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.

Role of new molecular approaches for the early diagnosis of bladder cancer in clinical practice

There is an urgent need to improve the performance of urine cytology for the diagnosis of bladder cancer. In preliminary studies, telomerase activity evaluated by telomeric repeat amplification protocol (TRAP) assay and chromosomal aneuploidy detected by fluorescence in situ hybridization (FISH) in the diagnosis of bladder cancer have produced important results. Urine cell-free (UCF) DNA has also been proposed as a potential marker for early bladder cancer diagnosis. In the first study the diagnostic performance of TRAP assay and FISH analysis was assessed, while the second study evaluated the potential role of UCF DNA integrity in early bladder cancer diagnosis. In the first cross-sectional study, 289 consecutive patients who presented with urinary symptoms underwent cystoscopy and cytology evaluation. In the second study, UCF DNA was isolated from 51 bladder cancer patients, 46 symptomatic patients, and 32 healthy volunteers. c-Myc, BCAS1 and HER2 gene sequences longer than 250 bp were quantified by real time PCR to verify UCF DNA integrity. In the first study, sensitivity and specificity were 0.39 and 0.83, respectively, for cytology; 0.66 and 0.72 for TRAP; 0.78 and 0.60 for the cytology and TRAP combination; 0.78 and 0.78 for the cytology, TRAP and FISH combination; and 0.65 and 0.93 for the TRAP and FISH combination. In the second study, at the best cutoff of 0.1 ng/µl, UCF DNA integrity analysis showed a sensitivity of 0.73 and a specificity of 0.84 in healthy individuals and 0.83 in symptomatic patients. The preliminary results suggest that these biomarkers could potentially be used for the early diagnosis of bladder cancer, especially in high-risk populations (e.g, symptomatic individuals exposed to occupational risk) who may benefit from the use of noninvasive diagnostic tests in terms of cost-benefit.

Integrated molecular analysis of endometrial carcinoma: translation of biomarker profiles into the clinical practice

The Cancer Genome Atlas (TCGA) collaborative project identified four distinct prognostic groups of endometrial carcinoma (EC) based on molecular alterations: (i) the ultramutated subtype that encompassed POLE mutated (POLE) cases; (ii) the hypermutated subtype, characterized by MisMatch Repair deficiency (MMRd); (iii) the copy-number high subtype, with p53 abnormal/mutated features (p53abn); (iv) the copy-number low subtype, known as No Specific Molecular Profile (NSMP). Although the prognostic value of TCGA molecular classification, NSMP tumors present a wide variability in molecular alterations and biological aggressiveness. This study aims to investigate the impact of ARID1A and CTNNB1/β-catenin alterations by targeted Next-generation sequencing (NGS) and immunohistochemistry (IHC) in a consecutive series of 125 molecularly classified ECs. NGS and IHC were used to assign surrogate TCGA groups and to identify molecular alterations of multiple target genes including POLE, PTEN, ARID1A, CTNNB1, TP53. Associations with clinicopathologic parameters, molecular subtypes, and outcomes identified NSMP category as the most heterogeneous group in terms of clinicopathologic features and outcome. Integration of surrogate TCGA molecular classification with ARID1A and β-catenin analysis showed NSMP cases with ARID1A mutation characterized by the worst outcome with early recurrence, while NSMP tumors with ARID1A wild-type and β-catenin alteration had indolent clinicopathologic features and no recurrence. This study indicates how the identification of ARID1A and β-catenin alterations in EC represents a simple and effective way to characterize NSMP tumor aggressiveness and metastatic potential.

Omission of axillary clearance in patients with early breast cancer and positive sentinel node biopsy treated with conservative surgery: application of the ACOSOG Z011 trial in clinical practice

