Approaches and criteria for provenance in biomedical data sets/workflows: a scoping review (Preprint)

2021 ◽  
Author(s):  
Kerstin Gierend ◽  
Frank Krüger ◽  
Dagmar Waltemath ◽  
Maximilian Fünfgeld ◽  
Atinkut Alamirrew Zeleke ◽  
...  

BACKGROUND Provenance supports the understanding of data genesis and it is a key factor to ensure the trustworthiness of the digital objects containing (sensitive) scientific data. Provenance information contributes to a better understanding of scientific results and fosters collaboration on existing data as well as data-sharing. This encompasses defining comprehensive concepts and standards for transparency and traceability, reproducibility, validity and quality assurance during clinical and scientific data workflows and/or research. OBJECTIVE The aim of this scoping review is to investigate approaches and challenges for provenance tracking as well as disclosing current knowledge gaps in the area. The review covers modeling aspects as well as metadata frameworks for capturing meaningful and usable provenance information during creation, collection and processing of (sensitive) scientific biomedical data. The objective of the review also includes the examination of quality aspects of provenance criteria. METHODS The scoping review will follow the methodological framework by Arksey and O'Malley. Relevant publications will be obtained by querying PubMed and Web of Science. All articles in English language will be included, within the time period between 2006 and 23-March 2021. Database retrieval will be accompanied by manual search for grey literature. Potential publications will then be exported into a reference management software, and duplicates will be removed. Afterwards, the obtained set of papers will be transferred into a systematic review management tool. All publications will be screened, extracted and analyzed: title and abstract screening will be carried out by 4 independent reviewers. Majority vote is required for consent to eligibility of articles based on defined inclusion and exclusion criteria. Full-text reading will be performed independently by 2 reviewers and in the last step key information will be extracted on a template which has been evaluated by the reviewers beforehand. If agreement cannot be reached, the conflict will be resolved by a domain expert. Charted data will be analyzed by categorizing and summarizing the individual data items based on the research questions. Tabular or graphical overviews will be given, if applicable. RESULTS The reporting follows the extension of the PRISMA statements for scoping reviews (PRISMA-ScR). Electronic database searches in PubMed and Web of Science resulted in 469 matches after deduplication. As of June 2021, the scoping review is in the full text screening stage. The data extraction using the pretested charting template will follow the full text screening stage. We expect the scoping review report to be completed by the end of 2021. CONCLUSIONS Information about the origin of healthcare data has a major impact on the quality and the reusability of scientific results as well as follow-up activities. This scoping review will provide information about current approaches, challenges or knowledge gaps with provenance tracking in biomedical sciences.

2021 ◽  
Vol 10 (3) ◽  
pp. e001293
Author(s):  
Victoria Bohm ◽  
Diane Lacaille ◽  
Nicole Spencer ◽  
Claire EH Barber

ObjectiveBalanced scorecards (BSCs) were developed in the early 1990s in corporate settings as a strategic performance management tool that emphasised measurement from multiple perspectives. Since their introduction, BSCs have been adapted for a variety of industries, including to healthcare settings. The aim of this scoping review was to describe the application of BSCs in healthcare.MethodsMedline, Embase and CINHAL databases were searched using keywords and medical subject headings for ‘balanced scorecard’ and related terms from 1992 to 17/04/2020. Title and abstract screening and full text review were conducted in duplicate by two reviewers. Studies describing the development and/or implementation of a BSC in a healthcare setting were included. Data were abstracted using pilot-tested forms and reviewed for key themes and findings.Results8129 records were identified and 841 underwent a full text review. 87 articles were included. Over 26 countries were represented and the majority of BSCs were applied at a local level (54%) in hospital settings (41%). While almost all discussed Kaplan and Norton’s original BSC (97%), only 69% described alignment with a strategic plan. Patients/family members were rarely involved in development teams (3%) which typically were comprised of senior healthcare leaders/administrators. Only 21% of BSCs included perspectives using identical formatting to the original BSC description. Lessons learnt during development addressed three main themes: scorecard design, stakeholder engagement and feasibility.ConclusionsBSC frameworks have been used in various healthcare settings but frequently undergo adaptation from the original description in order to suit a specific healthcare context. Future BSCs should aim to include patients/families to promote patient-centred healthcare systems. Considering the heterogeneity evident in development approaches, methodological guidance in this area is warranted.


