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Galaxy correlations and the BAO in a void universe: structure formation as a test of the Copernican Principle
(IOP Publishing, 19) February, Sean; Clarkson, Chris; Maartens, Roy
A suggested solution to the dark energy problem is the void model, where accelerated expansion is replaced by Hubble-scale inhomogeneity. In these models, density perturbations grow on a radially inhomogeneous background. This large scale inhomogeneity distorts the spherical Baryon Acoustic Oscillation feature into an ellipsoid which implies that the bump in the galaxy correlation function occurs at different scales in the radial and transverse correlation functions. We compute these for the first time, under the approximation that curvature gradients do not couple the scalar modes to vector and tensor modes. The radial and transverse correlation functions are very different from those of the concordance model, even when the models have the same average BAO scale. This implies that if void models are fine-tuned to satisfy average BAO data, there is enough extra information in the correlation functions to distinguish a void model from the concordance model. We expect these new features to remain when the full perturbation equations are solved, which means that the radial and transvers.
Open Access
Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context
(Public Library of Science, 25) Candresse, T; Filloux, D; Muhire, B; Julian, C; Galzi, S; Fort, G; Bernardo, P; Daugrois, J-H; Fernandez, E; Martin, D P; Varsani, A; Roumagnac, P
Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share .91% genomewide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.
Open Access
Bayesian inference for radio observations
(Oxford University Press, 25) Lochner, Michelle; Natarajan, Iniyan; Zwart, Jonathan T L; Smirnov, Oleg; Bassett, Bruce A; Oozeer, Nadeem; Kunz, Martin
New telescopes like the Square Kilometre Array (SKA) will push into a new sensitivity regime and expose systematics, such as direction-dependent effects, that could previously be ignored. Current methods for handling such systematics rely on alternating best estimates of instrumental calibration and models of the underlying sky, which can lead to inadequate uncertainty estimates and biased results because any correlations between parameters are ignored. These deconvolution algorithms produce a single image that is assumed to be a true representation of the sky, when in fact it is just one realization of an infinite ensemble of images compatible with the noise in the data. In contrast, here we report a Bayesian formalism that simultaneously infers both systematics and science. Our technique, Bayesian Inference for Radio Observations (BIRO), determines all parameters directly from the raw data, bypassing image-making entirely, by sampling from the joint posterior probability distribution. This enables it to derive both correlations and accurate uncertainties, making use of the flexible software MEQTREES to model the sky and telescope simultaneously. We demonstrate BIRO with two simulated sets of Westerbork Synthesis Radio Telescope data sets. In the first, we perform joint estimates of 103 scientific (flux densities of sources) and instrumental (pointing errors, beamwidth and noise) parameters. In the second example, we perform source separation with BIRO. Using the Bayesian evidence, we can accurately select between a single point source, two point sources and an extended Gaussian source, allowing for ‘super-resolution’ on scales much smaller than the synthesized beam.
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ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations
(Oxford University Press, 27) Chimusa, Emile R; Mbiyavanga, Mamana; Mazandu, Gaston K; Mulder, Nicola J
Despite numerous successful Genome-wide Association Studies (GWAS), detecting variants that have low disease risk still poses a challenge. GWAS may miss disease genes with weak genetic effects or strong epistatic effects due to the single-marker testing approach commonly used. GWAS may thus generate false negative or inconclusive results, suggesting the need for novel methods to combine effects of single nucleotide polymorphisms within a gene to increase the likelihood of fully characterizing the susceptibility gene. Results: We developed ancGWAS, an algebraic graph-based centrality measure that accounts for linkage disequilibrium in identifying significant disease sub-networks by integrating the association signal from GWAS data sets into the human protein–protein interaction (PPI) network. We validated ancGWAS using an association study result from a breast cancer data set and the simulation of interactive disease loci in the simulation of a complex admixed population, as well as pathway-based GWAS simulation. This new approach holds promise for deconvoluting the interactions between genes underlying the pathogenesis of complex diseases. Results obtained yield a novel central breast cancer sub-network of the human interactome implicated in the proteoglycan syndecan-mediated signaling events pathway which is known to play a major role in mesenchymal tumor cell proliferation, thus providing further insights into breast cancer pathogenesis.
