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.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Funzionalizzazione della mandibola dopo ricostruzione con lembo libero rivascolarizzato di fibula "single strut". Al di là del deficit di verticalità.

Obiettivi: Valutare la modalità  più efficace per la riabilitazione funzionale del limbo libero di fibula "single strut", dopo ampie resezioni per patologia neoplastica maligna del cavo orale. Metodi: Da una casistica di 62 ricostruzioni microvascolari con limbo libero di fibula, 11 casi sono stati selezionati per essere riabilitati mediante protesi dentale a supporto implantare. 6 casi sono stati trattati senza ulteriori procedure chirurgiche ad eccezione dell'implantologia (gruppo 1), affrontando il deficit di verticalità  della fibula attraverso la protesi dentaria, mentre i restanti casi sono stati trattati con la distrazione osteogenetica (DO) della fibula prima della riabilitazione protesica (gruppo 2). Il deficit di verticalità  fibula/mandibola è stato misurato. I criteri di valutazione utilizzati includono la misurazione clinica e radiografica del livello osseo e dei tessuti molli peri-implantari, ed il livello di soddisfazione del paziente attraverso un questionario appositamente redatto. Risultati: Tutte le riabilitazioni protesiche sono costituite da protesi dentali avvitate su impianti. L'età  media è di 52 anni, il rapporto uomini/donne è di 6/5. Il numero medio di impianti inseriti nelle fibule è di 5. Il periodo massimo di follow-up dopo il carico masticatorio è stato di 30 mesi per il gruppo 1 e di 38.5 mesi (17-81) di media per il gruppo 2. Non abbiamo riportato complicazioni chirurgiche. Nessun impianto è stato rimosso dai pazienti del gruppo 1, la perdita media di osso peri-implantare registrata è stata di 1,5 mm. Nel gruppo 2 sono stati riportati un caso di tipping linguale del vettore di distrazione durante la fase di consolidazione e un caso di frattura della corticale basale in assenza di formazione di nuovo osso. L'incremento medio di osso in verticalità è stato di 13,6 mm (12-15). 4 impianti su 32 (12.5%) sono andati persi dopo il periodo di follow-up. Il riassorbimento medio peri-implantare, è stato di 2,5 mm. Conclusioni: Le soluzioni più utilizzate per superare il deficit di verticalità  del limbo libero di fibula consistono nell'allestimento del lembo libero di cresta iliaca, nel posizionare la fibula in posizione ideale da un punto di vista protesico a discapito del profilo osseo basale, l'utilizzo del lembo di fibula nella versione descritta come "double barrel", nella distrazione osteogenetica della fibula. La nostra esperienza concerne il lembo libero di fibula che nella patologia neoplastica maligna utilizziamo nella versione "single strut", per mantenere disponibili tutte le potenzialità  di lunghezza del peduncolo vascolare, senza necessità  di innesti di vena. Entrambe le soluzioni, la protesi dentale ortopedica e la distrazione osteogenetica seguita da protesi, entrambe avvitate su impianti, costituiscono soluzioni soddisfacenti per la riabilitazione funzionale della fibula al di là  del suo deficit di verticalità . La prima soluzione ha preso spunto dall'osservazione dei buoni risultati della protesi dentale su impianti corti, avendo un paragonabile rapporto corona/radice, la DO applicata alla fibula, sebbene sia risultata una metodica con un numero di complicazioni più elevato ed un maggior livello di riassorbimento di osso peri-implantare, costituisce in ogni caso una valida opzione riabilitativa, specialmente in caso di notevole discrepanza mandibulo/fibulare. Decisiva è la scelta del percorso terapeutico dopo una accurata valutazione di ogni singolo caso. Vengono illustrati i criteri di selezione provenienti dalla nostra esperienza.

