The recent morpho-tectonic history of the Vaalputs radioactive waste repository and environs

Thesis submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY Johannesburg, 1998This study deals with a region in the Northern Province, centred around Vaalputs, the National Radioactive Waste Disposal site. The study area constitutes two distinct geomorphological terrains: the western section consists of rugged, mountainous, granitic terrane, with steep cliffs that include weathered and silicified basement; the eastern section consists of the generally reatureless, gently undulating Bushmanland Plateau. The latter is characterized by low-amplitude palaeo-dunes which have a north-northeasterly trend. Precambrian crystalline rocks belonging to the Namaqualand Metamorphic Complex and late Palaeozoic (Karoo) rocks form the basement to Cretaceous and Cenozoic deposits in the region. Seismic studies in the Vaalputs area have indicated that there is appreciable seismic activity over a broad region of the northern Cape. In addition, satellite images and aerial photographs have recorded the presence of a network of lineaments in recent cover. The objectives of this study were to obtain a better understanding of the Late-Mesozoic and Cenozoic tectonic history of the region. Geomorphological, sedimentological and geological episodes were identified, described and correlated to the major tectonic events in the area. During the Late-Cretaceous the Dasdap Formation was deposited as a result of uplift along the marginal escarpment (west coast), in an alluvial fan setting. Crater sediments overlying olivine melilitites and kimberlites were also deposited contemporaneously with the Dasdap Formation. The late Cretaceous saw tropical conditions which caused extensive deep weathering and silicification of the Namaqualand Metamorphic Complex and the Dasdap Formation. This wet period was terminated approximately at the end of the Cretaceous with the onset of aridification. Tectonism largely in the form of reactivated older structures caused differences in the elevation of the palaeo-weathered and silicified surfaces and the initial deepening of a north-northwest oriented graben. Continued deepening of the graben during the Tertiary allowed for the deposition of the fluvial (floodouts) and aeolian Vaalputs sediments. Calcrete horizons preserved in the Vaalputs sequence of sediments indicate drier interludes and define previous land surfaces during tectonically less active periods or during periods of lower sediment supply. Postdepositional alteration and bioturbation resulted in the generally structureless and massive sediments of the Vaalputs Formation Overall desiccation throughout the Cenozoic finally gave rise to the aeolian dominated Gordonia Formation and present day microenvironments, consisting predominantly of aeolian deposits, deflation pans, and lag deposits. The source of the Gordonia sediments is primarily the underlying Vaalputs Formation which is in a state of degradation. Surface processes (primarily aeolian) have reworked and modified the surface into longitudinal dunes with a transverse component. Since the Cretaceous two primary stress fields have given rise to the numerous tectonic products observed in the study area. The study area is affected by two important uplift axes: the Griqualand-Transvaal and the Kamiesberge axes, which were active between the Miocene and the Plio-Pleistocene. On a regional scale the larger and older Pan African age (700 Ma.) faults are predominantly north-northwesterly trending and have been reactivated. At about 60 Ma ago, the minimum principal stress was most probably oriented to the NW causing extensive dip-slip faulting with a northeasterly strike. The stress field, active during most of the Cenozoic, had an ENE oriented minimum principal horizontal stress, and accompanied the development of a fault-bound sedimentary basin, which was filled by the sediments of the Vaalputs Formation. This stress field is probably still active as evidenced by numerous recent structural features

Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study

Background: Deep learning (DL) can extract predictive and prognostic biomarkers from routine pathology slides in colorectal cancer. For example, a DL test for the diagnosis of microsatellite instability (MSI) in CRC has been approved in 2022. Current approaches rely on convolutional neural networks (CNNs). Transformer networks are outperforming CNNs and are replacing them in many applications, but have not been used for biomarker prediction in cancer at a large scale. In addition, most DL approaches have been trained on small patient cohorts, which limits their clinical utility. Methods: In this study, we developed a new fully transformer-based pipeline for end-to-end biomarker prediction from pathology slides. We combine a pre-trained transformer encoder and a transformer network for patch aggregation, capable of yielding single and multi-target prediction at patient level. We train our pipeline on over 9,000 patients from 10 colorectal cancer cohorts. Results: A fully transformer-based approach massively improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training on a large multicenter cohort, we achieve a sensitivity of 0.97 with a negative predictive value of 0.99 for MSI prediction on surgical resection specimens. We demonstrate for the first time that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem. Interpretation: A fully transformer-based end-to-end pipeline trained on thousands of pathology slides yields clinical-grade performance for biomarker prediction on surgical resections and biopsies. Our new methods are freely available under an open source license

