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Code archive corresponding to the manuscript submission: "Quantifying the Optimism of Naive Cross-Validation for Binary Outcome Prediction with Repeated-Measures Predictors: A Simulation Study and Clinical Illustration."
The editors of BMC Medical Research Methodology would like to thank all our reviewers who have contributed to the journal in Volume 15 (2015).
BACKGROUND: An observed decrease of physician scientists in medical practice has generated much recent interest in increasing the exposure of research programs in medical school. The aim of this study was to review the experience and attitudes regarding research by medical students in Canada. METHODS: An anonymous, cross-sectional, self-report questionnaire was administered to second and fourth year students in three medical schools in Ontario between February and May of 2005. Questions were primarily closed-ended and consisted of Likert scales. Descriptive and correlative statistics were used to analyze the responses between students of different years and previous research experience. RESULTS: There was a 47% (327/699) overall response rate to the questionnaire. Despite 87% of respondents reporting that they had been involved in some degree of research prior to medical school, 43% report that they have not been significantly involved in research activity during medical school and 24% had no interest in any participation. There were significant differences in the attitudes towards research endeavors during medical school between students in their fourth year compared to second year. The greatest barriers to involvement in research in medical school appear to be time, availability of research mentors, formal teaching of research methodology and the perception that the student would not receive appropriate acknowledgement for work put towards a research project. CONCLUSION: The results of this self-report survey outline the significant differences in attitudes towards mandatory research as a component of critical inquiry and scholarship in the undergraduate curriculum in Ontario medical schools.
BACKGROUND: Problem-based learning (PBL) is a pedagogical approach that shifts the role of the teacher to the student (student-centered) and is based on self-directed learning. Although PBL has been adopted in undergraduate and postgraduate medical education, the effectiveness of the method is still under discussion. The author's purpose was to appraise available international evidence concerning to the effectiveness and usefulness of PBL methodology in undergraduate medical teaching programs. METHODS: The authors applied the Arksey and O'Malley framework to undertake a scoping review. The search was carried out in February 2021 in PubMed and Web of Science including all publications in English and Spanish with no limits on publication date, study design or country of origin. RESULTS: The literature search identified one hundred and twenty-four publications eligible for this review. Despite the fact that this review included many studies, their design was heterogeneous and only a few provided a high scientific evidence methodology (randomized design and/or systematic reviews with meta-analysis). Furthermore, most were single-center experiences with small sample size and there were no large multi-center studies. PBL methodology obtained a high level of satisfaction, especially among students. It was more effective than other more traditional (or lecture-based methods) at improving social and communication skills, problem-solving and self-learning skills. Knowledge retention and academic performance weren't worse (and in many studies were better) than with traditional methods. PBL was not universally widespread, probably because requires greater human resources and continuous training for its implementation. CONCLUSION: PBL is an effective and satisfactory methodology for medical education. It is likely that through PBL medical students will not only acquire knowledge but also other competencies that are needed in medical professionalism.
BACKGROUND: This study aims to review the literature regarding the barriers to sampling, recruitment, participation, and retention of members of socioeconomically disadvantaged groups in health research and strategies for increasing the amount of health research conducted with socially disadvantaged groups. METHODS: A systematic review with narrative synthesis was conducted. Searches of electronic databases Medline, PsychInfo, EMBASE, Social Science Index via Web of Knowledge and CINHAL were conducted for English language articles published up to May 2013. Qualitative and quantitative studies as well as literature reviews were included. Articles were included if they reported attempts to increase disadvantaged group participation in research, or the barriers to research with disadvantaged groups. Groups of interest were those described as socially, culturally or financially disadvantaged compared to the majority of society. Eligible articles were categorised according to five phases of research: 1) sampling, 2) recruitment and gaining consent, 3) data collection and measurement, 4) intervention delivery and uptake, and 5) retention and attrition. RESULTS: In total, 116 papers from 115 studies met inclusion criteria and 31 previous literature reviews were included. A comprehensive summation of the major barriers to working with various disadvantaged groups is provided, along with proposed strategies for addressing each of the identified types of barriers. Most studies of strategies to address the barriers were of a descriptive nature and only nine studies reported the results of randomised trials. CONCLUSIONS: To tackle the challenges of research with socially disadvantaged groups, and increase their representation in health and medical research, researchers and research institutions need to acknowledge extended timeframes, plan for higher resourcing costs and operate via community partnerships.
