A pH optode based on thymol blue: application to determination of CO2 using flow injection analysis system

An optode based on thymol blue (TB), an acid-based indicator, has been constructed and evaluated as a detector in FIA system for CO2 determination. The dye was chemically immobilised on the surface of a bifurcated glass optical fibre bundle, using silanisation in organic media. In FIA system, hydrogen carbonate or carbonate samples are injected in a buffer carrier solution, and then are mixed with phosphoric acid solution to generate CO2, which diffuses through a PTFE membrane, in order to be collected in an acceptor carrier fluid, pumped towards to detection cell, in which the optode was adapted. The proposed system presents two linear response ranges, from 1.0 x 10-3 to 1.0 x 10-2 mol l-1, and from 2.0 x 10-2 to 0.10 mol l-1. The sampling frequency was 11 sample h-1, with good repeatability (R.S.D < 4 %, n = 10). In flow conditions the optode lifetime was 170 h. The system was applied in the analysis of commercial mineral water and the results obtained in the hydrogen carbonate determination did not differ significantly from those obtained by potentiometry, at a confidence level of 95 %.

Development of a warning system for wheat blast caused by Pyricularia grisea

Wheat (Triticum aestivum L.) blast caused by Pyricularia grisea is a new disease in Brazil and no resistant cultivars are available. The interactions between temperature and wetness durations have been used in many early warning systems. Hence, growth chamber experiments to assess the effect of different temperatures (10, 15, 20, 25, 30 and 35ºC) and the duration of spike-wetness (0, 5, 10, 15, 20, 25, 30, 35 and 40 hours) on the intensity of blast in cultivar BR23 were carried out. Each temperature formed an experiment and the duration of wetness the treatments. The highest blast intensity was observed at 30°C and increased as the duration of the wetting period increased while the lowest occurred at 25°C and 10 hours of spike wetness. Regardless of the temperature, no symptoms occurred when the wetting period was less than 10 hours but at 25°C and a 40 h wetting period blast intensity exceeded 85%. These variations in blast intensity as a function of temperature are explained by a generalized beta model and as a function of the duration of spike wetness by the Gompertz model. Disease intensity was modeled as a function of both temperature and the durations of spike wetness and the resulting equation provided a precise description of the response of P. grisea to temperatures and the durations of spike wetness. This model was used to construct tables that can be used to predict the intensity of P. grisea wheat blast based on the temperatures and the durations of wheat spike wetness obtained in the field.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Broadband excitation in the system identification of active magnetic bearing rotor systems

One of the targets of the climate and energy package of the European Union is to increase the energy efficiency in order to achieve a 20 percent reduction in primary energy use compared with the projected level by 2020. The energy efficiency can be improved for example by increasing the rotational speed of large electrical drives, because this enables the elimination of gearboxes leading to a compact design with lower losses. The rotational speeds of traditional bearings, such as roller bearings, are limited by mechanical friction. Active magnetic bearings (AMBs), on the other hand, allow very high rotational speeds. Consequently, their use in large medium- and high-speed machines has rapidly increased. An active magnetic bearing rotor system is an inherently unstable, nonlinear multiple-input, multiple-output system. Model-based controller design of AMBs requires an accurate system model. Finite element modeling (FEM) together with the experimental modal analysis provides a very accurate model for the rotor, and a linearized model of the magneticactuators has proven to work well in normal conditions. However, the overall system may suffer from unmodeled dynamics, such as dynamics of foundation or shrink fits. This dynamics can be modeled by system identification. System identification can also be used for on-line diagnostics. In this study, broadband excitation signals are adopted to the identification of an active magnetic bearing rotor system. The broadband excitation enables faster frequency response function measurements when compared with the widely used stepped sine and swept sine excitations. Different broadband excitations are reviewed, and the random phase multisine excitation is chosen for further study. The measurement times using the multisine excitation and the stepped sine excitation are compared. An excitation signal design with an analysis of the harmonics produced by the nonlinear system is presented. The suitability of different frequency response function estimators for an AMB rotor system are also compared. Additionally, analytical modeling of an AMB rotor system, obtaining a parametric model from the nonparametric frequency response functions, and model updating are discussed in brief, as they are key elements in the modeling for a control design. Theoretical methods are tested with a laboratory test rig. The results conclude that an appropriately designed random phase multisine excitation is suitable for the identification of AMB rotor systems.

