Quantifying error and bias in sampling thin carboniferous reef types

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 Masters in Engineering. 13st October 2015This study examines the history of underground face sampling since the earliest writers documented their findings regarding the method. An historical review of the errors associated with sampling is followed by a discussion of findings from a number of underground investigations. The thesis examines how errors introduced during and after sample extraction are responsible for error and bias. A Simulated Chip Sample Model was created and used to evaluate the nature of sampling errors and bias. Learning’s from this model include an understanding of the effects of sample extraction on variations in grade and precision. The effects of sample shape on error were considered and the aspect ratio of the sample was found to be a critical factor in minimising error It was found that if the homogeneity of the ore material decrease the error increase proportionally, despite the extraction error remaining constant. During extraction the material will be biased and the effect of using accumulation values will amplify the error and bias in samples; the error and bias in this case is secondary and has nothing to do with the extraction error. The historical ideas about error being a consequence of the nugget effect have been shown to be false; variability between samples in this case is a direct result of poor sample extraction rather than the occurrence of large gold grains in the ore. The thesis also identified sources of sampling bias and two distinct types, namely the soft-reef bias and waste-discard bias were identified. The perception that soft-reef bias is the main contributor to the deterioration of the MCF was found not to be the case. This finding is based on a comparison between chip sampling and perfect sampling, in the form of so-called “coffin samples”, that indicated there is no bias between these sample types. Other possibilities for sample error and bias were investigated and found to be related to human preference for selecting material that had to be discarded during or immediately after the sample had been taken. This was confirmed by a survey of 70 samplers with different experience levels and from different mines, who indicated the same preferences when selecting material they chose to discard from the sample material collected. The waste-discard bias is a better contender for introducing bias serious enough to affect the MCF because it occurs at each and every sample site, unlike the soft-reef bias. This type of bias was shown to mimic the soft-reef bias using the Simulated Chip Sample Model. Chip sampling has been the simplest and at the same time most misunderstood sampling method there has ever been, but it has stood the test of time and is shown to be without a meaningful replacement. Despite the appearance of poor extraction compared to other methods, chip sampling is an acceptable technique when one understands and eliminates biases during and after extraction

Analysis and design of simple antenna geometries for broadband high frequency communications.

A thesis submitted to the Faculty of Engineering. University of the Witwatersrand. Johannesburg in fulfilment of the requirements for the degree of Doctor of Philosophy.The general argument of the thesis is that the design of broadband antennas demands a thorough understanding of the factors influencing the current distribution on antenna wires. Specifically. current distribution concepts are used to improve the evaluation and design of small broadband antennas for the high frequency (HF) 2 to 30 MHz range. The current distribution on an antenna governs its input impedance, radiation efficiency and radiation patterns. (Abbreviation abstract)Andrew Chakane 201

The Practice of Oral Medicine in South Africa

Oral medicine is a clinical discipline, practiced by periodontists, which concerns itself mostly with the nonsurgical management of oral mucosal diseases. Many of these diseases are rare and the discipline less well known – making it essential to identify the obstacles this discipline faces. The purpose of this study was to describe the private and academic practice of Oral Medicine. A self-administered, internet-based, questionnaire was distributed to South African periodontists which questioned the clinician’s competency, diseases managed, special investigations performed, referral sources, proportional time and monetary distribution of the discipline, and perceived barriers to the practice. Twenty-six periodontists completed the questionnaire. In comparison to periodontology and implantology, periodontists generally feel less competent, spend less time on, and receive less money from Oral Medicine. Lack of awareness of the speciality (55.6% - 59.3%) was identified as the biggest constraint, with only 11.2% of referrals received from medical doctors. Immune-mediated diseases (29.3%) and benign neoplasms (26.5%) are managed the most, and surgical biopsies (80.2%) are used most regularly to diagnose oral mucosal disease. Oral Medicine is still a lesser-known clinical speciality. Despite the heavy burden of HIV-related oral disease and oral mucosal malignancies, this speciality remains underutilised

Biochemical mechanisms for tolerance of citrus rootstocks against Phytophthora nicotianae

