Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

Transitions in Contentious Behaviour in Infancy and Later Aggressive Conduct Problems

Background. Individual trajectories toward aggression originate in early infancy, before there is intent to harm. We focused on infants who were contentious, i.e., prone to engage in anger and use of physical force with other people, and examined change in levels of contentiousness between 6 and 12 months of age with reference to later aggressive conduct problems.
Sample. The CCDS is a nationally representative sample of 321 firstborn children whose families were recruited from antenatal clinics in two National Health Service Trusts.
Method. Mothers, fathers, and a third family member or friend who knew infants well completed the Cardiff Infant Contentiousness Scale (CICS) at 6 months, which was stable form 6 to 12 months, and validated by direct observation of infants’ use of force against peers. Primary caregivers again completed the CICS at 12 months, and up to three informants completed the Child Behaviour Check List at mean ages of 36 and 84 months. We used Latent Transition Analysis to identify different groups of infants in respect to their patterns of contentiousness from 6 to 12 months.
Results
Three ordered classes of contentiousness from low to high were found at 6 and 12 months. Infants exposed to greater family adversity were more likely to move into the high-contentious class from 6 to 12 months. Higher contentiousness in infancy predicted more aggressive conduct problems at 33 months and thereafter.
Conclusions
Infants exposed to family adversity are already at disadvantage by 6 months and likely to escalate in their anger and aggressiveness over time.

Characterisation of polyethylene powders for rotational moulding and effect of powder size and shape on densification behaviour

The particle size, shape and distribution of a range of rotational moulding polyethylenes (PEs) ground to powder was investigated using a novel visual data acquisition and analysis system (TP Picture®), developed by Total Petrochemicals. Differences in the individual particle shape factors of the powder samples were observed and correlations with the grinding conditions were determined. When heated, the bubble dissolution behaviour of the same powders was investigated and the shape factor correlated with densification rate, bubble size and bubble distribution.

Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Navigating uncertain waters: a critical review of inferring foraging behaviour from location and dive data in pinnipeds

In the last thirty years, the emergence and progression of biologging technology has led to great advances in marine predator ecology. Large databases of location and dive observations from biologging devices have been compiled for an increasing number of diving predator species (such as pinnipeds, sea turtles, seabirds and cetaceans), enabling complex questions about animal activity budgets and habitat use to be addressed. Central to answering these questions is our ability to correctly identify and quantify the frequency of essential behaviours, such as foraging. Despite technological advances that have increased the quality and resolution of location and dive data, accurately interpreting behaviour from such data remains a challenge, and analytical methods are only beginning to unlock the full potential of existing datasets. This review evaluates both traditional and emerging methods and presents a starting platform of options for future studies of marine predator foraging ecology, particularly from location and two-dimensional (time-depth) dive data. We outline the different devices and data types available, discuss the limitations and advantages of commonly-used analytical techniques, and highlight key areas for future research. We focus our review on pinnipeds - one of the most studied taxa of marine predators - but offer insights that will be applicable to other air-breathing marine predator tracking studies. We highlight that traditionally-used methods for inferring foraging from location and dive data, such as first-passage time and dive shape analysis, have important caveats and limitations depending on the nature of the data and the research question. We suggest that more holistic statistical techniques, such as state-space models, which can synthesise multiple track, dive and environmental metrics whilst simultaneously accounting for measurement error, offer more robust alternatives. Finally, we identify a need for more research to elucidate the role of physical oceanography, device effects, study animal selection, and developmental stages in predator behaviour and data interpretation.

