Effectiveness of Personal Protective Measures to Prevent Lyme Disease

Use of protective clothing and tick repellents on the skin or clothing while outdoors is 40% and 20% effective, respectively

Massive parallelism for combinatorial problems by hardware acceleration with an application to the label switching problem

A dissertation submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science in Engineering.This dissertation proposes an approach to solving hard combinatorial problems in massively parallel architectures using parallel metaheuristics. Combinatorial problems are common in many scientific fields. Scientific progress is constrained by the fact that, even using state of the art algorithms, solving hard combinatorial problems can take days or weeks. This is the case with the Label Switching Problem (LSP) in the field of Bioinformatics. In this field, prior work to solve the LSP has resulted in the program CLUMPP (CLUster Matching and Permutation Program). CLUMPP focuses solely on the use of a sequential, classical heuristic, and has had success in smaller low complexity problems. By contrast this dissertation proposes the Parallel Solvers model for the acceleration of hard combinatorial problems. This model draws on the commonalities evident in algorithms and strategies in metaheuristics. After investigating the effectiveness of the mechanisms apparent in the Parallel Solvers model with regards to the LSP, the author developed DePermute, an algorithm which can be used to solve the LSP significantly faster. Results were generated from time based testing of simulated data, as well as data freely available on the Internet as part of various projects. An investigation into the effectiveness of DePermute was carried out on a CPU (Central Processing Unit) based computer. The time based testing was carried out on a CPU based computer and on a Graphics Processing Unit (GPU) attached to a CPU host computer. The dissertation also proposes the design of an Field Programmable Gate Arrays (FGPA) based implementation of DePermute. Using Parallel Solvers, in the DePermute algorithm, the time taken for population group sizes, K, ranging from K = 5 to 20 was improved by up to two orders of magnitude using the GPU implementation and aggressive settings for CLUMPP. The CPU implementation, while slower than the GPU implementation still outperforms CLUMPP, using aggressive settings, marginally and usually with better quality. In addition it outperforms CLUMPP by at least an order of magnitude when CLUMPP is set to use higher quality settings. Combinatorial problems can be very difficult. Parallel Solvers has been effective in the field of Bioinformatics in solving the LSP. This dissertation proposes that it might assist in the reasoning and design of algorithms in other fields.MT201

Swahili exercises. Compiled for the Universities' mission to Central Africa,

Mode of access: Internet

Measuring the Force Production of the Hormogonia of Mastigocladus laminosus

The cyanobacterium Mastigocladus laminosus forms hormogonia, which glide slowly away from the parent colony by extruding slime out of nozzles. Using video microscopy, we observed hormogonia embedded in and moving through 1–4% agar solutions with an average velocity of 0.5 μm/s. Agar is non-Newtonian and is subject to shear-thinning so that its viscosity greatly increases at low shear rates. We measured the viscosity of these agar solutions at the very low shear rates appropriate for gliding hormogonia and found it to vary from 1 to 52 million centipoise. Then, by applying a Newtonian drag coefficient for a 100-μm-long, cigar-shaped hormogonium, we found that it produced a force of several million pN. A typical hormogonium has 10–100 thousand 9-nm-wide slime extrusion nozzles. Wolgemuth et al. have proposed hydration-driven swelling of the polyelectrolyte slime ejected from these nozzles as the force production mechanism, and our experiment found a large nozzle force that was consistent with this hypothesis. Average single nozzle force depended on viscosity, being large when the viscosity was high: 71 pN in 3% and 126 pN in 4% agar

Environmental Health implications of global climate change

First published as an Advance Article on the web 4th August 2005 This paper reviews the background that has led to the now almost-universally held opinion in the scientific community that global climate change is occurring and is inescapably linked with anthropogenic activity. The potential implications to human health are considerable and very diverse. These include, for example, the increased direct impacts of heat and of rises in sea level, exacerbated air and water-borne harmful agents, and—associated with all the preceding—the emergence of environmental refugees. Vector-borne diseases, in particular those associated with blood-sucking arthropods such as mosquitoes, may be significantly impacted, including redistribution of some of those diseases to areas not previously affected. Responses to possible impending environmental and public health crises must involve political and socio-economic considerations, adding even greater complexity to what is already a difficult challenge. In some areas, adjustments to national and international public health practices and policies may be effective, at least in the short and medium terms. But in others, more drastic measures will be required. Environmental monitoring

Lipidomic Analysis of Dynamic Eicosanoid Responses during the Induction and Resolution of Lyme Arthritis*

Eicosanoids and other bioactive lipid mediators are indispensable regulators of biological processes, as demonstrated by the numerous inflammatory diseases resulting from their dysregulation, including cancer, hyperalgesia, atherosclerosis, and arthritis. Despite their importance, a robust strategy comparable with gene or protein array technology for comprehensively analyzing the eicosanoid metabolome has not been forthcoming. We have developed liquid chromatography-tandem mass spectrometry methodology that quantitatively and comprehensively analyzes the eicosanoid metabolome and utilized this approach to characterize eicosanoid production during experimental Lyme arthritis in mice infected with the bacterium Borrelia burgdorferi. Eicosanoids were extracted throughout infection from the joints of Lyme arthritis-resistant and -susceptible mice and subjected to lipidomic profiling. We identified temporal and quantitative differences between these mouse strains in the production of eicosanoids, which correlated with differences in arthritis development. The eicosanoid biosynthetic enzyme cyclooxygenase (COX)-2 has been implicated in the regulation of Lyme arthritis pathology, and subsequent lipidomic profiling of B. burgdorferi-infected COX-2−/− mice identified reductions not only in COX-2 products but, surprisingly, also significant off-target reductions in 5-lipoxygenase metabolites. Our results demonstrate the utility of a comprehensive lipidomic approach for identifying potential contributors to disease pathology and may facilitate the development of more precisely targeted treatment strategies

Dietary Fish Oil Substitution Alters the Eicosanoid Profile in Ankle Joints of Mice during Lyme Infection

Dietary ingestion of (n-3) PUFA alters the production of eicosanoids and can suppress chronic inflammatory and autoimmune diseases. The extent of changes in eicosanoid production during an infection of mice fed a diet high in (n-3) PUFA, however, has not, to our knowledge, been reported. We fed mice a diet containing either 18% by weight soybean oil (SO) or a mixture with fish oil (FO), FO:SO (4:1 ratio), for 2 wk and then infected them with Borrelia burgdorferi. We used an MS-based lipidomics approach and quantified changes in eicosanoid production during Lyme arthritis development over 21 d. B. burgdorferi infection induced a robust production of prostanoids, mono-hydroxylated metabolites, and epoxide-containing metabolites, with 103 eicosanoids detected of the 139 monitored. In addition to temporal and compositional changes in the eicosanoid profile, dietary FO substitution increased the accumulation of 15-deoxy PGJ(2), an antiinflammatory metabolite derived from arachidonic acid. Chiral analysis of the mono-hydroxylated metabolites revealed they were generated from primarily nonenzymatic mechanisms. Although dietary FO substitution reduced the production of inflammatory (n-6) fatty acid-derived eicosanoids, no change in the host inflammatory response or development of disease was detected