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.

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.

Topological analysis of singularity loci for serial and parallel manipulators

Singularities of robot manipulators have been intensely studied in the last decades by researchers of many fields. Serial singularities produce some local loss of dexterity of the manipulator, therefore it might be desirable to search for singularityfree trajectories in the jointspace. On the other hand, parallel singularities are very dangerous for parallel manipulators, for they may provoke the local loss of platform control, and jeopardize the structural integrity of links or actuators. It is therefore utterly important to avoid parallel singularities, while operating a parallel machine. Furthermore, there might be some configurations of a parallel manipulators that are allowed by the constraints, but nevertheless are unreachable by any feasible path. The present work proposes a numerical procedure based upon Morse theory, an important branch of differential topology. Such procedure counts and identify the singularity-free regions that are cut by the singularity locus out of the configuration space, and the disjoint regions composing the configuration space of a parallel manipulator. Moreover, given any two configurations of a manipulator, a feasible or a singularity-free path connecting them can always be found, or it can be proved that none exists. Examples of applications to 3R and 6R serial manipulators, to 3UPS and 3UPU parallel wrists, to 3UPU parallel translational manipulators, and to 3RRR planar manipulators are reported in the work.

Path planning for image based visual servoing

This thesis deals with Visual Servoing and its strictly connected disciplines like projective geometry, image processing, robotics and non-linear control. More specifically the work addresses the problem to control a robotic manipulator through one of the largely used Visual Servoing techniques: the Image Based Visual Servoing (IBVS). In Image Based Visual Servoing the robot is driven by on-line performing a feedback control loop that is closed directly in the 2D space of the camera sensor. The work considers the case of a monocular system with the only camera mounted on the robot end effector (eye in hand configuration). Through IBVS the system can be positioned with respect to a 3D fixed target by minimizing the differences between its initial view and its goal view, corresponding respectively to the initial and the goal system configurations: the robot Cartesian Motion is thus generated only by means of visual informations. However, the execution of a positioning control task by IBVS is not straightforward because singularity problems may occur and local minima may be reached where the reached image is very close to the target one but the 3D positioning task is far from being fulfilled: this happens in particular for large camera displacements, when the the initial and the goal target views are noticeably different. To overcame singularity and local minima drawbacks, maintaining the good properties of IBVS robustness with respect to modeling and camera calibration errors, an opportune image path planning can be exploited. This work deals with the problem of generating opportune image plane trajectories for tracked points of the servoing control scheme (a trajectory is made of a path plus a time law). The generated image plane paths must be feasible i.e. they must be compliant with rigid body motion of the camera with respect to the object so as to avoid image jacobian singularities and local minima problems. In addition, the image planned trajectories must generate camera velocity screws which are smooth and within the allowed bounds of the robot. We will show that a scaled 3D motion planning algorithm can be devised in order to generate feasible image plane trajectories. Since the paths in the image are off-line generated it is also possible to tune the planning parameters so as to maintain the target inside the camera field of view even if, in some unfortunate cases, the feature target points would leave the camera images due to 3D robot motions. To test the validity of the proposed approach some both experiments and simulations results have been reported taking also into account the influence of noise in the path planning strategy. The experiments have been realized with a 6DOF anthropomorphic manipulator with a fire-wire camera installed on its end effector: the results demonstrate the good performances and the feasibility of the proposed approach.

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.

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.

Use of computer algebra in the calculation of Feynman diagrams

The increasing precision of current and future experiments in high-energy physics requires a likewise increase in the accuracy of the calculation of theoretical predictions, in order to find evidence for possible deviations of the generally accepted Standard Model of elementary particles and interactions. Calculating the experimentally measurable cross sections of scattering and decay processes to a higher accuracy directly translates into including higher order radiative corrections in the calculation. The large number of particles and interactions in the full Standard Model results in an exponentially growing number of Feynman diagrams contributing to any given process in higher orders. Additionally, the appearance of multiple independent mass scales makes even the calculation of single diagrams non-trivial. For over two decades now, the only way to cope with these issues has been to rely on the assistance of computers. The aim of the xloops project is to provide the necessary tools to automate the calculation procedures as far as possible, including the generation of the contributing diagrams and the evaluation of the resulting Feynman integrals. The latter is based on the techniques developed in Mainz for solving one- and two-loop diagrams in a general and systematic way using parallel/orthogonal space methods. These techniques involve a considerable amount of symbolic computations. During the development of xloops it was found that conventional computer algebra systems were not a suitable implementation environment. For this reason, a new system called GiNaC has been created, which allows the development of large-scale symbolic applications in an object-oriented fashion within the C++ programming language. This system, which is now also in use for other projects besides xloops, is the main focus of this thesis. The implementation of GiNaC as a C++ library sets it apart from other algebraic systems. Our results prove that a highly efficient symbolic manipulator can be designed in an object-oriented way, and that having a very fine granularity of objects is also feasible. The xloops-related parts of this work consist of a new implementation, based on GiNaC, of functions for calculating one-loop Feynman integrals that already existed in the original xloops program, as well as the addition of supplementary modules belonging to the interface between the library of integral functions and the diagram generator.