As dimensões individual e coletiva no ensino exploratório da matemática

Relatório de Estágio apresentado à Escola Superior de Educação de Lisboa para obtenção do grau de mestre em Ensino do 1.º e 2.º Ciclos do Ensino Básico

A coupled movement and bioenergetics model to explore the spawning migration of anchovy in the Bay of Biscay

Adult anchovies in the Bay of Biscay perform north to south migration from late winter to early summer for spawning. However, what triggers and drives the geographic shift of the population remains unclear and poorly understood. An individual-based fish model has been implemented to explore the potential mechanisms that control anchovy's movement routes toward its spawning habitats. To achieve this goal, two fish movement behaviors – gradient detection through restricted area search and kinesis – simulated fish response to its dynamic environment. A bioenergetics model was used to represent individual growth and reproduction along the fish trajectory. The environmental forcing (food, temperature) of the model was provided by a coupled physical–biogeochemical model. We followed a hypothesis-testing strategy to actualize a series of simulations using different cues and computational assumptions. The gradient detection behavior was found as the most suitable mechanism to recreate the observed shift of anchovy distribution under the combined effect of sea-surface temperature and zooplankton. In addition, our results suggested that southward movement occurred more actively from early April to middle May following favorably the spatio-temporal evolution of zooplankton and temperature. In terms of fish bioenergetics, individuals who ended up in the southern part of the bay presented better condition based on energy content, proposing the resulting energy gain as an ecological explanation for this migration. The kinesis approach resulted in a moderate performance, producing distribution pattern with the highest spread. Finally, model performance was not significantly affected by changes on the starting date, initial fish distribution and number of particles used in the simulations, whereas it was drastically influenced by the adopted cues.

Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging

This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.

A comparison of the physiological demands of rugby union match-play when determined by absolute (ABS) or individual (IND) velocity bands in Global Positioning System (GPS) analysis

Since turning professional in 1995 there have been considerable advances in the research on the demands of rugby union, largely using Global Positioning System (GPS) analysis over the last 10 years. A systematic review on the use of GPS, particularly the setting of absolute (ABS) and individual (IND) velocity bands in field based, intermittent, high-intensity (HI) team sports was undertaken. From 3669 records identified, 38 studies were included for qualitative analysis. Little agreement on the definition of movement intensities within team sports was found, only three papers, all on rugby union, had used IND bands, with only one comparing ABS and IND methods. Thus, the aim of this study was to determine if there is a difference in the demands within positions when comparing ABS and IND methods for GPS analysis and if these differences are significantly different between the forward and back positional groups. A total of 214 data files were recorded from 26 players in 17 matches of the 2015/2016 Scottish BT Premiership. ABS velocity zones 1-7 were set at 1) 0-6, 2) 6.1-11, 3) 11.1-15, 4) 15.1-18, 5) 18.1-21, 6) 21.1-15 and 7) 25.1-40km.h-1 while IND zones 1-7 were 1) <20, 2) 20-40, 3) 40-50, 4) 50-70, 5) 70-80, 6) 80-95 and 7) 95-100% of player’s individually determined maximum velocity (Vmax). A 40m sprint test measured Vmax using OptaPro S4 10 Hz (catapult, Australia) GPS units to derive IND bands. The same GPS units were worn during matches. GPS outputs analysed were % distance, % time, high intensity efforts (HIEs) over 18.1 km.h-1 / 70% max velocity and repeated high intensity efforts (RHIEs) which consists of three HIEs in 21secs. General linear model (GLM) analysis identified a significant difference in the measurement of % total distance covered, between the ABS and IND methods in all zones for forwards (p<0.05) and backs (p<0.05). This difference was also significant between forwards and backs in zones 1, shown as mean difference ± standard deviation (3.7±0.7%), 6 (1.2±0.4%) and 7 (1.0±0.0%) respectively (p<0.05). Percentage time estimations were significantly different between ABS and IND analysis within forwards in zones 1 (1.7±1.7%), 2 (-2.9±1.3%), 3 (1.9±0.8%), 4 (-1.4±0.8%) and 5 (0.2±0.4%), and within backs in zones 1 (-10±1.5%), 2 (-1.2±1.1%), 3 (1.8±0.9%) and 5 (0.6±0.5%) (p<0.05). The difference between groups was significant in zones 1, 2, 4 and 5 (p<0.05). The number of HIEs was significantly different between forwards and backs in zones 6 (6±2) and 7 (3±2). RHIEs were significantly different between ABS and IND for forwards (1±2, p<0.05) although not between groups. Until more research on the differences in ABS and IND methods is carried out, then neither can be deemed a criterion method. In conclusion, there are significant differences between the ABS and IND methods of GPS analysis of the physical demands of rugby union, which must be considered when used to inform training load and recovery to improve performance and reduce injuries.

