Global Standards to Expedite Learning From Medical Research Data.
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ABSTRACT:
SUBMITTER: Hudson LD
PROVIDER: S-EPMC6039196 | biostudies-literature | 2018 Jul
REPOSITORIES: biostudies-literature
Publications
Global Standards to Expedite Learning From Medical Research Data.
Hudson Lynn D LD Kush Rebecca D RD Navarro Almario Eileen E Seigneuret Nathalie N Jackson Tammy T Jauregui Barbara B Jordan David D Fitzmartin Ronald R Zhou F Liz FL Malone James K JK Galvez Jose J Becnel Lauren B LB
Clinical and translational science 20180426 4
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Project description:ImportanceIncreased wait times and long lengths of stay in emergency departments (EDs) are associated with poor patient outcomes. Systems to improve ED efficiency would be useful. Specifically, minimizing the time to diagnosis by developing novel workflows that expedite test ordering can help accelerate clinical decision-making.ObjectiveTo explore the use of machine learning-based medical directives (MLMDs) to automate diagnostic testing at triage for patients with common pediatric ED diagnoses.Design, setting, and participantsMachine learning models trained on retrospective electronic health record data were evaluated in a decision analytical model study conducted at the ED of the Hospital for Sick Children Toronto, Canada. Data were collected on all patients aged 0 to 18 years presenting to the ED from July 1, 2018, to June 30, 2019 (77 219 total patient visits).ExposureMachine learning models were trained to predict the need for urinary dipstick testing, electrocardiogram, abdominal ultrasonography, testicular ultrasonography, bilirubin level testing, and forearm radiographs.Main outcomes and measuresModels were evaluated using area under the receiver operator curve, true-positive rate, false-positive rate, and positive predictive values. Model decision thresholds were determined to limit the total number of false-positive results and achieve high positive predictive values. The time difference between patient triage completion and test ordering was assessed for each use of MLMD. Error rates were analyzed to assess model bias. In addition, model explainability was determined using Shapley Additive Explanations values.ResultsThere was a total of 42 238 boys (54.7%) included in model development; mean (SD) age of the children was 5.4 (4.8) years. Models obtained high area under the receiver operator curve (0.89-0.99) and positive predictive values (0.77-0.94) across each of the use cases. The proposed implementation of MLMDs would streamline care for 22.3% of all patient visits and make test results available earlier by 165 minutes (weighted mean) per affected patient. Model explainability for each MLMD demonstrated clinically relevant features having the most influence on model predictions. Models also performed with minimal to no sex bias.Conclusions and relevanceThe findings of this study suggest the potential for clinical automation using MLMDs. When integrated into clinical workflows, MLMDs may have the potential to autonomously order common ED tests early in a patient's visit with explainability provided to patients and clinicians.
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Project description:Integration between information systems is critical, especially in the healthcare domain, since interoperability requirements are related to patients' data confidentiality, safety, and satisfaction. The goal of this study is to propose a solution based on the integration between queue management solution (QMS) and the electronic medical records (EMR), using Health Level Seven (HL7) protocols and Extensible Markup Language (XML). The proposed solution facilitates the patient's self-check-in within a healthcare organization in UAE. The solution aims to help in minimizing the waiting times within the outpatient department through early identification of patients who hold the Emirates national ID cards, i.e., whether an Emirati or expatriates. The integration components, solution design, and the custom-designed XML and HL7 messages were clarified in this paper. In addition, the study includes a simulation experiment through control and intervention weeks with 517 valid appointments. The experiment goal was to evaluate the patient's total journey and each related clinical stage by comparing the "routine-based identification" with the "patient's self-check-in" processes in case of booked appointments. As a key finding, the proposed solution is efficient and could reduce the "patient's journey time" by more than 14 minutes and "time to identify" patients by 10 minutes. There was also a significant drop in the waiting time to triage and the time to finish the triage process. In conclusion, the proposed solution is considered innovative and can provide a positive added value for the patient's whole journey.
