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Characterisation of RNase Y in H. pylori: a non-essential enzyme involved in the processing of cag-PAI non coding RNA 1 (CncR1) sRNA
Get PDFThe importance of Helicobacter pylori as a human pathogen is underlined by the plethora of diseases it is responsible for. The capacity of H. pylori to adapt to the restricted host-associated environment andto evade the host immune response largely depends on a streamlined signalling network. The peculiar H. pylori small genome size combined with its paucity of transcriptional regulators highlights the relevance of post-transcriptional regulatory mechanisms as small non-coding RNAs (sRNAs). However, among the 8 RNases represented in H. pylori genome, a regulator guiding sRNAs metabolism is still not well studied.
We investigated for the first time the physiological role in H. pylori G27 strain of the RNase Y enzyme.
In the first line of research we provide a comprehensive characterization of the RNase Y activity by analysing its genomic organization and the factors that orchestrate its expression. Then, based on bioinformatic prediction models, we depict the most relevant determinants of RNase Y function, demonstrating a correlation of both structure and domain organization with orthologues represented in Gram-positive bacteria. To unveil the post-transcriptional regulatory effect exerted by the RNase Y, we compared the transcriptome of an RNase Y knock-out mutant to the parental wild type strain by RNA-seq approach.
In the second line of research we characterized the activity of this single strand specific endoribonuclease on cag-PAI non coding RNA 1 (CncR1) sRNA. We found that deletion or inactivation of RNase Y led to the accumulation of a 3’-extended CncR1 (CncR1-L) transcript over time. Moreover, beneath its increased half-life, CncR1-L resembled a CncR1 inactive phenotype.
Finally, we focused on the characterization of the in vivo interactome of CncR1. We set up a preliminary MS2-affinity purification coupled with RNA-sequencing (MAPS) approach and we evaluated the enrichment of specific targets, demonstrating the suitability of the technique in the H. pylori G27 strain
A coupled ocean-atmosphere system for short term forecasting in the southern european seas
Get PDFThis coupled model combines two state-of-the-art numerical models, NEMO for the oceanic component and WRF for the atmospheric component and implements them at an appropriate resolution.
The oceanic model has been implemented starting from the Mediterranean Forecasting System with a resolution of 1/24° and the domain was extended to exactly match the grid of a newly implemented atmospheric model for the same area. The uncoupled ocean model has been validated against SST observed data, both in the simulation of an extreme event and in the short-term forecast of two seasonal periods. A new setup of the model was successfully tested in which the downward radiative fluxes were prescribed from atmospheric forecasts.
Various physical schemes, domain, boundary, and initial conditions were tested with the atmospheric model to obtain the best representation of medicane Ianos. The heat fluxes calculated by the uncoupled models were compared to determine which setup gave the best energy balance between the components of the coupled model.
The coupling strategy used is the traditional one, where the ocean is driven by the surface stress, heat fluxes, and radiative fluxes computed in the atmospheric component, which in turn receives the SST and surface currents.
As expected, the overall skills of the coupled model are slightly degraded compared to the uncoupled models, even though the positioning and timing of the cyclone at the time of the landfall is enhanced.
The mean heat fluxes do not change compared to the uncoupled model, whereas the pattern of the shortwave radiation and latent heat is changed. Moreover, the two energy fluxes are larger in absolute values than those calculated with the MFS formulas. The fact that they have opposite signs give raise to a compensation error that limits the overall degradation of the coupled simulation
First steps in underwater photogrammetry with the support of an unmanned underwater vehicle
Get PDFThe evolution of modern and increasingly sensitive image sensors, the increasingly compact design of the cameras, and the recent emergence of low-cost cameras allowed the Underwater Photogrammetry to become an infallible and irreplaceable technique used to estimate the structure of the seabed with high accuracy. Within this context, the main topic of this work is the Underwater Photogrammetry from a geomatic point of view and all the issues associated with its implementation, in particular with the support of Unmanned Underwater Vehicles. Questions such as: how does the technique work, what is needed to deal with a proper survey, what tools are available to apply this technique, and how to resolve uncertainties in measurement will be the subject of this thesis. The study conducted can be divided into two major parts: one devoted to several ad-hoc surveys and tests, thus a practical part, another supported by the bibliographical research. However the main contributions are related to the experimental section, in which two practical case studies are carried out in order to improve the quality of the underwater survey of some calibration platforms. The results obtained from these two experiments showed that, the refractive effects due to water and underwater housing can be compensated by the distortion coefficients in the camera model, but if the
aim is to achieve high accuracy then a model that takes into account the configuration of the underwater housing, based on ray tracing, must also be coupled. The major contributions that this work brought are: an overview of the practical issues when performing surveys exploiting an UUV prototype, a method to reach a reliable accuracy in the 3D reconstructions without the use of an underwater local geodetic network, a guide for who addresses underwater photogrammetry topics for the first time, and the use of open-source environments
Growth performance, gut health, and metabolism of broilers under thermoneutral and heat stress conditions: multidisciplinary studies on the effects of nutritional strategies and genotype
Get PDFThis PhD project aimed to (i) investigate the effects of three nutritional strategies (supplementation of a synbiotic, a muramidase, or arginine) on growth performance, gut health, and metabolism of broilers fed without antibiotics under thermoneutral and heat stress conditions and to (ii) explore the impacts of heat stress on hypothalamic regulation of feed intake in three broiler lines from diverse stages of genetic selection and in the red jungle fowl, the ancestor of domestic chickens.
