Pattern recognition analysis on heavy ion reaction data

One of the problems in the analysis of nucleus-nucleus collisions is to get information on the value of the impact parameter b. This work consists in the application of pattern recognition techniques aimed at associating values of b to groups of events. To this end, a support vec- tor machine (SVM) classifier is adopted to analyze multifragmentation reactions. This method allows to backtracing the values of b through a particular multidimensional analysis. The SVM classification con- sists of two main phase. In the first one, known as training phase, the classifier learns to discriminate the events that are generated by two different model:Classical Molecular Dynamics (CMD) and Heavy- Ion Phase-Space Exploration (HIPSE) for the reaction: 58Ni +48 Ca at 25 AMeV. To check the classification of events in the second one, known as test phase, what has been learned is tested on new events generated by the same models. These new results have been com- pared to the ones obtained through others techniques of backtracing the impact parameter. Our tests show that, following this approach, the central collisions and peripheral collisions, for the CMD events, are always better classified with respect to the classification by the others techniques of backtracing. We have finally performed the SVM classification on the experimental data measured by NUCL-EX col- laboration with CHIMERA apparatus for the previous reaction.

De Novo Design of secondary structures: Synthesis and conformational studies

Chemists have long sought to extrapolate the power of biological catalysis and recognition to synthetic systems. These efforts have focused largely on low molecular weight catalysts and receptors; however, biological systems themselves rely almost exclusively on polymers, proteins and RNA, to perform complex chemical functions. Proteins and RNA are unique in their ability to adopt compact, well-ordered conformations, and specific folding provides precise spatial orientation of the functional groups that comprise the “active site”. These features suggest that identification of new polymer backbones with discrete and predictable folding propensities (“foldamers”) will provide a basis for design of molecular machines with unique capabilities. The foldamer approach complements current efforts to design unnatural properties into polypeptides and polynucleotides. The aim of this thesis is the synthesis and conformational studies of new classes of foldamers, using a peptidomimetic approach. Moreover their attitude to be utilized as ionophores, catalysts, and nanobiomaterials were analyzed in solution and in the solid state. This thesis is divided in thematically chapters that are reported below. It begins with a very general introduction (page 4) which is useful, but not strictly necessary, to the expert reader. It is worth mentioning that paragraph I.3 (page 22) is the starting point of this work and paragraph I.5 (page 32) isrequired to better understand the results of chapters 4 and 5. In chapter 1 (page 39) is reported the synthesis and conformational analysis of a novel class of foldamers containing (S)-β3-homophenylglycine [(S)-β3-hPhg] and D- 4-carboxy-oxazolidin-2-one (D-Oxd) residues in alternate order is reported. The experimental conformational analysis performed in solution by IR, 1HNMR, and CD spectroscopy unambiguously proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic foldamers and might be useful in the mimicry of native peptides. In chapter 2 cyclo-(L-Ala-D-Oxd)3 and cyclo-(L-Ala-DOxd) 4 were prepared in the liquid phase with good overall yields and were utilized for bivalent ions chelation (Ca2+, Mg2+, Cu2+, Zn2+ and Hg2+); their chelation skill was analyzed with ESI-MS, CD and 1HNMR techniques and the best results were obtained with cyclo-(L-Ala-D-Oxd)3 and Mg2+ or Ca2+. Chapter 3 describes an application of oligopeptides as catalysts for aldol reactions. Paragraph 3.1 concerns the use of prolinamides as catalysts of the cross aldol addition of hydroxyacetone to aromatic aldeydes, whereas paragraphs 3.2 and 3.3 are about the catalyzed aldol addition of acetone to isatins. By means of DFT and AIM calculations, the steric and stereoelectronic effects that control the enantioselectivity in the cross-aldol addition of acetone to isatin catalysed by L-proline have been studied, also in the presence of small quantities of water. In chapter 4 is reported the synthesis and the analysis of a new fiber-like material, obtained from the selfaggregation of the dipeptide Boc-L-Phe-D-Oxd-OBn, which spontaneously forms uniform fibers consisting of parallel infinite linear chains arising from singleintermolecular N-H···O=C hydrogen bonds. This is the absolute borderline case of a parallel β-sheet structure. Longer oligomers of the same series with general formula Boc-(L-Phe-D-Oxd)n-OBn (where n = 2-5), are described in chapter 5. Their properties in solution and in the solid state were analyzed, in correlation with their attitude to form intramolecular hydrogen bond. In chapter 6 is reported the synthesis of imidazolidin-2- one-4-carboxylate and (tetrahydro)-pyrimidin-2-one-5- carboxylate, via an efficient modification of the Hofmann rearrangement. The reaction affords the desired compounds from protected asparagine or glutamine in good to high yield, using PhI(OAc)2 as source of iodine(III).