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The effect of sulfide concentrate mineralogy and texture on Reactive Oxygen Species (ROS) generation
(Elsevier, ROS) Jones, Gavin C; Becker, Megan; van Hille, Robert P; Harrison, Susan T L
The generation of Reactive Oxygen Species (ROS), H2O2 and radical dotOH, has been observed from sulfide mineral containing particles in acidic solutions. The implications of this phenomenon, as a potential microbial stress-causing effect, have been studied previously with respect to thermophilic bioleaching performance in the presence of finely milled pyrite and chalcopyrite concentrates. In this study, the effect of sulfide mineralogy on ROS generation in the absence of microbes under physicochemical conditions typical for the bioleach environment was investigated. The mineralogical and elemental composition of eleven different samples containing sulfide mineral was obtained. These Au, Cu and other base metal-containing sulfide mineral concentrates as well as a milled whole ore of low Cu grade were tested for ROS generation. The whole ore sample and two refractory Au concentrates containing approximately 50% pyrite, generated significantly less ROS compared to the base metal-containing concentrates when compared on a constant surface area loading basis. Sulfide mineral-related variables were correlated with ROS generation. A significant difference was observed between FeS2 and CuFeS2 grades separately, whereas a combined measure of both minerals present in samples showed a consistently strong correlation to ROS generation. The Cu grade, total Cu-containing sulfides and the chalcopyrite content of Cu-containing samples correlated well with ROS generation. However, a common deterministic variable with a strong association to increased ROS generation was not found. A sub-set of samples were subjected to QEMSCAN® for textural analysis. Results suggested that a decrease in sulfide mineral liberation, caused by gangue silicate mineral occlusion to solution, resulted in decreased reactivity as shown in one of the Au-containing samples. Well-liberated chalcopyrite and pyrite phases corresponded to increased reactivity of samples. Pyrite, which was present in all of the reactive samples, was shown to be associated with other sulfide minerals, implicating its importance in galvanic interactions. Micro-analysis of chalcopyrite and pyrite phases from highly reactive samples showed an abundance of particles with extensive cracking and the possible presence of secondary transformation phases (szomolnokite). These results suggest that sulfide mineralogy, liberation and extent of physical processing affect sulfide mineral concentrate reactivity in acidic solutions.
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The Emancipation of Transkei
(Royal Institute of International Affairs, 1977-01) Schrire, Robert
On 26 October 1976 the South African Government granted the Transkei, a 37,000 sq. kilometre territory on the south-east coast of the Cape Province, independence. With the exception of South Africa, no state has recognized Transkei and, indeed, the United Nations explicitly condemned South Africa. Why has so much attention been lavished on a territory that on the surface appears to be devoid of any importance? South African and foreign opinion leaders perceived that the importance of Transkeian independence lay in its significance as part of the larger South African situation and it is therefore necessary to examine Transkei within the broader context of South African domestic and external policies.
Open Access
Intra-osseous synovial sarcoma.
(1982) Rose, A G; Uys, C J; Brawn, E
Intra-osseous synovial sarcoma is very rare and its mode of origin is conjectural. Our patient's tumour was situated within the lower femur. The sited of origin of the few intra-osseous synovial sarcomas so far documented may support the concept of intra-osseous synovial rests.
Open Access
Diamphotoxin: the arrow poison of the Kung bushmen
(1983) DE LA HARPE, J; REICH, E; REICH, K; DOWDLE, E
Purification de la diamphotoxine et étude de ses caractéristiques pharmacologiques et biochimiques.
