Using Hadoop to implement a semantic method for assessing the quality of medical data

Recent technological advances in modern healthcare have lead to a vast wealth of patient data being collected. This data is not only utilised for diagnosis but also has the potential to be used for medical research. However, there are often many errors in datasets used for medical research, with one study finding error rates ranging from 2.3% to 26.9% in a selection of medical research databases. Previous methods of automatically assessing data quality have often relied on threshold rules. These rules can sometimes miss errors requiring complex domain knowledge to correctly identify. To combat this, a semantic framework has been developed to assess the quality of medical data expressed in the form of linked open data. Early work in this direction revealed that existing triplestores are unable to cope with the large amounts of medical data. In this thesis, a system for storing and querying medical RDF data using Hadoop is de-veloped. This approach enables the creation of an inherently parallel framework that will scale the workload across a cluster. Unlike existing solutions, this framework uses highly optimised joining strategies to enable the completion of eight separate SPARQL queries, comprising over eighty distinct joins, in only two Map/Reduce iterations. Results are pre-sented comparing both na¨ıve and optimised versions of the solution against Jena TDB, demonstrating the superior performance of the Hadoop system and its viability for assess-ing the quality of medical data

The "linked evidence approach" to assess medical tests: a critical analysis

Objectives: A linked evidence approach (LEA) is the synthesis of systematically acquired evidence on the accuracy of a medical test, its impact on clinical decision making and the effectiveness of consequent treatment options. We aimed to assess the practical utility of this methodology and to develop a decision framework to guide its use. Methods: As Australia has lengthy experience with LEA, we reviewed health technology assessment (HTA) reports informing reimbursement decisions by the Medical Services Advisory Committee (August 2005 to March 2012). Eligibility was determined according to predetermined criteria and data were extracted on test characteristics, evaluation methodologies, and reported difficulties. Fifty percent of the evidence-base was independently analyzed by a second reviewer. Results: Evaluations of medical tests for diagnostic (62 percent), staging (27 percent), and screening (6 percent) purposes were available for eighty-nine different clinical indications. Ninety-six percent of the evaluations used either the full LEA methodology or an abridged version (where evidence is linked through to management changes but not patient outcomes). Sixty-one percent had the full evidence linkage. Twenty-five percent of test evaluations were considered problematic; all involving LEA (n = 22). Problems included: determining test accuracy with an imperfect reference standard (41 percent); assessing likely treatment effectiveness in test positive patients when the new test is more accurate than the comparator (18 percent); and determining probable health benefits in those symptomatic patients ruled out using the test (13 percent). A decision framework was formulated to address these problems. Conclusions: LEA is useful for evaluating medical tests but a stepped approach should be followed to determine what evidence is required for the synthesis.Tracy Merlin, Samuel Lehman, Philip Ryan, Janet E. Hille

Linking Emergency Medical Services and Emergency Department Data to Improve Overdose Surveillance in North Carolina

Introduction Linking emergency medical services (EMS) data to emergency department (ED) data enables assessing the continuum of care and evaluating patient outcomes. We developed novel methods to enhance linkage performance and analysis of EMS and ED data for opioid overdose surveillance in North Carolina. Methods We identified data on all EMS encounters in North Carolina during January 1–November 30, 2017, with documented naloxone administration and transportation to the ED. We linked these data with ED visit data in the North Carolina Disease Event Tracking and Epidemiologic Collection Tool. We manually reviewed a subset of data from 12 counties to create a gold standard that informed developing iterative linkage methods using demographic, time, and destination variables. We calculated the proportion of suspected opioid overdose EMS cases that received International Classification of Diseases, Tenth Revision, Clinical Modification diagnosis codes for opioid overdose in the ED. Results We identified 12 088 EMS encounters of patients treated with naloxone and transported to the ED. The 12-county subset included 1781 linkage-eligible EMS encounters, with historical linkage of 65.4% (1165 of 1781) and 1.6% false linkages. Through iterative linkage methods, performance improved to 91.0% (1620 of 1781) with 0.1% false linkages. Among statewide EMS encounters with naloxone administration, the linkage improved from 47.1% to 91.1%. We found diagnosis codes for opioid overdose in the ED among 27.2% of statewide linked records. Practice Implications Through an iterative linkage approach, EMS–ED data linkage performance improved greatly while reducing the number of false linkages. Improved EMS–ED data linkage quality can enhance surveillance activities, inform emergency response practices, and improve quality of care through evaluating initial patient presentations, field interventions, and ultimate diagnoses

