Structure-activity relationships from in vitro efficacies of the thiazolide series against the intracellular apicomplexan protozoan Neospora caninum

Nitazoxanide (2-acetolyloxy-N-(5-nitro 2-thiazolyl) benzamide; NTZ) represents the parent compound of a novel class of broad-spectrum anti-parasitic compounds named thiazolides. NTZ is active against a wide variety of intestinal and tissue-dwelling helminths, protozoa, enteric bacteria and a number of viruses infecting animals and humans. While potent, this poses a problem in practice, since this obvious non-selectivity can lead to undesired side effects in both humans and animals. In this study, we used real time PCR to determine the in vitro activities of 29 different thiazolides (NTZ-derivatives), which carry distinct modifications on both the thiazole- and the benzene moieties, against the tachyzoite stage of the intracellular protozoan Neospora caninum. The goal was to identify a highly active compound lacking the undesirable nitro group, which would have a more specific applicability, such as in food animals. By applying self-organizing molecular field analysis (SOMFA), these data were used to develop a predictive model for future drug design. SOMFA performs self-alignment of the molecules, and takes into account the steric and electrostatic properties, in order to determine 3D-quantitative structure activity relationship models. The best model was obtained by overlay of the thiazole moieties. Plotting of predicted versus experimentally determined activity produced an r2 value of 0.8052 and cross-validation using the "leave one out" methodology resulted in a q2 value of 0.7987. A master grid map showed that large steric groups at the R2 position, the nitrogen of the amide bond and position Y could greatly reduce activity, and the presence of large steric groups placed at positions X, R4 and surrounding the oxygen atom of the amide bond, may increase the activity of thiazolides against Neospora caninum tachyzoites. The model obtained here will be an important predictive tool for future development of this important class of drugs.

Self-organized defensive behavior in honeybees

We investigated the defensive behavior of honeybees under controlled experimental conditions. During an attack on two identical targets, the spatial distribution of stings varied as a function of the total number of stings, evincing the classic “pitchfork bifurcation” phenomenon of nonlinear dynamics. The experimental results support a model of defensive behavior based on a self-organizing mechanism. The model helps to explain several of the characteristic features of the honeybee defensive response: (i) the ability of the colony to localize and focus its attack, (ii) the strong variability between different hives in the intensity of attack, as well as (iii) the variability observed within the same hive, and (iv) the ability of the colony to amplify small differences between the targets.

How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum

When individual amoebae of the cellular slime mold Dictyostelium discoideum are starving, they aggregate to form a multicellular migrating slug, which moves toward a region suitable for culmination. The culmination of the morphogenesis involves complex cell movements that transform a mound of cells into a globule of spores on a slender stalk. The movement has been likened to a “reverse fountain,” whereby prestalk cells in the upper part form a stalk that moves downwards and anchors to the substratum, while prespore cells in the lower part move upwards to form the spore head. So far, however, no satisfactory explanation has been produced for this process. Using a computer simulation that we developed, we now demonstrate that the processes that are essential during the earlier stages of the morphogenesis are in fact sufficient to produce the dynamics of the culmination stage. These processes are cAMP signaling, differential adhesion, cell differentiation, and production of extracellular matrix. Our model clarifies the processes that generate the observed cell movements. More specifically, we show that periodic upward movements, caused by chemotactic motion, are essential for successful culmination, because the pressure waves they induce squeeze the stalk downwards through the cell mass. The mechanisms revealed by our model have a number of self-organizing and self-correcting properties and can account for many previously unconnected and unexplained experimental observations.