Open Access
Interaction of nucleotides and cations with the (Ca2+, Mg2+)-ATPase of sarcoplasmic reticulum as determined by fluorescence changes of bound 1-anilino-8-naphthalenesulfonate
(1983) Arav, R; Aderem, A A; Berman, M C
The changes in fluorescence of 1-anilino-8-naphthalenesulfonate (ANS-) have been used to determine binding of ligands to the (Ca2+, Mg2+)-ATPase of sarcoplasmic reticulum vesicles, isolated from rabbit skeletal muscle. ANS- binds to sarcoplasmic reticulum membranes with an apparent Kd of 3.8 X 10(-5) M. The binding of ANS- had no effect on Ca2+ transport or Ca2+-dependent ATPase activity. EGTA, by binding endogenous Ca2+, increased the fluorescence intensity of bound ANS- by 10-12%. Subsequent addition of ATP, ADP, or Ca2+, in the presence or absence of Mg2+, reversed this change of fluorescence. The binding parameters, as determined by these decreases in fluorescence intensity, were as follows: for ATP, Kd = 1.0 X 10(-5) M, nH = 0.80; for ADP, Kd = 1.2 X 10(-5) M, nH = 0.89; and for Ca2+, Kd = 3.4 X 10(-7) M, nH = 1.8. The binding parameters for ITP and for the nonhydrolyzable analogue, adenyl-5'-yl-beta, gamma-methylene)diphosphate, were similar to those of ATP, but GDP, IDP, CDP, AMP, and cAMP had lower apparent affinities. Millimolar concentrations of pyrophosphate also decreased the fluorescence of bound ANS-, whereas orthophosphate caused a small (2-3%) increase in fluorescence in Ca2+-free media. Vanadate, in the presence of EGTA, decreased the fluorescence of bound ANS-with half-maximal effect at 4 X 10(-5) M. The changes of fluorescence intensity of bound ANS- appear to reflect conformational changes of the (Ca2+, Mg2+)-ATPase, consequent to ligand binding, with the low and high fluorescence intensity species corresponding to the E1 and E2 conformations, respectively. These appear to reflect similar conformational states of the (Ca2+, Mg2+)-ATPase to those reported by changes in intrinsic tryptophan fluorescence (DuPont, Y. (1976) Biochem, Biophys. Res. Commun. 71, 544-550).
Open Access
Eighteenth Century Cape Society and its Historiography: Culture, Race, and Class
(Taylor & Francis, 1983) Giliomee, Hermann
The revisionist literature of the 1970s approached social stratification in South Africa with the insistence that proper 'weighting' of the race and class factors should occur. Arguing that class and not racial consciousness was the key determinant of social structure in pre-industrial South Africa, it concluded that eighteenth century Cape society in certain areas of the colony was characterised by greater fluidity than the caste system of the AmericanSouth or industrialised South Africa. George Fredrickson's comparative analysis of American and South African history rejects the first mentioned approach but agrees with the conclusion. This article argues that Fredrickson erred by characterising Cape society as being largely based on class and a permeable colour line. The extent to which Cape Town or frontier society can be categorised as such was limited,while the agrarian Western Cape, in terms of manumission rates and the incidence of mixed marriages, was one of the most rigid caste societies in the world.The article concludes by observing that only by studying how political and class relationships reinforced each other can the full complexity of eighteenth century Cape society be revealed.
