Statistical methods for biomedical signal analysis and processing

Statistical modelling and statistical learning theory are two powerful analytical frameworks for analyzing signals and developing efficient processing and classification algorithms. In this thesis, these frameworks are applied for modelling and processing biomedical signals in two different contexts: ultrasound medical imaging systems and primate neural activity analysis and modelling. In the context of ultrasound medical imaging, two main applications are explored: deconvolution of signals measured from a ultrasonic transducer and automatic image segmentation and classification of prostate ultrasound scans. In the former application a stochastic model of the radio frequency signal measured from a ultrasonic transducer is derived. This model is then employed for developing in a statistical framework a regularized deconvolution procedure, for enhancing signal resolution. In the latter application, different statistical models are used to characterize images of prostate tissues, extracting different features. These features are then uses to segment the images in region of interests by means of an automatic procedure based on a statistical model of the extracted features. Finally, machine learning techniques are used for automatic classification of the different region of interests. In the context of neural activity signals, an example of bio-inspired dynamical network was developed to help in studies of motor-related processes in the brain of primate monkeys. The presented model aims to mimic the abstract functionality of a cell population in 7a parietal region of primate monkeys, during the execution of learned behavioural tasks.

Teleconnections between Ethiopian summer rainfall and sea surface temperature: part I. Observation and modelling

In this study, the oceanic regions that are associated with anomalous Ethiopian summer rains were identified and the teleconnection mechanisms that give rise to these associations have been investigated. Because of the complexities of rainfall climate in the horn of Africa, Ethiopia has been subdivided into six homogeneous rainfall zones and the influence of SST anomalies was analysed separately for each zone. The investigation made use of composite analysis and modelling experiments. Two sets of composites of atmospheric fields were generated, one based on excess/deficit rainfall anomalies and the other based on warm/cold SST anomalies in specific oceanic regions. The aim of the composite analysis was to determine the link between SST and rainfall in terms of large scale features. The modelling experiments were intended to explore the causality of these linkage. The results show that the equatorial Pacific, the midlatitude northwest Pacific and the Gulf of Guinea all exert an influence on the summer rainfall in various part of the country. The results demonstrate that different mechanisms linked to sea surface temperature control variations in rainfall in different parts of Ethiopia. This has important consequences for seasonal forecasting models which are based on statistical correlations between SST and seasonal rainfall totals. It is clear that such statistical models should take account of the local variations in teleconnections.

Meta-analysis of strategies to control nitrate leaching in irrigated agricultural systems and their effects on crop yield.

Nitrate leaching (NL) is an important N loss process in irrigated agriculture that imposes a cost on the farmer and the environment. A meta-analysis of published experimental results from agricultural irrigated systems was conducted to identify those strategies that have proven effective at reducing NL and to quantify the scale of reduction that can be achieved. Forty-four scientific articles were identified which investigated four main strategies (water and fertilizer management, use of cover crops and fertilizer technology) creating a database with 279 observations on NL and 166 on crop yield. Management practices that adjust water application to crop needs reduced NL by a mean of 80% without a reduction in crop yield. Improved fertilizer management reduced NL by 40%, and the best relationship between yield and NL was obtained when applying the recommended fertilizer rate. Replacing a fallow with a non-legume cover crop reduced NL by 50% while using a legume did not have any effect on NL. Improved fertilizer technology also decreased NL but was the least effective of the selected strategies. The risk of nitrate leaching from irrigated systems is high, but optimum management practices may mitigate this risk and maintain crop yields while enhancing environmental sustainability.

Modelling nitrous oxide emissions from mown-grass and grain-cropping systems : Testing and sensitivity analysis of DailyDayCent using high frequency measurements

The lead author, Nimai Senapati (Post doc), was funded by the European community’s Seventh Framework programme (FP2012-2015) under grant agreement no. 262060 (ExpeER). The research leading to these results has received funding principally from the ANR (ANR-11-INBS-0001), AllEnvi, CNRS-INSU. We would like to thank the National Research Infrastructure ‘Agro-écosystèmes, Cycles Biogéochimique et Biodiversité (SOERE-ACBB http://www.soere-acbb.com/fr/) for their support in field experiment. We are deeply indebted to Christophe deBerranger, Xavier Charrier for their substantial technical assistance and Patricia Laville for her valuables suggestion regarding N2O flux estimation.

