Development and characterization of a scaffold-free 3D spheroid model of iPSC-derived human cardiomyocytes

Purpose: Cardiomyocytes are terminally differentiated cells in the adult heart and ischemia and cardiotoxic compounds can lead to cell death and irreversible decline of cardiac function. As testing platforms, isolated organs and primary cells from rodents have been the standard in research and toxicology, but there is a need for better models that more faithfully recapitulate native human biology. Hence, a new in vitro model comprising the advantages of 3D cell culture and the availability of induced pluripotent stem cells (iPSC) from human origin was developed and characterized. Methods: Human cardiomyocytes (CMs) derived from induced pluripotent stem cells (iPSCs) were studied in standard 2D culture and as cardiac microtissues (MTs) formed in hanging drops. 2D cultures were examined using immunofluorescence microscopy and Western blotting while the cardiac MTs were subjected to immunofluorescence, contractility, and pharmacological investigations. Results: iPSC-derived CMs in 2D culture showed well-formed myofibrils, cell-cell contacts positive for connexin-43, and other typical cardiac proteins. The cells reacted to pro-hypertrophic growth factors with a substantial increase in myofibrils and sarcomeric proteins. In hanging drop cultures, iPSC-derived cardiomyocytes formed spheroidal MTs within 4 days showing a homogeneous tissue structure with well-developed myofibrils extending throughout the whole spheroid without a necrotic core. MTs showed spontaneous contractions for more than 4 weeks that were recorded by optical motion tracking, sensitive to temperature, and responsive to electrical pacing. Contractile pharmacology was tested with several agents known to modulate cardiac rate and viability. Calcium-transients underlay the contractile activity and were also responsive to electrical stimulation, caffeine-induced Ca2+-release, extracellular calcium levels. Conclusions: 3D culture using iPSC-derived human cardiomyocytes provides an organoid human-based cellular platform that is free of necrosis and recapitulates vital cardiac functionality, thereby providing new and promising relevant model for the evaluation and development of new therapies and detection of cardiotoxicity.