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Constitutional change and the issue of reform: A Review of the Buthelezi Commission and President's Council Constitutional Reports
(UNISA Press, 1983-01) Schrire, Robert
One of the recent growth industries in our political life is in the field of constitutional proposals. From the government side we have had among others the Theron Commission, the Parliamentary Select Committee on the Constitution, and three President's Council reports. An election in 1977 was ostensibly fought at least in part, over the merits of the National Party constitutional proposals. Much of 1982 was dominated by news of the government's new constitutional proposals which precipitated a National Party split and then absorbed most of the efforts of its four provincial party congresses. Outside of government considerable attention has also been paid to constitutional matters. In 1978 a major conference was held in Pietermaritzburg to examine the then constitutional proposals of the National Party and several other constitutional conferences and workshops have subsequently taken place. Indeed the theme of the most recent meeting of the Political Science Association of South Africa was constitutional reform and political stability. In KwaZulu Chief Buthelezi appointed a constitutional commission while the Coloured Persons Representative Council produced its own constitutional proposals before it was disbanded. The opposition parties too have paid more attention to constitutional issues than in the past and both the PFP and the NRP have specific and carefully worked out proposals. Clearly however, the proposals with the greatest political significance are those of the National Party and the Buthelezi Commission, because they are the products of the two largest political groupings in South Africa; the Afrikaners and the Zulus. This review article will therefore be devoted to an analysis of these two reports.
Open Access
Strange particle production in pp and pN reactions
(1984) Greiner, Walter; Koch, Peter; Rafelski, Johann
A statistical model of particle production valid for a wide range of Feynman x is developed and applied to describe strange particle production in hadronic collisions. Predictions of relative abundances of multiply strange hadrons are made which compare well with the available fragmentary data.
Open Access
DNA hypermethylation in sodium butyrate-treated WI-38 fibroblasts
(1986) PARKER, M Iqbal; de Haa, Judy B; Gevers, Wieland
Sodium butyrate is very often used to alter gene expression in cultured cells. In this study, we examined the effects of this compound on various cellular events in WI-38 human embryonic lung fibroblasts in culture. During a 16-20-h treatment at sodium butyrate concentrations of between 5 and 20 mM, no adverse effects on cell morphology were observed. However, cell division and DNA synthesis were reversibly inhibited, the latter by 85, 80, and 70% at sodium butyrate concentrations of 5, 10, and 20 mM, respectively. Although overall protein synthetic activity was not significantly affected, RNA synthesis decreased to 76% of the control values at a sodium butyrate concentration of 5 mM. Butyrate treatment also caused hypermethylation of DNA cytosines as determined by differential digestion by MspI/HpaII restriction endonucleases and by high performance liquid chromatography analysis of the DNA. The 5-methylcytosine content of the DNA in untreated WI-38 fibroblasts was 2.94 +/- 0.46% of total cytosine residues, while in cultures treated with 5, 10, and 20 mM sodium butyrate, these values were 5.76 +/- 0.28, 5.91 +/- 0.37, and 6.8 +/- 0.44%, respectively. An interesting feature is that this hypermethylation occurred in DNA which was synthesized in the presence of sodium butyrate (newly synthesized) as well as in DNA which had been synthesized before butyrate administration (pre-existing DNA). The hypermethylated state was conserved only in the former situation, since the methylcytosines were rapidly lost in the subsequent generation in the latter case. It would therefore appear that methylcytosines are maintained after cell replication only if they are generated on newly synthesized DNA.
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The rhetoric and reality of local government reform
(Taylor & Francis (Routledge), 1986) Cameron, Robert
N. Dewar, in his article; 'Municipal Government under the New South African Constitution: Who Gets What, Where, Who Decides, and Who Decides Who Decides?' Social Dynamics, Vol. 11(2), argues that the new local government legislation could lead to individual ethnic groups having the space to enact legislation which could precipitate fundamental changes to national level structures. This paper argues against this view because there is a great difference between the stated government commitment to devolution of power and the reality of local government legislation which is characterised by increased state centralisation of powers. Both forms of local government structures, Regional Services Councils and Primary Local Authorities, are going to be under such tight state control that the possibility of using them to challenge national structures is negligible. Local government restructuring must be seen as part of a broader state strategy to defuse political unrest and restructure the economy. This article will show how contradictory objectives of this strategy at local government level are primarily responsible for the discrepancy between government rhetoric and reality.
