8,396 research outputs found

    Environmental surveillance for Salmonella Typhi as a tool to estimate the incidence of typhoid fever in low-income populations.

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    Background: The World Health Organisation recommends prioritised use of recently prequalified typhoid conjugate vaccines in countries with the highest incidence of typhoid fever. However, representative typhoid surveillance data are lacking in many low-income countries because of the costs and challenges of diagnostic clinical microbiology. Environmental surveillance (ES) of Salmonella Typhi in sewage and wastewater using molecular methods may offer a low-cost alternative, but its performance in comparison with clinical surveillance has not been assessed. Methods: We developed a harmonised protocol for typhoid ES and its implementation in communities in India and Malawi where it will be compared with findings from hospital-based surveillance for typhoid fever. The protocol includes methods for ES site selection based on geospatial analysis, grab and trap sample collection at sewage and wastewater sites, and laboratory methods for sample processing, concentration and quantitative polymerase chain reaction (PCR) to detect Salmonella Typhi. The optimal locations for ES sites based on digital elevation models and mapping of sewage and river networks are described for each community and their suitability confirmed through field investigation. We will compare the prevalence and abundance of Salmonella Typhi in ES samples collected each month over a 12-month period to the incidence of blood culture confirmed typhoid cases recorded at referral hospitals serving the study areas. Conclusions: If environmental detection of Salmonella Typhi correlates with the incidence of typhoid fever estimated through clinical surveillance, typhoid ES may be a powerful and low-cost tool to estimate the local burden of typhoid fever and support the introduction of typhoid conjugate vaccines. Typhoid ES could also allow the impact of vaccination to be assessed and rapidly identify circulation of drug resistant strains

    On the Robustness of ChatGPT: An Adversarial and Out-of-distribution Perspective

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    ChatGPT is a recent chatbot service released by OpenAI and is receiving increasing attention over the past few months. While evaluations of various aspects of ChatGPT have been done, its robustness, i.e., the performance to unexpected inputs, is still unclear to the public. Robustness is of particular concern in responsible AI, especially for safety-critical applications. In this paper, we conduct a thorough evaluation of the robustness of ChatGPT from the adversarial and out-of-distribution (OOD) perspective. To do so, we employ the AdvGLUE and ANLI benchmarks to assess adversarial robustness and the Flipkart review and DDXPlus medical diagnosis datasets for OOD evaluation. We select several popular foundation models as baselines. Results show that ChatGPT shows consistent advantages on most adversarial and OOD classification and translation tasks. However, the absolute performance is far from perfection, which suggests that adversarial and OOD robustness remains a significant threat to foundation models. Moreover, ChatGPT shows astounding performance in understanding dialogue-related texts and we find that it tends to provide informal suggestions for medical tasks instead of definitive answers. Finally, we present in-depth discussions of possible research directions.Comment: Technical report; code is at: https://github.com/microsoft/robustlear

    A Decision Support System for Economic Viability and Environmental Impact Assessment of Vertical Farms

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    Vertical farming (VF) is the practice of growing crops or animals using the vertical dimension via multi-tier racks or vertically inclined surfaces. In this thesis, I focus on the emerging industry of plant-specific VF. Vertical plant farming (VPF) is a promising and relatively novel practice that can be conducted in buildings with environmental control and artificial lighting. However, the nascent sector has experienced challenges in economic viability, standardisation, and environmental sustainability. Practitioners and academics call for a comprehensive financial analysis of VPF, but efforts are stifled by a lack of valid and available data. A review of economic estimation and horticultural software identifies a need for a decision support system (DSS) that facilitates risk-empowered business planning for vertical farmers. This thesis proposes an open-source DSS framework to evaluate business sustainability through financial risk and environmental impact assessments. Data from the literature, alongside lessons learned from industry practitioners, would be centralised in the proposed DSS using imprecise data techniques. These techniques have been applied in engineering but are seldom used in financial forecasting. This could benefit complex sectors which only have scarce data to predict business viability. To begin the execution of the DSS framework, VPF practitioners were interviewed using a mixed-methods approach. Learnings from over 19 shuttered and operational VPF projects provide insights into the barriers inhibiting scalability and identifying risks to form a risk taxonomy. Labour was the most commonly reported top challenge. Therefore, research was conducted to explore lean principles to improve productivity. A probabilistic model representing a spectrum of variables and their associated uncertainty was built according to the DSS framework to evaluate the financial risk for VF projects. This enabled flexible computation without precise production or financial data to improve economic estimation accuracy. The model assessed two VPF cases (one in the UK and another in Japan), demonstrating the first risk and uncertainty quantification of VPF business models in the literature. The results highlighted measures to improve economic viability and the viability of the UK and Japan case. The environmental impact assessment model was developed, allowing VPF operators to evaluate their carbon footprint compared to traditional agriculture using life-cycle assessment. I explore strategies for net-zero carbon production through sensitivity analysis. Renewable energies, especially solar, geothermal, and tidal power, show promise for reducing the carbon emissions of indoor VPF. Results show that renewably-powered VPF can reduce carbon emissions compared to field-based agriculture when considering the land-use change. The drivers for DSS adoption have been researched, showing a pathway of compliance and design thinking to overcome the ‘problem of implementation’ and enable commercialisation. Further work is suggested to standardise VF equipment, collect benchmarking data, and characterise risks. This work will reduce risk and uncertainty and accelerate the sector’s emergence

