Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

Abstract Background Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum. Results Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions. Conclusion The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.

Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients

Abstract Background Plasmodium vivax is the most widely distributed human malaria, responsible for 70–80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected. Methods A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10-30 was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology Results A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them. Conclusion These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.

A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical behavior displaying the degree of robustness typical of the biological cell cycle. The structure of our PGN model was inspired in well-established biological facts such as the existence of integrator subsystems, negative and positive feedback loops, and redundant signaling pathways. Our model represents genes interactions as stochastic processes and presents strong robustness in the presence of moderate noise and parameters fluctuations. A recently published deterministic yeast cell-cycle model does not perform as well as our PGN model, even upon moderate noise conditions. In addition, self stimulatory mechanisms can give our PGN model the possibility of having a pacemaker activity similar to the observed in the oscillatory embryonic cell cycle.

A contribution for developing more efficient dynamic modelling algorithms of parallel robots

Parallel kinematic structures are considered very adequate architectures for positioning and orienti ng the tools of robotic mechanisms. However, developing dynamic models for this kind of systems is sometimes a difficult task. In fact, the direct application of traditional methods of robotics, for modelling and analysing such systems, usually does not lead to efficient and systematic algorithms. This work addre sses this issue: to present a modular approach to generate the dynamic model and through some convenient modifications, how we can make these methods more applicable to parallel structures as well. Kane’s formulati on to obtain the dynamic equations is shown to be one of the easiest ways to deal with redundant coordinates and kinematic constraints, so that a suitable c hoice of a set of coordinates allows the remaining of the modelling procedure to be computer aided. The advantages of this approach are discussed in the modelling of a 3-dof parallel asymmetric mechanisms.

Cytosolic flagellin-induced lysosomal pathway regulates inflammasome-dependent and -independent macrophage responses

NAIP5/NLRC4 (neuronal apoptosis inhibitory protein 5/nucleotide oligomerization domain-like receptor family, caspase activation recruitment domain domain-containing 4) inflammasome activation by cytosolic flagellin results in caspase-1-mediated processing and secretion of IL-1β/IL-18 and pyroptosis, an inflammatory cell death pathway. Here, we found that although NLRC4, ASC, and caspase-1 are required for IL-1β secretion in response to cytosolic flagellin, cell death, nevertheless, occurs in the absence of these molecules. Cytosolic flagellin-induced inflammasome-independent cell death is accompanied by IL-1α secretion and is temporally correlated with the restriction of Salmonella Typhimurium infection. Despite displaying some apoptotic features, this peculiar form of cell death do not require caspase activation but is regulated by a lysosomal pathway, in which cathepsin B and cathepsin D play redundant roles. Moreover, cathepsin B contributes to NAIP5/NLRC4 inflammasome-induced pyroptosis and IL-1α and IL-1β production in response to cytosolic flagellin. Together, our data describe a pathway induced by cytosolic flagellin that induces a peculiar form of cell death and regulates inflammasome-mediated effector mechanisms of macrophages

Actualización, consolidación, migración y contingencia de un entorno hardware y software para la gestión de bases de datos

[ES]El objetivo de este Trabajo es el de actualizar un entorno de gestión de bases de datos existente a la versión 11.2 del software de bases de datos Oracle y a una plataforma hardware de última generación. Se migran con tiempo de parada cero varias bases de datos dispersas en distintos servidores a un entorno consolidado de dos nodos dispuestos en alta disponibilidad tipo "activo-activo" mediante Oracle RAC y respaldado por un entorno de contingencia totalmente independiente y sincronizado en tiempo real mediante Oracle GoldenGate. Se realiza un estudio del entorno actual y, realizando una estimación de crecimiento, se propone una configuración de hardware y software mínima para implementar con garantías de éxito los requerimientos del entorno de gestión de bases de datos a corto y medio plazo. Una vez adquirido el hardware, se lleva a cabo la instalación, actualización y configuración del Sistema Operativo y el acceso redundado de los servidores a la cabina de almacenamiento. Posteriormente se instala el software de clúster de Oracle, el software de la base de datos y se crea una instancia que albergará los esquemas requeridos de las bases de datos a consolidar. Seguidamente se migran los esquemas al entorno consolidado y se establece la replicación de éstos en tiempo real con la máquina de contingencia usando en ambos casos Oracle GoldenGate. Finalmente se crea y prueba un esquema de copias de seguridad que incluye copias lógicas y físicas de la propia base de datos y de archivos de configuración del clúster a partir de los cuales será posible restaurar el entorno completamente.

