Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Background: Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need to be made to the organism in order to achieve the desired biotechnological goal. As appropriate models to perform such an analysis are necessarily non-linear and typically non-convex, finding their global optimum is a challenging task. Canonical modeling techniques, such as Generalized Mass Action (GMA) models based on the power-law formalism, offer a possible solution to this problem because they have a mathematical structure that enables the development of specific algorithms for global optimization. Results: Based on the GMA canonical representation, we have developed in previous works a highly efficient optimization algorithm and a set of related strategies for understanding the evolution of adaptive responses in cellular metabolism. Here, we explore the possibility of recasting kinetic non-linear models into an equivalent GMA model, so that global optimization on the recast GMA model can be performed. With this technique, optimization is greatly facilitated and the results are transposable to the original non-linear problem. This procedure is straightforward for a particular class of non-linear models known as Saturable and Cooperative (SC) models that extend the power-law formalism to deal with saturation and cooperativity. Conclusions: Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task.

Definition of linear color models in the RGB vector color space to detect red peaches in orchard images taken under natural illumination

This work proposes the detection of red peaches in orchard images based on the definition of different linear color models in the RGB vector color space. The classification and segmentation of the pixels of the image is then performed by comparing the color distance from each pixel to the different previously defined linear color models. The methodology proposed has been tested with images obtained in a real orchard under natural light. The peach variety in the orchard was the paraguayo (Prunus persica var. platycarpa) peach with red skin. The segmentation results showed that the area of the red peaches in the images was detected with an average error of 11.6%; 19.7% in the case of bright illumination; 8.2% in the case of low illumination; 8.6% for occlusion up to 33%; 12.2% in the case of occlusion between 34 and 66%; and 23% for occlusion above 66%. Finally, a methodology was proposed to estimate the diameter of the fruits based on an ellipsoidal fitting. A first diameter was obtained by using all the contour pixels and a second diameter was obtained by rejecting some pixels of the contour. This approach enables a rough estimate of the fruit occlusion percentage range by comparing the two diameter estimates.

Les codes de l'obligations : méta-analyses pragmatologiques de l'application de méthodes en sciences sociales

Cette thèse rassemble une série de méta-analyses, c'est-à-dire d'analyses ayant pour objet des analyses produites par des sociologues (notamment celles résultant de l'application de méthodes de traitement des entretiens). Il s'agit d'une démarche réflexive visant les pratiques concrètes des sociologues. Celles-ci sont envisagées comme des activités gouvernées par des règles. Une part importante de cette thèse sera donc consacrée au développement d'un outil d'analyse « pragmatologique » (E. Durkheim), c'est-à-dire permettant l'étude des pratiques et des règles en rapport avec elles. Pour aborder les règles, la philosophie analytique d'inspiration wittgensteinienne apporte plusieurs propositions importantes. Les règles sont ainsi considérées comme des concepts d'air de famille : il n'y a pas de définitions communes recouvrant l'ensemble des règles. Pour étudier les règles, il convient alors de faire des distinctions à partir de leurs usages. Une de ces distinctions concerne la différence entre règles constitutives et règles régulatives : une règle constitutive crée une pratique (e.g. le mariage), alors qu'une règle régulative s'applique à des activités qui peuvent exister sans elle (e.g. les règles du savoir-vivre). L'activité méthodologique des sociologues repose et est contrainte par ces types de règles, qui sont pour l'essentiel implicites. Cette thèse vise donc à rendre compte, par la description et la codification des règles, du caractère normatif des méthodes dans les pratiques d'analyse de la sociologie. Elle insiste en particulier sur les limites logiques qu'instituent les règles constitutives, celles-ci rendant impossibles (et non pas interdites) certaines actions des sociologues. This thesis brings together a series of meta-analyzes, that is, analyzes that tackle analyzes produced by sociologists (notably those resulting from the application of methods in treating interviews). The approach is reflexive and aimed at the concrete practices of sociologists, considered as activities governed by rules. An important part of this thesis is therefore devoted to the development of a "pragmatological" analytical tool (Durkheim) to conduct a study of such practices and of the rules that govern them. To approach these rules, Wittgenstein-inspired analytic philosophy offers several important proposals. The rules are, at first, seen as concepts of family resemblance, assuming that there is no common definition accounting for all rules. In order to conduct the study of such rules, it is therefore necessary to discern how they are respectively used. One of these distinctions concerns the difference between constitutive rules and regulative rules: a constitutive rule creates a practice (for example marriage), while a regulative rule applies to activities that can exist outside of the rule (for example, the rules of etiquette). The methodological activity of sociologists relies on, and is constrained by these types of rules, which are essentially implicit. Through the description and codification of rules, this thesis aims to account for the normative character of methods governing analytical practices in sociology. Particular emphasis is on the logical limits established by constitutive rules, limits that render several of the sociologist's actions impossible (rather than forbidden).

