Micro Data Repositories: Increasing the Value of Research on the Web

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

ReShare and ReCollect: EPrints data repository solutions developed at the UK Data Archive

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Stiffness based trajectory planning and feedforward based vibration suppression control of parallel robot machines

The dissertation proposes two control strategies, which include the trajectory planning and vibration suppression, for a kinematic redundant serial-parallel robot machine, with the aim of attaining the satisfactory machining performance. For a given prescribed trajectory of the robot's end-effector in the Cartesian space, a set of trajectories in the robot's joint space are generated based on the best stiffness performance of the robot along the prescribed trajectory. To construct the required system-wide analytical stiffness model for the serial-parallel robot machine, a variant of the virtual joint method (VJM) is proposed in the dissertation. The modified method is an evolution of Gosselin's lumped model that can account for the deformations of a flexible link in more directions. The effectiveness of this VJM variant is validated by comparing the computed stiffness results of a flexible link with the those of a matrix structural analysis (MSA) method. The comparison shows that the numerical results from both methods on an individual flexible beam are almost identical, which, in some sense, provides mutual validation. The most prominent advantage of the presented VJM variant compared with the MSA method is that it can be applied in a flexible structure system with complicated kinematics formed in terms of flexible serial links and joints. Moreover, by combining the VJM variant and the virtual work principle, a systemwide analytical stiffness model can be easily obtained for mechanisms with both serial kinematics and parallel kinematics. In the dissertation, a system-wide stiffness model of a kinematic redundant serial-parallel robot machine is constructed based on integration of the VJM variant and the virtual work principle. Numerical results of its stiffness performance are reported. For a kinematic redundant robot, to generate a set of feasible joints' trajectories for a prescribed trajectory of its end-effector, its system-wide stiffness performance is taken as the constraint in the joints trajectory planning in the dissertation. For a prescribed location of the end-effector, the robot permits an infinite number of inverse solutions, which consequently yields infinite kinds of stiffness performance. Therefore, a differential evolution (DE) algorithm in which the positions of redundant joints in the kinematics are taken as input variables was employed to search for the best stiffness performance of the robot. Numerical results of the generated joint trajectories are given for a kinematic redundant serial-parallel robot machine, IWR (Intersector Welding/Cutting Robot), when a particular trajectory of its end-effector has been prescribed. The numerical results show that the joint trajectories generated based on the stiffness optimization are feasible for realization in the control system since they are acceptably smooth. The results imply that the stiffness performance of the robot machine deviates smoothly with respect to the kinematic configuration in the adjacent domain of its best stiffness performance. To suppress the vibration of the robot machine due to varying cutting force during the machining process, this dissertation proposed a feedforward control strategy, which is constructed based on the derived inverse dynamics model of target system. The effectiveness of applying such a feedforward control in the vibration suppression has been validated in a parallel manipulator in the software environment. The experimental study of such a feedforward control has also been included in the dissertation. The difficulties of modelling the actual system due to the unknown components in its dynamics is noticed. As a solution, a back propagation (BP) neural network is proposed for identification of the unknown components of the dynamics model of the target system. To train such a BP neural network, a modified Levenberg-Marquardt algorithm that can utilize an experimental input-output data set of the entire dynamic system is introduced in the dissertation. Validation of the BP neural network and the modified Levenberg- Marquardt algorithm is done, respectively, by a sinusoidal output approximation, a second order system parameters estimation, and a friction model estimation of a parallel manipulator, which represent three different application aspects of this method.

On Distributed Storage Codes

Distributed storage systems are studied. The interest in such system has become relatively wide due to the increasing amount of information needed to be stored in data centers or different kinds of cloud systems. There are many kinds of solutions for storing the information into distributed devices regarding the needs of the system designer. This thesis studies the questions of designing such storage systems and also fundamental limits of such systems. Namely, the subjects of interest of this thesis include heterogeneous distributed storage systems, distributed storage systems with the exact repair property, and locally repairable codes. For distributed storage systems with either functional or exact repair, capacity results are proved. In the case of locally repairable codes, the minimum distance is studied. Constructions for exact-repairing codes between minimum bandwidth regeneration (MBR) and minimum storage regeneration (MSR) points are given. These codes exceed the time-sharing line of the extremal points in many cases. Other properties of exact-regenerating codes are also studied. For the heterogeneous setup, the main result is that the capacity of such systems is always smaller than or equal to the capacity of a homogeneous system with symmetric repair with average node size and average repair bandwidth. A randomized construction for a locally repairable code with good minimum distance is given. It is shown that a random linear code of certain natural type has a good minimum distance with high probability. Other properties of locally repairable codes are also studied.

