Living bacteria rheology: Population growth, aggregation patterns, and collective behaviour under diferente shear flows

The activity of growing living bacteria was investigated using real-time and in situ rheology-in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus-strain COL and its isogenic cell wall autolysis mutant, RUSAL9-were considered in this work. For low bacteria density, strain COL forms small clusters, while the mutant, presenting deficient cell separation, forms irregular larger aggregates. In the early stages of growth, when subjected to a stationary shear, the viscosity of the cultures of both strains increases with the population of cells. As the bacteria reach the exponential phase of growth, the viscosity of the cultures of the two strains follows different and rich behaviors, with no counterpart in the optical density or in the population's colony-forming units measurements. While the viscosity of strain COL culture keeps increasing during the exponential phase and returns close to its initial value for the late phase of growth, where the population stabilizes, the viscosity of the mutant strain culture decreases steeply, still in the exponential phase, remains constant for some time, and increases again, reaching a constant plateau at a maximum value for the late phase of growth. These complex viscoelastic behaviors, which were observed to be shear-stress-dependent, are a consequence of two coupled effects: the cell density continuous increase and its changing interacting properties. The viscous and elastic moduli of strain COL culture, obtained with oscillatory shear, exhibit power-law behaviors whose exponents are dependent on the bacteria growth stage. The viscous and elastic moduli of the mutant culture have complex behaviors, emerging from the different relaxation times that are associated with the large molecules of the medium and the self-organized structures of bacteria. Nevertheless, these behaviors reflect the bacteria growth stage.

Virtual globes as a platform for developing spatial literacy

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Spatial data infrastructures model for developing countries: A case study of Nigeria

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Spatial analysis of avoidable hospitalizations due to tuberculosis in Ribeirao Preto, SP, Brazil (2006-2012)

ABSTRACT OBJECTIVE To describe the spatial distribution of avoidable hospitalizations due to tuberculosis in the municipality of Ribeirao Preto, SP, Brazil, and to identify spatial and space-time clusters for the risk of occurrence of these events. METHODS This is a descriptive, ecological study that considered the hospitalizations records of the Hospital Information System of residents of Ribeirao Preto, SP, Southeastern Brazil, from 2006 to 2012. Only the cases with recorded addresses were considered for the spatial analyses, and they were also geocoded. We resorted to Kernel density estimation to identify the densest areas, local empirical Bayes rate as the method for smoothing the incidence rates of hospital admissions, and scan statistic for identifying clusters of risk. Softwares ArcGis 10.2, TerraView 4.2.2, and SaTScanTM were used in the analysis. RESULTS We identified 169 hospitalizations due to tuberculosis. Most were of men (n = 134; 79.2%), averagely aged 48 years (SD = 16.2). The predominant clinical form was the pulmonary one, which was confirmed through a microscopic examination of expectorated sputum (n = 66; 39.0%). We geocoded 159 cases (94.0%). We observed a non-random spatial distribution of avoidable hospitalizations due to tuberculosis concentrated in the northern and western regions of the municipality. Through the scan statistic, three spatial clusters for risk of hospitalizations due to tuberculosis were identified, one of them in the northern region of the municipality (relative risk [RR] = 3.4; 95%CI 2.7–4,4); the second in the central region, where there is a prison unit (RR = 28.6; 95%CI 22.4–36.6); and the last one in the southern region, and area of protection for hospitalizations (RR = 0.2; 95%CI 0.2–0.3). We did not identify any space-time clusters. CONCLUSIONS The investigation showed priority areas for the control and surveillance of tuberculosis, as well as the profile of the affected population, which shows important aspects to be considered in terms of management and organization of health care services targeting effectiveness in primary health care.

Spatial dynamics of team sports exposed by Voronoi diagrams

Team sports represent complex systems: players interact continuously during a game, and exhibit intricate patterns of interaction, which can be identified and investigated at both individual and collective levels. We used Voronoi diagrams to identify and investigate the spatial dynamics of players' behavior in Futsal. Using this tool, we examined 19 plays of a sub-phase of a Futsal game played in a reduced area (20 m(2)) from which we extracted the trajectories of all players. Results obtained from a comparative analysis of player's Voronoi area (dominant region) and nearest teammate distance revealed different patterns of interaction between attackers and defenders, both at the level of individual players and teams. We found that, compared to defenders, larger dominant regions were associated with attackers. Furthermore, these regions were more variable in size among players from the same team but, at the player level, the attackers' dominant regions were more regular than those associated with each of the defenders. These findings support a formal description of the dynamic spatial interaction of the players, at least during the particular sub-phase of Futsal investigated. The adopted approach may be extended to other team behaviors where the actions taken at any instant in time by each of the involved agents are associated with the space they occupy at that particular time.

