Discriminative feature learning for multimodal classification

The purpose of this thesis is to tackle two related topics: multimodal classification and objective functions to improve the discriminative power of features. First, I worked on image and text classification tasks and performed many experiments to show the effectiveness of different approaches available in literature. Then, I introduced a novel methodology which can classify multimodal documents using singlemodal classifiers merging textual and visual information into images and a novel loss function to improve separability between samples of a dataset. Results show that exploiting multimodal data increases performances on classification tasks rather than using traditional single-modality methods. Moreover the introduced GIT loss function is able to enhance the discriminative power of features, lowering intra-class distance and raising inter-class distance between samples of a multiclass dataset

Integrating phenotypes and endotypes in chronic rhinosinusitis: a combined clinical and experimental approach.

Chronic rhinosinusitis (CRS) represents a hot and debated topic in rhinology because of its high prevalence, heterogeneity of clinical manifestations and unpredictability of disease course. The quite recent dichotomic classification of CRS with and without nasal polyps has proved to be too simplistic to fully explain CRS manifestations and the underlying pathogenetic mechanisms. Being either the same phenotype expression of substantially different pathogenic mechanisms or different phenotypes the expression of the same mechanism, a one-size-fit-all therapeutic approach turned out to be insufficient in a non-negligible proportion of patients. Moreover, considering the attempt of giving a classification cut at a biomolecular level, a diagnostic and prognostic approach exclusively limited to subjective and objective clinical parameters is inevitably failing in many ways. However, to date no other more effective markers are available to monitor the trend of the disease. The fact of dealing with an apparently very frequent pathology responsible for a strong discomfort on the QoL and a substantial economic impact requires a diagnostic and therapeutic appropriateness for an adequate allocation of resources within the standards of precision medicine. The development of systems for a uniform archiving and sharing of the experiences of each rhinological center would enhance the efforts of the scientific community in defining integrated and targeted care pathways. The present thesis reports the results and the practical implications of three different experimental studies about the implementation of data storage and sharing systems, methods of analysis of therapeutic outcomes and inflammatory biomarkers in CRS

Molecular characterization of a Mecp2Y120D mouse model and MeCP2 role in primary cilia formation: implications in Rett syndrome

Rett syndrome (RTT) is a neurological progressive disorder affecting about 1/10,000 new born females. Most cases of “classic” RTT are primarily ascribable to sporadic mutations in the X-linked MECP2 gene, encoding the multifunctional methyl-CpG-binding protein 2 (MeCP2). Studies of different mouse models of Mecp2 indicate that MeCP2 activities are modulated by a series of post-translational modifications. We generated a knockin mouse model harboring the human pathogenic tyrosine 120aspartic acid (Y120D) mutation in Mecp2. This mutation was found in a female patient affected by RTT. Studies carried out on Mecp2Y120D mouse line showed a surprisingly severe phenotype overlapping that of Mecp2 null mice. The obtained data showed that the Y120D mutation causes a significant reduction in protein levels of Mecp2 and a clear defect in its chromatin binding. Since our studies on tyrosine 120 phosphorylation allowed us to functionally connect MeCP2 with the centrosome, we investigated whether Mecp2 deficiency might lead to centrosomal dysfunctions also in neurons that represent the most affected cells in RTT. Thus, we undertook a study to determine whether MeCP2 is required for the proper formation of the primary cilium. Our studies demonstrate that loss of MeCP2 determines a defect in ciliogenesis in all tested cells including murine neurons and astrocytes and RTT patients’ fibroblasts. We have also observed a functional defect in the activation of the Sonic Hedgehog pathway. Both morphological and functional defects are rescued by the stabilization of microtubules with an histone deacetylase 6 inhibitor

DNA hypomethylation and hypermethylation in colorectal cancer initiation.