Background: Axillary lymph node dissection (ALND) in presence of sentinel lymph node (SLN) metastases has been the standard in breast cancer (BC) patients for many years. Today, after the publication of the ACOSOG Z0011 trial, ALND is a procedure restricted to a dwindling group of patients with a clearly metastatic axilla. Material and methods: This was a prospective observational trial involving two Italian Breast Units: Policlinico di Sant’Orsola and San Raffaele hospital. Objective was to evaluate that the omission of ALND in patients with cT1-2 cN0 BC undergoing breast conserving surgery (BCS) and histological finding of metastases in 1 or 2 SLN is not associated with a worse prognostic outcome. Primary endpoint was overall survival (OS). Secondary endpoints were disease free survival (DFS) and locoregional recurrence. All BC patients treated between the 1st of November 2020 and 31st of July 2023 with cT1-2 cN0 BC, preoperative negative axillary ultrasound and 1 or 2 metastatic SLN treated with sentinel node biopsy (SLNB) alone entered the study. Results: 795 cT1-2 cN0 BC patients underwent BCS and SLNB. Ninety patients were included. Median age was 60 (52-68) years. Seventy-five patients (83%) had T1 tumor and 15 (17%) T2. Median tumor size was 16 mm (11-19). The median SLN removed was 2 (1-3). Eighty-one patients had 1 positive SLN (90%), while 9 had 2 SLN metastasis (10%). 39 (43%) micrometastases were identified and 51 macrometastasis (57%). All patients underwent radiotherapy. Seventeen (19%) performed adjuvant chemotherapy. Two received immunotherapy with trastuzumab and pertuzumab. Endocrine therapy was given to 84 (93%). At a median follow-up of 19 months (IQR 13-23) OS and DFS were 100%. No loco-regional recurrence was seen. Conclusion: The preliminary results of our study confirm that omitting ALND in patients meeting Z011 criteria is oncologically safe and should be the standard of care.

Development of Clinical Decision Support Systems based on Mathematical Models of Physiological Systems