Adaption of the Creative Commons approach and the roaming concept to spatial data infrastructures (SDI)

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

SAKWeb – Spatial autocorrelation and kriging web, a W3 geocomputation perspective

A thesis submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Information Systems

A survey of e-learning content aggregation standards

As e-learning gradually evolved many specialized and disparate systems appeared to fulfil the needs of teachers and students, such as repositories of learning objects, authoring tools, intelligent tutors and automatic evaluators. This heterogeneity raises interoperability issues giving the standardization of content an important role in e-learning. This article presents a survey on current e-learning content aggregation standards focusing on their internal organization and packaging. This study is part of an effort to choose the most suitable specifications and standards for an e-learning framework called Ensemble defined as a conceptual tool to organize a network of e-learning systems and services for domains with complex evaluation.

Spatial metrics and Landsat data for urban landuse change detection: case of Addis Ababa, Ethiopia.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Demand Response Programs Definition Using Demand Price Elasticity to Define Consumers Aggregation for an Improved Remuneration Structure

The positioning of the consumers in the power systems operation has been changed in the recent years, namely due to the implementation of competitive electricity markets. Demand response is an opportunity for the consumers’ participation in electricity markets. Smart grids can give an important support for the integration of demand response. The methodology proposed in the present paper aims to create an improved demand response program definition and remuneration scheme for aggregated resources. The consumers are aggregated in a certain number of clusters, each one corresponding to a distinct demand response program, according to the economic impact of the resulting remuneration tariff. The knowledge about the consumers is obtained from its demand price elasticity values. The illustrative case study included in the paper is based on a 218 consumers’ scenario.

A plugin for spatial and thematic comparison in the cadastral domain.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Conservation GIS: Ontology and spatial reasoning for commonsense knowledge.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Remuneration Structure Definition for Distributed Generation Units and Demand Response Participants Aggregation

The implementation of competitive electricity markets has changed the consumers’ and distributed generation position power systems operation. The use of distributed generation and the participation in demand response programs, namely in smart grids, bring several advantages for consumers, aggregators, and system operators. The present paper proposes a remuneration structure for aggregated distributed generation and demand response resources. A virtual power player aggregates all the resources. The resources are aggregated in a certain number of clusters, each one corresponding to a distinct tariff group, according to the economic impact of the resulting remuneration tariff. The determined tariffs are intended to be used for several months. The aggregator can define the periodicity of the tariffs definition. The case study in this paper includes 218 consumers, and 66 distributed generation units.

Engineering Temporal and Spatial Aspects in OWL using Patterns

WWW is a huge, open, heterogeneous system, however its contents data is mainly human oriented. The Semantic Web needs to assure that data is readable and “understandable” to intelligent software agents, though the use of explicit and formal semantics. Ontologies constitute a privileged artifact for capturing the semantic of the WWW data. Temporal and spatial dimensions are transversal to the generality of knowledge domains and therefore are fundamental for the reasoning process of software agents. Representing temporal/spatial evolution of concepts and their relations in OWL (W3C standard for ontologies) it is not straightforward. Although proposed several strategies to tackle this problem but there is still no formal and standard approach. This work main goal consists of development of methods/tools to support the engineering of temporal and spatial aspects in intelligent systems through the use of OWL ontologies. An existing method for ontology engineering, Fonte was used as framework for the development of this work. As main contributions of this work Fonte was re-engineered in order to: i) support the spatial dimension; ii) work with OWL Ontologies; iii) and support the application of Ontology Design Patterns. Finally, the capabilities of the proposed approach were demonstrated by engineering time and space in a demo ontology about football.

S100A6 Amyloid Fibril Formation Is Calcium-modulated and Enhances Superoxide Dismutase-1 (SOD1) Aggregation

S100A6 is a small EF-hand calcium- and zinc-binding protein involved in the regulation of cell proliferation and cytoskeletal dynamics. It is overexpressed in neurodegenerative disorders and a proposed marker for Amyotrophic Lateral Sclerosis (ALS). Following recent reports of amyloid formation by S100 proteins, we investigated the aggregation properties of S100A6. Computational analysis using aggregation predictors Waltz and Zyggregator revealed increased propensity within S100A6 helices HI and HIV. Subsequent analysis of Thioflavin-T binding kinetics under acidic conditions elicited a very fast process with no lag phase and extensive formation of aggregates and stacked fibrils as observed by electron microscopy. Ca2+ exerted an inhibitory effect on the aggregation kinetics, which could be reverted upon chelation. An FT-IR investigation of the early conformational changes occurring under these conditions showed that Ca2+ promotes anti-parallel β-sheet conformations that repress fibrillation. At pH 7, Ca2+ rendered the fibril formation kinetics slower: time-resolved imaging showed that fibril formation is highly suppressed, with aggregates forming instead. In the absence of metals an extensive network of fibrils is formed. S100A6 oligomers, but not fibrils, were found to be cytotoxic, decreasing cell viability by up to 40%. This effect was not observed when the aggregates were formed in the presence of Ca2+. Interestingly, native S1006 seeds SOD1 aggregation, shortening its nucleation process. This suggests a cross-talk between these two proteins involved in ALS. Overall, these results put forward novel roles for S100 proteins, whose metal-modulated aggregation propensity may be a key aspect in their physiology and function.