Characterization of a reference material for BCR-ABL (M-BCR) mRNA quantitation by real-time amplification assays:towards new standards for gene expression measurements

Monitoring of BCR-ABL transcripts has become established practice in the management of chronic myeloid leukemia. However, nucleic acid amplification techniques are prone to variations which limit the reliability of real-time quantitative PCR (RQ-PCR) for clinical decision making, highlighting the need for standardization of assays and reporting of minimal residual disease (MRD) data. We evaluated a lyophilized preparation of a leukemic cell line (K562) as a potential quality control reagent. This was found to be relatively stable, yielding comparable respective levels of ABL, GUS and BCR-ABL transcripts as determined by RQ-PCR before and after accelerated degradation experiments as well as following 5 years storage at -20 degrees C. Vials of freeze-dried cells were sent at ambient temperature to 22 laboratories on four continents, with RQ-PCR analyses detecting BCR-ABL transcripts at levels comparable to those observed in primary patient samples. Our results suggest that freeze-dried cells can be used as quality control reagents with a range of analytical instrumentations and could enable the development of urgently needed international standards simulating clinically relevant levels of MRD.

Geotechnical monitoring using a combination of LIDAR, real-time dGPS, and electrical tomography to assess geotechnical risk of a coastal landslide.

The Antrim Coast Road stretching from the seaport of Larne in the East of Northern Ireland has a well-deserved reputation for being one of the most spectacular roads in Europe (Day, 2006). However the problematic geology; Jurassic Lias Clay and Triassic Mudstone overlain by Cretaceous Limestone and Tertiary Basalt, and environmental variables result in frequent instances of slope instability manifested in both shallow debris flows and occasional massive rotational movements, creating a geotechnical risk to this highway. This paper describes how a variety of techniques are being used to both assess instability and monitor movement of these active slopes near one site at Straidkilly Point, Glenarm. An in-depth understanding of the geology was obtained via boreholes, resistivity surveys and laboratory testing. Environmental variables recorded by an on-site weather station were correlated with measured pore water pressure and soil moisture infiltration data. Terrestrial LiDAR (TLS), with surveys carried out on a bi-monthly basis allowed for the generation of Digital Elevation Models (DEMs) of difference, highlighting areas of recent movement, accumulation and depletion. Morphology parameters were generated from the DEMs and include slope, curvature and multiple measures of roughness. Changes in the structure of the slope coupled with morphological parameters were characterised and linked to progressive failures from the temporal monitoring. In addition to TLS monitoring, Aerial LiDAR datasets were used for the spatio-morphological characterisation of the slope on a macro scale. A Differential Global Positioning System (dGPS) was also deployed on site to provide a real-time warning system for gross movements, which were also correlated with environmental conditions. Frequent electrical resistivity tomography (ERT) surveys were also implemented to provide a better understanding of long-term changes in soil moisture and help to define the complex geology. The paper describes how the data obtained via a diverse range of methods has been combined to facilitate a more informed management regime of geotechnical risk by the Northern Ireland Roads Service.

High Performance Real-time Pre-Processing for Fixed-Complexity Sphere Decoder

Pre-processing (PP) of received symbol vector and channel matrices is an essential pre-requisite operation for Sphere Decoder (SD)-based detection of Multiple-Input Multiple-Output (MIMO) wireless systems. PP is a highly complex operation, but relative to the total SD workload it represents a relatively small fraction of the overall computational cost of detecting an OFDM MIMO frame in standards such as 802.11n. Despite this, real-time PP architectures are highly inefficient, dominating the resource cost of real-time SD architectures. This paper resolves this issue. By reorganising the ordering and QR decomposition sub operations of PP, we describe a Field Programmable Gate Array (FPGA)-based PP architecture for the Fixed Complexity Sphere Decoder (FSD) applied to 4 × 4 802.11n MIMO which reduces resource cost by 50% as compared to state-of-the-art solutions whilst maintaining real-time performance.

Real-Time Channel Model Selection Using Windowed Received Signal Strength Measurements

This paper investigates the potential for using the windowed variance of the received signal strength to select from a set of predetermined channel models for a wireless ranging or localization system. An 868 MHz based measurement system was used to characterize the received signal strength (RSS) of the off-body link formed between two wireless nodes attached to either side of a human thorax and six base stations situated in the local surroundings.

