Toward Never-Ending Object Learning for Robots

Thesis (Ph.D.)--University of Washington, 2016-06

Robust multivariable control of complex biological processes

This paper addresses advanced control of a biological nutrient removal (BNR) activated sludge process. Based on a previously validated distributed parameter model of the BNR activated sludge process, we present robust multivariable controller designs for the process, involving loop shaping of plant model, robust stability and performance analyses. Results from three design case studies showed that a multivariable controller with stability margins of 0.163, 0.492 and 1.062 measured by the normalised coprime factor, multiplicative and additive uncertainties respectively give the best results for meeting performance robustness specifications. The controller robustly stabilises effluent nutrients in the presence of uncertainties with the behaviour of phosphorus accumulating organisms as well as to effectively attenuate major disturbances introduced as step changes. This study also shows that, performance of the multivariable robust controller is superior to multi-loops SISO PI controllers for regulating the BNR activated sludge process in terms of robust stability and performance and controlling the process using inlet feed flowrate is infeasible. (C) 2003 Elsevier Ltd. All rights reserved.

Modelling nucleation in wet granulation

Nucleation is the first stage in any granulation process where binder liquid first comes into contact with the powder. This paper investigates the nucleation process where binder liquid is added to a fine powder with a spray nozzle. The dimensionless spray flux approach of Hapgood et al. (Powder Technol. 141 (2004) 20) is extended to account for nonuniform spray patterns and allow for overlap of nuclei granules rather than spray drops. A dimensionless nuclei distribution function which describes the effects of the design and operating parameters of the nucleation process (binder spray characteristics, the nucleation area ratio between droplets and nuclei and the powder bed velocity) on the fractional surface area coverage of nuclei on a moving powder bed is developed. From this starting point, a Monte Carlo nucleation model that simulates full nuclei size distributions as a function of the design and operating parameters that were implemented in the dimensionless nuclei distribution function is developed. The nucleation model was then used to investigate the effects of the design and operating parameters on the formed nuclei size distributions and to correlate these effects to changes of the dimensionless nuclei distribution function. Model simulations also showed that it is possible to predict nuclei size distributions beyond the drop controlled nucleation regime in Hapgood's nucleation regime map. Qualitative comparison of model simulations and experimental nucleation data showed similar shapes of the nuclei size distributions. In its current form, the nucleation model can replace the nucleation term in one-dimensional population balance models describing wet granulation processes. Implementation of more sophisticated nucleation kinetics can make the model applicable to multi-dimensional population balance models.

Flotillins and the PHB domain protein family: Rafts, worms and anaesthetics

While our understanding of lipid microdomains has advanced in recent years, many aspects of their formation and dynamics are still unclear. In particular, the molecular determinants that facilitate the partitioning of integral membrane proteins into lipid raft domains are yet to be clarified. This review focuses on a family of raft-associated integral membrane proteins, termed flotillins, which belongs to a larger class of integral membrane proteins that carry an evolutionarily conserved domain called the prohibitin homology (PHB) domain. A number of studies now suggest that eucaryotic proteins carrying this domain have affinity for lipid raft domains. The PHB domain is carried by a diverse array of proteins including stomatin, podocin, the archetypal PHB protein, prohibitin, lower eucaryotic proteins such as the Dictyostelium discoideum proteins vacuolin A and vacuolin B and the Caenorhabditis elegans proteins unc-1, unc-24 and mec-2. The presence of this domain in some procaryotic proteins suggests that the PHB domain may constitute a primordial lipid recognition motif. Recent work has provided new insights into the trafficking and targeting of flotillin and other PHB domain proteins. While the function of this large family of proteins remains unclear, studies of the C. elegans PHB proteins suggest possible links to a class of volatile anaesthetics raising the possibility that these lipophilic agents could influence lipid raft domains. This review will discuss recent insights into the cell biology of flotillins and the large family of evolutionarily conserved PHB domain proteins.

