Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Abstract Background MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. Results In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots. Conclusions Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.

The humankind genome: from genetic diversity to the origin of human diseases

Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease’s etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.

Caratterizzazione meccanica di calcestruzzi fibrorinforzati con fibre d'acciaio

L’utilizzo di materiali compositi come i calcestruzzi fibrorinforzati sta diventando sempre più frequente e diffuso. Tuttavia la scelta di nuovi materiali richiede una approfondita analisi delle loro caratteristiche e dei loro comportamenti. I vantaggi forniti dall’aggiunta di fibre d’acciaio ad un materiale fragile, quale il calcestruzzo, sono legati al miglioramento della duttilità e all'aumento di assorbimento di energia. L’aggiunta di fibre permette quindi di migliorare il comportamento strutturale del composito, dando vita ad un nuovo materiale capace di lavorare non solo a compressione ma anche in piccola parte a trazione, ma soprattutto caratterizzato da una discreta duttilità ed una buona capacità plastica. Questa tesi ha avuto come fine l’analisi delle caratteristiche di questi compositi cementizi fibrorinforzati. Partendo da prove sperimentali classiche quali prove di trazione e compressione, si è arrivati alla caratterizzazione di questi materiali avvalendosi di una campagna sperimentale basata sull’applicazione della norma UNI 11039/2003. L’obiettivo principale di questo lavoro consiste nell’analizzare e nel confrontare calcestruzzi rinforzati con fibre di due diverse lunghezze e in diversi dosaggi. Studiando questi calcestruzzi si è cercato di comprendere meglio questi materiali e trovare un riscontro pratico ai comportamenti descritti in teorie ormai diffuse e consolidate. La comparazione dei risultati dei test condotti ha permesso di mettere in luce differenze tra i materiali rinforzati con l’aggiunta di fibre corte rispetto a quelli con fibre lunghe, ma ha anche permesso di mostrare e sottolineare le analogie che caratterizzano questi materiali fibrorinforzati. Sono stati affrontati inoltre gli aspetti legati alle fasi della costituzione di questi materiali sia da un punto di vista teorico sia da un punto di vista pratico. Infine è stato sviluppato un modello analitico basato sulla definizione di specifici diagrammi tensione-deformazione; i risultati di questo modello sono quindi stati confrontati con i dati sperimentali ottenuti in laboratorio.

Tools and methods for the quality assurance of force platforms in human movement analysis

The human movement analysis (HMA) aims to measure the abilities of a subject to stand or to walk. In the field of HMA, tests are daily performed in research laboratories, hospitals and clinics, aiming to diagnose a disease, distinguish between disease entities, monitor the progress of a treatment and predict the outcome of an intervention [Brand and Crowninshield, 1981; Brand, 1987; Baker, 2006]. To achieve these purposes, clinicians and researchers use measurement devices, like force platforms, stereophotogrammetric systems, accelerometers, baropodometric insoles, etc. This thesis focus on the force platform (FP) and in particular on the quality assessment of the FP data. The principal objective of our work was the design and the experimental validation of a portable system for the in situ calibration of FPs. The thesis is structured as follows: Chapter 1. Description of the physical principles used for the functioning of a FP: how these principles are used to create force transducers, such as strain gauges and piezoelectrics transducers. Then, description of the two category of FPs, three- and six-component, the signals acquisition (hardware structure), and the signals calibration. Finally, a brief description of the use of FPs in HMA, for balance or gait analysis. Chapter 2. Description of the inverse dynamics, the most common method used in the field of HMA. This method uses the signals measured by a FP to estimate kinetic quantities, such as joint forces and moments. The measures of these variables can not be taken directly, unless very invasive techniques; consequently these variables can only be estimated using indirect techniques, as the inverse dynamics. Finally, a brief description of the sources of error, present in the gait analysis. Chapter 3. State of the art in the FP calibration. The selected literature is divided in sections, each section describes: systems for the periodic control of the FP accuracy; systems for the error reduction in the FP signals; systems and procedures for the construction of a FP. In particular is detailed described a calibration system designed by our group, based on the theoretical method proposed by ?. This system was the “starting point” for the new system presented in this thesis. Chapter 4. Description of the new system, divided in its parts: 1) the algorithm; 2) the device; and 3) the calibration procedure, for the correct performing of the calibration process. The algorithm characteristics were optimized by a simulation approach, the results are here presented. In addiction, the different versions of the device are described. Chapter 5. Experimental validation of the new system, achieved by testing it on 4 commercial FPs. The effectiveness of the calibration was verified by measuring, before and after calibration, the accuracy of the FPs in measuring the center of pressure of an applied force. The new system can estimate local and global calibration matrices; by local and global calibration matrices, the non–linearity of the FPs was quantified and locally compensated. Further, a non–linear calibration is proposed. This calibration compensates the non– linear effect in the FP functioning, due to the bending of its upper plate. The experimental results are presented. Chapter 6. Influence of the FP calibration on the estimation of kinetic quantities, with the inverse dynamics approach. Chapter 7. The conclusions of this thesis are presented: need of a calibration of FPs and consequential enhancement in the kinetic data quality. Appendix: Calibration of the LC used in the presented system. Different calibration set–up of a 3D force transducer are presented, and is proposed the optimal set–up, with particular attention to the compensation of non–linearities. The optimal set–up is verified by experimental results.