This project was focused on identification of new valuable molecular risk factors for the onset of colorectal cancer (CRC), studying both KRAS/NRAS/BRAF/PIK3CA mutations and DNA global hypomethylation in the early events of colorectal carcinogenesis. We analyzed a cohort of 52 colorectal adenomas and 11 carcinomas derived from MAP subjects, 80 sporadic adenomas and 15 carcinomas and a control set of 36 FAP/AFAP adenomas. Moreover, we characterized the L1-MET transcript induced by L1 hypomethylation. We observed that the early steps of oxidative DNA damage in MAP carcinogenesis are characterized by a specific pattern of somatic mutations. We also found that MAP adenomas and carcinomas show a decreased DNA global methylation and specific L1-MET hypomethylation. Finally, we hypothesized that DNA hypomethylation and expression of L1-MET chimeric transcript may play an early role in colorectal carcinogenesis characterizing a subset of more aggressive precursor lesions and cancers. In the second part of the thesis, we studied the promoter of MutL homolog 1 (MLH1) in order to elucidate the relationship between methylation and risk/protective allele at rs1800734 during CRC progression. We confirmed the association of rs1800734 with microsatellite instability (MSI) in our own data. In 33 normal colon biopsies, small allele-specific differences exist only in methylation, but not gene expression. In contrast, allele-specific differences in both MLH1 methylation and expression are present in 35 MSI cancers. We showed that MLH1 transcriptional repression is dependent on DNA methylation and can be reversed by a methylation inhibitor. The rs1800734 allele influences the rate of methylation loss and amount of re-expression

Per una storia della comunicazione globale: dal Centro Mondiale di Andersen al Web.

The concept of global communication was defined through the comparison between the World Centre of Communication and the World Wide Web. This notion refers to the idea, spread in the nineteenth century, to create a system which ensure connection over long distances. Electrification, the construction of infrastructures and the use of media allowed to connect geographically distant places. This process, which began in the 19th century, ended its long and difficult path between the 80s and 90s of the 20th century with the advent of the World Wide Web. Well before Tim Berners Lee’s innovation, Norwegian sculptor Hendrik Christian Andersen developed an ideal project with similar objectives: The World Centre of Communication. Poorly studied by historiography in the field of technology and communication, this plan represented the hypothesis to create a universal communication system to connect different territories and spread information and knowledge throughout the globe. Unfortunately, this idea remained a utopia; while the Web has developed between the 80s and 90s of the twentieth century, becoming a real universal library of information open and accessible. Over time Lee’s innovation has gone into crisis. The digital giants have taken control of the network: through the algorithms - complex, opaque and invisible -, they have undermined the pedagogical and educational functions of the Web, supporting a commercial orientation

Metal nanoparticle permeation through the plasma membrane: Xenopus laevis oocytes as novel tools for membrane permeability evaluation and physico-chemical characterization of particle properties.

In this Ph.D. thesis several kinds of metal-based NPs were tested in Xenopus laevis oocytes, in order to understand the metal NP related toxicity. The mechanism of the metals entrance in the cell and the passive permeation hypothesis were investigated. The results can be categorized as follows: • The metallic NPs tested (Co, Fe, Ni) dissolve more than their oxide counterparts; however, they are unstable in suspension and their aggregation rate is fast. All these particles are not able to induce modifications in membrane biophysical parameters and in intracellular metal concentration, thereby excluding a direct membrane crossing mechanism for their internalization. • The metal oxide NPs which retain a population below 200 nm (Fe3O4, Co3O4) in suspension in experimental medium induced significant modifications in membrane biophysical parameters and in intracellular metal concentration. The effects are recorded only when the population of NPs smaller than 200 nm is present, namely only within 5 min from the particles addition to the medium; after this time range, effects on membrane become milder until they disappear, stating the complete fast recovery of the membrane. • The metal oxide NPs that never go below 200 nm (NiO, Fe2O3) in suspension in the experimental medium do not cross the membrane and do not modify neither intracellular metal concentration nor membrane biophysical parameters. • The surface coating modifies particles behavior in suspension in the experimental medium. The non-covalent coating by BSA stabilized the 200 nm population for Co3O4 and Fe3O4 NPs but abolished the modifications in intracellular metal concentration and in membrane biophysical parameters. The covalent coating by APTES of Fe2O3 NPs partially stabilized particles around 100 nm but failed to induce membrane crossing. The role of particle surface is thus crucial to achieve direct membrane crossing. Many of the studies conducted nowadays on direct membrane crossing rely on models, both in silico as well as in vitro, that are limited in replicating the biological complexity of the cells. Using voltage clamp and fluorescent probe on Xenopus Laevis oocytes may lay the foundation for an innovative screening platform, allowing to study the internalization and the effects on membrane. Xenopus laevis oocytes are easy to collect, maintain and prepare. They are flexible and adaptable to different culture conditions, allowing to study interactions in controlled environment. Moreover, Xenopus laevis oocytes can also be a useful tool to study and optimize targeted internalization. Their historical use as heterologous expression system is well known, selectively express target proteins to study specific internalization pathways of new modified nanoparticles will be one of the new goals for the therapeutic use of nanomaterial

