Clinical prediction modelling in oral health: A review of study quality and empirical examples of model development

Background Substantial efforts have been made to improve the reproducibility and reliability of scientific findings in health research. These efforts include the development of guidelines for the design, conduct and reporting of preclinical studies (ARRIVE), clinical trials (ROBINS-I, CONSORT), observational studies (STROBE), and systematic reviews and meta-analyses (PRISMA). In recent years, the use of prediction modelling has increased in the health sciences. Clinical prediction models use information at the individual patient level to estimate the probability of a health outcome(s). Such models offer the potential to assist in clinical decision-making and to improve medical care. Guidelines such as PROBAST (Prediction model Risk Of Bias Assessment Tool) have been recently published to further inform the conduct of prediction modelling studies. Related guidelines for the reporting of these studies, such as TRIPOD (Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis) instrument, have also been developed. Since the early 2000s, oral health prediction models have been used to predict the risk of various types of oral conditions, including dental caries, periodontal diseases and oral cancers. However, there is a lack of information on the methodological quality and reporting transparency of the published oral health prediction modelling studies. As a consequence, and due to the unknown quality and reliability of these studies, it remains unclear to what extent it is possible to generalise their findings and to replicate their derived models. Moreover, there remains a need to demonstrate the conduct of prediction modelling studies in oral health field following the contemporary guidelines. This doctoral project addresses these issues using two systematic reviews and two empirical analyses. This thesis is the first comprehensive and systematic project reviewing the study quality and demonstrating the use of registry data and longitudinal cohorts to develop clinical prediction models in oral health. Aims • To identify and examine the quality of existing prediction modelling studies in the major fields of oral health.• To demonstrate the conduct and reporting of a prediction modelling study following current guidelines, incorporating machine learning algorithms and accounting for multiple sources of biases. Methods As one of the most prevalent oral conditions, chronic periodontitis was chosen as the exemplar pathology for the first part of this thesis. A systematic review was conducted to investigate the existing prediction models for the incidence and progression of this condition. Based upon this initial overview, a more comprehensive critical review was conducted to assess the methodological quality and completeness of reporting for prediction modelling studies in the field of oral health. The risk of bias in the existing literature was assessed using the PROBAST criteria, and the quality of study reporting was measured in accordance with the TRIPOD guidelines. Following these two reviews, this research project demonstrated the conduct and reporting of a clinical prediction modelling study using two empirical examples. Two types of analyses that are commonly used for two different types of outcome data were adopted: survival analysis for censored outcomes and logistic regression analysis for binary outcomes. Models were developed to 1) predict the three- and five-year disease-specific survival of patients with oral and pharyngeal cancers, based on 21,154 cases collected by a large cancer registry program in the US, the Surveillance, Epidemiology and End Results (SEER) program, and 2) to predict the occurrence of acute and persistent pain following root canal treatment, based on the electronic dental records of 708 adult patients collected by the National Practice-Based Research Network. In these two case studies, all prediction models were developed in five steps: (i) framing the research question; (ii) data acquisition and pre-processing; (iii) model generation; (iv) model validation and performance evaluation; and (v) model presentation and reporting. In accordance with the PROBAST recommendations, the risk of bias during the modelling process was reduced in the following aspects: • In the first case study, three types of biases were taken into account: (i) bias due to missing data was reduced by adopting compatible methods to conduct imputation; (ii) bias due to unmeasured predictors was tested by sensitivity analysis; and (iii) bias due to the initial choice of modelling approach was addressed by comparing tree-based machine learning algorithms (survival tree, random survival forest and conditional inference forest) with the traditional statistical model (Cox regression). • In the second case study, the following strategies were employed: (i) missing data were addressed by multiple imputation with missing indicator methods; (ii) a multilevel logistic regression approach was adopted for model development in order to fit Table of Contents xi the hierarchical structure of the data; (iii) model complexity was reduced using the Least Absolute Shrinkage and Selection Operator (LASSO) for predictor selection; and (iv) the models’ predictive performance was evaluated comprehensively by using the Area Under the Precision Recall Curve (AUPRC) in addition to the Area Under the Receiver Operating Characteristic curve (AUROC); (v) finally, and most importantly, given the existing criticism in the research community concerning the gender-based and racial bias in risk prediction models, we compared the models’ predictive performance built with different sets of predictors (including a clinical set, a sociodemographic set and a combination of both, the ‘general’ set). Results The first and second review studies indicated that, in the field of oral health, the popularity of multivariable prediction models has increased in recent years. Bias and variance are two components of the uncertainty (e.g., the mean squared error) in model estimation. However, the majority of the existing studies did not account for various sources of bias, such as measurement error and inappropriate handling of missing data. Moreover, non-transparent reporting and lack of reproducibility of the models were also identified in the existing oral health prediction modelling studies. These findings provided motivation to conduct two case studies aimed at demonstrating adherence to the contemporary guidelines and to best practice. In the third study, comparable predictive capabilities between Cox regression and the non-parametric tree-based machine learning algorithms were observed for predicting the survival of patients with oral and pharyngeal cancers. For example, the C-index for a Cox model and a random survival forest in predicting three-year survival were 0.82 and 0.84, respectively. A novelty of this study was the development of an online calculator designed to provide an open and transparent estimation of patients’ survival probability for up to five years after diagnosis. This calculator has clinical translational potential and could aid in patient stratification and treatment planning, at least in the context of ongoing research. In addition, the transparent reporting of this study was achieved by following the TRIPOD checklist and sharing all data and codes. In the fourth study, LASSO regression suggested that pre-treatment clinical factors were important in the development of one-week and six-month postoperative pain following root canal treatment. Among all the developed multilevel logistic models, models with a clinical set of predictors yielded similar predictive performance to models with a general set of predictors, while the models with sociodemographic predictors showed the weakest predictive ability. For example, for predicting one-week postoperative pain, the AUROC for models with clinical, sociodemographic and general predictors were 0.82, 0.68 and 0,84, respectively, and the AUPRC were 0.66, 0.40 and 0.72, respectively. Conclusion The significance of this research project is twofold. First, prediction models have been developed for potential clinical use in the context of various oral conditions. Second, this research represents the first attempt to standardise the conduct of this type of studies in oral health research. This thesis presents three conclusions: 1) Adherence to contemporary best practice guidelines such as PROBAST and TRIPOD is limited in the field of oral health research. In response, this PhD project disseminates these guidelines and leverages their advantages to develop effective prediction models for use in dentistry and oral health. 2) Use of appropriate procedures, accounting for and adapting to multiple sources of bias in model development, produces predictive tools of increased reliability and accuracy that hold the potential to be implemented in clinical practice. Therefore, for future prediction modelling research, it is important that data analysts work towards eliminating bias, regardless of the areas in which the models are employed. 3) Machine learning algorithms provide alternatives to traditional statistical models for clinical prediction purposes. Additionally, in the presence of clinical factors, sociodemographic characteristics contribute less to the improvement of models’ predictive performance or to providing cogent explanations of the variance in the models, regardless of the modelling approach. Therefore, it is timely to reconsider the use of sociodemographic characteristics in clinical prediction modelling research. It is suggested that this is a proportionate and evidence based strategy aimed at reducing biases in healthcare risk prediction that may be derived from gender and racial characteristics inherent in sociodemographic data sets.Thesis (Ph.D.) -- University of Adelaide, School of Public Health, 202