Semantic middleware development for the Internet of Things

After the extraordinary spread of the World Wide Web during the last fifteen years, engineers and developers are pushing now the Internet to its next border. A new conception in computer science and networks communication has been burgeoning during roughly the last decade: a world where most of the computers of the future will be extremely downsized, to the point that they will look like dust at its most advanced prototypes. In this vision, every single element of our “real” world has an intelligent tag that carries all their relevant data, effectively mapping the “real” world into a “virtual” one, where all the electronically augmented objects are present, can interact among them and influence with their behaviour that of the other objects, or even the behaviour of a final human user. This is the vision of the Internet of the Future, which also draws ideas of several novel tendencies in computer science and networking, as pervasive computing and the Internet of Things. As it has happened before, materializing a new paradigm that changes the way entities interrelate in this new environment has proved to be a goal full of challenges in the way. Right now the situation is exciting, with a plethora of new developments, proposals and models sprouting every time, often in an uncoordinated, decentralised manner away from any standardization, resembling somehow the status quo of the first developments of advanced computer networking, back in the 60s and the 70s. Usually, a system designed after the Internet of the Future will consist of one or several final user devices attached to these final users, a network –often a Wireless Sensor Network- charged with the task of collecting data for the final user devices, and sometimes a base station sending the data for its further processing to less hardware-constrained computers. When implementing a system designed with the Internet of the Future as a pattern, issues, and more specifically, limitations, that must be faced are numerous: lack of standards for platforms and protocols, processing bottlenecks, low battery lifetime, etc. One of the main objectives of this project is presenting a functional model of how a system based on the paradigms linked to the Internet of the Future works, overcoming some of the difficulties that can be expected and showing a model for a middleware architecture specifically designed for a pervasive, ubiquitous system. This Final Degree Dissertation is divided into several parts. Beginning with an Introduction to the main topics and concepts of this new model, a State of the Art is offered so as to provide a technological background. After that, an example of a semantic and service-oriented middleware is shown; later, a system built by means of this semantic and service-oriented middleware, and other components, is developed, justifying its placement in a particular scenario, describing it and analysing the data obtained from it. Finally, the conclusions inferred from this system and future works that would be good to be tackled are mentioned as well. RESUMEN Tras el extraordinario desarrollo de la Web durante los últimos quince años, ingenieros y desarrolladores empujan Internet hacia su siguiente frontera. Una nueva concepción en la computación y la comunicación a través de las redes ha estado floreciendo durante la última década; un mundo donde la mayoría de los ordenadores del futuro serán extremadamente reducidas de tamaño, hasta el punto que parecerán polvo en sus más avanzado prototipos. En esta visión, cada uno de los elementos de nuestro mundo “real” tiene una etiqueta inteligente que porta sus datos relevantes, mapeando de manera efectiva el mundo “real” en uno “virtual”, donde todos los objetos electrónicamente aumentados están presentes, pueden interactuar entre ellos e influenciar con su comportamiento el de los otros, o incluso el comportamiento del usuario final humano. Ésta es la visión del Internet del Futuro, que también toma ideas de varias tendencias nuevas en las ciencias de la computación y las redes de ordenadores, como la computación omnipresente y el Internet de las Cosas. Como ha sucedido antes, materializar un nuevo paradigma que cambia la manera en que las entidades se interrelacionan en este nuevo entorno ha demostrado ser una meta llena de retos en el camino. Ahora mismo la situación es emocionante, con una plétora de nuevos desarrollos, propuestas y modelos brotando todo el rato, a menudo de una manera descoordinada y descentralizada lejos de cualquier estandarización, recordando de alguna manera el estado de cosas de los primeros desarrollos de redes de ordenadores avanzadas, allá por los años 60 y 70. Normalmente, un sistema diseñado con el Internet del futuro como modelo consistirá en uno o varios dispositivos para usuario final sujetos a estos usuarios finales, una red –a menudo, una red de sensores inalámbricos- encargada de recolectar datos para los dispositivos de usuario final, y a veces una estación base enviando los datos para su consiguiente procesado en ordenadores menos limitados en hardware. Al implementar un sistema diseñado con el Internet del futuro como patrón, los problemas, y más específicamente, las limitaciones que deben enfrentarse son numerosas: falta de estándares para plataformas y protocolos, cuellos de botella en el procesado, bajo tiempo de vida de las baterías, etc. Uno de los principales objetivos de este Proyecto Fin de Carrera es presentar un modelo funcional de cómo trabaja un sistema basado en los paradigmas relacionados al Internet del futuro, superando algunas de las dificultades que pueden esperarse y mostrando un modelo de una arquitectura middleware específicamente diseñado para un sistema omnipresente y ubicuo. Este Proyecto Fin de Carrera está dividido en varias partes. Empezando por una introducción a los principales temas y conceptos de este modelo, un estado del arte es ofrecido para proveer un trasfondo tecnológico. Después de eso, se muestra un ejemplo de middleware semántico orientado a servicios; después, se desarrolla un sistema construido por medio de este middleware semántico orientado a servicios, justificando su localización en un escenario particular, describiéndolo y analizando los datos obtenidos de él. Finalmente, las conclusiones extraídas de este sistema y las futuras tareas que sería bueno tratar también son mencionadas.

A Development Methodology to Facilitate the Integration of Smart Spaces into the Web of Things

How to create or integrate large Smart Spaces (considered as mash-ups of sensors and actuators) into the paradigm of ?Web of Things? has been the motivation of many recent works. A cutting-edge approach deals with developing and deploying web-enabled embedded devices with two major objectives: 1) to integrate sensor and actuator technologies into everyday objects, and 2) to allow a diversity of devices to plug to Internet. Currently, developers who want to use this Internet-oriented approach need have solid understanding about sensorial platforms and semantic technologies. In this paper we propose a Resource-Oriented and Ontology-Driven Development (ROOD) methodology, based on Model Driven Architecture (MDA), to facilitate to any developer the development and deployment of Smart Spaces. Early evaluations of the ROOD methodology have been successfully accomplished through a partial deployment of a Smart Hotel.

