During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequencing is presented. The method has been applied to several projects and further development by others has enabled even higher sample throughputs. Amplification of single cell genomes is a prerequisite for sequence analysis. Paper 2 evaluates four commercially available kits for whole genome amplification of single cells. The results show that coverage of the genome differs significantly among the protocols and as expected this has impact on the downstream analysis. In Paper 3, single cell genotyping by exome sequencing is used to confirm the presence of fat cells derived from donated bone marrow within the recipients’ fat tissue. Close to hundred single cells were exome sequenced and a subset was validated by whole genome sequencing. In the last paper, a new method for phasing (i.e. determining the physical connection of variant alleles) is presented. The method barcodes amplicons from single molecules in emulsion droplets. The barcodes can then be used to determine which variants were present on the same original DNA molecule. The method is applied to two variable regions in the bacterial 16S gene in a metagenomic sample. Thus, two of the papers (1 and 4) present development of new methods for increasing the throughput and information content of data from massively parallel sequencing. Paper 2 evaluates and compares currently available methods and in paper 3, a biological question is answered using some of these tools. / <p>QC 20160127</p>

The optimisation of image quality in medical imaging techniques is a significant factor in favourable patient prognoses. The number of counts in a nuclear medicine image is one factor in determining the diagnostic value of the image. The current study aims to determine the variation in counts in whole-body bone scan images with patient height and weight. Three separate studies were undertaken as part of the investigation. First, 65 whole-body bone scans were analysed together with patient height, weight, age and sex. Weight was found to the most important anatomy influence on image counts. However, significant influences from patient sex and age meant that a useful relationship between image counts and patient anatomy based solely on height and weight could not be determined. For the second study, a model of General Electric Millennium MG gamma camera was created and validated within the SIMIND Monte Carlo software. The results indicate that the model is an accurate representation of the gamma camera. Third, the 4D NCAT whole-body patient phantom was modified to represent the average male and female clinical study participants. The phantoms were used in conjunction with the gamma camera model to simulate the whole-body bone scan procedure. The counts in the simulated images were consistent with the average measured counts of the clinical study indicating that it is feasible to use the NCAT phantom for nuclear medicine bone imaging. However, the phantom’s method of activity distribution should be refined to allow a more realistic distribution of activity throughout the skeleton.

This study contributes to the growing body of formulaic language research that indicates that formulaic sequences (e.g., idioms, collocations, metaphors, and other conventionalized multi-word items) facilitate comprehension by reducing processing load (Wray, 2002). Expanding on Underwood et. al. (2004), this study combines corpus analysis and eye-movement data to assess the contribution of formulaicity to the comprehension of a whole, authentic text.Information regarding grammatical, lexical, and contextual conventions for each formulaic item in the text was obtained via the Collins COBUILD Online Corpus and the British National Corpus. Additionally, using an Applied Science Laboratories Eye Tracker, the eye movements of two native speakers and one non-native speaker of English were recorded and the fixations for formulaic sequences were compared. All eye movement data was interpreted in light of Goodman's Transactional model of reading (2003). Specifically, eye movements for each participant were compared across two conditions: 1) a condition comprised of the formulaic sequences in the text and 2) a baseline segment from the text which was free of formulaic items. Paired t-tests were performed for each participant to determine whether or not the eye movement behavior differed significantly in the two conditions. Data analysis indicates that both native and non-native readers of English showed significant differences in the eye movement patterns for the two conditions. However, these significant differences were reversed for the two participant groups. In the case of the native readers, the predictable nature of formulaic sequences facilitated the processing of written text, as evidenced by a significantly lower percentage of words fixated in the formulaic sequences in comparison with the percent of words fixated in the baseline condition. However, for the non-native readers, 1) lack of experience with the formulaic items and 2) their opaque nature appeared to hinder comprehension, resulting in a significantly higher percentage of words fixated in the formulaic condition than in the baseline, non-formulaic condition. This dissertation has implications for the fields of first and second language acquisition, particularly literacy theory and instruction.

No description available.

