Automatic Population of Structured Reports from Narrative Pathology Reports

There are a number of advantages for the use of structured pathology reports: they can ensure the accuracy and completeness of pathology reporting; it is easier for the referring doctors to glean pertinent information from them. The goal of this thesis is to extract pertinent information from free-text pathology reports and automatically populate structured reports for cancer diseases and identify the commonalities and differences in processing principles to obtain maximum accuracy. Three pathology corpora were annotated with entities and relationships between the entities in this study, namely the melanoma corpus, the colorectal cancer corpus and the lymphoma corpus. A supervised machine-learning based-approach, utilising conditional random fields learners, was developed to recognise medical entities from the corpora. By feature engineering, the best feature configurations were attained, which boosted the F-scores significantly from 4.2% to 6.8% on the training sets. Without proper negation and uncertainty detection, the quality of the structured reports will be diminished. The negation and uncertainty detection modules were built to handle this problem. The modules obtained overall F-scores ranging from 76.6% to 91.0% on the test sets. A relation extraction system was presented to extract four relations from the lymphoma corpus. The system achieved very good performance on the training set, with 100% F-score obtained by the rule-based module and 97.2% F-score attained by the support vector machines classifier. Rule-based approaches were used to generate the structured outputs and populate them to predefined templates. The rule-based system attained over 97% F-scores on the training sets. A pipeline system was implemented with an assembly of all the components described above. It achieved promising results in the end-to-end evaluations, with 86.5%, 84.2% and 78.9% F-scores on the melanoma, colorectal cancer and lymphoma test sets respectively

Transforming Research Methods in the Social Sciences

Social science researchers in the global South, and in South Africa particularly, utilise research methods in innovative ways in order to respond to contexts characterised by diversity, racial and political tensions, socioeconomic disparities and gender inequalities. These methods often remain undocumented – a gap that this book starts to address. Written by experts from various methodological fields, Transforming Research Methods in the Social Sciences is a comprehensive collation of original essays and cutting-edge research that demonstrates the variety of novel techniques and research methods available to researchers responding to these context-bound issues. It is particularly relevant for study and research in the fields of applied psychology, sociology, ethnography, biography and anthropology. In addition to their unique combination of conceptual and application issues, the chapters also include discussions on ethical considerations relevant to the method in similar global South contexts. Transforming Research Methods in the Social Sciences has much to offer to researchers, professionals and others involved in social science research both locally and internationally

Advanced Magnetic Resonance Imaging of Osteoarthritis

This thesis examines the potential utility of magnetic resonance (MR) quantitative imaging biomarkers (QIBs) of knee osteoarthritis (OA) for rapid assessment of treatment efficacy in experimental medicine studies. The development of treatments able to modify disease in OA is hampered by an inability to evaluate treatment response over a timeframe relevant to clinical trials. There are particular challenges in the experimental medicine setting due to the small numbers of participants and short follow-up duration relative to the expected time course of OA development and progression. Multiple MR QIBs of OA exist which may help address the problem of early evaluation of treatment response. However, their use in early phase studies has remained limited. Possible reasons for this include incomplete characterisation of the performance of QIBs in this setting and lack of head-to-head comparison of candidate QIBs to determine which would be optimal. This thesis aims to address these shortcomings and provide new information on the likely utility of MR QIBs in the setting of experimental medicine studies, as well as their potential for improving our general understanding of OA pathophysiology. I start by examining the reliability and ability to discriminate between OA and healthy knees of cartilage compositional MR imaging in a systematic review and meta-analysis. I then describe the development and validation of a novel semi-automatic surface-based method for analysing articular cartilage composition and morphology at the knee which may offer improved responsiveness and spatial localisation of change. Moving to QIBs of subchondral bone, I evaluate the association between measures of subchondral bone architecture derived from MR texture analysis and OA progression in the Osteoarthritis Initiative. The remainder of the thesis describes a prospective observational study where the utility of MR QIBs of synovium, subchondral bone and cartilage in experimental medicine studies is assessed. In summary, this thesis will inform decisions regarding the use of MR-based QIBs in future longitudinal and interventional studies. Their inclusion in experimental medicine studies may allow early assessment of treatment efficacy at a structural level and improve efficiency of treatment development pipelines.Funding: Addenbrooke's Charitable Trust, Experimental Medicine Initiative, non-investigator sponsored study grant from GlaxoSmithKlin

