Tick parasitism classification from noisy medical records

Much of the health information in the medical domain comes in the form of clinical narratives. The rich semantic information contained in these notes can be modeled to make inferences that assist the decision making process for medical practitioners, which is particularly important under time and resource constraints. However, the creation of such assistive tools is made difficult given the ubiquity of misspellings, unsegmented words and morphologically complex or rare medical terms. This reduces the coverage of vocabulary terms present in commonly used pretrained distributed word representations that are passed as input to parametric models that makes such predictions. This paper presents an ensemble architecture that combines indomain and general word embeddings to overcome these challenges, showing best performance on a binary classification task when compared to various other baselines. We demonstrate our approach in the context of the veterinary domain for the task of identifying tick parasitism from small animals. The best model shows 84.29% test accuracy, showing some improvement over models, which only use pretrained embeddings that are not specifically trained for the medical sub-domain of interest

Ecology of a host-parasite system : a study in temperate cave-dwelling bats

Tese de doutoramento em Biologia (Ecologia), apresentada à Universidade de Lisboa através da Faculdade de Ciências, 2009Os parasitas englobam, segundo algumas estimativas, cerca de metade das espécies conhecidas do planeta. Pela sua vasta distribuição e diversidade, associada ao elevado grau de adaptação ao meio onde vivem (i.e. os seus hospedeiros), o parasitismo pode ser considerado uma das formas de vida mais bem sucedidas. A transição de um estilo de vida livre para o parasitismo trouxe inúmeras vantagens a estes organismos, nomeadamente o uso de um ambiente mais estável, uma maior mobilidade, e a redução dos custos relacionados com várias funções vitais como a digestão e a procura de alimento, que passaram a ser maioritariamente desempenhados pelos seus hospedeiros. No entanto, no decorrer da evolução para esta forma de vida, os parasitas enfrentaram diversos desafios adaptativos, relacionados com as características intrínsecas dos seus hospedeiros. Neste contexto, a imprevisibilidade espacial e temporal de algumas espécies hospedeiras constitui um dos maiores obstáculos à conclusão do ciclo de vida de um parasita, dado dificultar significativamente a sua dispersão. Paralelamente, estes organismos tiveram de se adaptar à presença frequente de outras espécies de parasitas num mesmo hospedeiro, e explorando os mesmos recursos. Adicionalmente, devido à sua dependência em relação ao hospedeiro para uma reprodução e dispersão bem sucedidas, a maioria dos parasitas necessitou de evoluir de maneira a maximizar a exploração dos recursos do hospedeiro e ao mesmo tempo evitar a sua morte. A presente tese teve como principal objectivo contribuir para o conhecimento sobre os mecanismos desenvolvidos por alguns ectoparasitas para contornarem estes desafios e se adaptarem com sucesso à vida nos seus hospedeiros. Para tal, usaram-se duas espécies de morcegos de regiões temperadas, o morcego-de-peluche Miniopterus schreibersii e o morcego rato-grande Myotis myotis, e os seus ectoparasitas como sistemas modelo. Apesar dos morcegos se encontrarem geralmente fortemente parasitados, pouco se sabe sobre a dinâmica e o funcionamento destes sistemas parasita-hospedeiro. Para alcançar o objectivo delineado, foram estabelecidos quatro objectivos específicos, cada qual abordado num capítulo distinto da presente tese.Parasitism is one of the most successful modes of life displayed by living organisms. Thetransition to a parasitic lifestyle brought many advantages to parasites, namely a stable environment, mobility and a lesser investment in nutricional functions. However, it also entailed a set of adaptative challenges that had to be met by parasites. These had to find a way of dispersing between hosts often discontinuously distributed in space and time. Moreover, they had to adapt to the frequent presence of other potential competing parasites within the host's body. Lastly, due to their dependence on hosts for successfully reproducing and dispersing, parasites had to balance the exploitation of resources of a host with the need to keep it alive. The main aim of this thesis was to determine how bat ectoparasites have overcome some of these challenges and successfully adapted to their hosts, using two temperate-zone cave dwelling bats (Miniopterus schreibersii and Myotis myotis) and its ectoparasites as model systems. Results showed that a group of specific bat ectoparasites, the nycteribiids, was able to overcome the spatial unpredictability of its hosts within caves by evolving efficient sensorial mechanisms to locate them from a distance. In addition, some parasitic mites, ticks and nycteribiids were found to deal with the temporal unpredictability of their bat hosts, by maximising their reproduction during the reproductive period of bats, when more hosts were more available and particularly vulnerable. Results also showed that competition is likely to occur among bat parasite species, even if for shortterm periods, influencing the structure of their communities. Finally, a suggestion was found of potential costs induced by a parasitic mite on the body condition of its bat host. It is discussed how these potential costs may play a role in the social structure of the bat. Overall, this study provided evidences that bat parasites have tightly coevolved with their hosts. Some of conclusions discussed here are likely to apply to other host-parasite systems involving bats in temperate-zones.Fundação para a Ciência e Tecnologia (FCT), (SFRH/ BD/ 10717/2002

