Analyzing the dependence structure of microarray data: a copula–based approach

The main aim of this Ph.D. dissertation is the study of clustering dependent data by means of copula functions with particular emphasis on microarray data. Copula functions are a popular multivariate modeling tool in each field where the multivariate dependence is of great interest and their use in clustering has not been still investigated. The first part of this work contains the review of the literature of clustering methods, copula functions and microarray experiments. The attention focuses on the K–means (Hartigan, 1975; Hartigan and Wong, 1979), the hierarchical (Everitt, 1974) and the model–based (Fraley and Raftery, 1998, 1999, 2000, 2007) clustering techniques because their performance is compared. Then, the probabilistic interpretation of the Sklar’s theorem (Sklar’s, 1959), the estimation methods for copulas like the Inference for Margins (Joe and Xu, 1996) and the Archimedean and Elliptical copula families are presented. In the end, applications of clustering methods and copulas to the genetic and microarray experiments are highlighted. The second part contains the original contribution proposed. A simulation study is performed in order to evaluate the performance of the K–means and the hierarchical bottom–up clustering methods in identifying clusters according to the dependence structure of the data generating process. Different simulations are performed by varying different conditions (e.g., the kind of margins (distinct, overlapping and nested) and the value of the dependence parameter ) and the results are evaluated by means of different measures of performance. In light of the simulation results and of the limits of the two investigated clustering methods, a new clustering algorithm based on copula functions (‘CoClust’ in brief) is proposed. The basic idea, the iterative procedure of the CoClust and the description of the written R functions with their output are given. The CoClust algorithm is tested on simulated data (by varying the number of clusters, the copula models, the dependence parameter value and the degree of overlap of margins) and is compared with the performance of model–based clustering by using different measures of performance, like the percentage of well–identified number of clusters and the not rejection percentage of H0 on . It is shown that the CoClust algorithm allows to overcome all observed limits of the other investigated clustering techniques and is able to identify clusters according to the dependence structure of the data independently of the degree of overlap of margins and the strength of the dependence. The CoClust uses a criterion based on the maximized log–likelihood function of the copula and can virtually account for any possible dependence relationship between observations. Many peculiar characteristics are shown for the CoClust, e.g. its capability of identifying the true number of clusters and the fact that it does not require a starting classification. Finally, the CoClust algorithm is applied to the real microarray data of Hedenfalk et al. (2001) both to the gene expressions observed in three different cancer samples and to the columns (tumor samples) of the whole data matrix.

Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

A partial dependence factorial analysis to deal with selection bias in observational studis

This thesis presents a creative and practical approach to dealing with the problem of selection bias. Selection bias may be the most important vexing problem in program evaluation or in any line of research that attempts to assert causality. Some of the greatest minds in economics and statistics have scrutinized the problem of selection bias, with the resulting approaches – Rubin’s Potential Outcome Approach(Rosenbaum and Rubin,1983; Rubin, 1991,2001,2004) or Heckman’s Selection model (Heckman, 1979) – being widely accepted and used as the best fixes. These solutions to the bias that arises in particular from self selection are imperfect, and many researchers, when feasible, reserve their strongest causal inference for data from experimental rather than observational studies. The innovative aspect of this thesis is to propose a data transformation that allows measuring and testing in an automatic and multivariate way the presence of selection bias. The approach involves the construction of a multi-dimensional conditional space of the X matrix in which the bias associated with the treatment assignment has been eliminated. Specifically, we propose the use of a partial dependence analysis of the X-space as a tool for investigating the dependence relationship between a set of observable pre-treatment categorical covariates X and a treatment indicator variable T, in order to obtain a measure of bias according to their dependence structure. The measure of selection bias is then expressed in terms of inertia due to the dependence between X and T that has been eliminated. Given the measure of selection bias, we propose a multivariate test of imbalance in order to check if the detected bias is significant, by using the asymptotical distribution of inertia due to T (Estadella et al. 2005) , and by preserving the multivariate nature of data. Further, we propose the use of a clustering procedure as a tool to find groups of comparable units on which estimate local causal effects, and the use of the multivariate test of imbalance as a stopping rule in choosing the best cluster solution set. The method is non parametric, it does not call for modeling the data, based on some underlying theory or assumption about the selection process, but instead it calls for using the existing variability within the data and letting the data to speak. The idea of proposing this multivariate approach to measure selection bias and test balance comes from the consideration that in applied research all aspects of multivariate balance, not represented in the univariate variable- by-variable summaries, are ignored. The first part contains an introduction to evaluation methods as part of public and private decision process and a review of the literature of evaluation methods. The attention is focused on Rubin Potential Outcome Approach, matching methods, and briefly on Heckman’s Selection Model. The second part focuses on some resulting limitations of conventional methods, with particular attention to the problem of how testing in the correct way balancing. The third part contains the original contribution proposed , a simulation study that allows to check the performance of the method for a given dependence setting and an application to a real data set. Finally, we discuss, conclude and explain our future perspectives.