Food Safety, Security, Sustainability and Nutrition as Priority Objectives of the Food Sector

The future food systems will have to provide food and nutrition security while facing unprecedented sustainability challenges: this underlines the need for a transition to more sustainable food systems. Taking into account these premises and considering the complexity of food systems, this book aims to present original research articles, reviews, and commentaries concerning the following:Advancements in food and beverage;Dietary supplements, nutraceuticals, and functional food;Food allergy and public health;Food and nutritional toxicology;Food biotechnology and food processing;Food microbiology and food safety;Food packaging;Food safety and food inspection;Food security and environmental impacts;Food waste management;Nutrition and metabolism;Sustainable food systems and agro-ecological food production

The role of subchondral bone in osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis. Affected individuals commonly suffer with chronic pain, joint dysfunction, and reduced quality of life. OA also confers an immense burden on health services and economies. Current OA therapies are symptomatic and there are no therapies that modify structural progression. The lack of validated, responsive and reliable biomarkers represents a major barrier to the development of structure-modifying therapies. MRI provides tremendous insight into OA structural disease and has highlighted the importance of subchondral bone in OA. The hypothesis underlying this thesis is that novel quantitative imaging biomarkers of subchondral bone will provide valid measures for OA clinical trials. The Osteoarthritis Initiative (OAI) provided a large natural history database of knee OA to enable testing of the validity of these novel biomarkers. A systematic literature review identified independent associations between subchondral bone features with structural progression, pain and total knee replacement in peripheral joint OA. However very few papers examined the association of 3D bone shape with these patient-centred outcomes. A cross-sectional analysis of the OAI established a significant association between 3D bone area and conventional radiographic OA severity scores, establishing construct validity of 3D bone shape. A nested case-control analysis within the OAI determined that 3D bone shape was associated with the outcome of future total knee replacement, establishing predictive validity for 3D bone shape. A regression analysis within the OAI identified that 3D bone shape was associated with current knee symptoms but not incident symptoms, establishing evidence of concurrent but not predictive validity for new symptoms. In summary, 3D bone shape is an important biomarker of OA which has construct and predictive validity in knee OA. This thesis, along with parallel work on reliability and responsiveness provides evidence supporting its suitability for use in clinical trials

Safety and Reliability - Safe Societies in a Changing World

The contributions cover a wide range of methodologies and application areas for safety and reliability that contribute to safe societies in a changing world. These methodologies and applications include: - foundations of risk and reliability assessment and management - mathematical methods in reliability and safety - risk assessment - risk management - system reliability - uncertainty analysis - digitalization and big data - prognostics and system health management - occupational safety - accident and incident modeling - maintenance modeling and applications - simulation for safety and reliability analysis - dynamic risk and barrier management - organizational factors and safety culture - human factors and human reliability - resilience engineering - structural reliability - natural hazards - security - economic analysis in risk managemen

The impact of the Johannesburg Stock Exchange's alternative exchange on listed firm's performance and entrepreneurship