Substructuring approache in state space models for dynamic system parameters identification

In the recent decade, the request for structural health monitoring expertise increased exponentially in the United States. The aging issues that most of the transportation structures are experiencing can put in serious jeopardy the economic system of a region as well as of a country. At the same time, the monitoring of structures is a central topic of discussion in Europe, where the preservation of historical buildings has been addressed over the last four centuries. More recently, various concerns arose about security performance of civil structures after tragic events such the 9/11 or the 2011 Japan earthquake: engineers looks for a design able to resist exceptional loadings due to earthquakes, hurricanes and terrorist attacks. After events of such a kind, the assessment of the remaining life of the structure is at least as important as the initial performance design. Consequently, it appears very clear that the introduction of reliable and accessible damage assessment techniques is crucial for the localization of issues and for a correct and immediate rehabilitation. The System Identification is a branch of the more general Control Theory. In Civil Engineering, this field addresses the techniques needed to find mechanical characteristics as the stiffness or the mass starting from the signals captured by sensors. The objective of the Dynamic Structural Identification (DSI) is to define, starting from experimental measurements, the modal fundamental parameters of a generic structure in order to characterize, via a mathematical model, the dynamic behavior. The knowledge of these parameters is helpful in the Model Updating procedure, that permits to define corrected theoretical models through experimental validation. The main aim of this technique is to minimize the differences between the theoretical model results and in situ measurements of dynamic data. Therefore, the new model becomes a very effective control practice when it comes to rehabilitation of structures or damage assessment. The instrumentation of a whole structure is an unfeasible procedure sometimes because of the high cost involved or, sometimes, because it’s not possible to physically reach each point of the structure. Therefore, numerous scholars have been trying to address this problem. In general two are the main involved methods. Since the limited number of sensors, in a first case, it’s possible to gather time histories only for some locations, then to move the instruments to another location and replay the procedure. Otherwise, if the number of sensors is enough and the structure does not present a complicate geometry, it’s usually sufficient to detect only the principal first modes. This two problems are well presented in the works of Balsamo [1] for the application to a simple system and Jun [2] for the analysis of system with a limited number of sensors. Once the system identification has been carried, it is possible to access the actual system characteristics. A frequent practice is to create an updated FEM model and assess whether the structure fulfills or not the requested functions. Once again the objective of this work is to present a general methodology to analyze big structure using a limited number of instrumentation and at the same time, obtaining the most information about an identified structure without recalling methodologies of difficult interpretation. A general framework of the state space identification procedure via OKID/ERA algorithm is developed and implemented in Matlab. Then, some simple examples are proposed to highlight the principal characteristics and advantage of this methodology. A new algebraic manipulation for a prolific use of substructuring results is developed and implemented.

Analisi sperimentale e modellazione della conducibilità termica in materiali per la protezione passiva da incendio esterno