3D-based reconstruction using growing neural gas landmark: application to rapid prototyping in shoe last manufacturing

Customizing shoe manufacturing is one of the great challenges in the footwear industry. It is a production model change where design adopts not only the main role, but also the main bottleneck. It is therefore necessary to accelerate this process by improving the accuracy of current methods. Rapid prototyping techniques are based on the reuse of manufactured footwear lasts so that they can be modified with CAD systems leading rapidly to new shoe models. In this work, we present a shoe last fast reconstruction method that fits current design and manufacturing processes. The method is based on the scanning of shoe last obtaining sections and establishing a fixed number of landmarks onto those sections to reconstruct the shoe last 3D surface. Automated landmark extraction is accomplished through the use of the self-organizing network, the growing neural gas (GNG), which is able to topographically map the low dimensionality of the network to the high dimensionality of the contour manifold without requiring a priori knowledge of the input space structure. Moreover, our GNG landmark method is tolerant to noise and eliminates outliers. Our method accelerates up to 12 times the surface reconstruction and filtering processes used by the current shoe last design software. The proposed method offers higher accuracy compared with methods with similar efficiency as voxel grid.

Principles of the design of self-learning systems, USSR.

"Translation of the ... collection of reports" [entitled]: Print︠s︡ipy postroenii︠a︡ samoobuchaiushchikhsia sistem (romanized form) Kiev, 1962.

A modelling and simulation environment for self-aware and self-expressive systems

Self-awareness and self-expression are promising architectural concepts for embedded systems to be equipped with to match them with dedicated application scenarios and constraints in the avionic and space-flight industry. Typically, these systems operate in largely undefined environments and are not reachable after deployment for a long time or even never ever again. This paper introduces a reference architecture as well as a novel modelling and simulation environment for self-aware and self-expressive systems with transaction level modelling, simulation and detailed modelling capabilities for hardware aspects, precise process chronology execution as well as fine timing resolutions. Furthermore, industrial relevant system sizes with several self-aware and self-expressive nodes can be handled by the modelling and simulation environment.

A survey of self-awareness and its application in computing systems

Novel computing systems are increasingly being composed of large numbers of heterogeneous components, each with potentially different goals or local perspectives, and connected in networks which change over time. Management of such systems quickly becomes infeasible for humans. As such, future computing systems should be able to achieve advanced levels of autonomous behaviour. In this context, the system's ability to be self-aware and be able to self-express becomes important. This paper surveys definitions and current understanding of self-awareness and self-expression in biology and cognitive science. Subsequently, previous efforts to apply these concepts to computing systems are described. This has enabled the development of novel working definitions for self-awareness and self-expression within the context of computing systems.

Self-organising zooms for decentralised redundancy management in visual sensor networks

When visual sensor networks are composed of cameras which can adjust the zoom factor of their own lens, one must determine the optimal zoom levels for the cameras, for a given task. This gives rise to an important trade-off between the overlap of the different cameras’ fields of view, providing redundancy, and image quality. In an object tracking task, having multiple cameras observe the same area allows for quicker recovery, when a camera fails. In contrast having narrow zooms allow for a higher pixel count on regions of interest, leading to increased tracking confidence. In this paper we propose an approach for the self-organisation of redundancy in a distributed visual sensor network, based on decentralised multi-objective online learning using only local information to approximate the global state. We explore the impact of different zoom levels on these trade-offs, when tasking omnidirectional cameras, having perfect 360-degree view, with keeping track of a varying number of moving objects. We further show how employing decentralised reinforcement learning enables zoom configurations to be achieved dynamically at runtime according to an operator’s preference for maximising either the proportion of objects tracked, confidence associated with tracking, or redundancy in expectation of camera failure. We show that explicitly taking account of the level of overlap, even based only on local knowledge, improves resilience when cameras fail. Our results illustrate the trade-off between maintaining high confidence and object coverage, and maintaining redundancy, in anticipation of future failure. Our approach provides a fully tunable decentralised method for the self-organisation of redundancy in a changing environment, according to an operator’s preferences.

Self-aware and self-expressive camera networks

Smart cameras perform on-board image analysis, adapt their algorithms to changes in their environment, and collaborate with other networked cameras to analyze the dynamic behavior of objects. A proposed computational framework adopts the concepts of self-awareness and self-expression to more efficiently manage the complex tradeoffs among performance, flexibility, resources, and reliability. The Web extra at http://youtu.be/NKe31-OKLz4 is a video demonstrating CamSim, a smart camera simulation tool, enables users to test self-adaptive and self-organizing smart-camera techniques without deploying a smart-camera network.