Genomic molecular markers to monitor minimal residual disease with a non invasive liquid biopsy in breast cancer patients

Background Circulating cell free DNA (cfDNA) is one of the most intriguing and developing topic in the field of precision and personalized medicine. From 1977, when Leon and colleagues reported an increase in cfDNA in cancer patients, several studies have tried to explain and understand deeper how cfDNA is produced, lasts into the bloodstream, and what kind of information it contains and can be useful to detect and/or manage the disease. Liquid biopsy has already been approved to determine those patients that will benefit from an epidermal growth factor receptor (EGFR)-targeted therapy in non-small cell lung cancer (NSCLC). Nowadays, several studies on clinical applicability and clinical trials are on-going, in order to determine if information obtained from cfDNA can drive clinical decisions. Homologous recombination (HR) is a high-fidelity DNA repair mechanism involved in double-strand DNA (dsDNA) break repair. Recent studies have highlighted a broader involvement of HR status in BRCA wild type breast cancers (BC), in particular in triple negative BC (TNBC). Identification of mutations in the HR pathway can suggest the administration of a specific therapy, such as platinum agents or PARP inhibitors (PARPi). Material & Methods In this work we have collected fresh tissue and blood from 6 BC patients. Plasma was separated with two consecutive centrifugations to completely remove cell and cellular debris. We have extracted genomic DNA (gDNA) from fresh tissue and cfDNA from plasma using commercial kits. We have analysed in parallel both DNAs with the Homologous Recombination Solution™ kit (Sophia™ Genetics) that allows the identification of mutations in exonic regions of 16 genes involved in HR. Results All samples passed target enrichment and sequencing quality controls (QC). In 3 out of 6 patients no mutations were detected in both gDNA and cfDNA. Patients 1 and 6 had mutations in gDNA not detected in cfDNA. Patient 2 had 2 mutations in gDNA and only one of the two was detected in cfDNA. Conclusions This kit can be used to analyse cfDNA, as confirmed by QC reports. Interestingly, the identification of the mutation in TP53 in patient 2’s cfDNA supports the possibility to detect mutations with this kit. The higher variant fraction (VF) in cfDNA compared to gDNA can sustain the possibility to have a broader detection of heterogeneity. The non-recognition of mutations in cfDNA in patients carrying gDNA mutations can be ascribed to the reduced amount of cfDNA analysed and to the fact that tumoral DNA is only a fraction of the total cfDNA. Thus, the sample analysed can be unrepresentative of the circulating DNA pool. The analysis of a higher number of samples will give us a clearer idea of the applicability of this kit to monitor HR mutational status in cfDNA of BC patients, giving us statistical significance of detection

Assessment of portable and miniaturized sensors for the monitoring of human exposure to air pollutants

In the last years, several in-field campaigns have been conducted using portable and miniaturized monitors to evaluate the personal exposure to different pollutants. In general, this kind of monitors are characterized by worse metrological performance if compared to the traditional standard methods. Despite this disadvantage, portable and miniaturized monitors could be easily used across different applications, because their advantageous features, such as the capability to provide real-time measurement, the high spatial and temporal resolution of acquired data, the ability to adapt to different experimental designs and, especially, the ability to follow the subject in any activity. Finally, portable and miniaturized instruments can provide data acquired in the respiratory zone of the subject, following therefore the practices for a correct exposure assessment. Obviously, the best compromise between the analytical gold standard (in terms of precision, accuracy and instrumental sensitivity) and the gold standard in regard to the exposure assessment should be chosen. Therefore, in brief, principal aims of this thesis are (i) to evaluate the on-field performances of portable and miniaturized monitors for gaseous pollutants and airborne PM and (ii) to use these monitors in exposure assessment studies and (iii) to understand if data acquired via portable and miniaturized monitors could be useful in other fields of application, such as epidemiological studies or toxicological studies, in which the evaluation of the inhaled dose of pollutants could play a key role

