Contribution towards intelligent service management in wearable and ubiquitous devices

Hoy en día asistimos a un creciente interés por parte de la sociedad hacia el cuidado de la salud. Esta afirmación viene apoyada por dos realidades. Por una parte, el aumento de las prácticas saludables (actividad deportiva, cuidado de la alimentación, etc.). De igual manera, el auge de los dispositivos inteligentes (relojes, móviles o pulseras) capaces de medir distintos parámetros físicos como el pulso cardíaco, el ritmo respiratorio, la distancia recorrida, las calorías consumidas, etc. Combinando ambos factores (interés por el estado de salud y disponibilidad comercial de dispositivos inteligentes) están surgiendo multitud de aplicaciones capaces no solo de controlar el estado actual de salud, también de recomendar al usuario cambios de hábitos que lleven hacia una mejora en su condición física. En este contexto, los llamados dispositivos llevables (weareables) unidos al paradigma de Internet de las cosas (IoT, del inglés Internet of Things) permiten la aparición de nuevos nichos de mercado para aplicaciones que no solo se centran en la mejora de la condición física, ya que van más allá proponiendo soluciones para el cuidado de pacientes enfermos, la vigilancia de niños o ancianos, la defensa y la seguridad, la monitorización de agentes de riesgo (como bomberos o policías) y un largo etcétera de aplicaciones por llegar. El paradigma de IoT se puede desarrollar basándose en las existentes redes de sensores inalámbricos (WSN, del inglés Wireless Sensor Network). La conexión de los ya mencionados dispositivos llevables a estas redes puede facilitar la transición de nuevos usuarios hacia aplicaciones IoT. Pero uno de los problemas intrínsecos a estas redes es su heterogeneidad. En efecto, existen multitud de sistemas operativos, protocolos de comunicación, plataformas de desarrollo, soluciones propietarias, etc. El principal objetivo de esta tesis es realizar aportaciones significativas para solucionar no solo el problema de la heterogeneidad, sino también de dotar de mecanismos de seguridad suficientes para salvaguardad la integridad de los datos intercambiados en este tipo de aplicaciones. Algo de suma importancia ya que los datos médicos y biométricos de los usuarios están protegidos por leyes nacionales y comunitarias. Para lograr dichos objetivos, se comenzó con la realización de un completo estudio del estado del arte en tecnologías relacionadas con el marco de investigación (plataformas y estándares para WSNs e IoT, plataformas de implementación distribuidas, dispositivos llevables y sistemas operativos y lenguajes de programación). Este estudio sirvió para tomar decisiones de diseño fundamentadas en las tres contribuciones principales de esta tesis: un bus de servicios para dispositivos llevables (WDSB, Wearable Device Service Bus) basado en tecnologías ya existentes tales como ESB, WWBAN, WSN e IoT); un protocolo de comunicaciones inter-dominio para dispositivos llevables (WIDP, Wearable Inter-Domain communication Protocol) que integra en una misma solución protocolos capaces de ser implementados en dispositivos de bajas capacidades (como lo son los dispositivos llevables y los que forman parte de WSNs); y finalmente, la tercera contribución relevante es una propuesta de seguridad para WSN basada en la aplicación de dominios de confianza. Aunque las contribuciones aquí recogidas son de aplicación genérica, para su validación se utilizó un escenario concreto de aplicación: una solución para control de parámetros físicos en entornos deportivos, desarrollada dentro del proyecto europeo de investigación “LifeWear”. En este escenario se desplegaron todos los elementos necesarios para validar las contribuciones principales de esta tesis y, además, se realizó una aplicación para dispositivos móviles por parte de uno de los socios del proyecto (lo que contribuyó con una validación externa de la solución). En este escenario se usaron dispositivos llevables tales como un reloj inteligente, un teléfono móvil con sistema operativo Android y un medidor del ritmo cardíaco inalámbrico capaz de obtener distintos parámetros fisiológicos del deportista. Sobre este escenario se realizaron diversas pruebas de validación mediante las cuales se obtuvieron resultados satisfactorios. ABSTRACT Nowadays, society is shifting towards a growing interest and concern on health care. This phenomenon can be acknowledged by two facts: first, the increasing number of people practising some kind of healthy activity (sports, balanced diet, etc.). Secondly, the growing number of commercial wearable smart devices (smartwatches or bands) able to measure physiological parameters such as heart rate, breathing rate, distance or consumed calories. A large number of applications combining both facts are appearing. These applications are not only able to monitor the health status of the user, but also to provide recommendations about routines in order to improve the mentioned health status. In this context, wearable devices merged with the Internet of Things (IoT) paradigm enable the proliferation of new market segments for these health wearablebased applications. Furthermore, these applications can provide solutions for the elderly or baby care, in-hospital or in-home patient monitoring, security and defence fields or an unforeseen number of future applications. The introduced IoT paradigm can be developed with the usage of existing Wireless Sensor Networks (WSNs) by connecting the novel wearable devices to them. In this way, the migration of new users and actors to the IoT environment will be eased. However, a major issue appears in this environment: heterogeneity. In fact, there is a large number of operating systems, hardware platforms, communication and application protocols or programming languages, each of them with unique features. The main objective of this thesis is defining and implementing a solution for the intelligent service management in wearable and ubiquitous devices so as to solve the heterogeneity issues that are presented when dealing with interoperability and interconnectivity of devices and software of different nature. Additionally, a security schema based on trust domains is proposed as a solution to the privacy problems arising when private data (e.g., biomedical parameters or user identification) is broadcasted in a wireless network. The proposal has been made after a comprehensive state-of-the-art analysis, and includes the design of a Wearable Device Service Bus (WDSB) including the technologies collected in the requirement analysis (ESB, WWBAN, WSN and IoT). Applications are able to access the WSN services regardless of the platform and operating system where they are running. Besides, this proposal also includes the design of a Wearable Inter-Domain communication Protocols set (WIDP) which integrates lightweight protocols suitable to be used in low-capacities devices (REST, JSON, AMQP, CoAP, etc...). Furthermore, a security solution for service management based on a trustworthy domains model to deploy security services in WSNs has been designed. Although the proposal is a generic framework for applications based on services provided by wearable devices, an application scenario for testing purposes has been included. In this validation scenario it has been presented an autonomous physical condition performance system, based on a WSN, bringing the possibility to include several elements in an IoT scenario: a smartwatch, a physiological monitoring device and a smartphone. In summary, the general objective of this thesis is solving the heterogeneity and security challenges arising when developing applications for WSNs and wearable devices. As it has been presented in the thesis, the solution proposed has been successfully validated in a real scenario and the obtained results were satisfactory.

Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme

The RNA cleavage reaction catalyzed by the hairpin ribozyme shows biphasic kinetics, and chase experiments show that the slow phase of the reaction results from reversible substrate binding to an inactive conformational isomer. To investigate the structural basis for the heterogeneous kinetics, we have developed an enzymatic RNA modification method that selectively traps substrate bound to the inactive conformer and allows the two forms of the ribozyme-substrate complex to be separated and analyzed by using both physical and kinetic strategies. The inactive form of the complex was trapped by the addition of T4 RNA ligase to a cleavage reaction, resulting in covalent linkage of the 5′ end of the substrate to the 3′ end of the ribozyme and in selective and quantitative ablation of the slow kinetic phase of the reaction. This result indicates that the inactive form of the ribozyme-substrate complex can adopt a conformation in which helices 2 and 3 are coaxially stacked, whereas the active form does not have access to this conformation, because of a sharp bend at the helical junction that presumably is stabilized by inter-domain tertiary contacts required for catalytic activity. These results were used to improve the activity of the hairpin ribozyme by designing new interfaces between the two domains, one containing a non-nucleotidic orthobenzene linkage and the other replacing the two-way junction with a three-way junction. Each of these modified ribozymes preferentially adopts the active conformation and displays improved catalytic efficiency.

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

Effect of polymer microstructure on the docetaxel release and stability of polyurethane formulation

PurSil®AL20 (PUS), a copolymer of 4,4'-dicyclohexylmethane diisocyanate (HMDI), 1,4-butane diol (BD), poly-tetramethylene oxide (PTMO) and poly-dimethyl siloxane (PDMS) was investigated for stability as a vehicle for Docetaxel (DTX) delivery through oesophageal drug eluting stent (DES). On exposure to stability test conditions, it was found that DTX release rate declined at 4 and 40 °C. In order to divulge reasons underlying this, changes in DTX solid state as well as PUS microstructure were followed. It was found that re-crystallization of DTX in PDMS rich regions was reducing the drug release at both 4 °C and 40 °C samples. So far microstructural features have not been correlated with stability and drug release, and in this study we found that at 40 °C increase in microstructural domain sizes and the inter-domain distances (from ∼85 Å to 129 Å) were responsible for hindering the DTX release in addition to DTX re-crystallization.