Investigating Problem-Orientated Patient Pathways, Toothache to Treatment: ImPacT Study

Ph. D. ThesisAlmost one-third of adults will only seek professional dental care when suffering with acute dental pain rather than engaging in routine preventive dental care, so called problem-orientated dental attenders. These individuals can wait a long time before seeking care resulting in: greater impacts on everyday activities, and greater potential for serious adverse events. They can present to a range of services including emergency dental services, medical emergency departments, and general medical practitioners (GMPs). The reasons for this attendance pattern and care pathway are under-researched. To encourage these patients to engage in routine dental care it is important to build an understanding of: (1) why they only attend when symptomatic, (2) where they present and why. The aim of this thesis was to build an understanding of problem-orientated attendance to subsequently develop an intervention to encourage regular dental attendance. This thesis involved four studies. The first was a retrospective observational study examining dental attendances at Welsh GMPs. The second and third were qualitative studies exploring: (1) problem-orientated attenders’ perspectives and experiences of seeking repeated emergency dental care (2) adolescents’ experiences of dental care and their future plans for dental attendance. The final study co-designed an intervention to prevent problem-orientated dental attendance. Dental attendance rates at GMPs varied over the study period and appeared to relate to key policy change dates. Predictors of being a repeat dental attender included deprivation, residential area, and appointment outcome. Reasons for problemorientated attendance were complex and multifactorial, with overarching reasons related to knowledge and dentist characteristics. Adolescents faced multiple barriers to dental care-seeking as they transitioned to independence subsequently affecting decision-making to continue to seek regular care. Finally, an intervention was developed targeted at adolescents and young adults to encourage continued regular dental attendance as they transitioned to independence, hence preventing problemorientated attendance.National Institute for Health Research (NIHR), European Society of Endodontolog

