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- ItemA Cayley-Hamilton trace identity for 2 × 2 matrices over Lie-solvable rings(2012-01-18) Meyer J.; Szigeti J.; van Wyk L.First we construct an algebra satisfying the polynomial identity [[x,y],[u,v]]=0, but none of the stronger identities [x,y][u,v]=0 and [[x,y],z]=0. Then we exhibit a Cayley-Hamilton trace identity for 2×2 matrices with entries in a ring R satisfying [[x,y],[x,z]]=0 and 12∈R. © 2011 Elsevier Inc. All rights reserved.
- ItemA CFD study of wind patterns over a desert dune and the effect on seed dispersion(2011) Joubert E.C.; Harms T.M.; Muller A.; Hipondoka M.; Henschel J.R.
- ItemA mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism(2011-10-13) Geenen S.; du Preez F.B.; Reed M.; Frederik Nijhout H.; Gerry Kenna J.; Wilson I.D.; Westerhoff H.V.; Snoep J.L.One of the main pathways for the detoxification of reactive metabolites in the liver involves glutathione conjugation. Metabolic profiling studies have shown paradoxical responses in glutathione-related biochemical pathways. One of these is the increase in 5-oxoproline and ophthalmic acid concentrations with increased dosage of paracetamol. Experimental studies have thus far failed to resolve these paradoxes and the robustness of how these proposed biomarkers correlate with liver glutathione levels has been questioned. To better understand how these biomarkers behave in the glutathione system a kinetic model of this pathway was made. By using metabolic control analysis and by simulating biomarker levels under a variety of conditions, we found that 5-oxoproline and ophthalmic acid concentrations may not only depend on the glutathione but also on the methionine status of the cell. We show that neither of the two potential biomarkers are reliable on their own since they need additional information about the methionine status of the system to relate them uniquely to intracellular glutathione concentration. However, when both biomarkers are measured simultaneously a direct inference of the glutathione concentration can be made, irrespective of the methionine concentration in the system. © 2011 Elsevier B.V. All rights reserved.
- ItemA new antigen scanning strategy for monitoring HIV-1 specific T-cell immune responses(2012-01-18) Malnati M.S.; Heltai S.; Cosma A.; Reitmeir P.; Allgayer S.; Glashoff R.H.; Liebrich W.; Vardas E.; Imami N.; Westrop S.; Nozza S.; Tambussi G.; Butto S.; Fanales-Belasio E.; Ensoli B.; Ensoli F.; Tripiciano A.; Fortis C.; Lusso P.; Poli G.; Erfle V.; Holmes H.Delineation of the immune correlates of protection in natural infection or after vaccination is a mandatory step for vaccine development. Although the most recent techniques allow a sensitive and specific detection of the cellular immune response, a consensus on the best strategy to assess their magnitude and breadth is yet to be reached. Within the AIDS Vaccine Integrated Project (AVIP http://www.avip-eu.org) we developed an antigen scanning strategy combining the empirical-based approach of overlapping peptides with a vast array of database information. This new system, termed Variable Overlapping Peptide Scanning Design (VOPSD), was used for preparing two peptide sets encompassing the candidate HIV-1 vaccine antigens Tat and Nef. Validation of the VOPSD strategy was obtained by direct comparison with 15mer or 20mer peptide sets in a trial involving six laboratories of the AVIP consortium. Cross-reactive background responses were measured in 80 HIV seronegative donors (HIV-), while sensitivity and magnitude of Tat and Nef-specific T-cell responses were assessed on 90 HIV+ individuals. In HIV-, VOPSD peptides generated background responses comparable with those of the standard sets. In HIV-1+ individuals the VOPSD pools showed a higher sensitivity in detecting individual responses (Tat VOPSD vs. Tat 15mers or 20mers: p ≤ 0.01) as well as in generating stronger responses (Nef VOPSD vs. Nef 20mers: p < 0.001) than standard sets, enhancing both CD4 and CD8 T-cell responses. Moreover, this peptide design allowed a marked reduction of the peptides number, representing a powerful tool for investigating novel HIV-1 candidate vaccine antigens in cohorts of HIV-seronegative and seropositive individuals. © 2011 Elsevier B.V.