Numerosi incidenti verificatisi negli ultimi dieci anni in campo chimico e petrolchimico sono dovuti all’innesco di sostanze infiammabili rilasciate accidentalmente: per questo motivo gli scenari incidentali legati ad incendi esterni rivestono oggigiorno un interesse crescente, in particolar modo nell’industria di processo, in quanto possono essere causa di ingenti danni sia ai lavoratori ed alla popolazione, sia alle strutture. Gli incendi, come mostrato da alcuni studi, sono uno dei più frequenti scenari incidentali nell’industria di processo, secondi solo alla perdita di contenimento di sostanze pericolose. Questi eventi primari possono, a loro volta, determinare eventi secondari, con conseguenze catastrofiche dovute alla propagazione delle fiamme ad apparecchiature e tubazioni non direttamente coinvolte nell’incidente primario; tale fenomeno prende il nome di effetto domino. La necessità di ridurre le probabilità di effetto domino rende la mitigazione delle conseguenze un aspetto fondamentale nella progettazione dell’impianto. A questo scopo si impiegano i materiali per la protezione passiva da fuoco (Passive Fire Protection o PFP); essi sono sistemi isolanti impiegati per proteggere efficacemente apparecchiature e tubazioni industriali da scenari di incendio esterno. L’applicazione dei materiali per PFP limita l’incremento di temperatura degli elementi protetti; questo scopo viene raggiunto tramite l’impiego di differenti tipologie di prodotti e materiali. Tuttavia l’applicazione dei suddetti materiali fireproofing non può prescindere da una caratterizzazione delle proprietà termiche, in particolar modo della conducibilità termica, in condizioni che simulino l’esposizione a fuoco. Nel presente elaborato di tesi si è scelto di analizzare tre materiali coibenti, tutti appartenenti, pur con diversità di composizione e struttura, alla classe dei materiali inorganici fibrosi: Fibercon Silica Needled Blanket 1200, Pyrogel®XT, Rockwool Marine Firebatt 100. I tre materiali sono costituiti da una fase solida inorganica, differente per ciascuno di essi e da una fase gassosa, preponderante come frazione volumetrica. I materiali inorganici fibrosi rivestono una notevole importanza rispetto ad altri materiali fireproofing in quanto possono resistere a temperature estremamente elevate, talvolta superiori a 1000 °C, senza particolari modifiche chimico-fisiche. Questo vantaggio, unito alla versatilità ed alla semplicità di applicazione, li rende leader a livello europeo nei materiali isolanti, con una fetta di mercato pari circa al 60%. Nonostante l’impiego dei suddetti materiali sia ormai una realtà consolidata nell’industria di processo, allo stato attuale sono disponibili pochi studi relativi alle loro proprietà termiche, in particolare in condizioni di fuoco. L’analisi sperimentale svolta ha consentito di identificare e modellare il comportamento termico di tali materiali in caso di esposizione a fuoco, impiegando nei test, a pressione atmosferica, un campo di temperatura compreso tra 20°C e 700°C, di interesse per applicazioni fireproofing. Per lo studio delle caratteristiche e la valutazione delle proprietà termiche dei tre materiali è stata impiegata principalmente la tecnica Transient Plane Source (TPS), che ha consentito la determinazione non solo della conducibilità termica, ma anche della diffusività termica e della capacità termica volumetrica, seppure con un grado di accuratezza inferiore. I test sono stati svolti su scala di laboratorio, creando un set-up sperimentale che integrasse opportunamente lo strumento Hot Disk Thermal Constants Analyzer TPS 1500 con una fornace a camera ed un sistema di acquisizione dati. Sono state realizzate alcune prove preliminari a temperatura ambiente sui tre materiali in esame, per individuare i parametri operativi (dimensione sensori, tempi di acquisizione, etc.) maggiormente idonei alla misura della conducibilità termica. Le informazioni acquisite sono state utilizzate per lo sviluppo di adeguati protocolli sperimentali e per effettuare prove ad alta temperatura. Ulteriori significative informazioni circa la morfologia, la porosità e la densità dei tre materiali sono state ottenute attraverso stereo-microscopia e picnometria a liquido. La porosità, o grado di vuoto, assume nei tre materiali un ruolo fondamentale, in quanto presenta valori compresi tra 85% e 95%, mentre la frazione solida ne costituisce la restante parte. Inoltre i risultati sperimentali hanno consentito di valutare, con prove a temperatura ambiente, l’isotropia rispetto alla trasmissione del calore per la classe di materiali coibenti analizzati, l’effetto della temperatura e della variazione del grado di vuoto (nel caso di materiali che durante l’applicazione possano essere soggetti a fenomeni di “schiacciamento”, ovvero riduzione del grado di vuoto) sulla conducibilità termica effettiva dei tre materiali analizzati. Analoghi risultati, seppure con grado di accuratezza lievemente inferiore, sono stati ottenuti per la diffusività termica e la capacità termica volumetrica. Poiché è nota la densità apparente di ciascun materiale si è scelto di calcolarne anche il calore specifico in funzione della temperatura, di cui si