Bayesian models for spatio-temporal assessment of disease

This thesis has contributed to the advancement of knowledge in disease modelling by addressing interesting and crucial issues relevant to modelling health data over space and time. The research has led to the increased understanding of spatial scales, temporal scales, and spatial smoothing for modelling diseases, in terms of their methodology and applications. This research is of particular significance to researchers seeking to employ statistical modelling techniques over space and time in various disciplines. A broad class of statistical models are employed to assess what impact of spatial and temporal scales have on simulated and real data.

Impacts of agriculture on amphibians at multiple scales

Agriculture-mediated habitat loss and degradation together with climate change are among the greatest global threats to species, communities, and ecosystem functioning. During the last century, more than 50% of the world's wetlands have been lost and agricultural activities have subjected wetland species to increased isolation and decreased quality of habitats. Likewise, as a part of agricultural intensification, the use of pesticides has increased notably, and pesticide residues occur frequently in wetlands making the exposure of wetland organisms to pesticides highly probable. In this thesis, a set of ecotoxicological and landscape ecological studies were carried out to investigate pesticide-effects on tadpoles, and species-habitat relationships of amphibians in agricultural landscapes. The results show that the fitness of R. temporaria tadpoles can be negatively affected by sublethal pesticide concentrations, and that pesticides may increase the costs of response to natural environmental stressors. However, tadpoles may also be able to compensate for some of the negative effects of pesticides. The results further demonstrate that both historic and current-day agricultural land use can negatively impact amphibians, but that in some cases the costs of living in agricultural habitats may only become apparent when amphibians face other environmental stressors, such as drought. Habitat heterogeneity may, however, increase the persistence of amphibians in agricultural landscapes. Hence, the results suggest that amphibians are likely to be affected by agricultural processes that operate at several spatial and temporal scales, and that it is probable that various processes related to current-day agriculture will affect both larval and adult amphibians. The results imply that maintaining dense wetland patterns could enhance persistence of amphibian populations in agricultural habitats, and indicate that heterogeneous landscapes may lower the risk of regional amphibian population declines under extreme weather perturbations.

Influence of Spatial Scales on the Performance of Saturated Subsurface Flow and Transport Models

Numerical modeling of saturated subsurface flow and transport has been widely used in the past using different numerical schemes such as finite difference and finite element methods. Such modeling often involves discretization of the problem in spatial and temporal scales. The choice of the spatial and temporal scales for a modeling scenario is often not straightforward. For example, a basin-scale saturated flow and transport analysis demands larger spatial and temporal scales than a meso-scale study, which in turn has larger scales compared to a pore-scale study. The choice of spatial-scale is often dictated by the computational capabilities of the modeler as well as the availability of fine-scale data. In this study, we analyze the impact of different spatial scales and scaling procedures on saturated subsurface flow and transport simulations.

Space-Time Scales of Northward Propagation of Convection during Boreal Summer

This study uses precipitation estimates from the Tropical Rainfall Measuring Mission to quantify the spatial and temporal scales of northward propagation of convection over the Indian monsoon region during boreal summer. Propagating modes of convective systems in the intraseasonal time scales such as the Madden-Julian oscillation can interact with the intertropical convergence zone and bring active and break spells of the Indian summer monsoon. Wavelet analysis was used to quantify the spatial extent (scale) and center of these propagating convective bands, as well as the time period associated with different spatial scales. Results presented here suggest that during a good monsoon year the spatial scale of this oscillation is about 30 degrees centered around 10 degrees N. During weak monsoon years, the scale of propagation decreases and the center shifts farther south closer to the equator. A strong linear relationship is obtained between the center/scale of convective wave bands and intensity of monsoon precipitation over Indian land on the interannual time scale. Moreover, the spatial scale and its center during the break monsoon were found to be similar to an overall weak monsoon year. Based on this analysis, a new index is proposed to quantify the spatial scales associated with propagating convective bands. This automated wavelet-based technique developed here can be used to study meridional propagation of convection in a large volume of datasets from observations and model simulations. The information so obtained can be related to the interannual and intraseasonal variation of Indian monsoon precipitation.