Diel variation in movement patterns and habitat use by the near-threatened cabrera vole in mediterranean farmland

As variações circadianas no comportamento animal e o seu impacto nas populações constituem desafios importantes em ecologia e conservação. Nesta tese documentam-se as variações circadianas no uso do habitat e padrões de movimento pelo rato de Cabrera, em habitats Mediterrânicos fragmentados. O estudo baseou-se no radio-seguimento de indivíduos em habitats dominados por herbáceas e arbustos. Os resultados indicaram que a proporção de tempo despendido em deslocações, a distância percorrida, e a selecção do tipo de vegetação, estão fortemente interrelacionados, variando consideravelmente ao longo de diferentes períodos do dia. Os ratos movimentaram-se mais frequentemente e maiores distâncias nos períodos diurnos, durante os quais as áreas dominadas por herbáceas foram usadas mais intensivamente. Durante a estação seca houve alguma tendência para a diminuição dos movimentos durante as horas mais quentes. Estes resultados são discutidos no sentido de mostrar como indicadores comportamentais podem contribuir para melhorar a gestão e conservação da espécie; ABSTRACT: Understanding the circadian variations in species behaviour and its impacts on population is a challenging topic in ecology and conservation. This thesis documents the circadian variations in habitat use and movement patterns by Cabrera voles in fragmented Mediterranean farmland. The study was based on radiotracking data of individuals living in habitat patches dominated by wet grasses and shrubs. Results indicated that the proportion of time animals spent moving, the distance moved and the selection strength of vegetation were closely linked behavioural traits, which varied considerably across the 24 hour cycle. Voles moved more frequently and over larger distances during daytime, which was when wet grasses were used more intensively. During the dry season there was some tendency for a decrease in movement activity during the hottest hours of the day. These results are used to discuss how behavioural indicators may be useful to improve conservation management of the species.

More Than A Movement: Unpacking Contemporary Anti-Human Trafficking Efforts in Washington, D.C.

Trafficking in persons has attracted seemingly boundless attention over the last two decades and the work aimed at fighting it is best understood when this cause is contextualized against the backdrop of other social forces—economic, social, and cultural—shaping contemporary nonprofit activities. This project argues that the paid and volunteer labor that takes place in metro Washington, D.C., to combat trafficking in persons can be understood as both a movement and an industry. In addition to arguing that anti-trafficking work is part of a nonprofit industrial complex that situates activist and advocacy work firmly inside state and economic institutions, this project is concerned with the ways in which trafficking work and workers conduct their business collectively. As an organizational study, it identifies the key players in the D.C. region focused on this issue and traces their interactions, collaborations, and cooperation. Significantly, this project suggests that despite variations in objectives, methods, priorities, and characterizations of trafficking, thirty organizations in metro D.C. working on this issue “get along” because they are bound by the benign common goal of raising awareness. Awareness, in this context, is best understood as both a cultural anchor facilitating cohesion and as a social currency allowing groups to opt into joint efforts. The dissertation concludes that organizations centralize awareness in their collective activities over more drastic priorities around which consensus would need to be gained. This is a lost opportunity for making sense of the ways that individual bodies—men, women, and children—experience not just trafficking, but the world around them.