Technical innovations for the diagnosis and the rehabilitation of motor and perceptive impairments of the child with Cerebral Palsy

The treatment of the Cerebral Palsy (CP) is considered as the “core problem” for the whole field of the pediatric rehabilitation. The reason why this pathology has such a primary role, can be ascribed to two main aspects. First of all CP is the form of disability most frequent in childhood (one new case per 500 birth alive, (1)), secondarily the functional recovery of the “spastic” child is, historically, the clinical field in which the majority of the therapeutic methods and techniques (physiotherapy, orthotic, pharmacologic, orthopedic-surgical, neurosurgical) were first applied and tested. The currently accepted definition of CP – Group of disorders of the development of movement and posture causing activity limitation (2) – is the result of a recent update by the World Health Organization to the language of the International Classification of Functioning Disability and Health, from the original proposal of Ingram – A persistent but not unchangeable disorder of posture and movement – dated 1955 (3). This definition considers CP as a permanent ailment, i.e. a “fixed” condition, that however can be modified both functionally and structurally by means of child spontaneous evolution and treatments carried out during childhood. The lesion that causes the palsy, happens in a structurally immature brain in the pre-, peri- or post-birth period (but only during the firsts months of life). The most frequent causes of CP are: prematurity, insufficient cerebral perfusion, arterial haemorrhage, venous infarction, hypoxia caused by various origin (for example from the ingestion of amniotic liquid), malnutrition, infection and maternal or fetal poisoning. In addition to these causes, traumas and malformations have to be included. The lesion, whether focused or spread over the nervous system, impairs the whole functioning of the Central Nervous System (CNS). As a consequence, they affect the construction of the adaptive functions (4), first of all posture control, locomotion and manipulation. The palsy itself does not vary over time, however it assumes an unavoidable “evolutionary” feature when during growth the child is requested to meet new and different needs through the construction of new and different functions. It is essential to consider that clinically CP is not only a direct expression of structural impairment, that is of etiology, pathogenesis and lesion timing, but it is mainly the manifestation of the path followed by the CNS to “re”-construct the adaptive functions “despite” the presence of the damage. “Palsy” is “the form of the function that is implemented by an individual whose CNS has been damaged in order to satisfy the demands coming from the environment” (4). Therefore it is only possible to establish general relations between lesion site, nature and size, and palsy and recovery processes. It is quite common to observe that children with very similar neuroimaging can have very different clinical manifestations of CP and, on the other hand, children with very similar motor behaviors can have completely different lesion histories. A very clear example of this is represented by hemiplegic forms, which show bilateral hemispheric lesions in a high percentage of cases. The first section of this thesis is aimed at guiding the interpretation of CP. First of all the issue of the detection of the palsy is treated from historical viewpoint. Consequently, an extended analysis of the current definition of CP, as internationally accepted, is provided. The definition is then outlined in terms of a space dimension and then of a time dimension, hence it is highlighted where this definition is unacceptably lacking. The last part of the first section further stresses the importance of shifting from the traditional concept of CP as a palsy of development (defect analysis) towards the notion of development of palsy, i.e., as the product of the relationship that the individual however tries to dynamically build with the surrounding environment (resource semeiotics) starting and growing from a different availability of resources, needs, dreams, rights and duties (4). In the scientific and clinic community no common classification system of CP has so far been universally accepted. Besides, no standard operative method or technique have been acknowledged to effectively assess the different disabilities and impairments exhibited by children with CP. CP is still “an artificial concept, comprising several causes and clinical syndromes that have been grouped together for a convenience of management” (5). The lack of standard and common protocols able to effectively diagnose the palsy, and as a consequence to establish specific treatments and prognosis, is mainly because of the difficulty to elevate this field to a level based on scientific evidence. A solution aimed at overcoming the current incomplete treatment of CP children is represented by the clinical systematic adoption of objective tools able to measure motor defects and movement impairments. A widespread application of reliable instruments and techniques able to objectively evaluate both the form of the palsy (diagnosis) and the efficacy of the treatments provided (prognosis), constitutes a valuable method able to validate care protocols, establish the efficacy of classification systems and assess the validity of definitions. Since the ‘80s, instruments specifically oriented to the analysis of the human movement have been advantageously designed and applied in the context of CP with the aim of measuring motor deficits and, especially, gait deviations. The gait analysis (GA) technique has been increasingly used over the years to assess, analyze, classify, and support the process of clinical decisions making, allowing for a complete investigation of gait with an increased temporal and spatial resolution. GA has provided a basis for improving the outcome of surgical and nonsurgical treatments and for introducing a new modus operandi in the identification of defects and functional adaptations to the musculoskeletal disorders. Historically, the first laboratories set up for gait analysis developed their own protocol (set of procedures for data collection and for data reduction) independently, according to performances of the technologies available at that time. In particular, the stereophotogrammetric systems mainly based on optoelectronic technology, soon became a gold-standard for motion analysis. They have