Development of a real time polymerase chain reaction for quantitation of Schistosoma mansoni DNA

This report describes the development of a SYBR Green I based real time polymerase chain reaction (PCR) protocol for detection on the ABI Prism 7000 instrument. Primers targeting the gene encoding the SSU rRNA were designed to amplify with high specificity DNA from Schistosoma mansoni, in a real time quantitative PCR system. The limit of detection of parasite DNA for the system was 10 fg of purified genomic DNA, that means less than the equivalent to one parasite cell (genome ~580 fg DNA). The efficiency was 0.99 and the correlation coefficient (R²) was 0.97. When different copy numbers of the target amplicon were used as standards, the assay could detect at least 10 copies of the specific target. The primers used were designed to amplify a 106 bp DNA fragment (Tm 83ºC). The assay was highly specific for S. mansoni, and did not recognize DNA from closely related non-schistosome trematodes. The real time PCR allowed for accurate quantification of S. mansoni DNA and no time-consuming post-PCR detection of amplification products by gel electrophoresis was required. The assay is potentially able to quantify S. mansoni DNA (and indirectly parasite burden) in a number of samples, such as snail tissue, serum and feces from patients, and cercaria infested water. Thus, these PCR protocols have potential to be used as tools for monitoring of schistosome transmission and quantitative diagnosis of human infection.

Discovery of a 29-gene panel in peripheral blood mononuclear cells for the detection of colorectal cancer and adenomas using high throughput real-time PCR.

Colorectal cancer (CRC) is the second leading cause of cancer-related death in developed countries. Early detection of CRC leads to decreased CRC mortality. A blood-based CRC screening test is highly desirable due to limited invasiveness and high acceptance rate among patients compared to currently used fecal occult blood testing and colonoscopy. Here we describe the discovery and validation of a 29-gene panel in peripheral blood mononuclear cells (PBMC) for the detection of CRC and adenomatous polyps (AP). Blood samples were prospectively collected from a multicenter, case-control clinical study. First, we profiled 93 samples with 667 candidate and 3 reference genes by high throughput real-time PCR (OpenArray system). After analysis, 160 genes were retained and tested again on 51 additional samples. Low expressed and unstable genes were discarded resulting in a final dataset of 144 samples profiled with 140 genes. To define which genes, alone or in combinations had the highest potential to discriminate AP and/or CRC from controls, data were analyzed by a combination of univariate and multivariate methods. A list of 29 potentially discriminant genes was compiled and evaluated for its predictive accuracy by penalized logistic regression and bootstrap. This method discriminated AP >1cm and CRC from controls with a sensitivity of 59% and 75%, respectively, with 91% specificity. The behavior of the 29-gene panel was validated with a LightCycler 480 real-time PCR platform, commonly adopted by clinical laboratories. In this work we identified a 29-gene panel expressed in PBMC that can be used for developing a novel minimally-invasive test for accurate detection of AP and CRC using a standard real-time PCR platform.

Improving strategic decision-making with simulation based decision support systems

Combating climate change is one of the key tasks of humanity in the 21st century. One of the leading causes is carbon dioxide emissions due to usage of fossil fuels. Renewable energy sources should be used instead of relying on oil, gas, and coal. In Finland a significant amount of energy is produced using wood. The usage of wood chips is expected to increase in the future significantly, over 60 %. The aim of this research is to improve understanding over the costs of wood chip supply chains. This is conducted by utilizing simulation as the main research method. The simulation model utilizes both agent-based modelling and discrete event simulation to imitate the wood chip supply chain. This thesis concentrates on the usage of simulation based decision support systems in strategic decision-making. The simulation model is part of a decision support system, which connects the simulation model to databases but also provides a graphical user interface for the decisionmaker. The main analysis conducted with the decision support system concentrates on comparing a traditional supply chain to a supply chain utilizing specialized containers. According to the analysis, the container supply chain is able to have smaller costs than the traditional supply chain. Also, a container supply chain can be more easily scaled up due to faster emptying operations. Initially the container operations would only supply part of the fuel needs of a power plant and it would complement the current supply chain. The model can be expanded to include intermodal supply chains as due to increased demand in the future there is not enough wood chips located close to current and future power plants.