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Project description:Modern biomedical research is characterised by its high-throughput and interdisciplinary nature. Multiproject and consortium-based collaborations requiring meaningful analysis of multiple heterogeneous phenotypic datasets have become the norm; however, such analysis remains a challenge in many regions across the world. An increasing number of data harmonisation efforts are being undertaken by multistudy collaborations through either prospective standardised phenotype data collection or retrospective phenotype harmonisation. In this regard, the Phenotype Harmonisation Working Group (PHWG) of the Human Heredity and Health in Africa (H3Africa) consortium aimed to facilitate phenotype standardisation by both promoting the use of existing data collection standards (hosted by PhenX), adapting existing data collection standards for appropriate use in low- and middle-income regions such as Africa, and developing novel data collection standards where relevant gaps were identified. Ultimately, the PHWG produced 11 data collection kits, consisting of 82 protocols, 38 of which were existing protocols, 17 were adapted, and 27 were novel protocols. The data collection kits will facilitate phenotype standardisation and harmonisation not only in Africa but also across the larger research community. In addition, the PHWG aims to feed back adapted and novel protocols to existing reference platforms such as PhenX.
| S-EPMC10522421 | biostudies-literature
Project description: Not available
| S-EPMC9951373 | biostudies-literature
Project description:Biomedical informatics has traditionally adopted a linear view of the informatics process (collect, store and analyse) in translational medicine (TM) studies; focusing primarily on the challenges in data integration and analysis. However, a data management challenge presents itself with the new lifecycle view of data emphasized by the recent calls for data re-use, long term data preservation, and data sharing. There is currently a lack of dedicated infrastructure focused on the 'manageability' of the data lifecycle in TM research between data collection and analysis. Current community efforts towards establishing a culture for open science prompt the creation of a data custodianship environment for management of TM data assets to support data reuse and reproducibility of research results. Here we present the development of a lifecycle-based methodology to create a metadata management framework based on community driven standards for standardisation, consolidation and integration of TM research data. Based on this framework, we also present the development of a new platform (PlatformTM) focused on managing the lifecycle for translational research data assets.
| S-EPMC6692384 | biostudies-literature
Project description:BackgroundThe collection, storage, and analysis of large data sets are relevant in many sectors. Especially in the medical field, the processing of patient data promises great progress in personalized health care. However, it is strictly regulated, such as by the General Data Protection Regulation (GDPR). These regulations mandate strict data security and data protection and, thus, create major challenges for collecting and using large data sets. Technologies such as federated learning (FL), especially paired with differential privacy (DP) and secure multiparty computation (SMPC), aim to solve these challenges.ObjectiveThis scoping review aimed to summarize the current discussion on the legal questions and concerns related to FL systems in medical research. We were particularly interested in whether and to what extent FL applications and training processes are compliant with the GDPR data protection law and whether the use of the aforementioned privacy-enhancing technologies (DP and SMPC) affects this legal compliance. We placed special emphasis on the consequences for medical research and development.MethodsWe performed a scoping review according to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews). We reviewed articles on Beck-Online, SSRN, ScienceDirect, arXiv, and Google Scholar published in German or English between 2016 and 2022. We examined 4 questions: whether local and global models are "personal data" as per the GDPR; what the "roles" as defined by the GDPR of various parties in FL are; who controls the data at various stages of the training process; and how, if at all, the use of privacy-enhancing technologies affects these findings.ResultsWe identified and summarized the findings of 56 relevant publications on FL. Local and likely also global models constitute personal data according to the GDPR. FL strengthens data protection but is still vulnerable to a number of attacks and the possibility of data leakage. These concerns can be successfully addressed through the privacy-enhancing technologies SMPC and DP.ConclusionsCombining FL with SMPC and DP is necessary to fulfill the legal data protection requirements (GDPR) in medical research dealing with personal data. Even though some technical and legal challenges remain, for example, the possibility of successful attacks on the system, combining FL with SMPC and DP creates enough security to satisfy the legal requirements of the GDPR. This combination thereby provides an attractive technical solution for health institutions willing to collaborate without exposing their data to risk. From a legal perspective, the combination provides enough built-in security measures to satisfy data protection requirements, and from a technical perspective, the combination provides secure systems with comparable performance with centralized machine learning applications.
| S-EPMC10131784 | biostudies-literature
Project description:The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Project description:ObjectiveThe Multiple Chronic Conditions (MCCs) Electronic Care (e-Care) Plan project aims to establish care planning data standards for individuals living with MCCs. This article reports on the portion of the project focused on long COVID and presents the process of identifying and modeling data elements using the HL7 Fast Healthcare Interoperability Resources (FHIR) standard.Materials and methodsCritical data elements for managing long COVID were defined through a consensus-driven approach involving a Technical Expert Panel (TEP). This involved 2 stages: identifying data concepts and establishing electronic exchange standards.ResultsThe TEP-identified and -approved long COVID data elements were mapped to the HL7 US Core FHIR profiles for syntactic representation, and value sets from standard code systems were developed for semantic representation of the long COVID concepts.DiscussionEstablishing common long COVID data standards through this process, and representing them with the HL7 FHIR standard, facilitates interoperable data collection, benefiting care delivery and patient-centered outcomes research (PCOR) for long COVID. These standards may support initiatives including clinical and pragmatic trials, quality improvement, epidemiologic research, and clinical and social interventions.By building standards-based data collection, this effort accelerates the development of evidence to better understand and deliver effective long COVID interventions and patient and caregiver priorities within the context of MCCs and to advance the delivery of coordinated, person-centered care.ConclusionThe open, collaborative, and consensus-based approach used in this project will enable the sharing of long COVID-related health concerns, interventions, and outcomes for patient-centered care coordination across diverse clinical settings and will facilitate the use of real-world data for long COVID research.
