Dinosaur tracks in Triassic Molteno sediments: the earliest evidence of dinosaurs in South Africa?

A fossil tracksite containing well-preserved tridactyl footprints of bipedal theropod dinosaurs is reported from fluvial overbank deposits of Molteno age (Stormberg Group: Triassic) in the northeastern Cape Province, South Africa. They occur stratigraphically below the mudrocks of the Elliot Formation, in which dinosaur remains are comparatively common, and are taken to represent the earliest evidence for dinosaurs in South Africa. They also represent the earliest unequivocal evidence of tetrapods in Molteno deposits.Foundation for Research Development; Trustees of the Port Elizabeth Museu

Challenges of biobanking in South Africa to facilitate indigenous research in an environment burdened with human immunodeficiency virus, tuberculosis, and emerging non-communicable diseases

The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth and public health development. Increased SA research on these diseases and syndromes and the collection of associated biospecimens has ensured a plethora of biobanks created by individuals, albeit without the foresight of prospective and collective use by other local and international researchers. As the need for access to high-quality specimens in statistically relevant numbers has increased, so has the necessity for the development of national human biobanks in SA and across the Continent. The prospects of achieving sustainable centralized biobanks are still an emerging and evolving concept, primarily and recently driven by the launch of the H3Africa consortium, which includes the development of harmonized and standardized biobanking operating procedures. This process is hindered by a myriad of complex societal considerations and ethico-legal challenges. Efforts to consolidate and standardize biological sample collections are further compromised by the lack of full appreciation by national stakeholders of the biological value inherent in these collections, and the availability of high quality human samples with well-annotated data for future scientific research and development. Inadequate or nonexistent legislative structures that specifically regulate the storage, use, dispersal, and disposal of human biological samples are common phenomena and pose further challenges. Furthermore, concerns relating to consent for unspecific future uses, as well as access to information and data protection, are all new paradigms that require further consideration and public engagement. This article reviews important fundamental issues such as governance, ethics, infrastructure, and bioinformatics that are important foundational prerequisites for the establishment and evolution of successful human biobanking in South Africa.Web of Scienc

Lupus nephritis. Part I. Histopathological classification, activity and chronicity scores

CITATION: Bates, W. D. et al. 1991. Lupus nephritis. Part I. Histopathological classification, activity and chronicity scores. South African Medical Journal, 79:256-259.The original publication is available at http://www.samj.org.zaRenal biopsy has made a major contribution to the understanding and management of patients with lupus nephritis. In a 5-year retrospective study the renal morphology of 55 biopsies from 51 patients with lupus nephritis was classified acccrding to World Health Organisation criteria. In addition, semi-quantitative activity and chronicity scores were documented. The findings were similar to series from other parts of the world. Of the biopsies reviewed, 6 were class II, 13 class III, 32 class IV and 4 class V. In situations of overlap, segmental proliferative features determined the class to which a biopsy specimen was assigned. Twenty-five of the patients, all WHO class IV, showed activity scores in the severe range. Most of the activity score features were common and easily recognised but necrotising angiitis was only seen in 1 patient. Haematoxylin bodies were difficult to document and the nature and value of the haematoxylin body is questioned.Publisher’s versio

Metabolic, inflammatory and haemostatic effects of a low-dose continuous combined HRT in women with type 2 diabetes: potentially safer with respect to vascular risk?

BACKGROUND Conventional hormone replacement therapy (HRT) containing conjugated equine oestrogen (CEE) and medroxyprogesterone acetate (MPA) increases triglyceride, C- reactive protein (CRP) and coagulation Factor VII concentrations, potentially explaining their increased coronary heart disease (CHD) and stroke risk. OBJECTIVE To assess the metabolic effects of a continuous combined HRT containing 1 mg oestradiol and 0.5 mg norethisterone or matching placebo. DESIGN Double-blind, randomized placebo-controlled trial. PATIENTS Fifty women with type 2 diabetes. MEASUREMENTS Classical and novel risk factors for vascular disease. RESULTS Triglyceride concentration was not altered (P = 0.31, change in active arm relative to placebo) and low-density lipoprotein (LDL) cholesterol concentration declined 13% (P = 0.018). IL-6 concentration (mean difference -1.42 pg/ml, 95% CI: -2.55 to - 0.29 IU/dl, P = 0.015), Factor VII (-32 IU/dl, -43 to -21 IU/l, P lt 0.001) and tissue plasminogen activator antigen (by 13%, P = 0.005) concentrations fell, but CRP was not significantly altered (P = 0.62). Fasting glucose (P = 0.026) also declined significantly, but there are no significant effects on HBA1c, Factor IX or APC resistance. CONCLUSIONS HRT containing 1 mg oestradiol and 0.5 mg norethisterone may avoid the adverse metabolic effects potentially implicated in the elevated CHD and stroke risk induced by conventional higher dose HRT. This type of preparation may therefore be more suitable than conventional HRT for women at elevated CHD risk such as those with type 2 diabetes. Large randomized controlled trials of such low dose preparations, powered for cardiovascular end points, are now needed

Multicomponent signal unmixing from nanoheterostructures: overcoming the traditional challenges of nanoscale X-ray analysis via machine learning.