Do terrestrial ectoparasites disperse with penguins?

Dispersal plays a critical role in evolution. Rare long-distance movements can lead to allopatric speciation, whereas frequent movements can facilitate gene flow among disjunct populations and prevent divergence. Dispersal between populations of a species may be difficult to observe directly, and is often inferred from indirect measures such as species occurrence data. Increasingly, however, high resolution genomic data are being used to clarify dispersal and gene flow, in many cases contradicting past assumptions. Islands are excellent model regions for investigating dispersal as they offer replicated habitats with clear geographic boundaries. The sub-Antarctic comprises some of the most geographically isolated island ecosystems in the world, representing an ideal model system for assessing the evolutionary consequences of long-distance dispersal. Strong winds, circumpolar oceanic currents, and extreme climatic cycles are thought to have effectively isolated many sub-Antarctic ecosystems, but a growing body of molecular evidence is beginning to question this rhetoric, with numerous species showing connectivity across the region. Connectivity patterns are, however, complex and are not always predictable from an organism’s inferred dispersal capacity. With environmental change placing unprecedented pressure on isolated ecosystems, there is a pressing need for improved understanding of dispersal processes and population connectivity via genomic analyses of diverse taxa. A number of sub-Antarctic species exhibit gene flow across the region despite lacking active long-distance dispersal capabilities. Brooding, sedentary crustaceans have, for example, rafted on buoyant kelp across thousands of kilometres of open ocean in the sub-Antarctic. The close symbiotic or parasitic relationships that such species maintain with the kelp has resulted in whole communities dispersing together. Indeed, active dispersal is often limited in parasites, which can depend almost entirely on mobile hosts for long-distance movement. A parasite that is unable to travel far with its host would, therefore, be expected to show considerable phylogeographic structure. For example, penguins primarily travel underwater but are hosts to terrestrial ectoparasites (most commonly ticks - Ixodes spp.) when they come ashore to breed. Aquatic host movements may represent a challenge to the survival of penguin ticks, restricting gene flow across their range. This thesis first reviews connectivity patterns and challenges throughout the sub-Antarctic, and then uses a multidisciplinary approach (genomic and physiological data) to test whether some terrestrial parasites (ticks: Acari) are able to travel long distances at sea with their aquatically dispersing hosts (penguins). Results indicate that penguin ticks are physiologically resilient, and may be capable of surviving the conditions faced during aquatic penguin movements between colonies. However, these movements appear to be too sporadic to maintain gene flow across the ticks’ ranges, resulting in broad-scale geographic structure. In contrast, movement on fine scales (within colonies) is inferred – based on lack of genomic structure – to be common, possibly facilitated by social interactions of hosts. These results emphasise the important role of dispersal in isolated regions for range expansion and diversification, and highlight the adaptability of parasites to their hosts’ environments

Health and disease status of Australia's most critically endangered mammal the Gilbert's potoroo (Potorous gilbertii)