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Project description:BackgroundUniversities undertake the majority of publicly funded research in Germany and hence bear a responsibility to contribute to global health efforts. So far, involvement and impact of German medical faculties in global health are unknown. Our aim was to systematically asses and evaluate German medical faculties' contribution to global health related research and education, as well as their policies and practices concerning open access publishing and equitable licensing.MethodsWe assessed the involvement in global health of all 36 publicly funded medical faculties in Germany during 2010-2014 in three areas: innovation, access and education, using the following indicators: research funding and publications focused on global health or poverty-related and neglected diseases; open access publishing and policies promoting access to medical innovations worldwide; provision of global health education. Data were gathered from public databases, university websites and questionnaires sent to individual universities for validation and triangulation.ResultsThere was a high level of variability between institutions and indicators. The proportion of research funding for poverty-related and neglected diseases research ranged between 0.0-1.1%. The top five institutions received nearly 85% of the total poverty-related and neglected diseases research funding. 20 of 36 universities had an institutional open access publishing policy, 19 had an open access publishing fund, 16 had neither. Only one university reported having used an equitable licensing policy. 22 of 36 faculties provided some global health education, but only one of them included global health in their core undergraduate medical curriculum as a compulsory course with more than just single lectures.ConclusionObtained data indicate that global health and poverty-related and neglected diseases research at German medical faculties is highly concentrated in a few institutions, open-access publishing and equitable licensing policies are mostly absent, and only little global health education exists. Universities and government should address global health strategically in both research and education at medical faculties to reflect the country's economic and political weight and human resource potential.
| S-EPMC7170220 | biostudies-literature
Project description:BackgroundThe COVID-19 pandemic has forced medical schools to suspend on-campus live-sessions and shift to distance-learning (DL). This precipitous shift presented medical educators with a challenge, 'to create a "simulacrum" of the learning environment that students experience in classroom, in DL'. This requires the design of an adaptable and versatile DL-framework bearing in mind the theoretical underpinnings associated with DL. Additionally, effectiveness of such a DL-framework in content-delivery followed by its evaluation at the user-level, and in cognitive development needs to be pursued such that medical educators can be convinced to effectively adopt the framework in a competency-based medical programme.MainIn this study, we define a DL-framework that provides a 'simulacrum' of classroom experience. The framework's blueprint was designed amalgamating principles of: Garrison's community inquiry, Siemens' connectivism and Harasim's online-collaborative-learning; and improved using Anderson's DL-model. Effectiveness of the DL-framework in course delivery was demonstrated using the exemplar of fundamentals in epidemiology and biostatistics (FEB) course during COVID-19 lockdown. Virtual live-sessions integrated in the framework employed a blended-approach informed by instructional-design strategies of Gagne and Peyton. The efficiency of the framework was evaluated using first 2 levels of Kirkpatrick's framework. Of 60 students, 51 (85%) responded to the survey assessing perception towards DL (Kirkpatrick's Level 1). The survey-items, validated using exploratory factor analysis, were classified into 4-categories: computer expertise; DL-flexibility; DL-usefulness; and DL-satisfaction. The overall perception for the 4 categories, highlighted respondents' overall satisfaction with the framework. Scores for specific survey-items attested that the framework promoted collaborative-learning and student-autonomy. For, Kirkpatrick's Level 2 that is, cognitive-development, performance in FEB's summative-assessment of students experiencing DL was compared with students taught using traditional methods. Similar, mean-scores for both groups indicated that shift to DL didn't have an adverse effect on students' learning.ConclusionIn conclusion, we present here the design, implementation and evaluation of a DL-framework, which is an efficient pedagogical approach, pertinent for medical schools to adopt (elaborated using Bourdieu's Theory of Practice) to address students' learning trajectories during unprecedented times such as that during the COVID-19 pandemia.
| S-EPMC8981515 | biostudies-literature