Role of nitric oxide and endocannabinoids in synaptic plasticity in the perirhinal cortex and in visual recognition memory

Introduction and aims of the research Nitric oxide (NO) and endocannabinoids (eCBs) are major retrograde messengers, involved in synaptic plasticity (long-term potentiation, LTP, and long-term depression, LTD) in many brain areas (including hippocampus and neocortex), as well as in learning and memory processes. NO is synthesized by NO synthase (NOS) in response to increased cytosolic Ca2+ and mainly exerts its functions through soluble guanylate cyclase (sGC) and cGMP production. The main target of cGMP is the cGMP-dependent protein kinase (PKG). Activity-dependent release of eCBs in the CNS leads to the activation of the Gαi/o-coupled cannabinoid receptor 1 (CB1) at both glutamatergic and inhibitory synapses. The perirhinal cortex (Prh) is a multimodal associative cortex of the temporal lobe, critically involved in visual recognition memory. LTD is proposed to be the cellular correlate underlying this form of memory. Cholinergic neurotransmission has been shown to play a critical role in both visual recognition memory and LTD in Prh. Moreover, visual recognition memory is one of the main cognitive functions impaired in the early stages of Alzheimer’s disease. The main aim of my research was to investigate the role of NO and ECBs in synaptic plasticity in rat Prh and in visual recognition memory. Part of this research was dedicated to the study of synaptic transmission and plasticity in a murine model (Tg2576) of Alzheimer’s disease. Methods Field potential recordings. Extracellular field potential recordings were carried out in horizontal Prh slices from Sprague-Dawley or Dark Agouti juvenile (p21-35) rats. LTD was induced with a single train of 3000 pulses delivered at 5 Hz (10 min), or via bath application of carbachol (Cch; 50 μM) for 10 min. LTP was induced by theta-burst stimulation (TBS). In addition, input/output curves and 5Hz-LTD were carried out in Prh slices from 3 month-old Tg2576 mice and littermate controls. Behavioural experiments. The spontaneous novel object exploration task was performed in intra-Prh bilaterally cannulated adult Dark Agouti rats. Drugs or vehicle (saline) were directly infused into the Prh 15 min before training to verify the role of nNOS and CB1 in visual recognition memory acquisition. Object recognition memory was tested at 20 min and 24h after the end of the training phase. Results Electrophysiological experiments in Prh slices from juvenile rats showed that 5Hz-LTD is due to the activation of the NOS/sGC/PKG pathway, whereas Cch-LTD relies on NOS/sGC but not PKG activation. By contrast, NO does not appear to be involved in LTP in this preparation. Furthermore, I found that eCBs are involved in LTP induction, but not in basal synaptic transmission, 5Hz-LTD and Cch-LTD. Behavioural experiments demonstrated that the blockade of nNOS impairs rat visual recognition memory tested at 24 hours, but not at 20 min; however, the blockade of CB1 did not affect visual recognition memory acquisition tested at both time points specified. In three month-old Tg2576 mice, deficits in basal synaptic transmission and 5Hz-LTD were observed compared to littermate controls. Conclusions The results obtained in Prh slices from juvenile rats indicate that NO and CB1 play a role in the induction of LTD and LTP, respectively. These results are confirmed by the observation that nNOS, but not CB1, is involved in visual recognition memory acquisition. The preliminary results obtained in the murine model of Alzheimer’s disease indicate that deficits in synaptic transmission and plasticity occur very early in Prh; further investigations are required to characterize the molecular mechanisms underlying these deficits.