- ItemA Note on the Five Lemma(2011) Michael F.I.
- ItemA practical equation of state for non-spherical and asymmetric systems for application at high pressures. Part 2: Extension to mixtures(2011-10-13) Rand M.D.; Nieuwoudt I.; Schwarz C.E.; Knoetze J.H.In part I of this series the pure component PHCT-DNSK equation of state (EOS) was presented. In this paper the EOS is extended to describe mixtures, particularly asymmetric mixtures containing one or more low molecular weight spherical compound together with one or more high molecular weight chain-like compound. The EOS utilises theoretically correct mixing rules and is generally able to predict the correct trends quantitatively for binary mixtures, and in most cases outperform other EOSs. With the use of a small, temperature independent, interaction parameter the EOS is able to predict the phase behaviour of the investigated systems qualitatively. The EOS is able to predict the phase behaviour of a multi-component system containing one or more light components and a range of heavy hydrocarbons with improved accuracy compared to other EOSs at reduced computational times. © 2011 Canadian Society for Chemical Engineering.
- ItemA well-tested set of primers to amplify regions spread across the avian genome(2011-05-15) Kimball R.T.; Braun E.L.; Barker F.K.; Bowie R.C.K.; Braun M.J.; Chojnowski J.L.; Hackett S.J.; Han K.-L.; Harshman J.; Heimer-Torres V.; Holznagel W.; Huddleston C.J.; Marks B.D.; Miglia K.J.; Moore W.S.; Reddy S.; Sheldon F.H.; Smith J.V.; Witt C.C.; Yuri T.[No abstract available]
- ItemAccelerated skeletal muscle recovery after in vivo polyphenol administration(2012-02-15) Myburgh K.H.; Kruger M.J.; Smith C.Acute skeletal muscle damage results in fiber disruption, oxidative stress and inflammation. We investigated cell-specific contributions to the regeneration process after contusion-induced damage (rat gastrocnemius muscle) with or without chronic grape seed-derived proanthocyanidolic oligomer (PCO) administration. In this placebo-controlled study, male Wistar rats were subjected to PCO administration for 2 weeks, after which they were subjected to a standardised contusion injury. Supplementation was continued after injury. Immune and satellite cell responses were assessed, as well as oxygen radical absorption capacity and muscle regeneration. PCO administration resulted in a rapid satellite cell response with an earlier peak in activation (Pax7 +, CD56 +, at 4 h post-contusion) vs. placebo groups (PLA) (P<.001: CD56 + on Day 5 and Pax7 + on Day 7). Specific immune-cell responses in PLA followed expected time courses (neutrophil elevation on Day 1; sustained macrophage elevation from Days 3 to 5). PCO dramatically decreased neutrophil elevation to nonsignificant, while macrophage responses were normal in extent, but significantly earlier (peak between Days 1 and 3) and completely resolved by Day 5. Anti-inflammatory cytokine, IL-10, increased significantly only in PCO (Day 3). Muscle fiber regeneration (MHC f content and central nuclei) started earlier and was complete by Day 14 in PCO, but not in PLA. Thus, responses by three crucial cell types involved in muscle recovery were affected by in vivo administration of a specific purified polyphenol in magnitude (neutrophil), time course (macrophages), or time course and activation state (satellite cell), explaining faster effective regeneration in the presence of proanthocyanidolic oligomers. © 2011 Elsevier Inc. All rights reserved.
- ItemAddiction Research Centres and the Nurturing of Creativity: The Alcohol & Drug Abuse Research Unit at the South African Medical Research Council - strengthening substance abuse research and policy in South Africa Charles Parry etal. Alcohol and Drug Abuse Research Unit, South Africa(2012-01-18) Parry C.; Morojele N.; Myers B.; Pluddemann A.