Per un'etica della letteratura: la cornice il doppio legame nell'opera di J. M. Coetzee

The elusive fiction of J. M. Coetzee is not a work in which you can read fixed ethical stances. I suggest testing the potentialities of a logic based on frames and double binds in Coetzee's novels. A double bind is a dilemma in communication which consists on tho conflicting messages, with the result that you can’t successfully respond to neither. Jacques Derrida highlighted the strategic value of a way of thinking based on the double bind (but on frames as well), which enables to escape binary thinking and so it opens an ethical space, where you can make a choice out of a set of fixed rules and take responsibility for it. In Coetzee’s fiction the author himself can be considered in a double bind, seeing that he is a white South African writer who feels that his “task” can’t be as simply as choosing to represent faithfully the violence and the racism of the apartheid or of choosing to give a voice to the oppressed. Good intentions alone do not ensure protection against entering unwittingly into complicity with the dominant discourse, and this is why is important to make the frame in which one is always situated clearly visible and explicit. The logic of the double bind becomes the way in which moral problem are staged in Coetzee’s fiction as well: the opportunity to give a voice to the oppressed through the same language which co-opted to serve the cause of oppression, a relation with the otherness never completed, or the representability of evil in literature, of the secret and of the paradoxical implications of confession and forgiveness.

Origini dell'ucronia. La letteratura contro la storia

L’ucronia (Alternate History) è un fenomeno letterario ormai popolare e molto studiato, ma non lo sono altrettanto lo sue origini e i suoi rapporti con la storia “fatta con i se” (Counterfactual History), che risale a Erodoto e a Tito Livio. Solo nell’Ottocento alcuni autori, per vie largamente autonome, fecero della storia alternativa un genere di fiction: Louis Geoffroy con Napoléon apocryphe (1836), storia «della conquista del mondo e della monarchia universale», e Charles Renouvier con Uchronie. L’utopie dans l’histoire (1876), storia «della civiltà europea quale avrebbe potuto essere» se il cristianesimo fosse stato fermato nel II secolo. Questi testi intrattengono relazioni complesse con la letteratura dell’epoca di genere sia realistico, sia fantastico, ma altresì con fenomeni di altra natura: la storiografia, nelle sue forme e nel suo statuto epistemico, e ancor più il senso del possibile - o la filosofia della storia - derivato dall’esperienza della rivoluzione e dal confronto con le teorie utopistiche e di riforma sociale. Altri testi, prodotti in Inghilterra e negli Stati Uniti nello stesso periodo, esplorano le possibilità narrative e speculative del genere: tra questi P.s’ Correspondence di Nathaniel Hawthorne (1845), The Battle of Dorking di George Chesney (1871) e Hands Off di Edward Hale (1881); fino a una raccolta del 1931, If It Had Happened Otherwise, che anticipò molte forme e temi delle ucronie successive. Queste opere sono esaminate sia nel contesto storico e letterario in cui furono prodotte, sia con gli strumenti dell’analisi testuale. Una particolare attenzione è dedicata alle strategie di lettura prescritte dai testi, che subordinano i significati al confronto mentale tra gli eventi narrati e la serie dei fatti autentici. Le teorie sui counterfactuals prodotte in altri campi disciplinari, come la storia e la psicologia, arricchiscono la comprensione dei testi e dei loro rapporti con fenomeni extra-letterari.