è proposto una correlazione empirica. I risultati sperimentali, concordi per i tre materiali in esame, hanno mostrato un incremento della conducibilità termica con la temperatura, da valori largamente inferiori a 0,1 W/(m∙K) a temperatura ambiente, fino a 0,3÷0,4 W/(m∙K) a 700°C. La sostanziale similitudine delle proprietà termiche tra i tre materiali, appartenenti alla medesima categoria di materiali isolanti, è stata riscontrata anche per la diffusività termica, la capacità termica volumetrica ed il calore specifico. Queste considerazioni hanno giustificato l’applicazione a tutti i tre materiali in esame dei medesimi modelli per descrivere la conducibilità termica effettiva, ritenuta, tra le proprietà fisiche determinate sperimentalmente, la più significativa nel caso di esposizione a fuoco. Lo sviluppo di un modello per la conducibilità termica effettiva si è reso necessario in quanto i risultati sperimentali ottenuti tramite la tecnica Transient Plane Source non forniscono alcuna informazione sui contributi offerti da ciascun meccanismo di scambio termico al termine complessivo e, pertanto, non consentono una facile generalizzazione della proprietà in funzione delle condizioni di impiego del materiale. La conducibilità termica dei materiali coibenti fibrosi e in generale dei materiali bi-fasici tiene infatti conto in un unico valore di vari contributi dipendenti dai diversi meccanismi di scambio termico presenti: conduzione nella fase gassosa e nel solido, irraggiamento nelle superfici delle cavità del solido e, talvolta, convezione; inoltre essa dipende fortemente dalla temperatura e dalla porosità. Pertanto, a partire dal confronto con i risultati sperimentali, tra cui densità e grado di vuoto, l’obiettivo centrale della seconda fase del progetto è stata la scelta, tra i numerosi modelli a disposizione in letteratura per materiali bi-fasici, di cui si è presentata una rassegna, dei più adatti a descrivere la conducibilità termica effettiva nei materiali in esame e nell’intervallo di temperatura di interesse, fornendo al contempo un significato fisico ai contributi apportati al termine complessivo. Inizialmente la scelta è ricaduta su cinque modelli, chiamati comunemente “modelli strutturali di base” (Serie, Parallelo, Maxwell-Eucken 1, Maxwell-Eucken 2, Effective Medium Theory) [1] per la loro semplicità e versatilità di applicazione. Tali modelli, puramente teorici, hanno mostrato al raffronto con i risultati sperimentali numerosi limiti, in particolar modo nella previsione del termine di irraggiamento, ovvero per temperature superiori a 400°C. Pertanto si è deciso di adottare un approccio semi-empirico: è stato applicato il modello di Krischer [2], ovvero una media pesata su un parametro empirico (f, da determinare) dei modelli Serie e Parallelo, precedentemente applicati. Anch’esso si è rivelato non idoneo alla descrizione dei materiali isolanti fibrosi in esame, per ragioni analoghe. Cercando di impiegare modelli caratterizzati da forte fondamento fisico e grado di complessità limitato, la scelta è caduta sui due recenti modelli, proposti rispettivamente da Karamanos, Papadopoulos, Anastasellos [3] e Daryabeigi, Cunnington, Knutson [4] [5]. Entrambi presentavano il vantaggio di essere stati utilizzati con successo per materiali isolanti fibrosi. Inizialmente i due modelli sono stati applicati con i valori dei parametri e le correlazioni proposte dagli Autori. Visti gli incoraggianti risultati, a questo primo approccio è seguita l’ottimizzazione dei parametri e l’applicazione di correlazioni maggiormente idonee ai materiali in esame, che ha mostrato l’efficacia dei modelli proposti da Karamanos, Papadopoulos, Anastasellos e Daryabeigi, Cunnington, Knutson per i tre materiali analizzati. Pertanto l’obiettivo finale del lavoro è stato raggiunto con successo in quanto sono stati applicati modelli di conducibilità termica con forte fondamento fisico e grado di complessità limitato che, con buon accordo ai risultati sperimentali ottenuti, consentono di ricavare equazioni predittive per la stima del comportamento, durante l’esposizione a fuoco, dei materiali fireproofing in esame. Bologna, Luglio 2013 Riferimenti bibliografici: [1] Wang J., Carson J.K., North M.F., Cleland D.J., A new approach to modelling the effective thermal conductivity of heterogeneous materials. International Journal of Heat and Mass Transfer 49 (2006) 3075-3083. [2] Krischer O., Die wissenschaftlichen Grundlagen der Trocknungstechnik (The Scientific Fundamentals of Drying Technology), Springer-Verlag, Berlino, 1963. [3] Karamanos A., Papadopoulos A., Anastasellos D., Heat Transfer phenomena in fibrous insulating materials. (2004) Geolan.gr http://www.geolan.gr/sappek/docs/publications/article_6.pdf Ultimo accesso: 1 Luglio 2013. [4] Daryabeigi K., Cunnington G. R., and Knutson J. R., Combined Heat Transfer in High-Porosity High-Temperature Fibrous Insulation: Theory and Experimental Validation. Journal of Thermophysics and Heat Transfer 25 (2011) 536-546. [5] Daryabeigi K., Cunnington G.R., Knutson J.R., Heat Transfer Modeling for Rigid High-Temperature Fibrous Insulation. Journal of Thermophysics and Heat Transfer. AIAA Early Edition/1 (2012).

