Data Mining in Clinical Practice for the Quantification of Motor Impairment in Parkinson's Disease

Advances in biomedical signal acquisition systems for motion analysis have led to lowcost and ubiquitous wearable sensors which can be used to record movement data in different settings. This implies the potential availability of large amounts of quantitative data. It is then crucial to identify and to extract the information of clinical relevance from the large amount of available data. This quantitative and objective information can be an important aid for clinical decision making. Data mining is the process of discovering such information in databases through data processing, selection of informative data, and identification of relevant patterns. The databases considered in this thesis store motion data from wearable sensors (specifically accelerometers) and clinical information (clinical data, scores, tests). The main goal of this thesis is to develop data mining tools which can provide quantitative information to the clinician in the field of movement disorders. This thesis will focus on motor impairment in Parkinson's disease (PD). Different databases related to Parkinson subjects in different stages of the disease were considered for this thesis. Each database is characterized by the data recorded during a specific motor task performed by different groups of subjects. The data mining techniques that were used in this thesis are feature selection (a technique which was used to find relevant information and to discard useless or redundant data), classification, clustering, and regression. The aims were to identify high risk subjects for PD, characterize the differences between early PD subjects and healthy ones, characterize PD subtypes and automatically assess the severity of symptoms in the home setting.

Profilo molecolare dei linfomi post-trapianto

Fifty-two cases of monomorphic post-transplant lymphoproliferative disorders (M-PTLD), developed in patients undergone solid organ or bone marrow transplantation, were studied by the application of the tissue micro-array (TMA) technology. They included 50 cases of diffuse large B-cell lymphomas (DLBCL) and 2 Burkitt lymphomas (BL). In order to evaluate the immune-profile a large panel of antibodies was applied including several new markers (Cyclin D2, Cyclin D3, p27, PKC-β, FOXP-1 and Survivin) identified as negative prognostic factors in DLBCL of the immunocompetent patient. Out of 50 DLBCL, 23 cases (46%) had an Activated B Cell (ABC) phenotype, 8 (16%) a Germinal Centre B-cell (GCB) phenotype, and 11 (22%) an Unclassified (UC) phenotype. In 8 cases (16%) the subtype was not demonstrable due to sub-optimal preservation or loss of the tissue core. FISH analysis detected BCL2 gene amplification and MYC rearrangement. EBV was identified in 32 cases (64%) performing immunohistochemistry (LMP-1) and in situ hybridization (EBER). Clinical data and follow-up were available in all cases of malignant lymphomas but one. Thirty-two patients died for progression of disease or complications related to transplant (bleeding, bacterial infections, and multi-organ failure); 17 patients are actually alive and disease-free. M-PTLD are aggressive lymphomas characterized by very poor outcome. The neoplastic process is stimulated by a prolonged immunosuppressive status which is capable to induce alterations of the immune system and allow EBV reactivation in previously infected patients. Indeed EBV infection seems to be the most significant risk factor to predict the development of a PTLD while age, sex, site of involvement and type of transplant do not have significant correlation. Furthermore DLBCL arisen in a setting of immunodeficiency share phenotypic and molecular features with DLBCL of the immunocompetent patient. In particular, the former shows a high incidence of BCL2 gene amplification and this aberration typically correlates with “non-GCB” phenotype. Also M-PTLD do express prognostic markers (PKC-β, cyclin D2, FOXP-1, and Survivin): notably, in our study, PKC-β and FOXP-1 were frequently expressed and they were predictive of a shorter overall survival even in lymphomas recognized to have a good prognosis (GCB-type). Given the fact that such molecules are detectable at the time of the diagnosis, we postulate whether a “tailored” or more specific therapy might be applied in the management of the immune-compromised patient.

Evaluation of fluid transport processes in dental enamel. Methods to assess the relevance of enamel permeability in caries prevention and etching treatments.