Expressions- und Funktionsanalysen von "Tetraspan Vesicle Membrane Proteins" in Caenorhabditis elegans

Tetraspan vesicle membrane proteins (TVPs) sind ubiquitäre Komponenten von Transportvesikeln. Bei den Säugetieren unterscheidet man drei Familien, die Physine, Gyrine und SCAMPs (secretory carrier-associated membrane proteins). Ihre Funktion ist weitgehend unbekannt, es wird jedoch vermutet, dass sie eine Rolle bei der Vesikelbildung und der Vesikelrezirkulierung spielen. In Caenorhabditis elegans existiert von jeder Familie jeweils nur ein einziges Polypeptid: für die Physine Synaptophysin (SPH-1), für die Gyrine Synaptogyrin (SNG-1) und für die SCAMPs SCAMP (SCM-1). Ziel der Arbeit war es die Verteilung der C. elegans TVPs zu untersuchen und ihre Funktion unter besonderer Berücksichtigung der vesikelvermittelten synaptischen Kopplung zu bestimmen. Wenn die C. elegans TVPs in humanen Epithelzellen synthetisiert werden, lokalisieren sie in zytoplasmatischen Vesikeln. In Kotransfektionsexperimenten wurde gezeigt, dass sie größtenteils in den gleichen Strukturen enthalten sind. In C. elegans synthetisierte TVP-Reporterkonstrukte können in unterschiedlichen Geweben nachgewiesen werden. Dabei ist SNG-1 fast ausschließlich in Neuronen zu finden. SPH-1 und SCM-1 hingegen weisen komplexe und teilweise überlappende Verteilungsmuster auf. Während für SPH-1 eine starke Fluoreszenz im Pharynx, auf der apikalen Seite der Darmzellen oberhalb des sog. terminal webs und in adluminalen Regionen von exkretorischen Geweben gefunden wurde, war SCM-1 stark in der Muskulatur und den Coelomozyten vertreten. Die Expression von SCM-1 in Pharynx und Darm war deutlich schwächer. Die C. elegans TVPs werden früh in der Entwicklung ab der Gastrulation (SPH-1 und SCM-1) bzw. ab der Neurulation im sog. Komma-Stadium (SNG-1) produziert. Um die Funktion der TVPs in C. elegans zu untersuchen, wurden TVP-Mutanten analysiert. Durch Kombination aller drei TVP-Gen-Mutanten wurden TVP-Dreifachmutanten generiert. Diese wiesen keinen offensichtlichen Defekt im Bewegungsmuster auf, entwickelten sich normal und bildeten ein normales Nervensystem aus. Auch auf unterschiedliche chemische und physikalische Reize in sensorischen Tests reagierten die TVP-Dreifachmutanten in gleicher Weise wie Wildtyptiere. Ebenso zeigen die TVP-Dreifachmutanten elektrophysiologisch unter normalen Bedingungen keine anormalen Reaktionsmuster. In ultrastrukturellen Untersuchungen wurde lediglich eine signifikant erhöhte Anzahl Clathrin-ummantelter Vesikel in cholinergen Synapsen gefunden. Erst unter Stressbedingungen, hervorgerufen durch den GABA-Antagonisten Pentylentetrazol (PTZ), wiesen sowohl die TVP-Dreifach- als auch die TVP-Einzelmutanten eine deutlich erhöhte Krampfbereitschaft auf. Zusammengenommen zeigen die Analysen, dass TVPs zwar für grundlegende neuronale Prozesse nicht notwendig sind, dass sie aber auf der anderen Seite vermutlich an alternativen redundanten Wegen der Neurotransmitterfreisetzung beteiligt sind.

