A novel generative adversarial networks modelling for the class imbalance problem in high dimensional omics data

Class imbalance remains a large problem in high-throughput omics analyses, causing bias towards the over-represented class when training machine learning-based classifiers. Oversampling is a common method used to balance classes, allowing for better generalization of the training data. More naive approaches can introduce other biases into the data, being especially sensitive to inaccuracies in the training data, a problem considering the characteristically noisy data obtained in healthcare. This is especially a problem with high-dimensional data. A generative adversarial network-based method is proposed for creating synthetic samples from small, high-dimensional data, to improve upon other more naive generative approaches. The method was compared with ‘synthetic minority over-sampling technique’ (SMOTE) and ‘random oversampling’ (RO). Generative methods were validated by training classifiers on the balanced data

Should we reduce the use of plastics in agriculture?

Plastic use in agriculture has transformed agricultural systems worldwide, facilitating the production of fresh produce in yield-limiting conditions, extend the growing season and improving the food security of many regions. As global food systems come under increasing pressure from the future impacts of climate change and other global crises, the need to provide a stable, readily available supply of healthy, nutritious produce is increasingly important. Whilst plasticulture is considered an effective measure to maintain food security and increase agricultural productivity, there is a global call to reduce plastic use in agriculture. The impact of plastics from ‘cradle-to-grave’ are overwhelmingly negative, thought to compromise long-term agricultural productivity, human and planetary health. Even though there is an urgent call to reduce plastic use in agriculture, we are not equipped with an adequate knowledge base to assess and reevaluate plasticulture. Our understanding of plasticulture and its importance in food systems has not yet been comprehensively assessed. In parallel, the implications of plastic use in agricultural systems are not fully understood, in particular the quantification of microplastics in agricultural soils and risks to future agroecosystem functioning. This thesis presents a review of the UK food system and a meta-analysis to explore the relative importance of plasticulture. The meta-analysis found that plasticulture is key to increasing the yield of globally-important crops in agricultural systems worldwide. This is followed by a nationwide survey, soil archive analysis and a mesocosm experiment that investigate microplastic concentrations, fate and impacts in agricultural soils. The nationwide survey suggests that plastic crop covers are a significant contributor of microplastics to agricultural soils. Analysis of the Rothamsted soil archive revealed that agricultural soils are receptors of microplastic pollution from different agricultural sources and non-agricultural sources which predate modern plasticulture. A mesocosm experiment was used to determine the effects of microplastics on soil and crop health, as well as the influence of soil and crop type on microplastic transport. The results from the mesocosm experiment indicate microplastics pollution affects agroecosystem functioning. This thesis is an essential contribution to producing a comprehensive assessment of plastic use in agriculture in future food systems. The findings from this thesis highlight an urgent need to reassess plastic use in agriculture. Sustainable plasticulture will be vital to build the resilience of a future food system that prioritises human and planetary health

Sustainable production of healthy, affordable food in the UK:The pros and cons of plasticulture

An evolving green agenda as the UK seeks to achieve ‘net zero’ in greenhouse gas emissions by 2050, coupled with our new trading relationship with the European Union, is resulting in new government policies, which will be disruptive to Britain's traditional food and farming practices. These policies encourage sustainable farming and land-sparing to restore natural habitats and will provide an opportunity to address issues such as high emissions of GHGs and dwindling biodiversity resulting from many intensive agricultural practices. To address these and other food challenges such as global conflicts and health issues, Britain will need a revolution in its food system. The aim of this paper is to make the case for such a food revolution where additional healthy food for the UK population is produced in-country in specialised production units for fruits and vegetables developed on sites previously considered unsuitable for crop production. High crop productivity can be achieved in low-cost controlled environments, making extensive use of novel crop science and modern controlled-environment technology. Such systems must be operated with very limited environmental impact. In recent years, growth in the application of plasticulture in UK horticulture has driven some increases in crop yield, quality and value. However, the environmental cost of plastic production and plastic pollution is regarded as a generational challenge that faces the earth system complex. The distribution of plastic waste is ubiquitous, with a significant pollution load arising from a range of agricultural practices. The primary receptor of agriplastic pollution is agricultural soil. Impacts of microplastics on crop productivity and quality and also on human health are only now being investigated. This paper explores the possibility that we can mitigate the adverse environmental effects of agriplastics and thereby exploit the potential of plasticulture to enhance the productivity and positive health impact of UK horticulture