Computational methods for genome screening

Motivation An actual issue of great interest, both under a theoretical and an applicative perspective, is the analysis of biological sequences for disclosing the information that they encode. The development of new technologies for genome sequencing in the last years, opened new fundamental problems since huge amounts of biological data still deserve an interpretation. Indeed, the sequencing is only the first step of the genome annotation process that consists in the assignment of biological information to each sequence. Hence given the large amount of available data, in silico methods became useful and necessary in order to extract relevant information from sequences. The availability of data from Genome Projects gave rise to new strategies for tackling the basic problems of computational biology such as the determination of the tridimensional structures of proteins, their biological function and their reciprocal interactions. Results The aim of this work has been the implementation of predictive methods that allow the extraction of information on the properties of genomes and proteins starting from the nucleotide and aminoacidic sequences, by taking advantage of the information provided by the comparison of the genome sequences from different species. In the first part of the work a comprehensive large scale genome comparison of 599 organisms is described. 2,6 million of sequences coming from 551 prokaryotic and 48 eukaryotic genomes were aligned and clustered on the basis of their sequence identity. This procedure led to the identification of classes of proteins that are peculiar to the different groups of organisms. Moreover the adopted similarity threshold produced clusters that are homogeneous on the structural point of view and that can be used for structural annotation of uncharacterized sequences. The second part of the work focuses on the characterization of thermostable proteins and on the development of tools able to predict the thermostability of a protein starting from its sequence. By means of Principal Component Analysis the codon composition of a non redundant database comprising 116 prokaryotic genomes has been analyzed and it has been showed that a cross genomic approach can allow the extraction of common determinants of thermostability at the genome level, leading to an overall accuracy in discriminating thermophilic coding sequences equal to 95%. This result outperform those obtained in previous studies. Moreover, we investigated the effect of multiple mutations on protein thermostability. This issue is of great importance in the field of protein engineering, since thermostable proteins are generally more suitable than their mesostable counterparts in technological applications. A Support Vector Machine based method has been trained to predict if a set of mutations can enhance the thermostability of a given protein sequence. The developed predictor achieves 88% accuracy.

ParTec and KarnUMa-Digital tools as a help for freshman learning

[EN]Freshman students always present lower success rates than other levels of students. Digital systems is a course usually taught at first year studentsand its success rate is not very high. In this work we introduce three digital tools to improve freshman learning designed for easy use and one of them is a tool for mobile terminals that can be used as a game. The first tool is ParTec and is used to implement and test the partition technique. This technique is used to eliminate redundant states in finite state machines. This is a repetitive task that students do not like to perform. The second tool is called KarnUMa and is used for simplifying logic functions through Karnaugh Maps. Simplifying logical functions is a core task for this course and although students usually perform this task better than other tasks, it can still be improved. The third tool is a version of KarnUMa, designed for mobile devices. All the tools are available online for download and have been a helpful tool for students.