The chemical composition of core-shell nanoparticle clusters have been determined through principal component analysis (PCA) and independent component analysis (ICA) of an energy-dispersive X-ray (EDX) spectrum image (SI) acquired in a scanning transmission electron microscope (STEM). The method blindly decomposes the SI into three components, which are found to accurately represent the isolated and unmixed X-ray signals originating from the supporting carbon film, the shell, and the bimetallic core. The composition of the latter is verified by and is in excellent agreement with the separate quantification of bare bimetallic seed nanoparticles.D.R. acknowledges support from the Royal Society’s Newton International Fellowship scheme. B.R.K. thanks the U.K. EPSRC for financial support (EP/J500380/1). F.d.l.P. and C.D. acknowledge funding from the ERC under grant no. 259619 PHOTO EM. P.A.M and P.B. acknowledges financial support from the European Research Council under the European Union’s Seventh Framework Programme (FP7/ 2007-2013)/ERC grant agreement 291522-3DIMAGE. P.A.M. also acknowledges financial support from the European Union’s Seventh Framework Programme of the European Commission: ESTEEM2, contract number 312483.This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b00449

Globally sparse PLS regression

Volume 56 ; Print ISBN : 978-1-4614-8282-6Partial least squares (PLS) regression combines dimensionality reduction and prediction using a latent variable model. It provides better predictive ability than principle component analysis by taking into account both the independent and re- sponse variables in the dimension reduction procedure. However, PLS suffers from over-fitting problems for few samples but many variables. We formulate a new criterion for sparse PLS by adding a structured sparsity constraint to the global SIMPLS optimization. The constraint is a sparsity-inducing norm, which is useful for selecting the important variables shared among all the components. The optimization is solved by an augmented Lagrangian method to obtain the PLS components and to perform variable selection simultaneously. We propose a novel greedy algorithm to overcome the computation difficulties. Experiments demonstrate that our approach to PLS regression attains better performance with fewer selected predictor

Impact of Hormone Replacement Therapy on Exercise Training-Induced Improvements in Insulin Action in Sedentary Overweight Adults

Exercise training (ET) and hormone replacement therapy (HRT) are both recognized influences on insulin action, but the influence of HRT on responses to ET has not been examined. In order to determine if HRT use provided additive benefits for the response of insulin action to ET, we evaluated the impact of HRT use on changes in insulin during the course of a randomized, controlled, aerobic ET intervention. Subjects at baseline were sedentary, dyslipidemic, and overweight. These individuals were randomized to six months of one of three aerobic ET interventions or continued physical inactivity. In 206 subjects, an insulin sensitivity index (SI) was obtained with a frequently sampled intravenous glucose tolerance test pre- and post-ET. Baseline and post-intervention fitness, regional adiposity, general adiposity, skeletal muscle biochemistry and histology, and serum lipoproteins were measured as other putative mediators influencing insulin action. Two-way analyses of variance were used to determine if gender or HRT use influenced responses to exercise training. Linear modeling was used to determine if predictors for response in SI differed by gender or HRT use. Women who used HRT (HRT+) demonstrated significantly greater improvements in SI with ET than women not using HRT (HRT-). In those HRT+ women, plasma triglyceride change best correlated with change in SI. For HRT- women, capillary density change, and for men, subcutaneous adiposity change, best correlated with change in SI. In summary, in an ET intervention, HRT use appears associated with more robust responses in insulin action. Also, relationships between ET induced changes in insulin action and potential mediators of change in insulin action are different for men, and for women on or off HRT. These findings have implications for the relative utility of ET for improving insulin action in middle-aged men and women, particularly in the setting of differences in HRT use. Address Originally published Metabolism, Vol. 57, No. 7, July 200

Comparative transcriptomic analysis reveals similarities and dissimilarities in saccharomyces cerevisiae wine strains response to nitrogen availability

Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations

A selected history of South African inflation perceptions: The question matters

This paper provides a selected historical overview of inflation perception surveys undertaken in South Africa between 2006 and 2010 with a view to assessing the nature of the link between inflation perceptions and inflation expectations in the latest 2012 survey. These surveys are undertaken to assess the perceptions of respondents on the degree in which historic inflation figures reflect perceptions of actual inflation, and to find some link to inflation expectations. All the earlier pilot studies on inflation perceptions and the representative samples undertaken between 2006 and 2010 (in total six pilot studies, three representative samples and one survey among central bank employees) failed to show any link between inflation perceptions and inflation expectations. These findings cast some doubt on the premise that a policy of inflation targeting anchors inflation expectations in the current rate of inflation and therefore in the announced inflation target policy rate. In response to the earlier survey results, the question on inflation perceptions was put in different ways to respondents in the most-recent (2012) inflation perception survey to retest the hypothesis that inflation perceptions and inflation expectations are linked. The findings of this survey are analysed in this paper. These findings show a possible link to inflation expectations, and will be the subject of further research. The conclusion on the assessment of inflation perceptions is that the question matters.KIM201