This study’s primary objective is to determine the impact that the JSE’s AltX has on listed firm’s performance and the level of entrepreneurship in South Africa. Its secondary objective was to quantitatively determine whether there exists a link between increased capitalisation of the AltX and the expansionary drive of listed firms, as well as to ascertain the impact that the listing requirements of the AltX has on the broad-based black economic empowerment (B-BBEE) score performance of listed firms. In order to achieve the methodological objectives of this study, mixed methods was used to measure this phenomenon which led to the development of an integrated model for the JSE’s AltX listed firms, as well as for intending small and medium enterprises (SMEs) that might want to list. Accordingly, the researcher employed pragmatic research paradigm and conducted two types of analysis. Firstly, quantitative analysis which is based on primary and secondary data was conducted followed by a qualitative analysis based on a qualitative semi-structured case study. It was found that the JSE's AltX positively impacts on the performance of listed firms and the level of entrepreneurship in South Africa. Most especially as increased capitalisation levels was positively linked with the expansionary drive of these registered firms. And that the listing requirements of the AltX had a net positive effect on the B-BBEE score performance of these companies. Practically, by virtue of being listed many SMEs would generate enough capital and buzz to facilitate their expansion. This study also contributes to new knowledge by recommending that the JSE's AltX develop a custom-made business-friendly targeted listing procedure. Just as policy makers are encouraged to create a one-stop-shop investment portal which would streamline the activities of government agencies for the benefit of Small, Medium and Micro-Enterprises (SMMEs) in South Africa. The researcher proposes that future research would extend beyond South Africa, across the SADC, Africa or even across continents. Besides, a 3-level multi-level modelling (MLM) equation testing procedure was conducted to test the efficacy of firm listing, using IBM SPSS Statistics version 27 statistical software package. Quantitative analysis, comprising: quantitative analysis of primary data from survey questionnaire (investigated whether location or sector impacts on firm performance), and quantitative analysis of secondary data (determined if the number of both SMMEs and the JSE's AltX listed companies impacts on firm performance and the level of entrepreneurship in South Africa). Using participants' sample from sixty JSE's AltX listed firms who were either CEOs/directors/top management team members, and ten interviewees (i.e. for the qualitative analysis, comprising: qualitative analysis of primary data from semi-structured case study), this study's triangulated findings and conclusions became more valid and reliable. Evidence provided by the ensuing econometric analysis suggests that: Firstly, firms that are listed on the JSE’s AltX were more likely to perform better than their unlisted peers (i.e. both formal and informal SMMEs). Thus, this helped listed firms to improve their company’s performance, corporate profile, loan amount and profits, as well as assisted in securing a major investor for the firm. Besides, it was observed that the variation in the dataset occurred within sectors between the JSE's AltX variable parameters at Level 1. This positively impacted on the AltX market capitalisation, total number of employed personnel, foreign assets, as well as the total equity and liabilities of the JSE's AltX listed firms. Secondly, listing on the JSE’s AltX was found to be positively associated with the level of entrepreneurship in South Africa. There was evidence that listing boosted the level of creativity and innovation in South Africa, as well as encouraged entrepreneurial risk taking, and also increased business confidence levels. Furthermore, it was observed that the variation in the dataset occurred within sectors between the JSE's AltX variable parameters at Level 1. Likewise, the turnover, AltX market capitalisation, the total investments and loans, as well as the earnings yield of the JSE's AltX listed firms were positively linked with the level of entrepreneurship in South Africa. Thirdly, the rising share capitalisation of listed firms on the AltX was linked to an increased likelihood for company expansion. In addition, listing led to international firm exposure and industry position consolidation. However, the corporate bonds and equities sold by these listed firms on the AltX did not guaranty the long-term sustainability of their business. Also, it was observed that the variation in the dataset occurred within sectors between the JSE's AltX variable parameters at Level 1. Correspondingly, the qualitative case analysis indicated that listing on the AltX led to a high yield but with lower multiples, higher return on equity, joint ventures and acquisitions, share ownership dilution, debt reduction, more capital disbursement and risk diversification, and it also led to firm growth and economic development, which was good. Fourthly, higher compliance requirements for listing on the AltX, increased the likelihood that there would be improvements in quoted B-BBEE performance score. Equally, the implementation of good governance systems like the B-BBEE by listed firms made them more attractive to stakeholders. On the other hand, when the B-BBEE score of these listed firms becomes the regressand, listing had an undesirable effect on their value added, patents and trademarks in relation to company performance. This study therefore opens-up a new vista for examining the performance of listed firms in South Africa, which is a significant contribution to new knowledge.Business ManagementD. Phil. (Management Studies (Entrepreneurship)