Il ruolo del collicolo superiore nell'orientamento spaziale

This thesis was aimed at verifying the role of the superior colliculus (SC) in human spatial orienting. To do so, subjects performed two experimental tasks that have been shown to involve SC’s activation in animals, that is a multisensory integration task (Experiment 1 and 2) and a visual target selection task (Experiment 3). To investigate this topic in humans, we took advantage of neurophysiological finding revealing that retinal S-cones do not send projections to the collicular and magnocellular pathway. In the Experiment 1, subjects performed a simple reaction-time task in which they were required to respond as quickly as possible to any sensory stimulus (visual, auditory or bimodal audio-visual). The visual stimulus could be an S-cone stimulus (invisible to the collicular and magnocellular pathway) or a long wavelength stimulus (visible to the SC). Results showed that when using S-cone stimuli, RTs distribution was simply explained by probability summation, indicating that the redundant auditory and visual channels are independent. Conversely, with red long-wavelength stimuli, visible to the SC, the RTs distribution was related to nonlinear neural summation, which constitutes evidence of integration of different sensory information. We also demonstrate that when AV stimuli were presented at fixation, so that the spatial orienting component of the task was reduced, neural summation was possible regardless of stimulus color. Together, these findings provide support for a pivotal role of the SC in mediating multisensory spatial integration in humans, when behavior involves spatial orienting responses. Since previous studies have shown an anatomical asymmetry of fibres projecting to the SC from the hemiretinas, the Experiment 2 was aimed at investigating temporo-nasal asymmetry in multisensory integration. To do so, subjects performed monocularly the same task shown in the Experiment 1. When spatially coincident audio-visual stimuli were visible to the SC (i.e. red stimuli), the RTE depended on a neural coactivation mechanism, suggesting an integration of multisensory information. When using stimuli invisible to the SC (i.e. purple stimuli), the RTE depended only on a simple statistical facilitation effect, in which the two sensory stimuli were processed by independent channels. Finally, we demonstrate that the multisensory integration effect was stronger for stimuli presented to the temporal hemifield than to the nasal hemifield. Taken together, these findings suggested that multisensory stimulation can be differentially effective depending on specific stimulus parameters. The Experiment 3 was aimed at verifying the role of the SC in target selection by using a color-oddity search task, comprising stimuli either visible or invisible to the collicular and magnocellular pathways. Subjects were required to make a saccade toward a target that could be presented alone or with three distractors of another color (either S-cone or long-wavelength). When using S-cone distractors, invisible to the SC, localization errors were similar to those observed in the distractor-free condition. Conversely, with long-wavelength distractors, visible to the SC, saccadic localization error and variability were significantly greater than in either the distractor-free condition or the S-cone distractors condition. Our results clearly indicate that the SC plays a direct role in visual target selection in humans. Overall, our results indicate that the SC plays an important role in mediating spatial orienting responses both when required covert (Experiments 1 and 2) and overt orienting (Experiment 3).

