Contact network epidemiology: Mathematical methods of modeling a mutating pathogen on a two-type network

With the threat of diseases like Sudden Acute Respiratory Syndrome (SARS) and Avian Flu that can lead to global pandemics, it is important to be able to understand how diseases spread through a population and predict how many people will become infected. It is also important to learn how preventative treatments affect disease spread. Public health officials must prepare a different vaccine each year to deal with a different influenza strain. Furthermore, it is important to be able to determine how effective a particular vaccination strategy will be in the event of a limited vaccine supply. The most common mathematical model of epidemic disease is based on the assumption that the population is homogenously mixed. That is, every member of the population is identical in how many other individuals he interacts with and every infected individual has the potential to spread disease to every other individual. However, these assumptions are unrealistic. To create a better model, the basic assumption of homogeneous mixing is removed. To do this, the population is modeled as a contact network. In a contact network, the population is represented by dots connected by lines. Each member is represented by a dot, or node, with disease-causing interactions between two members of a population represented by lines, or edges, between two nodes. This models the structure that exists in human populations by allowing individuals in a population to infect only a limited number of other individuals and allowing the number of contacts to vary between individuals. Much is already understood about how network structure affects disease dynamics. This thesis uses the contact network model to study the impact of network structure on the dynamics of a mutating pathogen. By distributing the contacts within the population in different ways, the effect of the network's structure on the extent of the disease is observed. Given the distribution of contacts on the network and the probability that an individual spreads the disease to a contact, the average sizes of a small outbreak (that which spreads to only a few people) and a large epidemic (that which spreads to a fixed proportion of the population, no matter the size) are calculated. These calculations are computed for different contact distributions and for a range of transmissibility values. Furthermore, these calculations are checked against simulations of the disease spreading over contact networks. This thesis also generalizes the contact network model to allow for both treated and untreated individuals in a population. In this generalization, not only does the number of contacts vary between individuals, but the probability of transmission also differs between treated and untreated individuals. This thesis shows that the contact network model with pathogen evolution is similar to the basic model. It also shows that the predictions made by the model are supported by simulation in some cases but not in other. Furthermore, it shows a contact network model that incorporates two different kinds of nodes. Lastly, it shows that this new model reduces to the basic model under certain conditions.Mathematic

Application of the wetland fish index to Northern Great Lakes marshes with emphasis on Georgian Bay coastal wetlands

The wetland fish index (WFI), a published indicator of wetland condition that ranks wetlands based on tolerance offish species to degraded water-quality conditions, had been developed with data from 40 wetlands located exclusively in the southern portion of the Great Lakes basin (Erie, Ontario, and Michigan). No data had been included from wetlands of the northern Great Lakes (Superior and Huron) and especially those of eastern and northern Georgian Bay, where many wetlands are still unaffected by human activities. We demonstrate why application of the WFI for the lower lakes (WFILower) can yield biased scores when applied to data for upper lakes wetlands. We then develop a basin-wide index to include data from 60 other coastal wetlands located in the northern portion of the basin, including 32 from Georgian Bay. Inclusion of northern sites in development of a basin-wide WFI (WFIBasin) still produced index scores that were positively correlated with water-quality conditions as indicated by water quality index scores. We explain why use of the basin-wide WFI is better than one developed specifically for upper lakes (WFIUpper). Overall, WFIBasin scores were higher in the northern lakes (Superior 3.49, Georgian Bay 3.67, Huron 3.62) than in the southern lakes (Michigan 3.33, Erie 3.12, Ontario 3.09). WFI scores are only minimally affected by inter-annual variation, which allows for its use for long-term monitoring. We recommend that the WFIBasin be used when managers need to manage at a scale across the entire Great Lakes basin

Comparative study of ecological indices for assessing human-induced disturbance in coastal wetlands of the Laurentian Great Lakes

Several ecological indices have been developed to evaluate the wetland quality in the Laurentian Great Lakes. One index, the water quality index (WQI) can be widely applied to wetlands and produces accurate measurements of wetland condition. The WQI measures the degree of water quality degradation as a result of nutrient enrichment and road runoff. The wetland fish index (WFI), wetland zooplankton index (WZI), and the wetland macrophyte index (WMI), are all derived from the statistical relationships of biotic communities along a gradient of deteriorating water quality. Compared to the WQI, these indices are less labor-intensive, cost less, and have the potential to produce immediate results. We tested the relative sensitivity of each biotic index for 32 Great Lakes wetlands relative to the WQI and to each other. The WMI (r2 = 0.84) and WFI (r2 = 0.75) had significant positive relationships (P < 0.0001) with the WQI in a linear and polynomial fashion. Slopes of the WMI and WFI were similar when comparing the polynomial regressions (ANCOVA; P = 0.117) but intercepts were significantly different (P = 0.004). The WZI had a positive relationship with the WQI in degraded wetlands and a negative relationship in minimally impacted wetlands. The strengths and weaknesses of each index can be explained by the interactions among fish, zooplankton, aquatic plants and water chemistry. The distribution of different species indicative of low and high quality in each index provides insight into the relative wetland community composition in different parts of the Great Lakes and helps to explain the differences in index scores when different organisms are used. Our findings suggest that the WMI and WFI produce comparable results but the WZI should not be used in the minimally impacted wetlands without further study. © 2008 Elsevier Ltd. All rights reserved