Monitoring and modelling the three-dimensional flow of water under drip irrigation

The interpretation of soil water dynamics under drip irrigation systems is relevant for crop production as well as on water use and management. In this study a three-dimensional representation of the flow of water under drip irrigation is presented. The work includes analysis of the water balance at point scale as well as area-average, exploring uncertainties in water balance estimations depending on the number of locations sampled. The water flow was monitored by detailed profile water content measurements before irrigation, after irrigation and 24 h later with a dense array of soil moisture access tubes radially distributed around selected drippers. The objective was to develop a methodology that could be used on selected occasions to obtain 'snap shots' of the detailed three-dimensional patterns of soil moisture. Such patterns are likely to be very complex, as spatial variability will be induced for a number of reasons, such as strong horizontal gradients in soil moisture, variations between individual sources in the amount of water applied and spatial variability is soil hydraulic properties. Results are compared with a widely used numerical model, Hydrus-2D. The observed dynamic of the water content distribution is in good agreement with model simulations, although some discrepancies concerning the horizontal distribution of the irrigation bulb are noted due to soil heterogeneity. (c) 2006 Elsevier B.V. All rights reserved.

Análisis y diseño de multiplicadores y mezcladores mediante el método de Monte Carlo en la banda de THz = Analysis and design of multipliers and mixers via Monte Carlo modelling at THz bands

La región del espectro electromagnético comprendida entre 100 GHz y 10 THz alberga una gran variedad de aplicaciones en campos tan dispares como la radioastronomía, espectroscopíamolecular, medicina, seguridad, radar, etc. Los principales inconvenientes en el desarrollo de estas aplicaciones son los altos costes de producción de los sistemas trabajando a estas frecuencias, su costoso mantenimiento, gran volumen y baja fiabilidad. Entre las diferentes tecnologías a frecuencias de THz, la tecnología de los diodos Schottky juega un importante papel debido a su madurez y a la sencillez de estos dispositivos. Además, los diodos Schottky pueden operar tanto a temperatura ambiente como a temperaturas criogénicas, con altas eficiencias cuando se usan como multiplicadores y con moderadas temperaturas de ruido en mezcladores. El principal objetivo de esta tesis doctoral es analizar los fenómenos físicos responsables de las características eléctricas y del ruido en los diodos Schottky, así como analizar y diseñar circuitos multiplicadores y mezcladores en bandas milimétricas y submilimétricas. La primera parte de la tesis presenta un análisis de los fenómenos físicos que limitan el comportamiento de los diodos Schottky de GaAs y GaN y de las características del espectro de ruido de estos dispositivos. Para llevar a cabo este análisis, un modelo del diodo basado en la técnica de Monte Carlo se ha considerado como referencia debido a la elevada precisión y fiabilidad de este modelo. Además, el modelo de Monte Carlo permite calcular directamente el espectro de ruido de los diodos sin necesidad de utilizar ningún modelo analítico o empírico. Se han analizado fenómenos físicos como saturación de la velocidad, inercia de los portadores, dependencia de la movilidad electrónica con la longitud de la epicapa, resonancias del plasma y efectos no locales y no estacionarios. También se ha presentado un completo análisis del espectro de ruido para diodos Schottky de GaAs y GaN operando tanto en condiciones estáticas como variables con el tiempo. Los resultados obtenidos en esta parte de la tesis contribuyen a mejorar la comprensión de la respuesta eléctrica y del ruido de los diodos Schottky en condiciones de altas frecuencias y/o altos campos eléctricos. También, estos resultados han ayudado a determinar las limitaciones de modelos numéricos y analíticos usados en el análisis de la respuesta eléctrica y del ruido electrónico en los diodos Schottky. La segunda parte de la tesis está dedicada al análisis de multiplicadores y mezcladores mediante una herramienta de simulación de circuitos basada en la técnica de balance armónico. Diferentes modelos basados en circuitos equivalentes del dispositivo, en las ecuaciones de arrastre-difusión y en la técnica de Monte Carlo se han considerado en este análisis. El modelo de Monte Carlo acoplado a la técnica de balance armónico se ha usado como referencia para evaluar las limitaciones y el rango de validez de modelos basados en circuitos equivalentes y en las ecuaciones de arrastredifusión para el diseño de circuitos multiplicadores y mezcladores. Una notable característica de esta herramienta de simulación es que permite diseñar circuitos Schottky teniendo en cuenta tanto la respuesta eléctrica como el ruido generado en los dispositivos. Los resultados de las simulaciones presentados en esta parte de la tesis, tanto paramultiplicadores comomezcladores, se han comparado con resultados experimentales publicados en la literatura. El simulador que integra el modelo de Monte Carlo con la técnica de balance armónico permite analizar y diseñar circuitos a frecuencias superiores a 1 THz. ABSTRACT The terahertz region of the electromagnetic spectrum(100 GHz-10 THz) presents a wide range of applications such as radio-astronomy, molecular spectroscopy, medicine, security and radar, among others. The main obstacles for the development of these applications are the high production cost of the systems working at these frequencies, highmaintenance, high volume and low reliability. Among the different THz technologies, Schottky technology plays an important rule due to its maturity and the inherent simplicity of these devices. Besides, Schottky diodes can operate at both room and cryogenic temperatures, with high efficiency in multipliers and moderate noise temperature in mixers. This PhD. thesis is mainly concerned with the analysis of the physical processes responsible for the characteristics of the electrical response and noise of Schottky diodes, as well as the analysis and design of frequency multipliers and mixers at millimeter and submillimeter wavelengths. The first part of the thesis deals with the analysis of the physical phenomena limiting the electrical performance of GaAs and GaN Schottky diodes and their noise performance. To carry out this analysis, a Monte Carlo model of the diode has been used as a reference due to the high accuracy and reliability of this diode model at millimeter and submillimter wavelengths. Besides, the Monte Carlo model provides a direct description of the noise spectra of the devices without the necessity of any additional analytical or empirical model. Physical phenomena like velocity saturation, carrier inertia, dependence of the electron mobility on the epilayer length, plasma resonance and nonlocal effects in time and space have been analysed. Also, a complete analysis of the current noise spectra of GaAs and GaN Schottky diodes operating under static and time varying conditions is presented in this part of the thesis. The obtained results provide a better understanding of the electrical and the noise responses of Schottky diodes under high frequency and/or high electric field conditions. Also these results have helped to determine the limitations of numerical and analytical models used in the analysis of the electrical and the noise responses of these devices. The second part of the thesis is devoted to the analysis of frequency multipliers and mixers by means of an in-house circuit simulation tool based on the harmonic balance technique. Different lumped equivalent circuits, drift-diffusion and Monte Carlo models have been considered in this analysis. The Monte Carlo model coupled to the harmonic balance technique has been used as a reference to evaluate the limitations and range of validity of lumped equivalent circuit and driftdiffusion models for the design of frequency multipliers and mixers. A remarkable feature of this reference simulation tool is that it enables the design of Schottky circuits from both electrical and noise considerations. The simulation results presented in this part of the thesis for both multipliers and mixers have been compared with measured results available in the literature. In addition, the Monte Carlo simulation tool allows the analysis and design of circuits above 1 THz.