Cancer is one of the major causes of worldwide mortality. Imaging plays a vital role in the staging, follow-up, and evaluation of therapeutic response in cancer patients. Whole-body (WB) magnetic resonance imaging (MRI), as a non-ionizing imaging technique, is a promising procedure to assess tumor spreading in a single examination. New MRI technological developments now enable the application of diffusion-weighted imaging (DWI) of the entire body. DWI reflects the random motion of water molecules and provides functional information of body tissues. DWI can be quantified with the use of the apparent diffusion coefficient (ADC). The aim of this dissertation was to demonstrate the value of WB MRI including DWI in cancer patients. WB MRI including DWI, 18F-NaF PET/CT, and bone scintigraphy was performed on 49 patients with newly diagnosed, high-risk prostate cancer, for the purpose of detecting bone metastases. WB DWI showed higher specificity, but lower sensitivity compared to 18F-NaF PET/CT. In addition, WB MRI including DWI, and CT of the chest and abdomen was performed in 23 patients with malignant melanoma. We concluded that WB MRI could not completely supplant CT for the staging of malignant melanoma, especially with respect to the detection of lesions in the chest region. In this study, WB MRI and DWI were able to detect more bone lesions compared to CT, and showed several lesions outside the CT field of view, reinforcing the advantage of whole-body examination. WB MRI, including DWI, was performed in 71 patients with testicular cancer. This modality demonstrated its feasibility for use in the follow-up of such patients. WB MRI, including DWI, and 18F-FDG PET-CT, were carried out in 50 patients with malignant lymphoma. Both these imaging modalities proved to be promising approaches for predicting clinical outcomes and discriminating between different subtypes of lymphomas. In conclusion, WB MRI, including DWI, is an evolving technique that is continuing to undergo technical refinement. Standardization of image acquisition and analysis will be invaluable, allowing for more accurate comparison between studies, and widespread application of this technique in clinical practice. Both WB MRI, including DWI and PET/CT, have their particular strengths and weaknesses in the evaluation of metastatic disease. DWI and PET/CT are different functional techniques, so that combinations of these techniques may provide complementary and more comprehensive information of tumor tissue.

Early pregnancy is characterized by complex interactions between blood vessels, leukocytes, and conceptus-derived trophoblasts within the gestational uterus. Uterine Natural Killer (uNK) cells become the most abundant leukocyte during decidualization and produce a wide array of angiogenic factors, yet little is known regarding their early pregnancy functions. To characterize the role(s) of uNK cells, whole mount in situ immunohistochemistry of live early implant sites was performed. A timecourse examination of murine early pregnancy (virgin, and gd4.5-9.5) implantation sites was performed. Comparison of Gd6.5, 8.5 and 9.5 implant sites from BALB/c+/+ controls (BALB/c) and BALB/c-Rag2-/-Il2rg-/- (alymphoid) identified anomalies that result from the absence of lymphocytes. In alymphoid decidua basalis, mesometrial angiogenesis was widespread but pruning of nascent vessels within alymphoid decidua basalis was deficient. As early gestation progressed, vessels of alymphoid decidua basalis showed no evidence for remodeling. Alymphoid implantation sites showed ~24h delay in uterine lumen closure and embryonic development. To determine if uNK cells would normalize the anomalies observed in alymphoid implantation sites, adoptive cell transfer of NK+ B- T- marrow to alymphoid mice was performed. All of the above anomalies were reversed by adoptive transfer of NK+B-T- marrow. My results suggest that uNK cells support vascular growth and development which ensures the decidua can support the growing conceptus early in pregnancy prior to formation and function of the placenta. Human decidual NK cells may fill similar roles and be important targets for strategies designed to correct intra-uterine growth restriction. / Thesis (Master, Anatomy & Cell Biology) -- Queen's University, 2013-08-02 08:42:06.487

