packing arrangements.
The bulk polymorph screening of OSCs was approached with conventional solution mediated recrystallization experiments like evaporation, slurry maturation, anti-solvent precipitation, etc. Each of the polymorphs were inspected for their relative stability and the kinetics of transformation was evaluated. Polymorphism in thin films was also investigated for selected OSCs. Non-equilibrium methods like, thermal gradient and solution shearing were employed to examine the nucleation, crystal growth and morphology in controlled crystallization conditions. After careful analysis of crystal phases in bulk and thin films, OFETs have been fabricated by optimizing the manufacturing conditions and the hole mobility values were extracted. The charge transport property of the OSCs tested for OFETs was supported by the ionization potential and transfer integrals calculation. An attempt to correlate the solid-state structure to electronic properties was carried out. For some of the molecules, mechanical properties have been also investigated, as the response to mechanical stress is highly susceptible to packing arrangements and the intermolecular interaction energy contributions.
Additionally, collaborative research was carried out by solving and analysing the crystal structures of six oligorylene molecules
The linguistic background and the tradition of the Hebrew language of the Secunda (second column of Origen's Hexapla)
Get PDFLe terme Secunda désigne la deuxième colonne de la synopse hexaplaire d’Origène. Cette synopse comportait six colonnes, d’où le nom Hexapla utilisé pour la désigner : la première contenait le texte hébreu original de l’Ancien Testament, la deuxième (Secunda) sa transcription phonétique en caractères grecs, les quatre autres les différentes traductions grecques de la Bible. La présence de graphèmes de vocaliques grecs dans la Secunda permet de mener une étude grammaticale complète de cette source, d’un point de vue phonétique et morphologique. Il manque encore actuellement une recherche qui développe le rapport entre la tradition hébraïque de la Secunda, telle qu’elle ressort de la transcription, et les autres traditions hébraïques attestées : celles sans graphèmes vocaliques (c’est-à-dire la tradition samaritaine et le corpus qumranien) et les traditions plus tardives et vocalisées pendant la période médiévale (les traditions massorétique tibérienne, babylonienne et palestinienne). Ce dernier point est précisément l’objet de cette thèse, qui vise à mieux comprendre le statut de l’hébreu de la Secunda, ses relations avec les autres traditions hébraïques et sa place dans l’histoire de la langue. Cette question est abordée à travers différentes étapes : en partant d’une étude phonétique et morphologique de la langue hébraïque de la colonne, on arrive à une hypothèse de datation qui permet une comparaison directe entre l’hébreu hexaplaire et les autres traditions mentionnées ci-dessus. La comparaison entre la Secunda et les autres traditions est cruciale pour situer correctement la Secunda dans l’histoire de la langue hébraïque : au niveau synchronique, elle permet de mettre en évidence ses éléments dialectaux, documentés dans les transcriptions de la Secunda et dans les traditions de la même époque ; au niveau diachronique, elle fournit des terminus ante ou post quem pour des phénomènes bien attestés dans les traditions tardives.The term Secunda refers to the second column of Origen’s synopsis of Hexapla. This synopsis consisted of six columns, from which comes the name Hexapla employed to designate it: the first column contained the original Hebrew text of the Old Testament, the second (Secunda) its phonetic transcription in Greek characters, the other four the different Greek translations of the Bible. The presence of Greek vowel graphemes in the Secunda makes possible to conduct a comprehensive grammatical study of that source, phonetically and morphologically. At present there is still a lack of research that develops the relationship between the Hebrew language tradition of the Secunda, as emerging from the transcription, and the other attested Hebrew language traditions: those without vowel graphemes (i.e., the Samaritan tradition and the Qumran corpus) and the later, vocalized in the medieval period (the Tiberian, Babylonian and the Palestinian). The latter point is precisely the subject of this thesis, which aims to better understand the Hebrew language status of Secunda, its relation to other traditions of Hebrew and its place in the history of the language. This issue is approached through different stages: moving from a phonetic and morphological study of the Hebrew language of the column, we arrive at a dating hypothesis that allows for a direct comparison between the hexaplaric Hebrew and the other traditions mentioned above. The comparison between the Secunda and the other traditions is crucial to correctly situating the Secunda in the history of the Hebrew language: at the synchronic level, it serves the function of highlighting its dialectal elements, documented in the transcriptions of the Secunda and in the traditions of the same epoch; at the diachronic level, it provides a terminus ante or post quem for phenomena well attested in the late traditions
Real-time anomaly detection of gamma-ray bursts for the Cherenkov Telescope Array using deep learning
Get PDFThe Cherenkov Telescope Array (CTA) will be the next-generation ground-based observatory to study the universe in the very-high-energy domain. The observatory will rely on a Science Alert Generation (SAG) system to analyze the real-time data from the telescopes and generate science alerts. The SAG system will play a crucial role in the search and follow-up of transients from external alerts, enabling multi-wavelength and multi-messenger collaborations. It will maximize the potential for the detection of the rarest phenomena, such as gamma-ray bursts (GRBs), which are the science case for this study.
This study presents an anomaly detection method based on deep learning for detecting gamma-ray burst events in real-time. The performance of the proposed method is evaluated and compared against the Li&Ma standard technique in two use cases of serendipitous discoveries and follow-up observations, using short exposure times. The method shows promising results in detecting GRBs and is flexible enough to allow real-time search for transient events on multiple time scales. The method does not assume background nor source models and doe not require a minimum number of photon counts to perform analysis, making it well-suited for real-time analysis.