Counter-propagating dual-trap optical tweezers based on linear momentum conservation

We present a dual-trap optical tweezers setup which directly measures forces using linear momentum conservation. The setup uses a counter-propagating geometry, which allows momentum measurement on each beam separately. The experimental advantages of this setup include low drift due to all-optical manipulation, and a robust calibration (independent of the features of the trapped object or buffer medium) due to the force measurement method. Although this design does not attain the high-resolution of some co-propagating setups, we show that it can be used to perform different single molecule measurements: fluctuation-based molecular stiffness characterization at different forces and hopping experiments on molecular hairpins. Remarkably, in our setup it is possible to manipulate very short tethers (such as molecular hairpins with short handles) down to the limit where beads are almost in contact. The setup is used to illustrate a novel method for measuring the stiffness of optical traps and tethers on the basis of equilibrium force fluctuations, i.e., without the need of measuring the force vs molecular extension curve. This method is of general interest for dual trap optical tweezers setups and can be extended to setups which do not directly measure forces.

Anticipating linear stochastic differential equations driven by a Lévy process

In this paper we study the existence of a unique solution for linear stochastic differential equations driven by a Lévy process, where the initial condition and the coefficients are random and not necessarily adapted to the underlying filtration. Towards this end, we extend the method based on Girsanov transformations on Wiener space and developped by Buckdahn [7] to the canonical Lévy space, which is introduced in [25].

Hierarchical linear models in Psychiatry: A bibliometric study

Development of research methods requires a systematic review of their status. This study focuses on the use of Hierarchical Linear Modeling methods in psychiatric research. Evaluation includes 207 documents published until 2007, included and indexed in the ISI Web of Knowledge databases; analyses focuses on the 194 articles in the sample. Bibliometric methods are used to describe the publications patterns. Results indicate a growing interest in applying the models and an establishment of methods after 2000. Both Lotka"s and Bradford"s distributions are adjusted to the data.

Source separation techniques applied to linear prediction

The prediction filters are well known models for signal estimation, in communications, control and many others areas. The classical method for deriving linear prediction coding (LPC) filters is often based on the minimization of a mean square error (MSE). Consequently, second order statistics are only required, but the estimation is only optimal if the residue is independent and identically distributed (iid) Gaussian. In this paper, we derive the ML estimate of the prediction filter. Relationships with robust estimation of auto-regressive (AR) processes, with blind deconvolution and with source separation based on mutual information minimization are then detailed. The algorithm, based on the minimization of a high-order statistics criterion, uses on-line estimation of the residue statistics. Experimental results emphasize on the interest of this approach.

Exploring Non-linear Transformations for an Entropybased Voice Activity Detector

In this paper we explore the use of non-linear transformations in order to improve the performance of an entropy based voice activity detector (VAD). The idea of using a non-linear transformation comes from some previous work done in speech linear prediction (LPC) field based in source separation techniques, where the score function was added into the classical equations in order to take into account the real distribution of the signal. We explore the possibility of estimating the entropy of frames after calculating its score function, instead of using original frames. We observe that if signal is clean, estimated entropy is essentially the same; but if signal is noisy transformed frames (with score function) are able to give different entropy if the frame is voiced against unvoiced ones. Experimental results show that this fact permits to detect voice activity under high noise, where simple entropy method fails.