been successfully applied especially for scientific purposes. Nowadays the optoelectronic systems have significantly improved their performances in term of spatial and temporal resolution, however many laboratories continue to use the protocols designed on the technology available in the ‘70s and now out-of-date. Furthermore, these protocols are not coherent both for the biomechanical models and for the adopted collection procedures. In spite of these differences, GA data are shared, exchanged and interpreted irrespectively to the adopted protocol without a full awareness to what extent these protocols are compatible and comparable with each other. Following the extraordinary advances in computer science and electronics, new systems for GA no longer based on optoelectronic technology, are now becoming available. They are the Inertial and Magnetic Measurement Systems (IMMSs), based on miniature MEMS (Microelectromechanical systems) inertial sensor technology. These systems are cost effective, wearable and fully portable motion analysis systems, these features gives IMMSs the potential to be used both outside specialized laboratories and to consecutive collect series of tens of gait cycles. The recognition and selection of the most representative gait cycle is then easier and more reliable especially in CP children, considering their relevant gait cycle variability. The second section of this thesis is focused on GA. In particular, it is firstly aimed at examining the differences among five most representative GA protocols in order to assess the state of the art with respect to the inter-protocol variability. The design of a new protocol is then proposed and presented with the aim of achieving gait analysis on CP children by means of IMMS. The protocol, named ‘Outwalk’, contains original and innovative solutions oriented at obtaining joint kinematic with calibration procedures extremely comfortable for the patients. The results of a first in-vivo validation of Outwalk on healthy subjects are then provided. In particular, this study was carried out by comparing Outwalk used in combination with an IMMS with respect to a reference protocol and an optoelectronic system. In order to set a more accurate and precise comparison of the systems and the protocols, ad hoc methods were designed and an original formulation of the statistical parameter coefficient of multiple correlation was developed and effectively applied. On the basis of the experimental design proposed for the validation on healthy subjects, a first assessment of Outwalk, together with an IMMS, was also carried out on CP children. The third section of this thesis is dedicated to the treatment of walking in CP children. Commonly prescribed treatments in addressing gait abnormalities in CP children include physical therapy, surgery (orthopedic and rhizotomy), and orthoses. The orthotic approach is conservative, being reversible, and widespread in many therapeutic regimes. Orthoses are used to improve the gait of children with CP, by preventing deformities, controlling joint position, and offering an effective lever for the ankle joint. Orthoses are prescribed for the additional aims of increasing walking speed, improving stability, preventing stumbling, and decreasing muscular fatigue. The ankle-foot orthosis (AFO), with a rigid ankle, are primarily designed to prevent equinus and other foot deformities with a positive effect also on more proximal joints. However, AFOs prevent the natural excursion of the tibio-tarsic joint during the second rocker, hence hampering the natural leaning progression of the whole body under the effect of the inertia (6). A new modular (submalleolar) astragalus-calcanear orthosis, named OMAC, has recently been proposed with the intention of substituting the prescription of AFOs in those CP children exhibiting a flat and valgus-pronated foot. The aim of this section is thus to present the mechanical and technical features of the OMAC by means of an accurate description of the device. In particular, the integral document of the deposited Italian patent, is provided. A preliminary validation of OMAC with respect to AFO is also reported as resulted from an experimental campaign on diplegic CP children, during a three month period, aimed at quantitatively assessing the benefit provided by the two orthoses on walking and at qualitatively evaluating the changes in the quality of life and motor abilities. As already stated, CP is universally considered as a persistent but not unchangeable disorder of posture and movement. Conversely to this definition, some clinicians (4) have recently pointed out that movement disorders may be primarily caused by the presence of perceptive disorders, where perception is not merely the acquisition of sensory information, but an active process aimed at guiding the execution of movements through the integration of sensory information properly representing the state of one’s body and of the environment. Children with perceptive impairments show an overall fear of moving and the onset of strongly unnatural walking schemes directly caused by the presence of perceptive system disorders. The fourth section of the thesis thus deals with accurately defining the perceptive impairment exhibited by diplegic CP children. A detailed description of the clinical signs revealing the presence of the perceptive impairment, and a classification scheme of the clinical aspects of perceptual disorders is provided. In the end, a functional reaching test is proposed as an instrumental test able to disclosure the perceptive impairment. References 1. Prevalence and characteristics of children with cerebral palsy in Europe. Dev Med Child Neurol. 2002 Set;44(9):633-640. 2. Bax M, Goldstein M, Rosenbaum P, Leviton A, Paneth N, Dan B, et al. Proposed definition and classification of cerebral palsy, April 2005. Dev Med Child Neurol. 2005 Ago;47(8):571-576. 3. Ingram TT. A study of cerebral palsy in the childhood population of Edinburgh. Arch. Dis. Child. 1955 Apr;30(150):85-98. 4. Ferrari A, Cioni G. The spastic forms of cerebral palsy : a guide to the assessment of adaptive functions. Milan: Springer; 2009. 5. Olney SJ, Wright MJ. Cerebral Palsy. Campbell S et al. Physical Therapy for Children. 2nd Ed. Philadelphia: Saunders. 2000;:533-570. 6. Desloovere K, Molenaers G, Van Gestel L, Huenaerts C, Van Campenhout A, Callewaert B, et al. How can push-off be preserved during use of an ankle foot orthosis in children with hemiplegia? A prospective controlled study. Gait Posture. 2006 Ott;24(2):142-151.

