Improving Data Quality in an Institutional Clinical Trial Data Repository to Support Patient-Trial Matching

Institutional clinical data repositories often suffer from poor data quality, creating demand for advanced natural language processing (NLP) tools to support secondary use tasks. The need to address specific data quality issues and link unstructured aggregated institutional clinical trial summaries with their ClinicalTrials.gov records inspired the work in this project. A modern language representation model, the Bidirectional Encoder Representations from Transformers (BERT) model, has shown promise in many NLP tasks and been the basis for other BERT-based models pre-trained with domain-specific resources. My thesis aimed to evaluate the abilities of biomedical-domain-specific BERT models to discriminate between pairs of clinical trial texts belonging to the same trial (“matches”) and those belonging to different trials (“mismatches”), using trial titles and eligibility criteria (EC). Trials records from an institutional repository were paired with trial records from the Database for Aggregate Analysis of ClinicalTrials.gov. Next, BERT and six biomedical-domain-specific BERT models computed semantic similarity scores between the trial titles and trial EC for each trial pairing. I evaluated the models using the difference in median similarity scores between matched and mismatched pairs. I also examined model performance by analyzing the overlap between matched and mismatched pairs' kernel density estimate (KDE) plots. Lastly, I conducted exploratory analyses using different similarity score thresholds to convert score outputs into binary match/mismatch classifications and evaluated model performance using the standard metrics of recall and precision; the true negative rate and accuracy were also calculated. SciBERT was the only domain-specific model to demonstrate a greater difference in median similarity between matched and mismatched pairs (0.153; 0.061) than BERT (0.098; 0.051). BlueBERT had the smallest KDE overlap between matched and mismatched titles (0.057) followed by Bio+Clinical BERT (0.061) and PubMedBERT (tied with CODER; 0.066), while PubMedBERT had the smallest KDE overlap between matched and mismatched EC (0.110) followed by CODER (0.111) and BioBERT (0.122). Bio+Clinical BERT and PubMedBERT had the best title classification performance, while Bio+Clinical BERT and CODER had the best EC classification performance. Domain-specific models outperformed BERT in all evaluation methods used, but larger studies with more balanced datasets are required to determine the generalizability of this claim

A cost minimisation analysis of a telepaediatric otolaryngology service

Background: Paediatric ENT services in regional areas can be provided through telemedicine (tele-ENT) using videoconferencing or with a conventional outpatient department ENT service (OPD-ENT) in which patients travel to see the specialist. The objective of this study was to identify the least-cost approach to providing ENT services for paediatric outpatients

Evidence for models of diagnostic service provision in the community: literature mapping exercise and focused rapid reviews

Background Current NHS policy favours the expansion of diagnostic testing services in community and primary care settings. Objectives Our objectives were to identify current models of community diagnostic services in the UK and internationally and to assess the evidence for quality, safety and clinical effectiveness of such services. We were also interested in whether or not there is any evidence to support a broader range of diagnostic tests being provided in the community. Review methods We performed an initial broad literature mapping exercise to assess the quantity and nature of the published research evidence. The results were used to inform selection of three areas for investigation in more detail. We chose to perform focused reviews on logistics of diagnostic modalities in primary care (because the relevant issues differ widely between different types of test); diagnostic ultrasound (a key diagnostic technology affected by developments in equipment); and a diagnostic pathway (assessment of breathlessness) typically delivered wholly or partly in primary care/community settings. Databases and other sources searched, and search dates, were decided individually for each review. Quantitative and qualitative systematic reviews and primary studies of any design were eligible for inclusion. Results We identified seven main models of service that are delivered in primary care/community settings and in most cases with the possible involvement of community/primary care staff. Not all of these models are relevant to all types of diagnostic test. Overall, the evidence base for community- and primary care-based diagnostic services was limited, with very few controlled studies comparing different models of service. We found evidence from different settings that these services can reduce referrals to secondary care and allow more patients to be managed in primary care, but the quality of the research was generally poor. Evidence on the quality (including diagnostic accuracy and appropriateness of test ordering) and safety of such services was mixed. Conclusions In the absence of clear evidence of superior clinical effectiveness and cost-effectiveness, the expansion of community-based services appears to be driven by other factors. These include policies to encourage moving services out of hospitals; the promise of reduced waiting times for diagnosis; the availability of a wider range of suitable tests and/or cheaper, more user-friendly equipment; and the ability of commercial providers to bid for NHS contracts. However, service development also faces a number of barriers, including issues related to staffing, training, governance and quality control. Limitations We have not attempted to cover all types of diagnostic technology in equal depth. Time and staff resources constrained our ability to carry out review processes in duplicate. Research in this field is limited by the difficulty of obtaining, from publicly available sources, up-to-date information about what models of service are commissioned, where and from which providers. Future work There is a need for research to compare the outcomes of different service models using robust study designs. Comparisons of ‘true’ community-based services with secondary care-based open-access services and rapid access clinics would be particularly valuable. There are specific needs for economic evaluations and for studies that incorporate effects on the wider health system. There appears to be no easy way of identifying what services are being commissioned from whom and keeping up with local evaluations of new services, suggesting a need to improve the availability of information in this area. Funding The National Institute for Health Research Health Services and Delivery Research programme

Management of CRPS secondary to preganglionic C8 nerve root avulsion: a case report and literature review

Background: Cervical nerve root avulsion is a well-documented result of high-velocity motor vehicle accidents (MVAs). In up to 21% of cases, preganglionic cervical root avulsion can result in a complex regional pain syndrome (CRPS) impacting the quality of life for patients already impaired by motor, sensory, and autonomic dysfunction. The optimal treatment strategies include repeated stellate ganglion blocks (SBGs). Case Description: A 43-year-old male sustained a high-velocity MVA resulting in the left C8 nerve root avulsion. This resulted in weakness in the C8 distribution, tactile allodynia, and dysesthesias. The magnetic resonance imaging demonstrated an abnormal signal ventral to the C8-T1 level. As the patient was not considered a candidate for surgical intervention secondary to the attendant brachial plexus injury, a C7-C8 epidural steroid injection was performed; this did not provide improvement. Before placing a spinal cord stimulator, the patient underwent a series of six ultrasound-guided SBGs performed 2 weeks apart; there was 75% improvement in pain and strength. Six years later, the patient continues to do well while receiving SBGs 4 times a year. Conclusion: A preganglionic cervical nerve root avulsion should not be a contraindication for a stellate ganglion block in a patient with established CRPS

Recent decline in the use of invasive neurocritical care monitoring for traumatic brain injury: A case report

Background: In this article, we discuss the dramatic decline in the utilization of invasive cranial monitoring of patients with traumatic brain injury (TBI). Case Description: A 52-year-old male presented with a severe TBI following a motor vehicle accident. The initial computed tomography scan showed a subdural hematoma, and the patient underwent a craniotomy. However, preoperatively, intraoperatively, and postoperatively, the critical care team never utilized invasive cranial monitoring. Therefore, when the patient expired several weeks later due to multiorgan failure, his death was in part attributed to the neurocritical care specialists\u27 failure to employ invasive cranial monitoring techniques. Conclusion: Evidence-based and defensive medicine, cost containment, and a lack of leadership have contributed to neurocritical care specialists\u27 increased failure to utilize invasive hemodynamic and neurological monitoring for TBI