An assessment of the physical drivers for farm dam distribution in Midlands KwaZulu Natal, using GIS and Remote Sensing

This research proposal is done in partial fulfillment of the requirements of the Master of Science degree in GIS and Remote Sensing at Witwatersrand University, Johannesburg, South Africa March 2018.The interest in farm dams emanates mainly from their use for livestock watering, irrigation and fisheries enhancement on a sustainable basis. While management information on large dams in South Africa is largely available, it is lacking for farm dams which cumulatively store large volumes of water. As a result they are barely considered as part of the water resources of a river basin. Data acquisition methods for obtaining information about farm dams are costly, time consuming and labour intensive. This study was an attempt to map farm dams and establish the factors driving their spatial distribution pattern in the Midlands, KwaZulu-Natal, South Africa, using cost effective, time saving and less laborious GIS and remote sensing techniques. A classified April 2017 Landsat 8 satellite image was used to identify all water bodies in the Umgeni River basin U2 quaternary catchment (U2) while Google Earth was subsequently employed for differentiating farm dams from other water bodies. There were approximately 2000 water bodies that were identified by the classification. These included large national dams, pools in golf courses, ponds and disused mine dumps. A total of 864 farm dams in the U2 region quaternary catchment was observed. Six physical factors, namely slope, aspect, elevation, land use, soil type and geology were assessed to establish to what extent they influenced the siting of farm dams. The results indicated the importance of soils and land use as farm dams were mainly found in clusters in areas where agricultural farm land is also found since water is required for crop and livestock production. The influence of other factors such as slope, geology and elevation were observed in the spatial distribution maps. They all gave significant p-values in their univariate analysis. Of the six variables only aspect gave non-significant results while the rest were significant. A binary multivariate logistic regression was created for forecasting future farm dam sites and to establish which sites are poorly sited. The other four factors were fitted to the model except aspect and geology type which had no significant p-values in the model. The model had an Akaike information criterion (AIC) score of 293.42 and had the best combination of variables relative to other models. It was validated using 500 farm dam sites and it predicted 86% correctly.LG201

Optimal Piecewise Linear Regression Algorithm for QSAR Modelling

Quantitative Structure‐Activity Relationship (QSAR) models have been successfully applied to lead optimisation, virtual screening and other areas of drug discovery over the years. Recent studies, however, have focused on the development of models that are predictive but often not interpretable. In this article, we propose the application of a piecewise linear regression algorithm, OPLRAreg, to develop both predictive and interpretable QSAR models. The algorithm determines a feature to best separate the data into regions and identifies linear equations to predict the outcome variable in each region. A regularisation term is introduced to prevent overfitting problems and implicitly selects the most informative features. As OPLRAreg is based on mathematical programming, a flexible and transparent representation for optimisation problems, the algorithm also permits customised constraints to be easily added to the model. The proposed algorithm is presented as a more interpretable alternative to other commonly used machine learning algorithms and has shown comparable predictive accuracy to Random Forest, Support Vector Machine and Random Generalised Linear Model on tests with five QSAR data sets compiled from the ChEMBL database