Local Binary Patterns in Focal-Plane Processing. Analysis and Applications

Feature extraction is the part of pattern recognition, where the sensor data is transformed into a more suitable form for the machine to interpret. The purpose of this step is also to reduce the amount of information passed to the next stages of the system, and to preserve the essential information in the view of discriminating the data into different classes. For instance, in the case of image analysis the actual image intensities are vulnerable to various environmental effects, such as lighting changes and the feature extraction can be used as means for detecting features, which are invariant to certain types of illumination changes. Finally, classification tries to make decisions based on the previously transformed data. The main focus of this thesis is on developing new methods for the embedded feature extraction based on local non-parametric image descriptors. Also, feature analysis is carried out for the selected image features. Low-level Local Binary Pattern (LBP) based features are in a main role in the analysis. In the embedded domain, the pattern recognition system must usually meet strict performance constraints, such as high speed, compact size and low power consumption. The characteristics of the final system can be seen as a trade-off between these metrics, which is largely affected by the decisions made during the implementation phase. The implementation alternatives of the LBP based feature extraction are explored in the embedded domain in the context of focal-plane vision processors. In particular, the thesis demonstrates the LBP extraction with MIPA4k massively parallel focal-plane processor IC. Also higher level processing is incorporated to this framework, by means of a framework for implementing a single chip face recognition system. Furthermore, a new method for determining optical flow based on LBPs, designed in particular to the embedded domain is presented. Inspired by some of the principles observed through the feature analysis of the Local Binary Patterns, an extension to the well known non-parametric rank transform is proposed, and its performance is evaluated in face recognition experiments with a standard dataset. Finally, an a priori model where the LBPs are seen as combinations of n-tuples is also presented

Effects of heat treatment and storage temperature on the use of açaí drink by nutraceutical and beverage industries

This study assesses the storage temperature effect on the anthocyanins of pasteurized and unpasteurized açaí pulp. The data was obtained using a pasteurized and lyophilized pulp (PLP) to evaluate the temperature effect (0, 25, and 40 °C). Part of non-pasteurized frozen pulp (NPP) was pasteurized (NPP-P) at 90 °C for 30 seconds; both pulps were stored at 40 °C. The anthocyanin content reduction in the drink was evaluated from the half-life time (t1/2), activation energy (Ea), temperature quotient (Q10), and the reaction rate constant (k). The t1/2 of the PLP anthocyanins stored at 40 °C was 1.8 times less than that stored at 25 °C and 15 times less than that stored at 0 °C; therefore, the higher temperatures decreased the stability of anthocyanins. The pasteurization increased the t1/2 by 6.6 times (10.14 hours for NPP and 67.28 hours for NPP-P). The anthocyanin degradation on NPP-P followed a first order kinetic, while NPP followed a second order kinetic; thus it can be said that the pasteurization process can improve the preservation of anthocyanins in the pulp.

Volatile profile and physical, chemical, and biochemical changes in fresh cut watermelon during storage

Existing data about the aroma of fresh-cut watermelon and the metabolic changes that occur with minimal processing are scarce. Given the close relationship that exists between aroma, texture, and quality characteristics, it is necessary to investigate the changes in the volatile profile and texture of watermelon, a fruit extensively sold in supermarket chains throughout Brazil. The objective of this work was to analyze the volatile profile using solid phase microextraction (SPME) as well as texture changes in fresh-cut watermelon stored at 5 °C for ten days. Chromatography associated with sensory analysis (sniffing) led us to conclude that 9-carbon (C9) alcohols and aldehydes are the major responsible for the flavor and aroma of minimally processed watermelon stored at 5 ± 1 °C/90 ± 5% RH for ten days, and also that the aroma diminishes in intensity with storage, but it does not affect the final quality of the product. It was noted that the amount of drained liquid, soluble pectin, and weight loss increased during storage concurrently with a reduction in firmness and a structural breakdown of the cells. Pectin methyl esterase activity remained constant and polygalacturonase activity was not detected.