The phrase “miner” is comparatively non-specific as mining is seen as a multi-disciplinary industry that includes several diverse professions and trades (Donoghue, 2004). One of the functions within mining is the operation of earth moving equipment (EME) such as haul trucks, dozers, excavators and graders. EME are generally used to shift large amounts of earth, dig foundations and landscape areas. In this study whole-body vibration (WBV) and noise exposure of earth moving equipment (EME) operators were assessed, at an opencast coalmine in South Africa. The aim was to evaluate and quantify the levels of exposure in different EME types, as well as to compare old with new EME, in order to estimate if machine hours contribute to higher noise and vibration levels. WBV and noise levels of the Production and Rehabilitation operations were compared, to determine whether different activities led to different exposures. Internationally accepted standardised methods, ISO 2631-1 for WBV and SANS 10083:2012 for noise were followed and correctly calibrated instrumentation was used. WBV measurements were conducted with a tri-axial seat pad accelerometer (SVAN 958) and personal noise dosimeters (Casella 35 X) were used for noise measurements. Measurements were taken over a period of four months. With regards to the European Union (EU) limit (1.15 m/s2) and the EU action limit (0.5 m/s2) it was noted that operators of EME within the Production operation were not exposed to WBV levels above the EU limit, but 77% of these operators were exposed to WBV levels above the EU action limit. It was also evident that 45% of operators’ vibration exposure levels were within the Health Guidance Caution Zone (HGCZ) of 0.45 – 0.90 m/s2. Within the Rehabilitation operation, 9% of operators were exposed to WBV levels above the EU limit and 55% above the EU action limit. Furthermore 50% was within the HGCZ. With regards to the noise Occupational exposure limit (OEL) of 85 dB(A) as stated by the Mine Health and Safety Regulations (MHSR) it was noted that 27% of operators within the Production operation were exposed to noise levels above the limit and for operators within the Rehabilitation operation 14% were reported to be exposed at or above the limit. Statistically significant difference in noise exposure was found between the Production operation and Rehabilitation operation. Results indicated that the majority of EME operators were exposed to high noise levels, in some cases exceeding the 85 dB(A) OEL. A significant positive correlation was found between noise exposure levels and machine hours. Thus higher noise levels were observed as machine operating hours increased. It was found that operators were exposed predominantly to vibration and noise levels below the limits. However the Dozer group within the Production and Rehabilitation operations in some cases exceeded the vibration and noise legal limit. High exposure levels within the Dozer group can be attributed to the fact that these EME types mostly perform activities in uneven areas and the tracks on which these Dozers move also contribute to higher vibration levels due to a lack of a suspension. Controls should be implemented as far as is reasonably practicable to ensure that operators are not exposed above recommended or permissible levels for each hazard. Continuous improvement of the maintenance plan for all EME and regularly grading and maintaining travelling ways are some of the controls that will contribute to lower vibration and noise levels. Operators exposed to high noise levels should use hearing protective devices as an early on preventative measure to reduce noise exposure levels. / MSc (Occupational Hygiene), North-West University, Potchefstroom Campus, 2014

This study explores the global health diplomacy phenomenon by focusing on how and why health is integrated into foreign policy. Over the last decade or so, precipitated primarily by a growing concern about the need to strengthen global health security and deliver on the Millennium Development Goals, foreign policymakers have been paying more attention to health as a foreign policy concern and several countries have adopted formal global health policy positions and/or strategies. To elucidate a deeper and clearer understanding of how and why health is integrated into foreign policy, this thesis used a case study research design that incorporated literature and document review and interviews with twenty informants to conduct an in-depth analysis of the United Kingdom’s (UK) Health is Global: A UK Government Strategy 2008-13. Health is Global represents the first example of a formal national global health strategy developed using a multi-stakeholder process. Briefer background case reviews of three nations that are leaders in global health diplomacy - Brazil, Norway and Switzerland, were also conducted to inform the analysis of the in-depth case. Policy analysis included categorizing data into five areas: context (why?), content (what?), actors (who?), process (how?) and impact (so what?). The Multiple Streams Model of Policymaking and Fidler’s health and foreign policy conceptualizations - revolution, remediation and regression - were used to analyze the findings. Based on this analysis, the primary reason that the countries examined have decided to focus more on global health is self-interest - to protect national and international security and their economic interests. Investing in global health was also seen as a way to enhance a state’s international reputation. In terms of self-interest, Brazil was an outlier, however. International solidarity and health as a human right have been the driving forces behind its long-term investment in development cooperation to date. Investing in health for normative reasons was also a prevalent through weaker theme in the UK, Swiss and Norwegian cases. The study highlighted the critical role that policy entrepreneurs who cross the domains of international relations and health play in the global health policymaking process. In regards to advancing a conceptual understanding of global health diplomacy, the findings propose that the whole-of-government global health policymaking process is a form of global health diplomacy. The thesis elucidated factors that underpin this process as well as lessons for other nations, in particular, Canada. While ascertaining the impact of national global health strategies was not the main objective of this thesis, the study provided an initial look at the impact of these policy instruments and processes. Such impacts include better collaboration across government actors leading to enhanced policy coherence and a more strategic focus on global health. Finally, some have argued of late that the global health revolution is over due to the current world economic crisis. Considering the level of interest in whole-of-government global health strategies and the ever growing and sophisticated world-wide global health policy community, based on this thesis, the global health revolution is alive and well.