Fingerprint Recognition: Enhancement, Feature Extraction and Automatic Evaluation of Algorithms

The identification of people by measuring some traits of individual anatomy or physiology has led to a specific research area called biometric recognition. This thesis is focused on improving fingerprint recognition systems considering three important problems: fingerprint enhancement, fingerprint orientation extraction and automatic evaluation of fingerprint algorithms. An effective extraction of salient fingerprint features depends on the quality of the input fingerprint. If the fingerprint is very noisy, we are not able to detect a reliable set of features. A new fingerprint enhancement method, which is both iterative and contextual, is proposed. This approach detects high-quality regions in fingerprints, selectively applies contextual filtering and iteratively expands like wildfire toward low-quality ones. A precise estimation of the orientation field would greatly simplify the estimation of other fingerprint features (singular points, minutiae) and improve the performance of a fingerprint recognition system. The fingerprint orientation extraction is improved following two directions. First, after the introduction of a new taxonomy of fingerprint orientation extraction methods, several variants of baseline methods are implemented and, pointing out the role of pre- and post- processing, we show how to improve the extraction. Second, the introduction of a new hybrid orientation extraction method, which follows an adaptive scheme, allows to improve significantly the orientation extraction in noisy fingerprints. Scientific papers typically propose recognition systems that integrate many modules and therefore an automatic evaluation of fingerprint algorithms is needed to isolate the contributions that determine an actual progress in the state-of-the-art. The lack of a publicly available framework to compare fingerprint orientation extraction algorithms, motivates the introduction of a new benchmark area called FOE (including fingerprints and manually-marked orientation ground-truth) along with fingerprint matching benchmarks in the FVC-onGoing framework. The success of such framework is discussed by providing relevant statistics: more than 1450 algorithms submitted and two international competitions.

The effect of osmolytes on protein fold stability at the single-molecule level

By pulling and releasing the tension on protein homomers with the Atomic Force Miscroscope (AFM) at different pulling speeds, dwell times and dwell distances, the observed force-response of the protein can be fitted with suitable theoretical models. In this respect we developed mathematical procedures and open-source computer codes for driving such experiments and fitting Bell’s model to experimental protein unfolding forces and protein folding frequencies. We applied the above techniques to the study of proteins GB1 (the B1 IgG-binding domain of protein G from Streptococcus) and I27 (a module of human cardiac titin) in aqueous solutions of protecting osmolytes such as dimethyl sulfoxide (DMSO), glycerol and trimethylamine N-oxide (TMAO). In order to get a molecular understanding of the experimental results we developed an Ising-like model for proteins that incorporates the osmophobic nature of their backbone. The model benefits from analytical thermodynamics and kinetics amenable to Monte-Carlo simulation. The prevailing view used to be that small protecting osmolytes bridge the separating beta-strands of proteins with mechanical resistance, presumably shifting the transition state to significantly higher distances that correlate with the molecular size of the osmolyte molecules. Our experiments showed instead that protecting osmolytes slow down protein unfolding and speed-up protein folding at physiological pH without shifting the protein transition state on the mechanical reaction coordinate. Together with the theoretical results of the Ising-model, our results lend support to the osmophobic theory according to which osmolyte stabilisation is a result of the preferential exclusion of the osmolyte molecules from the protein backbone. The results obtained during this thesis work have markedly improved our understanding of the strategy selected by Nature to strengthen protein stability in hostile environments, shifting the focus from hypothetical protein-osmolyte interactions to the more general mechanism based on the osmophobicity of the protein backbone.