Image analysis for assessing broiler breeder behavior response to thermal environment

The research proposes a methodology for assessing broiler breeder response to changes in rearing thermal environment. The continuous video recording of a flock analyzed may offer compelling evidences of thermal comfort, as well as other indications of welfare. An algorithm for classifying specific broiler breeder behavior was developed. Videos were recorded over three boxes where 30 breeders were reared. The boxes were mounted inside an environmental chamber were ambient temperature varied from cold to hot. Digital images were processed based on the number of pixels, according to their light intensity variation and binary contrast allowing a sequence of behaviors related to welfare. The system used the default of x, y coordinates, where x represents the horizontal distance from the top left of the work area to the point P, and y is the vertical distance. The video images were observed, and a grid was developed for identifying the area the birds stayed and the time they spent at that place. The sequence was analyzed frame by frame confronting the data with specific adopted thermal neutral rearing standards. The grid mask overlapped the real bird image. The resulting image allows the visualization of clusters, as birds in flock behave in certain patterns. An algorithm indicating the breeder response to thermal environment was developed.

Software for design of experiments and response modelling of cake ltration applications

Filtration is a widely used unit operation in chemical engineering. The huge variation in the properties of materials to be ltered makes the study of ltration a challenging task. One of the objectives of this thesis was to show that conventional ltration theories are di cult to use when the system to be modelled contains all of the stages and features that are present in a complete solid/liquid separation process. Furthermore, most of the ltration theories require experimental work to be performed in order to obtain critical parameters required by the theoretical models. Creating a good overall understanding of how the variables a ect the nal product in ltration is somewhat impossible on a purely theoretical basis. The complexity of solid/liquid separation processes require experimental work and when tests are needed, it is advisable to use experimental design techniques so that the goals can be achieved. The statistical design of experiments provides the necessary tools for recognising the e ects of variables. It also helps to perform experimental work more economically. Design of experiments is a prerequisite for creating empirical models that can describe how the measured response is related to the changes in the values of the variable. A software package was developed that provides a ltration practitioner with experimental designs and calculates the parameters for linear regression models, along with the graphical representation of the responses. The developed software consists of two software modules. These modules are LTDoE and LTRead. The LTDoE module is used to create experimental designs for di erent lter types. The lter types considered in the software are automatic vertical pressure lter, double-sided vertical pressure lter, horizontal membrane lter press, vacuum belt lter and ceramic capillary action disc lter. It is also possible to create experimental designs for those cases where the variables are totally user de ned, say for a customized ltration cycle or di erent piece of equipment. The LTRead-module is used to read the experimental data gathered from the experiments, to analyse the data and to create models for each of the measured responses. Introducing the structure of the software more in detail and showing some of the practical applications is the main part of this thesis. This approach to the study of cake ltration processes, as presented in this thesis, has been shown to have good practical value when making ltration tests.

Software for design of experiments and response modelling of cake filtration applications

Filtration is a widely used unit operation in chemical engineering. The huge variation in the properties of materials to be ltered makes the study of ltration a challenging task. One of the objectives of this thesis was to show that conventional ltration theories are di cult to use when the system to be modelled contains all of the stages and features that are present in a complete solid/liquid separation process. Furthermore, most of the ltration theories require experimental work to be performed in order to obtain critical parameters required by the theoretical models. Creating a good overall understanding of how the variables a ect the nal product in ltration is somewhat impossible on a purely theoretical basis. The complexity of solid/liquid separation processes require experimental work and when tests are needed, it is advisable to use experimental design techniques so that the goals can be achieved. The statistical design of experiments provides the necessary tools for recognising the e ects of variables. It also helps to perform experimental work more economically. Design of experiments is a prerequisite for creating empirical models that can describe how the measured response is related to the changes in the values of the variable. A software package was developed that provides a ltration practitioner with experimental designs and calculates the parameters for linear regression models, along with the graphical representation of the responses. The developed software consists of two software modules. These modules are LTDoE and LTRead. The LTDoE module is used to create experimental designs for di erent lter types. The lter types considered in the software are automatic vertical pressure lter, double-sided vertical pressure lter, horizontal membrane lter press, vacuum belt lter and ceramic capillary action disc lter. It is also possible to create experimental designs for those cases where the variables are totally user de ned, say for a customized ltration cycle or di erent piece of equipment. The LTRead-module is used to read the experimental data gathered from the experiments, to analyse the data and to create models for each of the measured responses. Introducing the structure of the software more in detail and showing some of the practical applications is the main part of this thesis. This approach to the study of cake ltration processes, as presented in this thesis, has been shown to have good practical value when making ltration tests.

