Reconstruction and analysis of the NF-kB pathway interactome: a systems biology approach

Background. One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. A prominent mediator of inflammation is the transcription factor NF-kB, that acts as key transcriptional regulator of many genes coding for pro-inflammatory cytokines. Many different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory network characterized by high complexity. NF-kB signaling has been proposed to be responsible of inflammaging. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling and interaction network: the NF-kB pathway interactome. Methods. The study has been carried out following a workflow for gathering information from literature as well as from several pathway and protein interactions databases, and for integrating and analyzing existing data and the relative reconstructed representations by using the available computational tools. Strong manual intervention has been necessarily used to integrate data from multiple sources into mathematically analyzable networks. The reconstruction of the NF-kB interactome pursued with this approach provides a starting point for a general view of the architecture and for a deeper analysis and understanding of this complex regulatory system. Results. A “core” and a “wider” NF-kB pathway interactome, consisting of 140 and 3146 proteins respectively, were reconstructed and analyzed through a mathematical, graph-theoretical approach. Among other interesting features, the topological characterization of the interactomes shows that a relevant number of interacting proteins are in turn products of genes that are controlled and regulated in their expression exactly by NF-kB transcription factors. These “feedback loops”, not always well-known, deserve deeper investigation since they may have a role in tuning the response and the output consequent to NF-kB pathway initiation, in regulating the intensity of the response, or its homeostasis and balance in order to make the functioning of such critical system more robust and reliable. This integrated view allows to shed light on the functional structure and on some of the crucial nodes of thet NF-kB transcription factors interactome. Conclusion. Framing structure and dynamics of the NF-kB interactome into a wider, systemic picture would be a significant step toward a better understanding of how NF-kB globally regulates diverse gene programs and phenotypes. This study represents a step towards a more complete and integrated view of the NF-kB signaling system.

Comparative Analysis of Alternative Hybrid Systems for Automotive Applications

The main objective of this work was to investigate the impact of different hybridization concepts and levels of hybridization on fuel economy of a standard road vehicle where both conventional and non-conventional hybrid architectures are treated exactly in the same way from the point of view of overall energy flow optimization. Hybrid component models were developed and presented in detail as well as the simulations results mainly for NEDC cycle. The analysis was performed on four different parallel hybrid powertrain concepts: Hybrid Electric Vehicle (HEV), High Speed Flywheel Hybrid Vehicle (HSF-HV), Hydraulic Hybrid Vehicle (HHV) and Pneumatic Hybrid Vehicle (PHV). In order to perform equitable analysis of different hybrid systems, comparison was performed also on the basis of the same usable system energy storage capacity (i.e. 625kJ for HEV, HSF and the HHV) but in the case of pneumatic hybrid systems maximal storage capacity was limited by the size of the systems in order to comply with the packaging requirements of the vehicle. The simulations were performed within the IAV Gmbh - VeLoDyn software simulator based on Matlab / Simulink software package. Advanced cycle independent control strategy (ECMS) was implemented into the hybrid supervisory control unit in order to solve power management problem for all hybrid powertrain solutions. In order to maintain State of Charge within desired boundaries during different cycles and to facilitate easy implementation and recalibration of the control strategy for very different hybrid systems, Charge Sustaining Algorithm was added into the ECMS framework. Also, a Variable Shift Pattern VSP-ECMS algorithm was proposed as an extension of ECMS capabilities so as to include gear selection into the determination of minimal (energy) cost function of the hybrid system. Further, cycle-based energetic analysis was performed in all the simulated cases, and the results have been reported in the corresponding chapters.

Experimental analysis on the use of CCC systems to analyze the in-situ bearing capacity of C&D materials

Compaction is one of the most important processes in roadway construction. It is needed to achieve high quality and uniformity of pavement materials, which in turn better ensure long lasting performance.