Context-aware wireless networks

This thesis investigates context-aware wireless networks, capable to adapt their behavior to the context and the application, thanks to the ability of combining communication, sensing and localization. Problems of signals demodulation, parameters estimation and localization are addressed exploiting analytical methods, simulations and experimentation, for the derivation of the fundamental limits, the performance characterization of the proposed schemes and the experimental validation. Ultrawide-bandwidth (UWB) signals are in certain cases considered and non-coherent receivers, allowing the exploitation of the multipath channel diversity without adopting complex architectures, investigated. Closed-form expressions for the achievable bit error probability of novel proposed architectures are derived. The problem of time delay estimation (TDE), enabling network localization thanks to ranging measurement, is addressed from a theoretical point of view. New fundamental bounds on TDE are derived in the case the received signal is partially known or unknown at receiver side, as often occurs due to propagation or due to the adoption of low-complexity estimators. Practical estimators, such as energy-based estimators, are revised and their performance compared with the new bounds. The localization issue is addressed with experimentation for the characterization of cooperative networks. Practical algorithms able to improve the accuracy in non-line-of-sight (NLOS) channel conditions are evaluated on measured data. With the purpose of enhancing the localization coverage in NLOS conditions, non-regenerative relaying techniques for localization are introduced and ad hoc position estimators are devised. An example of context-aware network is given with the study of the UWB-RFID system for detecting and locating semi-passive tags. In particular a deep investigation involving low-complexity receivers capable to deal with problems of multi-tag interference, synchronization mismatches and clock drift is presented. Finally, theoretical bounds on the localization accuracy of this and others passive localization networks (e.g., radar) are derived, also accounting for different configurations such as in monostatic and multistatic networks.

The Dynamics of Passive Torsional Fatigue Test Rigs: Innovative Applications of Universal Joints

The dynamics of a passive back-to-back test rig have been characterised, leading to a multi-coordinate approach for the analysis of arbitrary test configurations. Universal joints have been introduced into a typical pre-loaded back-to-back system in order to produce an oscillating torsional moment in a test specimen. Two different arrangements have been investigated using a frequency-based sub-structuring approach: the receptance method. A numerical model has been developed in accordance with this theory, allowing interconnection of systems with two-coordinates and closed multi-loop schemes. The model calculates the receptance functions and modal and deflected shapes of a general system. Closed form expressions of the following individual elements have been developed: a servomotor, damped continuous shaft and a universal joint. Numerical results for specific cases have been compared with published data in literature and experimental measurements undertaken in the present work. Due to the complexity of the universal joint and its oscillating dynamic effects, a more detailed analysis of this component has been developed. Two models have been presented. The first represents the joint as two inertias connected by a massless cross-piece. The second, derived by the dynamic analysis of a spherical four-link mechanism, considers the contribution of the floating element and its gyroscopic effects. An investigation into non-linear behaviour has led to a time domain model that utilises the Runge-Kutta fourth order method for resolution of the dynamic equations. It has been demonstrated that the torsional receptances of a universal joint, derived using the simple model, result in representation of the joint as an equivalent variable inertia. In order to verify the model, a test rig has been built and experimental validation undertaken. The variable inertia of a universal joint has lead to a novel application of the component as a passive device for the balancing of inertia variations in slider-crank mechanisms.