    Assessing performance of artificial neural networks and re-sampling techniques for healthcare datasets.

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    Re-sampling methods to solve class imbalance problems have shown to improve classification accuracy by mitigating the bias introduced by differences in class size. However, it is possible that a model which uses a specific re-sampling technique prior to Artificial neural networks (ANN) training may not be suitable for aid in classifying varied datasets from the healthcare industry. Five healthcare-related datasets were used across three re-sampling conditions: under-sampling, over-sampling and combi-sampling. Within each condition, different algorithmic approaches were applied to the dataset and the results were statistically analysed for a significant difference in ANN performance. The combi-sampling condition showed that four out of the five datasets did not show significant consistency for the optimal re-sampling technique between the f1-score and Area Under the Receiver Operating Characteristic Curve performance evaluation methods. Contrarily, the over-sampling and under-sampling condition showed all five datasets put forward the same optimal algorithmic approach across performance evaluation methods. Furthermore, the optimal combi-sampling technique (under-, over-sampling and convergence point), were found to be consistent across evaluation measures in only two of the five datasets. This study exemplifies how discrete ANN performances on datasets from the same industry can occur in two ways: how the same re-sampling technique can generate varying ANN performance on different datasets, and how different re-sampling techniques can generate varying ANN performance on the same dataset

    Omics measures of ageing and disease susceptibility

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    While genomics has been a major field of study for decades due to relatively inexpensive genotyping arrays, the recent advancement of technology has also allowed the measure and study of various “omics”. There are now numerous methods and platforms available that allow high throughput and high dimensional quantification of many types of biological molecules. Traditional genomics and transcriptomics are now joined by proteomics, metabolomics, glycomics, lipidomics and epigenomics. I was lucky to have access to a unique resource in the Orkney Complex Disease Study (ORCADES), a cohort of individuals from the Orkney Islands that are extremely deeply annotated. Approximately 1000 individuals in ORCADES have genomics, proteomics, lipidomics, glycomics, metabolomics, epigenomics, clinical risk factors and disease phenotypes, as well as body composition measurements from whole body scans. In addition to these cross-sectional omics and health related measures, these individuals also have linked electronic health records (EHR) available, allowing the assessment of the effect of these omics measures on incident disease over a ~10-year follow up period. In this thesis I use this phenotype rich resource to investigate the relationship between multiple types of omics measures and both ageing and health outcomes. First, I used the ORCADES data to construct measures of biological age (BA). The idea that there is an underlying rate at which the body deteriorates with age that varies between individuals of the same chronological age, this biological age, would be more indicative of health status, functional capacity and risk of age-related diseases than chronological age. Previous models estimating BA (ageing clocks) have predominantly been built using a single type of omics assay and comparison between different omics ageing clocks has been limited. I performed the most exhaustive comparison of different omics ageing clocks yet, with eleven clocks spanning nine different omics assays. I show that different omics clocks overlap in the information they provide about age, that some omics clocks track more generalised ageing while others track specific disease risk factors and that omics ageing clocks are prognostic of incident disease over and above chronological age. Second, I assessed whether individually or in multivariable models, omics measures are associated with health-related risk factors or prognostic of incident disease over 10 years post-assessment. I show that 2,686 single omics biomarkers are associated with 10 risk factors and 44 subsequent incident diseases. I also show that models built using multiple biomarkers from whole body scans, metabolomics, proteomics and clinical risk factors are prognostic of subsequent diabetes mellitus and that clinical risk factors are prognostic of incident hypertensive disorders, obesity, ischaemic heart disease and Framingham risk score. Third, I investigated the genetic architecture of a subset of the proteomics measures available in ORCADES, specifically 184 cardiovascular-related proteins. Combining genome-wide association (GWAS) summary statistics from ORCADES and 17 other cohorts from the SCALLOP Consortium, giving a maximum sample size of 26,494 individuals, I performed 184 genome-wide association meta-analyses (GWAMAs) on the levels of these proteins circulating in plasma. I discovered 592 independent significant loci associated with the levels of at least one protein. I found that between 8-37% of these significant loci colocalise with known expression quantitative trait loci (eQTL). I also find evidence of causal associations between 11 plasma protein levels and disease susceptibility using Mendelian randomisation, highlighting potential candidate drug targets