A nationwide assessment of microplastic abundance in agricultural soils: The influence of plastic crop covers within the United Kingdom

Societal Impact Statement Agricultural soils are substantial receptors of plastic pollution. Plastic crop covers, a facet of agriplastics, may represent an important contribution to microplastic load in agricultural soils. The authors present a nationwide study of agricultural soils in the United Kingdom, comparing microplastic load between sites where plastic crop covers are and are not used for carrot and potato production. Sites where plastic crop covers were used received a higher microplastic load compared with sites where no plastic crop cover was used. The effects of microplastic pollution are largely unknown, requiring further research to determine the impact on soil, crop and human health. Summary Agricultural soils are substantial receptors of plastic pollution, with agriplastics potentially making an important contribution to the overall microplastic load to agricultural soils. The intensive use and mismanagement of plastic crop covers, particularly plastic mulch films, nets and fleeces, represent a pollution pathway. In this study, we have analysed the microplastic concentrations in agricultural soils in 324 samples from 108 sites across the United Kingdom, where carrots or potatoes were grown, using a combined digestion and density separation method. Microplastics were stained with Nile Red and quantified using fluorescence microscopy. Microplastic concentrations ranged from 1320 to 8190 particles kg−1, with a mean of 3680 ± 129.1 particles kg−1. Where no plastic crop covers were used for potato and carrot production, a mean of 2667 ± 84.1 particles kg−1 were detected. At sites where plastic crop covers were used in the past 10 years, a mean of 4689 ± 147.1 particles kg−1 were recorded. There was a significant difference in microplastic abundance between sites where plastic crop covers were and were not used (p ≤ 0.001), confirming that plastic crop covers are an important source of microplastics to agricultural soils. Further studies are needed to investigate microplastic occurrence in the environment to better understand their impact on soil, crops and human health

A nationwide assessment of microplastic abundance in agricultural soils:The influence of plastic crop covers within the United Kingdom

Societal Impact Statement: Agricultural soils are substantial receptors of plastic pollution. Plastic crop covers, a facet of agriplastics, may represent an important contribution to microplastic load in agricultural soils. The authors present a nationwide study of agricultural soils in the United Kingdom, comparing microplastic load between sites where plastic crop covers are and are not used for carrot and potato production. Sites where plastic crop covers were used received a higher microplastic load compared with sites where no plastic crop cover was used. The effects of microplastic pollution are largely unknown, requiring further research to determine the impact on soil, crop and human health. Summary: Agricultural soils are substantial receptors of plastic pollution, with agriplastics potentially making an important contribution to the overall microplastic load to agricultural soils. The intensive use and mismanagement of plastic crop covers, particularly plastic mulch films, nets and fleeces, represent a pollution pathway. In this study, we have analysed the microplastic concentrations in agricultural soils in 324 samples from 108 sites across the United Kingdom, where carrots or potatoes were grown, using a combined digestion and density separation method. Microplastics were stained with Nile Red and quantified using fluorescence microscopy. Microplastic concentrations ranged from 1320 to 8190 particles kg−1, with a mean of 3680 ± 129.1 particles kg−1. Where no plastic crop covers were used for potato and carrot production, a mean of 2667 ± 84.1 particles kg−1 were detected. At sites where plastic crop covers were used in the past 10 years, a mean of 4689 ± 147.1 particles kg−1 were recorded. There was a significant difference in microplastic abundance between sites where plastic crop covers were and were not used (p ≤ 0.001), confirming that plastic crop covers are an important source of microplastics to agricultural soils. Further studies are needed to investigate microplastic occurrence in the environment to better understand their impact on soil, crops and human health

Agricultural fertilisers contribute substantially to microplastic concentrations in UK soils

Since their invention, plastics have driven a revolution in behavior in all aspects of our lives, including agriculture. In-use and as a waste material, plastics degrade and accumulate in agricultural systems. Accumulation of plastic pollution in agricultural systems has negative impacts on human health and agricultural productivity but little is known about concentrations of microplastics in soils. Here we used a historical time series to examine changes to microplastic concentrations in agricultural soils over time. Microplastics were stained with Nile Red and quantified using fluorescence microscopy. We demonstrate that microplastic concentrations increased at higher rates in soils that are amended with either organic or inorganic fertiliser between 1966 and 2022, suggesting that agricultural fertilisers are an important contributor to microplastic concentrations in agricultural soils over time. This study provides evidence that agricultural soils are receptors and reservoirs of microplastic pollution, a legacy which is growing over time