Explaining tourists´ support for environmental protection

Any movement towards sustainable tourism is dependent not only upon the industry and other key stakeholders but also the demand side, namely the tourists. Yet, there is a limited literature from the demand point of view. In this area, contributions to an understanding of tourists’ support to sustainable development are necessary. This paper analyzes the main determinants in tourist behavior regarding the environmental considerations when they are making decisions about their holiday plans. General literature on this issue highlights the need to consider socio-economic variables of the individual as well as the attributes related of their style of living. If the econometric model takes into account all these variables simultaneously, then the linkage between contextual changes and tourists´ behaviour is enriched and it may be estimated more accurately. In this sense, a multilevel approach using a random-intercept logistic models is proposed, since tourists belong to a country are affected by the same contextual variables. The analysis comprises a joint dataset composed by microdata belong to the survey Attitudes of Europeans Towards Tourism, which corresponds to Flash Eurobarometer 281, macrodata from Eurostat (GDP in pps and GDP growth) and additional variables profiles from the 2005 Environmental Sustainability Index. Country-specific effects are calculated across the EU-27 countries, which corroborated that attitudes to the sustainable tourism are heterogeneous geo-graphically. The higher the level of GDP, the lower the level of tourists´ support. These results could be explained because tourists of richer countries already have to pay more tax for envi-ronmental protection. Age, gender and educational attainment are relevant. Motivations for travelling, size of the community, type of the destination, and environmental sustainability indi-cators of the place of residence are also important factors.

Modelling reactive and proactive behaviour in simulation

This research investigated the simulation model behaviour of a traditional and combined discrete event as well as agent based simulation models when modelling human reactive and proactive behaviour in human centric complex systems. A departmental store was chosen as human centric complex case study where the operation system of a fitting room in WomensWear department was investigated. We have looked at ways to determine the efficiency of new management policies for the fitting room operation through simulating the reactive and proactive behaviour of staff towards customers. Once development of the simulation models and their verification had been done, we carried out a validation experiment in the form of a sensitivity analysis. Subsequently, we executed a statistical analysis where the mixed reactive and proactive behaviour experimental results were compared with some reactive experimental results from previously published works. Generally, this case study discovered that simple proactive individual behaviour could be modelled in both simulation models. In addition, we found the traditional discrete event model performed similar in the simulation model output compared to the combined discrete event and agent based simulation when modelling similar human behaviour.

European lobster (Homarus gammarus) larvae under an acidification scenario: addressing biochemical, development and behaviour responses

A acidificação dos oceanos constitui uma problemática global e a realidade de que está, efetivamente, a acontecer não é uma consideração subjetiva. A Acidificação dos oceanos provocada por emissões de dióxido de carbono de origem antropogénica tem vindo a reduzir o pH das águas superficiais do Oceano e projeções preveem a continuidade deste processo. Embora muita investigação tenha sido desenvolvida no âmbito dos invertebrados que calcificam, tais como moluscos e crustáceos, poucos consideraram o estudo de efeitos ao nível sub-celular para avaliar stress oxidativo ou respostas funcionais do metabolismo energético em tais condições, interligando vários níveis de organização biológica. O objetivo do presente estudo foi o de avaliar os efeitos da exposição a diferentes níveis-alvo de pCO2 (controlo: 370 μatm; aumentado: 710 μatm) e de pH (controlo: 8.15; reduzido: 7.85) em parâmetros de crescimento bem como avaliar respostas comportamentais e bioquímicas relacionadas com stress oxidativo e metabolismo energético durante o desenvolvimento larvar de um crustáceo decápode. Este cenário de acidificação está de acordo com os RCPs previstos pelo Painel Intergovernamental para as Alterações Climáticas (IPCC, 2014) para o ano 2100. Para o presente estudo, foi utilizado o crustáceo Homarus gammarus (L.) – sendo uma espécie com elevado valor comercial, que tem vindo a sofrer elevada pressão de pesca em águas Europeias. Fêmeas adultas provenientes da costa Atlântica Oeste Portuguesa foram obtidas de um retalhista local. Após a eclosão em ambiente laboratorial controlado, larvas provenientes da mesma progenitora foram expostas às condições acima descritas desde o momento da eclosão até à chegada ao Estádio III. A sobrevivência individual e ocorrência de ecdise foram avaliados individualmente de 12h em 12h. Réplicas de cada tratamento foram recolhidas em momentos específicos durante o Estádio I (primeiro estádio larvar) e Estádio III (último estádio larvar) para análise morfométrica e de crescimento (peso fresco e comprimento carapaça) e respostas bioquímicas. Os biomarcadores analisados incluíram parâmetros relacionados com stress oxidativo e danos (atividade da enzima superóxido dismutase (SOD), peroxidação lipídica (LPO) e danos no DNA) e metabolismo energético (atividade da cadeia transportadora de eletrões (ETS) e da enzima lactato desidrogenase (LDH) e quantificação de Hidratos de Carbono). Os resultados obtidos sugerem que a sobrevivência diminui e que o período inter-muda é afetado durante a exposição a cenários de acidificação. No que respeita aos parâmetros de crescimento/morfométricos, larvas do cenário de acidificação apresentam uma tendência para crescimento diminuído, menor peso e comprimento de carapaça. As análises bioquímicas realizadas indicam a ocorrência de stress oxidativo sob condições de acidificação. Respostas ao nível do metabolismo energético não variaram significativamente entre tratamentos. Os resultados apontam também para que fases larvares possam possuir um sistema antioxidante ainda em desenvolvimento, tornando-as mais suscetíveis ao stress oxidativo. As fases larvares são uma fase vulnerável e crucial no ciclo de vida das espécies, influenciando o recrutamento e a renovação de stocks. Este estudo contribui para um melhor entendimento sobre a vulnerabilidade desta espécie num cenário de alterações climáticas – Acidificação dos oceanos – ao endereçar os mecanismos envolvidos nas respostas deste crustáceo a este agente causador de stress.

