Modular Instrumentation for Controlling and Monitoring In-Vitro Cultivation Environment and Image-based Functionality Measurements of Human Stem Cells

Artificial animal cell culture was successfully developed by Ross Harrison in 1907. But it was not until the 1940’s and 1950’s that several developments occurred, which expedited the cell culturing in-vitro (C-Vitro) to be a consistent and reproducible technique to study isolated living-cells in a controlled environment. Currently, CVitro is one of the major tools in cellular and molecular biology both in the academia and industry. They are extensively utilised to study the cellular physiology/biochemistry, to screen drugs/therapeutic compounds, to understand the effects of drugs/toxic compounds and also to identify the pathways of carcinogenesis/mutagenesis. It is also used in large scale manufacturing of vaccines and therapeutic proteins. In any experimental setup, it is important that the C-Vitro model should represent the physiological phenomena of interest with reasonable accuracy so that all experimental results are statistically consistent and reproducible. In this direction, sensors and measurement systems play important roles in in-situ detection and/or control/manipulation of cells/tissues/environment. This thesis aimed to develop new technology for tailored cell culturing and integrated measurements. Firstly, design and assembly of a portable Invert-upright microscope interchangeable modular cell culturing platform (iuCMP) was envisioned. In contrast to conventional methods, micro-scaled systems mimic the cells' natural microenvironment more precisely, facilitating accurate and tractable models. The iuCMP integrates modular measurement schemes with a mini culture chamber using biocompatible cell-friendly materials, automated environment-control (temperature and gas concentrations), oxygen sensing and simultaneous functional measurements (electrophysiological and image-based). Time lapse microscopy is very useful in cell biology, but integration of advanced >i>in-vitro/device based biological systems (e.g. lab/organ/body-on-chips, or mini-bioreactors/microfluidic systems) into conventional microscopes can be challenging in several circumstances due to multiple reasons. But in iuCMP the main advantage is, the microscope can be switched either as an inverted or as an upright system and therefore can accommodate virtually any in-vitro device. It can capture images from regions that are otherwise inaccessible by conventional microscopes, for example, cells cultured on physical or biochemical sensor systems. The modular design also allows accommodating more sensor or measurement systems quite freely. We have demonstrated the system for video-based beating analysis of cardiomyocytes, cell orientation analysis on nanocellulose, and simultaneous long-term in-situ microscopy with oxygen and temperature sensing in hypoxia. In an example application, the system was utilised for long-term temperature stressing and simultaneous mechanobiological analysis of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). For this the iuCMP together with a temperature sensor plate (TSP) and a novel non-invasive beating analysis software (CMaN—cardiomyocyte function analysis tool, scripted as a subpart of this thesis), was applied for automated temperature response studies in hiPSC-CM cultures. In-situ temperature sensing is usually challenging with bulky external sensors, but TSPs solved this issue. In the temperature response study, we showed that the relationship between hiPSC-CM beating frequency and temperature is non-linear and measured the Q10 temperature coefficients. Moreover, we observed the hiPSC-CM contractile networking, including propagation of the action potential signal between dissociated clusters and their non-invasive measurements. It was the first case where these events were reported in hiPSC-CM clusters and their noninvasive measurements by image processing. The software CMaN comes with a user-friendly interface and, is equipped with features for batch processing, movement centre detection and cluster finding. It can extract six different signals of the contractile motion of cardiomyocytes (clusters or single cells) per processing. This ensures a minimum of one useful beating signal even in the cases of complex beating videos. On the processing end, compared to similar tools, CMaN is faster, more sensitive, and computationally less expensive and allows ROI based processing. In the case of healthy cells, the waveform of the signal from the CMaN resembles an ECG signal with positive and negative segments, allowing the computation of contraction and relaxation features separately. In addition to iuCMP, a Modular optical pH measurement