Decision making and decision support in service systems

This thesis is a literature study that develops a conceptual model of decision making and decision support in service systems. The study is related to the Ä-Logi, Intelligent Service Logic for Welfare Sector Services research project, and the objective of the study is to develop the necessary theoretical framework to enable further research based on the research project results and material. The study first examines the concepts of service and service systems, focusing on understanding the characteristics of service systems and their implications for decision making and decision support to provide the basis for the development of the conceptual model. Based on the identified service system characteristics, an integrated model of service systems is proposed that views service systems through a number of interrelated perspectives that each offer different, but complementary, implications on the nature of decision making and the requirements for decision support in service systems. Based on the model, it is proposed that different types of decision making contexts can be identified in service systems that may be dominated by different types of decision making processes and where different types of decision support may be required, depending on the characteristics of the decision making context and its decision making processes. The proposed conceptual model of decision making and decision support in service systems examines the characteristics of decision making contexts and processes in service systems, and their typical requirements for decision support. First, a characterization of different types of decision making contexts in service systems is proposed based on the Cynefin framework and the identified service system characteristics. Second, the nature of decision making processes in service systems is proposed to be dual, with both rational and naturalistic decision making processes existing in service systems, and having an important and complementary role in decision making in service systems. Finally, a characterization of typical requirements for decision support in service systems is proposed that examines the decision support requirements associated with different types of decision making processes in characteristically different types of decision making contexts. It is proposed that decision support for the decision making processes that are based on rational decision making can be based on organizational decision support models, while decision support for the decision making processes that are based on naturalistic decision making should be based on supporting the decision makers’ situation awareness and facilitating the development of their tacit knowledge of the system and its tasks. Based on the proposed conceptual model a further research process is proposed. The study additionally provides a number of new perspectives on the characteristics of service systems, and the nature of decision making and requirements for decision support in service systems that can potentially provide a basis for further discussion and research, and support the practice alike.

Effective Data Management Enables Intelligent Utility Management

Instrumentation and automation plays a vital role to managing the water industry. These systems generate vast amounts of data that must be effectively managed in order to enable intelligent decision making. Time series data management software, commonly known as data historians are used for collecting and managing real-time (time series) information. More advanced software solutions provide a data infrastructure or utility wide Operations Data Management System (ODMS) that stores, manages, calculates, displays, shares, and integrates data from multiple disparate automation and business systems that are used daily in water utilities. These ODMS solutions are proven and have the ability to manage data from smart water meters to the collaboration of data across third party corporations. This paper focuses on practical, utility successes in the water industry where utility managers are leveraging instantaneous access to data from proven, commercial off-the-shelf ODMS solutions to enable better real-time decision making. Successes include saving $650,000 / year in water loss control, safeguarding water quality, saving millions of dollars in energy management and asset management. Immediate opportunities exist to integrate the research being done in academia with these ODMS solutions in the field and to leverage these successes to utilities around the world.

Real-Time Flood Forecasting Systems In Flanders

As a highly urbanized and flood prone region, Flanders has experienced multiple floods causing significant damage in the past. In response to the floods of 1998 and 2002 the Flemish Environment Agency, responsible for managing 1 400 km of unnavigable rivers, started setting up a real time flood forecasting system in 2003. Currently the system covers almost 2 000 km of unnavigable rivers, for which flood forecasts are accessible online (www.waterinfo.be). The forecasting system comprises more than 1 000 hydrologic and 50 hydrodynamic models which are supplied with radar rainfall, rainfall forecasts and on-site observations. Forecasts for the next 2 days are generated hourly, while 10 day forecasts are generated twice a day. Additionally, twice daily simulations based on percentile rainfall forecasts (from EPS predictions) result in uncertainty bands for the latter. Subsequent flood forecasts use the most recent rainfall predictions and observed parameters at any time while uncertainty on the longer-term is taken into account. The flood forecasting system produces high resolution dynamic flood maps and graphs at about 200 river gauges and more than 3 000 forecast points. A customized emergency response system generates phone calls and text messages to a team of hydrologists initiating a pro-active response to prevent upcoming flood damage. The flood forecasting system of the Flemish Environment Agency is constantly evolving and has proven to be an indispensable tool in flood crisis management. This was clearly the case during the November 2010 floods, when the agency issued a press release 2 days in advance allowing water managers, emergency services and civilians to take measures.

Sviluppo di un sistema miniaturizzato per il controllo real-time di assetto di nano e microsatelliti

Microsatelliti e nanosatelliti, come ad esempio i Cubesat, sono carenti di sistemi integrati di controllo d’assetto e di manovra orbitale. Lo scopo di questa tesi è stato quello di realizzare un sistema compatibile con Cubesat di una unità, completo di attuatori magnetici e attuatori meccanici, comprendente tutti i sensori e l’elettronica necessaria per il suo funzionamento, creando un dispositivo totalmente indipendente dal veicolo su cui è installato, capace di funzionare sia autonomamente che ricevendo comandi da terra. Nella tesi sono descritte le campagne di simulazioni numeriche effettuate per validare le scelte tecnologiche effettuate, le fasi di sviluppo dell’elettronica e della meccanica, i test sui prototipi realizzati e il funzionamento del sistema finale. Una integrazione così estrema dei componenti può implicare delle interferenze tra un dispositivo e l’altro, come nel caso dei magnetotorquer e dei magnetometri. Sono stati quindi studiati e valutati gli effetti della loro interazione, verificandone l’entità e la validità del progetto. Poiché i componenti utilizzati sono tutti di basso costo e di derivazione terrestre, è stata effettuata una breve introduzione teorica agli effetti dell’ambiente spaziale sull’elettronica, per poi descrivere un sistema fault-tolerant basato su nuove teorie costruttive. Questo sistema è stato realizzato e testato, verificando così la possibilità di realizzare un controller affidabile e resistente all’ambiente spaziale per il sistema di controllo d’assetto. Sono state infine analizzate alcune possibili versioni avanzate del sistema, delineandone i principali aspetti progettuali, come ad esempio l’integrazione di GPS e l’implementazione di funzioni di determinazione d’assetto sfruttando i sensori presenti a bordo.