Max Bill in Italia . Lo spazio logico dell'architettura

I Max Bill is an intense giornata of a big fresco. An analysis of the main social, artistic and cultural events throughout the twentieth century is needed in order to trace his career through his masterpieces and architectures. Some of the faces of this hypothetical mural painting are, among others, Le Corbusier, Walter Gropius, Ernesto Nathan Rogers, Kandinskij, Klee, Mondrian, Vatongerloo, Ignazio Silone, while the backcloth is given by artistic avant-gardes, Bauhaus, International Exhibitions, CIAM, war events, reconstruction, Milan Triennali, Venice Biennali, the School of Ulm. Architect, even though more known as painter, sculptor, designer and graphic artist, Max Bill attends the Bauhaus as a student in the years 1927-1929, and from this experience derives the main features of a rational, objective, constructive and non figurative art. His research is devoted to give his art a scientific methodology: each work proceeds from the analysis of a problem to the logical and always verifiable solution of the same problem. By means of composition elements (such as rhythm, seriality, theme and its variation, harmony and dissonance), he faces, with consistent results, themes apparently very distant from each other as the project for the H.f.G. or the design for a font. Mathematics are a constant reference frame as field of certainties, order, objectivity: ‘for Bill mathematics are never confined to a simple function: they represent a climate of spiritual certainties, and also the theme of non attempted in its purest state, objectivity of the sign and of the geometrical place, and at the same time restlessness of the infinity: Limited and Unlimited ’. In almost sixty years of activity, experiencing all artistic fields, Max Bill works, projects, designs, holds conferences and exhibitions in Europe, Asia and Americas, confronting himself with the most influencing personalities of the twentieth century. In such a vast scenery, the need to limit the investigation field combined with the necessity to address and analyse the unpublished and original aspect of Bill’s relations with Italy. The original contribution of the present research regards this particular ‘geographic delimitation’; in particular, beyond the deep cultural exchanges between Bill and a series of Milanese architects, most of all with Rogers, two main projects have been addressed: the realtà nuova at Milan Triennale in 1947, and the Contemporary Art Museum in Florence in 1980. It is important to note that these projects have not been previously investigated, and the former never appears in the sources either. These works, together with the most well-known ones, such as the projects for the VI and IX Triennale, and the Swiss pavilion for the Biennale, add important details to the reference frame of the relations which took place between Zurich and Milan. Most of the occasions for exchanges took part in between the Thirties and the Fifties, years during which Bill underwent a significant period of artistic growth. He meets the Swiss progressive architects and the Paris artists from the Abstraction-Création movement, enters the CIAM, collaborates with Le Corbusier to the third volume of his Complete Works, and in Milan he works and gets confronted with the events related to post-war reconstruction. In these years Bill defines his own working methodology, attaining an artistic maturity in his work. The present research investigates the mentioned time period, despite some necessary exceptions. II The official Max Bill bibliography is naturally wide, including spreading works along with ones more devoted to analytical investigation, mainly written in German and often translated into French and English (Max Bill himself published his works in three languages). Few works have been published in Italian and, excluding the catalogue of the Parma exhibition from 1977, they cannot be considered comprehensive. Many publications are exhibition catalogues, some of which include essays written by Max Bill himself, some others bring Bill’s comments in a educational-pedagogical approach, to accompany the observer towards a full understanding of the composition processes of his art works. Bill also left a great amount of theoretical speculations to encourage a critical reading of his works in the form of books edited or written by him, and essays published in ‘Werk’, magazine of the Swiss Werkbund, and other international reviews, among which Domus and Casabella. These three reviews have been important tools of analysis, since they include tracks of some of Max Bill’s architectural works. The architectural aspect is less investigated than the plastic and pictorial ones in all the main reference manuals on the subject: Benevolo, Tafuri and Dal Co, Frampton, Allenspach consider Max Bill as an artist proceeding in his work from Bauhaus in the Ulm experience . A first filing of his works was published in 2004 in the monographic issue of the Spanish magazine 2G, together with critical essays by Karin Gimmi, Stanislaus von Moos, Arthur Rüegg and Hans Frei, and in ‘Konkrete Architektur?’, again by Hans Frei. Moreover, the monographic essay on the Atelier Haus building by Arthur Rüegg from 1997, and the DPA 17 issue of the Catalonia Polytechnic with contributions of Carlos Martì, Bruno Reichlin and Ton Salvadò, the latter publication concentrating on a few Bill’s themes and architectures. An urge to studying and going in depth in Max Bill’s works was marked in 2008 by the centenary of his birth and by a recent rediscovery of Bill as initiator of the ‘minimalist’ tradition in Swiss architecture. Bill’s heirs are both very active in promoting exhibitions, researching and publishing. Jakob Bill, Max Bill’s son and painter himself, recently published a work on Bill’s experience in Bauhaus, and earlier on he had published an in-depth study on ‘Endless Ribbons’ sculptures. Angela Thomas Schmid, Bill’s wife and art historian, published in end 2008 the first volume of a biography on Max Bill and, together with the film maker Eric Schmid, produced a documentary film which was also presented at the last Locarno Film Festival. Both biography and documentary concentrate on Max Bill’s political involvement, from antifascism and 1968 protest movements to Bill experiences as Zurich Municipality councilman and member of the Swiss Confederation Parliament. In the present research, the bibliography includes also direct sources, such as interviews and original materials in the form of letters correspondence and graphic works together with related essays, kept in the max+binia+jakob bill stiftung archive in Zurich. III The results of the present research are organized into four main chapters, each of them subdivided into four parts. The first chapter concentrates on the research field, reasons, tools and methodologies employed, whereas the second one consists of a short biographical note organized by topics, introducing the subject of the research. The third chapter, which includes unpublished events, traces the historical and cultural frame with particular reference to the relations between Max Bill and the Italian scene, especially Milan and the architects Rogers and Baldessari around the Fifties, searching the themes and the keys for interpretation of Bill’s architectures and investigating the critical debate on the reviews and the plastic survey through sculpture. The fourth and last chapter examines four main architectures chosen on a geographical basis, all devoted to exhibition spaces, investigating Max Bill’s composition process related to the pictorial field. Paintings has surely been easier and faster to investigate and verify than the building field. A doctoral thesis discussed in Lausanne in 1977 investigating Max Bill’s plastic and pictorial works, provided a series of devices which were corrected and adapted for the definition of the interpretation grid for the composition structures of Bill’s main architectures. Four different tools are employed in the investigation of each work: a context analysis related to chapter three results; a specific theoretical essay by Max Bill briefly explaining his main theses, even though not directly linked to the very same work of art considered; the interpretation grid for the composition themes derived from a related pictorial work; the architecture drawing and digital three-dimensional model. The double analysis of the architectural and pictorial fields is functional to underlining the relation among the different elements of the composition process; the two fields, however, cannot be compared and they stay, in Max Bill’s works as in the present research, interdependent though self-sufficient. IV An important aspect of Max Bill production is self-referentiality: talking of Max Bill, also through Max Bill, as a need for coherence instead of a method limitation. Ernesto Nathan Rogers describes Bill as the last humanist, and his horizon is the known world but, as the ‘Concrete Art’ of which he is one of the main representatives, his production justifies itself: Max Bill not only found a method, but he autonomously re-wrote the ‘rules of the game’, derived timeless theoretical principles and verified them through a rich and interdisciplinary artistic production. The most recurrent words in the present research work are synthesis, unity, space and logic. These terms are part of Max Bill’s vocabulary and can be referred to his works. Similarly, graphic settings or analytical schemes in this research text referring to or commenting Bill’s architectural projects were drawn up keeping in mind the concise precision of his architectural design. As for Mies van der Rohe, it has been written that Max Bill took art to ‘zero degree’ reaching in this way a high complexity. His works are a synthesis of art: they conceptually encompass all previous and –considered their developments- most of contemporary pictures. Contents and message are generally explicitly declared in the title or in Bill’s essays on his artistic works and architectural projects: the beneficiary is invited to go through and re-build the process of synthesis generating the shape. In the course of the interview with the Milan artist Getulio Alviani, he tells how he would not write more than a page for an essay on Josef Albers: everything was already evident ‘on the surface’ and any additional sentence would be redundant. Two years after that interview, these pages attempt to decompose and single out the elements and processes connected with some of Max Bill’s works which, for their own origin, already contain all possible explanations and interpretations. The formal reduction in favour of contents maximization is, perhaps, Max Bill’s main lesson.