2020 ◽  
Author(s):  
Pat Camp ◽  
Mirha Girt ◽  
Alix Wells ◽  
Adeeb Malas ◽  
Maryke Peter ◽  
...  

BACKGROUND Indigenous people in Canada, the United States, Australia, and New Zealand experience an increased burden of chronic diseases compared to non-Indigenous people in these countries. Lack of necessary services and culturally relevant care for Indigenous people contributes to this burden. Many Indigenous communities have implemented systems, such as virtual care, to improve chronic disease management. Virtual care has extended beyond videoconferencing to include more advanced technologies, such as remote biometric monitoring devices. However, given the historical and ongoing Western intrusion into Indigenous day to day life, these technologies may seem more invasive and thus require additional research on their acceptability and utility within Indigenous populations. OBJECTIVE The objective of this paper is to present the protocol for a scoping review, which aims to map existing evidence. This study is based on the following guiding research question: What are the characteristics of virtual care use by Indigenous adult populations in Canada, the United States, Australia, and New Zealand? The subquestions are related to the technology used, health conditions and nature of the virtual care, cultural safety, and key concepts for effective use. METHODS This scoping review protocol is informed by the methodology described by the Joanna Briggs Institute and is supplemented by the frameworks proposed by Arksey and O’Malley and Levac et al. A search for published and gray literature, written in English, and published between 2000 and present will be completed utilizing electronic databases and search engines, including MEDLINE, CINAHL, Embase, Indigenous Peoples of North America, Australian Indigenous HealthInfoNet, Informit, and Native Health Database. Search results will be uploaded to the review software, Covidence, for title and abstract screening before full-text screening begins. This process will be repeated for gray literature. Upon completion, a data abstraction tool will organize the relevant information into categorical formations. RESULTS The search strategy has been confirmed, and the screening of titles and abstracts is underway. As of October 2020, we have identified over 300 articles for full-text screening. CONCLUSIONS Previous reviews have addressed virtual care within Indigenous communities. However, new virtual care technologies have since emerged; subsequently, additional literature has been published. Mapping and synthesizing this literature will inform new directions for research and discussion. CLINICALTRIAL INTERNATIONAL REGISTERED REPORT PRR1-10.2196/21860


10.2196/21860 ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. e21860
Author(s):  
Pat Camp ◽  
Mirha Girt ◽  
Alix Wells ◽  
Adeeb Malas ◽  
Maryke Peter ◽  
...  

Background Indigenous people in Canada, the United States, Australia, and New Zealand experience an increased burden of chronic diseases compared to non-Indigenous people in these countries. Lack of necessary services and culturally relevant care for Indigenous people contributes to this burden. Many Indigenous communities have implemented systems, such as virtual care, to improve chronic disease management. Virtual care has extended beyond videoconferencing to include more advanced technologies, such as remote biometric monitoring devices. However, given the historical and ongoing Western intrusion into Indigenous day to day life, these technologies may seem more invasive and thus require additional research on their acceptability and utility within Indigenous populations. Objective The objective of this paper is to present the protocol for a scoping review, which aims to map existing evidence. This study is based on the following guiding research question: What are the characteristics of virtual care use by Indigenous adult populations in Canada, the United States, Australia, and New Zealand? The subquestions are related to the technology used, health conditions and nature of the virtual care, cultural safety, and key concepts for effective use. Methods This scoping review protocol is informed by the methodology described by the Joanna Briggs Institute and is supplemented by the frameworks proposed by Arksey and O’Malley and Levac et al. A search for published and gray literature, written in English, and published between 2000 and present will be completed utilizing electronic databases and search engines, including MEDLINE, CINAHL, Embase, Indigenous Peoples of North America, Australian Indigenous HealthInfoNet, Informit, and Native Health Database. Search results will be uploaded to the review software, Covidence, for title and abstract screening before full-text screening begins. This process will be repeated for gray literature. Upon completion, a data abstraction tool will organize the relevant information into categorical formations. Results The search strategy has been confirmed, and the screening of titles and abstracts is underway. As of October 2020, we have identified over 300 articles for full-text screening. Conclusions Previous reviews have addressed virtual care within Indigenous communities. However, new virtual care technologies have since emerged; subsequently, additional literature has been published. Mapping and synthesizing this literature will inform new directions for research and discussion. International Registered Report Identifier (IRRID) PRR1-10.2196/21860


Author(s):  
Saryu Sharma ◽  
Hana Kim ◽  
Havan Harris ◽  
Amanda Haberstroh ◽  
Heather Harris Wright ◽  
...  