Behaviour Driven Development for Multi-Agent Systems

This paper presents a testing methodology to apply Behaviour Driven Development (BDD) techniques while developing Multi-Agent Systems (MAS), so called BEhavioural Agent Simple Testing (BEAST) methodology. It is supported by the developed open source framework (BEAST Tool) which automatically generates test cases skeletons from BDD scenarios specifications. The developed framework allows testing MASs based on JADE or JADEX platforms and offers a set of configurable Mock Agents which allow the execution of tests while the system is under development. BEAST tool has been validated in the development of a MAS for fault diagnosis in FTTH (Fiber To The Home) networks.

Methodologies for implement video decoders over multiprocessor platforms

The latest video coding standards developed, like HEVC (High Efficiency Video Coding, approved in January 2013), require for their implementation the use of devices able to support a high computational load. Considering that currently it is not enough the usage of one unique Digital Signal Processor (DSP), multicore devices have appeared recently in the market. However, due to its novelty, the working methodology that allows produce solutions for these configurations is in a very initial state, since currently the most part of the work needs to be performed manually. In consequence, the objective set consists on finding methodologies that ease this process. The study has been focused on extend a methodology, under development, for the generation of solutions for PCs and embedded systems. During this study, the standards RVC (Reconfigurable Video Coding) and HEVC have been employed, as well as DSPs of the Texas Instruments company. In its development, it has been tried to address all the factors that influence both the development and deployment of these new implementations of video decoders, ranging from tools up to aspects of the partitioning of algorithms, without this can cause a drop in application performance. The results of this study are the description of the employed methodology, the characterization of the software migration process and performance measurements for the HEVC standard in an RVC-based implementation. RESUMEN Los estándares de codificación de vídeo desarrollados más recientemente, como HEVC (High Efficiency Video Coding, aprobado en enero de 2013), requieren para su implementación el uso de dispositivos capaces de soportar una elevada carga computacional. Teniendo en cuenta que actualmente no es suficiente con utilizar un único Procesador Digital de Señal (DSP), han aparecido recientemente dispositivos multinúcleo en el mercado. Sin embargo, debido a su novedad, la metodología de trabajo que permite elaborar soluciones para tales configuraciones se encuentra en un estado muy inicial, ya que actualmente la mayor parte del trabajo debe realizarse manualmente. En consecuencia, el objetivo marcado consiste en encontrar metodologías que faciliten este proceso. El estudio se ha centrado en extender una metodología, en desarrollo, para la generación de soluciones para PC y sistemas empotrados. Durante dicho estudio se han empleado los estándares RVC (Reconfigurable Video Coding) y HEVC, así como DSPs de la compañía Texas Instruments. En su desarrollo se ha tratado de atender a todos los factores que influyen tanto en el desarrollo como en la puesta en marcha de estas nuevas implementaciones de descodificadores de vídeo; abarcando desde las herramientas a utilizar hasta aspectos del particionado de los algoritmos, sin que por ello se produzca una reducción en el rendimiento de las aplicaciones. Los resultados de este estudio son una descripción de la metodología empleada, la caracterización del proceso de migración de software, y medidas de rendimiento para el estándar HEVC en una implementación basada en RVC.

An online failure prediction system for private IaaS platforms

The size and complexity of cloud environments make them prone to failures. The traditional approach to achieve a high dependability for these systems relies on constant monitoring. However, this method is purely reactive. A more proactive approach is provided by online failure prediction (OFP) techniques. In this paper, we describe a OFP system for private IaaS platforms, currently under development, that combines di_erent types of data input, including monitoring information, event logs, and failure data. In addition, this system operates at both the physical and virtual planes of the cloud, taking into account the relationships between nodes and failure propagation mechanisms that are unique to cloud environments.

Case study on mobile applications UX: effect of the usage of a crosss-platform development framework

Cross-platform development frameworks for mobile applications promise important advantages in cost cuttings and easy maintenance, posing as a very good option for organizations interested in the design of mobile applications for several platforms. Given that platform conventions are especially important for the User eXperience (UX) of mobile applications, the usage of framework where the same code defines the behavior of the app in different platforms could have negative impact in the UX. The objetive of this study is comparing the cross-platform and the native approach for being able to determine if the selected development approach has any impact on the users in terms of UX. To be able to set a base line under this subject, study on cross-platform frameworks was performed to select the most appropriate one from a UX point of view. In order to achieve the objectives of this work, two development teams have developed two versions of the same application; one using framework that generates Android and iOS versions automatically, and another team developing native versions of the same application. The alternative versions for each platform have been evaluated with 37 users with a combination of a laboratory usability test and a longitudinal study. The results show that differences are minimal in the Android version, but in iOS, even if a reasonable good UX can be obtained with the usage of this framework by an UX-conscious design team, a higher level of UX can be obtained directly developing in native code.