Theoretical and Experimental Analysis of micro-CHP Energy Systems

In the framework of the micro-CHP (Combined Heat and Power) energy systems and the Distributed Generation (GD) concept, an Integrated Energy System (IES) able to meet the energy and thermal requirements of specific users, using different types of fuel to feed several micro-CHP energy sources, with the integration of electric generators of renewable energy sources (RES), electrical and thermal storage systems and the control system was conceived and built. A 5 kWel Polymer Electrolyte Membrane Fuel Cell (PEMFC) has been studied. Using experimental data obtained from various measurement campaign, the electrical and CHP PEMFC system performance have been determinate. The analysis of the effect of the water management of the anodic exhaust at variable FC loads has been carried out, and the purge process programming logic was optimized, leading also to the determination of the optimal flooding times by varying the AC FC power delivered by the cell. Furthermore, the degradation mechanisms of the PEMFC system, in particular due to the flooding of the anodic side, have been assessed using an algorithm that considers the FC like a black box, and it is able to determine the amount of not-reacted H2 and, therefore, the causes which produce that. Using experimental data that cover a two-year time span, the ageing suffered by the FC system has been tested and analyzed.

Discrete Event Systems based Design Patterns for Diagnosability Analysis of Automated Manufacturing Systems

The main goal of this thesis is to facilitate the process of industrial automated systems development applying formal methods to ensure the reliability of systems. A new formulation of distributed diagnosability problem in terms of Discrete Event Systems theory and automata framework is presented, which is then used to enforce the desired property of the system, rather then just verifying it. This approach tackles the state explosion problem with modeling patterns and new algorithms, aimed for verification of diagnosability property in the context of the distributed diagnosability problem. The concepts are validated with a newly developed software tool.

Analysis of Two Component Systems in Group B Streptococcus Shows that RgfAC and the Novel FspSR Modulate Virulence and Bacterial Fitness

Group B Streptococcus (GBS), in its transition from commensal to pathogen, will encounter diverse host environments and thus require coordinately controlling its transcriptional responses to these changes. This work was aimed at better understanding the role of two component signal transduction systems (TCS) in GBS pathophysiology through a systematic screening procedure. We first performed a complete inventory and sensory mechanism classification of all putative GBS TCS by genomic analysis. Five TCS were further investigated by the generation of knock-out strains, and in vitro transcriptome analysis identified genes regulated by these systems, ranging from 0.1-3% of the genome. Interestingly, two sugar phosphotransferase systems appeared differently regulated in the knock-out mutant of TCS-16, suggesting an involvement in monitoring carbon source availability. High throughput analysis of bacterial growth on different carbon sources showed that TCS-16 was necessary for growth of GBS on fructose-6-phosphate. Additional transcriptional analysis provided further evidence for a stimulus-response circuit where extracellular fructose-6-phosphate leads to autoinduction of TCS-16 with concomitant dramatic up-regulation of the adjacent operon encoding a phosphotransferase system. The TCS-16-deficient strain exhibited decreased persistence in a model of vaginal colonization and impaired growth/survival in the presence of vaginal mucoid components. All mutant strains were also characterized in a murine model of systemic infection, and inactivation of TCS-17 (also known as RgfAC) resulted in hypervirulence. Our data suggest a role for the previously unknown TCS-16, here named FspSR, in bacterial fitness and carbon metabolism during host colonization, and also provide experimental evidence for TCS-17/RgfAC involvement in virulence.

Synthesis and conformational analysis of heteroaromatic atropisomeric systems

The research work reported in this Thesis was held along two main lines of research. The first and main line of research is about the synthesis of heteroaromatic compounds with increasing steric hindrance, with the aim of preparing stable atropisomers. The main tools used for the study of these dynamic systems, as described in the Introduction, are DNMR, coupled with line shape simulation and DFT calculations, aimed to the conformational analysis for the prediction of the geometries and energy barriers to the trasition states. This techniques have been applied to the research projects about: • atropisomers of arylmaleimides; • atropisomers of 4-arylpyrazolo[3,4-b]pyridines; • study of the intramolecular NO2/CO interaction in solution; • study on 2-arylpyridines. Parallel to the main project, in collaboration with other groups, the research line about determination of the absolute configuration was followed. The products, deriving form organocatalytic reactions, in many cases couldn’t be analyzed by means of X-Ray diffraction, making necessary the development of a protocol based on spectroscopic methodologies: NMR, circular dichroism and computational tools (DFT, TD-DFT) have been implemented in this scope. In this Thesis are reported the determination of the absolute configuration of: • substituted 1,2,3,4-tetrahydroquinolines; • compounds from enantioselective Friedel-Crafts alkylation-acetalization cascade of naphthols with α,β-unsaturated cyclic ketones; • substituted 3,4-annulated indoles.