system (MO-pH) for 24/7 non-contact cell culture measurements was also developed. The MO-pH incorporates modular sterilisable optical parts and is used in phenol-red medium cell cultures. The modular assembly of MO-pH cassettes is unique and reusable. Measurements are carried out in a closed flow system without wasting any culture medium and requires no special manual attention or recalibrations during culture. Furthermore, a new absorption correction model was put forward that minimised errors caused e.g. by biolayers in spectrometric pH measurement, which improved the pH measurement accuracy. MO-pH has been applied in long-term human adipose stem cells (hASC) expansion cultures in CO2 dependent and independent media. Additionally, the MO-pH was also utilised to comprehend the behaviour of pH, temperature and humidity in water jacked incubators as well as to record the pH response as a function of temperature in the presence and absence of CO2 in the context of stem cell cultures. The resulting plots clearly showed the interplay between measured parameters indicating a few stress sources present all through the culture. Additionally, it provided an overall picture of behaviour of critical control parameters in an incubator and pointed out the need for bioprocess systems with automatic process monitoring and smart control for maximum yield, optimal growth and maintenance of the cells. Besides, we also integrated MO-pH into flasks with reclosable lids (RL-F) and tested its applicability in stem cell cultures. A standalone system around an RL-F flask was built by combining the cell culture, medium perfusion and optical measurements. The developed RL-F system has been successfully tested in ASC-differentiation cultures. Finally, a few trial experiments for image-based pH estimation aimed for iuCMP have also been carried out. This includes tests with LCD illumination, optical projection tomography, and webcam systems. In reality, the pH is not distributed uniformly in tissues, and has shown a gradient of up to 1.0 pH unit within 1 cm distance. Therefore, producing reliable pH maps also in in-vitro can be important in understanding various common pathologies and location of lesions. A reliable and adequately developed long-term pH mapping method will be an important addition into the iuCMP

Transaction Generator - Tool for Network-on-Chip Benchmarking

This thesis focuses on benchmarking on-chip communication networks. Multiprocessor System-on-Chips (MP-SoC) utilizing the Network-on-Chip (NoC) paradigm are becoming more prominent. Required communication capabilities differ considerably among the diverse set of application categories. A standard and commonly used benchmarking methodology for networks is needed to ease finding a suitable network topology and its configuration parameters for those applications. This thesis presents a simulation based tool Transaction Generator (TG) for evaluating NoCs. TG conforms the Open Core Protocol - International Partnership (OCP-IP) NoC benchmarking group's proposed methodology. TG relies on abstract task graphs made after real Multiprocessor System-on-Chip (MP-SoC) applications or synthetic test cases. TG simulates the workload tasks on Processing Elements (PEs) and generates the network traffc accordingly and collects statistics. TG was initially introduced in 2003 and this thesis presents the current state of the tool and the modifications made. The work for this thesis includes refactoring the whole program from a TCL and C++ SystemC 1 based code generator to a C++ SystemC 2 based dynamic simulation kernel. In addition to the refactoring, new features were implemented, such as memory modeling with the Accurate Dynamic Random Access Memory (DRAM) Model (ADM) package, possibility of simulating Mobile Computing System Lab (MCSL) NoC Tra c Patterns workload models and diversity to modeling the workload. The current implementation of TG consists of 10k lines of code for the simulator core, the result of this thesis, and 50k lines of code for the support programs and example NoC models. Thesis presents 3 example use cases requiring around 100 simulations, which can be executed and analyzed in a work day with the TG

GNSS array-based acquisition: theory and implementation