This thesis evaluated in vivo and in vitro enamel permeability in different physiological and clinical conditions by means of SEM inspection of replicas of enamel surface obtained from polyvinyl siloxane impressions subsequently later cast in polyether impression ma-terial. This technique, not invasive and risk-free, allows the evaluation of fluid outflow from enamel surface and is able to detect the presence of small quantities of fluid, visu-alized as droplets. Fluid outflow on enamel surface represents enamel permeability. This property has a paramount importance in enamel physiolgy and pathology although its ef-fective role in adhesion, caries pathogenesis and prevention today is still not fully under-stood. The aim of the studies proposed was to evaluate enamel permeability changes in differ-ent conditions and to correlate the findings with the actual knowledge about enamel physiology, caries pathogenesis, fluoride and etchinhg treatments. To obtain confirmed data the replica technique has been supported by others specific techniques such as Ra-man and IR spectroscopy and EDX analysis. The first study carried out visualized fluid movement through dental enamel in vivo con-firmed that enamel is a permeable substrate and demonstrated that age and enamel per-meability are closely related. Examined samples from subjects of different ages showed a decreasing number and size of droplets with increasing age: freshly erupted permanent teeth showed many droplets covering the entire enamel surface. Droplets in permanent teeth were prominent along enamel perikymata. These results obtained through SEM inspection of replicas allowed innovative remarks in enamel physiology. An analogous testing has been developed for evaluation of enamel permeability in primary enamel. The results of this second study showed that primary enamel revealed a substantive permeability with droplets covering the entire enamel sur-face without any specific localization accordingly with histological features, without changes during aging signs of post-eruptive maturation. These results confirmed clinical data that showed a higher caries susceptibility for primary enamel and suggested a strong relationship between this one and enamel permeability. Topical fluoride application represents the gold standard for caries prevention although the mechanism of cariostatic effect of fluoride still needs to be clarified. The effects of topical fluoride application on enamel permeability were evaluated. Particularly two dif-ferent treatments (NaF and APF), with different pH, were examined. The major product of topical fluoride application was the deposition of CaF2-like globules. Replicas inspec-tion before and after both treatments at different times intervals and after specific addi-tional clinical interventions showed that such globule formed in vivo could be removed by professional toothbrushing, sonically and chemically by KOH. The results obtained in relation to enamel permeability showed that fluoride treatments temporarily reduced enamel water permeability when CaF2-like globules were removed. The in vivo perma-nence of decreased enamel permeability after CaF2 globules removal has been demon-strated for 1 h for NaF treated teeth and for at least 7 days for APF treated teeth. Important clinical consideration moved from these results. In fact the caries-preventing action of fluoride application may be due, in part, to its ability to decrease enamel water permeability and CaF2 like-globules seem to be indirectly involved in enamel protection over time maintaining low permeability. Others results obtained by metallographic microscope and SEM/EDX analyses of or-thodontic resins fluoride releasing and not demonstrated the relevance of topical fluo-ride application in decreasing the demineralization marks and modifying the chemical composition of the enamel in the treated area. These data obtained in both the experiments confirmed the efficacy of fluoride in caries prevention and contribute to clarify its mechanism of action. Adhesive dentistry is the gold standard for caries treatment and tooth rehabilitation and is founded on important chemical and physical principles involving both enamel and dentine substrates. Particularly acid etching of dental enamel enamel has usually employed in bonding pro-cedures increasing microscopic roughness. Different acids have been tested in the litera-ture suggesting several etching procedures. The acid-induced structural transformations in enamel after different etching treatments by means of Raman and IR spectroscopy analysis were evaluated and these findings were correlated with enamel permeability. Conventional etching with 37% phosphoric acid gel (H3PO4) for 30 s and etching with 15 % HCl for 120 s were investigated. Raman and IR spectroscopy showed that the treatment with both hydrochloric and phosphoric acids induced a decrease in the carbonate content of the enamel apatite. At the same time, both acids induced the formation of HPO42- ions. After H3PO4 treatment the bands due to the organic component of enamel decreased in intensity, while in-creased after HCl treatment. Replicas of H3PO4 treated enamel showed a strongly reduced permeability while replicas of HCl 15% treated samples showed a maintained permeability. A decrease of the enamel organic component, as resulted after H3PO4 treatment, involves a decrease in enamel permeability, while the increase of the organic matter (achieved by HCl treat-ment) still maintains enamel permeability. These results suggested a correlation between the amount of the organic matter, enamel permeability and caries. The results of the different studies carried out in this thesis contributed to clarify and improve the knowledge about enamel properties with important rebounds in theoretical and clinical aspects of Dentistry.

