New approaches to open problems in gene expression microarray data

In the past decade, the advent of efficient genome sequencing tools and high-throughput experimental biotechnology has lead to enormous progress in the life science. Among the most important innovations is the microarray tecnology. It allows to quantify the expression for thousands of genes simultaneously by measurin the hybridization from a tissue of interest to probes on a small glass or plastic slide. The characteristics of these data include a fair amount of random noise, a predictor dimension in the thousand, and a sample noise in the dozens. One of the most exciting areas to which microarray technology has been applied is the challenge of deciphering complex disease such as cancer. In these studies, samples are taken from two or more groups of individuals with heterogeneous phenotypes, pathologies, or clinical outcomes. these samples are hybridized to microarrays in an effort to find a small number of genes which are strongly correlated with the group of individuals. Eventhough today methods to analyse the data are welle developed and close to reach a standard organization (through the effort of preposed International project like Microarray Gene Expression Data -MGED- Society [1]) it is not unfrequant to stumble in a clinician's question that do not have a compelling statistical method that could permit to answer it.The contribution of this dissertation in deciphering disease regards the development of new approaches aiming at handle open problems posed by clinicians in handle specific experimental designs. In Chapter 1 starting from a biological necessary introduction, we revise the microarray tecnologies and all the important steps that involve an experiment from the production of the array, to the quality controls ending with preprocessing steps that will be used into the data analysis in the rest of the dissertation. While in Chapter 2 a critical review of standard analysis methods are provided stressing most of problems that In Chapter 3 is introduced a method to adress the issue of unbalanced design of miacroarray experiments. In microarray experiments, experimental design is a crucial starting-point for obtaining reasonable results. In a two-class problem, an equal or similar number of samples it should be collected between the two classes. However in some cases, e.g. rare pathologies, the approach to be taken is less evident. We propose to address this issue by applying a modified version of SAM [2]. MultiSAM consists in a reiterated application of a SAM analysis, comparing the less populated class (LPC) with 1,000 random samplings of the same size from the more populated class (MPC) A list of the differentially expressed genes is generated for each SAM application. After 1,000 reiterations, each single probe given a "score" ranging from 0 to 1,000 based on its recurrence in the 1,000 lists as differentially expressed. The performance of MultiSAM was compared to the performance of SAM and LIMMA [3] over two simulated data sets via beta and exponential distribution. The results of all three algorithms over low- noise data sets seems acceptable However, on a real unbalanced two-channel data set reagardin Chronic Lymphocitic Leukemia, LIMMA finds no significant probe, SAM finds 23 significantly changed probes but cannot separate the two classes, while MultiSAM finds 122 probes with score >300 and separates the data into two clusters by hierarchical clustering. We also report extra-assay validation in terms of differentially expressed genes Although standard algorithms perform well over low-noise simulated data sets, multi-SAM seems to be the only one able to reveal subtle differences in gene expression profiles on real unbalanced data. In Chapter 4 a method to adress similarities evaluation in a three-class prblem by means of Relevance Vector Machine [4] is described. In fact, looking at microarray data in a prognostic and diagnostic clinical framework, not only differences could have a crucial role. In some cases similarities can give useful and, sometimes even more, important information. The goal, given three classes, could be to establish, with a certain level of confidence, if the third one is similar to the first or the second one. In this work we show that Relevance Vector Machine (RVM) [2] could be a possible solutions to the limitation of standard supervised classification. In fact, RVM offers many advantages compared, for example, with his well-known precursor (Support Vector Machine - SVM [3]). Among these advantages, the estimate of posterior probability of class membership represents a key feature to address the similarity issue. This is a highly important, but often overlooked, option of any practical pattern recognition system. We focused on Tumor-Grade-three-class problem, so we have 67 samples of grade I (G1), 54 samples of grade 3 (G3) and 100 samples of grade 2 (G2). The goal is to find a model able to separate G1 from G3, then evaluate the third class G2 as test-set to obtain the probability for samples of G2 to be member of class G1 or class G3. The analysis showed that breast cancer samples of grade II have a molecular profile more similar to breast cancer samples of grade I. Looking at the literature this result have been guessed, but no measure of significance was gived before.

Comportamento elastodinamico di meccanismi in catena chiusa bilanciati: analisi numerica e sperimentale di un quadrilatero articolato

The study presented in this work deals with the investigation of the effects produced by two common techniques of static balancing on the dynamic performances of closed-chain linkages, taking into account the compliance of the mechanism components. The long-term goal of the research consists in determining an optimal balancing strategy for parallel spatial manipulators. The present contribution is a starting point and it focuses on the planar four-bar linkage, intended as the simplest example of closed-chain mechanism. The elastodynamic behaviour of an unbalanced four-bar linkage and two balanced ones, respectively obtained by mass and elastic balancing, is investigated by means of both numerical simulations and experimental tests. The purpose of this work is to obtain preliminary results, to be refined and broadened in future developments

Analysis and Implementation of Multiphase-Multilevel Inverter for Open-Winding Loads

