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Deferred slanted-edge analysis: A unified approach to Spatial Frequency Response measurement on distorted images and Colour Filter Array subsets
(2018-03) Van den Bergh, Frans
The slanted-edge method of spatial frequency response (SFR) measurement is usually applied to grayscale images under the assumption that any distortion of the expected straight edge is negligible. By decoupling the edge orientation and position estimation step from the edge spread function construction step, it is shown in this paper that the slanted-edge method can be extended to allow it to be applied to images suffering from significant geometric distortion, such as produced by equiangular fisheye lenses. This same decoupling also allows the slanted-edge method to be applied directly to Bayer-mosaicked images so that the SFR of the color filter array subsets can be measured directly without the unwanted influence of demosaicking artifacts. Numerical simulation results are presented to demonstrate the efficacy of the proposed deferred slanted-edge method in relation to existing methods.
Defining the South African acute respiratory infectious disease season
(2023-01) Motlogeloa, O; Fitchett, JM; Sweijd, Neville A
The acute respiratory infectious disease season, or colloquially the “flu season”, is defined as the annually recurring period characterized by the prevalence of an outbreak of acute respiratory infectious diseases. It has been widely agreed that this season spans the winter period globally, but the precise timing or intensity of the season onset in South Africa is not well defined. This limits the efficacy of the public health sector to vaccinate for influenza timeously and for health facilities to synchronize efficiently for an increase in cases. This study explores the statistical intensity thresholds in defining this season to determine the start and finish date of the acute respiratory infectious disease season in South Africa. Two sets of data were utilized: public-sector hospitalization data that included laboratory-tested RSV and influenza cases and private-sector medical insurance claims under ICD 10 codes J111, J118, J110, and J00. Using the intensity threshold methodology proposed by the US CDC in 2017, various thresholds were tested for alignment with the nineteen-week flu season as proposed by the South African NICD. This resulted in varying thresholds for each province. The respiratory disease season commences in May and ends in September. These findings were seen in hospitalization cases and medical insurance claim cases, particularly with influenza-positive cases in Baragwanath hospital for the year 2019. These statistically determined intensity thresholds and timing of the acute respiratory infectious disease season allow for improved surveillance and preparedness among the public and private healthcare.
Efficacy of a plant-produced clade 2.3.4.4 H5 influenza virus-like particle vaccine in layer hens
(2022-06) Abolnik, C; O'Kennedy, Maretha M; Murphy, MA; Wandrag, DBR
Outbreaks caused by Goose/Guangdong H5 highly pathogenic avian influenza (HPAI)-lineage viruses continue to occur in unprecedented numbers throughout Eurasia, the Middle East and Africa, causing billions of dollars in economic losses and the deaths or destruction of hundreds of millions of poultry, and pose a zoonotic threat. Here, a recombinant virus-like particle (VLP) displaying the hemagglutinin protein of a clade 2.3.4.4b H5N8 HPAI strain was produced in tobacco plants (Nicotiana benthamiana) and its immunogenicity with four commercial adjuvants was compared in layer hens. After two immunizations with 250 hemagglutinating unit doses, hens that received intramuscular injections of H5 VLPs formulated with Emulsigen D, Emulsigen P or Montanide ISA 71VG seroconverted with hemagglutination inhibition geometric mean titres (GMTs) of 7.3 log2 (± 1.17), 8 log2 (± 1.08) and 7.9 log2 (±1.07), respectively, but the GMT of hens inoculated by eye drop with VLPs plus Carbigen only reached 2.05 log2 (± 1.64). The H5 VLP plus Emulsigen-P vaccinated hens and a sham-vaccinated group were then challenged with a high dose of the homologous H5N8 HPAI virus. Vaccinated hens were completely protected and showed no clinical signs, whereas the sham-vaccinated birds all died within 3–4 days. The average oropharyngeal shedding in vaccinated hens was reduced by 3,487-fold and 472-fold on days 2 and 3 post challenge, respectively, whereas average cloacal shedding was reduced by 2,360,098-fold and 15,608-fold on days 2 and 3, respectively, compared to the sham-vaccinated controls. No virus was detected in the vaccinated hens after day 8 post challenge, and the plant-produced H5 VLP vaccine completely prevented H5N8 HPAI virus transmission to eggs. This highly efficacious, safe and non-toxic plant-produced H5 VLP vaccine with DIVA (differentiation of infected from vaccinated animals) capability could be rapidly produced with a yield of at least 85,000 doses per Kg of plant leaf material.
