Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

On Real-Time Monitoring And Control For Efficient Management Of Drinking Water Networks: Barcelona Case Study

Drinking water utilities in urban areas are focused on finding smart solutions facing new challenges in their real-time operation because of limited water resources, intensive energy requirements, a growing population, a costly and ageing infrastructure, increasingly stringent regulations, and increased attention towards the environmental impact of water use. Such challenges force water managers to monitor and control not only water supply and distribution, but also consumer demand. This paper presents and discusses novel methodologies and procedures towards an integrated water resource management system based on advanced ICT technologies of automation and telecommunications for largely improving the efficiency of drinking water networks (DWN) in terms of water use, energy consumption, water loss minimization, and water quality guarantees. In particular, the paper addresses the first results of the European project EFFINET (FP7-ICT2011-8-318556) devoted to the monitoring and control of the DWN in Barcelona (Spain). Results are split in two levels according to different management objectives: (i) the monitoring level is concerned with all the aspects involved in the observation of the current state of a system and the detection/diagnosis of abnormal situations. It is achieved through sensors and communications technology, together with mathematical models; (ii) the control level is concerned with computing the best suitable and admissible control strategies for network actuators as to optimize a given set of operational goals related to the performance of the overall system. This level covers the network control (optimal management of water and energy) and the demand management (smart metering, efficient supply). The consideration of the Barcelona DWN as the case study will allow to prove the general applicability of the proposed integrated ICT solutions and their effectiveness in the management of DWN, with considerable savings of electricity costs and reduced water loss while ensuring the high European standards of water quality to citizens.

Adaptive, Decentralized, And Real-Time Sampling Strategies For Resource Constrained Hydraulic And Hydrologic Sensor Networks

We discuss the development and performance of a low-power sensor node (hardware, software and algorithms) that autonomously controls the sampling interval of a suite of sensors based on local state estimates and future predictions of water flow. The problem is motivated by the need to accurately reconstruct abrupt state changes in urban watersheds and stormwater systems. Presently, the detection of these events is limited by the temporal resolution of sensor data. It is often infeasible, however, to increase measurement frequency due to energy and sampling constraints. This is particularly true for real-time water quality measurements, where sampling frequency is limited by reagent availability, sensor power consumption, and, in the case of automated samplers, the number of available sample containers. These constraints pose a significant barrier to the ubiquitous and cost effective instrumentation of large hydraulic and hydrologic systems. Each of our sensor nodes is equipped with a low-power microcontroller and a wireless module to take advantage of urban cellular coverage. The node persistently updates a local, embedded model of flow conditions while IP-connectivity permits each node to continually query public weather servers for hourly precipitation forecasts. The sampling frequency is then adjusted to increase the likelihood of capturing abrupt changes in a sensor signal, such as the rise in the hydrograph – an event that is often difficult to capture through traditional sampling techniques. Our architecture forms an embedded processing chain, leveraging local computational resources to assess uncertainty by analyzing data as it is collected. A network is presently being deployed in an urban watershed in Michigan and initial results indicate that the system accurately reconstructs signals of interest while significantly reducing energy consumption and the use of sampling resources. We also expand our analysis by discussing the role of this approach for the efficient real-time measurement of stormwater systems.

Leakage Detection And Localization Method Based On A Hybrid Inverse/Direct Modelling Approach Suitable For Handling Multiple-Leak Scenarios

When an accurate hydraulic network model is available, direct modeling techniques are very straightforward and reliable for on-line leakage detection and localization applied to large class of water distribution networks. In general, this type of techniques based on analytical models can be seen as an application of the well-known fault detection and isolation theory for complex industrial systems. Nonetheless, the assumption of single leak scenarios is usually made considering a certain leak size pattern which may not hold in real applications. Upgrading a leak detection and localization method based on a direct modeling approach to handle multiple-leak scenarios can be, on one hand, quite straightforward but, on the other hand, highly computational demanding for large class of water distribution networks given the huge number of potential water loss hotspots. This paper presents a leakage detection and localization method suitable for multiple-leak scenarios and large class of water distribution networks. This method can be seen as an upgrade of the above mentioned method based on a direct modeling approach in which a global search method based on genetic algorithms has been integrated in order to estimate those network water loss hotspots and the size of the leaks. This is an inverse / direct modeling method which tries to take benefit from both approaches: on one hand, the exploration capability of genetic algorithms to estimate network water loss hotspots and the size of the leaks and on the other hand, the straightforwardness and reliability offered by the availability of an accurate hydraulic model to assess those close network areas around the estimated hotspots. The application of the resulting method in a DMA of the Barcelona water distribution network is provided and discussed. The obtained results show that leakage detection and localization under multiple-leak scenarios may be performed efficiently following an easy procedure.