Synbiotic improved feed efficiency and footpad health, increased Firmicutes and reduced Bacteroidetes in the ceca of birds kept in thermoneutral conditions, while did not mitigate the impacts of heat stress on growth performance.
Under optimal thermal conditions, muramidase increased final body weight and reduced cumulative feed intake and feed conversion ratio in a dose-dependent way. The highest dose reduced the risk of footpad lesions, cecal alpha diversity, the Firmicutes to Bacteroidetes ratio, and butyrate producers, increased Bacteroidaceae and Lactobacillaceae, plasmatic levels of bioenergetic metabolites, and reduced the levels of pro-oxidant metabolites. The same dose, however, failed to reduce the effects of heat stress on growth performance.
Arginine supplementation improved growth rate, final body weight, and feed efficiency, increased plasmatic levels of arginine and creatine and hepatic levels of creatine and essential amino acids, reduced alpha diversity, Firmicutes, and Proteobacteria (especially Escherichia coli), and increased Bacteroidetes and Lactobacillus salivarius in the ceca of thermoneutral birds. No arginine-mediated attenuation of heat stress was found. Heat stress altered protein metabolism and caused the accumulation of antioxidant and protective molecules in oxidative stress-sensitive tissues. Arginine supplementation, however, may have partially counterbalanced the effects of heat stress on energy homeostasis.
Stable gene expression of (an)orexigenic neuropeptides was found in the four chicken populations studied, but responses to hypoxia and heat stress appeared to be related to feed intake regulation
Role of second trimester ultrasound in prediction of newborns neurologic damage after maternal Cytomegalovirus infection
Get PDFObjective
To find a correlation between cerebral symptoms at birth and abnormalities found at anomaly scan, through the analysis of sensitivity of the anomaly scan in the prediction of severe CMV neonatal disease.
Methods - Design, Setting, Population
This was a retrospective collection of all cases of primary congenital CMV infection reported in our unit (Obstetrics and Perinatal Medicine, Policlinico di S Orsola, IRCSS, Bologna) over a period of 9 years (2013–2022). Only cases of fetal infection following confirmed maternal primary infection in the first trimester (MPI) and newborns with confirmed CMV infection on blood/saliva or urine were included.
Results
Between 2014 and 2022, 69 fetuses had an antenatal diagnosis of primary CMV infection. The infection occurred after MPI in the first, second, and third trimester in 63.7% (43/69), 27.5% (19/69), and 10% (7/69) of cases, respectively. Second-trimester assessment by anomaly scan was abnormal in 10/69 (15%) fetuses: 5/69 (7%) had an extracerebral STA and 5/69 (7%) had a cerebral STA. Normal anomaly scan was found in 59/69 (86%) fetuses. When looking at all fetuses infected in the first trimester, 12.5% (5/40) underwent TOP and 45% (18/40) had symptoms at birth. A mean follow-up of 22.4 months (range 12–48 months) was available for 68/69 (99%) live born neonates.