Behaviour and applications of elastic waves in structures and metamaterials

The present thesis focuses on elastic waves behaviour in ordinary structures as well as in acousto-elastic metamaterials via numerical and experimental applications. After a brief introduction on the behaviour of elastic guided waves in the framework of non-destructive evaluation (NDE) and structural health monitoring (SHM) and on the study of elastic waves propagation in acousto-elastic metamaterials, dispersion curves for thin-walled beams and arbitrary cross-section waveguides are extracted via Semi-Analytical Finite Element (SAFE) methods. Thus, a novel strategy tackling signal dispersion to locate defects in irregular waveguides is proposed and numerically validated. Finally, a time-reversal and laser-vibrometry based procedure for impact location is numerically and experimentally tested. In the second part, an introduction and a brief review of the basic definitions necessary to describe acousto-elastic metamaterials is provided. A numerical approach to extract dispersion properties in such structures is highlighted. Afterwards, solid-solid and solid-fluid phononic systems are discussed via numerical applications. In particular, band structures and transmission power spectra are predicted for 1P-2D, 2P-2D and 2P-3D phononic systems. In addition, attenuation bands in the ultrasonic as well as in the sonic frequency regimes are experimentally investigated. In the experimental validation, PZTs in a pitch-catch configuration and laser vibrometric measurements are performed on a PVC phononic plate in the ultrasonic frequency range and sound insulation index is computed for a 2P-3D phononic barrier in the sonic frequency range. In both cases the numerical-experimental results comparison confirms the existence of the numerical predicted band-gaps. Finally, the feasibility of an innovative passive isolation strategy based on giant elastic metamaterials is numerically proved to be practical for civil structures. In particular, attenuation of seismic waves is demonstrated via finite elements analyses. Further, a parametric study shows that depending on the soil properties, such an earthquake-proof barrier could lead to significant reduction of the superstructure displacement.

Feedback linearization of antagonistically actuated variable stiffness joints with twisted string actuators

The work of this thesis is on the implementation of a variable stiffness joint antagonistically actuated by a couple of twisted-string actuator (TSA). This type of joint is possible to be applied in the field of robotics, like UB Hand IV (the anthropomorphic robotic hand developed by University of Bologna). The purposes of the activities are to build the joint dynamic model and simultaneously control the position and stiffness. Three different control approaches (Feedback linearization, PID, PID+Feedforward) are proposed and validated in simulation. To improve the properties of joint stiffness, a joint with elastic element is taken into account and discussed. To the end, the experimental setup that has been developed for the experimental validation of the proposed control approaches.