Performance analysis of ray-tracing assisted beamforming techniques for future mm-wave wireless systems.

Il progetto di tesi riguarda principalmente la progettazione di moderni sistemi wireless, come 5G o WiGig, operanti a onde millimetriche, attraverso lo studio di una tecnica avanzata detta Beamforming, che, grazie all'utilizzo di antenne direttive e compatte, permette di superare limiti di link budget dovuti alle alte frequenze e introdurre inoltre diversità spaziale alla comunicazione. L'obiettivo principale del lavoro è stato quello di valutare, tramite simulazioni numeriche, le prestazioni di alcuni diversi schemi di Beamforming integrando come tool di supporto un programma di Ray Tracing capace di fornire le principali informazioni riguardo al canale radio. Con esso infatti è possibile sia effettuare un assessment generale del Beamforming stesso, ma anche formulare i presupposti per innovative soluzioni, chiamate RayTracing-assisted- Beamforming, decisamente promettenti per futuri sviluppi così come confermato dai risultati.

Reparation and enforcement of judgments : a comparative analysis of the European and Inter-American human rights systems

The inter-American human rights system has been conceived following the example of the European system under the European Convention on Human Rights (ECHR) before it was modified by Protocol No 11. However, two important differences exist. First, the authority of the European Court of Human Rights (ECtHR) to order reparation has been strictly limited by the principle of subsidiarity. Thus, the ECtHR's main function is to determine whether the ECHR has been violated. Beyond the declaratory effect of its judgments, according to Article 41 ECHR, it may only "afford just satisfaction to the injured party". The powers of the Inter-American Court of Human Rights (IACtHR) were conceived in a much broader fashion in Article 63 of the American Convention on Human Rights (ACHR), giving the Court the authority to order a variety of individual and general measures aimed at obtaining restitutio in integrum. The first main part of this thesis shows how both Courts have developed their reparation practice and examines the advantages and disadvantages of each approach. Secondly, the ECtHR's rather limited reparation powers have, interestingly, been combined with an elaborate implementation system that includes several of the Council of Europe's organs, principally the Committee of Ministers. In the Inter-American System, no dedicated mechanism was implemented to oversee compliance with the IACtHR's judgments. The ACHR limits itself to inviting the Court to point out in its annual reports the cases that have not been complied with and to propose measures to be adopted by the General Assembly of the Organization of American States. The General Assembly, however, hardly ever took action. The IACtHR has therefore filled this gap by developing a proper procedure to oversee compliance with its judgments. Both the European and the American solutions to ensure compliance are presented and compared in the second main part of this thesis. Finally, based on the results of both main parts, a comparative analysis of the reparation practice and the execution results in both human rights systems is being provided, aimed at developing proposals for the improvement of the functioning of either human rights protection system.

Qualitatitive and quantitative analysis of fish spoilage processes for development of new food monitoring systems

This study investigates the growth and metabolite production of microorganisms causing spoilage of Atlantic cod (Gadus morhua) fillets packaged under air and modified atmosphere (60 % CO2, 40 % O2). Samples were provided by two different retailers (A and B). Storage of packaged fillets occurred at 4 °C and 8 °C. Microbiological quality and metabolite production of cod fillets stored in MAP 4 °C, MAP 8 °C and air were monitored during 13 days, 7 days and 3 days of storage, respectively. Volatile compounds concentration in the headspace were quantified by Selective ion flow tube mass spectrometry and a correlation with microbiological spoilage was studied. The onset of volatile compounds detection was observed to be mostly around 7 log cfu/g of total psychrotrophic count. Trimethylamine and dimethyl sulfide were found to be the dominant volatiles in all of the tested storage conditions, nevertheless there was no close correlation between concentrations of each main VOC and percentages of rejection based on sensory evaluation. According to results it was concluded that they cannot be considered as only indicators of the quality of cod fillets stored in modified atmosphere and air.