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.

Development discourse in Romania: from Socialism to EU Membership

With their accession to the European Union, twelve new countries - Romania among them - (re)entered the international community of international donors. In the history of development aid this can be seen as a unique event: it is for the first time in history that such a large number of countries become international donors, with such short notice and in such a particular context that sees some scholars announcing the ‘death’ of development. But in spite of what might be claimed regarding the ‘end’ of the development era, development discourse seems to be rather vigorous and in good health: it is able to extert an undeniable force of attraction over the twelve countries that, in a matter of years, have already convinced themselves of its validity and adhered to its main tenets. This thesis collects evidence for improving our understanding of this process that sees the co-optation of twelve new countries to the dominant theory and practice of development cooperation. The evidence collected seems to show that one of the tools employed by the promoters of this co-optation process is that of constructing the ‘new’ Member States as ‘new’, inexpert donors that need to learn from the ‘old’ ones. By taking a case-study approach, this thesis gathers data that suggests that conceiving of the ‘twelve’ as ‘new’ donors is both historically inaccurate and value-ladden. On one hand, Romania’s case-study illustrates how in the (socialist) past at least one in the group of the twelve was particularly conversant in the discourse of international development. On the other hand, the process of co-optation, while being presented as a knowledgeproducing process, can also be seen as an ignorance-producing procedure: Romania, along with its fellow new Member States, takes the opportunity of ‘building its capacity’ and ‘raising its awareness’ of development cooperation along the line drawn by the European Union, but at the same time it seems to un-learn and ‘lower’ its awareness of development experience in the (socialist) past. This is one possible reading of this thesis. At a different level, this thesis can also be seen as an attempt to account of almost five decades of international development discourse in one specific country – Romania – in three different socio-political contexts: the socialist years (up to the year 1989), the ‘transition years’ (from 1989 to the pre-accession years) and the membership to the European Union. In this second reading, the thesis seeks to illustrate how – contrary to widespread beliefs – before 1989 Romania’s international development discourse was particularly vivid: in the most varied national and international settings President Ceausescu unfolded an extensive discursive activity on issues pertaining to international development; generous media coverage of affairs concerning the developing countries and their fight for development was the rule rather than the exception; the political leadership wanted the Romanians not only to be familiarized with (or ‘aware of’ to use current terminology) matters of underdevelopment, but also to prove a sense of solidarity with these countries, as well as a sense of pride for the relations of ‘mutual help’ that were being built with them; finally, international development was object of academic attention and the Romanian scholars were able not only to reflect on major developments, but could also formulate critical positions towards the practices of development aid. Very little remains of all this during the transition years, while in the present those who are engaged in matters pertaining to international development do so with a view of building Romania as an EU-compliant donor.