In the last years of research, I focused my studies on different physiological problems. Together with my supervisors, I developed/improved different mathematical models in order to create valid tools useful for a better understanding of important clinical issues. The aim of all this work is to develop tools for learning and understanding cardiac and cerebrovascular physiology as well as pathology, generating research questions and developing clinical decision support systems useful for intensive care unit patients. I. ICP-model Designed for Medical Education We developed a comprehensive cerebral blood flow and intracranial pressure model to simulate and study the complex interactions in cerebrovascular dynamics caused by multiple simultaneous alterations, including normal and abnormal functional states of auto-regulation of the brain. Individual published equations (derived from prior animal and human studies) were implemented into a comprehensive simulation program. Included in the normal physiological modelling was: intracranial pressure, cerebral blood flow, blood pressure, and carbon dioxide (CO2) partial pressure. We also added external and pathological perturbations, such as head up position and intracranial haemorrhage. The model performed clinically realistically given inputs of published traumatized patients, and cases encountered by clinicians. The pulsatile nature of the output graphics was easy for clinicians to interpret. The manoeuvres simulated include changes of basic physiological inputs (e.g. blood pressure, central venous pressure, CO2 tension, head up position, and respiratory effects on vascular pressures) as well as pathological inputs (e.g. acute intracranial bleeding, and obstruction of cerebrospinal outflow). Based on the results, we believe the model would be useful to teach complex relationships of brain haemodynamics and study clinical research questions such as the optimal head-up position, the effects of intracranial haemorrhage on cerebral haemodynamics, as well as the best CO2 concentration to reach the optimal compromise between intracranial pressure and perfusion. We believe this model would be useful for both beginners and advanced learners. It could be used by practicing clinicians to model individual patients (entering the effects of needed clinical manipulations, and then running the model to test for optimal combinations of therapeutic manoeuvres). II. A Heterogeneous Cerebrovascular Mathematical Model Cerebrovascular pathologies are extremely complex, due to the multitude of factors acting simultaneously on cerebral haemodynamics. In this work, the mathematical model of cerebral haemodynamics and intracranial pressure dynamics, described in the point I, is extended to account for heterogeneity in cerebral blood flow. The model includes the Circle of Willis, six regional districts independently regulated by autoregulation and CO2 reactivity, distal cortical anastomoses, venous circulation, the cerebrospinal fluid circulation, and the intracranial pressure-volume relationship. Results agree with data in the literature and highlight the existence of a monotonic relationship between transient hyperemic response and the autoregulation gain. During unilateral internal carotid artery stenosis, local blood flow regulation is progressively lost in the ipsilateral territory with the presence of a steal phenomenon, while the anterior communicating artery plays the major role to redistribute the available blood flow. Conversely, distal collateral circulation plays a major role during unilateral occlusion of the middle cerebral artery. In conclusion, the model is able to reproduce several different pathological conditions characterized by heterogeneity in cerebrovascular haemodynamics and can not only explain generalized results in terms of physiological mechanisms involved, but also, by individualizing parameters, may represent a valuable tool to help with difficult clinical decisions. III. Effect of Cushing Response on Systemic Arterial Pressure. During cerebral hypoxic conditions, the sympathetic system causes an increase in arterial pressure (Cushing response), creating a link between the cerebral and the systemic circulation. This work investigates the complex relationships among cerebrovascular dynamics, intracranial pressure, Cushing response, and short-term systemic regulation, during plateau waves, by means of an original mathematical model. The model incorporates the pulsating heart, the pulmonary circulation and the systemic circulation, with an accurate description of the cerebral circulation and the intracranial pressure dynamics (same model as in the first paragraph). Various regulatory mechanisms are included: cerebral autoregulation, local blood flow control by oxygen (O2) and/or CO2 changes, sympathetic and vagal regulation of cardiovascular parameters by several reflex mechanisms (chemoreceptors, lung-stretch receptors, baroreceptors). The Cushing response has been described assuming a dramatic increase in sympathetic activity to vessels during a fall in brain O2 delivery. With this assumption, the model is able to simulate the cardiovascular effects experimentally observed when intracranial pressure is artificially elevated and maintained at constant level (arterial pressure increase and bradicardia). According to the model, these effects arise from the interaction between the Cushing response and the baroreflex response (secondary to arterial pressure increase). Then, patients with severe head injury have been simulated by reducing intracranial compliance and cerebrospinal fluid reabsorption. With these changes, oscillations with plateau waves developed. In these conditions, model results indicate that the Cushing response may have both positive effects, reducing the duration of the plateau phase via an increase in cerebral perfusion pressure, and negative effects, increasing the intracranial pressure plateau level, with a risk of greater compression of the cerebral vessels. This model may be of value to assist clinicians in finding the balance between clinical benefits of the Cushing response and its shortcomings. IV. Comprehensive Cardiopulmonary Simulation Model for the Analysis of Hypercapnic Respiratory Failure We developed a new comprehensive cardiopulmonary model that takes into account the mutual interactions between the cardiovascular and the respiratory systems along with their short-term regulatory mechanisms. The model includes the heart, systemic and pulmonary circulations, lung mechanics, gas exchange and transport equations, and cardio-ventilatory control. Results show good agreement with published patient data in case of normoxic and hyperoxic hypercapnia simulations. In particular, simulations predict a moderate increase in mean systemic arterial pressure and heart rate, with almost no change in cardiac output, paralleled by a relevant increase in minute ventilation, tidal volume and respiratory rate. The model can represent a valid tool for clinical practice and medical research, providing an alternative way to experience-based clinical decisions. In conclusion, models are not only capable of summarizing current knowledge, but also identifying missing knowledge. In the former case they can serve as training aids for teaching the operation of complex systems, especially if the model can be used to demonstrate the outcome of experiments. In the latter case they generate experiments to be performed to gather the missing data.

Valutazione clinica, clinicopatologica e quantificazione di IgG e IgM in corso di leishmaniosi canina: studio retrospettivo