Il microcredito in alcuni Paesi europei: strumento polimorfo tra inclusione sociale e sviluppo finanziario.

La tesi analizza il fenomeno del microcredito in Europa, approfondendo le cause che hanno reso necessaria l’introduzione di questo strumento finanziario anche in economie profondamente diverse da quella in cui ha avuto origine ed esamina le trasformazioni che lo strumento ha subito durante il suo processo di adattamento ai paesi evoluti. Lo studio esamina il microcredito in Francia, Inghilterra, Spagna e Germania, soffermandosi ad analizzare, in ognuno dei suddetti Stati, la disciplina giuridica adottata (qualora esistente), le istituzioni micro finanziarie esistenti, le caratteristiche del settore e le fonti di finanziamento. L’obiettivo dell’analisi è pertanto quello di comprendere come nei Paesi europei convivano contemporaneamente modelli di microcredito profondamente diversi, a seconda del contesto economico, politico e sociale nel quale trovano applicazione. La tesi si concentra ad analizzare il microcredito in Italia, valutando il rapporto esistente tra questo strumento finanziario ed il problema dell’esclusione sociale, dell’immigrazione e dell’usura. Lo studio approfondisce, inoltre, la disciplina giuridica del microcredito adottata in Italia dopo le recenti modifiche introdotte dal D.lgs n. 169/2012. Il lavoro si sofferma ad analizzare, altresì, se e quali interventi, a livello internazionale ed europeo, sono stati programmati per dare al microcredito una cornice legislativa unitaria e per promuoverne lo sviluppo. L’attività di ricerca infine è volta a valutare, sulla base delle esperienze descritte dalla letteratura del settore, gli effetti prodotti dal microcredito, nonché ad approfondire alcune problematiche comuni ai programmi adottati negli Stati europei, quali la sostenibilità delle istituzioni di microcredito, la dipendenza dai sussidi e l’applicazione di tassi di interesse elevati. La tesi si conclude con l’analisi del rapporto esistente tra microcredito e crisi finanziaria, in un periodo storico in cui le politiche per l’occupazione ed il sostegno alla piccola impresa sono fondamentali per stimolare la ripresa economica.

L’espace urbain indien dans la littérature européenne au XXème siecle. Pour une perspective post-orientaliste.

L'affermarsi della teoria della « imaginative geography » di Edward Saïd (Orientalism, 1978), nell'arco degli ultimi trent'anni, ha imposto un orientamento prettamente sociopolitico, gramsciano e foucaultiano alla critica del testo, proponendo un'unica soluzione interpretativa per un corpus eterogeneo di testi (scientifici e artistici, antichi e moderni) accomunati dal fatto di « rappresentare l'Oriente ». La costruzione europea dello spazio orientale, dice Saïd, non rappresenta solo un misconoscimento dell'Altro, ma una sua rappresentazione tendenziosa e finalizzata a sostenere la macchina dell'imperialismo occidentale. In particolare, la rappresentazione « femminilizzata » della geografia orientale (come luogo dell'exploit del maschio bianco) preparebbe e accompagnerebbe l'impresa di assoggettamento politico e di sfruttamento economico dei paesi ad Est dell'Europa. Se Orientalism ha conosciuto fortune alterne dall'anno della sua apparizione, negli ultimi anni una vera e propria corrente anti-saidiana ha preso forza, soprattutto in ambito francese. Attraverso l'analisi di circa trenta opere francesi, belga, inglesi e italiane del Novecento, questa tesi cerca di visualizzare i limiti teorici della prospettiva saidiana rivolgendosi a un esame della rappresentazione dello spazio urbano indiano nella letteratura europea contemporanea. Nello specifico, uno studio delle nuove strutture e dei nuovi modelli della femminilizzazione dello spazio orientale indiano cercherà di completare – superandolo in direzione di un « post-orientalismo » – il riduzionismo della prospettiva saidiana.