Dispersal and metacommunity dynamics in a soft-sediment benthic system : how well is the seafloor connected?

Connectivity depends on rates of dispersal between communities. For marine soft-sediment communities continued small-scale dispersal as post-larvae and as adults can be equally important in maintaining community composition, as initial recruitment of substrate by pelagic larvae. In this thesis post-larval dispersal strategies of benthic invertebrates, as well as mechanisms by which communities are connected were investigated. Such knowledge on dispersal is scarce, due to the difficulties in actually measuring dispersal directly in nature, and dispersal has not previously been quantified in the Baltic Sea. Different trap-types were used underwater to capture dispersing invertebrates at different sites, while in parallel measuring waves and currents. Local community composition was found to change predictably under varying rates of dispersal and physical connectivity (waves and currents). This response was, however, dependent on dispersal-related traits of taxa. Actively dispersing taxa will be relatively better at maintaining their position, as they are not as dependent on hydrodynamic conditions for dispersal and will be less prone to be passively transported by currents. Taxa also dispersed in relative proportions that were distinctly different from resident community composition and a significant proportion (40 %) of taxa were found to lack a planktonic larval life-stage. Community assembly was re-started in a large-scale manipulative field experiment over one year across several sites, which revealed how patterns of community composition (α-, β- and λ-diversity) change depending on rates of dispersal. Results also demonstrated that in response to small-scale disturbance, initial recruitment was by nearby-dominant species after which other species arrived from successively further away. At later assembly time, the number of coexisting species increased beyond what was expected purely by local niche requirements (species sorting), transferring regional differences in community composition (β-diversity) to the local scale (α-diversity, mass effect). Findings of this thesis complement more theoretical studies in metacommunity ecology by demonstrating that understanding how and when individuals disperse relative to underlying environmental heterogeneity is key to interpreting how patterns of diversity change across different spatial scales. Such information from nature is critical when predicting responses to, for example, different types of disturbances or management actions in conservation.

Experimental poisoning of goats by Ipomoea carnea subsp. fistulosa in Argentina: a clinic and pathological correlation with special consideration on the central nervous system

Ipomoea carnea subsp. fistulosa, aguapei or mandiyura, is responsible for lysosomal storage in goats. The shrub contains several alkaloids, mainly swansonine which inhibits lysosomal α-mannosidase and Golgi mannosidase II. Poisoning occurs by inhibition of these hydrolases. There is neuronal vacuolation, endocrine dysfunction, cardiovascular and gastrointestinal injury, and immune disorders. Clinical signs and pathology of the experimental poisoning of goats by Ipomoea carnea in Argentina are here described. Five goats received fresh leaves and stems of Ipomoea. At the beginning, the goats did not consume the plant, but later, it was preferred over any other forage. High dose induced rapid intoxication, whereas with low doses, the course of the toxicosis was more protracted. The goats were euthanized when they were recumbent. Cerebrum, cerebellum, medulla oblongata, pons and colliculi, were routinely processed for histology. In nine days, the following clinical signs developed: abnormal fascies, dilated nostrils and abnormal postures of the head, cephalic tremors and nystagmus, difficulty in standing. Subsequently, the goats had a tendency to fall, always to the left, with spastic convulsions. There was lack in coordination of voluntary movements due to Purkinje and deep nuclei neurons damage. The cochlear reflex originated hyperreflexia, abnormal posture, head movements and tremors. The withdrawal reflex produced flexor muscles hypersensitivity at the four legs, later depression and stupor. Abnormal responses to sounds were related to collicular lesions. Thalamic damage altered the withdrawal reflex, showing incomplete reaction. The observed cervical hair bristling was attributed to a thalamic regulated nociceptive response. Depression may be associated with agonists of lysergic acid contained in Ipomoea. These clinical signs were correlated with lesions in different parts of the CNS.

System-level characterization of Th2 cell development and immune cell responses to ZnO and TiO2 nanoparticles