Real-time estimation of battery internal temperature based on a simplified thermoelectric model

Li-ion batteries have been widely used in the EVs, and the battery thermal management is a key but challenging part of the battery management system. For EV batteries, only the battery surface temperature can be measured in real-time. However, it is the battery internal temperature that directly affects the battery performance, and large temperature difference may exist between surface and internal temperatures, especially in high power demand applications. In this paper, an online battery internal temperature estimation method is proposed based on a novel simplified thermoelectric model. The battery thermal behaviour is first described by a simplified thermal model, and battery electrical behaviour by an electric model. Then, these two models are interrelated to capture the interactions between battery thermal and electrical behaviours, thus offer a comprehensive description of the battery behaviour that is useful for battery management. Finally, based on the developed model, the battery internal temperature is estimated using an extended Kalman filter. The experimental results confirm the efficacy of the proposed method, and it can be used for online internal temperature estimation which is a key indicator for better real-time battery thermal management.

Electron-phonon thermalization in a scalable method for real-time quantum dynamics

We present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.

Dielectrics in a time-dependent electric field: a real-time approach based on density-polarization functional theory

In the presence of a (time-dependent) macroscopic electric field the electron dynamics of dielectrics cannot be described by the time-dependent density only. We present a real-time formalism that has the density and the macroscopic polarization P as key quantities. We show that a simple local function of P already captures long-range correlation in linear and nonlinear optical response functions. Specifically, after detailing the numerical implementation, we examine the optical absorption, the second- and third-harmonic generation of bulk Si, GaAs, AlAs and CdTe at different level of approximation. We highlight links with ultranonlocal exchange-correlation functional approximations proposed within linear response time-dependent density functional theory framework.

Real-Time Multiple Event Detection and Classification Using Moving Window PCA

This paper proposes a method for the detection and classification of multiple events in an electrical power system in real-time, namely; islanding, high frequency events (loss of load) and low frequency events (loss of generation). This method is based on principal component analysis of frequency measurements and employs a moving window approach to combat the time-varying nature of power systems, thereby increasing overall situational awareness of the power system. Numerical case studies using both real data, collected from the UK power system, and simulated case studies, constructed using DigSilent PowerFactory, for islanding events, as well as both loss of load and generation dip events, are used to demonstrate the reliability of the proposed method.

NanoStreams: Codesigned Microservers for Edge Analytics in Real Time

NanoStreams explores the design, implementation,and system software stack of micro-servers aimed at processingdata in-situ and in real time. These micro-servers can serve theemerging Edge computing ecosystem, namely the provisioningof advanced computational, storage, and networking capabilitynear data sources to achieve both low latency event processingand high throughput analytical processing, before consideringoff-loading some of this processing to high-capacity datacentres.NanoStreams explores a scale-out micro-server architecture thatcan achieve equivalent QoS to that of conventional rack-mountedservers for high-capacity datacentres, but with dramaticallyreduced form factors and power consumption. To this end,NanoStreams introduces novel solutions in programmable & con-figurable hardware accelerators, as well as the system softwarestack used to access, share, and program those accelerators.Our NanoStreams micro-server prototype has demonstrated 5.5×higher energy-efficiency than a standard Xeon Server. Simulationsof the microserver’s memory system extended to leveragehybrid DDR/NVM main memory indicated 5× higher energyefficiencythan a conventional DDR-based system. 

Satellite DNA as a target for TaqMan real-time PCR detection of the pinewood nematode, Bursaphelenchus xylophilus

The pinewood nematode (PWN), Bursaphelenchus xylophilus , is a major pathogen of conifers, which impacts on forest health, natural ecosystem stability and international trade. As a consequence, it has been listed as a quarantine organism in Europe. A real-time PCR approach based on TaqMan chemistry was developed to detect this organism. Specific probe and primers were designed based on the sequence of the Msp I satellite DNA family previously characterized in the genome of the nematode. The method proved to be specific in tests with target DNA from PWN isolates from worldwide origin. From a practical point of view, detection limit was 1 pg of target DNA or one individual nematode. In addition, PWN genomic DNA or single individuals were positively detected in mixed samples in which B. xylophilius was associated with the closely related non-pathogenic species B. mucronatus , up to the limit of 0.01% or 1% of the mixture, respectively. The real-time PCR assay was also used in conjunction with a simple DNA extraction method to detect PWN directly in artificially infested wood samples. These results demonstrate the potential of this assay to provide rapid, accurate and sensitive molecular identification of the PWN in relation to pest risk assessment in the field and quarantine regulation.