Diffusion-driven transport in clayrock formations

Clay mineral-rich sedimentary formations are currently under investigation to evaluate their potential use as host formations for installation of deep underground disposal facilities for radioactive waste (e.g. Boom Clay (BE), Opalinus Clay (CH), Callovo-Oxfordian argillite (FR)). The ultimate safety of the corresponding repository concepts depends largely on the capacity of the host formation to limit the flux towards the biosphere of radionuclides (RN) contained in the waste to acceptably low levels. Data for diffusion-driven transfer in these formations shows extreme differences in the measured or modelled behaviour for various radionuclides, e. g. between halogen RN (Cl-36, I-129) and actinides (U-238,U-235, Np-237, Th-232, etc.), which result from major differences between RN of the effects on transport of two phenomena: diffusion and sorption. This paper describes recent research aimed at improving understanding of these two phenomena, focusing on the results of studies carried out during the EC Funmig IP on clayrocks from the above three formations and from the Boda formation (HU). Project results regarding phenomena governing water, cation and anion distribution and mobility in the pore volumes influenced by the negatively-charged surfaces of clay minerals show a convergence of the modelling results for behaviour at the molecular scale and descriptions based on electrical double layer models. Transport models exist which couple ion distribution relative to the clay-solution interface and differentiated diffusive characteristics. These codes are able to reproduce the main trends in behaviour observed experimentally, e.g. D-e(anion) < D-e(HTO) < D-e(cation) and D-e(anion) variations as a function of ionic strength and material density. These trends are also well-explained by models of transport through ideal porous matrices made up of a charged surface material. Experimental validation of these models is good as regards monovalent alkaline cations, in progress for divalent electrostatically-interacting cations (e.g. Sr2+) and still relatively poor for 'strongly sorbing', high K-d cations. Funmig results have clarified understanding of how clayrock mineral composition, and the corresponding organisation of mineral grain assemblages and their associated porosity, can affect mobile solute (anions, HTO) diffusion at different scales (mm to geological formation). In particular, advances made in the capacity to map clayrock mineral grain-porosity organisation at high resolution provide additional elements for understanding diffusion anisotropy and for relating diffusion characteristics measured at different scales. On the other hand, the results of studies focusing on evaluating the potential effects of heterogeneity on mobile species diffusion at the formation scale tend to show that there is a minimal effect when compared to a homogeneous property model. Finally, the results of a natural tracer-based study carried out on the Opalinus Clay formation increase confidence in the use of diffusion parameters measured on laboratory scale samples for predicting diffusion over geological time-space scales. Much effort was placed on improving understanding of coupled sorption-diffusion phenomena for sorbing cations in clayrocks. Results regarding sorption equilibrium in dispersed and compacted materials for weakly to moderately sorbing cations (Sr2+, Cs+, Co2+) tend to show that the same sorption model probably holds in both systems. It was not possible to demonstrate this for highly sorbing elements such as Eu(III) because of the extremely long times needed to reach equilibrium conditions, but there does not seem to be any clear reason why such elements should not have similar behaviour. Diffusion experiments carried out with Sr2+, Cs+ and Eu(III) on all of the clayrocks gave mixed results and tend to show that coupled diffusion-sorption migration is much more complex than expected, leading generally to greater mobility than that predicted by coupling a batch-determined K-d and Ficks law based on the diffusion behaviour of HTO. If the K-d measured on equivalent dispersed systems holds as was shown to be the case for Sr, Cs (and probably Co) for Opalinus Clay, these results indicate that these cations have a D-e value higher than HTO (up to a factor of 10 for Cs+). Results are as yet very limited for very moderate to strongly sorbing species (e.g. Co(II), Eu(III), Cu(II)) because of their very slow transfer characteristics. (C) 2011 Elsevier Ltd. All rights reserved.

MODEL UPDATING AND STRUCTURAL HEALTH MONITORING OF HORIZONTAL AXIS WIND TURBINES VIA ADVANCED SPINNING FINITE ELEMENTS AND STOCHASTIC SUBSPACE IDENTIFICATION METHODS

Wind energy has been one of the most growing sectors of the nation’s renewable energy portfolio for the past decade, and the same tendency is being projected for the upcoming years given the aggressive governmental policies for the reduction of fossil fuel dependency. Great technological expectation and outstanding commercial penetration has shown the so called Horizontal Axis Wind Turbines (HAWT) technologies. Given its great acceptance, size evolution of wind turbines over time has increased exponentially. However, safety and economical concerns have emerged as a result of the newly design tendencies for massive scale wind turbine structures presenting high slenderness ratios and complex shapes, typically located in remote areas (e.g. offshore wind farms). In this regard, safety operation requires not only having first-hand information regarding actual structural dynamic conditions under aerodynamic action, but also a deep understanding of the environmental factors in which these multibody rotating structures operate. Given the cyclo-stochastic patterns of the wind loading exerting pressure on a HAWT, a probabilistic framework is appropriate to characterize the risk of failure in terms of resistance and serviceability conditions, at any given time. Furthermore, sources of uncertainty such as material imperfections, buffeting and flutter, aeroelastic damping, gyroscopic effects, turbulence, among others, have pleaded for the use of a more sophisticated mathematical framework that could properly handle all these sources of indetermination. The attainable modeling complexity that arises as a result of these characterizations demands a data-driven experimental validation methodology to calibrate and corroborate the model. For this aim, System Identification (SI) techniques offer a spectrum of well-established numerical methods appropriated for stationary, deterministic, and data-driven numerical schemes, capable of predicting actual dynamic states (eigenrealizations) of traditional time-invariant dynamic systems. As a consequence, it is proposed a modified data-driven SI metric based on the so called Subspace Realization Theory, now adapted for stochastic non-stationary and timevarying systems, as is the case of HAWT’s complex aerodynamics. Simultaneously, this investigation explores the characterization of the turbine loading and response envelopes for critical failure modes of the structural components the wind turbine is made of. In the long run, both aerodynamic framework (theoretical model) and system identification (experimental model) will be merged in a numerical engine formulated as a search algorithm for model updating, also known as Adaptive Simulated Annealing (ASA) process. This iterative engine is based on a set of function minimizations computed by a metric called Modal Assurance Criterion (MAC). In summary, the Thesis is composed of four major parts: (1) development of an analytical aerodynamic framework that predicts interacted wind-structure stochastic loads on wind turbine components; (2) development of a novel tapered-swept-corved Spinning Finite Element (SFE) that includes dampedgyroscopic effects and axial-flexural-torsional coupling; (3) a novel data-driven structural health monitoring (SHM) algorithm via stochastic subspace identification methods; and (4) a numerical search (optimization) engine based on ASA and MAC capable of updating the SFE aerodynamic model.