Data Mining in Clinical Practice for the Quantification of Motor Impairment in Parkinson's Disease

Advances in biomedical signal acquisition systems for motion analysis have led to lowcost and ubiquitous wearable sensors which can be used to record movement data in different settings. This implies the potential availability of large amounts of quantitative data. It is then crucial to identify and to extract the information of clinical relevance from the large amount of available data. This quantitative and objective information can be an important aid for clinical decision making. Data mining is the process of discovering such information in databases through data processing, selection of informative data, and identification of relevant patterns. The databases considered in this thesis store motion data from wearable sensors (specifically accelerometers) and clinical information (clinical data, scores, tests). The main goal of this thesis is to develop data mining tools which can provide quantitative information to the clinician in the field of movement disorders. This thesis will focus on motor impairment in Parkinson's disease (PD). Different databases related to Parkinson subjects in different stages of the disease were considered for this thesis. Each database is characterized by the data recorded during a specific motor task performed by different groups of subjects. The data mining techniques that were used in this thesis are feature selection (a technique which was used to find relevant information and to discard useless or redundant data), classification, clustering, and regression. The aims were to identify high risk subjects for PD, characterize the differences between early PD subjects and healthy ones, characterize PD subtypes and automatically assess the severity of symptoms in the home setting.

Genetische und funktionelle Analyse von Vesikelmembranprotein-Mutanten in Maus und Caenorhabditis elegans

Tetraspan vesicle membrane proteins (TVPs) sind konservierte, ubiquitär vorkommende Membranproteine synaptischer Vesikel und zytoplasmatischer Transportvesikel. Bei Säugetieren lassen sie sich in die Physine, Gyrine und SCAMPs (secretory carrier-associated membrane proteins) unterteilen, die im Nematoden C. elegans jeweils nur durch ein einzelnes Polypeptid vertreten sind (Synaptophysin-1 [SPH-1], Synaptogyrin-1 [SNG-1] und SCAMP-1 [SCM-1]). Obwohl den TVPs eine Beteiligung bei der Regulation des Vesikelzyklus zugesprochen wurde, sind Synaptophysin-1-Knockout-Mäuse und vollständig TVP-defiziente Würmer gesund und weisen nur geringgradige Veränderungen auf. In dieser Arbeit sollten daher zum einen genomweite komparative Transkriptomanalysen durchgeführt werden, um mögliche Kompensationsmechanismen in der Maus und C. elegans zu finden, zum anderen sollten mit Hilfe pharmakologischer Stressassays und genetischer Verfahren Schwachstellen und Redundanzen identifiziert werden. Erstaunlicherweise konnten durch Affymetrix GeneChip-Analysen der RNA in der Retina von Synaptophysin-1-/--Mäusen keine differenziell exprimierten Gene gefunden werden. Bei der Untersuchung der C. elegans-TVP-Dreifachmutante wurden hingegen 17 Gene mit erhöhter und 3 mit erniedrigter Transkription identifiziert. Die Befunde für 12 hochregulierte Gene wurden durch quantitative Real-Time RT-PCR bestätigt. Das am stärksten hochregulierte Gen arf-1.1 kodiert für eine GTPase, die vermutlich an der Regulation der Vesikelbildung beteiligt ist. Von den ebenso identifizierten Genen cdr-2, cdr-4 und pgp-9 ist bekannt, dass sie in Stresssituationen, z. B. in Gegenwart von Cadmium, verstärkt transkribiert werden. ugt-62 und ugt-19 kodieren für Glucuronosyltransferasen. Für arf-1.1, cdr-2, ugt-62 sowie für das Gen T16G1.6, das für eine coiled-coil-Domäne kodiert, wurden im Folgenden fluoreszierende Promoterkonstrukte hergestellt, um Koexpressionsmuster mit TVPs zu bestimmen. Es stellte sich heraus, dass alle vier Promoterkonstrukte im Darm zusammen mit SPH-1 und SCM-1 im Darm transkribiert werden. Mit fluoreszierenden Translationschimären konnte weiterhin gezeigt werden, dass ARF-1.1 und CDR-2 mit den Darm-spezifischen TVPs im apikalen Bereich der Darmzellen kolokalisieren. Um mehr über die Funktion von TVPs im Vesikelzyklus zu erfahren, wurden pharmakologische und genetische Analysen von Würmern durchgeführt, in denen die Expression des Neuronen-spezifischen SNG-1 verändert ist. Deletion oder Überexpression führte zu einer Resistenz gegenüber dem Acetylcholinesterase-Inhibitor Aldicarb und zu erhöhter Empfindlichkeit gegenüber dem GABA-Rezeptor-Antagonisten Pentylentetrazol. Auf genetischer Ebene zeigte sich, dass sng-1 synthetisch mit den Genen für Synaptotagmin-1, Endophilin A sowie Synaptojanin wirkt. Die beobachteten Effekte weisen auf alternative Funktionen in der synaptischen Übertragung hin und unterstützen zugleich die Hypothese, dass SNG-1 im synaptischen Vesikelzyklus eine wichtige Funktion erfüllt, die möglicherweise einem noch unbekannten redundanten Kompartiment-spezifischen Signalweg der synaptischen Transmission zuzuordnen ist.