Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

Synonymous relationships among biomedical terms are extensively annotated within specialized terminologies, implying that synonymy is important for practical computational applications within this field. It remains unclear, however, whether text mining actually benefits from documented synonymy and whether existing biomedical thesauri provide adequate coverage of these linguistic relationships. In this study, we examine the impact and extent of undocumented synonymy within a very large compendium of biomedical thesauri. First, we demonstrate that missing synonymy has a significant negative impact on named entity normalization, an important problem within the field of biomedical text mining. To estimate the amount synonymy currently missing from thesauri, we develop a probabilistic model for the construction of synonym terminologies that is capable of handling a wide range of potential biases, and we evaluate its performance using the broader domain of near-synonymy among general English words. Our model predicts that over 90% of these relationships are currently undocumented, a result that we support experimentally through “crowd-sourcing.” Finally, we apply our model to biomedical terminologies and predict that they are missing the vast majority (>90%) of the synonymous relationships they intend to document. Overall, our results expose the dramatic incompleteness of current biomedical thesauri and suggest the need for “next-generation,” high-coverage lexical terminologies.</p

Mosquitoes of southern England and northern Wales: identification, ecology and host selection

As early as 1901, ecological and epidemiological studies were conducted to understand malaria transmission in the UK. Unfortunately, following the eradication of malaria after WWII, ecological studies on local mosquito species has been intermittent, leading to a significant gap in knowledge of the current habitat preference, distribution and vector capabilities of the 33 recorded species. This lack of current information makes the assessment of possible transmission of enzoonotic diseases such as Chikungunya and West Nile virus in UK difficult. Thus the overall purpose of this thesis was to facilitate the identification of potential vector species through the documentation and characterisation of the ecology of adult and larval stages, and the host selection of British mosquitoes, in southern England and northern Wales. A total of 13 out the 33 documented species are assessed in this study. Of which members of the Maculipennis and Pipiens Group comprised the bulk of the adult and immature collections respectively. The development of the ITS2 PCR-RFLP assay in this study allowed the identification of the three members of the Maculipennis Group, which revealed the widespread occurrence of the recently documented An. daciae in almost all localities sampled. While previously published assays discriminating the Pipiens Complex, did not yield congruent results questioning the prior identification methods and the validity of the taxonomic status of its members. In addition, host-specific primers designed herein to determine host selection in local mosquitoes revealed an indiscriminate host selection by An. atroparvus, An. daciae, An. messeae and Cx. pipiens thus indicating their potential role as vectors in the UK

Biomechanics and Functional Morphology of Amblypygid Predation

Amblypygids, colloquially known as whip spiders, are a charismatic order of arachnids that a characterised a unique pair of spined pedipalp appendages. Amblypygid pedipalps are hypothesised to primarily function as a prey capture device. However, the pedipalp is also used in several other functions including territorial contest and courtship, opening the possibility that the appendage could also be under the influence of sexual selection. There exists a vast degree of morphological diversity within the pedipalp, with relative length spanning nearly an order of magnitude across the group and spination varying markedly both within- and between species. The amblypygid pedipalp is therefore subject to multiple selective pressures, and both its external morphology and kinematics likely reflect this. Thus, the amblypygid pedipalp provides an ideal structure through which to study the evolution of morphological traits subject to multiple selective pressures, and the potential evolutionary trade-offs that may arise. Despite this, amblypygid pedipalp morphology and kinematics remains poorly quantified and little comparative work has been carried across the group. Here, I aim to quantify intra- and interspecific trends in amblypygid pedipalp shape and prey capture kinematics for the first time, using modern morphometric techniques and high-speed videography. In this work I present a comprehensive review of sexual dimorphism in arachnids and identify the common drivers behind this phenomenon. Building on this, I quantify sexual dimorphism in pedipalp size and shape in a single species of amblypygid using a novel geometric morphometric approach. This is followed by an broad analysis of intraspecific and interspecific trends in shape complexity of pedipalps using Elliptical Fourier Analysis. Finally, I draw a link between form and function by quantifying and comparing prey capture kinematics in a morphologically diverse set of amblypygids, using high-speed videography and motion analysis. This work provides new insights into amblypygid 8 pedipalp diversity and posits the possibility of an evolutionary trade-off between increased pedipalp length, for use in display in courtship and territorial contest, and strike performance during prey capture

Mosquitoes of southern England and northern Wales : identification, ecology and host selection

As early as 1901, ecological and epidemiological studies were conducted to understand malaria transmission in the UK. Unfortunately, following the eradication of malaria after WWII, ecological studies on local mosquito species has been intermittent, leading to a significant gap in knowledge of the current habitat preference, distribution and vector capabilities of the 33 recorded species. This lack of current information makes the assessment of possible transmission of enzoonotic diseases such as Chikungunya and West Nile virus in UK difficult. Thus the overall purpose of this thesis was to facilitate the identification of potential vector species through the documentation and characterisation of the ecology of adult and larval stages, and the host selection of British mosquitoes, in southern England and northern Wales. A total of 13 out the 33 documented species are assessed in this study. Of which members of the Maculipennis and Pipiens Group comprised the bulk of the adult and immature collections respectively. The development of the ITS2 PCR-RFLP assay in this study allowed the identification of the three members of the Maculipennis Group, which revealed the widespread occurrence of the recently documented An. daciae in almost all localities sampled. While previously published assays discriminating the Pipiens Complex, did not yield congruent results questioning the prior identification methods and the validity of the taxonomic status of its members. In addition, host-specific primers designed herein to determine host selection in local mosquitoes revealed an indiscriminate host selection by An. atroparvus, An. daciae, An. messeae and Cx. pipiens thus indicating their potential role as vectors in the UK.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Managing software evolution in embedded systems

Verhoef, C. [Promotor]Klusener, A.S. [Copromotor

Eleutherodactylus ridens (Pygmy Rainfrog) Predation

Workers of the large ponerine ant Paraponera clavata typically forage on small to medium-sized arthropods or collect pieces of plants or nectar but have been suspected of predating small vertebrates