Nurses' perception on the impact of technology on nursing care practice in the intensive care unit: a grounded theory approach

Using Charmaz's (2006) constructivist grounded theory methodology, this study sought to establish a theory that explains how nurses perceive the influence of technology on their nursing care practises. This study used individual in-depth interviews and participant observation as a primary data collection method. In addition, participant observations were conducted before participant interviews to understand the phenomenon and practises in the ICU and corroborate with the participants' stories. During semi-structured face-to-face interviews, 19 staff nurses, one nursing manager and one medical assistant from an adult general ICU at a public hospital in Malaysia shared their experiences. The grounded theory of the emancipatory practise of ICU nurses was developed by a continuous comparison analysis of transcribed interview data. The predicament of practice was explored within the context of the theme 'navigating through complexity,' which implies that nurses were confronted with a conflicting situation that prompted them to gravitate toward a more "technologized" rather than humanised approach. This option might lead to professional value conflicts and a feeling of powerlessness. In order to reconcile the conflict, nurses attempt to shape their ideal professional identity by incorporating humane and technological values into the care of their patients. A new care paradigm is incorporated into the professional identity that accommodates human needs from a technological standpoint. Emancipatory practise in the context of this research, refers to the practise in which nurses have the opportunity to self-reflect and become conscious of the significance of striking a balance between humanistic nursing and technological care. This awareness assists nurses in constructing a viable professional identity within an environment heavily influenced by technology. Emancipatory practise entails the practise that is not only done but also developed and altered as nurses attempt to construct and reconfigure how to operate in a 'complex and dynamic environment due to pervasive technology. A new practice that prioritise both technological advancements and humanistic nursing would be gaining traction, and this theory provided the health care authorities with a realistic assessment of the nursing workload necessary to facilitate this transformation

The development and initial validation of an outcome measure for children and young people with life-limiting and life-threatening conditions

BackgroundThere is no validated outcome measure for use in children's palliative care outside of sub-Saharan Africa. Development of such a measure is required to realise the benefits of patient-centred outcome measure use that has been demonstrated in adult palliative care. Previous research into what is important to children and young people with life-limiting and life-threatening conditions has primarily focused on those with a cancer diagnosis. Much of this pre-existing research focuses on the perspectives of proxies, rather than those of the child or young person.AimTo develop an outcome measure, the children's palliative outcome scale (C-POS), for use by children and young people with life-limiting and life-threatening conditions and their families, and to establish face and content validity, comprehensiveness, comprehensibility, feasibility, and acceptability of use.MethodsA sequential mixed-methods study was conducted in three phases, following the principles of patient-reported outcome measurement design described by Rothrock and the Consensus-based Standards for the selection of health Measurement Instruments (COSMIN).Phase 1 - gathering inputA systematic review was conducted with the aim of appraising the evidence on optimal recall period, response format and mode of administration to enable children and young people to participate in self-reporting on their health outcomes. A young person's advisory group was also consulted on the same topic.To inform face and content validity of C-POS a semi-structured qualitative interview study was conducted to seek the perspectives of children and young people, their parents/carers and siblings, health care professionals and NHS commissioners on priority symptoms, concerns, and care priorities. Participants were also asked to identify their preferences for the design of C-POS, in terms of recall period, response scale format and administration mode.Phase 2 - item generationPart 1: Parents and professionals with experience in caring for a child or young person with a life-limiting or life-threatening condition participated in a three-round modified ranking-type Delphi survey with the aim of establishing which outcomes identified in phase 1 of this thesis should be included in C-POS.Part 2: The young person’s advisory group were asked to select their priority outcomes from the items ranked in rounds 2 and 3 of the Delphi survey.Part 3: An item generation meeting was conducted with key stakeholders to develop initial C-POS versions based on the evidence collected so far.Phase 3 - item improvementCross-sectional cognitive interview study to establish acceptability, comprehensiveness, and comprehension of the initial C-POS versions within the target population.ResultsPhase 1 - gathering inputSystematic review: Findings showed that children under five years old cannot validly and reliably self-report health outcomes. Face scales demonstrated better psychometric properties than visual analogue or Likert scales. Computerised and paper scales generally show equivalent construct validity and children prefer computerised measures. Children seven years old and younger often think dichotomously so may need two response options. Those over eight years old can reliably use a three-point scale.Qualitative interview study: 106 participants were recruited: 26 children, 40 parents, 13 siblings, 15 health care professionals and 12 commissioners. Children found a short recall period and a visually appealing measure with 10 questions or fewer most acceptable. Children with life-limiting conditions were more familiar with using rating scales such as numeric and Likert than their healthy siblings and emphasised the importance of completing the measure alongside interactions with a healthcare professional. Parents assumed that electronic completion methods would be most feasible and acceptable but a small number of children preferred paper measures.Participants described many inter-related symptoms, concerns and care priorities impacting on all aspects of life. Data revealed an overarching theme of pursuing ‘normality’, described as children’s desire to undertake usual childhood activities. Parents need support with practical aspects of care to help realise this desire for normality.Phase 2 - item generationPart 1: Delphi survey (n=82). Ranking agreement between participants increased over the rounds, indicating movement towards consensus. Agreement between professional and parent ranking was poor. Professionals prioritised physical symptoms, whereas parents prioritised psychosocial and practical concerns.Part 2: 22 children and young people attended the young person's advisory group. They prioritised items related to living a ‘normal life’ such as seeing friends and attending school, in addition to items prioritised by the adult participants in the Delphi survey.Part 3: 22 participants attended the item generation meeting. Fiveage/developmental stage appropriPhase 3 - item improvementForty-eight individuals participated (36 parents; 12 children) in cognitive testing of the C-POS versions. This revealed challenges in the acceptability of some items for parents of non-verbal children and refinements were made. C-POS content and length were acceptable, and all questions were considered important. Parents reported that completing a measure that asks about what matters may be distressing but this is anticipated and acceptable.ConclusionsThis thesis demonstrates the development of the first UK patient-centred outcome measure for use with children and young people with life-limiting and life-threatening conditions and their families. By following established methodological criteria for patient-centred outcome measure development this thesis demonstrates that CPOS has robust face and content validity and is feasible and acceptable for use within the target population.</div