A DHA14 drug efflux gene from Xanthomonas albilineans confers high-level albicidin antibiotic resistance in Escherichia coli

Aims: Identification of a gene for self-protection from the antibiotic-producing plant pathogen Xanthomonas albilineans, and functional testing by heterologous expression. Methods and Results: Albicidin antibiotics and phytotoxins are potent inhibitors of prokaryote DNA replication. A resistance gene (albF) isolated by shotgun cloning from the X. albilineans albicidin-biosynthesis region encodes a protein with typical features of DHA14 drug efflux pumps. Low-level expression of albF in Escherichia coli increased the MIC of albicidin 3000-fold, without affecting tsx-mediated albicidin uptake into the periplasm or resistance to other tested antibiotics. Bioinformatic analysis indicates more similarity to proteins involved in self-protection in polyketide-antibiotic-producing actinomycetes than to multi-drug resistance pumps in other Gram-negative bacteria. A complex promoter region may co-regulate albF with genes for hydrolases likely to be involved in albicidin activation or self-protection. Conclusions: AlbF is the first apparent single-component antibiotic-specific efflux pump from a Gram-negative antibiotic producer. It shows extraordinary efficiency as measured by resistance level conferred upon heterologous expression. Significance and Impact of the Study: Development of the clinical potential of albicidins as potent bactericidial antibiotics against diverse bacteria has been limited because of low yields in culture. Expression of albF with recently described albicidin-biosynthesis genes may enable large-scale production. Because albicidins are X. albilineans pathogenicity factors, interference with AlbF function is also an opportunity for control of the associated plant disease.

On parameter estimation in population models

We describe methods for estimating the parameters of Markovian population processes in continuous time, thus increasing their utility in modelling real biological systems. A general approach, applicable to any finite-state continuous-time Markovian model, is presented, and this is specialised to a computationally more efficient method applicable to a class of models called density-dependent Markov population processes. We illustrate the versatility of both approaches by estimating the parameters of the stochastic SIS logistic model from simulated data. This model is also fitted to data from a population of Bay checkerspot butterfly (Euphydryas editha bayensis), allowing us to assess the viability of this population. (c) 2006 Elsevier Inc. All rights reserved.

Analysis of trigonometric implicit Runge-Kutta methods

Using generalized collocation techniques based on fitting functions that are trigonometric (rather than algebraic as in classical integrators), we develop a new class of multistage, one-step, variable stepsize, and variable coefficients implicit Runge-Kutta methods to solve oscillatory ODE problems. The coefficients of the methods are functions of the frequency and the stepsize. We refer to this class as trigonometric implicit Runge-Kutta (TIRK) methods. They integrate an equation exactly if its solution is a trigonometric polynomial with a known frequency. We characterize the order and A-stability of the methods and establish results similar to that of classical algebraic collocation RK methods. (c) 2006 Elsevier B.V. All rights reserved.

DNA Motifs Suppressing TLR9 Responses

Immune cells respond to bacterial DNA containing unmethylated CpG motifs via Toll-like receptor 9 (TLR9). Given the apparent role of TLR9 in development of systemic lupus erythernatosus (SLE), there is interest in the development of TLR9 inhibitors. TLR9-mediated responses are reported to be inhibited by a confusing variety of different DNA sequences and structures. To aid characterization, we have provisionally categorized TLR9-inhibitory oligodeoxynucleoti des (ODN) into 4 classes, on the basis of sequence and probable mode of action. Class I are short G-rich ODN, which show sequence-specific inhibition of all TLR9 responses, and may be direct competitive inhibitors for DNA binding to TLR9. Class II are telomeric repeat motifs that inhibit STAT signaling, and thus are not specific to TLR9 responses. Because Class II ODN are generally made as 24-base phosphorothioate-modified ODN (PS-ODN), they also fall into Class IV, defined as long PS-ODN, which inhibit TLR9 responses in a sequence-nonspecific manner. Class III includes oligo (dG) that forms a 4-stranded structure and inhibits DNA uptake. The Class I G-rich motifs show the most promise as selective and potent TLR9 inhibitors for therapeutic applications.