Métamorphoses de l'Image des Tartares dans la littérature européenne du XXème siècle

Ce travail doctoral analyse le changement de l’image des Tartares dans la littérature européenne en langue allemande, anglaise, française et italienne du XXe siècle par l’étude de trois figures : la horde mongole, Gengis-khan et Khoubilaï-khan. Il soutient la thèse que, grâce à quelques facteurs historico-culturels comme la remise en question du concept de barbarie, l’essor des totalitarismes, l’ouverture de la Mongolie vers l’Occident, la redécouverte de l’Histoire secrète des Mongols et la fortune de Le divisament dou monde, au cours du XXe siècle, l’image littéraire des gengiskhanides de négative devient positive. Cette étude se compose d’une introduction, de trois chapitres et d’une conclusion. Dans l’introduction, on analyse la formation de l’image des Tartares et son évolution jusqu’à la fin du XIXe siècle, on retrace les facteurs historico-culturels qui la remettent au goût du jour et en provoquent le changement au XXe siècle et on présente le travail. Dans le premier chapitre, on se penche sur la prosopographie des Tartares dans les textes littéraires du XXe siècle, en la confrontant avec leur représentation dans l’art contemporain. Dans le deuxième chapitre, on étudie la façon des Tartares de se rapporter aux autres au sein de la société dans les textes littéraires du XXe siècle. Dans le troisième chapitre, on examine les lieux des gengiskhanides dans les textes littéraires du XXe siècle. Enfin, dans la conclusion, les données acquises au moyen de l’analyse conduite sont confrontées et interprétées. Le changement de l’image des Tartares va de pair avec une Europe qui, après avoir fait l’expérience de deux guerres mondiales, avoir assisté aux revendications de la décolonisation et avoir introjecté la thèse freudienne du « malaise dans la civilisation », remet en discussion sa façon de concevoir la barbarie et l’Altérité.

Raccontare la storia al tempo delle crisi

La ricerca analizza il tema della relazione tra storia e narrazione nella letteratura degli ultimi quindici anni in tre contesti nazionali: Italia, Spagna e Portogalo. Per indagare un campo così vasto si sono identificate tre direttrici principali connesse tra loro, coincidenti con tre "crisi": la crisi del rapporto tra letteratura e mercato, la crisi del concetto di verità e la crisi dello stato nazione. Attraverso le riflessioni sul postmoderno (Lyotard, Jameson Hutcheon) e l’analisi di Bourdieu si indaga il rapporto tra mercato e autore letterario, facendo particolare riferimento ai percorsi letterari di Rafael Chirbes, Mia Couto e Wu Ming. Il tema della forma letteraria è invece letto atttraverso le analisi di Hutcheon e analizzando i testi di Helder Macedo (Pedro e Paula), Isaac Rosa (¡Otra maldita novela sobre la guerra civil!) e Tommaso De Lorenzis-Guido Favale (L’aspra stagione). La crisi del concetto di verità viene analizzata alla luce del dibattito sulla storiografia nella seconda metà del Novecento. In particolare si evidenzia la tensione tra Hayden White e Carlo Ginzuburg. Per evidenziare come le relazioni di potere influenzino la narrazione della storia si fa inoltre riferimento alle analisi di Michel Foucault, Michel de Certeau, Stephen Greenbaltt e Gayatri Spivak. Si analizzano quindi Anatomía de un instante, di Javier Cercas, Romanzo criminale, di Giancarlo de Cataldo e As três vidas, di João Tordo. Infine ci si riferisce alla crisi dello stato-nazione individuando una tensione tra le analisi di György Lukács e Franco Moretti, e allargando la riflessione agli studi sociologici di Immanuel Wallerstein e Saskia Sassen. Inoltre, attraverso i testi di Benedict Anderson, Homi B. Bhabha, José Saramao e Eduardo Lourenço si articola una riflessione sull’immaginario politico nazionale. I testi analizzati sono Victus, di Albert Sánchez Piñol, Pro Patria, di Ascanio Celestini e A voz da terra di Miguel Real.