Spectrum shaping and its application: spread-spectrum clock generator and circuits for ultra wide band

Electromagnetic spectrum can be identified as a resource for the designer, as well as for the manufacturer, from two complementary points of view: first, because it is a good in great demand by many different kind of applications; second, because despite its scarce availability, it may be advantageous to use more spectrum than necessary. This is the case of Spread-Spectrum Systems, those systems in which the transmitted signal is spread over a wide frequency band, much wider, in fact, than the minimum bandwidth required to transmit the information being sent. Part I of this dissertation deals with Spread-Spectrum Clock Generators (SSCG) aiming at reducing Electro Magnetic Interference (EMI) of clock signals in integrated circuits (IC) design. In particular, the modulation of the clock and the consequent spreading of its spectrum are obtained through a random modulating signal outputted by a chaotic map, i.e. a discrete-time dynamical system showing chaotic behavior. The advantages offered by this kind of modulation are highlighted. Three different prototypes of chaos-based SSCG are presented in all their aspects: design, simulation, and post-fabrication measurements. The third one, operating at a frequency equal to 3GHz, aims at being applied to Serial ATA, standard de facto for fast data transmission to and from Hard Disk Drives. The most extreme example of spread-spectrum signalling is the emerging ultra-wideband (UWB) technology, which proposes the use of large sections of the radio spectrum at low amplitudes to transmit high-bandwidth digital data. In part II of the dissertation, two UWB applications are presented, both dealing with the advantages as well as with the challenges of a wide-band system, namely: a chaos-based sequence generation method for reducing Multiple Access Interference (MAI) in Direct Sequence UWB Wireless-Sensor-Networks (WSNs), and design and simulations of a Low-Noise Amplifier (LNA) for impulse radio UWB. This latter topic was studied during a study-abroad period in collaboration with Delft University of Technology, Delft, Netherlands.

The Enhanced Single-dish Control System and wide surveys of compact sources

The Italian radio telescopes currently undergo a major upgrade period in response to the growing demand for deep radio observations, such as surveys on large sky areas or observations of vast samples of compact radio sources. The optimised employment of the Italian antennas, at first constructed mainly for VLBI activities and provided with a control system (FS – Field System) not tailored to single-dish observations, required important modifications in particular of the guiding software and data acquisition system. The production of a completely new control system called ESCS (Enhanced Single-dish Control System) for the Medicina dish started in 2007, in synergy with the software development for the forthcoming Sardinia Radio Telescope (SRT). The aim is to produce a system optimised for single-dish observations in continuum, spectrometry and polarimetry. ESCS is also planned to be installed at the Noto site. A substantial part of this thesis work consisted in designing and developing subsystems within ESCS, in order to provide this software with tools to carry out large maps, spanning from the implementation of On-The-Fly fast scans (following both conventional and innovative observing strategies) to the production of single-dish standard output files and the realisation of tools for the quick-look of the acquired data. The test period coincided with the commissioning phase for two devices temporarily installed – while waiting for the SRT to be completed – on the Medicina antenna: a 18-26 GHz 7-feed receiver and the 14-channel analogue backend developed for its use. It is worth stressing that it is the only K-band multi-feed receiver at present available worldwide. The commissioning of the overall hardware/software system constituted a considerable section of the thesis work. Tests were led in order to verify the system stability and its capabilities, down to sensitivity levels which had never been reached in Medicina using the previous observing techniques and hardware devices. The aim was also to assess the scientific potential of the multi-feed receiver for the production of wide maps, exploiting its temporary availability on a mid-sized antenna. Dishes like the 32-m antennas at Medicina and Noto, in fact, offer the best conditions for large-area surveys, especially at high frequencies, as they provide a suited compromise between sufficiently large beam sizes to cover quickly large areas of the sky (typical of small-sized telescopes) and sensitivity (typical of large-sized telescopes). The KNoWS (K-band Northern Wide Survey) project is aimed at the realisation of a full-northern-sky survey at 21 GHz; its pilot observations, performed using the new ESCS tools and a peculiar observing strategy, constituted an ideal test-bed for ESCS itself and for the multi-feed/backend system. The KNoWS group, which I am part of, supported the commissioning activities also providing map-making and source-extraction tools, in order to complete the necessary data reduction pipeline and assess the general system scientific capabilities. The K-band observations, which were carried out in several sessions along the December 2008-March 2010 period, were accompanied by the realisation of a 5 GHz test survey during the summertime, which is not suitable for high-frequency observations. This activity was conceived in order to check the new analogue backend separately from the multi-feed receiver, and to simultaneously produce original scientific data (the 6-cm Medicina Survey, 6MS, a polar cap survey to complete PMN-GB6 and provide an all-sky coverage at 5 GHz).