It was established that although the phytoalexin scoparone is associated with resistance/tolerance of citrus rootstocks to stem cancer caused by Phytophthora citrophthora, it does not dictate tolerance to root rot caused by P. nicotianae. It can therefore not be used as an indicator for tolerance to root rot. Results of the current study show that increase in total soluble phenolic concentrations in citrus roots after inoculation plays a key role in tolerance of citrus rootstocks against P. nicotianae root rot. Elevation of the levels of total phenolic compounds is therefore a part of the mechanism involved in rootstock resistance. As far as could be established, this finding has not been reported before in citrus. Determination of total soluble phenolics in citrus roots can therefore be used as a parameter in the screening of rootstocks for tolerance to P. nicotianae. Application of the systemic fungicide fosetyl-Al increased the total soluble phenolic concentrations in the roots more than infection with the pathogen alone. This provides evidence that the elevation of phenolic levels is involved in the mechanism of action of fosetyl-Al in control of Phytophthora root rot, therefore supporting an indirect antifungal mode of action. A unique chemical compound (U82) has been discovered that is associated only with tolerant rootstocks. If this yellow compound is a viable marker for resistance, it will certainly be a breakthrough in rootstock resistance research. Such a unique compound that is only associated with tolerant rootstocks could potentially be used in developing a more reliable high throughput screening technique for citrus rootstock resistance.Dissertation (MSc (Microbiology and Plant Pathology))--University of Pretoria, 2006.Microbiology and Plant Pathologyunrestricte

Geophysical And Geotechnical Investigation Of The Effect Of Blasting And Open Cast Mining On Worked-out Underground Mines And Modes Of Failure Of These Workings

To make the method of coalmining known as 'strip-mining' economically viable extremely large amounts of explosive need co be detonated in any one particular blast. This is to ensure enough rock is broken co keep the large earthmoving machinery, used in this type of mining, productive. This type of coal-mining operation was undertaken at Rieespruit Opencast Colliery in the Eastern Transvaal. Adjacent to this colliery is an exiting underground coalmine, and it was feared that the large amount of energy released by the surface blasting would be sufficient to damage the coal pillars. The investigation of the above problem formed the basis of this dissertation. Moving-coil seismometers were installed underground in what was considered^ a representative pillar, and continuous records of ground particle motion due to blasting were obtained from these instruments. Further field instrumentation consist of tape-recording decks and electronic packages to amplify and record the seismic signals was located on surface in an instrument hut built specifically for this purpose. The object of obtaining the above records was to establish damage criteria, whereby change weight could be estimated, for given distances from the blast to the underground workings, which would not cause appreciable damage underground. Propagation laws were established relating peak particle velocity, which is widely used as an indicator of possible damage, to the distance from the blast and either the square root or cube-root of the maximum charge weight per delay. These results are presented graphically and could be used to determine allowable charge weights to ensure a certain particle velocity is not exceeded

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Laboratory evaluation of a specimen transport medium for downstream molecular processing of sputum samples to detect Mycobacterium tuberculosis

BACKGROUND : Modern molecular-based approaches for the detection of Mycobacterium tuberculosis in sputum samples promise quicker and more accurate detection of cases. However, processing sputum samples at central diagnostic facilities provides a diagnostic approach, but requires a safe and efficient system that is not affected by transport delays and ambient temperature to be feasible. We evaluated the technical properties of PrimeStore®-Molecular Transport Medium(PS-MTM) for its ability to inactivate mycobacteria, ensuring stability of DNA over time at ambient temperatures and to assess the compatibility of the transport medium with DNA extraction systems. METHODS : Assessment of the transport medium for application of sputum samples processed for the detection of M. tuberculosis included the inactivation of M. tuberculosis in spiked sputum samples, compatibility of the medium with three commercial nucleic extraction systems and stability of DNA in the medium at ambient temperature over 28 days. We further performed a clinical laboratory evaluation on 256 sputum specimens sent for tuberculosis investigation. RESULTS : Complete inactivation ofM. tuberculosis occurredwithin 30 min of exposure at a ratio of 1:3 for sputumto PS-MTM. Sputum specimen in PS-MTMshowed very good compatibility with automated bead-based extraction systems, producing high DNA output (estimated lower limits of detection: ~170 CFU/ml). Furthermore, PS-MTM samples remained stable over 28 days at ambient temperature displaying no significant change over time in Ctvalues (b5% on a mean starting value of 22.47). Of the 256 clinical sputumspecimens, 10.2%were culture positive and 11.0% were positive by real-time PCR of PS-MTM samples. CONCLUSIONS : Collecting and transporting sputum from TB suspects in PS-MTM offer safe transport at ambient temperature, DNA stability for extended periods without cooling and specimens directly suitable for molecular testing. This novel approach may support introduction and further scale-up of molecular diagnostics for TB in resource-limited settings.http://www.elsevier.com/locate/jmicmeth2016-10-31hb201

Field evaluation of a novel preservation medium to transport sputum specimens for molecular detection of Mycobacterium tuberculosis in a rural African setting

