Integrated geophysical investigation of the Karoo Basin, South Africa

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy Johannesburg, August 2015 School of Geosciences, University of the WitwatersrandThe possibility of extensive shale gas resources in the main Karoo Basin has resulted in a renewed focus on the basin, and particularly the Whitehill Formation. The main Karoo Basin has been the subject of geological studies since before the 1920s, but geophysical data provides an opportunity to shed new light on the basin architecture and formation. In this thesis, I use regional gravity, magnetic and borehole data over the basin, as well as vintage seismic data in the southern part of the basin. Modern computational capacity allows for more information to be extracted from these seismic data, and for these data to be better integrated with potential field data. The integration of datasets in a three-dimensional model (3D) has allowed for a better understanding of the shape of the basin and its internal structure, in turn shedding light on basin formation. A new depth map of the basin constructed using this extensive database confirms that the basin deepens from on- to off-craton. The basin is deepest along the northern boundary of the Cape Fold Belt (CFB), with a depth of ~4000 m in the southwestern Karoo and ~5000 m in the southeastern part of the basin. Sediment thickness ranges from ~5500 to 6000 m. The Whitehill Formation along this boundary reaches a depth of ~ 3000 m in the southwest and ~4000 m in the southeast. Despite limited boreholes in this region, the basin appears to broadly deepen to the southeast. These seismic and borehole data also allow for mapping of the Cape Supergroup pinch-out below the Karoo basin (32.6°S for the Bokkeveld and 32.4°S for the Table Mountain Group), with the basin reaching a thickness of around 4 km just north of the CFB. The gravity effect of these sediments in the south is not sufficient to account for the low of the Cape Isostatic Anomaly near Willowmore and Steytlerville. This ~45 mGal Bouguer gravity low dominates the central region of the southern Karoo at the northern border of the CFB. The seismic data for the first time show uplift of lower-density shales of the Ecca Group (1800 – 2650 kg/m3) in this region, and structural and seismic data suggest that these lower density sediments continue to depth of 11 to 12 km along normal and thrust faults in this region. Two-dimensional density models show that these shallow crustal features, as well as deeper lower crust compared to surrounding regions, account for the anomaly. These seismic and borehole data also allow for constraints to be placed on the distribution and geometry of the dolerite intrusions that intruded the basin after its formation, and in some cases impacted on the shale layer, to be constrained. The highest concentrations of dolerites are found in the northwest and east of the basin, pointing towards two magma sources. The region of lowest concentration is in the south-central part of the basin. Here the intrusions are confined to the Beaufort Group, ~1000 m shallower than the shale reservoir, suggesting it should be the focus of exploration efforts. These dolerite sills are shown to be between 5 and 30 km wide and are saucer-shaped with ~ 800 m vertical extent, and dips of between 2° and 8° on the edges. The sheets in the south of the basin extend for over 150 km, dipping at between 3° and 13°, and are imaged down to ~ 5 km. This change in dip of the sheets is linked to deformation within the Cape Fold Belt, with greater dips closer to the belt, although these sheets do not appear to intrude strata dipping at more than 15 to 20°. In order to understand the shape of the Karoo basin and construct a 3D model of the basin, an understanding is needed of the underlying basement rocks. The Beattie Magnetic Anomaly (BMA) that stretches across the entire southern part of the basin forms part of the basement Namaqua-Natal Belt. Filtered magnetic data confirm that the Namaqua and Natal Belts are two separate regions with different magnetic characteristics, which is taken into account during modelling. The BMA is shown to be part of a group of linear magnetic anomalies making up the Natal Belt. The anomaly itself will therefore not have an individual effect on basin formation, and the effect of the Natal Belt as a whole will have to be investigated. An in-depth study of outcrops associated with one of these linear magnetic anomalies on the east coast of South Africa suggest the BMA can be attributed to regions of highly magnetic (10 to 100 x 10-3 SI) supracrustal rocks in Proterozoic shear zones. Along two-dimensional magnetic models in the southwestern Karoo constrained by seismic data, these magnetic zones are modelled as dipping slabs with horizontal extents of ~20-60 km and vertical extents of ~10-15 km. Body densities range from 2800- 2940 kg/m3 and magnetic susceptibilities from 10 to 100 x 10-3 SI. These, as well as other geophysical and geological constraints, are used to construct a 3D model of the basin down to 300 km. Relatively well-constrained crustal structure allows for inversion modelling of lithospheric mantle densities using GOCE satellite gravity data, with results in-line with xenolith data. These results confirm the existence of lower density mantle below the craton (~3270 kg/m3) that could contribute to the buoyancy of the craton, and an almost 50 kg/m3 density increase in the lithospheric mantle below the surrounding Proterozoic belts. It is this change in lithospheric density along with changes in Moho depths that isostatically compensate a large portion of South Africa’s high topography (<1200 m). The topography higher than 1200 m along the edge of the plateau, along the Great Escarpment, are shown to be accommodated by an asthenospheric buoyancy anomaly with a density contrast of around 40 kg/m3, while still mimicking the Bouguer gravity field. These findings are in line with recent tomographic studies below Africa suggesting an “African Superplume” or “Large Low Velocity Seismic Province” in the deep mantle. The basin sediment thickness maps were further used to investigate the formation of the main Karoo Basin. This was accomplished by studying the past flexure of the Whitehill Formation using north-south two-dimensional (2D) profiles. Deepening of the formation from ~3000 m in the southwest to ~4000 m in the southeast is explained using the concept of isostasy, i.e., an infinite elastic beam that is subjected to an increasing load size across the Cape Fold Belt. Load height values increase from 4 km in the southwest to 8 km in the southeast. This larger load is attributed here to “locking” along a subduction zone further to the south. The effective elastic thickness (Te) of the beam also increases from around 50 km over the Namaqua and Natal Belts in the southwest to 80 km over the Kaapvaal Craton and Natal Belt in the southeast. The changes in Te values do not correlate with changes in terrane, i.e., a north to south change, as previously though. The large extent and shape of the Karoo basin can therefore, in general, be explained as a flexural basin, with the strength of the basement increasing towards the southeast. Therefore, while factors such as mantle flow could have contributed towards basin formation, reducing the load size needed, it is no longer necessary in order to account for the large extent of the basin. This flexure model breaks down further to the southeast, most likely due to a very high Te value. This could be the reason for later plate break in this region during Gondwana breakup. It is inferred that this increase in Te is linked to the buoyancy anomaly in the asthenospheric mantle