La Pace Calda. La nascita del movimento antinucleare negli Stati Uniti e in Gran Bretagna, 1957-1963

The aim of this proposal is to offer an alternative perspective on the study of Cold War, since insufficient attention is usually paid to those organizations that mobilized against the development and proliferation of nuclear weapons. The antinuclear movement began to mobilize between the 1950s and the 1960s, when it finally gained the attention of public opinion, and helped to build a sort of global conscience about nuclear bombs. This was due to the activism of a significant part of the international scientific community, which offered powerful intellectual and political legitimization to the struggle, and to the combined actions of the scientific and organized protests. This antinuclear conscience is something we usually tend to consider as a fait accompli in contemporary world, but the question is to show its roots, and the way it influenced statesmen and political choices during the period of nuclear confrontation of the early Cold War. To understand what this conscience could be and how it should be defined, we have to look at the very meaning of the nuclear weapons that has deeply modified the sense of war. Nuclear weapons seemed to be able to destroy human beings everywhere with no realistic forms of control of the damages they could set off, and they represented the last resource in the wide range of means of mass destruction. Even if we tend to consider this idea fully rational and incontrovertible, it was not immediately born with the birth of nuclear weapons themselves. Or, better, not everyone in the world did immediately share it. Due to the particular climate of Cold War confrontation, deeply influenced by the persistence of realistic paradigms in international relations, British and U.S. governments looked at nuclear weapons simply as «a bullet». From the Trinity Test to the signature of the Limited Test Ban Treaty in 1963, many things happened that helped to shift this view upon nuclear weapons. First of all, more than ten years of scientific protests provided a more concerned knowledge about consequences of nuclear tests and about the use of nuclear weapons. Many scientists devoted their social activities to inform public opinion and policy-makers about the real significance of the power of the atom and the related danger for human beings. Secondly, some public figures, as physicists, philosophers, biologists, chemists, and so on, appealed directly to the human community to «leave the folly and face reality», publicly sponsoring the antinuclear conscience. Then, several organizations leaded by political, religious or radical individuals gave to this protests a formal structure. The Campaign for Nuclear Disarmament in Great Britain, as well as the National Committee for a Sane Nuclear Policy in the U.S., represented the voice of the masses against the attempts of governments to present nuclear arsenals as a fundamental part of the international equilibrium. Therefore, the antinuclear conscience could be defined as an opposite feeling to the development and the use of nuclear weapons, able to create a political issue oriented to the influence of military and foreign policies. Only taking into consideration the strength of this pressure, it seems possible to understand not only the beginning of nuclear negotiations, but also the reasons that permitted Cold War to remain cold.

Very Long Baseline Interferometry in Italy Wide-field VLBI imaging and astrometry and prospects for an Italian VLBI network including the Sardinia Radio Telescope