Software Tools For Large Scale Interactive Hydrodynamic Modeling

Running hydrodynamic models interactively allows both visual exploration and change of model state during simulation. One of the main characteristics of an interactive model is that it should provide immediate feedback to the user, for example respond to changes in model state or view settings. For this reason, such features are usually only available for models with a relatively small number of computational cells, which are used mainly for demonstration and educational purposes. It would be useful if interactive modeling would also work for models typically used in consultancy projects involving large scale simulations. This results in a number of technical challenges related to the combination of the model itself and the visualisation tools (scalability, implementation of an appropriate API for control and access to the internal state). While model parallelisation is increasingly addressed by the environmental modeling community, little effort has been spent on developing a high-performance interactive environment. What can we learn from other high-end visualisation domains such as 3D animation, gaming, virtual globes (Autodesk 3ds Max, Second Life, Google Earth) that also focus on efficient interaction with 3D environments? In these domains high efficiency is usually achieved by the use of computer graphics algorithms such as surface simplification depending on current view, distance to objects, and efficient caching of the aggregated representation of object meshes. We investigate how these algorithms can be re-used in the context of interactive hydrodynamic modeling without significant changes to the model code and allowing model operation on both multi-core CPU personal computers and high-performance computer clusters.

An evolving possibilistic fuzzy modeling approach for value-at-risk estimation

Market risk exposure plays a key role for nancial institutions risk management. A possible measure for this exposure is to evaluate losses likely to incurwhen the price of the portfolio's assets declines using Value-at-Risk (VaR) estimates, one of the most prominent measure of nancial downside market risk. This paper suggests an evolving possibilistic fuzzy modeling approach for VaR estimation. The approach is based on an extension of the possibilistic fuzzy c-means clustering and functional fuzzy rule-based modeling, which employs memberships and typicalities to update clusters and creates new clusters based on a statistical control distance-based criteria. ePFM also uses an utility measure to evaluate the quality of the current cluster structure. Computational experiments consider data of the main global equity market indexes of United States, London, Germany, Spain and Brazil from January 2000 to December 2012 for VaR estimation using ePFM, traditional VaR benchmarks such as Historical Simulation, GARCH, EWMA, and Extreme Value Theory and state of the art evolving approaches. The results show that ePFM is a potential candidate for VaR modeling, with better performance than alternative approaches.

Semiparametric modeling of the spatial distribution of occupational accident risk in the casual labor market, Piracicaba, southeast Brazil

The objective of this study was to estimate the spatial distribution of work accident risk in the informal work market in the urban zone of an industrialized city in southeast Brazil and to examine concomitant effects of age, gender, and type of occupation after controlling for spatial risk variation. The basic methodology adopted was that of a population-based case-control study with particular interest focused on the spatial location of work. Cases were all casual workers in the city suffering work accidents during a one-year period; controls were selected from the source population of casual laborers by systematic random sampling of urban homes. The spatial distribution of work accidents was estimated via a semiparametric generalized additive model with a nonparametric bidimensional spline of the geographical coordinates of cases and controls as the nonlinear spatial component, and including age, gender, and occupation as linear predictive variables in the parametric component. We analyzed 1,918 cases and 2,245 controls between 1/11/2003 and 31/10/2004 in Piracicaba, Brazil. Areas of significantly high and low accident risk were identified in relation to mean risk in the study region (p < 0.01). Work accident risk for informal workers varied significantly in the study area. Significant age, gender, and occupational group effects on accident risk were identified after correcting for this spatial variation. A good understanding of high-risk groups and high-risk regions underpins the formulation of hypotheses concerning accident causality and the development of effective public accident prevention policies.

Modeling of weeds interference periods in bean

Objetivou-se com este trabalho determinar o período de convivência anterior à interferência das plantas daninhas (PAI) e o período anterior ao dano no rendimento econômico (PADRE) na cultura do feijão, em diferentes espaçamentos (0,45 e 0,60 m) e densidade de plantas (10 e 15 plantas m-1). Os tratamentos foram constituídos de períodos de convivência entre a cultura e as plantas daninhas (0 a 10, 0 a 20, 0 a 30, 0 a 40, 0 a 50, 0 a 60, 0 a 70 e 0 a 80 dias), mais uma testemunha sem convívio com as plantas daninhas. Adotou-se o delineamento experimental de blocos casualizados, com quatro repetições. Os períodos anteriores à interferência (PAI) da cultura foram de 23, 27, 13 e 19 dias após emergência, e os períodos anteriores ao dano no rendimento econômico (PADRE), de 10, 9, 8 e 8 dias, para os tratamentos com espaçamento de 0,45 m e densidades de semeadura de 10 e 15 plantas m-1 e para aqueles com espaçamento de 0,60 m e densidades de semeadura de 10 e 15 plantas m-1, respectivamente, o que reduziu a produtividade de grãos em 63, 50, 42 e 57%, respectivamente, com a presença das plantas daninhas durante todo o ciclo do feijoeiro.