Testing of Android testing tools: development of a benchmark for the evaluation

With the ever growing trend of smart phones and tablets, Android is becoming more and more popular everyday. With more than one billion active users i to date, Android is the leading technology in smart phone arena. In addition to that, Android also runs on Android TV, Android smart watches and cars. Therefore, in recent years, Android applications have become one of the major development sectors in software industry. As of mid 2013, the number of published applications on Google Play had exceeded one million and the cumulative number of downloads was more than 50 billionii. A 2013 survey also revealed that 71% of the mobile application developers work on developing Android applicationsiii. Considering this size of Android applications, it is quite evident that people rely on these applications on a daily basis for the completion of simple tasks like keeping track of weather to rather complex tasks like managing one’s bank accounts. Hence, like every other kind of code, Android code also needs to be verified in order to work properly and achieve a certain confidence level. Because of the gigantic size of the number of applications, it becomes really hard to manually test Android applications specially when it has to be verified for various versions of the OS and also, various device configurations such as different screen sizes and different hardware availability. Hence, recently there has been a lot of work on developing different testing methods for Android applications in Computer Science fraternity. The model of Android attracts researchers because of its open source nature. It makes the whole research model more streamlined when the code for both, application and the platform are readily available to analyze. And hence, there has been a great deal of research in testing and static analysis of Android applications. A great deal of this research has been focused on the input test generation for Android applications. Hence, there are a several testing tools available now, which focus on automatic generation of test cases for Android applications. These tools differ with one another on the basis of their strategies and heuristics used for this generation of test cases. But there is still very little work done on the comparison of these testing tools and the strategies they use. Recently, some research work has been carried outiv in this regard that compared the performance of various available tools with respect to their respective code coverage, fault detection, ability to work on multiple platforms and their ease of use. It was done, by running these tools on a total of 60 real world Android applications. The results of this research showed that although effective, these strategies being used by the tools, also face limitations and hence, have room for improvement. The purpose of this thesis is to extend this research into a more specific and attribute-­‐ oriented way. Attributes refer to the tasks that can be completed using the Android platform. It can be anything ranging from a basic system call for receiving an SMS to more complex tasks like sending the user to another application from the current one. The idea is to develop a benchmark for Android testing tools, which is based on the performance related to these attributes. This will allow the comparison of these tools with respect to these attributes. For example, if there is an application that plays some audio file, will the testing tool be able to generate a test input that will warrant the execution of this audio file? Using multiple applications using different attributes, it can be visualized that which testing tool is more useful for which kinds of attributes. In this thesis, it was decided that 9 attributes covering the basic nature of tasks, will be targeted for the assessment of three testing tools. Later this can be done for much more attributes to compare even more testing tools. The aim of this work is to show that this approach is effective and can be used on a much larger scale. One of the flagship features of this work, which also differentiates it with the previous work, is that the applications used, are all specially made for this research. The reason for doing that is to analyze just that specific attribute in isolation, which the application is focused on, and not allow the tool to get bottlenecked by something trivial, which is not the main attribute under testing. This means 9 applications, each focused on one specific attribute. The main contributions of this thesis are: A summary of the three existing testing tools and their respective techniques for automatic test input generation of Android Applications. • A detailed study of the usage of these testing tools using the 9 applications specially designed and developed for this study. • The analysis of the obtained results of the study carried out. And a comparison of the performance of the selected tools.