Development of original analytical methods for the therapeutic drug monitoring of CNS druges: Antipsychotics, Antidepressants and Anxiolytics-hypnotics

Great strides have been made in the last few years in the pharmacological treatment of neuropsychiatric disorders, with the introduction into the therapy of several new and more efficient agents, which have improved the quality of life of many patients. Despite these advances, a large percentage of patients is still considered “non-responder” to the therapy, not drawing any benefits from it. Moreover, these patients have a peculiar therapeutic profile, due to the very frequent application of polypharmacy, attempting to obtain satisfactory remission of the multiple aspects of psychiatric syndromes. Therapy is heavily individualised and switching from one therapeutic agent to another is quite frequent. One of the main problems of this situation is the possibility of unwanted or unexpected pharmacological interactions, which can occur both during polypharmacy and during switching. Simultaneous administration of psychiatric drugs can easily lead to interactions if one of the administered compounds influences the metabolism of the others. Impaired CYP450 function due to inhibition of the enzyme is frequent. Other metabolic pathways, such as glucuronidation, can also be influenced. The Therapeutic Drug Monitoring (TDM) of psychotropic drugs is an important tool for treatment personalisation and optimisation. It deals with the determination of parent drugs and metabolites plasma levels, in order to monitor them over time and to compare these findings with clinical data. This allows establishing chemical-clinical correlations (such as those between administered dose and therapeutic and side effects), which are essential to obtain the maximum therapeutic efficacy, while minimising side and toxic effects. It is evident the importance of developing sensitive and selective analytical methods for the determination of the administered drugs and their main metabolites, in order to obtain reliable data that can correctly support clinical decisions. During the three years of Ph.D. program, some analytical methods based on HPLC have been developed, validated and successfully applied to the TDM of psychiatric patients undergoing treatment with drugs belonging to following classes: antipsychotics, antidepressants and anxiolytic-hypnotics. The biological matrices which have been processed were: blood, plasma, serum, saliva, urine, hair and rat brain. Among antipsychotics, both atypical and classical agents have been considered, such as haloperidol, chlorpromazine, clotiapine, loxapine, risperidone (and 9-hydroxyrisperidone), clozapine (as well as N-desmethylclozapine and clozapine N-oxide) and quetiapine. While the need for an accurate TDM of schizophrenic patients is being increasingly recognized by psychiatrists, only in the last few years the same attention is being paid to the TDM of depressed patients. This is leading to the acknowledgment that depression pharmacotherapy can greatly benefit from the accurate application of TDM. For this reason, the research activity has also been focused on first and second-generation antidepressant agents, like triciclic antidepressants, trazodone and m-chlorophenylpiperazine (m-cpp), paroxetine and its three main metabolites, venlafaxine and its active metabolite, and the most recent antidepressant introduced into the market, duloxetine. Among anxiolytics-hypnotics, benzodiazepines are very often involved in the pharmacotherapy of depression for the relief of anxious components; for this reason, it is useful to monitor these drugs, especially in cases of polypharmacy. The results obtained during these three years of Ph.D. program are reliable and the developed HPLC methods are suitable for the qualitative and quantitative determination of CNS drugs in biological fluids for TDM purposes.

Genetic and environmental factors associated with the risk of cognitive decline and dementia

AD is the most common age related neurodegenerative disease in the industrialized world. Clinically AD is defined as a progressing decline of cognitive functions. Neuropathologically, AD is characterized by the aggregation of b-amyloid (Ab) peptide in the form of extracellular senile plaques, and hyperphosphorlylated tau protein in the form of intracellular neurofibrillary tangles. These neuropathological hallmarks are often accompanied by abundant microvascular damage and pronounced inflammation of the affected brain regions. In this thesis we investigated several aspects of AD focusing on the genetic aspect. We confirmed that Alpha 1 antichymotrypsin (ACT), an acute phase protein, was associated to AD subjects, being plasma levels higher in AD cases than controls. In addition, in a GWA study we demonstrated that two different gene, Clusterin and CR1 were strongly associated to AD. A single gene association not explain such a complex disease like AD. The goal should be to created a network of genetic, phenotypic and clinical data associated to AD. We used a new algorithm, the ANNs, aimed to map variables and search for connectivity among variables. We found specific variables associated to AD like cholesterol levels, the presence of variation in HMGCR enzyme and the age. Other factors such as the BMI, the amount of HDL and blood folate levels were also associated with AD. Pathogen infections, above all viral infections, have been previously associated to AD. The hypothesis suggests that virus and in particular herpes virus could enter the brain when an individual becomes older, perhaps because of a decline in the immune system. Our new hypothesis is that the presence of SNPs in our GWA gene study results in a genetic signature that might affect individual brain susceptibility to infection by herpes virus family during aging.