Asthma and allergy are common diseases and their prevalence is increasing. One of the hypotheses that explains this trend is exposure to inhalable chemicals such as traffi c-related air pollution. Epidemiological research supports this theory, as a correlation between environmental chemicals and allergic respiratory diseases has been found. In addition to ambient airborne particles, one may be exposed to engineered nanosized materials that are actively produced due to their favorable physico-chemical properties compared to their bulk size counterparts. On the cellular level, improper activity of T helper (Th) cells has been connected to allergic reactions. Th cells can differentiate into functionally different effector subsets, which are identifi ed according to their characteristic cytokine profi les resulting in specifi c ability to communicate with other cells. Th2 cells activate humoral immunity and stimulate eradication of extracellular pathogens. However, persistent predominance of Th2 cells is involved in a development of number of allergic diseases. The cytokine environment at the time of antigen recognition is the major factor determining the polarization of a naïve Th cell. Th2 cell differentiation is initiated by IL4, which signals via transcription factor STAT6. Although the importance of this pathway has been evaluated in the mouse studies, the signaling components involved have been largely unknown. The aim of this thesis was to identify molecules, which are under the control of IL4 and STAT6 in Th cells. This was done by using system-level analysis of STAT6 target genes at genome, mRNA and protein level resulting in identifi cation of various genes previously not connected to Th2 cell phenotype acquisition. In the study, STAT6-mediated primary and secondary target genes were dissection from each other and a detailed transcriptional kinetics of Th2 cell polarization of naïve human CD4+ T cells was collected. Integration of these data revealed the hierarchy of molecular events that mediates the differentiation towards Th2 cell phenotype. In addition, the results highlighted the importance of exploiting proteomics tools to complement the studies on STAT6 target genes identifi ed through transcriptional profi ling. In the last subproject, the effects of the exposure with ZnO and TiO2 nanoparticles was analyzed in Jurkat T cell line and in primary human monocyte-derived macrophages and dendritic cells to evaluate their toxicity and potential to cause infl ammation. Identifi cation of ZnO-derived gene expression showed that the same nanoparticles may elicit markedly distinctive responses in different cell types, thus underscoring the need for unbiased profi ling of target genes and pathways affected. The results gave additional proof that the cellular response to nanosized ZnO is due to leached Zn2+ ions. The approach used in ZnO and TiO2 nanoparticle study demonstrated the value of assessing nanoparticle responses through a toxicogenomics approach. The increased knowledge of Th2 cell signaling will hopefully reveal new therapeutic nodes and eventually improve our possibilities to prevent and tackle allergic infl ammatory diseases.

Effect of oral administration of Propionibacterium acnes on growth performance, DTH response and anti-OVA titers in goat kids

Immunostimulants are susbstances that stimuli the response of effector cells to activate the immune response such as antigen uptake, cytokine release or antibody response. These substances can increase resistence to infection by different types of microorganisms, reducing dependence of antibiotics used in livestock animals. Recent reports have demonstrated the positive effect of Propionibacterium acnes (P. acnes) to control animal diseases. In this study, we evaluated the effect of the non-specific immunostimulant P. acnes on immunological functions and growth performance in goat kids. Twenty five goat kids served as control group (A) and another 25 animals received P. acnes being the experimental group (B). Kids were challenged with ovalbumin (OVA) to assess humoral immunity. To assess in vivo cell immunity, delayed type hypersensitivity (DTH) test with phytohemagglutinin (PHA) was used, clinical signs and body weight were recorded each week until 9 weeks of age when the experiment ended. Blood samples were obtained to analyze serum proteins fractions and anti-OVA specific antibodies. No clinical signs of disease and no differences (p>0.05) on body weight between groups were recorded (7.32±0.81 kg in group A, 7.13±0.65 kg in group B). Goat kids from group B had more total protein (59.8±5g/l) and albumin levels (32.8±3.3g/l) than goat kids from group A (56.6±5.7 g/l, 29.6±3.9 g/l respectively) (p<0.05). DTH response in goat kids from group B on day 42 was higher (p<0.05) than group A. At day 63, goat kids from group receiving P. acnes had higher percentage (85.4) of anti-OVA IgM titers (p<0.05) than control group (57.7). In conclusion, the results showed that oral administration of P. acnes to goat kids improved some aspects of the immune system of the animals and it could be used to control goat diseases.

Distribution of immune response cells in the pelvic urethra and the prepuce of rams