Characterization of fold-related fractures in the carbonate rocks of the Cingoli anticline, northern Apennines, Italy

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different structures, such as joints, faults, pressure solution seams, and deformation bands. Defining the development of fracture systems related to the folding process is significant both for theoretical and practical purposes. Fracture systems are useful constrains in order to understand the kinematical evolution of the fold. Furthermore, understanding the relationships between folding and fracturing provides a noteworthy contribution for reconstructing the geodynamic and the structural evolution of the studied area. Moreover, as fold-related fractures influence fluid flow through rocks, fracture systems are relevant for energy production (geothermal studies, methane and CO2 , storage and hydrocarbon exploration), environmental and social issues (pollutant distribution, aquifer characterization). The PhD project shows results of a study carried out in a multilayer carbonate anticline characterized by different mechanical properties. The aim of this study is to understand the factors which influence the fracture formation and to define their temporal sequence during the folding process. The studied are is located in the Cingoli anticline (Northern Apennines), which is characterized by a pelagic multilayer characterized by sequences with different mechanical stratigraphies. A multi-scale analysis has been made in several outcrops located in different structural positions. This project shows that the conceptual sketches proposed in literature and the strain distribution models outline well the geometrical orientation of most of the set of fractures observed in the Cingoli anticline. On the other hand, the present work suggests the relevance of the mechanical stratigraphy in particular controlling the type of fractures formed (e.g. pressure solution seams, joints or shear fractures) and their subsequent evolution. Through a multi-scale analysis, and on the basis of the temporal relationship between fracture sets and their orientation respect layering, I also suggest a conceptual model for fracture systems formation.

Advanced Techniques for Face Recognition under Challenging Environments

Automatically recognizing faces captured under uncontrolled environments has always been a challenging topic in the past decades. In this work, we investigate cohort score normalization that has been widely used in biometric verification as means to improve the robustness of face recognition under challenging environments. In particular, we introduce cohort score normalization into undersampled face recognition problem. Further, we develop an effective cohort normalization method specifically for the unconstrained face pair matching problem. Extensive experiments conducted on several well known face databases demonstrate the effectiveness of cohort normalization on these challenging scenarios. In addition, to give a proper understanding of cohort behavior, we study the impact of the number and quality of cohort samples on the normalization performance. The experimental results show that bigger cohort set size gives more stable and often better results to a point before the performance saturates. And cohort samples with different quality indeed produce different cohort normalization performance. Recognizing faces gone after alterations is another challenging problem for current face recognition algorithms. Face image alterations can be roughly classified into two categories: unintentional (e.g., geometrics transformations introduced by the acquisition devide) and intentional alterations (e.g., plastic surgery). We study the impact of these alterations on face recognition accuracy. Our results show that state-of-the-art algorithms are able to overcome limited digital alterations but are sensitive to more relevant modifications. Further, we develop two useful descriptors for detecting those alterations which can significantly affect the recognition performance. In the end, we propose to use the Structural Similarity (SSIM) quality map to detect and model variations due to plastic surgeries. Extensive experiments conducted on a plastic surgery face database demonstrate the potential of SSIM map for matching face images after surgeries.