Research work carried out in focusing a novel multiphase-multilevel ac motor drive system much suitable for low-voltage high-current power applications. In specific, six-phase asymmetrical induction motor with open-end stator winding configuration, fed from four standard two-level three-phase voltage source inverters (VSIs). Proposed synchronous reference frame control algorithm shares the total dc source power among the 4 VSIs in each switching cycle with three degree of freedom. Precisely, first degree of freedom concerns with the current sharing between two three-phase stator windings. Based on modified multilevel space vector pulse width modulation shares the voltage between each single VSIs of two three-phase stator windings with second and third degree of freedom, having proper multilevel output waveforms. Complete model of whole ac motor drive based on three-phase space vector decomposition approach was developed in PLECS - numerical simulation software working in MATLAB environment. Proposed synchronous reference control algorithm was framed in MATLAB with modified multilevel space vector pulse width modulator. The effectiveness of the entire ac motor drives system was tested. Simulation results are given in detail to show symmetrical and asymmetrical, power sharing conditions. Furthermore, the three degree of freedom are exploited to investigate fault tolerant capabilities in post-fault conditions. Complete set of simulation results are provided when one, two and three VSIs are faulty. Hardware prototype model of quad-inverter was implemented with two passive three-phase open-winding loads using two TMS320F2812 DSP controllers. Developed McBSP (multi-channel buffered serial port) communication algorithm able to control the four VSIs for PWM communication and synchronization. Open-loop control scheme based on inverse three-phase decomposition approach was developed to control entire quad-inverter configuration and tested with balanced and unbalanced operating conditions with simplified PWM techniques. Both simulation and experimental results are always in good agreement with theoretical developments.

Fenomeni di transizione degli organismi edilizi, criteri operativi di inserimento ambientale e procedure di intervento

La presente tesi indaga le potenzialità, in termini di criteri operativi di inserimento ambientale e procedure di intervento, che possono derivare dall’analisi dei fenomeni insediativi facendo riferimento ai concetti di ‘transizione’ e ‘resilienza’. L’attuale periodo di crisi sembra scaturire dal disequilibrio di due fattori: le esigenze umane e l’ambiente. La contestualizzazione degli interventi, il graduale adattamento alle risorse ambientali locali e la valorizzazione dei processi “dal basso” sembrano consentire di riappropriarsi sia del valore identitario dei luoghi, dando risposta ai problemi di natura sociale evidenziati, sia della eco-compatibilità delle trasformazioni, del corretto utilizzo delle risorse energetiche e della gestione delle dinamiche economiche, in risposta ai problemi ambientali analizzati. Il prefigurare applicazioni pratiche del modello di trasformazione indagato alla scala edilizia, utilizzando tavole parametriche di analisi del costruito, viste d’insieme planivolumetriche ed elaborazioni di dati e immagini, può consentire la gestione di eventuali fasi di programmazione e di pianificazione da parte delle amministrazioni finalizzate a favorire e non ostacolare i presenti e futuri fenomeni di transizione. Particolarmente significativa appare l’analisi delle diverse tendenze di ricerca progettuale in atto, con riferimento a contributi caratterizzati da un’impostazione fenomenologica e tipo-morfologica, che dimostra l’attualità degli argomenti affrontati. La ricerca di Dottorato si conclude con l’applicazione dei criteri operativi di inserimento ambientale e delle procedure di intervento individuati ad uno specifico caso di studio.

Silicon Photonics Integrated Circuits for Flexible Optical Systems

This dissertation deals with the design and the characterization of novel reconfigurable silicon-on-insulator (SOI) devices to filter and route optical signals on-chip. Design is carried out through circuit simulations based on basic circuit elements (Building Blocks, BBs) in order to prove the feasibility of an approach allowing to move the design of Photonic Integrated Circuits (PICs) toward the system level. CMOS compatibility and large integration scale make SOI one of the most promising material to realize PICs. The concepts of generic foundry and BB based circuit simulations for the design are emerging as a solution to reduce the costs and increase the circuit complexity. To validate the BB based approach, the development of some of the most important BBs is performed first. A novel tunable coupler is also presented and it is demonstrated to be a valuable alternative to the known solutions. Two novel multi-element PICs are then analysed: a narrow linewidth single mode resonator and a passband filter with widely tunable bandwidth. Extensive circuit simulations are carried out to determine their performance, taking into account fabrication tolerances. The first PIC is based on two Grating Assisted Couplers in a ring resonator (RR) configuration. It is shown that a trade-off between performance, resonance bandwidth and device footprint has to be performed. The device could be employed to realize reconfigurable add-drop de/multiplexers. Sensitivity with respect to fabrication tolerances and spurious effects is however observed. The second PIC is based on an unbalanced Mach-Zehnder interferometer loaded with two RRs. Overall good performance and robustness to fabrication tolerances and nonlinear effects have confirmed its applicability for the realization of flexible optical systems. Simulated and measured devices behaviour is shown to be in agreement thus demonstrating the viability of a BB based approach to the design of complex PICs.

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.