Role of orography in modulating space-time scales of convection over South Asia

Propagation of convective systems in the meridional direction during boreal summer is responsible for active and break phases of monsoon over south Asia. This region is unique in the world in its characteristics of monsoon variability and is in close proximity of mountains like the Himalayas. Here, using an atmospheric general circulation model, we try to understand the role of orography in determining spatial and temporal scales of these convective systems. Absence of orography (noGlOrog) decreased the simulated seasonal mean precipitation over India by 23 % due to delay in onset by about a month vis-a-vis the full-mountain case. In noGlOrog, poleward propagations were absent during the delayed period prior to onset. Post-onset, both simulations had similar patterns of poleward propagations. The spatial and temporal scales of propagating clouds bands were determined using wavelet analysis. These scales were found to be different in full-mountain and no-mountain experiments in June-July. However, after the onset of monsoon in noGlOrog, these scales become similar to that with orography. Simulations with two different sets of convection schemes confirmed this result. Further analysis shows that the absence (presence) of meridional propagations during early (late) phase of summer monsoon in noGlOrog was associated with weaker (stronger) vertical shear of zonal wind over south Asia. Our study shows that orography plays a major role in determining the time of onset over the Indian region. However, after onset, basic characteristics of propagating convective systems and therefore the monthly precipitation over India, are less sensitive to the presence of orography and are modulated by moist convective processes.

Temporal and spatial variations in the quality of water in El Gergal Reservior, Seville, Spain

It is often difficult to define ‘water quality’ with any degree of precision. One approach is that suggested by Battarbee (1997) and is based on the extent to which individual lakes have changed compared with their natural ‘baseline’ status. Defining the base-line status of artificial lakes and reservoirs however, is, very difficult. In ecological terms, the definition of quality must include some consideration of their functional characteristics and the extent to which these characteristics are self-sustaining. The challenge of managing lakes in a sustainable way is particularly acute in semi-arid, Mediterranean countries. Here the quality of the water is strongly influenced by the unpredictability of the rainfall as well as year-to-year variations in the seasonal averages. Wise management requires profound knowledge of how these systems function. Thus a holistic approach must be adopted and the factors influencing the seasonal dynamics of the lakes quantified over a range of spatial and temporal scales. In this article, the authors describe some of the ways in which both long-term and short-term changes in the weather have influenced the seasonal and spatial dynamics of phytoplankton in El Gergal, a water supply reservoir situated in the south of Spain. The quality of the water stored in this reservoir is typically very good but surface blooms of algae commonly appear during warm, calm periods when the water level is low. El Gergal reservoir is managed by the Empresa Municipal de Abastecimiento y Saneamiento (EMASESA) and supplies water for domestic, commercial and industrial use to an area which includes the city of Seville and twelve of its surrounding towns (ca. 1.3 million inhabitants). El Gergal is the last of two reservoirs in a chain of four situated in the Rivera de Huelva basin, a tributary of the Guadalquivir river. It was commissioned by EMASESA in 1979 and since then the company has monitored its main limnological parameters on, at least, a monthly basis and used this information to improve the management of the reservoir. As a consequence of these intensive studies the physical, chemical and biological information acquired during this period makes the El Gergal database one of the most complete in Spain. In this article the authors focus on three ‘weather-related’ effects that have had a significant impact on the composition and distribution of phytoplankton in El Gergal: (i) the changes associated with severe droughts; (ii) the spatial variations produced by short-term changes in the weather; (iii) the impact of water transfers on the seasonal dynamics of the dinoflagellate Ceratium.

Ontogenetic and temporal variability in the fat content and fatty acid composition of Atlantic herring (Clupea harengus) from the Bay of Fundy, Canada

Atlantic herring (Clupea harengus) is an ecologically and economically valuable species in many food webs, yet surprisingly little is known about the variation in the nutritional quality of these fish. Atlantic herring collected from 2005 through 2008 from the Bay of Fundy, Canada, were examined for variability in their nutritional quality by using total lipid content (n=889) and fatty acid composition (n=551) as proxies for nutritional value. A significant positive relationship was found between fish length and total lipid content. Atlantic herring also had significantly different fatty acid signatures by age. Fish from 2005 had significantly lower total lipid content than fish from 2006 through 2008, and all years had significantly different fatty acid signatures. Summer fish were significantly fatter than winter fish and had significantly different fatty acid signatures. For all comparisons (ontogenetic, annual, and seasonal) percent concentrations of omega-3, -6, and long-chain monounsaturated fatty acids were the most important for distinguishing between the fatty acid signatures of fish. This study underscores the importance of quantifying variation in prey quality synoptically with prey quantity in food webs over ontogenetic and temporal scales when evaluating the effect of prey nutritional quality on predators and on modeling trophic dynamics.