Open Access
Redistribution of strangeness between quark-gluon plasma and hadronic gas
(1987) Rafelski, J
In a baryon-rich hadronic gas s-quarks, unlike antistrange quarks, can be found in baryonic degrees of freedom. This abundance asymmetry induces an associated asymmetry in the otherwise symmetric quark-gluon plasma section of the fireball volume. The magnitude of this effect is established as a function of thermodynamic variables and experimental consequences are explored.
Open Access
Attitudes to adverse drug reactions and their reporting among medical practitioners
(1987) Robins, A H; Weir, M; Biersteker, E M
The adverse drug reaction (ADR) reporting rate within the medical profession is exceptionally low, and doctors' approaches and attitudes to ADRs were explored through personal structured interviews. The total sample comprised 104 doctors in private practice, divided into three groups: 59 general practitioners, 26 medical specialists and 19 surgical specialists. Certain differences emerged between the groups. The surgical group observed far fewer ADRs than the other groups and not a single member had ever reported an ADR. A significantly larger number of medical specialists considered it necessary to report an ADR to an outside agency, while general practitioners tended to believe that only newly released medicines required ADR reporting. However, few doctors of any specialty regarded ADR reporting as part of the action they would take in their handling of ADRs in practice. The commonest explanation advanced for the marked underreporting of ADRs was that unusual or serious reactions were very infrequent and the common or trivial ones did not warrant reporting. Apathy and indifference were rated as the next most pertinent influence in non-compliance, while such factors as fear of personal consequences (e.g. criticism, medicolegal action) and uncertainty about what to report were deemed to be relatively unimportant.
Open Access
Modelling techniques for biological reaction systems: 1 Mathematical description and model representation
(Water Research Commission, 1988) Billing, Alison Emslie; Dold, Peter Lorimer
This paper is the first in a series of three which deals with modelling and numeric techniques for biological reaction systems. A matrix for ma rov1des a usef\11. method for model presentation. The matrix ensures clarity as to the compounds, processes, reaction terms and s01chio.metry compnsmg the model. It allows ready comparison of different models and facilitates incorporating the model in a computer slffiulauon program.
Open Access
On the approximation of the spectrum of the Stokes operator
(1989) Geveci, Tunc; Reddy, B Daya; Pearce, Howard T
On obtient des estimations d'erreur pour le calcul approché des valeurs propres de l'opérateur de Stokes. Ces estimations sont valables pour les versions régularisées des méthodes mixtes qui satisfont la condition uniforme de Ladyzhenskaya-Babuška-Brezzi.
Open Access
Infantile fibrosarcoma presenting as shoulder dystocia A case report
(1989) Puzey, MS; Innes, DF; van der Elst, C W
The International Society for Burns Injuries (ISBI) has published guidelines for the management of multiple or mass burns casualties, and recommends that 'each country has or should have a disaster planning system that addresses its own particular needs.' The need for a national burns disaster plan integrated with national and provincial disaster planning was discussed at the South African Burns Society Congress in 2009, but there was no real involvement in the disaster planning prior to the 2010 World Cup; the country would have been poorly prepared had there been a burns disaster during the event. This article identifies some of the lessons learnt and strategies derived from major burns disasters and burns disaster planning from other regions. Members of the South African Burns Society are undertaking an audit of burns care in South Africa to investigate the feasibility of a national burns disaster plan. This audit (which is still under way) also aims to identify weaknesses of burns care in South Africa and implement improvements where necessary.
Open Access
Causation and the concomitant issue of apportionment with reference to gross income in South African income- tax law
(Juta Law, 1989) Emslie, Trevor; Jooste, Richard
The objective of this article is twofold: first, to set out the correct role, in our view, of the notion of causation in the application of two elements of the definition of gross income-the characterization of an amount as being from a source within the Republic (or not) and as being of a capital nature (or not); and secondly, to ascertain the apportionment implications where two or more causae with differing tax consequences are found to have given rise to the receipt or accrual of a single amount.