- ItemAn analytical pore-scale, shear stress model for purely viscous non-Newtonian fluids traversing porous media(2011-10-13) Cloete M.; Smit G.J.F.An analytical model for incompressible, generalized Newtonian fluids traversing different types of porous media is proposed. This model is based on the volume averaging of the governing equations. Interstitial quantities are obtained through means of a pore-scale model. For flow through porous media, in the Darcy regime, the interstitial fluid-solid interaction component is written in terms of the interstitial wall shear stress. The wall shear stress is obtained by assuming simple velocity profiles in the interstitial channels. Approximations are made in order to obtain explicit expressions for the wall shear stress in terms of the average interstitial channel velocities. The final analytical expressions obtained for predicting the flow through porous media can easily be implemented numerically and allow for a wide variety of practical implementations. Generalized Newtonian fluids traversing a porous structure adjacent to a free-flow domain were modelled numerically. The results for Newtonian fluids were compared to an analytical model from literature. © 2011 Elsevier Inc. All rights reserved.
- ItemAn effective fabrication method for ultra thin aluminum structures(2011-10-13) de Jager N.J.; Perold W.J.; Buttner U.In this paper we discuss the various effects on resistivity of thin metal films, concluding that grain boundary scattering and the material's electron-mean-free-path are the dominant factors. We also present an effective procedure for the fabrication of patterned ultra thin aluminum (sub 100 nm thick) structures on thermally grown SiO2 substrates, the results of which are compared to other commonly used electrode fabrication methods. A general 4-point probe measurement of an as-deposited 60 nm aluminum film's resistivity was performed. We also found our unique wet-etching method to deliver reproducible results with varying film thickness and yielding a favorable environment for the integration of nanomaterials. © 2011.
- ItemAn experimental evaluation of the leaching kinetics of PGM-containing Ni-Cu-Fe-S Peirce Smith converter matte, under atmospheric leach conditions(2011-05-15) van Schalkwyk R.F.; Eksteen J.J.; Petersen J.; Thyse E.L.; Akdogan G.In a first stage atmospheric leach in a typical Sherritt Ni-Cu matte leach process, a Ni-Cu-Fe-S Peirce Smith converter matte is contacted with recycled copper spent electrolyte (an aqueous copper sulphate/sulphuric acid solution) at 85 °C with the purpose of dissolving nickel, while simultaneously removing copper from solution. In the PGM industry, copper removal is also important because it serves as a leading indicator in the removal of Ir, Rh, and Ru from the spent electrolyte. The matte mainly consists of heazlewoodite, chalcocite/djurleite, a Ni-Cu alloy phase and inert spinel minerals (magnetite and trevorite). Nickel is leached from the matte by two mechanisms: (i) leaching by sulphuric acid and oxygen; and (ii) an anaerobic metal exchange reaction (cementation and metathesis) between cupric ions in solution and nickel in the matte, which is also responsible for the removal of copper from solution. This study investigates the oxidative and non-oxidative leaching of converter matte in a laboratory batch reactor, with attention specifically being given to the effects of initial copper and acid concentrations and their effects on leaching kinetics. Experimental conditions were varied based on a 2N experimental design. The availability of oxygen for acid-leaching reactions was found to be the most important factor influencing copper removal and nickel extraction. A 63% nickel extraction could be achieved during oxidative tests vs. 22% in a non-oxidative test. This also indicates that cementation did not take place to a significant degree and that nickel leaching mostly took place via leaching by acid and oxygen. It is suspected that the low degree of copper removal can be attributed to the solids/reactants ratio was employed in tests. The initial copper and acid concentrations did not have a significant effect on the rate of nickel extraction or the total amount of nickel extracted. The rate of copper removal was not significantly influenced by the initial copper concentration, but copper removal was affected by the initial acid concentration. In oxidative tests with high initial acid concentrations, the rate at which copper was leached from the matte was faster than the rate of cementation. The results suggest that operating under high initial acid conditions could interfere with copper removal with no significant benefit in terms of nickel extraction. The results allow the regression of rate expressions. © 2010 Elsevier Ltd. All rights reserved.