The Gilbert's potoroo (Potorous gilbertii) is a small marsupial endemic to the Two Peoples Bay Nature Reserve in the south-west of Western Australia. The Gilbert's potoroo is classified as Australia's most critically endangered mammal (IUCN 2006) with an estimated population of only 35 individuals. This thesis examines the health and disease status of the Gilbert's potoroo, presenting a strong case for the relatively new concept of disease as a potential threatening factor and modifier of population decline. Specific diseases, including Cryptococcus, ectoparasitism, endoparasitism, haemoparasitism, Toxoplasma and a novel Treponema organism are extensively studied. An assessment of the clinical significance of these diseases is made, and management strategies are recommended to minimise the impact of these diseases on both the wild and captive population. The novel Treponema organism which clinically presents with tenacious, green discharge and an associated balanoposthitis in males is molecularly characterized. Epidemiological studies show the effects of this agent on reproductive function and a penicillin-based treatment regime is trialled in the analogous long-nosed potoroo (Potorous tridactylus) with a recommendation to then trial this treatment regime in the critically endangered Gilbert's potoroo. Standard haematological and urinalysis findings are tabulated to form reference ranges for this species. A treatment regime for Cryptococcus in the analogous long-nosed potoroo is reported and parasitological findings, including the identification of a novel tick species are discussed. This thesis addresses key health issues, which have subsequently been incorporated into the Recovery Plan of the Gilbert's potoroo. A document encompassing multiple disciplines and expertise to support the recovery of this critically endangered marsupial in its current environment. In addition, this thesis outlines a recommended health monitoring and treatment protocol for future translocation procedures and provides a working example of the emerging importance of health monitoring in threatened species recovery programs

93rd Annual Meeting of the Virginia Academy of Science: Proceedings

Full proceedings of the 93rd Annual Meeting of the Virginia Academy of Science, May 21-23, 2015, James Madison University, Harrisonburg, Virgini

Using haematology and biochemistry to investigate the health and evolutionary biology of eastern grey kangaroos (Macropus giganteus)

Land clearing has detrimental and long-lasting impacts on natural ecosystems and biodiversity, yet land clearing is accelerating world-wide. The eastern grey kangaroo (Macropus giganteus) is a large common macropod that can reach high densities on cleared land. Despite their apparent success, kangaroo populations are susceptible to food shortages and increased disease risk. Developing a broad understanding of the drivers of kangaroo health is required to establish a benchmark to study poor health. This thesis aimed to develop an evidence-based tool that characterises kangaroo health. Species-specific haematological reference intervals (RI) were developed using blood samples collected from up to 245 animals from four sites across New South Wales and the Australian Capital Territory. Results showed that abiotic factors are critical determinants of kangaroo health outcomes. A health investigation was then performed, utilising the developed RIs, on a population of kangaroos in which health and welfare issues. This kangaroo population was from Look At Me Now Headland (LAMN) in NSW and was found to have widespread disease (parasitism and non-regenerative anaemia) and nutritional deficiencies stemming from a high population density, prolonged drought and reduced grazing habitat. The risk factors associated with parasitism were explored by examining potential selection pressures driving the evolution of kangaroos. An experiment was done to examine the influence of testosterone suppression on health parameters, parasite burdens and movement patterns in male kangaroos. While there was no effect of testosterone on these factors during the ten-week suppression period, a trend for reduced parasite burdens in kangaroos with supressed testosterone was evident. The findings of this thesis emphasise that regional planning must consider habitat connectivity for kangaroo populations to prevent overabundance and enhance positive outcomes for the health and welfare of the species