Exogenous abscisic acid inhibits the water-loss of postharvest romaine lettuce during storage by inducing stomatal closure

Abstract Postharvest lettuce often lose water, thus affecting both its market value and consumer acceptance. However, the mechanism of the water-loss is still waiting well exploration. The aim of the present study was to investigate the effect of a foliar application of ABA on the fresh weight-loss and the chlorophyll content of postharvest lettuce as well as its association with the regulation of stomata. The present data demonstrated that exogenously application of ABA, in a concentration range of 0 to 100 µM, significantly lowered the fresh weight-loss of postharvest lettuce. ABA also delayed chlorophyll reduction during ambient storage, but this protective effect was ABA concentration-dependent. Among the tested ABA concentrations, 50 µM or lower ABA produced an inhibition effect on chlorophyll degradation in postharvest lettuce leaves. The results demonstrated that the exogenous ABA treatment can obviously reduce the transpiration rate of lettuce leaves by promoting the stomatal closure of postharvest lettuce, therefore eventually delay fresh weight-loss. The present study primarily showed that the application of exogenous ABA, which originated from a naturally-produced phytohormone, has a great potential in retaining the freshness of postharvest lettuce that is stored in an ambient condition, although possible practical application still need to be further evaluated.

Optical and photoelectric properties of dry bacteriorhodopsin sensors

In this thesis, bacteriorhodopsin (BR) photosensor’s optical and electrical properties were studied. The BR sensor consisted of a dry film with BR in polyvinyl alcohol and covered with transparent conductors. In the experiments the BR photocycle was started with two lasers. The characteristics of the BR sensor were measured in two ways. The first approach was theoretical and it required knowing the laser parameters. The second way required assembling a measurement setup for the optical response measurements. However, no measurable results were obtained due to low laser power. The photoelectric response was measured in the experiments with two laser systems and the amplifier was tested. In the experiment with a Cavitar laser, the photoelectric response was obtained. In the experiment with FemtoFiber Pro laser, the photoelectric response was not measured. The expected amplitude of the response was obtained. The experimental data was analyzed and possible solutions for reducing the interference were given.

Performance Degradation Modelling and Techno-Economic Analysis of Lithium-Ion Battery Energy Storage Systems

Transmission system operators and distribution system operators are experiencing new challenges in terms of reliability, power quality, and cost efficiency. Although the potential of energy storages to face those challenges is recognized, the economic implications are still obscure, which introduce the risk into the business models. This thesis aims to investigate the technical and economic value indicators of lithium-ion battery energy storage systems (BESS) in grid-scale applications. In order to do that, a comprehensive performance lithium-ion BESS model with degradation effects estimation is developed. The model development process implies literature review on lifetime modelling, use, and modification of previous study progress, building the additional system parts and integrating it into a complete tool. The constructed model is capable of describing the dynamic behavior of the BESS voltage, state of charge, temperature and capacity loss. Five control strategies for BESS unit providing primary frequency regulation are implemented, in addition to the model. The questions related to BESS dimensioning and the end of life (EoL) criterion are addressed. Simulations are performed with one-month real frequency data acquired from Fingrid. The lifetime and cost-benefit analysis of the simulation results allow to compare and determine the preferable control strategy. Finally, the study performs the sensitivity analysis of economic profitability with variable size, EoL and system price. The research reports that BESS can be profitable in certain cases and presents the recommendations.