Exploring functional dynamics of innovation for inclusive development: Event history analysis of an ICT4D project
(2021-08) Maarsingh, B; Grobbelaar, SS; Uriona-Maldonado, M; Herselman, Martha E
Information and Communication Technologies for Development (ICT4D) projects aim to improve the living conditions of marginalized communities. However, ICT4D interventions have high failure rates. We draw on the Technological Innovation for Inclusive Development Systems (TI4IDS) framework, which argues that ICT4D projects are embedded in a system affected by many different actors, stakeholders and institutions. We analyze this through a qualitative exploratory case study of an ICT4D project for Elderly Rural Women in Mafarafara in Limpopo, South Africa. We map a set of TI4IDS functions through event history analysis (EHA) to explore how ICT4D projects may be implemented. We draw conclusions regarding the dynamic exhibited in the projects and show how the focus shifted from the development of knowledge and guidance of search to knowledge diffusion during the uptake of the technology with a more significant focus on resource mobilization and market formulation towards the later phases.
In living colour – South African aquatic scientists make a splash in biodiversity campaign
(2024-01) Lain, Elisabeth J; Smith, Marié E
A new age of satellite remote sensing is upon us. High-tech sensors capable of imaging the earth at over 100 spectral wavebands are now a reality. These sensors, known as hyperspectral radiometers, capture very fine spectral features of the colours emitted from the surface of the earth and its water bodies, offering opportunities for improved satellite-based environmental monitoring. South African researchers are primed and ready to make use of these new technologies to derive water quality parameters from hyperspectral radiometric measurements by applying it towards monitoring our diverse estuaries, dams and oceans. So writes Lisl Lain and Marie Smith of CSIR.
Land use induced land cover changes and future scenarios in extent of Miombo woodland and Dambo ecosystems in the Copperbelt province of Zambia
(2021-08) Malunga, MM; Cho, Moses A; Chirwa, PW; Yerokun, OA
The pattern of Miombo woodland conversion to other land uses and the attendant impacts on vital Miombo ecosystems such as dambos is not well understood. Using the Copperbelt province of Zambia as a case study, we assessed the spatio-temporal patterns of Miombo woodland and dambo conversion to other land uses between 1984 and 2016 and predicted the changes to 2050. The effects of land use land cover change (LULCC) on the extent of Miombo woodlands and dambos was determined by intersecting layers of croplands, settlements, plantations, grasslands and barelands on woodland and dambo pixels. Prediction of future LULCC was done using the land change modeller (LCM) in TerrSet. It was observed that in the period between 1984 and 2016, woodlands decreased by 17.9% while dambos increased by 4.9%. The two classes were predicted to lose 26.4% and 2.0%, respectively, by 2050. Conversion to cropland was the highest contributor to woodland loss, accounting for 57.5% of total loss by 2016, and projected to reach 67.6% by 2050. Similarly, establishment of cropland was shown to result into 53.5% (2016) and 58.9% (2050) of loss of dambos. Expansion of croplands caused a decline in woodlands and dambos. Therefore, sustainable agriculture should be adopted.
Multi-threaded compression of Earth observation time-series data
(2017-03) Swanepoel, Derick; Van den Bergh, Frans
Earth observation data are typically compressed using general-purpose single-threaded compression algorithms that operate at a fraction of the bandwidth of modern storage and processing systems. We present evidence that recently developed multi-threaded compression codecs offer substantial benefits over widely used single-threaded codecs in terms of compression efficiency when applied to a selection of moderate resolution imaging spectroradiometer (MODIS) datasets stored in the HDF5 format. Compression codecs from the LZ77 and Rice families are shown to vary in efficacy when applied to different MODIS data products, highlighting the need for compression strategies to be tailored to different classes of data. We also introduce LPC-Rice, a new multi-threaded codec, that performs particularly well when applied to time-series data.