A rigorous foundation for pattern based design models

This paper presents a way to describe design patterns rigorously based on role concepts. Rigorous pattern descriptions are a key aspect for patterns to be used as rules for model evolution in the MDA context, for example. We formalize the role concepts commonly used in defining design patterns as a role metamodel using Object-Z. Given this role metamodel, individual design patterns are specified generically as a formal pattern role model using Object-Z. We also formalize the properties that must be captured in a class model when a design pattern is deployed. These properties are defined generically in terms of role bindings from a pattern role model to a class model. Our work provides a precise but abstract approach for pattern definition and also provides a precise basis for checking the validity of pattern usage in designs.

CONSELHO DE CLASSE E SÉRIE PARTICIPATIVO: DIFÍCIL APRENDIZAGEM PARA UMA PRÁTICA DEMOCRÁTICA

A presente pesquisa, de natureza qualitativa, está direcionada à análise das políticas educacionais ligadas à democratização da gestão escolar e demais processos escolares ligados à avaliação. Nesse contexto, é evidenciado o Conselho de Classe e Série, pois esse vem se concretizando como um dos espaços que favorecem a participação de pais e alunos, tornando-se fator determinante para a qualidade da democratização da gestão escolar e do ensino-aprendizagem. A pesquisa desenvolveu-se em três momentos: (1) análise da documentação escolar; (2) estudo de caso em duas instituições escolares da Rede Pública de São Paulo e (3) entrevistas com pais, alunos, professores e gestores que serviram de parâmetros para saber como estão realizadas as reuniões de Conselho de Classe e Série. Os objetivos da pesquisa foram voltados para verificar como vem sendo estruturada a participação da comunidade na construção da gestão democrática da escola, principalmente nas práticas do Conselho de Classe e Série.(AU)

Blood type classification using computer vision and machine learning

In emergency situations, where time for blood transfusion is reduced, the O negative blood type (the universal donor) is administrated. However, sometimes even the universal donor can cause transfusion reactions that can be fatal to the patient. As commercial systems do not allow fast results and are not suitable for emergency situations, this paper presents the steps considered for the development and validation of a prototype, able to determine blood type compatibilities, even in emergency situations. Thus it is possible, using the developed system, to administer a compatible blood type, since the first blood unit transfused. In order to increase the system’s reliability, this prototype uses different approaches to classify blood types, the first of which is based on Decision Trees and the second one based on support vector machines. The features used to evaluate these classifiers are the standard deviation values, histogram, Histogram of Oriented Gradients and fast Fourier transform, computed on different regions of interest. The main characteristics of the presented prototype are small size, lightweight, easy transportation, ease of use, fast results, high reliability and low cost. These features are perfectly suited for emergency scenarios, where the prototype is expected to be used.

Mathematical methods in power system stability studies

In this thesis various mathematical methods of studying the transient and dynamic stabiIity of practical power systems are presented. Certain long established methods are reviewed and refinements of some proposed. New methods are presented which remove some of the difficulties encountered in applying the powerful stability theories based on the concepts of Liapunov. Chapter 1 is concerned with numerical solution of the transient stability problem. Following a review and comparison of synchronous machine models the superiority of a particular model from the point of view of combined computing time and accuracy is demonstrated. A digital computer program incorporating all the synchronous machine models discussed, and an induction machine model, is described and results of a practical multi-machine transient stability study are presented. Chapter 2 reviews certain concepts and theorems due to Liapunov. In Chapter 3 transient stability regions of single, two and multi~machine systems are investigated through the use of energy type Liapunov functions. The treatment removes several mathematical difficulties encountered in earlier applications of the method. In Chapter 4 a simple criterion for the steady state stability of a multi-machine system is developed and compared with established criteria and a state space approach. In Chapters 5, 6 and 7 dynamic stability and small signal dynamic response are studied through a state space representation of the system. In Chapter 5 the state space equations are derived for single machine systems. An example is provided in which the dynamic stability limit curves are plotted for various synchronous machine representations. In Chapter 6 the state space approach is extended to multi~machine systems. To draw conclusions concerning dynamic stability or dynamic response the system eigenvalues must be properly interpreted, and a discussion concerning correct interpretation is included. Chapter 7 presents a discussion of the optimisation of power system small sjgnal performance through the use of Liapunov functions.