- ItemAn Investigation into the Influence of Socioeconomic Variables on Gestational Body Mass Index in Pregnant Women Living in a Peri-Urban Settlement, South Africa(2011) Davies H.R.; Visser J.; Tomlinson M.; Rotherham-Borus M.J.; LeRoux I.; Gissane C.Maternal and child mortality rates are still unacceptably high in South Africa. The health status of women in peri-urban areas has been influenced by political and socio-economic factors. Examining socio-economic variables (SEV) in a population aids in the explanation of the impact of social structures on an individual. Risk factors can then be established and pregnant women in these higher risk groups can be identified and given additional support during pregnancy. The aim of this study was to investigate the association between SEV and gestational Body Mass Index (GBMI) in a peri-urban settlement, South Africa. This was a sub-study of the Philani Mentor Mothers' Study (2009-2010). Maternal anthropometry and SEV were obtained from 1,145 participants. Multinomial regression was used to analyse the data. Household income was the only SEV that was significantly associated with GBMI. The odds of being underweight rather than normal weight during pregnancy increase by a factor of 2.145 (P < 0.05) for those who had a household income lower than R2000 per month. All other SEV were not significant. Logistic regression was therefore not carried out. Women who had a lower income were at risk of having a lower GBMI during pregnancy. This can lead to adverse birth outcomes such as premature birth, low birth weight, height and head circumference. Public health policy needs to be developed to include optimal nutrition health promotion strategies targeting women with a low income ante and post-natally. Once implemented, they need to be evaluated to assess the impact on maternal and child mortality. © 2011 Springer Science+Business Media, LLC.
- ItemAn Overview of Nitrogen Cycling in a Semiarid Savanna: Some Implications for Management and Conservation in a Large African Park(2011) Coetsee C.; Jacobs S.; Govender N.
- ItemAn ultrastructural investigation of the surface microbiota present on the leaves and reproductive structures of the resurrection plant Myrothamnus flabellifolia(2011-05-15) Moore J.P.; Waldron M.; Lindsey G.G.; Farrant J.M.; Brandt W.F.The leaves, flower and stems of the southern African angiosperm resurrection plant Myrothamnus flabellifolia were investigated at the ultrastructural level to determine the source of previously reported fungal contamination. Fungal mycelia and hyphae of the genera Aspergillus and Penicillium were found localized to the hydathodes of the leaves and stigmatic surfaces of the female flowers in both desiccated and hydrated specimens. A waxy bacterium of the genus Bacillus was found to colonise the waxy epidermal surfaces of the leaves and flowers which was also where fungal cells were found to be absent. It is suggested that the wax like deposits within the leaves and stems as well as over the epidermal surface prevent the growth of the fungal organisms. These fungi opportunistically invade moist surfaces, such as the floral stigmas, during periods of moisture availability and may thus negatively impact plant development. © 2010 SAAB.
- ItemAnalytical techniques for wine analysis : an African perspective; a review(2012-02-22) De Villiers, A.; Alberts, P.; Tredoux, A. G. J.; Nieuwoudt, HeleneAnalytical chemistry is playing an ever-increasingly important role in the global wine industry. Chemical analysis of wine is essential in ensuring product safety and conformity to regulatory laws governing the international market, as well as understanding the fundamental aspects of grape and wine production to improve manufacturing processes. Within this field, advanced instrumental analysis methods have been exploited more extensively in recent years. Important advances in instrumental analytical techniques have also found application in the wine industry. This review aims to highlight the most important developments in the field of instrumental wine and grape analysis in the African context. The focus of this overview is specifically on the application of advanced instrumental techniques, including spectroscopic and chromatographic methods. Recent developments in wine and grape analysis and their application in the African context are highlighted, and future trends are discussed in terms of their potential contribution to the industry. © 2011 Elsevier B.V. All rights reserved.