La leishmaniosi canina (LCan) causata da Leishmania infantum rappresenta un’importante zoonosi in molte aree del mondo ed il cane rappresenta il principale reservoir del parassita per l’uomo. Il tipo di risposta immunitaria che i soggetti colpiti mettono in atto condiziona fortemente la progressione della malattia: animali che non sviluppano un’adeguata risposta immunitaria cellulo-mediata mostrano la sintomatologia clinica nonostante abbiano una forte ma inefficace risposta umorale che contribuisce al peggioramento della sintomatologia clinica. L’obbiettivo dello studio è stato quello valutare da un punto di vista descrittivo il segnalamento, i segni clinici e clinicopatologici dei pazienti affetti da leishmaniosi portati in visita presso il Dipartimento di Scienze Mediche Veterinarie nel periodo compreso da Gennaio 2002 a Marzo 2012 con particolare attenzione sull’impatto della patologia renale e dell’anemia nel quadro clinico della LCan. In base ai risultati ottenuti è stato possibile affermare che la leishmaniosi canina è una patologia relativamente frequente nella nostra realtà clinica universitaria e che presenta caratteristiche cliniche e clinicopatologiche simili a quelle riportate in letteratura. I nostri risultati preliminari suggeriscono che in questa malattia il coinvolgimento renale e le conseguenze sistemiche che ne derivano possono essere predominanti a livello clinico e laboratoristico. La gravità del quadro clinico appare associata in maniera significativa all’entità della risposta umorale e del successivo coinvolgimento glomerulare nel contesto di una risposta infiammatoria sistemica cronica. Successivamente, sono state misurate le concentrazioni di IgG ed IgM in corso di follow-up in alcuni dei soggetti inclusi nello studio e sottoposti a differenti trattamenti anti-leishmania. Dai risultati preliminari ottenuti nel nostro lavoro è stato possibile affermare che in corso di trattamento le concentrazioni di tali immunoglobuline subiscono una riduzione progressiva confermando pertanto l’efficacia del trattamento anti-leishmania non solo nella remissione della sintomatologia clinica ma anche nel ripristino della normale risposta umorale.

Il ruolo della Narrative in Medical Ethics, Medical Practice e Medical Education. Elementi di ricerca

La mia tesi di dottorato ha ad oggetto lo studio e l’analisi del ruolo della Narrative all’interno di tre ambiti, quali Medical Ethics, Clinical Practice e Medical Education. La tesi è strutturata in 4 capitoli: i primi tre vanno a comporre la parte teorica mentre nel quarto capitolo viene riportata una ricerca sul campo da me svolta negli Stati Uniti. Nel primo capitolo, analizzo il ruolo della narrative all’interno della Medical Ethics specificando che cosa si intenda con etica narrativa, quali sono le motivazione alla base del suo sviluppo e chi sono i suoi principali esponenti. In questo capitolo, inoltre, esamino i problemi che l’etica narrativa solleva suggerendo un nuovo modo in cui essa si integra alla riflessione bioetica. Il secondo capitolo è dedicato al contributo della narrative nella Medical Practice investigando sia le modalità attraverso le quali il paziente può avvalersi della narrazione per analizzare la sua esperienza di malattia sia la cosiddetta Medicina Narrativa. Il terzo capitolo è dedicato all'analisi delle Medical Humanities, ossia di quelle discipline che all’interno della Medical Education si stanno rivelando strumenti efficaci per una formazione più equilibrata e completa dei professionisti della salute. Il quarto capitolo, invece, è dedicato alla descrizione di una ricerca svolta presso l’University of California – Irvine . Durante questa esperienza ho frequentato i corsi del Program in Medical Humanities and Arts diretto dalla Prof.ssa J. Shapiro, (programma in vigore da 13 anni e implementato allo scopo di migliorare alcune competenze nei futuri medici quali: l'empatia, l’altruismo, la compassione e la predisposizione alla cura verso i pazienti, oltre che per affinare le comunicazione clinica e la capacità di osservazione) e intervistato gli studenti che hanno preso parte a queste lezioni.

Inertial and magnetic sensors for upper limb kinematics: modeling, calibration, sensor fusion and clinical applications

The primary aim of the research activity presented in this PhD thesis was the development of an innovative hardware and software solution for creating a unique tool for kinematics and electromyographic analysis of the human body in an ecological setting. For this purpose, innovative algorithms have been proposed regarding different aspects of inertial and magnetic data elaboration: magnetometer calibration and magnetic field mapping (Chapter 2), data calibration (Chapter 3) and sensor-fusion algorithm. Topics that may conflict with the confidentiality agreement between University of Bologna and NCS Lab will not be covered in this thesis. After developing and testing the wireless platform, research activities were focused on its clinical validation. The first clinical study aimed to evaluate the intra and interobserver reproducibility in order to evaluate three-dimensional humero-scapulo-thoracic kinematics in an outpatient setting (Chapter 4). A second study aimed to evaluate the effect of Latissimus Dorsi Tendon Transfer on shoulder kinematics and Latissimus Dorsi activation in humerus intra - extra rotations (Chapter 5). Results from both clinical studies have demonstrated the ability of the developed platform to enter into daily clinical practice, providing useful information for patients' rehabilitation.