Space division multiple access for wireless sensor networks

This dissertation proposed a self-organizing medium access control protocol (MAC) for wireless sensor networks (WSNs). The proposed MAC protocol, space division multiple access (SDMA), relies on sensor node position information and provides sensor nodes access to the wireless channel based on their spatial locations. SDMA divides a geographical area into space divisions, where there is one-to-one map between the space divisions and the time slots. Therefore, the MAC protocol requirement is the sensor node information of its position and a prior knowledge of the one-to-one mapping function. The scheme is scalable, self-maintaining, and self-starting. It provides collision-free access to the wireless channel for the sensor nodes thereby, guarantees delay-bounded communication in real time for delay sensitive applications. This work was divided into two parts: the first part involved the design of the mapping function to map the space divisions to the time slots. The mapping function is based on a uniform Latin square. A Uniform Latin square of order k = m 2 is an k x k square matrix that consists of k symbols from 0 to k-1 such that no symbol appears more than once in any row, in any column, or in any m x in area of main subsquares. The uniqueness of each symbol in the main subsquares presents very attractive characteristic in applying a uniform Latin square to time slot allocation problem in WSNs. The second part of this research involved designing a GPS free positioning system for position information. The system is called time and power based localization scheme (TPLS). TPLS is based on time difference of arrival (TDoA) and received signal strength (RSS) using radio frequency and ultrasonic signals to measure and detect the range differences from a sensor node to three anchor nodes. TPLS requires low computation overhead and no time synchronization, as the location estimation algorithm involved only a simple algebraic operation.

Contributions to 3D Data Registration and Representation

Nowadays, new computers generation provides a high performance that enables to build computationally expensive computer vision applications applied to mobile robotics. Building a map of the environment is a common task of a robot and is an essential part to allow the robots to move through these environments. Traditionally, mobile robots used a combination of several sensors from different technologies. Lasers, sonars and contact sensors have been typically used in any mobile robotic architecture, however color cameras are an important sensor due to we want the robots to use the same information that humans to sense and move through the different environments. Color cameras are cheap and flexible but a lot of work need to be done to give robots enough visual understanding of the scenes. Computer vision algorithms are computational complex problems but nowadays robots have access to different and powerful architectures that can be used for mobile robotics purposes. The advent of low-cost RGB-D sensors like Microsoft Kinect which provide 3D colored point clouds at high frame rates made the computer vision even more relevant in the mobile robotics field. The combination of visual and 3D data allows the systems to use both computer vision and 3D processing and therefore to be aware of more details of the surrounding environment. The research described in this thesis was motivated by the need of scene mapping. Being aware of the surrounding environment is a key feature in many mobile robotics applications from simple robotic navigation to complex surveillance applications. In addition, the acquisition of a 3D model of the scenes is useful in many areas as video games scene modeling where well-known places are reconstructed and added to game systems or advertising where once you get the 3D model of one room the system can add furniture pieces using augmented reality techniques. In this thesis we perform an experimental study of the state-of-the-art registration methods to find which one fits better to our scene mapping purposes. Different methods are tested and analyzed on different scene distributions of visual and geometry appearance. In addition, this thesis proposes two methods for 3d data compression and representation of 3D maps. Our 3D representation proposal is based on the use of Growing Neural Gas (GNG) method. This Self-Organizing Maps (SOMs) has been successfully used for clustering, pattern recognition and topology representation of various kind of data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models without considering time constraints. Self-organising neural models have the ability to provide a good representation of the input space. In particular, the Growing Neural Gas (GNG) is a suitable model because of its flexibility, rapid adaptation and excellent quality of representation. However, this type of learning is time consuming, specially for high-dimensional input data. Since real applications often work under time constraints, it is necessary to adapt the learning process in order to complete it in a predefined time. This thesis proposes a hardware implementation leveraging the computing power of modern GPUs which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). Our proposed geometrical 3D compression method seeks to reduce the 3D information using plane detection as basic structure to compress the data. This is due to our target environments are man-made and therefore there are a lot of points that belong to a plane surface. Our proposed method is able to get good compression results in those man-made scenarios. The detected and compressed planes can be also used in other applications as surface reconstruction or plane-based registration algorithms. Finally, we have also demonstrated the goodness of the GPU technologies getting a high performance implementation of a CAD/CAM common technique called Virtual Digitizing.