- ItemAntibodies reactive to Plasmodium falciparum serine repeat antigen in children with Burkitt lymphoma from Ghana(2011-10-13) Guech-Ongey M.; Yagi M.; Palacpac N.M.Q.; Emmanuel B.; Talisuna A.O.; Bhatia K.; Stefan D.C.; Biggar R.J.; Nkrumah F.; Neequaye J.; Tougan T.; Horii T.; Mbulaiteye S.M.The role of protective immunity to Plasmodium falciparum (Pf) malaria in Burkitt lymphoma (BL) is unknown. We investigated the association between BL and antibodies reactive to SE36 antigen, a recombinant protein based on P. falciparum serine repeat antigen 5 gene, targeted by protective malaria immune responses. Cases were children (0-14 years) enrolled at the Korle-Bu Teaching Hospital, Accra, Ghana, during 1965-1994 with BL confirmed by histology or cytology (92% of cases). Controls were apparently healthy children enrolled contemporaneous to the cases from the nearest neighbor house to the case house and were age,- sex-frequency-matched to the cases. Anti-SE36 IgG antibodies were measured using enzyme-linked absorbent immunoassays (ELISAs). SE36 titers were estimated by extrapolating ELISA optical density readings to a standard fitting curve. Anti-SE36 titers were log-transformed for analysis. Odds ratios (ORs) and two-sided 95% confidence intervals (95% CIs) were estimated using unconditional logistic regression. The mean log endpoint dilution titers were 0.63 logs lower in cases than in controls (8.26 [SD 1.68] vs. 8.89 [SD 1.75], Student's t-test, p = 0.019). Lower titers were observed in cases than controls aged 0-4 years (p = 0.05) and in those aged 5-14 years (p = 0.06). Low and medium tertiles of anti-SE36 IgG antibodies were associated with increased OR for BL ([OR 1.67, 95% CI 1.21-2.31] and [OR 1.33, 95% CI 0.96-1.86], respectively, ptrend = 0.002) in analyses adjusting for age, sex, calendar period and test plate. Our findings suggest that compared to similarly aged children enrolled from the same community, children with BL in Ghana have lower antibodies to SE36 antigen. © 2011 UICC.
- ItemAre linear measurements and computerized volumetric ratios determined from axial MRI useful for diagnosing hydrocephalus in children with tuberculous meningitis?(2011) von Bezing H.; Andronikou S.; van Toorn R.; Douglas T.Purpose: This study aimed to evaluate linear measurements and computerized volumetric ratios on axial magnetic resonance imaging (MRI) scans against the diagnosis of hydrocephalus in children with tuberculous meningitis (TBM). Methods: MRI scans and clinical notes of children with culture positive TBM were reviewed. Patients with surgical drainage of ventricles were considered positive for hydrocephalus. Alternatively, predefined radiological criteria of hydrocephalus in combination with any clinical criteria were considered positive for hydrocephalus. Axial T2-weighted MRI scans were used for measurement by a radiologist. Linear measurements included the Evans index, frontal-occipital horn ratio, and frontal-occipital horn width ratio. Computer-assisted segmentation of the MRI volume was performed on a slice-by-slice basis using the number of pixels comprising each region to calculate the ratios: ventricular volume: brain volume and cerebrospinal fluid (CSF)/(brain + CSF) for all slices and for a single slice at the level of the lateral ventricles. Results: Twenty-two children (mean age 3.7 years) comprised ten patients with a 'final' diagnosis of hydrocephalus (six communicating, four non-communicating). None of the linear measurements showed a statistical correlation with the 'final' diagnosis of hydrocephalus. The frontal-occipital horn width ratio (FOHWR) (p = 0.09) was the closest to demonstrate statistical significance. The highest sensitivity was attained with FOR (90%) followed by FOHWR (85%). The highest specificity was reached with FOHWR (70%). Volumetric ratios were inferior to linear measures. Conclusion: Linear measures of hydrocephalus in TBM were more reliable than volumetric ratios. Hydrocephalus can be quantified most reliably using the FOHWR. This is useful for serial follow-up and for research of TBM. © 2011 Springer-Verlag.