A case study on cross-platform development frameworks for mobile applications and UX

Cross-platform development frameworks for mobile applications promise important advantages in cost cuttings and easy maintenance, posing as a very good option for organizations interested in the design of mobile applications for several platforms. Given that platform conventions are especially important for the User eXperience (UX) of mobile applications, the usage of a framework where the same code defines the behavior of the app in different platforms could have a negative impact in the UX. This paper describes a study where two independent teams have designed two different versions of a mobile application, one using a framework that generates Android and iOS versions automatically, and another team using native tools. The alternative versions for each platform have been evaluated with 37 users with a combination of a laboratory usability test and a longitudinal study. The results show that differences are minimal in the Android platform, but in iOS, even if a reasonably good UX can be obtained with the usage of this framework by an UX-conscious design team, a higher level of UX can be obtained directly developing with a native tool.

A real case of a cognitive multiplayer game: design and development of the iOS client in Swift and its cloud architecture

as tecnologías emergentes como el cloud computing y los dispositivos móviles están creando una oportunidad sin precedentes para mejorar el sistema educativo, permitiendo tanto a los educadores personalizar y mejorar la experiencia de aprendizaje, como facilitar a los estudiantes que adquieran conocimientos sin importar dónde estén. Por otra parte, a través de técnicas de gamificacion será posible promover y motivar a los estudiantes a que aprendan materias arduas haciendo que la experiencia sea más motivadora. Los juegos móviles pueden ser el camino correcto para dar soporte a esta experiencia de aprendizaje mejorada. Este proyecto integra el diseño y desarrollo de una arquitectura en la nube altamente escalable y con alto rendimiento, así como el propio cliente de iOS, para dar soporte a una nueva version de Temporis, un juego móvil multijugador orientado a reordenar eventos históricos en una línea temporal (e.j. historia, arte, deportes, entretenimiento y literatura). Temporis actualmente está disponible en Google Play. Esta memoria describe el desarrollo de la nueva versión de Temporis (Temporis v.2.0) proporcionando detalles acerca de la mejora y adaptación basados en el Temporis original. En particular se describe el nuevo backend hecho en Go sobre Google App Engine creado para soportar miles de usuarios, asó como otras características por ejemplo como conseguir enviar noticaciones push desde la propia plataforma. Por último, el cliente de iOS en Temporis v.2.0 se ha desarrollado utilizando las últimas y más relevantes tecnologías, prestando especial atención a Swift (el lenguaje de programación nuevo de Apple, que es seguro y rápido), el Paradigma Funcional Reactivo (que ayuda a construir aplicaciones altamente interactivas además de a minimizar errores) y la arquitectura VIPER (una arquitectura que sigue los principios SOLID, se centra en la separación de asuntos y favorece la reutilización de código en otras plataformas). ABSTRACT Emerging technologies such as cloud computing and mobile devices are creating an unprecedented opportunity for enhancing the educational system, letting both educators customize and improve the learning experience, and students acquire knowledge regardless of where they are. Moreover, through gamification techniques it would be possible to encourage and motivate students to learn arduous subjects by making the experience more motivating. Mobile games can be a perfect vehicle to support this enhanced learning experience. This project integrates the design and development of a highly scalable and performant cloud architecture, as well as the iOS client that uses it, in order to provide support to a new version of Temporis, a mobile multiplayer game focused on ordering time-based (e.g. history, art, sports, entertainment and literature) in a timeline that currently is available on Google Play. This work describes the development of the new Temporis version (Temporis v.2.0), providing details about improvements and details on the adaptation of the original Temporis. In particular, the new Google App Engine backend is described, which was created to support thousand of users developed in Go language are provided, in addition to other features like how to achieve push notications in this platform. Finally, the mobile iOS client developed using the latest and more relevant technologies is explained paying special attention to Swift (Apple's new programming language, that is safe and fast), the Functional Reactive Paradigm (that helps building highly interactive apps while minimizing bugs) and the VIPER architecture (a SOLID architecture that enforces separation of concerns and makes it easy to reuse code for other platforms).