No. 69: Calibrating Informal Cross-Border Trade in Southern Africa

Informal cross-border trade (ICBT) is a significant feature of regional trade and international mobility in Southern Africa. The exact number of participants and economic importance of this trade is unknown because no official statistics are collected. Despite its obvious presence at every border post throughout the SADC region, ICBT remains largely invisible to policy-makers. Indeed, in government circles it is more often associated with smuggling, tax evasion and illegality than with innovation, enterprise and job creation. On the research side, there is a growing body of case study evidence that ICBT plays a critical role in poverty alleviation, food security and household livelihoods in Southern Africa. But its overall character and significance is unknown. With this in mind, SAMP initiated a project to examine cross-border regional trade at a selection of important border posts throughout the region. This research led to a number of country reports that provided rich insights into ICBT in particular countries. This report combines the data collected by each of the country teams and analyses the data set as a whole. The first issue addressed in the report is whether ICBT traders are a homogenous group. The research shows that this is far from being the case and that more attention needs to be paid to different types of traders and trading activity. Second, the report examines the activities of cross-border traders including the types of goods traded, the sources of those goods and where they are sold. While the majority of traders purchase goods from formal outlets in their countries of destination, most of these goods enter the informal economy on their return home. Third, the report examines financial transactions at the borders showing that most traders pay extremely small amounts of duty, which hardly justifies the effort of collecting it. On the other hand, only a small minority collect the VAT they are owed when they leave the country of purchase. Finally, the report itemizes the problems and challenges faced by informal traders when crossing borders. In total, the SAMP survey covered 20 land border posts connecting 11 Southern African countries using a threefold methodology. First, all people crossing through the selected border posts were monitored over a 10-day period and the number of ICBT traders counted. Second, the interactions of traders with customs officials were observed and the types, value and volumes of goods declared and duties paid were recorded. Third, a sample of traders was interviewed using an origin and destination (O&D) survey. During the course of the exercise, more than 205,000 people, including 85,000 traders, were counted passing through these border posts. The transactions of over 5,500 traders with customs officials were monitored and over 4,500 traders were interviewed. The study demonstrates that informal cross-border is a complex phenomenon and not uniform across the region, or even through border posts of the same country. However, the overall volume of trade, duties paid and VAT foregone, as well as the types of goods and where they are produced, indicate that this sector of regional trade should be given much greater attention and support by governments of the region as well as regional organizations such as the Common Market for Eastern and Southern Africa (COMESA), SADC and the Southern African Customs Union (SACU). The major findings at the regional level were as follows: Demographically, women comprise a significant proportion of traders and constitute the majority of traders crossing through nearly half of the border posts surveyed, including one of the busiest at Beit Bridge between South Africa and Zimbabwe. At the same time, an unexpectedly large number of men were also involved in ICBT. Malawi and Zambia had significantly more male than female traders, for example. Most ICBT is bilateral in character; that is, traders tend to operate between their home country and one other country. Trading into a third country is comparatively rare. At the same time, the vast majority of traders crossing into a country with goods to sell are citizens of that country. ICBT by traders of other nationalities is uncommon. Although South Africa is a major source of goods purchased by traders, the absence of South African informal traders was very noticeable. The reasons why South Africans do not participate in ICBT requires further exploration but it stands in marked contrast to formal sector regional trade where South African companies predominate. ICBT is a neglected market opportunity for small-scale South African entrepreneurs and the obstacles to their participation need to be better understood. The majority of traders travelled frequently to other countries for short visits (sometimes for less than a day) to buy goods to sell in their home country, or to sell goods that they had bought for that purpose in their home country. Only 13% of respondents bought and sold goods while travelling (two-way trading). Frequency of tracel also varied both within and between countries, with traders in the Namibian (42%) and Zambian (25%) surveys being most likely to travel every day. Others travel at least once a week (Mozambique, 67%; Zambia, 34%). Some travel less frequently, but at least once a month. Very few stay more than a month in another country. The types of goods carried by informal cross-border traders vary widely, but at most borders the trade was dominated by food, especially groceries and fresh produce. Again, there was considerable variability at different borders. New clothes, household and electrical goods comprised a significant proportion of the stock of some cross-border traders. Other goods identified in the survey included second-hand clothing, petrol, alcohol, car parts and construction materials. Traders mostly source their goods from the formal sector of destination countries. A small proportion obtain their goods from informal markets in other countries. Many traders acted as wholesale importers of goods, selling the goods they carried across borders to vendors in informal markets. Others sold from their own stalls in informal markets, door to door, or to networks of family, friends and other individuals. A small proportion sold to retailers and restaurants in the formal sector. The value of goods carried by traders indicates the complexity and diversity of this sector. A significant cohort of traders appeared to be survivalists as many said they carried less than ZAR500 worth of goods. However, at least some of these traders travel frequently with low-value loads, rather than infrequently with high-value loads. Most traders travelled with loads in the range of ZAR1,001-5,000. A small cohort of traders travelled with loads worth more than ZAR15,000. Informal traders make a relatively significant contribution to duties collected at border posts. During the 10-day survey period at the 20 border posts, ZAR3,750,000 was collected from 1,780 traders. Duties collected varied between and within border posts. In some surveys the value of duties paid per trader was less than ZAR50. Interestingly, duties were being incorrectly collected at some borders between Southern African Customs Union countries (for example, between Botswana and Swaziland and South Africa). Traders said they were willing to pay duties, but wanted amounts reduced and the process to be more transparent. Although most traders buy their goods in the formal sector, few claim VAT when leaving the country of purchase. Many did not know they could do this while others said that the systems are too complex and time consuming. Traders who do not claim VAT back make an unintended contribution to the fiscus of the country where they buy their goods. Responses to questions about treatment from officials at the borders were generally positive but varied between and within border posts. Larger and busier posts generally received less favourable reviews. The scope and scale of informal cross-border trade across the SADC suggests that it makes a significant contribution to regional trade and the retail economies of the region and is consistent with the stated aims of both the SADC and COMESA to promote intra-regional trade. Small-scale cross-border trade could, if promoted and supported, provide a route to the development of pro-poor trade policies that could have a direct impact at the household level. If trade policies for the region are to be successful, the activities of these entrepreneurs need to be included in planning processes. ICBT comprises a significant component of regional economic activity for most countries in Southern Africa. It is highly visible at border posts throughout the region. Only amongst policy-makers and governments does it remain largely invisible