This Dissertation addresses the signal acquisition problem using antenna arrays in the general framework of Global Navigation Satellite Systems (GNSS) receivers. The term GNSS classi es those navigation systems based on a constellation of satellites, which emit ranging signals useful for positioning. Although the American GPS is already available, which coexists with the renewed Russian Glonass, the forthcoming European contribution (Galileo) along with the Chinese Compass will be operative soon. Therefore, a variety of satellite constellations and signals will be available in the next years. GNSSs provide the necessary infrastructures for a myriad of applications and services that demand a robust and accurate positioning service. The positioning availability must be guaranteed all the time, specially in safety-critical and mission-critical services. Examining the threats against the service availability, it is important to take into account that all the present and the forthcoming GNSSs make use of Code Division Multiple Access (CDMA) techniques. The ranging signals are received with very low precorrelation signal-to-noise ratio (in the order of ���22 dB for a receiver operating at the Earth surface). Despite that the GNSS CDMA processing gain o ers limited protection against Radio Frequency interferences (RFI), an interference with a interference-to-signal power ratio that exceeds the processing gain can easily degrade receivers' performance or even deny completely the GNSS service, specially conventional receivers equipped with minimal or basic level of protection towards RFIs. As a consequence, RFIs (either intentional or unintentional) remain as the most important cause of performance degradation. A growing concern of this problem has appeared in recent times. Focusing our attention on the GNSS receiver, it is known that signal acquisition has the lowest sensitivity of the whole receiver operation, and, consequently, it becomes the performance bottleneck in the presence of interfering signals. A single-antenna receiver can make use of time and frequency diversity to mitigate interferences, even though the performance of these techniques is compromised in low SNR scenarios or in the presence of wideband interferences. On the other hand, antenna arrays receivers can bene t from spatial-domain processing, and thus mitigate the e ects of interfering signals. Spatial diversity has been traditionally applied to the signal tracking operation of GNSS receivers. However, initial tracking conditions depend on signal acquisition, and there are a number of scenarios in which the acquisition process can fail as stated before. Surprisingly, to the best of our knowledge, the application of antenna arrays to GNSS signal acquisition has not received much attention. This Thesis pursues a twofold objective: on the one hand, it proposes novel arraybased acquisition algorithms using a well-established statistical detection theory framework, and on the other hand demonstrates both their real-time implementation feasibility and their performance in realistic scenarios. The Dissertation starts with a brief introduction to GNSS receivers fundamentals, providing some details about the navigation signals structure and the receiver's architecture of both GPS and Galileo systems. It follows with an analysis of GNSS signal acquisition as a detection problem, using the Neyman-Pearson (NP) detection theory framework and the single-antenna acquisition signal model. The NP approach is used here to derive both the optimum detector (known as clairvoyant detector ) and the sov called Generalized Likelihood Ratio Test (GLRT) detector, which is the basis of almost all of the current state-of-the-art acquisition algorithms. Going further, a novel detector test statistic intended to jointly acquire a set of GNSS satellites is obtained, thus reducing both the acquisition time and the required computational resources. The eff ects of the front-end bandwidth in the acquisition are also taken into account. Then, the GLRT is extended to the array signal model to obtain an original detector which is able to mitigate temporally uncorrelated interferences even if the array is unstructured and moderately uncalibrated, thus becoming one of the main contributions of this Dissertation. The key statistical feature is the assumption of an arbitrary and unknown covariance noise matrix, which attempts to capture the statistical behavior of the interferences and other non-desirable signals, while exploiting the spatial dimension provided by antenna arrays. Closed form expressions for the detection and false alarm probabilities are provided. Performance and interference rejection capability are modeled and compared both to their theoretical bound. The proposed array-based acquisition algorithm is also compared to conventional acquisition techniques performed after blind null-steering beamformer approaches, such as the power minimization algorithm. Furthermore, the detector is analyzed under realistic conditions, accounting for the presence of errors in the covariance matrix estimation, residual Doppler and delay errors, and signal quantization e ects. Theoretical results are supported by Monte Carlo simulations. As another main