Assessing preventable hospitalisation indicators (APHID): protocol for a data-linkage study using cohort study and administrative data

Introduction Potentially preventable hospitalisation (PPH) has been adopted widely by international health systems as an indicator of the accessibility and overall effectiveness of primary care. The Assessing Preventable Hospitalisation InDicators (APHID) study will validate PPH as a measure of health system performance in Australia and Scotland. APHID will be the first large-scale study internationally to explore longitudinal relationships between primary care and PPH using detailed person-level information about health risk factors, health status and health service use. Methods and analysis APHID will create a new longitudinal data resource by linking together data from a large-scale cohort study (the 45 and Up Study) and prospective administrative data relating to use of general practitioner (GP) services, dispensing of pharmaceuticals, emergency department presentations, hospital admissions and deaths. We will use these linked person-level data to explore relationships between frequency, volume, nature and costs of primary care services, hospital admissions for PPH diagnoses, and health outcomes, and factors that confound and mediate these relationships. Using multilevel modelling techniques, we will quantify the contributions of person-level, geographic-level and service-level factors to variation in PPH rates, including socioeconomic status, country of birth, geographic remoteness, physical and mental health status, availability of GP and other services, and hospital characteristics. Ethics and dissemination Participants have consented to use of their questionnaire data and to data linkage. Ethical approval has been obtained for the study. Dissemination mechanisms include engagement of policy stakeholders through a reference group and policy forum, and production of summary reports for policy audiences in parallel with the scientific papers from the study.</p

What should we assess in practice?

Aim: This article reports on a PhD study and follow up work undertaken to review and develop a tool for assessment of practice. Background: The assessment of practice in nursing and midwifery education and, other health professions has been the source of concern, criticism and research for a number of years with the conclusion that it might not be possible to develop an assessment tool that could encompass all aspects of professional practice. Methods: A qualitative evaluation study was undertaken using the naturalistic method of inquiry. A combination of tools was used in order to collect the data and enable progressive focusing and cross checking of the findings. These included documentary analysis, a questionnaire and focus group and individual interviews. The data was collected from documents analysis, focus group interviews, individual interviews and questionnaires. Results: The results showed that the assessment tool in use at the time did not encompass all criteria assessors used and six areas were identified as those to include in any future tool. Conclusion: The six areas identified by subjects as those to include in any assessment tool were further developed with specific statements so that they could be used within a tool. Implications for nursing management and education: Within the changing nature of health care there is a need to review whether the tool used for assessing pre-registration education of nursing and midwifery students practice is ‘fit for purpose’

Assessing the impact of England's National Health Service R&D Health Technology Assessment program using the "payback" approach

Copyright © Cambridge University Press 2009Objectives: This study assesses the impact of the English National Health Service (NHS) Health Technology Assessment (HTA) program using the "payback" framework.Methods: A survey of lead investigators of all research projects funded by the HTA program 1993-2003 supplemented by more detailed case studies of sixteen projects.Results: Of 204 eligible projects, replies were received from 133 or 65 percent. The mean number of peer-reviewed publications per project was 2.9. Seventy-three percent of projects claimed to have had had an impact on policy and 42 percent on behavior. Technology Assessment Reports for the National Institute for Health and Clinical Excellence (NICE) had fewer than average publications but greater impact on policy. Half of all projects went on to secure further funding. The case studies confirmed the survey findings and indicated factors associated with impact.Conclusions: The HTA program performed relatively well in terms of "payback." Facilitating factors included the program's emphasis on topics that matter to the NHS, rigorous methods and the existence of "policy customers" such as NICE