Statistical methods for analysis and processing of medical ultrasound: applications to segmentation and restoration

In this thesis two major topics inherent with medical ultrasound images are addressed: deconvolution and segmentation. In the first case a deconvolution algorithm is described allowing statistically consistent maximum a posteriori estimates of the tissue reflectivity to be restored. These estimates are proven to provide a reliable source of information for achieving an accurate characterization of biological tissues through the ultrasound echo. The second topic involves the definition of a semi automatic algorithm for myocardium segmentation in 2D echocardiographic images. The results show that the proposed method can reduce inter- and intra observer variability in myocardial contours delineation and is feasible and accurate even on clinical data.

Timing per l'inserimento in lista dei pazienti affetti da fibrosi cistica che necessitano di trapianto polmonare: casistica di un centro regionale di riferimento

Timing of waiting list entrance for patients with cystic fibrosis in need of pulmonary transplant: the experience of a regional referral centre Objective: Evaluation of parameters that can predict a rapid decay of general conditions of patients affected by Cystic Fibrosis (CF) with no specific criteria to be candidate to pulmonary transplant. Material and methods: Fifteen patients with CF who died for complications and 8 who underwent lung transplantation in the 2000-2010 decade, were enrolled. Clinical data 2 years before the event (body max index, FEV1%, number of EV antibiotic treatments per year, colonization with Methicillin-resistant Staphylococcus aureus (MRSA), pseudomonas aeruginosa mucosus, burkholderia cepacia, pulmonary allergic aspergilosis) were compared among the 2 groups. Results: Mean FEV1% was significantly higher and mean number of antibiotic treatment was lower in deceased than in the transplanted patients (p<0.002 and p<0.001 respectively). Although in patients who died there were no including criteria to enter the transplant list 2 years before the exitus, suggestive findings such as low BMI (17.3), high incidence of hepatic pathology (33.3%), diabetes (50%), and infections with MRSA infection (25%), Pseudomonas aeruginosa (83.3%) and burkholderia cepacia (8.3%) were found with no statistical difference with transplanted patients, suggesting those patients were at risk of severe prognosis. In patients who died, females were double than males. Conclusion: While evaluating patients with CF, negative prognostic factors such as the ones investigated in this study, should be considered to select individuals with high mortality risk who need stricter therapeutical approach and follow up. Inclusion of those patients in the transplant waiting list should be taken into account.

Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

Aging in human liver and skeletal muscle: studies on proteasomes

Aging is a complex phenomenon that affects organs and tissues at a different rate. With advancing age, the skeletal muscle undergoes a progressive loss of mass and strength, a process known as sarcopenia that leads to a decreased mobility and increased risk of falls and invalidity. On the other side, another organ such as the liver that is endowed with a peculiar regenerative capacity seems to be only marginally affected by aging. Accordingly, clinical data indicate that liver transplantation from aged subjects has, in specific conditions, function and duration comparable to those achievable with grafts of liver from young donors. The molecular mechanisms involved in these peculiar aging patterns are still largely unknown, but it is conceivable that protein degradation machineries might play an important role, as they are responsible for the maintenance of cellular homeostasis. Indeed, it has been suggested that alteration of proteostasis may contribute to the onset and progression of several age-related pathological conditions, including skeletal muscle wasting and sarcopenia, as well as to the aging phenotypes. The ubiquitin-proteasome system (UPS) is one of the most important cellular pathways for intracellular degradation of short-lived as well as damaged proteins. To date, studies on the age-related modifications of proteasomes in liver and skeletal muscle were performed prevalently in rodents, with controversial results, while only preliminary observations have been obtained in human liver and skeletal muscle. In this scenario, we want to investigate and characterize in humans the age-related modifications of proteasomes of these two different organs.