A computer software system for integration and analysis of grid-based remote sensing data with other natural resource data. Remote Sensing Project

A computer-based information system is described designed to assist in the integration of commonly available spatial data for regional planning and resource analysis. The Resource Analysis Program (RAP) provides a variety of analytical and mapping phases for single factor or multi-factor analyses. The unique analytical and graphic capabilities of RAP are demonstrated with a study conducted in Windsor Township, Eaton County, Michigan. Soil, land cover/use, topographic and geological maps were used as a data base to develope an eleven map portfolio. The major themes of the portfolio are land cover/use, non-point water pollution, waste disposal, and ground water recharge

Land use inventory through merging of LANDSAT (satellite), aerial photography and map sources

There are no author-identified significant results in this report

Ventriculoperitoneal shunt failures at Red Cross War Memorial Children's Hospital

Introduction: Ventriculoperitoneal shunt (VP shunt) insertion is one of the mainstays of treatment of hydrocephalus and although very effective, a high rate of shunt failure persists globally. The purpose of the study was to quantify the ventriculoperitoneal shunt failure rate at Red Cross War Memorial Children’s Hospital (RCWMCH) and assess potential factors contributing to shunt failures. Methods: A retrospective review of VP shunts done at RCWMCH between August 2015 through December 2019 was performed. Operative notes, discharge summaries and patient folders were reviewed to collect information about patient age, aetiology of hydrocephalus, index vs revision shunt, shunt system and other noticeable variables. Overall shunt failure was recorded. Univariate and multivariate models were used to determine causal relationship. Results: Four hundred and ninety-four VP shunt operations were performed on 340 patients with 48.8% being index shunts and 51.2% revision shunts. The average patient age was 3.4 months. The total VP shunt failure rate over the study period was 31.2%, with a 7.3% infection rate, 13.6% blockage and 3.6% disconnection rate. The most common aetiologies were post-infectious hydrocephalus 29.4%, myelomeningocele 19.7% and premature intraventricular haemorrhage 14.1%. Orbis-sigma II (OSVII), distal slit valves and antibiotic-impregnated catheters were used most frequently. Failure rates were highest in the revision group, 34.7% compared to 27.3% in index shunts. Sixty-five percent (65%) of the head circumferences measured were above the + 3 Z score (> 90th centile). Conclusion: VP shunt failure occurs most commonly in revision surgery, and care should be taken at the index operation to reduce failure risk. Surgeon level, duration of surgery, aetiology of hydrocephalus and shunt system used did not influence overall failure rates. A closer look at larger head circumferences, their effect on shunt systems and the socio-economic factors behind late presentations should be investigated further in the future

Biomarkers of cerebral injury and inflammation in pediatric tuberculous meningitis

Background Tuberculous meningitis (TBM) leads to death or disability in half the affected individuals. Tools to assess severity and predict outcome are lacking. Neuro-specific biomarkers could serve as markers of the severity and evolution of brain injury, but have not been widely explored in TBM. We examined biomarkers of neurological injury (neuromarkers) and inflammation in pediatric TBM and their association with outcome. Methods Blood and cerebrospinal fluid (CSF) of children with TBM and hydrocephalus taken on admission and over 3 weeks were analysed for neuromarkers S100B, neuron-specific enolase (NSE) and glial fibrillary acidic protein (GFAP), and multiple inflammatory markers. Results were compared with 2 control groups; patients with 1) a fatty filum (abnormal filum terminale of the spinal cord), and 2) pulmonary tuberculosis (pTB). Imaging was conducted on admission and at 3 weeks. Outcome was assessed at 6 months. Results Data were collected from 44 TBM cases (median age 3.3 [0.3–13.1] years), 11 fatty filum (median age 2.8 [0.8–8] years) and 9 pTB controls (median age 3.7 [1.3–11.8] years). Seven cases (16%) died and 16 (36%) had disabilities. Neuromarkers and inflammatory markers were elevated in CSF on admission and for up to 3 weeks, but not in serum. Initial and highest concentrations in week 1 of S100B and NSE were associated with poor outcome, as were highest concentration overall and an increasing profile over time in S100B, NSE and GFAP. Combined neuromarker concentrations increased over time in patients who died, whereas inflammatory markers decreased. Cerebral infarcts were associated with highest overall neuromarker concentrations and an increasing profile over time. Tuberculomas were associated with elevated IL-12p40, IP-10 and MCP-1 concentrations, whereas infarcts were associated with elevated TNF-α, MIP-1α, IL-6 and IL-8. Conclusion CSF neuromarkers are promising biomarkers of injury severity and are predictive of mortality. An increasing trend suggested ongoing brain injury, even though markers of inflammation declined with treatment. These findings could offer novel insight into the pathophysiology of TBM

The pharmacokinetics of enteral antituberculosis drugs in patients requiring intensive care