Potential opportunities to convert waste to bio-based chemicals at an industrial scale in South Africa
(2023-10) Mandree, PM; Thopil, GA; Ramchuran, Santosh O
Globally, greater than 30% of waste is disposed of in some form of landfill, and it is estimated that annual waste-related emissions will increase by up to 76% by 2050. Emissions arising from fossil fuel-derived products and waste disposal in landfills have prompted the development of alternative technologies that utilize renewable resources. Biomass feedstock is being investigated globally to produce renewable fuels and chemicals. Globally, crop-based biomass and waste biomass are the major feedstocks for chemical production, and the market value of crop-based biomass is expected to increase at the fastest rate. South America, Europe, and North America are currently the global leaders in renewable or bio-based chemical production. In South Africa (SA), the country is still heavily reliant on landfilling as a waste solution. Wastes from agricultural production processes in SA are considered promising feedstocks for beneficiation opportunities to produce bio-based chemicals. The second-generation (2G) agricultural feedstocks that can be used in SA include fruit waste; sugarcane by-products and waste; forestry, timber, pulp, and paper waste; and invasive alien plants. Fermentation, or “green chemistry” technologies, can be used to convert various feedstocks into bio-based chemicals. Bio-based chemicals may be used as drop-in substitutes for existing petrochemical products, for use in end-user industries such as automotive and transportation, textiles, pharmaceuticals, consumer and home appliances, healthcare, and food and beverages. Bioethanol, specifically, can be used in transport fuel, as feedstock for power generation, as an energy source for fuel cells along with hydrogen, and as feedstock in the chemicals industry. Bio-butanol, an olefin derivative, can be used as a drop-in replacement for petroleum-based butanol in all its applications. Different monomers of bio-based chemicals can be used to produce biopolymers, polyhydroxyalkanoates (PHAs), and polylactic acid (PLA), which are subsequently used to produce bioplastics. A total of 25 bio-based chemicals and the technology used to produce them are summarized in this paper. Overall, bioethanol remains the dominant sugar platform product globally. Drawing on global trends, the potential options for the South African market include bioethanol, n-butanol, acetic acid, and lactic acid. It is estimated that the conversion of 70% of the lignocellulosic biomass available in SA would meet 24% of the country’s liquid fuel requirement as a bioethanol equivalent. The most feasible sources of lignocellulosic biomass or waste for beneficiation in SA are generated by the agricultural sector, including sugarcane by-products and waste. Taking into consideration the abundance of lignocellulosic biomass, adequate market segment sizes, and socio-economic factors, it is apparent that there are potential opportunities to investigate the co-production of bioethanol with lactic acid or other bio-based chemicals on an industrial scale.
Robust edge spread function construction methods to counter poor sample spacing uniformity in the slanted-edge method
(2019-06) Van den Bergh, Frans
The slanted-edge method describes an algorithm for measuring the spatial frequency response (SFR) of digital imaging systems. The method can be applied to edges oriented at nearly any angle, but there are some angles that cause simplistic implementations of the algorithm to fail, or produce inaccurate measurements. These angle-dependent phenomena are demonstrated to stem from a lack of uniformity in supersample spacing in the edge spread function (ESF). Two well-known slanted-edge implementation variants are adapted to minimize edge orientation dependent errors. These robust slanted-edge implementations are demonstrated yield accurate measurements, regardless of edge orientation angle or moderate image noise.
Sustainable co-management of acid mine drainage with struvite synthesis effluent: Pragmatic synergies in circular economy
(2023-04) Masindi, Vhahangwele; Mbhele, Nkhangweleni R; Foteinis, Spyros
Herein, the alkaline supernatant of a struvite recovery system from municipal wastewater was successfully co-managed with acid mine drainage (AMD). Various ratios (v/v) of AMD to struvite supernatant were examined, and the quality of the passively co-treated effluent and of the generated sludge were examined using state-of-the-art analytical techniques including ICP-OES, FE-SEM/FIB/EDX, XRD, XRF, and FTIR. The optimum ratio was 1:9, where metals and sulphate were largely removed from AMD, i.e., from higher to lower score Fe (~100%) = Pb (~100%) = Ni (99.6%) = Cu (96%) = As (95%) = Al (93.7%) = Zn (92.7%) > Ca (90.5%) > Mn (90%) = Cr (90%) > sulphate (88%) > Mg (85.7%), thus implying that opportunities for mineral recovery could be pursued. The pH of the final effluent was regulated to acceptable discharge levels, i.e., 6.5 instead of 2.2 (AMD) and 10.5 (struvite supernatant), while a notable reduction in the electrical conductivity further implied the attenuation of contaminants. Overall, results suggest the feasibility of the passive co-treatment of these wastewater matrices and that opportunities for direct scaling up exist (e.g., using waste stabilization ponds). Furthermore, apart from the initial recovery of struvite from municipal wastewater, metals could also be recovered from AMD and water could be reclaimed, therefore introducing circular economy and zero liquid discharge in wastewater treatment and management.