Anaerobic Digestion Project Working Guide: A Case Study Analysis and Procedural Summary of Anaerobic Digester Projects for the United States Agricultural Sector

Renewable energy such as biomass has given markets, including dairy farms, an effective approach to reducing the costs of sustaining a profitable business. Anaerobic digestion systems offer dairy farms a very effective way to reduce manure odor, comply with soil and water pollution regulations, manufacture compost for general market sales, produce irrigation capacity and generate on-site electricity as well as the ability to sell excess electricity back to the local utilities. This project defines anaerobic digestion technologies and practices, analyzes case studies and presents a step-by-step anaerobic digestion project startup checklist. The result is an anaerobic digestion project working guide that acts as a tool to aid dairy farmers in their own potential anaerobic digestion project.

Will improved access to capital dampen the need for more agricultural land? A CGE analysis of agricultural capital markets and world-wide biofuel policies. Factor Markets Working Paper No. 48, May 2013

This paper analyses the consequences of enhanced biofuel production in regions and countries of the world that have announced plans to implement or expand on biofuel policies. The analysis considers biofuel policies implemented as binding blending targets for transportation fuels. The chosen quantitative modelling approach is two-fold: it combines the analysis of biofuel policies in a multi-sectoral economic model (MAGNET) with systematic variation of the functioning of capital and labour markets. This paper adds to existing research by considering biofuel policies in the EU, the US and various other countries with considerable agricultural production and trade, such as Brazil, India and China. Moreover, the application multi-sectoral modelling system with different assumptions on the mobility of factor markets allows for the observation of changes in economic indicators under different conditions of how factor markets work. Systematic variation of factor mobility indicates that the ‘burden’ of global biofuel policies is not equally distributed across different factors within agricultural production. Agricultural land, as the pre-dominant and sector-specific factor, is, regardless of different degrees of inter-sectoral or intra-sectoral factor mobility, the most important factor limiting the expansion of agricultural production. More capital and higher employment in agriculture will ease the pressure on additional land use – but only partly. To expand agricultural production at global scale requires both land and mobile factors adapted to increase total factor productivity in agriculture in the most efficient way.