Soft sediment ecology of Lough Hyne Marine Reserve - spatial and temporal patterns

Distribution of soft sediment benthic fauna and the environmental factors affecting them were studied, to investigate changes across spatial and temporal scales. Investigations took place at Lough Hyne Marine Reserve using a range of methods. Data on the sedimentation rates of organic and inorganic matter were collected at monthly intervals for one year at a number of sites around the Lough, by use of vertical midwater-column sediment traps. Sedimentation of these two fractions were not coupled; inorganic matter sedimentation depended on hydrodynamic and weather factors, while the organic matter sedimentation was more complex, being dependent on biological and chemical processes in the water column. The effects of regular hypoxic episodes on benthic fauna due to a natural seasonal thermocline were studied in the deep Western Trough, using camera-equipped remotely-operated vehicle to follow transects, on a three-monthly basis over one year. In late summer, the area below the thermocline of the Western Trough was devoid of visible fauna. Decapod crustaceans were the first taxon to make use of ameliorating oxygen conditions in autumn, by darting below the thermocline depth, most likely to scavenge. This was indicated by tracks that they left on the surface of the Trough floor. Some species, most noticeably Fries’ goby Lesueurigobius friesii, migrated below the thermocline depth when conditions were normoxic and established semi-permanent burrows. Their population encompassed all size classes, indicating that this habitat was not limited to juveniles of this territorial species. Recolonisation by macrofauna and burrowing megafauna was studied during normoxic conditions, from November 2009 to May 2010. Macrofauna displayed a typical post-disturbance pattern of recolonisation with one species, the polychaete Scalibregma inflatum, occurring at high abundance levels in March 2010. In May, this population had become significantly reduced and a more diverse community was established. The abundance of burrowing infauna comprising decapods crabs and Fries’ gobies, was estimated by identifying and counting their distinctive burrow structures. While above the summer thermocline depth, burrow abundance increased in a linear fashion, below the thermocline depth a slight reduction of burrow abundance occurred in May, when oxygen conditions deteriorated again. The majority of the burrows occurring in May were made by Fries’ gobies, which are thought to encounter low oxygen concentrations in their burrows. Reduction in burrow abundance of burrowing shrimps Calocaris macandreae and Callianassa subterranea (based on descriptions of burrow structures from the literature), from March to May, might be related to their reduced activity in hypoxia, leading to loss of structural burrow maintenance. Spatial and temporal changes to macrofaunal assemblage structures were studied seasonally for one year across 5 sites in the Lough and subject to multivariate statistical analysis. Assemblage structures were significantly correlated with organic matter levels in the sediment, the amounts of organic matter settling out of the water column one month before macrofaunal sampling took place as well as current speed and temperature. This study was the first to investigate patterns and processes in the Lough soft sediment ecology across all 3 basins on a temporal and spatial scale. An investigation into the oceanographic aspects of the development, behaviour and break-down of the summer thermocline of Lough Hyne was performed in collaboration with researchers from other Irish institutions.

A review of spatial and temporal variation in grey and common seal diet in the United Kingdom and Ireland

Knowledge about the diet of fish-eating predators is critical when evaluating conflicts with the fishing industry. Numerous primary studies have examined the diet of grey seals Halichoerus grypus and common seals Phoca vitulina in a bid to understand the ecology of these predators. However, studies of large-scale spatial and temporal variation in seal diet are limited. Therefore this review combines the results of seal diet studies published between 1980 and 2000 to examine how seal diet varies at a range of spatial and temporal scales. Our results revealed extensive spatial variation in gadiform, perciform and flatfish consumption, likely reflecting variation in prey availability. Flatfish and gadiform consumption varied between years, reflecting changes in fish assemblages as a consequence of factors such as varying fishing pressures, climate change and natural fluctuations in populations. Perciform and gadiform consumption varied seasonally: in addition there was a significant interaction between season and seal species, indicating that grey and common seals exhibited different patterns of seasonal variation in their consumption of Perciformes and Gadiformes. Multivariate analysis of grey seal diet revealed spatial variation at a much smaller scale, with different species dominating the diet in different areas. The existence of spatial and temporal variation in seal diet emphasizes that future assessments of the impact of seal populations should not be based on past or localized estimates of diet and highlights the need for up-to-date, site specific estimates of diet composition in the context of understanding and resolving seal/fisheries conflict. © 2012 Marine Biological Association of the United Kingdom.