Controle Adaptativo Robusto para Filtros Ativos de Potência Paralelo

Conventional control strategies used in shunt active power filters (SAPF) employs real-time instantaneous harmonic detection schemes which is usually implements with digital filters. This increase the number of current sensors on the filter structure which results in high costs. Furthermore, these detection schemes introduce time delays which can deteriorate the harmonic compensation performance. Differently from the conventional control schemes, this paper proposes a non-standard control strategy which indirectly regulates the phase currents of the power mains. The reference currents of system are generated by the dc-link voltage controller and is based on the active power balance of SAPF system. The reference currents are aligned to the phase angle of the power mains voltage vector which is obtained by using a dq phase locked loop (PLL) system. The current control strategy is implemented by an adaptive pole placement control strategy integrated to a variable structure control scheme (VS-APPC). In the VS-APPC, the internal model principle (IMP) of reference currents is used for achieving the zero steady state tracking error of the power system currents. This forces the phase current of the system mains to be sinusoidal with low harmonics content. Moreover, the current controllers are implemented on the stationary reference frame to avoid transformations to the mains voltage vector reference coordinates. This proposed current control strategy enhance the performance of SAPF with fast transient response and robustness to parametric uncertainties. Experimental results are showing for determining the effectiveness of SAPF proposed control system

Contribuições à análise de robustez de sistemas de controle usando redes neurais

This work develops a robustness analysis with respect to the modeling errors, being applied to the strategies of indirect control using Artificial Neural Networks - ANN s, belong to the multilayer feedforward perceptron class with on-line training based on gradient method (backpropagation). The presented schemes are called Indirect Hybrid Control and Indirect Neural Control. They are presented two Robustness Theorems, being one for each proposed indirect control scheme, which allow the computation of the maximum steady-state control error that will occur due to the modeling error what is caused by the neural identifier, either for the closed loop configuration having a conventional controller - Indirect Hybrid Control, or for the closed loop configuration having a neural controller - Indirect Neural Control. Considering that the robustness analysis is restrict only to the steady-state plant behavior, this work also includes a stability analysis transcription that is suitable for multilayer perceptron class of ANN s trained with backpropagation algorithm, to assure the convergence and stability of the used neural systems. By other side, the boundness of the initial transient behavior is assured by the assumption that the plant is BIBO (Bounded Input, Bounded Output) stable. The Robustness Theorems were tested on the proposed indirect control strategies, while applied to regulation control of simulated examples using nonlinear plants, and its results are presented

Modelagem e controle de um microveículo aéreo: uma aplicação de estabilidade robusta com a técnica backstepping em uma estrutura hexarrotor

In this Thesis, the development of the dynamic model of multirotor unmanned aerial vehicle with vertical takeoff and landing characteristics, considering input nonlinearities and a full state robust backstepping controller are presented. The dynamic model is expressed using the Newton-Euler laws, aiming to obtain a better mathematical representation of the mechanical system for system analysis and control design, not only when it is hovering, but also when it is taking-off, or landing, or flying to perform a task. The input nonlinearities are the deadzone and saturation, where the gravitational effect and the inherent physical constrains of the rotors are related and addressed. The experimental multirotor aerial vehicle is equipped with an inertial measurement unit and a sonar sensor, which appropriately provides measurements of attitude and altitude. A real-time attitude estimation scheme based on the extended Kalman filter using quaternions was developed. Then, for robustness analysis, sensors were modeled as the ideal value with addition of an unknown bias and unknown white noise. The bounded robust attitude/altitude controller were derived based on globally uniformly practically asymptotically stable for real systems, that remains globally uniformly asymptotically stable if and only if their solutions are globally uniformly bounded, dealing with convergence and stability into a ball of the state space with non-null radius, under some assumptions. The Lyapunov analysis technique was used to prove the stability of the closed-loop system, compute bounds on control gains and guaranteeing desired bounds on attitude dynamics tracking errors in the presence of measurement disturbances. The controller laws were tested in numerical simulations and in an experimental hexarotor, developed at the UFRN Robotics Laboratory

Estratégia de controle robusto para filtro ativo paralelo sem detecção de harmônicos de correntes