The transcriptome of equine peripheral blood mononuclear cells.

Complete transcriptomic data at high resolution are available only for a few model organisms with medical importance. The gene structures of non-model organisms are mostly computationally predicted based on comparative genomics with other species. As a result, more than half of the horse gene models are known only by projection. Experimental data supporting these gene models are scarce. Moreover, most of the annotated equine genes are single-transcript genes. Utilizing RNA sequencing (RNA-seq) the experimental validation of predicted transcriptomes has become accessible at reasonable costs. To improve the horse genome annotation we performed RNA-seq on 561 samples of peripheral blood mononuclear cells (PBMCs) derived from 85 Warmblood horses. The mapped sequencing reads were used to build a new transcriptome assembly. The new assembly revealed many alternative isoforms associated to known genes or to those predicted by the Ensembl and/or Gnomon pipelines. We also identified 7,531 transcripts not associated with any horse gene annotated in public databases. Of these, 3,280 transcripts did not have a homologous match to any sequence deposited in the NCBI EST database suggesting horse specificity. The unknown transcripts were categorized as coding and noncoding based on predicted coding potential scores. Among them 230 transcripts had high coding potential score, at least 2 exons, and an open reading frame of at least 300 nt. We experimentally validated 9 new equine coding transcripts using RT-PCR and Sanger sequencing. Our results provide valuable detailed information on many transcripts yet to be annotated in the horse genome.

Systems Biology Approaches to Probe Gene Regulation in Bacteria

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb). First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses and survive within resting macrophages. As a result, the method unveiled transcriptional regulators and associated regulons utilized by Mtb to establish a successful infection of macrophages throughout the first 14 days of infection. Additionally, this network-based analysis identified the production of Fe-S proteins coupled to lipid metabolism through the alkane hydroxylase complex as a possible strategy employed by Mtb to survive in the host. Second, I developed a network inference method to infer the small non-coding RNA (sRNA) regulatory network in Mtb. The method identifies sRNA-mRNA interactions by integrating a priori knowledge of possible binding sites with structure-driven identification of binding sites. The reconstructed network was useful to predict functional roles for the multitude of sRNAs recently discovered in the pathogen, being that several sRNAs were postulated to be involved in virulence-related processes. Finally, I applied a combined experimental and computational approach to study post-transcriptional repression mediated by small non-coding RNAs in bacteria. Specifically, a probabilistic ranking methodology termed rank-conciliation was developed to infer sRNA-mRNA interactions based on multiple types of data. The method was shown to improve target prediction in Escherichia coli, and therefore is useful to prioritize candidate targets for experimental validation.

Testing a Cloud Provider Network for Hybrid P2P and Cloud Streaming Architectures

The number of online real-time streaming services deployed over network topologies like P2P or centralized ones has remarkably increased in the recent years. This has revealed the lack of networks that are well prepared to respond to this kind of traffic. A hybrid distribution network can be an efficient solution for real-time streaming services. This paper contains the experimental results of streaming distribution in a hybrid architecture that consist of mixed connections among P2P and Cloud nodes that can interoperate together. We have chosen to represent the P2P nodes as Planet Lab machines over the world and the cloud nodes using a Cloud provider's network. First we present an experimental validation of the Cloud infrastructure's ability to distribute streaming sessions with respect to some key streaming QoS parameters: jitter, throughput and packet losses. Next we show the results obtained from different test scenarios, when a hybrid distribution network is used. The scenarios measure the improvement of the multimedia QoS parameters, when nodes in the streaming distribution network (located in different continents) are gradually moved into the Cloud provider infrastructure. The overall conclusion is that the QoS of a streaming service can be efficiently improved, unlike in traditional P2P systems and CDN, by deploying a hybrid streaming architecture. This enhancement can be obtained by strategic placing of certain distribution network nodes into the Cloud provider infrastructure, taking advantage of the reduced packet loss and low latency that exists among its datacenters.