contribution of this Dissertation, the second part of the work deals with the design and the implementation of a novel Field Programmable Gate Array (FPGA)-based GNSS real-time antenna-array receiver platform. The platform is intended to be used as a research tool tightly coupled with software de ned GNSS receivers. A complete signal reception chain including the antenna array and the multichannel phase-coherent RF front-end for the GPS L1/ Galileo E1 was designed, implemented and tested. The details of the digital processing section of the platform, such as the array signal statistics extraction modules, are also provided. The design trade-o s and the implementation complexities were carefully analyzed and taken into account. As a proof-of-concept, the problem of GNSS vulnerability to interferences was addressed using the presented platform. The array-based acquisition algorithms introduced in this Dissertation were implemented and tested under realistic conditions. The performance of the algorithms were compared to single antenna acquisition techniques, measured under strong in-band interference scenarios, including narrow/wide band interferers and communication signals. The platform was designed to demonstrate the implementation feasibility of novel array-based acquisition algorithms, leaving the rest of the receiver operations (mainly, tracking, navigation message decoding, code and phase observables, and basic Position, Velocity and Time (PVT) solution) to a Software De ned Radio (SDR) receiver running in a personal computer, processing in real-time the spatially- ltered signal sample stream coming from the platform using a Gigabit Ethernet bus data link. In the last part of this Dissertation, we close the loop by designing and implementing such software receiver. The proposed software receiver targets multi-constellation/multi-frequency architectures, pursuing the goals of e ciency, modularity, interoperability, and exibility demanded by user domains that require non-standard features, such as intermediate signals or data extraction and algorithms interchangeability. In this context, we introduce an open-source, real-time GNSS software de ned receiver (so-named GNSS-SDR) that contributes with several novel features such as the use of software design patterns and shared memory techniques to manage e ciently the data ow between receiver blocks, the use of hardware-accelerated instructions for time-consuming vector operations like carrier wipe-o and code correlation, and the availability to compile and run on multiple software platforms and hardware architectures. At this time of writing (April 2012), the receiver enjoys of a 2-dimensional Distance Root Mean Square (DRMS) error lower than 2 meters for a GPS L1 C/A scenario with 8 satellites in lock and a Horizontal Dilution Of Precision (HDOP) of 1.2.Esta tesis aborda el problema de la adquisición de la señal usando arrays de antenas en el marco general de los receptores de Sistemas Globales de Navegación por Satélite (GNSS). El término GNSS engloba aquellos sistemas de navegación basados en una constelación de satélites que emiten señales útiles para el posicionamiento. Aunque el GPS americano ya está disponible, coexistiendo con el renovado sistema ruso GLONASS, actualmente se está realizando un gran esfuerzo para que la contribución europea (Galileo), junto con el nuevo sistema chino Compass, estén operativos en breve. Por lo tanto, una gran variedad de constelaciones de satélites y señales estarán disponibles en los próximos años. Estos sistemas proporcionan las infraestructuras necesarias para una multitud de aplicaciones y servicios que demandan un servicio de posicionamiento confiable y preciso. La disponibilidad de posicionamiento se debe garantizar en todo momento, especialmente en los servicios críticos para la seguridad de las personas y los bienes. Cuando examinamos las amenazas de la disponibilidad del servicio que ofrecen los GNSSs, es importante tener en cuenta que todos los sistemas presentes y los sistemas futuros ya planificados hacen uso de técnicas de multiplexación por división de código (CDMA). Las señales transmitidas por los satélites son recibidas con una relación señal-ruido (SNR) muy baja, medida antes de la correlación (del orden de -22 dB para un receptor ubicado en la superficie de la tierra). A pesar de que la ganancia de procesado CDMA ofrece una protección inherente contra las interferencias de radiofrecuencia (RFI), esta protección es limitada. Una interferencia con una relación de potencia de interferencia a potencia de la señal que excede la ganancia de procesado puede degradar el rendimiento de los receptores o incluso negar por completo el servicio GNSS. Este riesgo es especialmente importante en