In this thesis the use of widefield imaging techniques and VLBI observations with a limited number of antennas are explored. I present techniques to efficiently and accurately image extremely large UV datasets. Very large VLBI datasets must be reduced into multiple, smaller datasets if today’s imaging algorithms are to be used to image them. I present a procedure for accurately shifting the phase centre of a visibility dataset. This procedure has been thoroughly tested and found to be almost two orders of magnitude more accurate than existing techniques. Errors have been found at the level of one part in 1.1 million. These are unlikely to be measurable except in the very largest UV datasets. Results of a four-station VLBI observation of a field containing multiple sources are presented. A 13 gigapixel image was constructed to search for sources across the entire primary beam of the array by generating over 700 smaller UV datasets. The source 1320+299A was detected and its astrometric position with respect to the calibrator J1329+3154 is presented. Various techniques for phase calibration and imaging across this field are explored including using the detected source as an in-beam calibrator and peeling of distant confusing sources from VLBI visibility datasets. A range of issues pertaining to wide-field VLBI have been explored including; parameterising the wide-field performance of VLBI arrays; estimating the sensitivity across the primary beam both for homogeneous and heterogeneous arrays; applying techniques such as mosaicing and primary beam correction to VLBI observations; quantifying the effects of time-average and bandwidth smearing; and calibration and imaging of wide-field VLBI datasets. The performance of a computer cluster at the Istituto di Radioastronomia in Bologna has been characterised with regard to its ability to correlate using the DiFX software correlator. Using existing software it was possible to characterise the network speed particularly for MPI applications. The capabilities of the DiFX software correlator, running on this cluster, were measured for a range of observation parameters and were shown to be commensurate with the generic performance parameters measured. The feasibility of an Italian VLBI array has been explored, with discussion of the infrastructure required, the performance of such an array, possible collaborations, and science which could be achieved. Results from a 22 GHz calibrator survey are also presented. 21 out of 33 sources were detected on a single baseline between two Italian antennas (Medicina to Noto). The results and discussions presented in this thesis suggest that wide-field VLBI is a technique whose time has finally come. Prospects for exciting new science are discussed in the final chapter.

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

Nuovo scaffold biomimetico per il trattamento delle lesioni osteocondrali: studio clinico pilota

Nel corso degli anni diverse sono le tecniche proposte per il trattamento delle lesioni osteocondrali, da quelle mini-invasive con stimolazione midollare fino a quelle più aggressive basate sul trapianto di tessuti autologhi o eterologhi. Tutti questi metodi hanno comunque dei difetti ed è questo il motivo per cui il trattamento delle lesioni osteocondrali rappresenta tuttora una sfida per il chirurgo ortopedico, in considerazione dell’alta specializzazione e del basso potere di guarigione del tessuto cartilagineo. Buoni risultati sono stati ottenuti con innesti bioingegnerizzati o matrici polimeriche impiantati nei siti danneggiati. La quantità di scaffolds in uso per la riparazione condrale ed osteocondrale è molto ampia; essi differiscono non solo per il tipo di materiali usati per la loro realizzazione, ma anche per la presenza di promotori di una o più linee cellulari , su base condrogenica o osteogenica. Quando ci si approccia ad una lesione condrale di grandi dimensioni, l’osso sub-condrale è anch’esso coinvolto e necessita di trattamento per ottenere il corretto ripristino degli strati articolari più superficiali. La scelta più giusta sembra essere un innesto osteocondrale bioingegnerizzato, pronto per l’uso ed immediatamente disponibile, che consenta di effettuare il trattamento in un unico tempo chirurgico. Sulla base di questo razionale, dopo uno studio preclinico animale e previa autorizzazione del comitato etico locale, abbiamo condotto uno studio clinico clinico pilota utilizzando un nuovo innesto biomimetico nanostrutturato per il trattamento di lesioni condrali ed osteocondrali del ginocchio; la sua sicurezza e maneggevolezza, così come la facile riproducibilità della tecnica chirurgica ed i risultati clinici ottenuti sono stati valutati nel tempo a 6, 12, 24, 36 e 48 mesi dall’impianto in modo da testare il suo potenziale intrinseco senza l’aggiunta di alcuna linea cellulare.

Le campagne di Piacenza tra VII e IX secolo: insediamenti e comunità

Al centro della seguente ricerca c'è il Piacentino, ossia il territorio che faceva capo alla città di Placentia in età altomedievale, più precisamente tra VII e IX secolo. L'aspetto su cui è concentrata l’analisi è quello dell’insediamento, rapportando le forme insediative alle comunità rurali e alle strutture del potere. Il Piacentino costituisce un contesto particolare, sia per la vicinanza alla capitale Pavia, sia per la presenza di enti patrimoniali molto importanti, quale il monastero di Bobbio, sia per l'estensione di vallate appenniniche che ne hanno protetto l'isolamento e impedito, fino al secolo IX inoltrato, l'insediamento di una forte aristocrazia. Ciò che sembra dedursi dall’analisi della documentazione (informatizzata) di VIII, ma soprattutto di IX secolo, è che la civitas di Piacenza, sede del conte e centro della diocesi, non costituiva di fatto il punto di riferimento per gli abitanti dell’intero territorio rurale. Dal punto di vista del possesso fondiario molti insediamenti erano autonomi. Ciò vale soprattutto per i siti di alcune zone collinari e per quelli dell’Appennino, mentre il discorso è da porsi in modo più sfumato per la pianura e per la zona dei prata vel campanea Placentina, ubicati immediatamente al di fuori della civitas. Lo studio della media e grande proprietà fondiaria ha permesso di registrare la frammentarietà dei possedimenti, ossia la loro dispersione nel sistema insediativo del comitato, la loro ubicazione e l’articolato intreccio proprietario, che in alcune zone sembra avere permesso l’esistenza di comunità locali piuttosto forti. L’attento esame della documentazione e il sicuro rimando alla bibliografia di riferimento hanno portato a risultati originali e significativi.