Urban forest invertebrates : how they shape and respond to the urban environment

Invertebrates comprise the most diversified animal group on Earth. Due to their long evolutionary history and small size, invertebrates occupy a remarkable range of ecological niches, and play an important role as "ecosystem engineers" by structuring networks of mutualistic and antagonistic ecological interactions in almost all terrestrial ecosystems. Urban forests provide critical ecosystem services to humans, and, as in other systems, invertebrates are central to structuring and maintaining the functioning of urban forests. Identifying the role of invertebrates in urban forests can help elucidate their importance to practitioners and the public, not only to preserve biodiversity in urban environments, but also to make the public aware of their functional importance in maintaining healthy greenspaces. In this review, we examine the multiple functional roles that invertebrates play in urban forests that contribute to ecosystem service provisioning, including pollination, predation, herbivory, seed and microorganism dispersal and organic matter decomposition, but also those that lead to disservices, primarily from a public health perspective, e.g., transmission of invertebrate-borne diseases. We then identify a number of ecological filters that structure urban forest invertebrate communities, such as changes in habitat structure, increased landscape imperviousness, microclimatic changes and pollution. We also discuss the complexity of ways that forest invertebrates respond to urbanisation, including acclimation, local extinction and evolution. Finally, we present management recommendations to support and conserve viable and diverse urban forest invertebrate populations into the future.Peer reviewe

Modelling vector-borne and other parasitic diseases. Proceedings of a workshop

Session one of this report highlights ILRAD's research programs and the modelling needs of ILRAD and FAO. Session two deals with vector and helminth population dynamics with particular reference to ticks, tsetse and helminth. Parasite transmission and host parasite interaction are discussed in sessions three and four respectively. These two sessions deal with theileria, trypanosomes and leishmania. Parasite variations and polymorphism is the topic of session five. Session six discusses the effect of disease control programs and session seven reviews modelling systems. The last two sessions deal with the application of modelling, and collection, collation, analysis and dissemination of data on vector-borne and other parasitic diseases

Life Cycle and Development of Diptera

Diptera, or true flies, are of considerable economic importance, as these flies have a valuable role as scavengers, parasitoids and predators of other insects, pollinators, food for predators, bio-indicators of water quality, and tools for scientific research. In nine chapters, this book examines various aspects of flies of the order Diptera as well as some types of mosquitos and midges. Topics covered include taxonomy, phylogeny, life cycle, feeding habits, population control strategies, and more. A unique chapter on forensic entomology is particularly interesting. Beautifully illustrated and expertly researched, this volume will appeal to entomologists, biologists, and naturalists

Beyond unwanted sound : noise, affect and aesthetic moralism

PhD ThesisThis thesis uses Baruch Spinoza’s notion of affect to critically rethink the correlation between noise, ‘unwantedness’ and ‘badness’. Against subject-oriented definitions, which understand noise to be constituted by a listener; and object-oriented definitions, which define noise as a type of sound; I focus on what it is that noise does. Using the relational philosophy of Michel Serres in combination with Spinoza’s philosophy of affects, I posit noise as a productive, transformative force and a necessary component of material relations. I consider the implications of this affective and relational model for two lineages: what I identify as a ‘conservative’ politics of silence, and a ‘transgressive’ politics of noise. The former is inherent to R. Murray Schafer’s ‘aesthetic moralism’, where noise is construed as ‘bad’ to silence’s ‘good’. Instead, I argue that noise’s ‘badness’ is secondary, relational and contingent. This ethico-affective understanding thus allows for silence that is felt to be destructive and noise that is pleasantly serendipitous. Noise’s positively productive capacity can be readily exemplified by the use of noise within music, whereby noise is used to create new sonic sensations. An ethicoaffective approach also allows for an affirmative (re)conceptualization of noise music, which moves away from rhetoric of failure, taboo and contradiction. In developing a relational, ethico-affective approach to noise, this thesis facilitates a number of key conceptual shifts. Firstly, it serves to de-centre the listening subject. According to this definition, noise does not need to be heard as unwanted in order to exist; indeed, it need not be heard at all. Secondly, this definition no longer constitutes noise according to a series of hierarchical dualisms. Consequently, the structural oppositions of noise/signal, noise/silence and noise/music are disrupted. Finally, noise is understood to be ubiquitous and foundational, rather than secondary and contingent: it is inescapable, unavoidable and necessary