Parasite-host relationships in the biological control of insects: strategies of immunoevasion/immunosuppression and interference of temperature on the lethality of entomoparasites.

In this PhD project were considered two aspects of the relationship between bio-insecticide and insect hosts: the first has been the study the mechanisms carried out by EPNs complexes (Steinernema carpocapsae - Xenorhabdus nematophila) to overcome or neutralize the immune system of the insect host. The success of the EPNs results mainly from immunological disabling induced by nematode and its symbionts by immunoevasion/immunosuppression process when released inside the host hemocoel. The functions of structures and molecular components of the surface of both nematodes and bacteria play a key role and we assessed the role of protein pools isolated against Galleria mellonella (Lepidoptera). The eluted compounds from live nematode possessed a slight cytotoxicity on the haemocytes, whereas those from live bacteria markedly affected the host cells’ viability. Bacterial proteins can inhibit the phagocytic activity, despite they strongly trigger the host prophenoloxidase-phenoloxidase system. The second part of the project is aimed to acquire useful information on host-parasite relations in the context of climate change and, we reconsidered the physical conditions (such as temperature) in which bioinsecticides are highly effective. We evaluated the effectiveness of different commercial bio-insecticides (Steinernema feltiae, Steinernema carpocapsae, Heterorhabditis bacteriophora and Bacillus thuringiensis) assessing the mortality rate induced in two insect models, Galleria mellonella (Lepidoptera) and Sarcophaga africa (Diptera) after conditioning at various temperatures (10, 20 and 30 °C); moreover, we investigated the effects of temperature on the basal humoral immunity (phenoloxidase and lysozyme activity)

Robust optimization in data envelopment analysis: extended theory and applications.

Performance evaluation of decision-making units (DMUs) via the data envelopment analysis (DEA) is confronted with multi-conflicting objectives, complex alternatives and significant uncertainties. Visualizing the risk of uncertainties in the data used in the evaluation process is crucial to understanding the need for cutting edge solution techniques to organizational decisions. A greater management concern is to have techniques and practical models that can evaluate their operations and make decisions that are not only optimal but also consistent with the changing environment. Motivated by the myriad need to mitigate the risk of uncertainties in performance evaluations, this thesis focuses on finding robust and flexible evaluation strategies to the ranking and classification of DMUs. It studies performance measurement with the DEA tool and addresses the uncertainties in data via the robust optimization technique. The thesis develops new models in robust data envelopment analysis with applications to management science, which are pursued in four research thrust. In the first thrust, a robust counterpart optimization with nonnegative decision variables is proposed which is then used to formulate new budget of uncertainty-based robust DEA models. The proposed model is shown to save the computational cost for robust optimization solutions to operations research problems involving only positive decision variables. The second research thrust studies the duality relations of models within the worst-case and best-case approach in the input – output orientation framework. A key contribution is the design of a classification scheme that utilizes the conservativeness and the risk preference of the decision maker. In the third thrust, a new robust DEA model based on ellipsoidal uncertainty sets is proposed which is further extended to the additive model and compared with imprecise additive models. The final thrust study the modelling techniques including goal programming, robust optimization and data envelopment to a transportation problem where the concern is on the efficiency of the transport network, uncertainties in the demand and supply of goods and a compromising solution to multiple conflicting objectives of the decision maker. Several numerical examples and real-world applications are made to explore and demonstrate the applicability of the developed models and their essence to management decisions. Applications such as the robust evaluation of banking efficiency in Europe and in particular Germany and Italy are made. Considering the proposed models and their applications, efficiency analysis explored in this research will correspond to the practical framework of industrial and organizational decision making and will further advance the course of robust management decisions