Evaluation of a broadly-based control model of fascioliasis (liver fluke) in Central Vietnam

Fascioliasis (liver fluke) is listed as one of the most important parasitic infections in humans and animals in the developing world, posing a considerable burden to human public and veterinary health globally (Mas-Coma, 2005). In Vietnam, the prevalence of fascioliasis has increased rapidly since the beginning of the 21st century and it has become a zoonosis of great public health importance, with Central Vietnam being most severely hit by the disease (Trieu, 2011). The rising prevalence of the disease has been reported in all 15 regional provinces of Vietnam, increasing from 1,500 cases during 2004-2005 to 9,985 cases in 2011 (Nguyen, 2011). To date, comprehensive strategies for fascioliasis control are not in place, and the only control of the disease is reliance on chemotherapy with triclabendazole (TCZ), recommended by the WHO as the drug of choice for the treatment of both acute and chronic fascioliasis in humans (WHO, 2007b). However, TCZ resistance has been reported in animals and in humans (Ortiz, Scarcella, Cerna, Rosales, Cabrera, Guzman, Lamenza and Solana, 2013). Although alternative fascioliasis control measures are recommended elsewhere, no typical example has been proven to be effective in practice (Nithiuthai, Anantaphruti, Waikagul and Gajadhar, 2004; Saba and Korkmaz, 2005). Furthermore, various models of foodborne trematode infection control have been introduced and tested for their effectiveness but none of them are complete and applicable to all situations (Nguyen, Nguyen, Bui and Tran, 2011). In the context of the unavailability of effective control measures of fascioliasis, the study of a broadly-based control model of fascioliasis in Central Vietnam was conducted to address the burden of the disease and promote the community’s health. The model, selectively adapted from the trial control model of fascioliasis by Nguyen et al. (2011) and the intervention model by Molyneux (2006), comprised five main components: vector control, health education, improvement of local health systems, involvement of concerned bodies, and chemotherapy. This study aims to implement and evaluate a broadly-based control model for fascioliasis in a community with high prevalence of fascioliasis in Central Vietnam (1) to determine the seroprevalence of human fascioliasis by laboratory methods prior to the interventions; (2) to describe the risk factors associated with fascioliasis infections by conducting surveys on knowledge, attitudes and practices (KAP), and undertaking household observations and snail counts; (3) to report on the implementation of a broadly-based control model for fascioliasis infection; (4) to evaluate the effectiveness in reducing the seroprevalence of human fascioliasis of the broadly-based control model, comparing its impact with that of a model of treatment of humans and cattle alone, and to treatment of humans only; and (5) to explore the positive and negative factors that motivate or impede the successful implementation of the broadly-based control model for fascioliasis in Central Vietnam