Crescita volumetrica dei miomi uterini: analisi dei fattori di rischio

I miomi uterini sono la neoplasia uterina più comune e colpiscono fino al 30% delle donne in età fertile. Nonostante l’elevata prevalenza, pochi studi in Letteratura hanno analizzato i fattori di rischio per la crescita dei miomi uterini, mostrando spesso dei risultati contrastanti. Nel nostro studio osservazionale prospettico sono state arruolate pazienti che rispettassero i criteri di inclusione e di esclusione, con diagnosi di miomi uterini evidenziati mediante ecografia eseguita presso i nostri ambulatori, a partire da giugno 2017. A partire da gennaio 2019, sono state ricercate mensilmente le pazienti precedentemente arruolate che erano tornate presso i nostri ambulatori per esecuzione di ulteriore ecografia, a distanza di 24 ± 5 mesi, fino a raggiungere il campione designato, cioè 450 pazienti totali. È stato, quindi, valutato il tasso di crescita annuo del mioma di maggiori dimensioni ed è stato utilizzato l'approccio polinomiale frazionario multivariabile per selezionare i fattori di rischio anamnestici ed ecografici legati all’incremento volumetrico. Circa la metà dei miomi uterini analizzati ha mostrato stabilità dimensionale nel corso del follow-up (crescita ≤10%), mentre la restante metà ha mostrato una crescita > 10%. Il solo fattore di rischio associato alla crescita volumetrica dei miomi uterini è risultato essere il volume del mioma durante l’ecografia di arruolamento (P = 0.001), quindi miomi di piccole dimensioni presentano un tasso di crescita maggiore rispetto ai miomi di grandi dimensioni. Lo studio ha raccolto la più ampia casistica in Letteratura nella valutazione del naturale andamento di modifica dimensionale dei miomi uterini. Sebbene siano necessari ulteriori studi con campione più ampio, questi dati possono fornire un utile supporto per eseguire un adeguato counselling con le pazienti nella pratica clinica quotidiana.

Fattori che influenzano l'esame angio-TC del distretto addominale nel cane: una revisione sistematica

Lo scopo dell’AngioTC è quello di ottenere un’opacizzazione adeguata del comparto vascolare esaminato, sincronizzata all’acquisizione della scansione TC. La distribuzione del mezzo di contrasto (mdc) e l’opacizzazione dei distretti corporei, definita enhancement, è influenzata da diversi fattori: relativi al paziente, al mdc o allo scanner TC. In Medicina Veterinaria sono presenti pochi studi indirizzati a valutare l’influenza di diversi fattori sull’enhancement. La ricerca è stata condotta seguendo le linee guida PRISMA (Preferred Reporting Items for Systematic Reviews, 2020). Il database online di diversi motori di ricerca scientifici (Web of Science, PubMed, Scopus e CABAbstract) è stato esaminato mediante combinazione di diverse parole chiave. Sono stati individuati 20 studi che rispettavano i criteri di inclusione, inseriti nel corpo finale della revisione sistematica e raggruppati sulla base della categoria di appartenenza. Si è visto come la quantità di tessuto adiposo addominale sull’enhancement rappresenti un fattore che permette di ridurre la dose di mezzo di contrasto utilizzato, riducendo effetti avversi o tossicità sull’animale. Per quanto riguarda l’iniezione del mdc, un fattore in grado di influenzare maggiormente l’enhancement sembra essere la velocità di trasporto dello Iodio, piuttosto che la durata di iniezione, soprattutto a livello arterioso ed epatico. Con uno scanner lento o una durata di scansione lunga, è consigliato utilizzare una durata fissa di iniezione del mdc per l’acquisizione delle diverse fasi vascolari. Al contrario, con scanner più performanti la tecnica di bolus tracking garantisce una maggior qualità tra le varie fasi vascolari. È indicato, infine, eseguire un flush con soluzione fisiologica al termine della somministrazione di mdc per incrementare l’enhancement arterioso e ridurre la dose di mdc somministrata. Questa revisione sistematica mette in evidenza alcuni fattori e può fare da base per l’ulteriore approfondimento di alcuni di questi fattori o per la valutazione altri non ancora esaminati in Medicina Veterinaria.