Optical properties of organic superconductor K-(BETS)2FeBr4 /

K-(BETS)2FeBr4 is a quasi-2D charge transfer organic metal with interesting electronic and magnetic properties. It undergoes a transition to an antiferromagnetic (AF) state at ambient pressure at the Neel temperature (T^^) = 2.5 K, as well as to a superconducting (SC) state at 1.1 K [1]. The temperature dependence of the electrical resistivity shows a small decrease at T;v indicating the resistivity drops as a result of the onset of the ordering of Fe'*''" spins. A sharp drop in the resistivity at 1.1 K is due to its superconducting transition. The temperature dependence of the susceptibility indicates an antiferromagnetic spin structure with the easy axis parallel to the a-axis. The specific heat at zero-field shows a large peak at about 2.4 K, which corresponds to the antiferromagnetic transition temperature (Tat) and no anomaly is observed around the superconducting transition temperature (1.1 K) demonstrating that the magnetically ordered state is not destroyed by the appearance of another phase transition (the superconducting transition) in the 7r-electron layers [1], [2]. This work presents an investigation of how the low frequency electromagnetic response is affected by the antiferromagnetic and superconducting states, as well as the onset of strong correlation. The location of the easy axis of three samples was determined and polarized thermal reflectance measurements of these «-(BETS)2FeBr4 samples oriented with their vertical axis along the a- and c axes were then carried out using a *He refrigerator cryostat and a Martin-Puplett type polarizing interferometer at various temperatures (T = 0.5 K, 1.4 K. 1.9 K, 2.8 K) above and below the superconducting state and/or antiferromagnetic state. Comparison of the SC state to the normal state along the o- and c-axes indicates a rising thermal reflectance at low frequencies (below 10 cm"' ) which may be a manifestation of the superconducting energy gap. A dip-Hke feature is detected at low frequencies (below 15 cm"') in the thermal reflectance plots which probe the antiferromagnetic state along the two axes, and may be due to the opening of a gap in the excitation spectrum as a result of the antiferromagnetism. In another set of experiments, thermal reflectance measurements carried out along the a- and c-axes at higher temperatures (10 K-80 K) show that the reflectivity decreases with increasing temperature to 60 K (the coherence temperature) above which it increases again. Comparison of the thermal reflectance plots along the a- and c-axes at higher temperatures reveals an anisotropy between these two axes. The Hagen-Rubens thermal reflectance plots corresponding to an average over the ac-plane were calculated using experimental hterature resistivity values. Comparison of the Hagen-Rubens plots with the experimental thermal reflectance along the a- and c-axes indicates that both exhibit the general trend of a decrease in thermal reflectance with increasing frequency, however the calculated Hagen-Rubens thermal reflectance at different temperatures is much lower than the experimental curves.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Optimization of p-cycle protection schemes in optical networks

La survie des réseaux est un domaine d'étude technique très intéressant ainsi qu'une préoccupation critique dans la conception des réseaux. Compte tenu du fait que de plus en plus de données sont transportées à travers des réseaux de communication, une simple panne peut interrompre des millions d'utilisateurs et engendrer des millions de dollars de pertes de revenu. Les techniques de protection des réseaux consistent à fournir une capacité supplémentaire dans un réseau et à réacheminer les flux automatiquement autour de la panne en utilisant cette disponibilité de capacité. Cette thèse porte sur la conception de réseaux optiques intégrant des techniques de survie qui utilisent des schémas de protection basés sur les p-cycles. Plus précisément, les p-cycles de protection par chemin sont exploités dans le contexte de pannes sur les liens. Notre étude se concentre sur la mise en place de structures de protection par p-cycles, et ce, en supposant que les chemins d'opération pour l'ensemble des requêtes sont définis a priori. La majorité des travaux existants utilisent des heuristiques ou des méthodes de résolution ayant de la difficulté à résoudre des instances de grande taille. L'objectif de cette thèse est double. D'une part, nous proposons des modèles et des méthodes de résolution capables d'aborder des problèmes de plus grande taille que ceux déjà présentés dans la littérature. D'autre part, grâce aux nouveaux algorithmes, nous sommes en mesure de produire des solutions optimales ou quasi-optimales. Pour ce faire, nous nous appuyons sur la technique de génération de colonnes, celle-ci étant adéquate pour résoudre des problèmes de programmation linéaire de grande taille. Dans ce projet, la génération de colonnes est utilisée comme une façon intelligente d'énumérer implicitement des cycles prometteurs. Nous proposons d'abord des formulations pour le problème maître et le problème auxiliaire ainsi qu'un premier algorithme de génération de colonnes pour la conception de réseaux protegées par des p-cycles de la protection par chemin. L'algorithme obtient de meilleures solutions, dans un temps raisonnable, que celles obtenues par les méthodes existantes. Par la suite, une formulation plus compacte est proposée pour le problème auxiliaire. De plus, nous présentons une nouvelle méthode de décomposition hiérarchique qui apporte une grande amélioration de l'efficacité globale de l'algorithme. En ce qui concerne les solutions en nombres entiers, nous proposons deux méthodes heurisiques qui arrivent à trouver des bonnes solutions. Nous nous attardons aussi à une comparaison systématique entre les p-cycles et les schémas classiques de protection partagée. Nous effectuons donc une comparaison précise en utilisant des formulations unifiées et basées sur la génération de colonnes pour obtenir des résultats de bonne qualité. Par la suite, nous évaluons empiriquement les versions orientée et non-orientée des p-cycles pour la protection par lien ainsi que pour la protection par chemin, dans des scénarios de trafic asymétrique. Nous montrons quel est le coût de protection additionnel engendré lorsque des systèmes bidirectionnels sont employés dans de tels scénarios. Finalement, nous étudions une formulation de génération de colonnes pour la conception de réseaux avec des p-cycles en présence d'exigences de disponibilité et nous obtenons des premières bornes inférieures pour ce problème.