Enhanced ethernet switching technology for adaptive hard real-time applications: Tecnologia de comutação ethernet melhorada para aplicações adaptativas e críticas de tempo-real

Os Sistemas Embarcados Distribuídos (SEDs) estão, hoje em dia, muito difundidos em vastas áreas, desde a automação industrial, a automóveis, aviões, até à distribuição de energia e protecção do meio ambiente. Estes sistemas são, essencialmente, caracterizados pela integração distribuída de aplicações embarcadas, autónomas mas cooperantes, explorando potenciais vantagens em termos de modularidade, facilidade de manutenção, custos de instalação, tolerância a falhas, entre outros. Contudo, o ambiente operacional onde se inserem estes tipos de sistemas pode impor restrições temporais rigorosas, exigindo que o sistema de comunicação subjacente consiga transmitir mensagens com garantias temporais. Contudo, os SEDs apresentam uma crescente complexidade, uma vez que integram subsistemas cada vez mais heterogéneos, quer ao nível do tráfego gerado, quer dos seus requisitos temporais. Em particular, estes subsistemas operam de forma esporádica, isto é, suportam mudanças operacionais de acordo com estímulos exteriores. Estes subsistemas também se reconfiguram dinamicamente de acordo com a actualização dos seus requisitos e, ainda, têm lidar com um número variável de solicitações de outros subsistemas. Assim sendo, o nível de utilização de recursos pode variar e, desta forma, as políticas de alocação estática tornam-se muito ineficientes. Consequentemente, é necessário um sistema de comunicação capaz de suportar com eficácia reconfigurações e adaptações dinâmicas. A tecnologia Ethernet comutada tem vindo a emergir como uma solução sólida para fornecer comunicações de tempo-real no âmbito dos SEDs, como comprovado pelo número de protocolos de tempo-real que foram desenvolvidos na última década. No entanto, nenhum dos protocolos existentes reúne as características necessárias para fornecer uma eficiente utilização da largura de banda e, simultaneamente, para respeitar os requisitos impostos pelos SEDs. Nomeadamente, a capacidade para controlar e policiar tráfego de forma robusta, conjugada com suporte à reconfiguração e adaptação dinâmica, não comprometendo as garantias de tempo-real. Esta dissertação defende a tese de que, pelo melhoramento dos comutadores Ethernet para disponibilizarem mecanismos de reconfiguração e isolamento de tráfego, é possível suportar aplicações de tempo-real críticas, que são adaptáveis ao ambiente onde estão inseridas.Em particular, é mostrado que as técnicas de projecto, baseadas em componentes e apoiadas no escalonamento hierárquico de servidores de tráfego, podem ser integradas nos comutadores Ethernet para alcançar as propriedades desejadas. Como suporte, é fornecida, também, uma solução para instanciar uma hierarquia reconfigurável de servidores de tráfego dentro do comutador, bem como a análise adequada ao modelo de escalonamento. Esta última fornece um limite superior para o tempo de resposta que os pacotes podem sofrer dentro dos servidores de tráfego, com base unicamente no conhecimento de um dado servidor e na hierarquia actual, isto é, sem o conhecimento das especifidades do tráfego dentro dos outros servidores. Finalmente, no âmbito do projecto HaRTES foi construído um protótipo do comutador Ethernet, o qual é baseado no paradigma “Flexible Time-Triggered”, que permite uma junção flexível de uma fase síncrona para o tráfego controlado pelo comutador e uma fase assíncrona que implementa a estrutura hierárquica de servidores referidos anteriormente. Além disso, as várias experiências práticas realizadas permitiram validar as propriedades desejadas e, consequentemente, a tese que fundamenta esta dissertação.