Improving out-domain PLDA speaker verification using unsupervised inter-dataset variability compensation approach

Experimental studies have found that when the state-of-the-art probabilistic linear discriminant analysis (PLDA) speaker verification systems are trained using out-domain data, it significantly affects speaker verification performance due to the mismatch between development data and evaluation data. To overcome this problem we propose a novel unsupervised inter dataset variability (IDV) compensation approach to compensate the dataset mismatch. IDV-compensated PLDA system achieves over 10% relative improvement in EER values over out-domain PLDA system by effectively compensating the mismatch between in-domain and out-domain data.

Inter-observer agreement for spectral- and time-domain optical coherence tomography image grading: a prospective study

The purpose of this study was to compare inter-observer agreement of Stratus™ OCT versus Spectralis™ OCT image grading in patients with neovascular age-related macular degeneration (AMD). Thirty eyes with neovascular AMD were examined with Stratus™ OCT and Spectralis™ OCT. Four different scan protocols were used for imaging. Three observers graded the images for the presence of various pathologies. Inter-observer agreement between OCT models was assessed by calculating intra-class correlation coefficients (ICC). In Stratus™ OCT highest interobserver agreement was found for subretinal fluid (ICC: 0.79), and in Spectralis™ OCT for intraretinal cysts (IRC) (ICC: 0.93). Spectralis™ OCT showed superior interobserver agreement for IRC and epiretinal membranes (ERM) (ICC(Stratus™): for IRC 0.61; for ERM 0.56; ICC(Spectralis™): for IRC 0.93; for ERM 0.84). Increased image resolution of Spectralis™ OCT did improve the inter-observer agreement for grading intraretinal cysts and epiretinal membranes but not for other retinal changes.

Eukaryotic translation elongation factor 1A (eEF1A) domain I from S. cerevisiae is required but not sufficient for inter-species complementation

Ethanolamine phosphoglycerol (EPG) is a protein modification attached exclusively to eukaryotic elongation factor 1A (eEF1A). In mammals and plants, EPG is linked to conserved glutamate residues located in eEF1A domains II and III, whereas in the unicellular eukaryote Trypanosoma brucei, only domain III is modified by a single EPG. A biosynthetic precursor of EPG and structural requirements for EPG attachment to T. brucei eEF1A have been reported, but nothing is known about the EPG modifying enzyme(s). By expressing human eEF1A in T. brucei, we now show that EPG attachment to eEF1A is evolutionarily conserved between T. brucei and Homo sapiens. In contrast, S. cerevisiae eEF1A, which has been shown to lack EPG is not modified in T. brucei. Furthermore, we show that eEF1A cannot functionally complement across species when using T. brucei and S. cerevisiae as model organisms. However, functional complementation in yeast can be obtained using eEF1A chimera containing domains II or III from other species. In contrast, yeast domain I is strictly required for functional complementation in S. cerevisiae.

Inter-agency working : good intentions and interaction dynamics

This paper explores inter-agency working and examines the implications of inter-agency operations for delivering multi-domain service outcomes. Cross-agency collaborative approaches to service delivery are suggested to provide the vehicle for achieving integrated service and policy goals. However, it is argued these need to be crafted ‘fit’ for purpose’ and may not be the requisite approach for all joint purposes. Moreover, some commentators suggest that the optimism about these partnership arrangements and cross-agency actions to resolve complex multi-dimensional problems may be misplaced and propose that further research into the actual rather than desired consequences of these arrangements may find that, at times, partnership working creates negative effects. While collaboration and partnerships are often framed as the way to achieve real breakthroughs in service delivery across agencies, there remain key challenges to interagency working. As more and insistent calls for agencies and other community actors to work together in resolving complex social problems are heeded, the implications of working across organizational boundaries need to be further investigated. This paper investigates cases of inter-agency programmes to understand the dimensions and limitations of inter-agency working. The paper concludes by offering a framework for better inter-agency working that has applicability across all sectors.

QoS-Based Web Service Scheduling Accommodating Inter-Service Dependencies Using Minimal-Conflict Hill-Climbing Repair Genetic Algorithm

In the filed of semantic grid, QoS-based Web service scheduling for workflow optimization is an important problem.However, in semantic and service rich environment like semantic grid, the emergence of context constraints on Web services is very common making the scheduling consider not only quality properties of Web services, but also inter service dependencies which are formed due to the context constraints imposed on Web services. In this paper, we present a repair genetic algorithm, namely minimal-conflict hill-climbing repair genetic algorithm, to address scheduling optimization problems in workflow applications in the presence of domain constraints and inter service dependencies. Experimental results demonstrate the scalability and effectiveness of the genetic algorithm.