Aim The aim of this scoping review is to identify the eye tracking paradigms and eye movement measures used to investigate auditory and reading comprehension deficits in persons with aphasia (PWA). Method MEDLINE via PubMed, Cochrane, CINAHL, Embase, PsycINFO, OTseeker, Scopus, Google Scholar, Grey Literature Database, and ProQuest Search (Dissertations & Theses) were searched for relevant studies. The Covidence software was used to manage the initial and full-text screening process for the search. Results and Discussion From a total of 1,803 studies, 68 studies were included for full-text screening. In addition, 418 records from gray literature were also screened. After full-text screening, 16 studies were included for this review—12 studies for auditory comprehension in PWA and four studies for reading comprehension in PWA. The review highlights the use of common eye tracking paradigms used to study language comprehension in PWA. We also discusse eye movement measures and how they help in assessing auditory and reading comprehension. Methodological challenges of using eye tracking are discussed. Conclusion The studies summarized in this scoping review provide evidence that the eye tracking methods are beneficial for studying auditory and reading comprehension in PWA.


2020 ◽  
Vol 17 (12) ◽  
pp. 1275-1284
Author(s):  
Eduardo L. Caputo ◽  
Felipe F. Reichert

Background: This scoping review aimed to identify the available evidence related to physical activity (PA) and the coronavirus disease (COVID-19) pandemic. Methods: A search in 6 databases (PubMed, Embase, SPORTDiscus, Scopus, Web of Science, and CINAHL) was conducted on July 23, 2020. Medical subject headings and keywords related to PA and COVID-19 were combined to conduct the online search, which covered the period from January to July 2020. Results: Overall, 1784 articles were retrieved. After duplicate removal and title, abstract, and full-text screening, 41 articles were included. Most of the included studies were quantitative and collected data through online interviews/questionnaires, with sample sizes larger than 100 and composed by adults and older adults. Changes in PA levels due to the COVID-19 pandemic were the most assessed outcome, followed by the association between mental health issues and PA. Only 2 studies assessed the direct effects of PA on COVID-19. Conclusion: Most of the evidence identified a decrease in PA levels due to social distancing measures and that PA might help to decrease the mental health burden related to the COVID-19 outbreak.


2021 ◽  
pp. tobaccocontrol-2021-056896
Author(s):  
Marzena Hiler ◽  
Anna-Sophie Weidner ◽  
Lynn C Hull ◽  
Allison N Kurti ◽  
Elena V Mishina

ObjectiveThis scoping review provides an overview of the existing literature on biomarkers of exposure from electronic nicotine delivery systems (ENDS) use and identifies gaps in existing knowledge.Data sourcesWe searched two international databases (PubMed and Web of Science) to identify relevant studies published from August 2013 to February 2021.Data selectionStudies were included if they assessed and compared biomarkers of exposure between exclusive ENDS users, non-users, exclusive cigarette smokers, dual users of ENDS and cigarettes or cigarette smokers who switch to ENDS.Data extraction and synthesisOf the 5074 studies identified, 188 studies met criteria and were selected for full-text screening. Of these, 27 studies were selected for inclusion and data extraction.ConclusionsConsistent, although limited, evidence shows that exclusive ENDS users have elevated levels of biomarkers of certain volatile organic compounds (VOCs; eg, acrylamide and acrylonitrile), metals (eg, cadmium and selenium) and propylene glycol compared with non-users; however, evidence for biomarkers of other toxicants (eg, acrolein, benzene and chromium) is mixed. Biomarkers of most VOCs are lower in ENDS users compared with cigarette smokers, and cigarette smokers who switch to ENDS consistently show reductions in VOC biomarkers. Evidence comparing metal exposures from exclusive ENDS use, cigarette smoking and dual use is mixed and depends on the metal. ENDS and e-liquid characteristics as well as use patterns may be associated with elevated exposure to VOCs and metals. Additional rigorous, controlled studies can assess biomarker exposures from ENDS use and inform the overall risk–benefit of ENDS use for different user populations.