Energy exchange in a dense urban environment – part I: temporal variability of long-term observations in central London

Though anthropogenic impacts on boundary layer climates are expected to be large in dense urban areas, to date very few studies of energy flux observations are available. We report on 3.5 years of measurements gathered in central London, UK. Radiometer and eddy covariance observations at two adjacent sites, at different heights, were analysed at various temporal scales and with respect to meteorological conditions, such as cloud cover. Although the evaporative flux is generally small due to low moisture availability and a predominately impervious surface, the enhancement following rainfall usually lasts for 12–18 h. As both the latent and sensible heat fluxes are larger in the afternoon, they maintain a relatively consistent Bowen ratio throughout the middle of the day. Strong storage and anthropogenic heat fluxes sustain high and persistently positive sensible heat fluxes. At the monthly time scale, the urban surface often loses more energy by this turbulent heat flux than is gained from net all-wave radiation. Auxiliary anthropogenic heat flux information suggest human activities in the study area are sufficient to provide this energy.

Uso do procedimento de bissecção temporal na avaliação de idosos com doença de Alzheimer: uma revisão sistemática

OBJETIVO: Realizar revisão sistemática de artigos que utilizaram o método de bissecção, para avaliar a percepção de tempo em idosos com doença de Alzheimer e analisar seus parâmetros. MÉTODO: As buscas dos artigos foram conduzidas no período de março a maio de 2011, nas seguintes bases de dados: Web of Science, Science Direct on Line, Biological Abstracts, PsychoInfo e Medline. As palavras-chave e operadores booleanos foram: interval timing ou perception of time ou time discrimination ou reproduction of time e Alzheimer's disease. Também foram realizadas buscas manuais nas referências dos artigos selecionados. RESULTADOS: Quatro artigos contemplavam todos os critérios de inclusão, nos quais foram encontradas grandes variações nos parâmetros utilizados no método. CONCLUSÃO: Pacientes com doença de Alzheimer apresentam prejuízos nas tarefas de bissecção de tempo, que podem ser explicados pelo declínio gradual nas habilidades que são utilizadas no teste de percepção de tempo. Há grandes variações nos intervalos de tempo utilizados. Neste contexto, há necessidade de mais estudos, controlados e randomizados, para investigar potenciais efeitos das variações nos intervalos de tempo do método de bissecção. Os resultados de tais estudos poderão contribuir para o estabelecimento de parâmetros mais adequados e fidedignos.

Reproductive Strategies of Brazilian Lizards of the Genus Tropidurus Rodrigues, 1987 (Squamata, Tropiduridae) in the Temporal and Spatial

Reproductive strategy is the set of adaptations that promote the most efficient way that the species will survive under the particular conditions of a determined environment. Understanding these adaptations is important and can help pinpoint populations indicator of environmental changes. Spermatogenesis is a measurable biological process of these adaptations in spatial and temporal scales. We analyzed the morphology of the testes and oviducts of the lizard species that comprise the genus Tropidurus, taking into account the geographical distribution and sympatric relations. For the analysis and the testes were removed from the middle part of the oviducts from Tropidurus etheridge, T oreadicus, T itambere, T spinulosus and T Guarani species, collected in different places in the Mato Grosso state, Brazil. The reproductive period is synchronous for males and females and occurs in September, October and November. Reproductive males were characterized. In the testes are seminiferous tubules with germ cells at different stages of spermatogenesis, with a high epithelium, at present light, free spermatozoa in the lumen and reduction of interstitial tissue. For females, the reproduction peak occurs when the oviduct epithelium is high with secretions and basal nucleus. These months are characterized in the sampled areas over a period of heavy rain and high temperatures. The decline of reproductive period was observed in both sexes, between April and August. Low reproduction in males is characterized by ample light, absence of sperm, only germ cells in the early stages of spermatogenesis are observed (a few spermatogonia and spermatocytes) and interstitial tissue wide. In females, the period of reproductive decline is marked by the absence of unicellular glands in the oviduct epithelium, with higher affinity with the dye. This period corresponds to low rainfall periods and lower temperatures. We propose an analysis of zoological samples; this is a proposal to facilitate the work of many researchers through access to the species, especially rare species.

Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa

Background: Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results: Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (R(ST) = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (R(ST) = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (R(ST) = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m similar to 0.094 - 0.097) in the Volta populations. Conclusions: This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view.