receptores convencionales equipados con un nivel mínimo o básico de protección frente las RFIs. Como consecuencia, las RFIs (ya sean intencionadas o no intencionadas), se identifican como la causa más importante de la degradación del rendimiento en GNSS. El problema esta causando una preocupación creciente en los últimos tiempos, ya que cada vez hay más servicios que dependen de los GNSSs Si centramos la atención en el receptor GNSS, es conocido que la adquisición de la señal tiene la menor sensibilidad de todas las operaciones del receptor, y, en consecuencia, se convierte en el factor limitador en la presencia de señales interferentes. Un receptor de una sola antena puede hacer uso de la diversidad en tiempo y frecuencia para mitigar las interferencias, aunque el rendimiento de estas técnicas se ve comprometido en escenarios con baja SNR o en presencia de interferencias de banda ancha. Por otro lado, los receptores basados en múltiples antenas se pueden beneficiar del procesado espacial, y por lo tanto mitigar los efectos de las señales interferentes. La diversidad espacial se ha aplicado tradicionalmente a la operación de tracking de la señal en receptores GNSS. Sin embargo, las condiciones iniciales del tracking dependen del resultado de la adquisición de la señal, y como hemos visto antes, hay un número de situaciones en las que el proceso de adquisición puede fallar. En base a nuestro grado de conocimiento, la aplicación de los arrays de antenas a la adquisición de la señal GNSS no ha recibido mucha atención, sorprendentemente. El objetivo de esta tesis doctoral es doble: por un lado, proponer nuevos algoritmos para la adquisición basados en arrays de antenas, usando como marco la teoría de la detección de señal estadística, y por otro lado, demostrar la viabilidad de su implementación y ejecución en tiempo real, así como su medir su rendimiento en escenarios realistas. La tesis comienza con una breve introducción a los fundamentos de los receptores GNSS, proporcionando algunos detalles sobre la estructura de las señales de navegación y la arquitectura del receptor aplicada a los sistemas GPS y Galileo. Continua con el análisis de la adquisición GNSS como un problema de detección, aplicando la teoría del detector Neyman-Pearson (NP) y el modelo de señal de una única antena. El marco teórico del detector NP se utiliza aquí para derivar tanto el detector óptimo (conocido como detector clarividente) como la denominada Prueba Generalizada de la Razón de Verosimilitud (en inglés, Generalized Likelihood Ratio Test (GLRT)), que forma la base de prácticamente todos los algoritmos de adquisición del estado del arte actual. Yendo más lejos, proponemos un nuevo detector diseñado para adquirir simultáneamente un conjunto de satélites, por lo tanto, obtiene una reducción del tiempo de adquisición y de los recursos computacionales necesarios en el proceso, respecto a las técnicas convencionales. El efecto del ancho de banda del receptor también se ha tenido en cuenta en los análisis. A continuación, el detector GLRT se extiende al modelo de señal de array de antenas para obtener un detector nuevo que es capaz de mitigar interferencias no correladas temporalmente, incluso utilizando arrays no estructurados y moderadamente descalibrados, convirtiéndose así en una de las principales aportaciones de esta tesis. La clave del detector es asumir una matriz de covarianza de ruido arbitraria y desconocida en el modelo de señal, que trata de captar el comportamiento estadístico de las interferencias y otras señales no deseadas, mientras que utiliza la dimensión espacial proporcionada por los arrays de antenas. Se han derivado las expresiones que modelan las probabilidades teóricas de detección y falsa alarma. El rendimiento del detector y su capacidad de rechazo a interferencias se han modelado y comparado con su límite teórico. El algoritmo propuesto también ha sido comparado con técnicas de adquisición convencionales, ejecutadas utilizando la salida de conformadores de haz que utilizan algoritmos de filtrado de interferencias, como el algoritmo de minimización de la potencia. Además, el detector se ha analizado bajo condiciones realistas, representadas con la presencia de errores en la estimación de covarianzas, errores residuales en la estimación del Doppler y el retardo de señal, y los efectos de la cuantificación. Los resultados teóricos se apoyan en simulaciones de Monte Carlo. Como otra contribución principal de esta tesis, la segunda parte del trabajo trata sobre el diseño y la implementación de una nueva plataforma para receptores GNSS en tiempo real basados en array de antenas que utiliza la tecnología de matriz programable de puertas lógicas (en ingles Field Programmable Gate Array (FPGA)). La