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Improved characterisation of clinical text through ontology-based vocabulary expansion.
No full textBACKGROUND
Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described by several concepts in the same or similar contexts across several ontologies. While these concepts describe the same entities, they contain different sets of complementary metadata. Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks.
RESULTS
We develop and present an algorithm that expands the set of labels associated with an ontology class using a combination of strict lexical matching and cross-ontology reasoner-enabled equivalency queries. Across all disease terms in the Disease Ontology, the approach found 51,362 additional labels, more than tripling the number defined by the ontology itself. Manual validation by a clinical expert on a random sampling of expanded synonyms over the Human Phenotype Ontology yielded a precision of 0.912. Furthermore, we found that annotating patient visits in MIMIC-III with an extended set of Disease Ontology labels led to semantic similarity score derived from those labels being a significantly better predictor of matching first diagnosis, with a mean average precision of 0.88 for the unexpanded set of annotations, and 0.913 for the expanded set.
CONCLUSIONS
Inter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. While the accuracy of the extended vocabulary is not perfect, it nevertheless led to a significantly improved ontology-based characterisation of patients from text in one setting. Furthermore, where run-on error is not acceptable, the technique can be used to provide candidate synonyms which can be checked by a domain expert
Protocol for a scoping review exploring the use of patient-reported outcomes in adult social care.
No full textINTRODUCTION
Patient-reported outcomes (PROs) are measures of a person's own views of their health, functioning and quality of life. They are typically assessed using validated, self-completed questionnaires known as patient-reported outcome measures (PROMs). PROMs are used in healthcare settings to support care planning, clinical decision-making, patient-practitioner communication and quality improvement. PROMs have a potential role in the delivery of social care where people often have multiple and complex long-term health conditions. However, the use of PROMs in this context is currently unclear. The objective of this scoping review is to explore the evidence relating to the use of PROMs in adult social care.
METHODS AND ANALYSES
The electronic databases Medline (Ovid), PsychInfo (Ovid), ASSIA (ProQuest), Social Care Online (SCIE), Web of Science and EMBASE (Ovid) were searched on 29 September 2020 to identify eligible studies and other publically available documents published since 2010. A grey literature search and hand searching of citations and reference lists of the included studies will also be undertaken. No restrictions on study design or language of publication will be applied. Screening and data extraction will be completed independently by two reviewers. Quality appraisal of the included documents will use the Critical Appraisal Skills Programme and AACODS (Authority, Accuracy, Coverage, Objectivity, Date, Significance) checklists. A customised data charting table will be used for data extraction, with analysis of qualitative data using the framework method. The review findings will be presented as tables and in a narrative summary.
ETHICS AND DISSEMINATION
Ethical review is not required as scoping reviews are a form of secondary data analysis that synthesise data from publically available sources. Review findings will be shared with service users and other relevant stakeholders and disseminated through a peer-reviewed publication and conference presentations. This protocol is registered on the Open Science Framework (www.osf.io)
Molecular Characterisation of Plasmids Encoding bla from Faecal Escherichia coli in Travellers Returning to the UK from South Asia.
No full textBACKGROUND
The global prevalence of ESBL-producing Escherichia coli is rising and is dominated by bla spread by plasmids. Travellers to South Asia from Western Europe have high rates of acquisition of faecal CTX-M-producing E. coli (CTX-M-EC).
AIMS
We aimed to determine the conjugative ability of CTX-M-EC acquired by healthy volunteers after travel to South Asia, the proportion of travel-acquired CTX-M-EC where bla is encoded on a plasmid versus on the bacterial chromosome, and the relatedness of travel-acquired CTX-M-EC plasmids to previously sequenced plasmids.
METHODS
Faecal samples were collected pre- and post-travel from 23 volunteers who visited South Asia, and the CTX-M-EC were cultured. After short- and long-read sequencing, ten plasmid sequences were identified and compared to previously sequenced plasmids in Genbank. Conjugation to E. coli K-12 was undertaken using filter mating.
FINDINGS
35% of CTX-M-EC isolates tested transferred the bla plasmid by conjugation. Travel-acquired CTX-M-EC carried bla on a plasmid in 62% of isolates, whereas 38% of isolates had bla on the chromosome. CTX-M-EC plasmids acquired after travel to South Asia have close homology to previously described epidemic plasmids which are widely disseminated in humans, animals, and the natural environment.
CONCLUSION
Globally successful epidemic plasmids are involved in the spread of CTX-M-EC. Targeted strategies may be used to displace such plasmids from the host strain as part of efforts in infection prevention and control in healthcare settings. Bacteria with bla plasmids were readily acquired by healthy volunteers and were carried on return to the UK, providing opportunities for onward dissemination
International Forum on Transfusion Practices in Haematopoietic Stem-Cell Transplantation: Responses.
No full textEndoscopy in patients on antiplatelet or anticoagulant therapy: British Society of Gastroenterology (BSG) and European Society of Gastrointestinal Endoscopy (ESGE) guideline update.
No full textThis is a collaboration between the British Society of Gastroenterology (BSG) and the European Society of Gastrointestinal Endoscopy (ESGE), and is a scheduled update of their 2016 guideline on endoscopy in patients on antiplatelet or anticoagulant therapy. The guideline development committee included representatives from the British Society of Haematology, the British Cardiovascular Intervention Society, and two patient representatives from the charities Anticoagulation UK and Thrombosis UK, as well as gastroenterologists. The process conformed to AGREE II principles, and the quality of evidence and strength of recommendations were derived using GRADE methodology. Prior to submission for publication, consultation was made with all member societies of ESGE, including BSG. Evidence-based revisions have been made to the risk categories for endoscopic procedures, and to the categories for risks of thrombosis. In particular a more detailed risk analysis for atrial fibrillation has been employed, and the recommendations for direct oral anticoagulants have been strengthened in light of trial data published since the previous version. A section has been added on the management of patients presenting with acute GI haemorrhage. Important patient considerations are highlighted. Recommendations are based on the risk balance between thrombosis and haemorrhage in given situations
Predictors for poor outcome for conservatively treated traumatic triangular fibrocartilage complex tears.