- ItemAssessment of observed and perceived changes in ecosystems over time, with special reference to the Sylt-Romo Bight, German Wadden Sea(2011-10-13) Baird, D.Examples of state changes in three aquatic ecosystems (the Neuse River estuary, NC, USA, the Kromme River estuary (St. Francis Bay, South Africa), the St. Marks National Wildlife Refuge, FL, USA) over time have been quantitatively assessed using ecological network analysis (ENA). A suite of ENA indices were compared among the multiple states of these ecosystems to illustrate the usefulness of ENA for describing differences among system states. Quantitative network models were constructed for the Sylt-Rømø Bight ecosystem and for the mussel bed subsystem of the Bight, depicting standing stocks of the living and non-living components and flow of carbon [a surrogate for energy] between them. These models consist of 59 compartments, and were assessed by means of ENA protocols. The impact of invasive species, such as the Pacific oyster, Crassostrea gigas, on existing mussel beds [of Mytilus edulis], and on predators [mainly birds] dependent on mussels for energy were assessed using AUTOMOD, a routine that predict the impact of species on each other within the ecosystem model. Predictive modelling clearly shows variability in bird biomass due to change in abundance of their important prey species at lower trophic levels. The simulations illustrated that the numbers of eider duck and oystercatcher in the Bight could be reduced to 50% of their current abundance within about 10 years at a 20%-40% reduction in prey biomass. Ecosystem properties calculated using ENA for the initial and alternate state of the Bight and the mussel beds after a simulated reduction of 40% in prey biomass show a decline in virtually all metrics (Total System Throughput, Development Capacity, Ascendency, Redundancy), system trophic efficiency, cycling, and system ratios (e.g. Average Mutual Information, Flow Diversity, Food Web Connectance). © 2011 Elsevier Ltd. All rights reserved.
- ItemAssociation of Cocaine- and Amphetamine-Related Transcript, Leptin and Leptin Receptor Gene Polymorphisms with Anthropometric Obesity Phenotype Indicators in South African Learners(2011) Yako Y.Y.; Fanampe B.L.; Hassan M.S.; Erasmus R.T.; van der Merwe L.; van Rensburg S.J.; Matsha T.E.Background/Aims: Obesity has increased rapidly in South African children and adolescents. Genes involved in appetite regulation have been extensively studied worldwide, but their role in the obesity phenotype in South African Black and mixed-ancestry school adolescents is unknown. Methods: Seven common polymorphisms in LEP, GHRL, CART and LEPR were analysed for genotype and haplotype association with anthropometric obesity phenotype indicators in South African Black and mixed-ancestry adolescent school learners. Results: The CART c.517A→G polymorphism was significantly associated with obesity susceptibility. The LEPR Lys109Arg G allele was associated with an average reduction of 2.36 kg/m2 in body mass index (BMI), 5.66 cm in waist circumference (WC) and 1.61 cm in mid-upper-arm circumference (MUAC). This was confirmed by haplotype analysis. Additionally, a haplotype of the LEP polymorphisms significantly increased BMI, MUAC and hip circumference, while LEPR haplotypes were associated with differences in MUAC. Conclusion: Our findings suggest that c.517A→G and Lys109Arg contribute to the variation in anthropometric obesity phenotype indicators observed among Black African and mixed-ancestry South African learners. Furthermore, haplotypes of LEP, LEPR and GHRL polymorphisms were associated with varying measurements of weight, BMI and WC. Further studies are required to confirm our results in a larger and homogeneous study population group. Copyright © 2011 S. Karger AG, Basel.