Wide-scale population genomics of Atlantic bluefin tuna (Thunnus thynnus) inferred by novel high-throughput technology

My PhD project was focused on Atlantic bluefin tuna, Thunnus thynnus, a fishery resource overexploited in the last decades. For a better management of stocks, it was necessary to improve scientific knowledge of this species and to develop novel tools to avoid collapse of this important commercial resource. To do this, we used new high throughput sequencing technologies, as Next Generation Sequencing (NGS), and markers linked to expressed genes, as SNPs (Single Nucleotide Polymorphisms). In this work we applied a combined approach: transcriptomic resources were used to build cDNA libreries from mRNA isolated by muscle, and genomic resources allowed to create a reference backbone for this species lacking of reference genome. All cDNA reads, obtained from mRNA, were mapped against this genome and, employing several bioinformatics tools and different restricted parameters, we achieved a set of contigs to detect SNPs. Once a final panel of 384 SNPs was developed, following the selection criteria, it was genotyped in 960 individuals of Atlantic bluefin tuna, including all size/age classes, from larvae to adults, collected from the entire range of the species. The analysis of obtained data was aimed to evaluate the genetic diversity and the population structure of Thunnus thynnus. We detect a low but significant signal of genetic differentiation among spawning samples, that can suggest the presence of three genetically separate reproduction areas. The adult samples resulted instead genetically undifferentiated between them and from the spawning populations, indicating a presence of panmictic population of adult bluefin tuna in the Mediterranean Sea, without different meta populations.

Conservation genetics of European wildcat (Felis silvestris silvestris): a wide and integrating analysis protocol for admixture inferences and population structure

Introgression of domestic cat genes into European wildcat (Felis silvestris silvestris) populations and reduction of wildcats’ range in Europe, leaded by habitat loss and fragmentation, are considered two of the main conservation problems for this endangered feline. This thesis addressed the questions related with the artificial hybridization and populations’ fragmentation, using a conservation genetics perspective. We combined the use of highly polymorphic loci, Bayesian statistical inferences and landscape analyses tools to investigate the origin of the geographic-genetic substructure of European wildcats (Felis silvestris silvestris) in Italy and Europe. The genetic variability of microsatellites evidenced that European wildcat populations currently distributed in Italy differentiated in, and expanded from two distinct glacial refuges during the Last Glacial Maximum. The genetic and geographic substructure detected between the eastern and western sides of the Apennine ridge, resulted by adaptation to specific ecological conditions of the Mediterranean habitats. European wildcat populations in Europe are strongly structured into 5 geographic-genetic macro clusters corresponding to: the Italian peninsular & Sicily; Balkans & north-eastern Italy; Germany eastern; central Europe; and Iberian Peninsula. Central European population might have differentiated in the extra-Mediterranean Würm ice age refuge areas (Northern Alps, Carpathians, and the Bulgarian mountain systems), while the divergence among and within the southern European populations might have resulted by the Pleistocene bio geographical framework of Europe, with three southern refugia localized in the Balkans, Italian Peninsula and Iberia Peninsula. We further combined the use of most informative autosomal SNPs with uniparental markers (mtDNA and Y-linked) for accurately detecting parental genotypes and levels of introgressive hybridization between European wild and domestic cats. A total of 11 hybrids were identified. The presence of domestic mitochondrial haplotypes shared with some wild individuals led us to hypnotize the possibility that ancient introgressive events might have occurred and that further investigation should be recommended.