Study of management decision making by ward sisters in a hospital and the effects on decision making after the implementation of a decision support sytem

This thesis considers management decision making at the ward level in hospitals especially by ward sisters, and the effectiveness of the intervention of a decision support system. Nursing practice theories were related to organisation and management theories in order to conceptualise a decision making framework for nurse manpower planning and deployment at the ward level. Decision and systems theories were explored to understand the concepts of decision making and the realities of power in an organisation. In essence, the hypothesis was concerned with changes in patterns of decision making that could occur with the intervention of a decision support system and that the degree of change would be governed by a set of `difficulty' factors within wards in a hospital. During the course of the study, a classification of ward management decision making was created, together with the development and validation of measuring instruments to test the research hypothesis. The decision support system used was rigorously evaluated to test whether benefits did accrue from its implementation. Quantitative results from sample wards together with qualitative information collected, were used to test this hypothesis and the outcomes postulated were supported by these findings. The main conclusion from this research is that a more rational approach to management decision making is feasible, using information from a decision support system. However, wards and ward sisters that need the most assistance, where the `difficulty' factors in the organisation are highest, benefit the least from this type of system. Organisational reviews are needed on these identified wards, involving managers and doctors, to reduce the levels of un-coordinated activities and disruption.

An advanced real-time predictive maintenance framework for large scale machine systems

This thesis introduces and develops a novel real-time predictive maintenance system to estimate the machine system parameters using the motion current signature. Recently, motion current signature analysis has been addressed as an alternative to the use of sensors for monitoring internal faults of a motor. A maintenance system based upon the analysis of motion current signature avoids the need for the implementation and maintenance of expensive motion sensing technology. By developing nonlinear dynamical analysis for motion current signature, the research described in this thesis implements a novel real-time predictive maintenance system for current and future manufacturing machine systems. A crucial concept underpinning this project is that the motion current signature contains infor­mation relating to the machine system parameters and that this information can be extracted using nonlinear mapping techniques, such as neural networks. Towards this end, a proof of con­cept procedure is performed, which substantiates this concept. A simulation model, TuneLearn, is developed to simulate the large amount of training data required by the neural network ap­proach. Statistical validation and verification of the model is performed to ascertain confidence in the simulated motion current signature. Validation experiment concludes that, although, the simulation model generates a good macro-dynamical mapping of the motion current signature, it fails to accurately map the micro-dynamical structure due to the lack of knowledge regarding performance of higher order and nonlinear factors, such as backlash and compliance. Failure of the simulation model to determine the micro-dynamical structure suggests the pres­ence of nonlinearity in the motion current signature. This motivated us to perform surrogate data testing for nonlinearity in the motion current signature. Results confirm the presence of nonlinearity in the motion current signature, thereby, motivating the use of nonlinear tech­niques for further analysis. Outcomes of the experiment show that nonlinear noise reduction combined with the linear reverse algorithm offers precise machine system parameter estimation using the motion current signature for the implementation of the real-time predictive maintenance system. Finally, a linear reverse algorithm, BJEST, is developed and applied to the motion current signature to estimate the machine system parameters.

Knowledge engineering for mental-health risk assessment and decision support

Mental-health risk assessment practice in the UK is mainly paper-based, with little standardisation in the tools that are used across the Services. The tools that are available tend to rely on minimal sets of items and unsophisticated scoring methods to identify at-risk individuals. This means the reasoning by which an outcome has been determined remains uncertain. Consequently, there is little provision for: including the patient as an active party in the assessment process, identifying underlying causes of risk, and eecting shared decision-making. This thesis develops a tool-chain for the formulation and deployment of a computerised clinical decision support system for mental-health risk assessment. The resultant tool, GRiST, will be based on consensual domain expert knowledge that will be validated as part of the research, and will incorporate a proven psychological model of classication for risk computation. GRiST will have an ambitious remit of being a platform that can be used over the Internet, by both the clinician and the layperson, in multiple settings, and in the assessment of patients with varying demographics. Flexibility will therefore be a guiding principle in the development of the platform, to the extent that GRiST will present an assessment environment that is tailored to the circumstances in which it nds itself. XML and XSLT will be the key technologies that help deliver this exibility.