Efficacia clinica dello stanozololo intrarticolare nella terapia dell'osteoartrosi di gomito nel cane

Il trattamento dell’osteoartrosi (OA) del cane è una sfida nella pratica clinica veterinaria. Molti trattamenti sono stati proposti, tuttavia la risposta clinica agli stessi non è sempre soddisfacente. Molti farmaci sono utilizzati per il trattamento dell’OA, tra cui farmaci anti-infiammatori non steroidei, corticosteroidi, ed inibitori della produzione dell’ossido nitrico. Lo stanozololo è un derivato sintetico del testosterone; oltre alle sue proprietà anaboliche/androgeniche , a basse dosi lo stanozololo ha un affinità per i recettori glucocorticoidi. Per questa attività antinfiammatoria e rigenerativa sui tessuti articolari danneggiati viene utilizzato nella degenerative joint desease del cavallo. Lo scopo di questo studio è stato di valutare l’efficacia clinica dello stanozololo intra-articolare a 15, 30, 45 e 60 giorni dal trattamento di gomiti con OA di cane. E’ stato eseguito uno studio cieco, multicentrico e randomizzato. Previo consenso informato, sono stati arruolati 48 cani, suddivisi in 3 gruppi e trattati con stanozololo, mavacoxib e con entrambi i farmaci. Sono state valutate zoppia, tollerabilità del trattamento, range of motion, e punteggio radiografico. Inoltre sono state stabilite e annoverate quantità e qualità del liquido sinoviale. Ai dati ottenuti sono stati applicati i test di Kruskal-Wallis, Chi-quadro e Fischer, i quali hanno dimostrato l’efficacia della terapia nei singoli gruppi e tra i diversi gruppi di studio. I risultati ottenuti hanno mostrato la riduzione di almeno un grado di zoppia e la riduzione della progressione dell’OA nei casi trattati con stanozololo. Si può quindi affermare che tale molecola per via intra-articolare può essere una valida alternativa per il trattamento dell’OA di gomito nel cane.

Fistole retto-vaginali Crohn-relate trattate mediante trasposizione del muscolo gracile: risultati a lungo termine e qualità della vita

OBIETTIVO: Le fistole retto-vaginali Crohn-relate hanno un impatto significativo sulla qualità della vita. Quando il canale anale è alterato da ulcerazioni e stenosi o in pazienti con difetti estesi del perineo, la chirurgia locale produce risultati insoddisfacenti. Lo scopo di questo studio è quello di valutare l'efficacia della trasposizione del muscolo gracile nelle fistole retto-vaginali Crohn-relate e determinare i suoi effetti sulla qualità della vita. MATERIALI E METODI: Da gennaio 2012 a ottobre 2014 sono state trattate 10 pazienti; sono state raccolte alcune variabili (età, BMI, il fumo, CDAI, setone perioperatorio, precedenti procedure, uso di immunomodulatori e steroidi). Tutte le pazienti sono state sottoposte ad ileostomia temporanea prima della graciloplastica. La percentuale di successo è stata misurata come numero di pazienti con fistola guarita dopo la chiusura della stomia. Sono stati utilizzati tre questionari prima della graciloplastica e 3 mesi dopo la chiusura della stomia al fine di valutare la qualità della vita (SF-36), l’ incontinenza fecale e la funzione sessuale. RISULTATI: La fistola retto-vaginale è stata chiusa in 9 pazienti su 10 dopo graciloplastica, con un follow-up medio di chiusura della stomia di 19 mesi (range 4 -34). È stata documentata una recidiva di RVF. Il tempo operatorio era 90-150 minuti (media, 120). La degenza postoperatoria era 7-16 giorni (media 10). Complicanze postoperatorie precoci includevano deiscenza delle suture perineali in 2 casi. Le complicanze a lungo termine includevano disestesia della cicatrice perineale. Nei dati post-operatori abbiamo riportato un miglioramento della qualità di vita, della funzione sessuale e della continenza fecale. CONCLUSIONI: La chiusura della fistola retto-vaginale utilizzando la trasposizione del muscolo gracile è associata a morbidità minima e un alto tasso di successo.