Elements of an individuals occupational exposure, such as their posture can affect their comfort during work, and also their long term musculoskeletal health. Knowledge as to the extent of the influence of particular aspects of the exposures can help in providing guidance on risk evaluation, and direct future technical design focus. In many situations the exposures interact, and even if the effects of individual exposures are understood, the interactions are often less so. This is certainly the case with off-road driving exposures. Specific investigations have focussed on the effects of vibration exposure, resulting in the development of international standards and guidelines on measurement and evaluation of exposure. Consideration of the posture of the operator can be accomplished through postural assessment tools, although none of the currently available methods are developed specifically for use within a vehicle environment. The issues of both the posture of the operator and the seated vibration exposure are particularly apparent in off-road agricultural driving environments, where the driving task dictates that operator is often required to maintain specific postures whilst also exposed to whole-body vibration. In agriculture, many of the tasks require the operator to maintain axially rotated postures to complete the task effectively. The analysis of the combined effects of the axial rotation of the operator and the whole-body vibration exposure has been limited to a few studies within the literature, and is currently poorly understood. The overall aim of the thesis was to assess the influence of axial rotation and whole-body vibration on the musculoskeletal discomfort of the neck and trunk, in order that the true extent of the exposure risk may be evaluated. A field study was conducted to determine the common characteristics of some typical exposures, to provide a basis for the laboratory studies. A survey of expert opinion was conducted, examining the knowledge and experience of experts in assessing the relative influence of axial rotation and whole-body vibration on operators musculoskeletal health. The main investigations of the thesis are focussed in the laboratory, where the objective and subjective effects of axial rotation (static and dynamic) and whole-body vibration were investigated. Objective measures included the investigation of muscular fatigue in response to exposures. The tasks investigated in the field study indicated that the exposures often exceed the EU Physical Agents Exposure Limit Value, and that the axial rotation is a large component of the postures required. The survey of expert opinion concluded that combined exposure to axial rotation and whole-body vibration would increase the risks of lower back pain, and that acknowledgement of combined exposures should be included when assessing for risk. The results of the laboratory studies indicated that the greatest discomfort was present when subjects were exposed to axial rotation in the neck and shoulders. Out of the 8 muscles investigated, at most 6 of the 8 indicated fatigue during an experimental exposure. The muscle group which was affected most by the exposures was the m. trapezius pars decendens. Findings demonstrated that when subjects were exposed to axial rotation and whole-body vibration they indicated discomfort and their muscles fatigued. However, there was poor correlation between the sites of discomfort and the location of muscular fatigue. The discomfort findings suggest that there is an increased risk of discomfort from experiencing axial rotation together with whole-body vibration. Investigations of muscular fatigue do not substantiate this finding.

Therapeutic education initiatives embodying a whole child approach can be seen to address the intellectual, emotional, bodily and spiritual as being part of a child’s educational self. Through designing and implementing the concept of “aesthetic life narratives” in a primary school classroom, my research produces a curricular example of how therapeutic notions such as those found in psychological thought can be integrated into contemporary Scottish education through narrative and aesthetic means, exemplifying how individual children can make sense of expressive processes and roles introduced to them in an educational context. The specific characteristics of the research space and the particular interactive quality of research participation also illustrate how different children are able to participate in a short-term emotional education intervention specifically designed to be empowering. At the same time, my experience shows that the complex dynamic between the subjective life of a researcher and the historical nature of a child’s experience with caregivers in their home life can shape educational/research experience, as well as its adult and child participants, in ways unanticipated. What transpired in the process of applying philosophical ideas to the real lives of children in my research produced ethical implications regarding critical reflexivity and the socio-cultural regard of the child that are of wider relevance to educators, researchers, counsellors and policy makers who interact with children in their own work.