The pathogens of the reproductive system in the male can penetrate and establish by ascending route, from to the prepuce to the urethra, accessory glands, epididymis and testicles. The aim of this paper is determine the distribution and number of cells involved in the immune response in prepuce and pelvic urethra of rams, without apparent clinical alterations in testicle, epididymis and prepuce. The distribution of some of the cells involved in the immune response at the level of the prepuce and the pelvic urethra was quantified in four one-year-old rams seronegative for B. ovis and A. seminis and without apparent lesions in the testicles, the epididymis, and the prepuce. At the moment of slaughter, samples were taken from the preputial fornix and the pelvic urethra and placed in 10% formalin and under freezing conditions. CD4, CD8, WC1, CD45RO, CD14 and CD1b cells were demonstrated by immunohistochemistry, and immunoglobulin-containing cells (ICC) of the IgA, IgG and IgM classes were demonstrated by immunofluorescence. The labeled cells present in the mucosa of both organs were counted with an image analyzer. The total number of cells was compared between both tissues and differentially between the epithelium and the connective tissue of the mucosa. Significant differences were found in the total number of CD4, CD45RO, and WC1 lymphocytes, in CD14 macrophages, and CD1b dendritic cells, with mean values being greater in the fornix than in the urethra (p<0.05) in all cases. Only dendritic cells were found in the prepuce. No differences were found in the number of CD8 lymphocytes between both organs. The ratio between each cell type in the connective and the intraepithelial tissues and between organs was 10/1 for CD4 in the fornix (p<0.05), against 7/1 in the urethra (p<0.05), while CD8 had a 1/1 distribution in both mucosae. The WC1 ratio was 5/1 in both mucosae (p<0.05). CD45RO labeling was 19/1 in the prepuce (p<0.05) and 1/1 in the urethra. IgA-containing cells did not show differences in the total number of cells in both tissues. In the urethra, no IgG-containing cells were observed and IgM-containing cells were scarce; in contrast, both cell types were present in the prepuce, in amounts greater than in the urethra (p<0.05). IgA-, IgG-, and IgM-containing cells were located in both organs in the mucosal connective tissue. The presence of antigen-presenting cells, macrophages, and dendritic cells, as well as of lymphocytes CD4, CD8 TCR γδ (WC1), IgA-, IgG and IgM positive cells, and CD45RO cells suggests that both mucosae may behave as inductive and effector sites for the mucosal immune response.

Pulse response based control for positive definite systems

Pulse Response Based Control (PRBC) is a recently developed minimum time control method for flexible structures. The flexible behavior of the structure is represented through a set of discrete time sequences, which are the responses of the structure due to rectangular force pulses. The rectangular force pulses are given by the actuators that control the structure. The set of pulse responses, desired outputs, and force bounds form a numerical optimization problem. The solution of the optimization problem is a minimum time piecewise constant control sequence for driving the system to a desired final state. The method was developed for driving positive semi-definite systems. In case the system is positive definite, some final states of the system may not be reachable. Necessary conditions for reachability of the final states are derived for systems with a finite number of degrees of freedom. Numerical results are presented that confirm the derived analytical conditions. Numerical simulations of maneuvers of distributed parameter systems have shown a relationship between the error in the estimated minimum control time and sampling interval

Response of Grilage-Like Structures by the Mobility Approach

This work presents an application of the Mobility Approach to the analysis of the power flow through grillage-like structures. Such structures are usually found in offshore platforms, supporting large and heavy machines. Different wave kinds (longitudinal, flexural and torsional) were initially considered in the power flow analysis between two beams joined in L. Beams excited by an in-plane point force showed strong coupling between longitudinal-flexural waves, while that for out-of-plane point force excitation, flexural-torsional waves coupling represents the most important mechanism of energy transmission. The response determination of grillages by the mobility approach requires the structure to be separated into simple beam-like structural components. Equations for rotations and displacements at the joints of all beams are written for as mobility functions, and moments and forces acting at the joints. A system of equations relating all such internal forces and moments is obtained. This approach was applied to simple grillages. Response results showed good agreement when compared to those provided by Finite Elements.

Non-Linear Unsteady Aerodynamic Response Approximation Using Multi-Layer Functionals

Non-linear functional representation of the aerodynamic response provides a convenient mathematical model for motion-induced unsteady transonic aerodynamic loads response, that accounts for both complex non-linearities and time-history effects. A recent development, based on functional approximation theory, has established a novel functional form; namely, the multi-layer functional. For a large class of non-linear dynamic systems, such multi-layer functional representations can be realised via finite impulse response (FIR) neural networks. Identification of an appropriate FIR neural network model is facilitated by means of a supervised training process in which a limited sample of system input-output data sets is presented to the temporal neural network. The present work describes a procedure for the systematic identification of parameterised neural network models of motion-induced unsteady transonic aerodynamic loads response. The training process is based on a conventional genetic algorithm to optimise the network architecture, combined with a simplified random search algorithm to update weight and bias values. Application of the scheme to representative transonic aerodynamic loads response data for a bidimensional airfoil executing finite-amplitude motion in transonic flow is used to demonstrate the feasibility of the approach. The approach is shown to furnish a satisfactory generalisation property to different motion histories over a range of Mach numbers in the transonic regime.