Dosimetria dos cones radiocirúrgicos Radionics de diâmetros de 5 mm a 50 mm para um feixe de 6 MV de um acelerador linear Mevatron MD digital

Os parâmetros dosimétricos de um feixe de raios X de pequeno diâmetro para um sistema de radiocirurgia comercial foram medidos em água com um detector de diodo de Si do tipo p. As razões tecido-máximo, o fator de espalhamento total e os perfis dos feixes a profundidades de 5 e 10 cm foram medidos para 17 feixes de diâmetros circulares de 5 mm a 50 mm, em incrementos de 2,5 mm. Os fatores de espalhamento totais caíram lentamente, de 0,947 para 0,888 entre os cones de 50 mm e 12,5 mm de diâmetro (variação de 7%); para os cones entre 10 mm e 5 mm de diâmetro, esta queda foi bem maior, de 0,854 para 0,666 (variação de 28%). Os valores obtidos para a relação tecido-máximo são consistentes com dados publicados. Os perfis dos feixes foram medidos nas direções x e y, e estão dentro de 0,2 mm para todos os cones entre as duas direções. A medida da largura à meia-altura se encontra dentro de 1 mm com o diâmetro nominal dos cones.

Implantação de um programa de controle de qualidade de um acelerador linear de 6 MeV de fótons

Este trabalho apresenta a parte operacional do processo final envolvido na implantação de um programa de controle de qualidade por meio de testes rotineiros mecânicos e de radiação. O programa de controle de qualidade, durante 35 meses, mostrou a estabilidade excelente deste acelerador.

On the Analysis and Control of a Linear Synchronous Servomotor with a Flexible Load

Industry's growing need for higher productivity is placing new demands on mechanisms connected with electrical motors, because these can easily lead to vibration problems due to fast dynamics. Furthermore, the nonlinear effects caused by a motor frequently reduce servo stability, which diminishes the controller's ability to predict and maintain speed. Hence, the flexibility of a mechanism and its control has become an important area of research. The basic approach in control system engineering is to assume that the mechanism connected to a motor is rigid, so that vibrations in the tool mechanism, reel, gripper or any apparatus connected to the motor are not taken into account. This might reduce the ability of the machine system to carry out its assignment and shorten the lifetime of the equipment. Nonetheless, it is usually more important to know how the mechanism, or in other words the load on the motor, behaves. A nonlinear load control method for a permanent magnet linear synchronous motor is developed and implemented in the thesis. The purpose of the controller is to track a flexible load to the desired velocity reference as fast as possible and without awkward oscillations. The control method is based on an adaptive backstepping algorithm with its stability ensured by the Lyapunov stability theorem. As a reference controller for the backstepping method, a hybrid neural controller is introduced in which the linear motor itself is controlled by a conventional PI velocity controller and the vibration of the associated flexible mechanism is suppressed from an outer control loop using a compensation signal from a multilayer perceptron network. To avoid the local minimum problem entailed in neural networks, the initial weights are searched for offline by means of a differential evolution algorithm. The states of a mechanical system for controllers are estimated using the Kalman filter. The theoretical results obtained from the control design are validated with the lumped mass model for a mechanism. Generalization of the mechanism allows the methods derived here to be widely implemented in machine automation. The control algorithms are first designed in a specially introduced nonlinear simulation model and then implemented in the physical linear motor using a DSP (Digital Signal Processor) application. The measurements prove that both controllers are capable of suppressing vibration, but that the backstepping method is superior to others due to its accuracy of response and stability properties.

Vaccine-Induced Linear Epitope-Specific Antibodies to Simian Immunodeficiency Virus SIVmac239 Envelope Are Distinct from Those Induced to the Human Immunodeficiency Virus Type 1 Envelope in Nonhuman Primates.

To evaluate antibody specificities induced by simian immunodeficiency virus (SIV) versus human immunodeficiency virus type 1 (HIV-1) envelope antigens in nonhuman primate (NHP), we profiled binding antibody responses to linear epitopes in NHP studies with HIV-1 or SIV immunogens. We found that, overall, HIV-1 Env IgG responses were dominated by V3, with the notable exception of the responses to the vaccine strain A244 Env that were dominated by V2, whereas the anti-SIVmac239 Env responses were dominated by V2 regardless of the vaccine regimen.