Decision support for lifecycle planning and risk management of small-scale biomass combined heat and power (bCHP) projects in the UK

Biomass is projected to account for approximately half of the new energy production required to achieve the 2020 primary energy target in the UK. Combined heat and power (CHP) bioenergy systems are not only a highly efficient method of energy conversion, at smaller-scales a significant proportion of the heat produced can be effectively utilised for hot water, space heating or industrial heating purposes. However, there are many barriers to project development and this has greatly inhibited deployment in the UK. Project viability is highly subjective to changes in policy, regulation, the finance market and the low cost incumbent; a high carbon centralised energy system. Unidentified or unmitigated barriers occurring during the project lifecycle may not only negatively impact on the project but could ultimately lead to project failure. The research develops a decision support system (DSS) for small-scale (500 kWe to 10 MWe) biomass combustion CHP project development and risk management in the early stages of a potential project’s lifecycle. By supporting developers in the early stages of project development with financial, scheduling and risk management analysis, the research aims to reduce the barriers identified and streamline decision-making. A fuzzy methodology is also applied throughout the developed DSS to support developers in handling the uncertain or approximate information often held at the early stages of the project lifecycle. The DSS is applied to a case study of a recently failed (2011) small-scale biomass CHP project to demonstrate its applicability and benefits. The application highlights that the proposed development within the case study was not viable. Moreover, further analysis of the possible barriers with the DSS confirmed that some possible modifications to be project could have improved this, such as a possible change of feedstock to a waste or residue, addressing the unnecessary land lease cost or by increasing heat utilisation onsite. This analysis is further supported by a practitioner evaluation survey that confirms the research contribution and objectives are achieved.

Bioenergy decision support systems:worth the effort?

The purpose of this research is to explore the disparity between the existing model-orientated bioenergy decision support system (DSS) functions and what is desired by practitioners, in particular bioenergy project developers. This research has compiled the published bioenergy project development models, to highlight the characteristics emphasised by academics. When contrasted against a UK practitioner’s perspective through the administration of a Likert style questionnaire, it is clear that the general DSS issues still persist. Finally, the research suggests how this ’theory-practice’ divide could be addressed. The research contribute

Towards the Problems of an Evaluation of Data Uncertainty in Decision Support Systems

The question of forming aim-oriented description of an object domain of decision support process is outlined. Two main problems of an estimation and evaluation of data and knowledge uncertainty in decision support systems – straight and reverse, are formulated. Three conditions being the formalized criteria of aimoriented constructing of input, internal and output spaces of some decision support system are proposed. Definitions of appeared and hidden data uncertainties on some measuring scale are given.

Development of hardware in the loop real-time control techniques for hybrid power systems involving distributed demands and sustainable energy sources

The future power grid will effectively utilize renewable energy resources and distributed generation to respond to energy demand while incorporating information technology and communication infrastructure for their optimum operation. This dissertation contributes to the development of real-time techniques, for wide-area monitoring and secure real-time control and operation of hybrid power systems. ^ To handle the increased level of real-time data exchange, this dissertation develops a supervisory control and data acquisition (SCADA) system that is equipped with a state estimation scheme from the real-time data. This system is verified on a specially developed laboratory-based test bed facility, as a hardware and software platform, to emulate the actual scenarios of a real hybrid power system with the highest level of similarities and capabilities to practical utility systems. It includes phasor measurements at hundreds of measurement points on the system. These measurements were obtained from especially developed laboratory based Phasor Measurement Unit (PMU) that is utilized in addition to existing commercially based PMU’s. The developed PMU was used in conjunction with the interconnected system along with the commercial PMU’s. The tested studies included a new technique for detecting the partially islanded micro grids in addition to several real-time techniques for synchronization and parameter identifications of hybrid systems. ^ Moreover, due to numerous integration of renewable energy resources through DC microgrids, this dissertation performs several practical cases for improvement of interoperability of such systems. Moreover, increased number of small and dispersed generating stations and their need to connect fast and properly into the AC grids, urged this work to explore the challenges that arise in synchronization of generators to the grid and through introduction of a Dynamic Brake system to improve the process of connecting distributed generators to the power grid.^ Real time operation and control requires data communication security. A research effort in this dissertation was developed based on Trusted Sensing Base (TSB) process for data communication security. The innovative TSB approach improves the security aspect of the power grid as a cyber-physical system. It is based on available GPS synchronization technology and provides protection against confidentiality attacks in critical power system infrastructures. ^

Real time mobile system for support in firefighting environments

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores