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.

Design of optical networks for advanced applications

Nowadays, computing is migrating from traditional high performance and distributed computing to pervasive and utility computing based on heterogeneous networks and clients. The current trend suggests that future IT services will rely on distributed resources and on fast communication of heterogeneous contents. The success of this new range of services is directly linked to the effectiveness of the infrastructure in delivering them. The communication infrastructure will be the aggregation of different technologies even though the current trend suggests the emergence of single IP based transport service. Optical networking is a key technology to answer the increasing requests for dynamic bandwidth allocation and configure multiple topologies over the same physical layer infrastructure, optical networks today are still “far” from accessible from directly configure and offer network services and need to be enriched with more “user oriented” functionalities. However, current Control Plane architectures only facilitate efficient end-to-end connectivity provisioning and certainly cannot meet future network service requirements, e.g. the coordinated control of resources. The overall objective of this work is to provide the network with the improved usability and accessibility of the services provided by the Optical Network. More precisely, the definition of a service-oriented architecture is the enable technology to allow user applications to gain benefit of advanced services over an underlying dynamic optical layer. The definition of a service oriented networking architecture based on advanced optical network technologies facilitates users and applications access to abstracted levels of information regarding offered advanced network services. This thesis faces the problem to define a Service Oriented Architecture and its relevant building blocks, protocols and languages. In particular, this work has been focused on the use of the SIP protocol as a inter-layers signalling protocol which defines the Session Plane in conjunction with the Network Resource Description language. On the other hand, an advantage optical network must accommodate high data bandwidth with different granularities. Currently, two main technologies are emerging promoting the development of the future optical transport network, Optical Burst and Packet Switching. Both technologies respectively promise to provide all optical burst or packet switching instead of the current circuit switching. However, the electronic domain is still present in the scheduler forwarding and routing decision. Because of the high optics transmission frequency the burst or packet scheduler faces a difficult challenge, consequentially, high performance and time focused design of both memory and forwarding logic is need. This open issue has been faced in this thesis proposing an high efficiently implementation of burst and packet scheduler. The main novelty of the proposed implementation is that the scheduling problem has turned into simple calculation of a min/max function and the function complexity is almost independent of on the traffic conditions.

Uniquitous internet middleware: architecture design and prototype evaluation

Technology advances in recent years have dramatically changed the way users exploit contents and services available on the Internet, by enforcing pervasive and mobile computing scenarios and enabling access to networked resources almost from everywhere, at anytime, and independently of the device in use. In addition, people increasingly require to customize their experience, by exploiting specific device capabilities and limitations, inherent features of the communication channel in use, and interaction paradigms that significantly differ from the traditional request/response one. So-called Ubiquitous Internet scenario calls for solutions that address many different challenges, such as device mobility, session management, content adaptation, context-awareness and the provisioning of multimodal interfaces. Moreover, new service opportunities demand simple and effective ways to integrate existing resources into new and value added applications, that can also undergo run-time modifications, according to ever-changing execution conditions. Despite service-oriented architectural models are gaining momentum to tame the increasing complexity of composing and orchestrating distributed and heterogeneous functionalities, existing solutions generally lack a unified approach and only provide support for specific Ubiquitous Internet aspects. Moreover, they usually target rather static scenarios and scarcely support the dynamic nature of pervasive access to Internet resources, that can make existing compositions soon become obsolete or inadequate, hence in need of reconfiguration. This thesis proposes a novel middleware approach to comprehensively deal with Ubiquitous Internet facets and assist in establishing innovative application scenarios. We claim that a truly viable ubiquity support infrastructure must neatly decouple distributed resources to integrate and push any kind of content-related logic outside its core layers, by keeping only management and coordination responsibilities. Furthermore, we promote an innovative, open, and dynamic resource composition model that allows to easily describe and enforce complex scenario requirements, and to suitably react to changes in the execution conditions.

Design, implementation and evaluation of a virtual laboratory for Computer Engineering Education

Broad consensus has been reached within the Education and Cognitive Psychology research communities on the need to center the learning process on experimentation and concrete application of knowledge, rather than on a bare transfer of notions. Several advantages arise from this educational approach, ranging from the reinforce of students learning, to the increased opportunity for a student to gain greater insight into the studied topics, up to the possibility for learners to acquire practical skills and long-lasting proficiency. This is especially true in Engineering education, where integrating conceptual knowledge and practical skills assumes a strategic importance. In this scenario, learners are called to play a primary role. They are actively involved in the construction of their own knowledge, instead of passively receiving it. As a result, traditional, teacher-centered learning environments should be replaced by novel learner-centered solutions. Information and Communication Technologies enable the development of innovative solutions that provide suitable answers to the need for the availability of experimentation supports in educational context. Virtual Laboratories, Adaptive Web-Based Educational Systems and Computer-Supported Collaborative Learning environments can significantly foster different learner-centered instructional strategies, offering the opportunity to enhance personalization, individualization and cooperation. More specifically, they allow students to explore different kinds of materials, to access and compare several information sources, to face real or realistic problems and to work on authentic and multi-facet case studies. In addition, they encourage cooperation among peers and provide support through coached and scaffolded activities aimed at fostering reflection and meta-cognitive reasoning. This dissertation will guide readers within this research field, presenting both the theoretical and applicative results of a research aimed at designing an open, flexible, learner-centered virtual lab for supporting students in learning Information Security.

Ahmedabad | Laboratorio di architettura moderna Il National Institute of Design (1961-68) fra contatti internazionali ed echi della tradizione

Oggetto della ricerca è lo studio del National Institute of Design (NID), progettato da Gautam Sarabhai e sua sorella Gira, ad Ahmedabad, assunta a paradigma del nuovo corso della politica che il Primo Ministro Nehru espresse nei primi decenni del governo postcoloniale. Obiettivo della tesi è di analizzare il fenomeno che unisce modernità e tradizione in architettura. La modernità indiana, infatti, nacque e si sviluppò con i caratteri di un Giano bifronte: da un lato, la politica del Primo Ministro Nehru favorì lo sviluppo dell’industria e della scienza; dall’altro, la visione di Gandhi mirava alla riscoperta del locale, delle tradizioni e dell’artigianato. Questi orientamenti influenzarono l’architettura postcoloniale. Negli anni ‘50 e ’60 Ahmedabad divenne la culla dell’architettura moderna indiana. Kanvinde, i Sarabhai, Correa, Doshi, Raje trovarono qui le condizioni per costruire la propria identità come progettisti e come intellettuali. I motori che resero possibile questo fermento furono principalmente due: una committenza di imprenditori illuminati, desiderosi di modernizzare la città; la presenza ad Ahmedabad, a partire dal 1951, dei maestri dell’architettura moderna, tra cui i più noti furono Le Corbusier e Kahn, invitati da quella stessa committenza, per la quale realizzarono edifici di notevole rilevanza. Ad Ahmedabad si confrontarono con forza entrambe le visioni dell’India moderna. Lo sforzo maggiore degli architetti indiani si espresse nel tentativo di conciliare i due aspetti, quelli che derivavano dalle influenze internazionali e quelli che provenivano dallo spirito della tradizione. Il progetto del NID è uno dei migliori esempi di questo esercizio di sintesi. Esso recupera nella composizione spaziale la lezione di Wright, Le Corbusier, Kahn, Eames ibridandola con elementi della tradizione indiana. Nell’uso sapiente della struttura modulare e a padiglione, della griglia ordinatrice a base quadrata, dell’integrazione costante fra spazi aperti, natura e architettura affiorano nell’edificio del NID echi di una cultura millenaria.