plataforma está destinada a ser utilizada como una herramienta de investigación estrechamente acoplada con receptores GNSS definidos por software. Se ha diseñado, implementado y verificado la cadena completa de recepción, incluyendo el array de antenas y el front-end multi-canal para las señales GPS L1 y Galileo E1. El documento explica en detalle el procesado de señal que se realiza, como por ejemplo, la implementación del módulo de extracción de estadísticas de la señal. Los compromisos de diseño y las complejidades derivadas han sido cuidadosamente analizadas y tenidas en cuenta. La plataforma ha sido utilizada como prueba de concepto para solucionar el problema presentado de la vulnerabilidad del GNSS a las interferencias. Los algoritmos de adquisición introducidos en esta tesis se han implementado y probado en condiciones realistas. El rendimiento de los algoritmos se comparó con las técnicas de adquisición basadas en una sola antena. Se han realizado pruebas en escenarios que contienen interferencias dentro de la banda GNSS, incluyendo interferencias de banda estrecha y banda ancha y señales de comunicación. La plataforma fue diseñada para demostrar la viabilidad de la implementación de nuevos algoritmos de adquisición basados en array de antenas, dejando el resto de las operaciones del receptor (principalmente, los módulos de tracking, decodificación del mensaje de navegación, los observables de código y fase, y la solución básica de Posición, Velocidad y Tiempo (PVT)) a un receptor basado en el concepto de Radio Definida por Software (SDR), el cual se ejecuta en un ordenador personal. El receptor procesa en tiempo real las muestras de la señal filltradas espacialmente, transmitidas usando el bus de datos Gigabit Ethernet. En la última parte de esta Tesis, cerramos ciclo diseñando e implementando completamente este receptor basado en software. El receptor propuesto está dirigido a las arquitecturas de multi-constalación GNSS y multi-frecuencia, persiguiendo los objetivos de eficiencia, modularidad, interoperabilidad y flexibilidad demandada por los usuarios que requieren características no estándar, tales como la extracción de señales intermedias o de datos y intercambio de algoritmos. En este contexto, se presenta un receptor de código abierto que puede trabajar en tiempo real, llamado GNSS-SDR, que contribuye con varias características nuevas. Entre ellas destacan el uso de patrones de diseño de software y técnicas de memoria compartida para administrar de manera eficiente el uso de datos entre los bloques del receptor, el uso de la aceleración por hardware para las operaciones vectoriales más costosas, como la eliminación de la frecuencia Doppler y la correlación de código, y la disponibilidad para compilar y ejecutar el receptor en múltiples plataformas de software y arquitecturas de hardware. A fecha de la escritura de esta Tesis (abril de 2012), el receptor obtiene un rendimiento basado en la medida de la raíz cuadrada del error cuadrático medio en la distancia bidimensional (en inglés, 2-dimensional Distance Root Mean Square (DRMS) error) menor de 2 metros para un escenario GPS L1 C/A con 8 satélites visibles y una dilución de la precisión horizontal (en inglés, Horizontal Dilution Of Precision (HDOP)) de 1.2

Advancements in Real-Time Simulation of Power and Energy Systems

Modern power and energy systems are characterized by the wide integration of distributed generation, storage and electric vehicles, adoption of ICT solutions, and interconnection of different energy carriers and consumer engagement, posing new challenges and creating new opportunities. Advanced testing and validation methods are needed to efficiently validate power equipment and controls in the contemporary complex environment and support the transition to a cleaner and sustainable energy system. Real-time hardware-in-the-loop (HIL) simulation has proven to be an effective method for validating and de-risking power system equipment in highly realistic, flexible, and repeatable conditions. Controller hardware-in-the-loop (CHIL) and power hardware-in-the-loop (PHIL) are the two main HIL simulation methods used in industry and academia that contribute to system-level testing enhancement by exploiting the flexibility of digital simulations in testing actual controllers and power equipment. This book addresses recent advances in real-time HIL simulation in several domains (also in new and promising areas), including technique improvements to promote its wider use. It is composed of 14 papers dealing with advances in HIL testing of power electronic converters, power system protection, modeling for real-time digital simulation, co-simulation, geographically distributed HIL, and multiphysics HIL, among other topics