The sitting active and prone passive lag test: a validity study in a symptomatic knee population

Purpose: This study aimed to determine the diagnostic utility of the sitting active and prone passive lag test in identifying terminal extension lag in unilaterally symptomatic knees. The lack of full extension at the knee leads to greater force of quadriceps activation, overloading of the weight bearing joints, abnormal gait mechanics, resulting in pain and dysfunction. Participants and Methods: Participants were randomly assigned and evaluated by two blinded examiners, to determine the presence of extension lag at the knee. The reproducibility of test results between examiners was determined, for reliability. In addition, the ability of the test to identify the presence of extension lag in symptomatic knees and absence of extension lag in asymptomatic knees was assessed, for validity. Results: The results revealed the test to possess an \u27almost perfect\u27 inter-rater reliability, high sensitivity, and moderate specificity. Conclusion: The sitting active and prone passive lag test may be incorporated as a reliable and valid test to determine the presence of terminal knee extension lag in a unilaterally symptomatic knee population

A modular, open-source information extraction framework for identifying clinical concepts and processes of care in clinical narratives

In this thesis, a synthesis is presented of the knowledge models required by clinical informa- tion systems that provide decision support for longitudinal processes of care. Qualitative research techniques and thematic analysis are novelly applied to a systematic review of the literature on the challenges in implementing such systems, leading to the development of an original conceptual framework. The thesis demonstrates how these process-oriented systems make use of a knowledge base derived from workflow models and clinical guidelines, and argues that one of the major barriers to implementation is the need to extract explicit and implicit information from diverse resources in order to construct the knowledge base. Moreover, concepts in both the knowledge base and in the electronic health record (EHR) must be mapped to a common ontological model. However, the majority of clinical guideline information remains in text form, and much of the useful clinical information residing in the EHR resides in the free text fields of progress notes and laboratory reports. In this thesis, it is shown how natural language processing and information extraction techniques provide a means to identify and formalise the knowledge components required by the knowledge base. Original contributions are made in the development of lexico-syntactic patterns and the use of external domain knowledge resources to tackle a variety of information extraction tasks in the clinical domain, such as recognition of clinical concepts, events, temporal relations, term disambiguation and abbreviation expansion. Methods are developed for adapting existing tools and resources in the biomedical domain to the processing of clinical texts, and approaches to improving the scalability of these tools are proposed and evalu- ated. These tools and techniques are then combined in the creation of a novel approach to identifying processes of care in the clinical narrative. It is demonstrated that resolution of coreferential and anaphoric relations as narratively and temporally ordered chains provides a means to extract linked narrative events and processes of care from clinical notes. Coreference performance in discharge summaries and progress notes is largely dependent on correct identification of protagonist chains (patient, clinician, family relation), pronominal resolution, and string matching that takes account of experiencer, temporal, spatial, and anatomical context; whereas for laboratory reports additional, external domain knowledge is required. The types of external knowledge and their effects on system performance are identified and evaluated. Results are compared against existing systems for solving these tasks and are found to improve on them, or to approach the performance of recently reported, state-of-the- art systems. Software artefacts developed in this research have been made available as open-source components within the General Architecture for Text Engineering framework

Natural language processing (NLP) for clinical information extraction and healthcare research

Introduction: Epilepsy is a common disease with multiple comorbidities. Routinely collected health care data have been successfully used in epilepsy research, but they lack the level of detail needed for in-depth study of complex interactions between the aetiology, comorbidities, and treatment that affect patient outcomes. The aim of this work is to use natural language processing (NLP) technology to create detailed disease-specific datasets derived from the free text of clinic letters in order to enrich the information that is already available. Method: An NLP pipeline for the extraction of epilepsy clinical text (ExECT) was redeveloped to extract a wider range of variables. A gold standard annotation set for epilepsy clinic letters was created for the validation of the ExECT v2 output. A set of clinic letters from the Epi25 study was processed and the datasets produced were validated against Swansea Neurology Biobank records. A data linkage study investigating genetic influences on epilepsy outcomes using GP and hospital records was supplemented with the seizure frequency dataset produced by ExECT v2. Results: The validation of ExECT v2 produced overall precision, recall, and F1 score of 0.90, 0.86, and 0.88, respectively. A method of uploading, annotating, and linking genetic variant datasets within the SAIL databank was established. No significant differences in the genetic burden of rare and potentially damaging variants were observed between the individuals with vs without unscheduled admissions, and between individuals on monotherapy vs polytherapy. No significant difference was observed in the genetic burden between people who were seizure free for over a year and those who experienced at least one seizure a year. Conclusion: This work presents successful extraction of epilepsy clinical information and explores how this information can be used in epilepsy research. The approach taken in the development of ExECT v2, and the research linking the NLP outputs, routinely collected health care data, and genetics set the way for wider research

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

Tune your brown clustering, please

Brown clustering, an unsupervised hierarchical clustering technique based on ngram mutual information, has proven useful in many NLP applications. However, most uses of Brown clustering employ the same default configuration; the appropriateness of this configuration has gone predominantly unexplored. Accordingly, we present information for practitioners on the behaviour of Brown clustering in order to assist hyper-parametre tuning, in the form of a theoretical model of Brown clustering utility. This model is then evaluated empirically in two sequence labelling tasks over two text types. We explore the dynamic between the input corpus size, chosen number of classes, and quality of the resulting clusters, which has an impact for any approach using Brown clustering. In every scenario that we examine, our results reveal that the values most commonly used for the clustering are sub-optimal