2021 ◽  
Author(s):  
Khalia Ackermann ◽  
Jannah Baker ◽  
Malcolm Green ◽  
Mary Fullick ◽  
Hilal Varinli ◽  
...  

BACKGROUND Sepsis is a significant cause of morbidity and mortality worldwide. Early detection of septic patients followed by rapid treatment initiation improves patient outcomes and saves lives. Hospitals are increasingly utilizing computerized clinical decision support (CCDS) systems for the rapid identification of adult septic patients. OBJECTIVE This scoping review aimed to systematically describe studies reporting on the use and evaluation of CCDS systems for early detection of adult sepsis inpatients. METHODS The protocol for this scoping review has been previously published. Ten electronic databases (MEDLINE, Embase, CINAHL, The Cochrane database, LILACS, Scopus, Web of Science, OpenGrey, clinicaltrials.gov, and PQDT) were comprehensively searched to identify relevant studies. Title, abstract, and full-text screening were performed by two independent reviewers using predefined eligibility criteria. Data charting was performed by one reviewer with a second reviewer double checking a random sample of studies. Any disagreements were discussed with input from a third reviewer. In this review we present the results for adult inpatients, including studies that do not specify patient age. RESULTS A search of the electronic databases retrieved 12139 studies following duplicate removal. We identified 124 studies for inclusion after title, abstract, full-text screening, and hand-searching were complete. Nearly all studies (n=121, 97.6%) were published after 2009. Half the studies were journal articles (n=65), and the remainder were conference abstracts and theses (n=54 and 5 respectively). Most studies used a single cohort (n=54; 43.5%) or before-after (n=42; 33.9%) approach. Of all 124 included studies, patient outcomes were the most frequently reported outcomes (n=107; 86.3%), followed by sepsis treatment and management (n=75; 60.5%), CCDS usability (n=14; 11.3%), and cost outcomes (n=9; 7.3%). For sepsis identification, the systemic inflammatory response syndrome (SIRS) criteria were the most commonly used, either alone (n=50; 40.3%), combined with organ dysfunction (n=28; 22.6%) or combined with other criteria (n=23; 18.5%). Over half of the CCDS systems (n=68; 54.8%) were implemented alongside other sepsis-related interventions. CONCLUSIONS The current body of literature investigating the implementation of CCDS systems for the early detection of adult sepsis inpatients is extremely diverse. There is substantial variability in study design, CCDS criteria and characteristics, and outcomes measured across the identified literature. Future research on CCDS system usability, cost, and impact on sepsis morbidity is needed. INTERNATIONAL REGISTERED REPORT RR2-10.2196/24899


2021 ◽  
pp. 152483802098556
Author(s):  
Mark A. Wood ◽  
Stuart Ross ◽  
Diana Johns

In the last decade, an array of smartphone apps have been designed to prevent crime, violence, and abuse. The evidence base of these apps has, however, yet to analyzed systematically. To rectify this, the aims of this review were (1) to establish the extent, range, and nature of research into smartphone apps with a primary crime prevention function; (2) to locate gaps in the primary crime prevention app literature; and (3) to develop a typology of primary crime prevention apps. Employing a scoping review methodology and following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, studies were identified via Web of Science, EBSCOhost, and Google Scholar. We included English-language research published between 2008 and 2020 that examined smartphone applications designed explicitly for primary crime prevention. Sixty-one publications met our criteria for review, out of an initial sample of 151 identified. Our review identified six types of crime prevention app examined in these publications: self-surveillance apps, decision aid apps, child-tracking apps, educational apps, crime-mapping/alert apps, and crime reporting apps. The findings of our review indicate that most of these forms of primary crime prevention apps have yet to be rigorously evaluated and many are not evidence-based in their design. Consequently, our review indicates that recent enthusiasm over primary crime prevention apps is not supported by an adequate evidence base.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1098.2-1099
Author(s):  
O. Russell ◽  
S. Lester ◽  
R. Black ◽  
C. Hill