Conclusion
Anomaly scan results to have a predictive positive value of 67% fetuses infected in the first trimester. Serial assessment by ultrasound is necessary to predict the risk of sequelae occurring in 35% following fetal infection in the first trimester of pregnancy. This combined evaluation by US and trimester of infection should be useful when counselling on the prognosis of cCMV infection
The right of access to public information
No full textTanto en Italia como en España las personas han reivindicado que el ordenamiento jurídico reconozca un verdadero derecho de todos a acceder a la información pública de manera libre. En parte, esto ha sido así por la desafección de los ciudadanos con el sistema político que los ha llevado a reivindicar un rol más preponderante en los procesos de toma de decisiones públicas y a exigir una mayor eficiencia en la lucha contra la corrupción en el sector público. Con el libre acceso a la información pública se favorecen ambas cosas, ya que la información que posee el sector público resulta valiosísima para que los ciudadanos puedan enjuiciar de manera crítica «cómo se toman las decisiones que les afectan, cómo se manejan los fondos públicos o bajo qué criterios actúan nuestras instituciones» -apartado I del preámbulo de la LTAIBG-.
Tradicionalmente, el derecho a acceder a los documentos públicos ha sido una cuestión vinculada al procedimiento administrativo y su ejercicio quedaba circunscrito a ser parte en el procedimiento. Este derecho ha sido el modelo seguido para la creación del derecho de acceso a la información público, aunque nace desvinculado del procedimiento administrativo en la medida en que tiene un fundamento democrático del que carece el derecho de acceso en el procedimiento administrativo.
En esta tesis doctoral estudiamos las normas que han hecho posible que en Italia y España se cree este nuevo derecho político en el siglo XXI y su fundamento democrático. Concretamente, en Italia han sido el Decreto Legislativo 33/2013 y el Decreto Legislativo 97/2016 y en España la LTAIBG, las normas que han configurado este nuevo derecho.In both Italy and Spain, people have demanded that the legal system recognise a genuine right for everyone to freely access public information. In part, this has been due to citizens' disaffection with the political system, which has led them to demand a greater role in public decision-making processes and to demand greater efficiency in the fight against corruption in the public sector. Free access to public information favours both, as the information held by the public sector is invaluable for citizens to critically assess "how decisions that affect them are made, how public funds are managed or under what criteria our institutions act" -section I of the preamble of the LTAIBG-.
Traditionally, the right of access to public documents has been an issue linked to the administrative procedure and its exercise was limited to being a party to the procedure. This right has been the model followed for the creation of the right of access to public information, although it is born detached from the administrative procedure insofar as it has a democratic basis that the right of access in the administrative procedure lacks.
In this doctoral thesis we study the rules that have made it possible in Italy and Spain to create this new political right in the 21st century and its democratic basis. Specifically, in Italy it has been Legislative Decree 33/2013 and Legislative Decree 97/2016 and in Spain the LTAIBG, the rules that have shaped this new right
Development of processes for the valorization of lignocellulosic biomass based on renewable energies
Get PDFThe world grapples with climate change from fossil fuel reliance, prompting Europe to pivot to renewable energy. Among renewables, biomass is a bioenergy and bio-carbon source, used to create high-value biomolecules, replacing fossil-based products. Alkyl levulinates, derived from biomass, hold promise as bio-additives and biofuels, especially via acid solvolysis of hexose sugars, necessitating further exploration. Alkyl levulinate's potential extends to converting into γ-valerolactone (GVL), a bio-solvent produced via hydrogenation with molecular-hydrogen. Hydrogen, a key reagent and energy carrier, aids renewable energy integration. This thesis delves into a biorefinery system study, aligning with sustainability goals, integrating biomass valorization, energy production, and hydrogen generation. It investigates optimizing technologies for butyl levulinate production and subsequent GVL hydrogenation. Sustainability remains pivotal, reflecting the global shift towards renewable and carbon bio-resources.
The research initially focuses on experimenting with the optimal technology for producing butyl levulinate from biomass-derived hexose fructose. It examines the solvolysis process, investigating optimal conditions, kinetic modeling, and the impact of solvents on fructose conversion.
The subsequent part concentrates on the technological aspect of hydrogenating butyl levulinate into GVL. It includes conceptual design, simulation, and optimization of the fructose-to-GVL process scheme based on process intensification.
In the final part, the study applies the process to a real case study in Normandy, France, adapting it to local biomass availability and wind energy. It defines a methodology for designing and integrating the energy-supply system, evaluating different scenarios. Sustainability assessment using economic, environmental, and social indicators culminates in an overall sustainability index, indicating scenarios integrating the GVL biorefinery system with wind power and hydrogen energy storage as promising due to high profitability and reduced environmental impact. Sensitivity analyses validate the methodology's reliability, potentially extending to other technological systems
Development of unsupervised learning methods with applications to life sciences data
Get PDFMachine Learning makes computers capable of performing tasks typically requiring human intelligence. A domain where it is having a considerable impact is the life sciences, allowing to devise new biological analysis protocols, develop patients’ treatments efficiently and faster, and reduce healthcare costs. This Thesis work presents new Machine Learning methods and pipelines for the life sciences focusing on the unsupervised field.