Future improvements involve further tests, relaxing some of the assumptions made in this study as well as post-trials correction of the detection significance. Moreover, the ability to detect other transient classes in different scenarios must be investigated for completeness. The system can be integrated within the SAG system of CTA and deployed on the onsite computing clusters. This would provide valuable insights into the method's performance in a real-world setting and be another valuable tool for discovering new transient events in real-time. Overall, this study makes a significant contribution to the field of astrophysics by demonstrating the effectiveness of deep learning-based anomaly detection techniques for real-time source detection in gamma-ray astronomy.Il Cherenkov Telescope Array (CTA) sarà l'osservatorio terrestre di prossima generazione per lo studio dell'universo nel dominio delle altissime energie. L'osservatorio sfrutterà il sistema software di Science Alert Generation (SAG) per l'analisi in tempo reale dei dati osservativi e per generare automaticamente allerte scientifiche. Il sistema SAG svolgerà un ruolo da protagonista nella ricerca e nel follow-up di fenomeni transienti a seguito di allerte esterne, consentendo collaborazioni multi-wavelength e multi-messenger. Massimizzerà la capacità di rilevare i fenomeni più rari, come i lampi di raggi gamma (GRBs), che sono il caso scientifico di questo studio.
Questo studio presenta una tecnica di anomaly detection basata sul deep learning per la rilevazione in tempo reale di GRBs. Le prestazioni della tecnica proposta sono valutate e confrontate con la tecnica standard di Li&Ma, nei due casi d'uso scientifici di serendipitous discoveries e follow-up observations, considerando brevi tempi di esposizione. La tecnica proposta mostra risultati promettenti e è abbastanza flessibile da consentire la ricerca di eventi transienti su più tempi scala. Non necessita di fare ipotesi sui modelli del background e della sorgente e non richiede un numero minimo di conteggi di fotoni per eseguire l'analisi, rendendola adatta per l'analisi in tempo reale.
Miglioramenti futuri includono ulteriori test, accantonando alcune delle ipotesi semplificative assunte in questo studio, così come la correzione post-trial della significatività di rilevazione. Inoltre, dovrà essere testata la capacità di rilevare altre classi di transienti oltre ai GRBs. L'integrazione all'interno del sistema SAG e la messa in produzione nei centri di calcolo onsite, fornirebbe preziose informazioni sulle prestazioni del metodo con dati non simulati. Nel complesso, questo studio fornisce un contributo significativo al campo dell'astrofisica delle alte energie e dimostra l'efficacia della tecnica di anomaly detection per la rilevazione in tempo reale di fenomeni transienti
Economic preferences in the health setting. Three case studies concerning the needs of breast cancer patients, pain management in oncology and extreme end-of-life decisions
Get PDFThe thesis describes three studies concerning the role of the Economic Preference set investigated in the Global Preference Survey (GPS) in the following cases:
1) the needs of women with breast cancer;
2) pain undertreament in oncology;
3) legal status of euthanasia and assisted suicide.
The analyses, based on regression techniques, were always conducted on the basis of aggregate data and revealed in all cases a possible role of the Economic Preferences studied, also resisting the concomitant effect of the other covariates that were considered from time to time. Regarding individual studies, the related conclusion are:
1) Economic Preferences appear to play a role in influencing the needs of women with breast cancer, albeit of non-trivial interpretation, statistically "resisting" the concomitant effect of the other independent variables considered. However, these results should be considered preliminary and need further confirmation, possibly with prospective studies conducted at the level of the individual;\ud
2) the results show a good degree of internal consistency with regard to pro-social GPS scores, since they are all found to be non-statistically significant and united, albeit only weakly in trend, by a negative correlation with the % of pain undertreated patients. Sharper, at least statistically, is the role of Patience and Willingness to Take Risk, although of more complex empirical interpretation.
3) the results seem to indicate an obvious role of Economic Preferences, however difficult to interpret empirically. Less evidence, at least on the inferential level, emerged, however, regarding variables that, based on common sense, should play an even more obvious role than Economic Preferences in orienting attitudes toward euthanasia and assisted suicide, namely Healthcare System, Legal Origin, and Kinship Tightness; striking, in particular, is the inability to prove a role for the dominant religious orientation even with a simple bivariate analysis
Artisanal food productions of animal origin: exploring food safety in the age of Whole Genome Sequencing
Get PDFThe artisanal food chain is enriched by a wide diversity of local food productions with delightful organoleptic characteristics and valuable nutritional properties. Despite their increasing worldwide popularity and appeal, several food safety challenges are addressed in artisanal facilities context suffering from less standardized processing conditions. In such scenario, recent advances in molecular typing and genomic surveillance (e.g., Whole Genome Sequencing [WGS]) represent an unprecedent solution capable of inferring sources of contamination as well as contributing to food safety along the artisanal food continuum.
The overall objective of this PhD thesis was to explore potential microbial hazards among different artisanal food productions of animal origins (dairy and meat-derived) typical of the food culture and heritage landscape belonging to Mediterranean countries. Three different studies were then carried out, specifically focussing on: 1) compare the seasonal variability of microbiological quality and potential occurrence of microbial hazards in two batches of Italian artisanal fermented dairy and meat productions; 2) Investigate genetic relationships as well as virulome and resistome of foodborne pathogens isolated within dairy and meat-derived productions located in Italy, Spain, Portugal and Morocco; 3) investigate the population structure, virulome, resistome and mobilome of Klebsiella spp. isolates collected from study 1, including an extended range of public sequences