QoS-based web service composition accommodating inter-service dependencies using minimal-conflict , hill-climbing repair genetic algorithm

In the field of semantic grid, QoS-based Web service composition is an important problem. In semantic and service rich environment like semantic grid, the emergence of context constraints on Web services is very common making the composition consider not only QoS properties of Web services, but also inter service dependencies and conflicts which are formed due to the context constraints imposed on Web services. In this paper, we present a repair genetic algorithm, namely minimal-conflict hill-climbing repair genetic algorithm, to address the Web service composition optimization problem in the presence of domain constraints and inter service dependencies and conflicts. Experimental results demonstrate the scalability and effectiveness of the genetic algorithm.

Three-dimensional geological modelling of the Galilee and central Eromanga basins, Australia: New insights into aquifer/aquitard geometry and potential influence of faults on inter-connectivity

Study region The Galilee and Eromanga basins are located in central Queensland, Australia. Both basins are components of the Great Artesian Basin which host some of the most significant groundwater resources in Australia. Study focus This study evaluates the influence of regional faults on groundwater flow in an aquifer/aquitard interbedded succession that form one of the largest Artesian Basins in the world. In order to assess the significance of regional faults as potential barriers or conduits to groundwater flow, vertical displacements of the major aquifers and aquitards were studied at each major fault and the general hydraulic relationship of units that are juxtaposed by the faults were considered. A three-dimensional (3D) geological model of the Galilee and Eromanga basins was developed based on integration of well log data, seismic surfaces, surface geology and elevation data. Geological structures were mapped in detail and major faults were characterised. New hydrological insights for the region Major faults that have been described in previous studies have been confirmed within the 3D geological model domain and a preliminary assessment of their hydraulic significance has been conducted. Previously unknown faults such as the Thomson River Fault (herein named) have also been identified in this study.

The introduction of an Inter-professional learning unit: staff and student perspectives

Background The School of Clinical Sciences comprises a number of health disciplines including podiatry, paramedic science, pharmacy, medical imaging and radiation therapy. A new inter-professional unit was introduced in 2014, which covered key introductory learnings applicable for future health practitioners. This study examined teaching staff and student perspectives about their experience with the new unit for first year students. Methods Qualitative interviews with teaching staff (n=9) and focus group interviews with students (5 groups which ranged in size from 4-30) were conducted. Extensive notes were taken during the interviews Issues emerging from the interviews were identified and organised according to themes and subthemes. Results Four major themes were identified namely: Something new; To be or not to be that is the question; Advantages of the new unit; and Areas for improvement. Previous staff experience with inter-professional learning (IPL) had been ad-hoc, whereas the new unit brought together several disciplines in a planned and deliberate way. There was strong philosophical agreement about the value of IPL but some debate about the extent to which the unit provided IPL experience. The unit was seen as assisting students’ social and academic adjustment to university and provided opportunity for professional socialisation, exposure to macro and micro aspects of the Australian health care system and various types of communication. For podiatry students it was their first opportunity to formally meet and work with other podiatry students and moved their identity from ‘university student’ to ‘podiatry student’. Other positives included providing the opportunity for staff and students to interact at an early stage with the perceived benefit of reducing attrition. Areas for unit improvement included institutional arrangements, unit administration aspects and assessment. Conclusion The unit was seen as beneficial by staff and students however, students were more polarised in their views than staff. There was a tension between feeling apart of and learning about one's own profession and feeling apart of and learning about the roles of other health professionals in relation to patient care and the health care system.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

Frequency domain turbo equalization for MIMO-CPSC systems with large delay spreads

In this paper, we consider low-complexity turbo equalization for multiple-input multiple-output (MIMO) cyclic prefixed single carrier (CPSC) systems in MIMO inter-symbol interference (ISI) channels characterized by large delay spreads. A low-complexity graph based equalization is carried out in the frequency domain. Because of the reduction in correlation among the noise samples that happens for large frame sizes and delay spreads in frequency domain processing, improved performance compared to time domain processing is shown to be achieved. This improved performance is attractive for equalization in severely delay spread ISI channels like ultrawideband channels and underwater acoustic channels.