Intra- and inter-hemispheric interactions in somatosensory processing of pain : dynamical causal modeling analysis of fMRI data

La douleur est une expérience perceptive comportant de nombreuses dimensions. Ces dimensions de douleur sont inter-reliées et recrutent des réseaux neuronaux qui traitent les informations correspondantes. L’élucidation de l'architecture fonctionnelle qui supporte les différents aspects perceptifs de l'expérience est donc une étape fondamentale pour notre compréhension du rôle fonctionnel des différentes régions de la matrice cérébrale de la douleur dans les circuits corticaux qui sous tendent l'expérience subjective de la douleur. Parmi les diverses régions du cerveau impliquées dans le traitement de l'information nociceptive, le cortex somatosensoriel primaire et secondaire (S1 et S2) sont les principales régions généralement associées au traitement de l'aspect sensori-discriminatif de la douleur. Toutefois, l'organisation fonctionnelle dans ces régions somato-sensorielles n’est pas complètement claire et relativement peu d'études ont examiné directement l'intégration de l'information entre les régions somatiques sensorielles. Ainsi, plusieurs questions demeurent concernant la relation hiérarchique entre S1 et S2, ainsi que le rôle fonctionnel des connexions inter-hémisphériques des régions somatiques sensorielles homologues. De même, le traitement en série ou en parallèle au sein du système somatosensoriel constitue un autre élément de questionnement qui nécessite un examen plus approfondi. Le but de la présente étude était de tester un certain nombre d'hypothèses sur la causalité dans les interactions fonctionnelle entre S1 et S2, alors que les sujets recevaient des chocs électriques douloureux. Nous avons mis en place une méthode de modélisation de la connectivité, qui utilise une description de causalité de la dynamique du système, afin d'étudier les interactions entre les sites d'activation définie par un ensemble de données provenant d'une étude d'imagerie fonctionnelle. Notre paradigme est constitué de 3 session expérimentales en utilisant des chocs électriques à trois différents niveaux d’intensité, soit modérément douloureux (niveau 3), soit légèrement douloureux (niveau 2), soit complètement non douloureux (niveau 1). Par conséquent, notre paradigme nous a permis d'étudier comment l'intensité du stimulus est codé dans notre réseau d'intérêt, et comment la connectivité des différentes régions est modulée dans les conditions de stimulation différentes. Nos résultats sont en faveur du mode sériel de traitement de l’information somatosensorielle nociceptive avec un apport prédominant de la voie thalamocorticale vers S1 controlatérale au site de stimulation. Nos résultats impliquent que l'information se propage de S1 controlatéral à travers notre réseau d'intérêt composé des cortex S1 bilatéraux et S2. Notre analyse indique que la connexion S1→S2 est renforcée par la douleur, ce qui suggère que S2 est plus élevé dans la hiérarchie du traitement de la douleur que S1, conformément aux conclusions précédentes neurophysiologiques et de magnétoencéphalographie. Enfin, notre analyse fournit des preuves de l'entrée de l'information somatosensorielle dans l'hémisphère controlatéral au côté de stimulation, avec des connexions inter-hémisphériques responsable du transfert de l'information à l'hémisphère ipsilatéral.

Electro-Optical Properties of Metal Phthalocyanines and Naphthalocyanines

The thesis deals with the preparation of chemical, optical, thermal and electrical characterization of five compounds, namely metal free naphthalocyanine, vanadyl napthalocyanine, zinc naphlocyanine, europium dinaphthalocyanine, and europium diphthalocyanine in the pristine and iodine-doped forms. Two important technological properties of these compounds have been investigated. The electrical properties are important in applications sensors and semiconductor lasers. Opto-thermal properties assume significance for optical imaging and data recording. The electrical properties were investigated by dc and ac techniques. This work has revealed some novel information on the conduction mechanism in five macrocyclic compounds and their iodine-doped forms. Also useful data on the thermal diffusivity of the target compounds have been obtained by optical techniques.