Using C. elegans to discover therapeutic compounds for ageing-associated neurodegenerative diseases

Age-associated neurodegenerative disorders such as Alzheimer’s disease are a major public health challenge, due to the demographic increase in the proportion of older individuals in society. However, the relatively few currently approved drugs for these conditions provide only symptomatic relief. A major goal of neurodegeneration research is therefore to identify potential new therapeutic compounds that can slow or even reverse disease progression, either by impacting directly on the neurodegenerative process or by activating endogenous physiological neuroprotective mechanisms that decline with ageing. This requires model systems that can recapitulate key features of human neurodegenerative diseases that are also amenable to compound screening approaches. Mammalian models are very powerful, but are prohibitively expensive for high-throughput drug screens. Given the highly conserved neurological pathways between mammals and invertebrates, Caenorhabditis elegans has emerged as a powerful tool for neuroprotective compound screening. Here we describe how C. elegans has been used to model various human ageing-associated neurodegenerative diseases and provide an extensive list of compounds that have therapeutic activity in these worm models and so may have translational potential

Lymphoepithelioma-like carcinoma of the vulva, an underrecognized entity? Case report with a single inguinal micrometastasis detected by sentinel node technique

This report describes an unusual EBV-negative lymphoepithelioma-like carcinoma of the vulva in a 73-year-old patient. The lesion was localised at the right minor labium and was resected by partial vulvectomy. A synchronous sentinel lymph node biopsy revealed a single micrometastasis in the right inguinal region, which prompted local radiotherapy. Follow-up nine months later showed only slight vulvar atrophy, without signs of local recurrence or distant metastases

Structural and petrological investigations of the Pretoria Saltpan Impact Crater and surrounding area

Thesis submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 1994The origin of the 1.13 kilometres-in-diameter Pretoria Saltpan crater, which is situated some 40 kilometres north-north-west of Pretoria has been a matter of controversy for the last century. [Abbreviated Abstract. Open document to view full version

Controls On the Genesis, Sedimentary Architecture, and Preservation Potential of Dryland Alluvial Successions In Stable Continental Interiors:Insights from the Incising Modder River, South Africa

Interpretations of the allogenic and autogenic controls on dryland alluvial successions are commonly hampered by incomplete knowledge of the sedimentology of modern dryland river floodplains, in part because of the limited subsurface sediment exposures available in typically stable or aggrading riverine settings. Along many valleys in the South African interior, however, river incision and associated formation of “dongas” (gullies and badland-type settings) provides extensive exposures of Cenozoic alluvial successions, which enable assessment of the controls on their genesis, sedimentary architecture, and preservation potential. This paper focuses on the incised Modder River at Erfkroon, Free State, located ∼ 1480 km (river distance) inland from the Atlantic Ocean. At Erfkroon, numerous dongas have formed in an ∼ 15-m-thick alluvial succession deposited within a narrow (\u3c 500 m) valley carved predominantly in erodible, fine-grained sedimentary rocks (“shales”). Facies associations include channel deposits that vary in texture from sandy gravel to silty sand, and overbank deposits consisting predominantly of sandy mud to muddy sand that have varying degrees of pedogenic overprinting. Younger deposits are stacked upon, crosscut, or onlap older deposits, indicating a complex history of cut and fill. Changing assemblages of associated fossil fauna and archaeological artifacts, luminescence ages, and paleosol characteristics demonstrate net sediment accumulation over at least the last 42 ka under humid to arid climatic conditions. By contrast, the present-day situation of deep channel and donga incision into bedrock appears to represent a new phase of sediment evacuation and valley deepening. Comparison with other incising dryland rivers in the South African interior suggests that: 1) while phases of cut and fill are driven largely by climatic fluctuations, major phases of incision into bedrock are controlled by breaching of downstream resistant rock barriers; 2) long-term sediment preservation is limited in narrow valleys that are subject to extended periods of base-level stability followed by episodic, major incisional phases, but is greater along broader valleys where rivers are undergoing lateral migration and more progressive long-term incision. Study of incising rivers such as the Modder can yield important insights into the controls on alluvial successions in stable continental interiors beyond the range of sea-level changes, which may help with the interpretation of inland alluvial valleys preserved in the geological record