Spatial and temporal patterns in ungulate-ecosystem interactions

Ungulates are important components of a variety of ecosystems worldwide. This dissertation integrates aspects of ungulate and forest ecology to increase our understanding of how they work together in ways that are of interest to natural resource managers, educators, and those who are simply curious about nature. Although animal ecology and ecosystem ecology are often studied separately, one of the general goals of this dissertation is to examine how they interact across spatial and temporal scales. Forest ecosystems are heterogeneous across a range of scales. Spatial and temporal habitat use patterns of forest ungulates tend to be congregated in patches where food and/or cover are readily available. Ungulates interact with ecosystem processes by selectively foraging on plants and excreting waste products in concentrated patches. Positive feedbacks may develop where these activities increase the value of habitat through soil fertilization or the alteration of plant chemistry and architecture. Heterogeneity in ecosystem processes and plant community structure, observed at both stand and local scales, may be the integrated outcome of feedbacks between ungulate behavior and abiotic resource gradients. The first chapter of this dissertation briefly discusses pertinent background information on ungulate ecology, with a focus on white-tailed deer (Odocoileus virginianus) in the Upper Great Lakes region and moose (Alces acles) in Isle Royale National Park, Michigan, USA. The second chapter demonstrates why ecological context is important for studying ungulate ecology in forest ecosystems. Excluding deer from eastern hemlock (Tsuga canadensis) stands, which deer use primarily as winter cover, resulted in less spatial complexity in soil reactive nitrogen and greater complexity in diffuse light compared to unfenced stands. The spatial patterning of herbaceous-layer cover was more similar to nitrogen where deer were present, and was a combination of nitrogen and light within deer exclosures. This relationship depends on the seasonal timing of deer habitat use because deer fertilize the soil during winter, but leave during the growing season. The third chapter draws upon an eight-year, 39-stand data set of deer fecal pellet counts in hemlock stands to estimate the amount of nitrogen that deer are depositing in hemlock stands each winter. In stands of high winter deer use, deer-excreted nitrogen inputs consistently exceeded those of atmospheric deposition at the stand scale. At the neighborhood scale, deer-excreted nitrogen was often in excess of atmospheric deposition due to the patchy distribution of deer habitat use. Spatial patterns in habitat use were consistent over the eight-year study at both stand and neighborhood scales. The fourth chapter explores how foraging selectivity by moose interacts with an abiotic resource gradient to influence forest structure and composition. Soil depth on Isle Royale varies from east to west according to glacial history. Fir saplings growing in deeper soils on the west side are generally more palatable forage for moose (lower foliar C:N) than those growing in shallower soils on the east side. Therefore, saplings growing in better conditions are less likely to reach the canopy due to moose browsing, and fir is a smaller overstory component on the west side. Lastly, chapter five focuses on issues surrounding eastern hemlock regeneration failure, which is a habitat type that is important to many wildlife species. Increasing hemlock on the landscape is complicated by several factors including disturbance regime and climate change, in addition to the influence of deer.

Time scales in cognitive neuroscience

Cognitive neuroscience boils down to describing the ways in which cognitive function results from brain activity. In turn, brain activity shows complex fluctuations, with structure at many spatio-temporal scales. Exactly how cognitive function inherits the physical dimensions of neural activity, though, is highly non-trivial, and so are generally the corresponding dimensions of cognitive phenomena. As for any physical phenomenon, when studying cognitive function, the first conceptual step should be that of establishing its dimensions. Here, we provide a systematic presentation of the temporal aspects of task-related brain activity, from the smallest scale of the brain imaging technique's resolution, to the observation time of a given experiment, through the characteristic time scales of the process under study. We first review some standard assumptions on the temporal scales of cognitive function. In spite of their general use, these assumptions hold true to a high degree of approximation for many cognitive (viz. fast perceptual) processes, but have their limitations for other ones (e.g., thinking or reasoning). We define in a rigorous way the temporal quantifiers of cognition at all scales, and illustrate how they qualitatively vary as a function of the properties of the cognitive process under study. We propose that each phenomenon should be approached with its own set of theoretical, methodological and analytical tools. In particular, we show that when treating cognitive processes such as thinking or reasoning, complex properties of ongoing brain activity, which can be drastically simplified when considering fast (e.g., perceptual) processes, start playing a major role, and not only characterize the temporal properties of task-related brain activity, but also determine the conditions for proper observation of the phenomena. Finally, some implications on the design of experiments, data analyses, and the choice of recording parameters are discussed.