Conventional control strategies used in shunt active power filters (SAPF) employs real-time instantaneous harmonic detection schemes which is usually implements with digital filters. This increase the number of current sensors on the filter structure which results in high costs. Furthermore, these detection schemes introduce time delays which can deteriorate the harmonic compensation performance. Differently from the conventional control schemes, this paper proposes a non-standard control strategy which indirectly regulates the phase currents of the power mains. The reference currents of system are generated by the dc-link voltage controller and is based on the active power balance of SAPF system. The reference currents are aligned to the phase angle of the power mains voltage vector which is obtained by using a dq phase locked loop (PLL) system. The current control strategy is implemented by an adaptive pole placement control strategy integrated to a variable structure control scheme (VS¡APPC). In the VS¡APPC, the internal model principle (IMP) of reference currents is used for achieving the zero steady state tracking error of the power system currents. This forces the phase current of the system mains to be sinusoidal with low harmonics content. Moreover, the current controllers are implemented on the stationary reference frame to avoid transformations to the mains voltage vector reference coordinates. This proposed current control strategy enhance the performance of SAPF with fast transient response and robustness to parametric uncertainties. Experimental results are showing for determining the effectiveness of SAPF proposed control system

Controle de Manipulador Redundante Utilizando Realimentação Visual

In conventional robot manipulator control, the desired path is specified in cartesian space and converted to joint space through inverse kinematics mapping. The joint references generated by this mapping are utilized for dynamic control in joint space. Thus, the end-effector position is, in fact, controlled indirectly, in open-loop, and the accuracy of grip position control directly depends on the accuracy of the available kinematic model. In this report, a new scheme for redundant manipulator kinematic control, based on visual servoing is proposed. In the proposed system, a robot image acquired through a CCD camera is processed in order to compute the position and orientation of each link of the robot arm. The robot task is specified as a temporal sequence of reference images of the robot arm. Thus, both the measured pose and the reference pose are specified in the same image space, and its difference is utilized to generate a cartesian space error for kinematic control purposes. The proposed control scheme was applied in a four degree-of-freedom planar redundant robot arm, experimental results are shown

Modelagem e controle adaptativo de uma planta didática de nível com instrumentação industrial

The control, automation and optimization areas help to improve the processes used by industry. They contribute to a fast production line, improving the products quality and reducing the manufacturing costs. Didatic plants are good tools for research in these areas, providing a direct contact with some industrial equipaments. Given these capabilities, the main goal of this work is to model and control a didactic plant, which is a level and flow process control system with an industrial instrumentation. With a model it is possible to build a simulator for the plant that allows studies about its behaviour, without any of the real processes operational costs, like experiments with controllers. They can be tested several times before its application in a real process. Among the several types of controllers, it was used adaptive controllers, mainly the Direct Self-Tuning Regulators (DSTR) with Integral Action and the Gain Scheduling (GS). The DSTR was based on Pole-Placement design and use the Recursive Least Square to calculate the controller parameters. The characteristics of an adaptive system was very worth to guarantee a good performance when the controller was applied to the plant

The dorsal raphe nucleus exerts opposed control on generalized anxiety and panic-related defensive responses in rats

It has been proposed that the ascending dorsal raphe (DR)-serotonergic (5-HT) pathway facilitates conditioned avoidance responses to potential or distal threat, while the DR-periventricular 5-HT pathway inhibits unconditioned flight reactions to proximal danger. Dysfunction on these pathways would be, respectively, related to generalized anxiety (GAD) and panic disorder (PD). To investigate this hypothesis, we microinjected into the rat DR the benzodiazepine inverse receptor agonist FG 7142, the 5-HT1A receptor agonist 8-OH-DPAT or the GABA(A) receptor agonist muscimol. Animals were evaluated in the elevated T-maze (ETM) and light/dark transition test. These models generate defensive responses that have been related to GAD and PD. Experiments were also conducted in the ETM 14 days after the selective lesion of DR serotonergic neurons by 5,7-dihydroxytriptamine (DHT). In all cases, rats were pre-exposed to one of the open arms of the ETM 1 day before testing. The results showed that FG 7142 facilitated inhibitory avoidance, an anxiogenic effect, while impairing one-way escape, an anxiolytic effect. 8-OH-DPAT, muscimol, and 5,7-DHT-induced lesions acted in the opposite direction, impairing inhibitory avoidance while facilitating one-way escape from the open arm. In the light/dark transition, 8-OH-DPAT and muscimol increased the time spent in the lighted compartment, an anxiolytic effect. The data supports the view that distinct DR-5-HT pathways regulate neural mechanisms underlying GAD and PD. (C) 2002 Elsevier B.V. B.V. All rights reserved.