At a methodological level, two methods are presented. The first is an “Ab Initio Local Principal Path” and it is a revised and improved version of a pre-existing algorithm in the manifold learning realm. The second contribution is an improvement over the Import Vector Domain Description (one-class learning) through the Kullback-Leibler divergence. It hybridizes kernel methods to Deep Learning obtaining a scalable solution, an improved probabilistic model, and state-of-the-art performances. Both methods are tested through several experiments, with a central focus on their relevance in life sciences. Results show that they improve the performances achieved by their previous versions.
At the applicative level, two pipelines are presented. The first one is for the analysis of RNA-Seq datasets, both transcriptomic and single-cell data, and is aimed at identifying genes that may be involved in biological processes (e.g., the transition of tissues from normal to cancer). In this project, an R package is released on CRAN to make the pipeline accessible to the bioinformatic Community through high-level APIs. The second pipeline is in the drug discovery domain and is useful for identifying druggable pockets, namely regions of a protein with a high probability of accepting a small molecule (a drug). Both these pipelines achieve remarkable results.
Lastly, a detour application is developed to identify the strengths/limitations of the “Principal Path” algorithm by analyzing Convolutional Neural Networks induced vector spaces. This application is conducted in the music and visual arts domains
Analysis and design considerations of resonator arrays for inductive power transfer systems
Get PDFIn the frame of inductive power transfer (IPT) systems, arrays of magnetically coupled resonators have received increasing attention as they are cheap and versatile due to their simple structure. They consist of magnetically coupled coils, which resonate with their self-capacitance or lumped capacitive networks. Of great industrial interest are planar resonator arrays used to power a receiver that can be placed at any position above the array. A thorough circuit analysis has been carried out, first starting from traditional two-coil IPT devices. Then, resonator arrays have been introduced, with particular attention to the case of arrays with a receiver. To evaluate the system performance, a circuit model based on original analytical formulas has been developed and experimentally validated. The results of the analysis also led to the definition of a new doubly-fed array configuration with a receiver that can be placed above it at any position. A suitable control strategy aimed at maximising the transmitted power and the efficiency has been also proposed. The study of the array currents has been carried out resorting to the theory of magneto-inductive waves, allowing useful insight to be highlighted. The analysis has been completed with a numerical and experimental study on the magnetic field distribution originating from the array. Furthermore, an application of the resonator array as a position sensor has been investigated. The position of the receiver is estimated through the measurement of the array input impedance, for which an original analytical expression has been also obtained. The application of this sensing technique in an automotive dynamic IPT system has been discussed. The thesis concludes with an evaluation of the possible applications of two-dimensional resonator arrays in IPT systems. These devices can be used to improve system efficiency and transmitted power, as well as for magnetic field shielding
Active control of sound radiated by vibrating surfaces on a McLaren supercar
Get PDFSound radiators based on forced vibrations of plates are becoming widely employed, mainly for active sound enhancement and noise cancelling systems, both in music and automotive environment. Active sound enhancement solutions based on electromagnetic shakers hence find increasing interest. Mostly diffused applications deal with active noise control (ANC) and active vibration control systems for improving the acoustic experience inside or outside the vehicle. This requires investigating vibrational and, consequently, vibro-acoustic characteristics of vehicles. Therefore, simulation and processing methods capable of reducing the calculation time and providing high-accuracy results, are strongly demanded. In this work, an ideal case study on rectangular plates in fully clamped conditions preceded a real case analysis on vehicle panels. The sound radiation generated by a vibrating flat or shallow surface can be calculated by means of Rayleigh’s integral. The analytical solution of the problem is here calculated implementing the equations in MATLAB. Then, the results are compared with a numerical model developed in COMSOL Multiphysics, employing Finite Element Method (FEM). A very good matching between analytical and numerical solutions is shown, thus the cross validation of the two methods is achieved. The shift to the real case study, on a McLaren super car, led to the development of a mixed analytical-numerical method. Optimum results were obtained with mini shakers excitement, showing good matching of the recorded SPL with the calculated one over all the selected frequency band. In addition, a set of directivity measurements of the hood were realized, to start studying the spatiality of sound, which is fundamental to active noise control systems