The human factors of computer input using a mouse device

This thesis investigates how people select items from a computer display using the mouse input device. The term computer mouse refers to a class of input devices which share certain features, but these may have different characteristics which influence the ways in which people use the device. Although task completion time is one of the most commonly used performance measures for input device evaluation, there is no consensus as to its definition. Furthermore most mouse studies fail to provide adequate assurances regarding its correct measurement.Therefore precise and accurate timing software were developed which permitted the recording of movement data which by means of automated analysis yielded the device movements made. Input system gain, an important task parameter, has been poorly defined and misconceptualized in most previous studies. The issue of gain has been clarified and investigated within this thesis. Movement characteristics varied between users and within users, even for the same task conditions. The variables of target size, movement amplitude, and experience exerted significant effects on performance. Subjects consistently undershot the target area. This may be a consequence of the particular task demands. Although task completion times indicated that mouse performance had stabilized after 132 trials the movement traces, even of very experienced users, indicated that there was still considerable room for improvement in performance, as indicated by the proportion of poorly made movements. The mouse input device was suitable for older novice device users, but they took longer to complete the experimental trials. Given the diversity and inconsistency of device movements, even for the same task conditions, caution is urged when interpreting averaged grouped data. Performance was found to be sensitive to; task conditions, device implementations, and experience in ways which are problematic for the theoretical descriptions of device movement, and limit the generalizability of such findings within this thesis.

Productivity analysis and measurement

The state of the art in productivity measurement and analysis shows a gap between simple methods having little relevance in practice and sophisticated mathematical theory which is unwieldy for strategic and tactical planning purposes, -particularly at company level. An extension is made in this thesis to the method of productivity measurement and analysis based on the concept of added value, appropriate to those companies in which the materials, bought-in parts and services change substantially and a number of plants and inter-related units are involved in providing components for final assembly. Reviews and comparisons of productivity measurement dealing with alternative indices and their problems have been made and appropriate solutions put forward to productivity analysis in general and the added value method in particular. Based on this concept and method, three kinds of computerised models two of them deterministic, called sensitivity analysis and deterministic appraisal, and the third one, stochastic, called risk simulation, have been developed to cope with the planning of productivity and productivity growth with reference to the changes in their component variables, ranging from a single value 'to• a class interval of values of a productivity distribution. The models are designed to be flexible and can be adjusted according to the available computer capacity expected accuracy and 'presentation of the output. The stochastic model is based on the assumption of statistical independence between individual variables and the existence of normality in their probability distributions. The component variables have been forecasted using polynomials of degree four. This model is tested by comparisons of its behaviour with that of mathematical model using real historical data from British Leyland, and the results were satisfactory within acceptable levels of accuracy. Modifications to the model and its statistical treatment have been made as required. The results of applying these measurements and planning models to the British motor vehicle manufacturing companies are presented and discussed.

Use of amino acids as counterions improves the solubility of the BCS II model drug, indomethacin

The number of new chemical entities (NCE) is increasing every day after the introduction of combinatorial chemistry and high throughput screening to the drug discovery cycle. One third of these new compounds have aqueous solubility less than 20µg/mL [1]. Therefore, a great deal of interest has been forwarded to the salt formation technique to overcome solubility limitations. This study aims to improve the drug solubility of a Biopharmaceutical Classification System class II (BCS II) model drug (Indomethacin; IND) using basic amino acids (L-arginine, L-lysine and L-histidine) as counterions. Three new salts were prepared using freeze drying method and characterised by FT-IR spectroscopy, proton nuclear magnetic resonance ((1)HNMR), Differential Scanning Calorimetry (DSC) and Thermogravimetric analysis (TGA). The effect of pH on IND solubility was also investigated using pH-solubility profile. Both arginine and lysine formed novel salts with IND, while histidine failed to dissociate the free acid and in turn no salt was formed. Arginine and lysine increased IND solubility by 10,000 and 2296 fold, respectively. An increase in dissolution rate was also observed for the novel salts. Since these new salts have improved IND solubility to that similar to BCS class I drugs, IND salts could be considered for possible waivers of bioequivalence.