Applying ontologies to business and systems modelling techniques and perspectives: Lessons learned

For many years in the area of business systems analysis and design, practitioners and researchers alike have been searching for some comprehensive basis on which to evaluate, compare, and engineer techniques that are promoted for use in the modelling of systems' requirements. To date, while many frameworks, factors, and facets have been forthcoming, none appear to be based on a sound theory. In light of this dilemma, over the last 10 years, attention has been devoted by researchers to the use of ontology to provide some theoretical basis for the advancement of the business systems modelling discipline. This paper outlines how we have used a particular ontology for this purpose over the last five years. In particular we have learned that the understandability and the applicability of the selected ontology must be clear for IS professionals, the results of any ontological evaluation must be tempered by economic efficiency considerations of the stakeholders involved, and ontologies may have to be focused for the business purpose and type of user involved in the modelling situation.

A methodology for analysis and control of discrete event dynamic systems

The rapid developments in computer technology have resulted in a widespread use of discrete event dynamic systems (DEDSs). This type of system is complex because it exhibits properties such as concurrency, conflict and non-determinism. It is therefore important to model and analyse such systems before implementation to ensure safe, deadlock free and optimal operation. This thesis investigates current modelling techniques and describes Petri net theory in more detail. It reviews top down, bottom up and hybrid Petri net synthesis techniques that are used to model large systems and introduces on object oriented methodology to enable modelling of larger and more complex systems. Designs obtained by this methodology are modular, easy to understand and allow re-use of designs. Control is the next logical step in the design process. This thesis reviews recent developments in control DEDSs and investigates the use of Petri nets in the design of supervisory controllers. The scheduling of exclusive use of resources is investigated and an efficient Petri net based scheduling algorithm is designed and a re-configurable controller is proposed. To enable the analysis and control of large and complex DEDSs, an object oriented C++ software tool kit was developed and used to implement a Petri net analysis tool, Petri net scheduling and control algorithms. Finally, the methodology was applied to two industrial DEDSs: a prototype can sorting machine developed by Eurotherm Controls Ltd., and a semiconductor testing plant belonging to SGS Thomson Microelectronics Ltd.

Analysis and optimisation of the performance of nonlinear optical communication systems

We investigate the feasibility of simultaneous suppressing of the amplification noise and nonlinearity, representing the most fundamental limiting factors in modern optical communication. To accomplish this task we developed a general design optimisation technique, based on concepts of noise and nonlinearity management. We demonstrate the immense efficiency of the novel approach by applying it to a design optimisation of transmission lines with periodic dispersion compensation using Raman and hybrid Raman-EDFA amplification. Moreover, we showed, using nonlinearity management considerations, that the optimal performance in high bit-rate dispersion managed fibre systems with hybrid amplification is achieved for a certain amplifier spacing – which is different from commonly known optimal noise performance corresponding to fully distributed amplification. Required for an accurate estimation of the bit error rate, the complete knowledge of signal statistics is crucial for modern transmission links with strong inherent nonlinearity. Therefore, we implemented the advanced multicanonical Monte Carlo (MMC) method, acknowledged for its efficiency in estimating distribution tails. We have accurately computed acknowledged for its efficiency in estimating distribution tails. We have accurately computed marginal probability density functions for soliton parameters, by numerical modelling of Fokker-Plank equation applying the MMC simulation technique. Moreover, applying a powerful MMC method we have studied the BER penalty caused by deviations from the optimal decision level in systems employing in-line 2R optical regeneration. We have demonstrated that in such systems the analytical linear approximation that makes a better fit in the central part of the regenerator nonlinear transfer function produces more accurate approximation of the BER and BER penalty. We present a statistical analysis of RZ-DPSK optical signal at direct detection receiver with Mach-Zehnder interferometer demodulation

The mechanism of ϕC31 integrase directionality : experimental analysis and computational modelling

Acknowledgments We thank Sally Rowland for helpful comments on the manuscript. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Design, modelling, simulation and integration of cyber physical systems: methods and applications

The main drivers for the development and evolution of Cyber Physical Systems (CPS) are the reduction of development costs and time along with the enhancement of the designed products. The aim of this survey paper is to provide an overview of different types of system and the associated transition process from mechatronics to CPS and cloud-based (IoT) systems. It will further consider the requirement that methodologies for CPS-design should be part of a multi-disciplinary development process within which designers should focus not only on the separate physical and computational components, but also on their integration and interaction. Challenges related to CPS-design are therefore considered in the paper from the perspectives of the physical processes, computation and integration respectively. Illustrative case studies are selected from different system levels starting with the description of the overlaying concept of Cyber Physical Production Systems (CPPSs). The analysis and evaluation of the specific properties of a sub-system using a condition monitoring system, important for the maintenance purposes, is then given for a wind turbine.