Progetto di reti Sensori Wireless e tecniche di Fusione Sensoriale

Ambient Intelligence (AmI) envisions a world where smart, electronic environments are aware and responsive to their context. People moving into these settings engage many computational devices and systems simultaneously even if they are not aware of their presence. AmI stems from the convergence of three key technologies: ubiquitous computing, ubiquitous communication and natural interfaces. The dependence on a large amount of fixed and mobile sensors embedded into the environment makes of Wireless Sensor Networks one of the most relevant enabling technologies for AmI. WSN are complex systems made up of a number of sensor nodes, simple devices that typically embed a low power computational unit (microcontrollers, FPGAs etc.), a wireless communication unit, one or more sensors and a some form of energy supply (either batteries or energy scavenger modules). Low-cost, low-computational power, low energy consumption and small size are characteristics that must be taken into consideration when designing and dealing with WSNs. In order to handle the large amount of data generated by a WSN several multi sensor data fusion techniques have been developed. The aim of multisensor data fusion is to combine data to achieve better accuracy and inferences than could be achieved by the use of a single sensor alone. In this dissertation we present our results in building several AmI applications suitable for a WSN implementation. The work can be divided into two main areas: Multimodal Surveillance and Activity Recognition. Novel techniques to handle data from a network of low-cost, low-power Pyroelectric InfraRed (PIR) sensors are presented. Such techniques allow the detection of the number of people moving in the environment, their direction of movement and their position. We discuss how a mesh of PIR sensors can be integrated with a video surveillance system to increase its performance in people tracking. Furthermore we embed a PIR sensor within the design of a Wireless Video Sensor Node (WVSN) to extend its lifetime. Activity recognition is a fundamental block in natural interfaces. A challenging objective is to design an activity recognition system that is able to exploit a redundant but unreliable WSN. We present our activity in building a novel activity recognition architecture for such a dynamic system. The architecture has a hierarchical structure where simple nodes performs gesture classification and a high level meta classifiers fuses a changing number of classifier outputs. We demonstrate the benefit of such architecture in terms of increased recognition performance, and fault and noise robustness. Furthermore we show how we can extend network lifetime by performing a performance-power trade-off. Smart objects can enhance user experience within smart environments. We present our work in extending the capabilities of the Smart Micrel Cube (SMCube), a smart object used as tangible interface within a tangible computing framework, through the development of a gesture recognition algorithm suitable for this limited computational power device. Finally the development of activity recognition techniques can greatly benefit from the availability of shared dataset. We report our experience in building a dataset for activity recognition. Such dataset is freely available to the scientific community for research purposes and can be used as a testbench for developing, testing and comparing different activity recognition techniques.

Structure learning of graphical models for task-oriented robot grasping

In the collective imaginaries a robot is a human like machine as any androids in science fiction. However the type of robots that you will encounter most frequently are machinery that do work that is too dangerous, boring or onerous. Most of the robots in the world are of this type. They can be found in auto, medical, manufacturing and space industries. Therefore a robot is a system that contains sensors, control systems, manipulators, power supplies and software all working together to perform a task. The development and use of such a system is an active area of research and one of the main problems is the development of interaction skills with the surrounding environment, which include the ability to grasp objects. To perform this task the robot needs to sense the environment and acquire the object informations, physical attributes that may influence a grasp. Humans can solve this grasping problem easily due to their past experiences, that is why many researchers are approaching it from a machine learning perspective finding grasp of an object using information of already known objects. But humans can select the best grasp amongst a vast repertoire not only considering the physical attributes of the object to grasp but even to obtain a certain effect. This is why in our case the study in the area of robot manipulation is focused on grasping and integrating symbolic tasks with data gained through sensors. The learning model is based on Bayesian Network to encode the statistical dependencies between the data collected by the sensors and the symbolic task. This data representation has several advantages. It allows to take into account the uncertainty of the real world, allowing to deal with sensor noise, encodes notion of causality and provides an unified network for learning. Since the network is actually implemented and based on the human expert knowledge, it is very interesting to implement an automated method to learn the structure as in the future more tasks and object features can be introduced and a complex network design based only on human expert knowledge can become unreliable. Since structure learning algorithms presents some weaknesses, the goal of this thesis is to analyze real data used in the network modeled by the human expert, implement a feasible structure learning approach and compare the results with the network designed by the expert in order to possibly enhance it.

Enhanced Mixed Integer Programming Techniques and Routing Problems

Mixed integer programming is up today one of the most widely used techniques for dealing with hard optimization problems. On the one side, many practical optimization problems arising from real-world applications (such as, e.g., scheduling, project planning, transportation, telecommunications, economics and finance, timetabling, etc) can be easily and effectively formulated as Mixed Integer linear Programs (MIPs). On the other hand, 50 and more years of intensive research has dramatically improved on the capability of the current generation of MIP solvers to tackle hard problems in practice. However, many questions are still open and not fully understood, and the mixed integer programming community is still more than active in trying to answer some of these questions. As a consequence, a huge number of papers are continuously developed and new intriguing questions arise every year. When dealing with MIPs, we have to distinguish between two different scenarios. The first one happens when we are asked to handle a general MIP and we cannot assume any special structure for the given problem. In this case, a Linear Programming (LP) relaxation and some integrality requirements are all we have for tackling the problem, and we are ``forced" to use some general purpose techniques. The second one happens when mixed integer programming is used to address a somehow structured problem. In this context, polyhedral analysis and other theoretical and practical considerations are typically exploited to devise some special purpose techniques. This thesis tries to give some insights in both the above mentioned situations. The first part of the work is focused on general purpose cutting planes, which are probably the key ingredient behind the success of the current generation of MIP solvers. Chapter 1 presents a quick overview of the main ingredients of a branch-and-cut algorithm, while Chapter 2 recalls some results from the literature in the context of disjunctive cuts and their connections with Gomory mixed integer cuts. Chapter 3 presents a theoretical and computational investigation of disjunctive cuts. In particular, we analyze the connections between different normalization conditions (i.e., conditions to truncate the cone associated with disjunctive cutting planes) and other crucial aspects as cut rank, cut density and cut strength. We give a theoretical characterization of weak rays of the disjunctive cone that lead to dominated cuts, and propose a practical method to possibly strengthen those cuts arising from such weak extremal solution. Further, we point out how redundant constraints can affect the quality of the generated disjunctive cuts, and discuss possible ways to cope with them. Finally, Chapter 4 presents some preliminary ideas in the context of multiple-row cuts. Very recently, a series of papers have brought the attention to the possibility of generating cuts using more than one row of the simplex tableau at a time. Several interesting theoretical results have been presented in this direction, often revisiting and recalling other important results discovered more than 40 years ago. However, is not clear at all how these results can be exploited in practice. As stated, the chapter is a still work-in-progress and simply presents a possible way for generating two-row cuts from the simplex tableau arising from lattice-free triangles and some preliminary computational results. The second part of the thesis is instead focused on the heuristic and exact exploitation of integer programming techniques for hard combinatorial optimization problems in the context of routing applications. Chapters 5 and 6 present an integer linear programming local search algorithm for Vehicle Routing Problems (VRPs). The overall procedure follows a general destroy-and-repair paradigm (i.e., the current solution is first randomly destroyed and then repaired in the attempt of finding a new improved solution) where a class of exponential neighborhoods are iteratively explored by heuristically solving an integer programming formulation through a general purpose MIP solver. Chapters 7 and 8 deal with exact branch-and-cut methods. Chapter 7 presents an extended formulation for the Traveling Salesman Problem with Time Windows (TSPTW), a generalization of the well known TSP where each node must be visited within a given time window. The polyhedral approaches proposed for this problem in the literature typically follow the one which has been proven to be extremely effective in the classical TSP context. Here we present an overall (quite) general idea which is based on a relaxed discretization of time windows. Such an idea leads to a stronger formulation and to stronger valid inequalities which are then separated within the classical branch-and-cut framework. Finally, Chapter 8 addresses the branch-and-cut in the context of Generalized Minimum Spanning Tree Problems (GMSTPs) (i.e., a class of NP-hard generalizations of the classical minimum spanning tree problem). In this chapter, we show how some basic ideas (and, in particular, the usage of general purpose cutting planes) can be useful to improve on branch-and-cut methods proposed in the literature.

The potential of the 3-UPU translational parallel manipulator and a procedure to select the best architecture

The 3-UPU three degrees of freedom fully parallel manipulator, where U and P are for universal and prismatic pair respectively, is a very well known manipulator that can provide the platform with three degrees of freedom of pure translation, pure rotation or mixed translation and rotation with respect to the base, according to the relative directions of the revolute pair axes (each universal pair comprises two revolute pairs with intersecting and perpendicular axes). In particular, pure translational parallel 3-UPU manipulators (3-UPU TPMs) received great attention. Many studies have been reported in the literature on singularities, workspace, and joint clearance influence on the platform accuracy of this manipulator. However, much work has still to be done to reveal all the features this topology can offer to the designer when different architecture, i.e. different geometry are considered. Therefore, this dissertation will focus on this type of the 3-UPU manipulators. The first part of the dissertation presents six new architectures of the 3-UPU TPMs which offer interesting features to the designer. In the second part, a procedure is presented which is based on some indexes, in order to allows the designer to select the best architecture of the 3-UPU TPMs for a given task. Four indexes are proposed as stiffness, clearance, singularity and size of the manipulator in order to apply the procedure.