Refined Estimation of Earthquake Source Parameters: Methods, Applications and Scaling Relationships

The objective of this work of thesis is the refined estimations of source parameters. To such a purpose we used two different approaches, one in the frequency domain and the other in the time domain. In frequency domain, we analyzed the P- and S-wave displacement spectra to estimate spectral parameters, that is corner frequencies and low frequency spectral amplitudes. We used a parametric modeling approach which is combined with a multi-step, non-linear inversion strategy and includes the correction for attenuation and site effects. The iterative multi-step procedure was applied to about 700 microearthquakes in the moment range 1011-1014 N•m and recorded at the dense, wide-dynamic range, seismic networks operating in Southern Apennines (Italy). The analysis of the source parameters is often complicated when we are not able to model the propagation accurately. In this case the empirical Green function approach is a very useful tool to study the seismic source properties. In fact the Empirical Green Functions (EGFs) consent to represent the contribution of propagation and site effects to signal without using approximate velocity models. An EGF is a recorded three-component set of time-histories of a small earthquake whose source mechanism and propagation path are similar to those of the master event. Thus, in time domain, the deconvolution method of Vallée (2004) was applied to calculate the source time functions (RSTFs) and to accurately estimate source size and rupture velocity. This technique was applied to 1) large event, that is Mw=6.3 2009 L’Aquila mainshock (Central Italy), 2) moderate events, that is cluster of earthquakes of 2009 L’Aquila sequence with moment magnitude ranging between 3 and 5.6, 3) small event, i.e. Mw=2.9 Laviano mainshock (Southern Italy).

Novel investigation methods in Computational Social Dynamics and Complex Systems

In this thesis the evolution of the techno-social systems analysis methods will be reported, through the explanation of the various research experience directly faced. The first case presented is a research based on data mining of a dataset of words association named Human Brain Cloud: validation will be faced and, also through a non-trivial modeling, a better understanding of language properties will be presented. Then, a real complex system experiment will be introduced: the WideNoise experiment in the context of the EveryAware european project. The project and the experiment course will be illustrated and data analysis will be displayed. Then the Experimental Tribe platform for social computation will be introduced . It has been conceived to help researchers in the implementation of web experiments, and aims also to catalyze the cumulative growth of experimental methodologies and the standardization of tools cited above. In the last part, three other research experience which already took place on the Experimental Tribe platform will be discussed in detail, from the design of the experiment to the analysis of the results and, eventually, to the modeling of the systems involved. The experiments are: CityRace, about the measurement of human traffic-facing strategies; laPENSOcosì, aiming to unveil the political opinion structure; AirProbe, implemented again in the EveryAware project framework, which consisted in monitoring air quality opinion shift of a community informed about local air pollution. At the end, the evolution of the technosocial systems investigation methods shall emerge together with the opportunities and the threats offered by this new scientific path.