Molecular tests are revolutionizing diagnosis of tuberculosis (TB). Disease burden is concentrated in resource-poor countries with inadequate infrastructure and capacity resulting in delays for specimens to reach the laboratory. We assessed the performance of an innovative method using a swab to inoculate sputum in a transport medium, PrimeStore® - Molecular Transport Medium (PS-MTM) for subsequent molecular detection of Mycobacterium tuberculosis at a centralized facility. A sputum specimen was obtained from suspected TB patients at rural healthcare facilities in South Africa and a swab taken and placed into PS-MTM from this specimen, prior to it being processed by either liquid culture or Xpert MTB/Rif assay (Xpert). A subset from a larger cohort study of a 141 patients was included for analysis, which included 47 laboratory-confirmed TB patients. M. tuberculosis was detected at 29% by culture, 29% by Xpert and 31% and 36% by real-time PCR of PS-MTM for the culture and Xpert specimen respectively. Concordance between the method under evaluation with culture was 82% (McNemar, p=0.55) and 84% (McNemar, p=0.05) for Xpert. Stratified by culture result, detection rate by real-time PCR of PS-MTM was similar to Xpert for patients with positive culture (p=0.32), but significantly higher if culture was negative (p=0.008). These results suggest that swab collection of sputum into PS-MTM provides a promising application for diagnosis of TB in rural healthcare settings thereby potentially improving the options available for the diagnosis of TB in countries incapable of applying decentralized high-tech molecular testing.Department of Medical Microbiology, University of Pretoria and Anova Health Institute.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-31562017-06-30hb2016Medical Microbiolog

Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains

A novel protocol for full-length Mycobacterium tuberculosis gene analysis of first- and second-line drug resistance was developed using the Ion Torrent Personal Genome Machine (PGM). Five genes—rpoB (rifampin), katG (isoniazid), pncA (pyrazinamide), gyrA (ofloxacin/fluoroquinolone), and rrs (aminoglycosides)—were amplified and sequenced, and results were compared to those obtained by genotypic Hain line probe assay (LPA) and phenotypic Bactec MGIT 960 analysis using 26 geographically diverse South African clinical isolates collected between July and November 2011. Ion Torrent sequencing exhibited 100% (26/26) concordance to phenotypic resistance obtained by MGIT 960 culture and genotypic rpoB and katG results by LPA. In several rifampin- resistant isolates, Ion Torrent sequencing revealed uncommon substitutions (H526R and D516G) that did not have a defined mutation by LPA. Importantly, previously uncharacterized mutations in rpoB (V194I), rrs (G878A), and pncA (Q122Stop) genes were observed. Ion Torrent sequencing may facilitate tracking and monitoring geographically diverse multidrug- resistant and extensively drug-resistant strains and could potentially be integrated into selected regional and reference settings throughout Africa, India, and China.http://jcm.asm.org/am201

Theology at the University of Pretoria - 100 years: (1917-2017) Past, present and future

In this scholarly book, a century’s theology presented by the Faculty of Theology at the University of Pretoria, is celebrated. All authors are academics or research associates of the University of Pretoria. A historical and futuristic overview with perspectives from the past, present and future, are examined. The past is not only portrayed by means of societal and scientific contributions and achievements, but the authors also reflect on malfunctions, ill behaviour and disappointments of church and theology, presented at the University of Pretoria within the South African context over 100 years. The book commences with a chapter in which institutional transformation is discussed, as well as the changes that demonstrate the role of the Faculty of Theology within a secular state university. It includes an explanation of the importance of research impact, research productivity and research reputation. Among various discipline indicators, the category Theology and Religion Studies plays a significant role in the measurement of world university rankings of universities. With regard to scientific and encyclopaedic content, the book focuses on the theological disciplines presented in the academic curricula: first the biblical sciences (Old and New Testament Studies), then the historical disciplines (Systematic Theology, Church History and Church Polity), and finally the practical disciplines (Practical Theology, Science of Religion and Missiology). The role of Religion Studies in a newly established Faculty of Theology and Religion not only enhances the diversity of interreligious tolerance and an atmosphere of dialogue, but it serves as platform to interconnect with the fields of Humanities, Social and Natural Sciences and other academic disciplines. In the conclusive part of the book, contributions highlight the role of the centres in the Faculty (Centre for Contextual Ministry and Centre for Sustainable Communities), as well as the continental and international footprints of the two theological journals whose title ownership is attached to the Faculty of Theology of the University of Pretoria, namely HTS Theological Studies and Verbum et Ecclesia. The methodology comprised in all the chapters amounts to a literature and contextual study. Since the book describes the histories of formal academic departments, these texts are of a descriptive, interpretative and critical character. Reference is made in some chapters to exegetical methods, like the historical critical methods. The target audience of the book is academic scholars and theologians, who specialise in the different fields of Theology, the Humanities and other Social Sciences. The book is also accessible to scholars of other academic disciplines outside these disciplines. The book comprises original research by several authors and is not plagiarised from other scientific publications of this nature