Systems dynamics approach for modelling South Africa’s response to COVID-19: A “what if” scenario
(2021-02) Mutanga, Shingirirai S; Ngungu, M; Tshililo, FP; Kaggwa, M
Background: Many countries in the world are still struggling to control COVID-19 pandemic. As of April 28, 2020, South Africa reported the highest number of COVID-19 cases in Sub- Sahara Africa. The country took aggressive steps to control the spread of the virus including setting a national command team for COVID-19 and putting the country on a complete lockdown for more than 100 days. Evidence across most countries has shown that, it is vital to monitor the progression of pandemics and assess the effects of various public health measures, such as lockdowns. Countries need to have scientific tools to assist in monitoring and assessing the effectiveness of mitigation interventions. The objective of this study was thus to assess the extent to which a systems dynamics model can forecast COVID-19 infections in South Africa and be a useful tool in evaluating government interventions to manage the epidemic through 'what if' simulations. Design and Methods: This study presents a systems dynamics model (SD) of the COVID-19 infection in South Africa, as one of such tools. The development of the SD model in this study is grounded in design science research which fundamentally builds on prior research of modelling complex systems. Results: The SD model satisfactorily replicates the general trend of COVID-19 infections and recovery for South Africa within the first 100 days of the pandemic. The model further confirms that the decision to lockdown the country was a right one, otherwise the country's health capacity would have been overwhelmed. Going forward, the model predicts that the level of infection in the country will peak towards the last quarter of 2020, and thereafter start to decline. Conclusions: Ultimately, the model structure and simulations suggest that a systems dynamics model can be a useful tool in monitoring, predicting and testing interventions to manage COVID-19 with an acceptable margin of error. Moreover, the model can be developed further to include more variables as more facts on the COVID-19 emerge.
Understanding diarrhoeal diseases in response to climate variability and drought in Cape Town, South Africa: A mixed methods approach
(2023-08) Lee, TT; Dalvie, MA; Röösli, MS; Merten, S; Kwiatkowski, M; Sweijd, Neville A; Cissé, G; Mahomed, H
Background: The climate of southern Africa is expected to become hotter and drier with more frequent severe droughts and the incidence of diarrhoea to increase. From 2015 to 2018, Cape Town, South Africa, experienced a severe drought which resulted in extreme water conservation efforts. We aimed to gain a more holistic understanding of the relationship between diarrhoea in young children and climate variability in a system stressed by water scarcity. Methods: Using a mixed-methods approach, we explored diarrhoeal disease incidence in children under 5 years between 2010 to 2019 in Cape Town, primarily in the public health system through routinely collected diarrhoeal incidence and weather station data. We developed a negative binomial regression model to understand the relationship between temperature, precipitation, and relative humidity on incidence of diarrhoea with dehydration. We conducted in-depth interviews with stakeholders in the fields of health, environment, and human development on perceptions around diarrhoea and health-related interventions both prior to and over the drought, and analysed them through the framework method. Results: From diarrhoeal incidence data, the diarrhoea with dehydration incidence decreased over the decade studied, e.g. reduction of 64.7% in 2019 [95% confidence interval (CI): 5.5–7.2%] compared to 2010, with no increase during the severe drought period. Over the hot dry diarrhoeal season (November to May), the monthly diarrhoea with dehydration incidence increased by 7.4% (95% CI: 4.5–10.3%) per 1 °C increase in temperature and 2.6% (95% CI: 1.7–3.5%) per 1% increase in relative humidity in the unlagged model. Stakeholder interviews found that extensive and sustained diarrhoeal interventions were perceived to be responsible for the overall reduction in diarrhoeal incidence and mortality over the prior decade. During the drought, as diarrhoeal interventions were maintained, the expected increase in incidence in the public health sector did not occur. Conclusions: We found that that diarrhoeal incidence has decreased over the last decade and that incidence is strongly influenced by local temperature and humidity, particularly over the hot dry season. While climate change and extreme weather events especially stress systems supporting vulnerable populations such as young children, maintaining strong and consistent public health interventions helps to reduce negative health impacts.

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