No. 02: The State of Urban Food Insecurity in Southern Africa

The number of people living in urban areas is rising rapidly in Southern Africa. By mid-century, the region is expected to be 60% urban. Rapid urbanization is leading to growing food insecurity in the region’s towns and cities. This paper presents the results of the first ever regional study of the prevalence of food insecurity in Southern Africa. The AFSUN food security household survey was conducted simultaneously in 2008-9 in 11 cities in 8 SADC countries. The results confirm high levels of food insecurity amongst the urban poor in terms of food availability, accessibility, reliability and dietary diversity. The survey provides important insights into the causes of food insecurity and the kinds of households that are most vulnerable to food insecurity. It also shows the heavy reliance of the urban poor on informal food sources and the growing importance of supermarket chains

How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality

The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays’ gene targets. This continuous quality monitoring rapidly identified delayed hybridization of in the Allplex & trade; SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; gene target failure in the TaqPath & trade; COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently gene delayed hybridization in the Xpress SARS-CoV-2 due to XBB.1.5. This near ;real-time; monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics

Microbe-host interplay in atopic dermatitis and psoriasis

Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis. The skin microbiota is analysed by 16S amplicon or whole genome sequencing and the skin transcriptome by microarrays, followed by integration of the data layers. We find that atopic dermatitis and psoriasis can be classified by distinct microbes, which differ from healthy volunteers microbiome composition. Atopic dermatitis is dominated by a single microbe (Staphylococcus aureus), and associated with a disease relevant host transcriptomic signature enriched for skin barrier function, tryptophan metabolism and immune activation. In contrast, psoriasis is characterized by co-occurring communities of microbes with weak associations with disease related gene expression. Our work provides a basis for biomarker discovery and targeted therapies in skin dysbiosis.Peer reviewe

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

A mathematical programming approach for sequential clustering of dynamic networks

A common analysis performed on dynamic networks is community structure detection, a challenging problem that aims to track the temporal evolution of network modules. An emerging area in this field is evolutionary clustering, where the community structure of a network snapshot is identified by taking into account both its current state as well as previous time points. Based on this concept, we have developed a mixed integer non-linear programming (MINLP) model, SeqMod, that sequentially clusters each snapshot of a dynamic network. The modularity metric is used to determine the quality of community structure of the current snapshot and the historical cost is accounted for by optimising the number of node pairs co-clustered at the previous time point that remain so in the current snapshot partition. Our method is tested on social networks of interactions among high school students, college students and members of the Brazilian Congress. We show that, for an adequate parameter setting, our algorithm detects the classes that these students belong more accurately than partitioning each time step individually or by partitioning the aggregated snapshots. Our method also detects drastic discontinuities in interaction patterns across network snapshots. Finally, we present comparative results with similar community detection methods for time-dependent networks from the literature. Overall, we illustrate the applicability of mathematical programming as a flexible, adaptable and systematic approach for these community detection problems

Deforestation rate and causes in Upper Manyame Sub-Catchment, Zimbabwe: Implications on achieving national climate change mitigation targets

The signing of the Paris Agreement at the UNFCCC Conference of the Parties (COP) 21 repositioned the global agenda toward sustainable forest management to address the threats of global warming. However, deforestation rates in many parts of the world continue to accelerate. The study evaluates the rate and causes of deforestation in Upper Manyame Sub-Catchment (UMSC) due to land use land cover (LULC) changes between 1990 and 2020. Landsat imagery analysis augmented by household questionnaire survey and key stakeholder interviews were used to assess the rate and cause of deforestation in UMSC. Over the 30 years, the sub-catchment lost 9.4% of its vegetation area due to land use changes. Vegetation loss was mainly due to urban expansion of Harare and its dormitory towns and the extensive peri‑urban agriculture mainly tobacco harvesting. Using the Markov Chain Cellular Automata model, the study estimated that in 2030 the catchment will lose approximately 3.3% of the current vegetation land cover area. This means a further reduction of the vegetation area from 20.1% to 16.8% in 2030. There is need for harmonisation of infrastructure development in Harare and the peri‑urban farming activities with policies that conserve forests such as the use of charcoal and eucalyptus plantations for curing tobacco instead of indigenous trees. This is critical if Zimbabwe is to meet its climate change mitigation targets in the Nationally Determined Contribution that promotes the implementation of Reducing Emissions from Deforestation and Forest Degradation (REDD+)