Multimethodological study of molecular recognition phenomena

The study of the bio-recognition phenomena behind a biological process is nowadays considered a useful tool to deeply understand physiological mechanisms allowing the discovery of novel biological target and the development of new lead candidates. Moreover, understanding this kind of phenomena can be helpful in characterizing absorption, distribution, metabolism, elimination and toxicity properties of a new drug (ADMET parameters). Recent estimations show that about half of all drugs in development fail to make it to the market because of ADMET deficiencies; thus a rapid determination of ADMET parameters in early stages of drug discovery would save money and time, allowing to choose the better compound and to eliminate any losers. The monitoring of drug binding to plasma proteins is becoming essential in the field of drug discovery to characterize the drug distribution in human body. Human serum albumin (HSA) is the most abundant protein in plasma playing a fundamental role in the transport of drugs, metabolites and endogenous factors; so the study of the binding mechanism to HSA has become crucial to the early characterization of the pharmacokinetic profile of new potential leads. Furthermore, most of the distribution experiments carried out in vivo are performed on animals. Hence it is interesting to determine the binding of new compounds to albumins from different species to evaluate the reliability of extrapolating the distribution data obtained in animals to humans. It is clear how the characterization of interactions between proteins and drugs determines a growing need of methodologies to study any specific molecular event. A wide variety of biochemical techniques have been applied to this purpose. High-performance liquid affinity chromatography, circular dichroism and optical biosensor represent three techniques that can be able to elucidate the interaction of a new drug with its target and with others proteins that could interfere with ADMET parameters.

Polymerizing activity and regulation of group B Streptococcus pilus 2a sortase C1

Group B Streptococcus [GBS; Streptococcus agalactiae] is the leading cause of life-threatening diseases in newborn and is also becoming a common cause of invasive diseases in non-pregnant, elderly and immune-compromised adults. Pili, long filamentous fibers protruding from the bacterial surface, have been discovered in GBS, as important virulence factors and vaccine candidates. Gram-positive bacteria build pili on their cell surface via a class C sortase-catalyzed transpeptidation mechanism from pilin protein substrates. Despite the availability of several crystal structures, pilus-related C sortases remain poorly characterized to date and their mechanisms of transpeptidation and regulation need to be further investigated. The available three-dimensional structures of these enzymes reveal a typical sortase fold except for the presence of a unique feature represented by an N-terminal highly flexible loop, known as the “lid”. This region interacts with the residues composing the catalytic triad and covers the active site, thus maintaining the enzyme in an auto-inhibited state and preventing the accessibility to the substrate. It is believed that enzyme activation may occur only after lid displacement from the catalytic domain. In this work we provide the first direct evidence of the regulatory role of the lid, demonstrating that it is possible to obtain in vitro an efficient polymerization of pilin subunits using an active C sortase lid mutant carrying a single residue mutation in the lid region. Moreover, biochemical analyses of this recombinant mutant reveal that the lid confers thermodynamic and proteolytic stability to the enzyme. A further characterization of this sortase active mutant showed promiscuity in the substrate recognition, as it is able to polymerize different LPXTG-proteins in vitro.

La rappresentazione cinematografica del mondo agropastorale nel documentario corto italiano (1939 - 1969)

L’obiettivo primario di questo lavoro è quello di esplorare un insieme di documentari corti italiani di tipo etnografico e sociologico. Questi film hanno ricevuto pochissima attenzione critica, mentre sono essenziali alla comprensione del periodo di storia italiana compreso fra gli ultimi anni del Regime fascista e la fine del “Miracolo economico”. La prima parte della tesi è dedicata alla descrizione del contesto economico, sociologico, politico in cui questi lavori sono stati prodotti. La seconda parte si concentra su circa un centinaio di documentari corti analizzati sulla base di tre diversi criteri. Innanzitutto li abbiamo considerati a partire da un punto di vista autoriale, secondariamente a partire dalle loro caratteristiche produttive e distributive e infine sulla base di un criterio regionale. A partire dalla discussione antropologica coeva riguardante la scomparsa dei mondi contadini e su una precisa ricerca d’archivio focalizzata sullo stesso tema, abbiamo poi comparato il risultato dell’analisi del corpus con altre forme filmiche di rappresentazione dello stesso soggetto. Oltre a far riemergere un gruppo di autori e film quasi dimenticati, questo lavoro intende lanciare uno sguardo sul veloce, conflittuale e sbilanciato cambiamento compreso fra i mondi rurali tradizionali e la modernità, che ha caratterizzato la società italiana degli anni Cinquanta e Sessanta.