A Delphi study to validate competency-based criteria to assess undergraduate midwifery students' competencies in the maternity ward

Background: workplace learning plays a crucial role in midwifery education. Twelve midwifery schools in Flanders (Belgium) aimed to implement a standardised and evidence-based method to learn and assess competencies in practice. This study focuses on the validation of competency-based criteria to guide and assess undergraduate midwifery students’ postnatal care competencies in the maternity ward. Method: an online Delphi study was carried out. During three consecutive sessions, experts from workplaces and schools were invited to score the assessment criteria as to their relevance and feasibility, and to comment on the content and their formulation. A descriptive quantitative analysis, and a qualitative thematic content analysis of the comments were carried out. A Mann-Whitney U-test was used to investigate diferences between expert groups. Findings:eleven competencies and fifty-six assessment criteria were found appropriate to assess midwifery students’ competencies in the maternity ward. Overall median scores were high and consensus was obtained for all criteria, except for one during the first round. Although all initial assessment criteria (N=89) were scored as relevant, some of them appeared not feasible in practice. Little difference was found between the expert groups. Comments mainly included remarks about concreteness and measurability. Conclusion: this study resulted in validated criteria to assess postnatal care competencies in the maternity ward

Conducting retrospective impact analysis to inform a medical research charity’s funding strategies: The case of Asthma UK

© 2013 Hanney et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.BACKGROUND: Debate is intensifying about how to assess the full range of impacts from medical research. Complexity increases when assessing the diverse funding streams of funders such as Asthma UK, a charitable patient organisation supporting medical research to benefit people with asthma. This paper aims to describe the various impacts identified from a range of Asthma UK research, and explore how Asthma UK utilised the characteristics of successful funding approaches to inform future research strategies. METHODS: We adapted the Payback Framework, using it both in a survey and to help structure interviews, documentary analysis, and case studies. We sent surveys to 153 lead researchers of projects, plus 10 past research fellows, and also conducted 14 detailed case studies. These covered nine projects and two fellowships, in addition to the innovative case studies on the professorial chairs (funded since 1988) and the MRC-Asthma UK Centre in Allergic Mechanisms of Asthma (the ‘Centre’) which together facilitated a comprehensive analysis of the whole funding portfolio. We organised each case study to capture whatever academic and wider societal impacts (or payback) might have arisen given the diverse timescales, size of funding involved, and extent to which Asthma UK funding contributed to the impacts. RESULTS: Projects recorded an average of four peer-reviewed journal articles. Together the chairs reported over 500 papers. All streams of funding attracted follow-on funding. Each of the various categories of societal impacts arose from only a minority of individual projects and fellowships. Some of the research portfolio is influencing asthma-related clinical guidelines, and some contributing to product development. The latter includes potentially major breakthroughs in asthma therapies (in immunotherapy, and new inhaled drugs) trialled by university spin-out companies. Such research-informed guidelines and medicines can, in turn, contribute to health improvements. The role of the chairs and the pioneering collaborative Centre is shown as being particularly important. CONCLUSIONS: We systematically demonstrate that all types of Asthma UK’s research funding assessed are making impacts at different levels, but the main societal impacts from projects and fellowships come from a minority of those funded. Asthma UK used the study’s findings, especially in relation to the Centre, to inform research funding strategies to promote the achievement of impact.This study was funded by Asthma UK

Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. Although each of the participating cancer centers is structured differently, and leaders' titles vary, we know firsthand there are similarities in both the issues we face and the solutions we achieve. As a consortium, we have initiated a dedicated listserv, an open-initiatives program, and targeted biannual face-to-face meetings. These meetings are a place to review our priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues we, as informatics leaders, individually face at our respective institutions and cancer centers. Here we provide a brief history of the CI4CC organization and meeting highlights from the latest CI4CC meeting that took place in Napa, California from October 14-16, 2019. The focus of this meeting was "intersections between informatics, data science, and population science." We conclude with a discussion on "hot topics" on the horizon for cancer informatics