No full textAIMS
The primary aim of this study was to assess if traumatic triangular fibrocartilage complex (TFCC) tears can be treated successfully with immobilization alone. Our secondary aims were to identify clinical factors that may predict a poor prognosis.
METHODS
This was a retrospective analysis of 89 wrists in 88 patients between January 2015 and January 2019. All patients were managed conservatively initially with either a short-arm or above-elbow custom-moulded thermoplastic splint for six weeks. Outcome measures recorded included a visual analogue scale for pain, Patient-Rated Wrist Evaluation, Disabilities of the Arm, Shoulder and Hand score, and the modified Mayo Wrist Score (MMWS). Patients were considered to have had a poor outcome if their final MMWS was less than 80 points, or if they required eventual surgical intervention. Univariate and logistic regression analyses were used to identify independent predictors for a poor outcome.
RESULTS
In total, 76% of wrists (42/55) treated with an above-elbow splint had a good outcome, compared to only 29% (10/34) with a short-arm splint (p < 0.001). The presence of a complete foveal TFCC tear (p = 0.009) and a dorsally subluxated distal radioulnar joint (DRUJ) (p = 0.032) were significantly associated with a poor outcome on univariate analysis. Sex, age, energy of injury, hand dominance, manual occupation, ulnar variance, and a delay in initial treatment demonstrated no significant association. Multiple logistic regression revealed that short-arm immobilization (p < 0.001) and DRUJ subluxation (p = 0.020) were significant independent predictive factors of an eventual poor outcome.
CONCLUSION
Nonoperative management of traumatic TFCC injuries with above-elbow immobilization is a viable treatment method, particularly in patients without DRUJ subluxation. Early surgery should be considered for patients with dorsal ulnar subluxation treated with short-arm splints to prevent prolonged morbidity. Cite this article: 2021;103-B(8):1386-1391
Mobile health for walking on the tightrope of optimal physical activity to reduce the risk of atrial fibrillation.
No full textTransforming clinical research by involving and empowering patients- the RATE-AF randomized trial.
No full textMolecular characterization of plasmids encoding bla from faecal Escherichia coli in travellers returning to the UK from South Asia.
No full textBACKGROUND
The global prevalence of extended-spectrum beta-lactamase-producing Escherichia coli is rising and is dominated by bla spread by plasmids. Travellers to South Asia from Western Europe have high rates of acquisition of faecal CTX-M-producing E. coli (CTX-M-EC).
AIMS
To determine the conjugative ability of CTX-M-EC acquired by healthy volunteers after travel to South Asia, the proportion of travel-acquired CTX-M-EC where bla is encoded on a plasmid vs on the bacterial chromosome, and the relatedness of travel-acquired CTX-M-EC plasmids to previously sequenced plasmids.
METHODS
Faecal samples were collected pre- and post-travel from 23 volunteers who visited South Asia, and CTX-M-EC were cultured. After short- and long-read sequencing, 10 plasmid sequences were identified and compared with previously sequenced plasmids in GenBank. Conjugation to E. coli K-12 was undertaken using filter mating.
FINDINGS
Thirty-five percent of CTX-M-EC isolates tested transferred the bla plasmid by conjugation. Travel-acquired CTX-M-EC carried bla on a plasmid in 62% of isolates, whereas 38% of isolates had bla on the chromosome. CTX-M-EC plasmids acquired after travel to South Asia had close homology to previously described epidemic plasmids which are widely disseminated in humans, animals and the natural environment.
CONCLUSION
Globally successful epidemic plasmids are involved in the spread of CTX-M-EC. Targeted strategies may be used to displace such plasmids from the host strain as part of efforts in infection prevention and control in healthcare settings. Bacteria with bla plasmids were readily acquired by healthy volunteers, and were carried on return to the UK, providing opportunities for onward dissemination
The evolution of sinus surgery in England in the last decade - An observational study.
No full textBackground and objective
Sinus surgery has seen significant changes over the years with advancements in instruments, endoscopes and imaging. This study aimed to use Hospital Episode Statistics (HES) data to review the total number of sinus related procedures performed in both adults and children across England and identify whether there were any trends across the study period. We predicted an increase in endoscopic sinus procedures with a decline in open approaches to the paranasal sinuses.
Methods
Data from HES was extracted for the years 2010-2019. The operative (OPCS-4) codes relevant to all sinus procedures between E12.1 and E17.9 were analysed. After examination of overall sinus related procedures, further subgroup analysis was performed with regards to open or endoscopic techniques.
Results
The total number of sinus procedures performed between 2010 and 2019 was 89,495. There was an increase in endoscopic surgeries by 21.1% and a decrease of open surgeries 35.3% during this time. There was an overall increase in maxillary, frontal and sphenoid sinus procedures, with a decrease in ethmoid sinus and lateral rhinotomy operations. There was an increase in the proportion of endoscopic cases overall by 5.7% and for all sinuses individually.
Conclusion
Overall, we see an increase in sinus surgery over the last 9 years from 2010 to 2019. These findings are in keeping with our initial hypotheses. Although our data set is limited by coding, and lack of patient factors, it represents most, if not all, of the data in England over a large study period. It is therefore useful to add to previous studies when demonstrating the increasing popularity of endoscopic sinus surgery over open procedures