Continuos Flow Single Cell Separation into Open Microwell Arrays

A novel design based on electric field-free open microwell arrays for the automated continuous-flow sorting of single or small clusters of cells is presented. The main feature of the proposed device is the parallel analysis of cell-cell and cell-particle interactions in each microwell of the array. High throughput sample recovery with a fast and separate transfer from the microsites to standard microtiter plates is also possible thanks to the flexible printed circuit board technology which permits to produce cost effective large area arrays featuring geometries compatible with laboratory equipment. The particle isolation is performed via negative dielectrophoretic forces which convey the particles’ into the microwells. Particles such as cells and beads flow in electrically active microchannels on whose substrate the electrodes are patterned. The introduction of particles within the microwells is automatically performed by generating the required feedback signal by a microscope-based optical counting and detection routine. In order to isolate a controlled number of particles we created two particular configurations of the electric field within the structure. The first one permits their isolation whereas the second one creates a net force which repels the particles from the microwell entrance. To increase the parallelism at which the cell-isolation function is implemented, a new technique based on coplanar electrodes to detect particle presence was implemented. A lock-in amplifying scheme was used to monitor the impedance of the channel perturbed by flowing particles in high-conductivity suspension mediums. The impedance measurement module was also combined with the dielectrophoretic focusing stage situated upstream of the measurement stage, to limit the measured signal amplitude dispersion due to the particles position variation within the microchannel. In conclusion, the designed system complies with the initial specifications making it suitable for cellomics and biotechnology applications.

Hardware/Software Design of Dynamic Real-Time Schedulers for Embedded Multiprocessor Systems

The new generation of multicore processors opens new perspectives for the design of embedded systems. Multiprocessing, however, poses new challenges to the scheduling of real-time applications, in which the ever-increasing computational demands are constantly flanked by the need of meeting critical time constraints. Many research works have contributed to this field introducing new advanced scheduling algorithms. However, despite many of these works have solidly demonstrated their effectiveness, the actual support for multiprocessor real-time scheduling offered by current operating systems is still very limited. This dissertation deals with implementative aspects of real-time schedulers in modern embedded multiprocessor systems. The first contribution is represented by an open-source scheduling framework, which is capable of realizing complex multiprocessor scheduling policies, such as G-EDF, on conventional operating systems exploiting only their native scheduler from user-space. A set of experimental evaluations compare the proposed solution to other research projects that pursue the same goals by means of kernel modifications, highlighting comparable scheduling performances. The principles that underpin the operation of the framework, originally designed for symmetric multiprocessors, have been further extended first to asymmetric ones, which are subjected to major restrictions such as the lack of support for task migrations, and later to re-programmable hardware architectures (FPGAs). In the latter case, this work introduces a scheduling accelerator, which offloads most of the scheduling operations to the hardware and exhibits extremely low scheduling jitter. The realization of a portable scheduling framework presented many interesting software challenges. One of these has been represented by timekeeping. In this regard, a further contribution is represented by a novel data structure, called addressable binary heap (ABH). Such ABH, which is conceptually a pointer-based implementation of a binary heap, shows very interesting average and worst-case performances when addressing the problem of tick-less timekeeping of high-resolution timers.

Cannabinoid system combined to classic targets for a new MTDL strategy: design and synthesis of natural inspired molecules for Alzheimer's disease

In this thesis is described the design and synthesis of potential agents for the treatment of the multifactorial Alzheimer’s disease (AD). Our multi-target approach was to consider cannabinoid system involved in AD, together with classic targets. In the first project, designed modifications were performed on lead molecule in order to increase potency and obtain balanced activities on fatty acid amide hydrolase and cholinesterases. A small library of compounds was synthesized and biological results showed increased inhibitory activity (nanomolar range) related to selected target. The second project was focused on the benzofuran framework, a privileged structure being a common moiety found in many biologically active natural products and therapeutics. Hybrid molecules were designed and synthesized, focusing on the inhibition of cholinesterases, Aβ aggregation, FAAH and on the interaction with CB receptors. Preliminary results showed that several compounds are potent CB ligands, in particular the high affinity for CB2 receptors, could open new opportunities to modulate neuroinflammation. The third and the fourth project were carried out at the IMS, Aberdeen, under the supervision of Prof. Matteo Zanda. The role of the cannabinoid system in the brain is still largely unexplored and the relationship between the CB1 receptors functional modification, density and distribution and the onset of a pathological state is not well understood. For this reasons, Rimonabant analogues suitable as radioligands were synthesized. The latter, through PET, could provide reliable measurements of density and distribution of CB1 receptors in the brain. In the fifth project, in collaboration with CHyM of York, the goal was to develop arginine analogues that are target specific due to their exclusively location into NOS enzymes and could work as MRI contrasting agents. Synthesized analogues could be suitable substrate for the transfer of polarization by p-H2 molecules through SABRE technique transforming MRI a more sensitive and faster technique.