Towards a real-time 3D object recognition pipeline on mobile GPGPU computing platforms using low-cost RGB-D sensors

In this project, we propose the implementation of a 3D object recognition system which will be optimized to operate under demanding time constraints. The system must be robust so that objects can be recognized properly in poor light conditions and cluttered scenes with significant levels of occlusion. An important requirement must be met: the system must exhibit a reasonable performance running on a low power consumption mobile GPU computing platform (NVIDIA Jetson TK1) so that it can be integrated in mobile robotics systems, ambient intelligence or ambient assisted living applications. The acquisition system is based on the use of color and depth (RGB-D) data streams provided by low-cost 3D sensors like Microsoft Kinect or PrimeSense Carmine. The range of algorithms and applications to be implemented and integrated will be quite broad, ranging from the acquisition, outlier removal or filtering of the input data and the segmentation or characterization of regions of interest in the scene to the very object recognition and pose estimation. Furthermore, in order to validate the proposed system, we will create a 3D object dataset. It will be composed by a set of 3D models, reconstructed from common household objects, as well as a handful of test scenes in which those objects appear. The scenes will be characterized by different levels of occlusion, diverse distances from the elements to the sensor and variations on the pose of the target objects. The creation of this dataset implies the additional development of 3D data acquisition and 3D object reconstruction applications. The resulting system has many possible applications, ranging from mobile robot navigation and semantic scene labeling to human-computer interaction (HCI) systems based on visual information.

Development and formulation of wax-based transdermal drug delivery systems

Topical and transdermal formulations are promising platforms for the delivery of drugs. A unit dose topical or transdermal drug delivery system that optimises the solubility of drugs within the vehicle provides a novel dosage form for efficacious delivery that also offers a simple manufacture technique is desirable. This study used Witepsol® H15 wax as a abase for the delivery system. One aspect of this project involved determination of the solubility of ibuprofen, flurbiprofen and naproxen in the was using microscopy, Higuchi release kinetics, HyperDSC and mathematical modelling techniques. Correlations between the results obtained via these techniques were noted with additional merits such as provision of valuable information on drug release kinetics and possible interactions between the drug and excipients. A second aspect of this project involved the incorporation of additional excipients: Tween 20 (T), Carbopol®971 (C) and menthol (M) to the wax formulation. On in vitro permeation through porcine skin, the preferred formulations were: ibuprofen (5% w/w) within Witepsol®H15 + 1% w/w T; flurbiprofen (10% w/w) within Witepsol®H15 + 1% w/w T; naproxen (5% w/w) within Witepsol®H15 + 1% w/w T + 1% C and sodium diclofenac (10% w/w) within Witepsol®H15 + 1% w/w T + 1% w/w T + 1% w/w C + 5% w/w M. Unit dose transdermal tablets containing ibuprofen and diclofenac were produced with improved flux compared to marketed products; Voltarol Emugel® demonstrated flux of 1.68x10-3 cm/h compared to 123 x 10-3 cm/h for the optimised product as detailed above; Ibugel Forte® demonstrated a permeation coefficient value of 7.65 x 10-3 cm/h compared to 8.69 x 10-3 cm/h for the optimised product as described above.

Unique reporter-based sensor platforms to monitor signalling in cells

Introduction - In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level. Methods - Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis. Findings - We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation. Conclusions - We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.

A "Cross-technology" Software Development Approach

Contemporary web-based software solutions are usually composed of many interoperating applications. Classical approach is the different applications of the solution to be created inside one technology/platform, e.g. Java-technology, .NET-technology, etc. Wide spread technologies/platforms practically discourage (and sometime consciously make impossible) the cooperation with elements of the concurrent technologies/platforms. To make possible the usage of attractive features of one technology/platform in another technology/platform some “cross-technology” approach is necessary. In the paper is discussed the possibility to combine two existing instruments – interoperability protocols and “lifting” of procedures – in order to obtain such cross-technology approach.

Development of an open architecture motion control system

A multipurpose open architecture motion control system was developed with three platforms for control and monitoring. The Visual Basic user interface communicated with the operator and gave instructions to the electronic components. The first platform had a BASIC Stamp based controller and three stepping motors. The second platform had a controller, amplifiers and two DC servomotors. The third platform had a DSP module. In this study, each platform was used on machine tools either to move the table or to evaluate the incoming signal. The study indicated that by using advanced microcontrollers, which use high-level languages, motor controllers, DSPs (Digital Signal Processor) and microcomputers, the motion control of different systems could be realized in a short time. Although, the proposed systems had some limitations, their jobs were performed effectively. ^