Developing chiropractic students clinical practice skills - elements of best practice : a qualitative exploratory descriptive study

Background Although chiropractic has 125 years as an established profession, scrutiny of the literature proves that few studies have examined the clinical education of chiropractic students with a call for research from academics. This thesis is significant as it develops knowledge that can inform chiropractic bodies and help them improve an essential component of chiropractic education: clinical skill development. Research Purpose and Aims The purpose of this study was to identify elements of best practices in clinical education by critically examining, exploring and describing the aspects of an exemplar chiropractic clinical program that develops students’ clinical practice skills for transition into practice. This study explored the innovative clinical program of a reputable American chiropractic institution providing a scaffolded clinical program across varied clinical settings, patient populations and amongst other health disciplines. Research Design A six-phase exploratory descriptive qualitative design (EDQD) study was conducted to explore and describe the phenomenon being examined (Flick, 2014). This design enabled the collection of information about perceptions and lived experiences of three stakeholder cohorts: clinical faculty members, students and new graduates. Methods Purposive sampling (of students and clinical faculty members) and snowball sampling techniques (of new graduates) were used to derive the sample. Data were collected in three cycles across a two-year period using in-depth, semi-structured interviews. Interviews were conducted with 15 clinical faculty members and eight new graduates, and semi-structured focus groups were conducted with 20 students. All data were audio recorded, transcribed and thematically analysed using an inductive approach. Findings Chiropractic clinical education programs ought to be developed within a framework that incorporates adult learner principles; situated, social and experiential learning theories. Valued was a student-centred learning experience that includes authentic and diverse clinical placements, supervision and mentoring from multiple clinical educators which enhances students’ access to varied perspectives of clinical practices that contributes to developing clinical skills and professional identity. Business knowledge and entrepreneurial skills was an area of deficiency, which is problematic when the objective is to build graduates’ independence in clinical practice and professional prospects are predominantly private practice (NBCE, 2020). Embedding evidence-based practice within curricula and clinical training for educators and students are necessary to ensure this becomes a part of clinical practice. Conclusion This thesis posits best practice in chiropractic clinical education consists of the following: (a) using a scaffolded longitudinal clinical program, (b) varying clinical placements and case mix, (c) supervision and mentoring from multiple clinical educators, (d) educating the clinical educator, (e) curricula designed around industry standards and desired graduate attributes and capabilities, (f) an evidence-based practice approach in the curricula and clinical context, (g) aligning business skills, knowledge and practices with the professional context and (h) interprofessional learning and practice opportunities. Although this study has made a contribution to scholarly discourse, there remain many gaps in our knowledge where further studies are needed.Doctor of Philosoph

Using the oral health and disease ontology to study dental outcomes in national dental PBRN practices

The use of electronic dental records (EDR) has grown rapidly over the past decade, but the development of methods to use EDR data for research and quality improvement is still in its infancy. In this study, we are investigating the feasibility of reusing semantically structured EDR data for research purposes. Our two use cases are to assess (1) longevity of posterior composite restorations (PCR) and (2) tooth loss following root canal treatment (RCT)

Congress UPV Proceedings of the 21ST International Conference on Science and Technology Indicators

This is the book of proceedings of the 21st Science and Technology Indicators Conference that took place in València (Spain) from 14th to 16th of September 2016. The conference theme for this year, ‘Peripheries, frontiers and beyond’ aimed to study the development and use of Science, Technology and Innovation indicators in spaces that have not been the focus of current indicator development, for example, in the Global South, or the Social Sciences and Humanities. The exploration to the margins and beyond proposed by the theme has brought to the STI Conference an interesting array of new contributors from a variety of fields and geographies. This year’s conference had a record 382 registered participants from 40 different countries, including 23 European, 9 American, 4 Asia-Pacific, 4 Africa and Near East. About 26% of participants came from outside of Europe. There were also many participants (17%) from organisations outside academia including governments (8%), businesses (5%), foundations (2%) and international organisations (2%). This is particularly important in a field that is practice-oriented. The chapters of the proceedings attest to the breadth of issues discussed. Infrastructure, benchmarking and use of innovation indicators, societal impact and mission oriented-research, mobility and careers, social sciences and the humanities, participation and culture, gender, and altmetrics, among others. We hope that the diversity of this Conference has fostered productive dialogues and synergistic ideas and made a contribution, small as it may be, to the development and use of indicators that, being more inclusive, will foster a more inclusive and fair world