Background:Socioeconomic status (SES) influences disease outcomes in rheumatoid arthritis (RA) patients. (1, 2) Differences in medication use could partly explain this association. (3) A scoping review was used to identify research conducted on this topic and determine what knowledge gaps remain.Objectives:To determine what research has been conducted on this topic, how this research has defined SES and medication use, and establish what knowledge gaps remain.Methods:MEDLINE, EMBASE and PsychInfo were searched from their inception until May 2019 for studies which assessed SES and medication use as outcome variables. Studies were included if they measured medication use and incorporated an SES measure as a comparator variable.SES was defined using any of the “PROGRESS” framework variables (4) including patients’ stated gender, age, educational attainment, employment, occupational class, personal income, marital status, health insurance coverage, area- (neighbourhood) level SES, or patients’ stated race and/or ethnicity. Medication use was broadly defined as either prescription or dispensation of a medicine, medication adherence, or delays in treatment. Data was extracted on studies’ primary objectives, measurement of specific SES measures, patients’ medication use, and whether studies assessed for differences in patients’ medication use according to SES variables.Results:1464 studies were identified by this search from which 74 studies were selected for inclusion, including 52 published articles. Studies’ publication year ranged from 1994-2019, and originated from 20 countries; most commonly from the USA.Studies measured a median of 4 SES variables (IQR 3-6), with educational achievement, area level SES and race/ethnicity the most frequently recorded.Likelihood of disease modifying antirheumatic drug (DMARD) prescription was the most frequent primary objective recorded.96% of studies reported on patients’ use of DMARDs, with glucocorticoids and analgesics being reported in fewer studies (51% and 23% respectively.)Most included studies found at least one SES measure to be significantly associated with differences in patients’ medication use. In some studies, however, this result was not necessarily drawn from the primary outcome and therefore may not have been adjusted for covariates.70% of published studies measuring patients’ income (n=14 of 20) and 58% of those that measured race/ethnicity (n=14 of 24) documented significant differences in patients’ medication use according to these SES variables, although the direction of this effect – whether it led to ‘greater’ or ‘lesser’ medication use – varied between studies.Conclusion:Multiple definitions of SES are used in studies of medication use in RA patients. Despite this, most identified studies found evidence of a difference in medication use by patient groups that differed by an SES variable, although how medication use differed was found to vary between studies. This latter observation may relate to contextual factors pertaining to differences in countries’ healthcare systems. Further prospective studies with clearly defined SES and medication use measures may help confirm the apparent association between SES and differences in medication use.References:[1]Jacobi CE, Mol GD, Boshuizen HC, Rupp I, Dinant HJ, Van Den Bos GA. Impact of socioeconomic status on the course of rheumatoid arthritis and on related use of health care services. Arthritis Rheum. 2003;49(4):567-73.[2]ERAS Study Group. Socioeconomic deprivation and rheumatoid disease: what lessons for the health service? ERAS Study Group. Early Rheumatoid Arthritis Study. Annals of the rheumatic diseases. 2000;59(10):794-9.[3]Verstappen SMM. The impact of socio-economic status in rheumatoid arthritis. Rheumatology (Oxford). 2017;56(7):1051-2.[4]O’Neill J, Tabish H, Welch V, Petticrew M, Pottie K, Clarke M, et al. Applying an equity lens to interventions: using PROGRESS ensures consideration of socially stratifying factors to illuminate inequities in health. J Clin Epidemiol. 2014;67(1):56-64.Acknowledgements:This research was supported by an Australian Government Research Training Program Scholarship.Disclosure of Interests:None declared


2021 ◽  
pp. 153944922110326
Author(s):  
Mary E. Stoykov ◽  
Courtney Heidle ◽  
Shamshir Kang ◽  
Lisa Lodesky ◽  
Lindsay E. Maccary ◽  
...  

Sensory priming is a technique to facilitate neuroplasticity and improve motor skills after injury. Common sensory priming modalities include peripheral nerve stimulation/somatosensory electrical stimulation (PNS/SES), transient functional deafferentation (TFD), and vibration. The aim of this study was to determine whether sensory priming with a motor intervention results in improved upper limb motor impairment or function after stroke. PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, and EMBASE were the databases used to search the literature in July 2020. This scoping review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and recommendations for the Cochrane collaboration. In total, 30 studies were included in the analysis: three studies examined TFD, 16 examined PNS/SES, 10 studied vibration, and one combined the three stimulation techniques. Most studies reported significant improvements for participants receiving sensory priming. Given the low risk, it may be advantageous to use sensory-based priming prior to or concurrent with upper limb training after stroke.


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