Changes in Fish Communities of Lake Ontario Coastal Wetlands before and after Remedial Action Plans

We conducted a change-detection analysis to determine if improvements in the habitat quality of coastal wetlands could be attributed to Remedial Action Plans (RAPs) of Lake Ontario. We used a 5-km buffer relative to each recent site to “resample” an existing database of spawning/nursery habitat from the early 1980s to derive a “historic” species list associated with thirteen representative wetlands sampled in 2001-2002. For each wetland, we calculated Wetland Fish Index (WFI) scores, which are relative measures of wetland quality having scores ranging from 1 to 5, indicating worst to best conditions, respectively. The mean WFI score of 3.16 for the recent era was significantly higher than that for the historic era of 2.79 (Wilcoxon sign-rank test; P=.04), and this is consistent with the conclusion that lakewide RAPs have been effective in recovering some of the ecological functions of degraded coastal wetlands of Lake Ontario.</jats:p

Impact of urbanization on the water quality, fish habitat, and fish community of a Lake Ontario marsh, Frenchman’s Bay

Frenchman's Bay is a barrier beach wetland with a highly urbanized watershed located east of Toronto, along the north shore of Lake Ontario. Degradation of water quality has reduced the historically large stand of emergent vegetation to fringe emergent beds to the north and south of the Bay. Altered hydrology and runoff from the urban watershed and a nearby major highway have resulted in poor water quality, and warmer waters at the northern site. By contrast, the southern site has considerably cleaner and cooler water, as it is influenced by exchange of good-quality water with Lake Ontario. These differences in water quality were reflected in the composition of the fish assemblages that were sampled at the two sites over a 2-year period. Comparisons with past studies indicate that the dominant fish community of Frenchman's Bay has been relatively stable for the last 20 years. Scores for the Wetland Fish Index, an indicator of wetland condition, were significantly higher in the south site than in the north site, which corresponded to significant differences in Water Quality Index scores. Although the northern portion of Frenchman's Bay shows clear signs of degradation, the southern portion contains important fish habitat for western Lake Ontario. © 2007 Springer Science+Business Media, LLC

Thioflavine-T and Congo Red reveal the polymorphism of insulin amyloid fibrils when probed by polarization-resolved fluorescence microscopy.

International audienceAmyloid fibrils are protein misfolding structures that involve a β-sheet structure and are associated with the pathologies of various neurodegenerative diseases. Here we show that Thioflavine-T and Congo Red, two major dyes used to image fibrils by fluorescence assays, can provide deep structural information when probed by means of polarization-resolved fluorescence microscopy. Unlike fluorescence anisotropy or fluorescence detected linear dichroism imaging, this technique allows to retrieve simultaneously both mean orientation and orientation dispersion of the dye, used here as a reporter of the fibril structure. We have observed that insulin amyloid fibrils exhibit a homogeneous behavior over the fibrils' length, confirming their structural uniformity. In addition, these results reveal the existence of various structures among the observed fibrils' population, in spite of a similar aspect when imaged with conventional fluorescence microscopy. This optical nondestructive technique opens perspectives for in vivo structural analyses or high throughput screening

Low is large: spatial location and pitch interact in voice-based body size estimation

The binding of incongruent cues poses a challenge for multimodal perception. Indeed, although taller objects emit sounds from higher elevations, low-pitched sounds are perceptually mapped both to large size and to low elevation. In the present study, we examined how these incongruent vertical spatial cues (up is more) and pitch cues (low is large) to size interact, and whether similar biases influence size perception along the horizontal axis. In Experiment 1, we measured listeners’ voice-based judgments of human body size using pitch-manipulated voices projected from a high versus a low, and a right versus a left, spatial location. Listeners associated low spatial locations with largeness for lowered-pitch but not for raised-pitch voices, demonstrating that pitch overrode vertical-elevation cues. Listeners associated rightward spatial locations with largeness, regardless of voice pitch. In Experiment 2, listeners performed the task while sitting or standing, allowing us to examine self-referential cues to elevation in size estimation. Listeners associated vertically low and rightward spatial cues with largeness more for lowered- than for raised-pitch voices. These correspondences were robust to sex (of both the voice and the listener) and head elevation (standing or sitting); however, horizontal correspondences were amplified when participants stood. Moreover, when participants were standing, their judgments of how much larger men’s voices sounded than women’s increased when the voices were projected from the low speaker. Our results provide novel evidence for a multidimensional spatial mapping of pitch that is generalizable to human voices and that affects performance in an indirect, ecologically relevant spatial task (body size estimation). These findings suggest that crossmodal pitch correspondences evoke both low-level and higher-level cognitive processes