Análise do jogo de goalball : modelação e interpretação dos padrões de jogo da Paralimpíada de Pequim 2008

Universidade Estadual de Campinas . Faculdade de Educação Física

Improvements on ICA mixture models for image pre-processing and segmentation

Today several different unsupervised classification algorithms are commonly used to cluster similar patterns in a data set based only on its statistical properties. Specially in image data applications, self-organizing methods for unsupervised classification have been successfully applied for clustering pixels or group of pixels in order to perform segmentation tasks. The first important contribution of this paper refers to the development of a self-organizing method for data classification, named Enhanced Independent Component Analysis Mixture Model (EICAMM), which was built by proposing some modifications in the Independent Component Analysis Mixture Model (ICAMM). Such improvements were proposed by considering some of the model limitations as well as by analyzing how it should be improved in order to become more efficient. Moreover, a pre-processing methodology was also proposed, which is based on combining the Sparse Code Shrinkage (SCS) for image denoising and the Sobel edge detector. In the experiments of this work, the EICAMM and other self-organizing models were applied for segmenting images in their original and pre-processed versions. A comparative analysis showed satisfactory and competitive image segmentation results obtained by the proposals presented herein. (C) 2008 Published by Elsevier B.V.

A mathematical view of biological complexity

This essay is a trial on giving some mathematical ideas about the concept of biological complexity, trying to explore four different attributes considered to be essential to characterize a complex system in a biological context: decomposition, heterogeneous assembly, self-organization, and adequacy. It is a theoretical and speculative approach, opening some possibilities to further numerical and experimental work, illustrated by references to several researches that applied the concepts presented here. (C) 2008 Elsevier B.V. All rights reserved.

Planeamento e optimização em redes celulares móveis auto-geridas assentes em LTE

O objectivo deste trabalho consiste em avaliar os benefícios das Self Organizing Networks (SON), no que concerne ao planeamento e optimização de redes Long Term Evolution (LTE), não só através do seu estudo, como também através do desenvolvimento e teste de algoritmos, que permitem avaliar o funcionamento de algumas das suas principais funções. O estudo efectuado sobre as SON permitiu identificar um conjunto de funções, tais como a atribuição automática de Physical Cell Id (PCI), o Automatic Neighbour Relation (ANR) e a optimização automática de parâmetros de handover, que permitem facilitar ou mesmo substituir algumas das tarefas mais comuns em planeamento e optimização de redes móveis celulares, em particular, redes LTE. Recorrendo a um simulador LTE destinado à investigação académica, em código aberto e desenvolvido em Matlab®, foi desenvolvido um conjunto de algoritmos que permitiram a implementação das funções em questão. Para além das funções implementadas, foram também introduzidas alterações que conferem a este simulador a capacidade de representar e simular redes reais, permitindo uma análise mais coerente dos algoritmos desenvolvidos. Os resultados obtidos, para além de evidenciarem claramente o benefício dos algoritmos desenvolvidos, foram ainda comparados com os obtidos pela ferramenta profissional de planeamento e optimização Atoll®, tendo-se verificado a franca proximidade de desempenho em algumas das funções. Finalmente, foi desenvolvida uma interface gráfica que permite o desenho, configuração e simulação de cenários, bem como a análise de resultados.