Physicochemical complexity in complex chemical systems

Self-replication and compartmentalization are two central properties thought to be essential for minimal life, and understanding how such processes interact in the emergence of complex reaction networks is crucial to exploring the development of complexity in chemistry and biology. Autocatalysis can emerge from multiple different mechanisms such as formation of an initiator, template self-replication and physical autocatalysis (where micelles formed from the reaction product solubilize the reactants, leading to higher local concentrations and therefore higher rates). Amphiphiles are also used in artificial life studies to create protocell models such as micelles, vesicles and oil-in-water droplets, and can increase reaction rates by encapsulation of reactants. So far, no template self-replicator exists which is capable of compartmentalization, or transferring this molecular scale phenomenon to micro or macro-scale assemblies. Here a system is demonstrated where an amphiphilic imine catalyses its own formation by joining a non-polar alkyl tail group with a polar carboxylic acid head group to form a template, which was shown to form reverse micelles by Dynamic Light Scattering (DLS). The kinetics of this system were investigated by 1H NMR spectroscopy, showing clearly that a template self-replication mechanism operates, though there was no evidence that the reverse micelles participated in physical autocatalysis. Active oil droplets, composed from a mixture of insoluble organic compounds in an aqueous sub-phase, can undergo processes such as division, self-propulsion and chemotaxis, and are studied as models for minimal cells, or protocells. Although in most cases the Marangoni effect is responsible for the forces on the droplet, the behaviour of the droplet depends heavily on the exact composition. Though theoretical models are able to calculate the forces on a droplet, to model a mixture of oils on an aqueous surface where compounds from the oil phase are dissolving and diffusing through the aqueous phase is beyond current computational capability. The behaviour of a droplet in an aqueous phase can only be discovered through experiment, though it is determined by the droplet's composition. By using an evolutionary algorithm and a liquid handling robot to conduct droplet experiments and decide which compositions to test next, entirely autonomously, the composition of the droplet becomes a chemical genome capable of evolution. The selection is carried out according to a fitness function, which ranks the formulation based on how well it conforms to the chosen fitness criteria (e.g. movement or division). Over successive generations, significant increases in fitness are achieved, and this increase is higher with more components (i.e. greater complexity). Other chemical processes such as chemiluminescence and gelation were investigated in active oil droplets, demonstrating the possibility of controlling chemical reactions by selective droplet fusion. Potential future applications for this might include combinatorial chemistry, or additional fitness goals for the genetic algorithm. Combining the self-replication and the droplet protocells research, it was demonstrated that the presence of the amphiphilic replicator lowers the interfacial tension between droplets of a reaction mixture in organic solution and the alkaline aqueous phase, causing them to divide. Periodic sampling by a liquid handling robot revealed that the extent of droplet fission increased as the reaction progressed, producing more individual protocells with increased self-replication. This demonstrates coupling of the molecular scale phenomenon of template self-replication to a macroscale physicochemical effect.