Background. There is a paucity of data on the pharmacokinetics of fixed-dose combination enteral antituberculosis treatment in critically ill patients. Objectives. To establish the pharmacokinetic profile of a fixed-dose combination of rifampicin, isoniazid, pyrazinamide and ethambutol given according to weight via a nasogastric tube to patients admitted to an intensive care unit (ICU). Methods. We conducted a prospective, observational study on 10 patients (mean age 32 years, 6 male) admitted to an ICU and treated for tuberculosis (TB). Serum concentrations of the drugs were determined at eight predetermined intervals over 24 hours by means of high-performance liquid chromatography. Results. The therapeutic maximum plasma concentration (Cmax) for rifampicin at time to peak concentration was achieved in only 4 patients, whereas 2 did not achieve therapeutic Cmax for isoniazid. No patient reached sub-therapeutic Cmax for pyrazinamide (6 were within and 4 above therapeutic range). Three patients reached sub-therapeutic Cmax for ethambutol, and 6 patients were within and 1 above the therapeutic range. Patients with a sub-therapeutic rifampicin level had a higher mean Acute Physiology and Chronic Health Evaluation II (APACHE II) score (p=0.03) and a lower estimated glomerular filtration rate (GFR) (p=0.03). Conclusions. A fixed-dose combination tablet, crushed and mixed with water, given according to weight via a nasogastric tube to patients with TB admitted to an ICU resulted in sub-therapeutic rifampicin plasma concentrations in the majority of patients, whereas the other drugs had a more favourable pharmacokinetic profile. Patients with a sub-therapeutic rifampicin concentration had a higher APACHE II score and a lower estimated GFR, which may contribute to suboptimal outcomes in critically ill patients. Studies in other settings have reported similar proportions of patients with ‘sub-therapeutic’ rifampicin concentrations

The pharmacokinetics of enteral antituberculosis drugs in patients requiring intensive care

The original publication is available at http://www.samj.org.zaBackground. There is a paucity of data on the pharmacokinetics of fixed-dose combination enteral antituberculosis treatment in critically ill patients. Objectives. To establish the pharmacokinetic profile of a fixed-dose combination of rifampicin, isoniazid, pyrazinamide and ethambutol given according to weight via a nasogastric tube to patients admitted to an intensive care unit (ICU). Methods. We conducted a prospective, observational study on 10 patients (mean age 32 years, 6 male) admitted to an ICU and treated for tuberculosis (TB). Serum concentrations of the drugs were determined at eight predetermined intervals over 24 hours by means of highperformance liquid chromatography. Results. The therapeutic maximum plasma concentration (Cmax) for rifampicin at time to peak concentration was achieved in only 4 patients, whereas 2 did not achieve therapeutic Cmax for isoniazid. No patient reached sub-therapeutic Cmax for pyrazinamide (6 were within and 4 above therapeutic range). Three patients reached sub-therapeutic Cmax for ethambutol, and 6 patients were within and 1 above the therapeutic range. Patients with a sub-therapeutic rifampicin level had a higher mean Acute Physiology and Chronic Health Evaluation II (APACHE II) score (p=0.03) and a lower estimated glomerular filtration rate (GFR) (p=0.03). Conclusions. A fixed-dose combination tablet, crushed and mixed with water, given according to weight via a nasogastric tube to patients with TB admitted to an ICU resulted in sub-therapeutic rifampicin plasma concentrations in the majority of patients, whereas the other drugs had a more favourable pharmacokinetic profile. Patients with a sub-therapeutic rifampicin concentration had a higher APACHE II score and a lower estimated GFR, which may contribute to suboptimal outcomes in critically ill patients. Studies in other settings have reported similar proportions of patients with ‘sub-therapeutic’ rifampicin concentrations.Publishers' Versio

Structural and luminescence imaging and characterisation of semiconductors in the scanning electron microscope

The scanning electron microscopy techniques of electron backscatter diffraction (EBSD), electron channelling contrast imaging (ECCI) and hyperspectral cathodoluminescence imaging (CL) provide complementary information on the structural and luminescence properties of materials rapidly and non-destructively, with a spatial resolution of tens of nanometres. EBSD provides crystal orientation, crystal phase and strain analysis, whilst ECCI is used to determine the planar distribution of extended defects over a large area of a given sample. CL reveals the influence of crystal structure, composition and strain on intrinsic luminescence and/or reveals defect-related luminescence. Dark features are also observed in CL images where carrier recombination at defects is non-radiative. The combination of these techniques is a powerful approach to clarifying the role of crystallography and extended defects on a materials' light emission properties. Here we describe the EBSD, ECCI and CL techniques and illustrate their use for investigating the structural and light emitting properties of UV-emitting nitride semiconductor structures. We discuss our investigations of the type, density and distribution of defects in GaN, AlN and AlGaN thin films and also discuss the determination of the polarity of GaN nanowires