    Physical phenomena controlling quiescent flame spread in porous wildland fuel beds

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    Despite well-developed solid surface flame spread theories, we still lack a coherent theory to describe flame spread through porous wildland fuel beds. This porosity results in additional complexity, reducing the thermal conductivity of the fuel bed, but allowing in-bed radiative and convective heat transfer to occur. While previous studies have explored the effect of fuel bed structure on the overall fire behaviour, there remains a need for further investigation of the effect of fuel structure on the underlying physical phenomena controlling flame spread. Through an extensive series of laboratory-based experiments, this thesis provides detailed, physics-based insights for quiescent flame spread through natural porous beds, across a range of structural conditions. Measurements are presented for fuel beds representative of natural field conditions within an area of the fire-prone New Jersey Pinelands National Reserve, which compliment a related series of field experiments conducted as part of a wider research project. Additional systematic investigation across a wider range of fuel conditions identified independent effects of fuel loading and bulk density on the spread rate, flame height and heat release rate. However, neither fuel loading nor bulk density alone provided adequate prediction of the resulting fire behaviour. Drawing on existing structural descriptors (for both natural and engineered fuel beds) an alternative parameter ασδ was proposed. This parameter (incorporating the fuel bed porosity (α), fuel element surface-to-volume ratio (σ), and the fuel bed height (δ)) was strongly correlated with the spread rate. One effect of the fuel bed structure is to influence the heat transfer mechanisms both above and within the porous fuel bed. Existing descriptions of radiation transport through porous fuel beds are often predicated on the assumption of an isotropic fuel bed. However, given their preferential angle of inclination, the pine needle beds in this study may not exhibit isotropic behaviour. Regardless, for the structural conditions investigated, horizontal heat transfer through the fuel bed was identified as the dominant heating mechanism within this quiescent flame spread scenario. However, the significance of heat transfer contributions from the above-bed flame generally increased with increasing ασδ value of the fuel bed. Using direct measurements of the heat flux magnitude and effective heating distance, close agreement was observed between experimentally observed spread rates and a simple thermal model considering only radiative heat transfer through the fuel bed, particularly at lower values of ασδ. Over-predictions occurred at higher ασδ values, or where other heat transfer terms were incorporated, which may highlight the need to include additional heat loss terms. A significant effect of fuel structure on the primary flow regimes, both within and above these porous fuel beds, was also observed, with important implications for the heat transfer and oxygen supply within the fuel bed. Independent effects of fuel loading and bulk density on both the buoyant and buoyancy-driven entrainment flow were observed, with a complex feedback cycle occurring between Heat Release Rate (HRR) and combustion behaviour. Generally, increases in fuel loading resulted in increased HRR, and therefore increased buoyant flow velocity, along with an increase in the velocity of flow entrained towards the combustion region. The complex effects of fuel structure in both the flaming and smouldering combustion phases may necessitate modifications to other common modelling approaches. The widely used Rothermel model under-predicted spread rate for higher bulk density and lower ασδ fuel beds. As previously suggested, an over-sensitivity to fuel bed height was observed, with experimental comparison indicating an under-prediction of reaction intensity at lower fuel heights. These findings have important implications particularly given the continuing widespread use of the Rothermel model, which continues to underpin elements of the BehavePlus fire modelling system and the US National Fire Danger Rating System. The physical insights, and modelling approaches, developed for this low-intensity, quiescent flame spread scenario, are applicable to common prescribed fire activities. It is hoped that this work (alongside complimentary laboratory and field experiments conducted by various authors as part of a wider multi-agency project (SERDP-RC2641)) will contribute to the emerging field of prescribed fire science, and help to address the pressing need for further development of fire prediction and modelling tools
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