Dependable wireless real-time communications for open environments

Wireless communication technologies have become widely adopted, appearing in heterogeneous applications ranging from tracking victims, responders and equipments in disaster scenarios to machine health monitoring in networked manufacturing systems. Very often, applications demand a strictly bounded timing response, which, in distributed systems, is generally highly dependent on the performance of the underlying communication technology. These systems are said to have real-time timeliness requirements since data communication must be conducted within predefined temporal bounds, whose unfulfillment may compromise the correct behavior of the system and cause economic losses or endanger human lives. The potential adoption of wireless technologies for an increasingly broad range of application scenarios has made the operational requirements more complex and heterogeneous than before for wired technologies. On par with this trend, there is an increasing demand for the provision of cost-effective distributed systems with improved deployment, maintenance and adaptation features. These systems tend to require operational flexibility, which can only be ensured if the underlying communication technology provides both time and event triggered data transmission services while supporting on-line, on-the-fly parameter modification. Generally, wireless enabled applications have deployment requirements that can only be addressed through the use of batteries and/or energy harvesting mechanisms for power supply. These applications usually have stringent autonomy requirements and demand a small form factor, which hinders the use of large batteries. As the communication support may represent a significant part of the energy requirements of a station, the use of power-hungry technologies is not adequate. Hence, in such applications, low-range technologies have been widely adopted. In fact, although low range technologies provide smaller data rates, they spend just a fraction of the energy of their higher-power counterparts. The timeliness requirements of data communications, in general, can be met by ensuring the availability of the medium for any station initiating a transmission. In controlled (close) environments this can be guaranteed, as there is a strict regulation of which stations are installed in the area and for which purpose. Nevertheless, in open environments, this is hard to control because no a priori abstract knowledge is available of which stations and technologies may contend for the medium at any given instant. Hence, the support of wireless real-time communications in unmanaged scenarios is a highly challenging task. Wireless low-power technologies have been the focus of a large research effort, for example, in the Wireless Sensor Network domain. Although bringing extended autonomy to battery powered stations, such technologies are known to be negatively influenced by similar technologies contending for the medium and, especially, by technologies using higher power transmissions over the same frequency bands. A frequency band that is becoming increasingly crowded with competing technologies is the 2.4 GHz Industrial, Scientific and Medical band, encompassing, for example, Bluetooth and ZigBee, two lowpower communication standards which are the base of several real-time protocols. Although these technologies employ mechanisms to improve their coexistence, they are still vulnerable to transmissions from uncoordinated stations with similar technologies or to higher power technologies such as Wi- Fi, which hinders the support of wireless dependable real-time communications in open environments. The Wireless Flexible Time-Triggered Protocol (WFTT) is a master/multi-slave protocol that builds on the flexibility and timeliness provided by the FTT paradigm and on the deterministic medium capture and maintenance provided by the bandjacking technique. This dissertation presents the WFTT protocol and argues that it allows supporting wireless real-time communication services with high dependability requirements in open environments where multiple contention-based technologies may dispute the medium access. Besides, it claims that it is feasible to provide flexible and timely wireless communications at the same time in open environments. The WFTT protocol was inspired on the FTT paradigm, from which higher layer services such as, for example, admission control has been ported. After realizing that bandjacking was an effective technique to ensure the medium access and maintenance in open environments crowded with contention-based communication technologies, it was recognized that the mechanism could be used to devise a wireless medium access protocol that could bring the features offered by the FTT paradigm to the wireless domain. The performance of the WFTT protocol is reported in this dissertation with a description of the implemented devices, the test-bed and a discussion of the obtained results.

Architecture for real-time coordination of multiple autonomous mobile units

Interest on using teams of mobile robots has been growing, due to their potential to cooperate for diverse purposes, such as rescue, de-mining, surveillance or even games such as robotic soccer. These applications require a real-time middleware and wireless communication protocol that can support an efficient and timely fusion of the perception data from different robots as well as the development of coordinated behaviours. Coordinating several autonomous robots towards achieving a common goal is currently a topic of high interest, which can be found in many application domains. Despite these different application domains, the technical problem of building an infrastructure to support the integration of the distributed perception and subsequent coordinated action is similar. This problem becomes tougher with stronger system dynamics, e.g., when the robots move faster or interact with fast objects, leading to tighter real-time constraints. This thesis work addressed computing architectures and wireless communication protocols to support efficient information sharing and coordination strategies taking into account the real-time nature of robot activities. The thesis makes two main claims. Firstly, we claim that despite the use of a wireless communication protocol that includes arbitration mechanisms, the self-organization of the team communications in a dynamic round that also accounts for variable team membership, effectively reduces collisions within the team, independently of its current composition, significantly improving the quality of the communications. We will validate this claim in terms of packet losses and communication latency. We show how such self-organization of the communications can be achieved in an efficient way with the Reconfigurable and Adaptive TDMA protocol. Secondly, we claim that the development of distributed perception, cooperation and coordinated action for teams of mobile robots can be simplified by using a shared memory middleware that replicates in each cooperating robot all necessary remote data, the Real-Time Database (RTDB) middleware. These remote data copies, which are updated in the background by the selforganizing communications protocol, are extended with age information automatically computed by the middleware and are locally accessible through fast primitives. We validate our claim showing a parsimonious use of the communication medium, improved timing information with respect to the shared data and the simplicity of use and effectiveness of the proposed middleware shown in several use cases, reinforced with a reasonable impact in the Middle Size League of RoboCup.

Preface to the special section on algorithms and architectures for real-time control

Rapid developments in microelectronics and computer science continue to fuel new opportunities for real-time control engineers. The ever-increasing system complexity and sophistication, environmental legislation, economic competition, safety and reliability constitute some of the driving forces for the research themes presented at the IFAC Workshop on Algorithms and Architectures for Real-Time Control (AARTC'2000). The Spanish Society for Automatic Control hosted AARTC'2000, which was held at Palma de Maiorca, Spain, from 15 to 17 May. This workshop was the sixth in the series.

Design and implementation of a real-time data acquisition system for the identification of dynamic temperature models in a hydroponic greenhouse

This text describes a real data acquisition and identification system implemented in a soilless greenhouse located at the University of Algarve (south of Portugal). Using the Real Time Workshop, Simulink, Matlab and the C programming language a system was developed to perform real-time data acquisition from a set of sensors.