Leonardo Ricci in the United States (1952-1972). A twenty-year American transfer as a turning experience in teaching and design.

The research solved the historiographic lacuna about Leonardo Ricci’s work in the United States focusing on the span 1952-1972 as a fundamental period for the architect's research, which moved from the project for the community space to macrostructures. The considered period is comprised between Ricci’s first travel to the United States and the date of his resignation from the University of Florida, one year before his resignation from the deanship of the faculty of architecture of Florence (1973). The research retraced philologically the stages of Ricci’s activity in the U.S.A. unveiling the premises and results of his American transfer, and to what extent it marked a turning period for his work as educator and designer and for the wider historiographic contest of the Sixties. The American transfer helped him grounding his belief in avoiding a priori morphological results in favor of what he called the “form-act” design method. Ricci’s research in the U.S.A. is described in his books Anonymous (XX century) and City of the Earth (unpublished). In them and in Ricci’s projects one common thread is traceable: the application of the “form-act” as the best tool to conceive urban design, a discipline established in the United States during Ricci’s first stay at M.I.T., in which he encountered the balance point between architecture and urban planning, between the architect’s sign and his being anonymous, between the collective and the individual dimension. With the notions of “anonymous architecture” and “form-act”, Urban Design and “open work” are the key words to understand Ricci’s work in the United States and in Italy. Urban design’s main goal to design the city as a collective work of art was the solution of that dychothomous research that enlivened Ricci’s work and one possible answer to that tension useful for him to seek the truth of architecture.

Processi e pratiche di Innovazione Responsabile: il ruolo dell' Advanced Design nella trasformazione collaborativa dei territori

La ricerca indaga il rapporto tra Design e Innovazione Responsabile calandolo all’interno della relazione tra territorio e pratiche collaborative guidate dal design, ma anche legate al patrimonio culturale immateriale e a un sistema di conoscenza a quintupla elica. La necessità emergente di cura del futuro porta a rivedere il contesto del territorio come campo strumentale per la trasformazione degli individui e della comunità e a domandarsi in che modo il design possa supportare questo cambiamento, abilitando la produzione di conoscenza collaborativa. La ricerca parte dal dimostrare come il modello di innovazione recentemente proposto dalla Comunità Europea attraverso il concetto di Responsible Research Innovation (RRI), poi ripreso nella nozione di Responsible Innovation (RI), sia un campo aperto e responsivo: se integrato con altre discipline, in particolare con il design, può supportare lo sviluppo di processi, politiche, prodotti, servizi e comportamenti che rispettino la relazione tra società, ambiente, identità individuale e collettiva e i ritmi ad essi connessi. Partendo dal contesto sopra descritto, ci si chiede come il design e il designer possano integrare le dimensioni RI nei processi di progettazione, per innovare in modo collaborativo i territori. Si individua quindi nell’Advanced Design la metodologia che, grazie alla sua natura anticipatrice, collaborativa, trasformativa, riesce a coniugarsi virtuosamente con l’approccio RI e supportare il cambiamento in atto. L’intersezione di questi elementi porta alla creazione del Modello Advanced Design per/con l’Innovazione Responsabile (ADIR): un sistema multidimensionale per gruppi di innovazione (quintupla elica) che hanno l’obiettivo di rigenerare in modo collaborativo e inclusivo i territori. L’esperienza sul campo ha confermato come la struttura del modello, formata da un corpus di semi-lavorati, permetta di creare un proprio ritmo, una compenetrazione tra azioni e forme progettuali volti a mantenere il senso di comunità e il coinvolgimento degli attori, a creare relazioni, a sviluppare una trasformazione continua.