In 2011, the National Institute on Aging and Alzheimer's Association created separate diagnostic recommendations for the preclinical, mild cognitive impairment, and dementia stages of Alzheimer's disease. Scientific progress in the interim led to an initiative by the National Institute on Aging and Alzheimer's Association to update and unify the 2011 guidelines. This unifying update is labeled a "research framework" because its intended use is for observational and interventional research, not routine clinical care. In the National Institute on Aging and Alzheimer's Association Research Framework, Alzheimer's disease (AD) is defined by its underlying pathologic processes that can be documented by postmortem examination or in vivo by biomarkers. The diagnosis is not based on the clinical consequences of the disease (i.e., symptoms/signs) in this research framework, which shifts the definition of AD in living people from a syndromal to a biological construct. The research framework focuses on the diagnosis of AD with biomarkers in living persons. Biomarkers are grouped into those of β amyloid deposition, pathologic tau, and neurodegeneration [AT(N)]. This ATN classification system groups different biomarkers (imaging and biofluids) by the pathologic process each measures. The AT(N) system is flexible in that new biomarkers can be added to the three existing AT(N) groups, and new biomarker groups beyond AT(N) can be added when they become available. We focus on AD as a continuum, and cognitive staging may be accomplished using continuous measures. However, we also outline two different categorical cognitive schemes for staging the severity of cognitive impairment: a scheme using three traditional syndromal categories and a six-stage numeric scheme. It is important to stress that this framework seeks to create a common language with which investigators can generate and test hypotheses about the interactions among different pathologic processes (denoted by biomarkers) and cognitive symptoms. We appreciate the concern that this biomarker-based research framework has the potential to be misused. Therefore, we emphasize, first, it is premature and inappropriate to use this research framework in general medical practice. Second, this research framework should not be used to restrict alternative approaches to hypothesis testing that do not use biomarkers. There will be situations where biomarkers are not available or requiring them would be counterproductive to the specific research goals (discussed in more detail later in the document). Thus, biomarker-based research should not be considered a template for all research into age-related cognitive impairment and dementia; rather, it should be applied when it is fit for the purpose of the specific research goals of a study. Importantly, this framework should be examined in diverse populations. Although it is possible that β-amyloid plaques and neurofibrillary tau deposits are not causal in AD pathogenesis, it is these abnormal protein deposits that define AD as a unique neurodegenerative disease among different disorders that can lead to dementia. We envision that defining AD as a biological construct will enable a more accurate characterization and understanding of the sequence of events that lead to cognitive impairment that is associated with AD, as well as the multifactorial etiology of dementia. This approach also will enable a more precise approach to interventional trials where specific pathways can be targeted in the disease process and in the appropriate people.
This literature review paper discusses the proper use of qualitative research methodology to discuss several aspects of the research for the improvement of the skill of the readers. During the last few decades, the use of qualitative research has been increased in many institutions. It can be used to explore several areas of human behavior for the development of organizations. The purpose of this study is to provide inspirations to the new researchers for the development of their qualitative articles. The paper analyzes the design of qualitative research giving some methodological suggestions to make it explicable to the reader. In this paper an attempt has been taken to study the background of the qualitative research methodologyin social sciences and some other related subjects, along with the importance, and main features of the study.
BACKGROUND: The syntheses of multiple qualitative studies can pull together data across different contexts, generate new theoretical or conceptual models, identify research gaps, and provide evidence for the development, implementation and evaluation of health interventions. This study aims to develop a framework for reporting the synthesis of qualitative health research. METHODS: We conducted a comprehensive search for guidance and reviews relevant to the synthesis of qualitative research, methodology papers, and published syntheses of qualitative health research in MEDLINE, Embase, CINAHL and relevant organisational websites to May 2011. Initial items were generated inductively from guides to synthesizing qualitative health research. The preliminary checklist was piloted against forty published syntheses of qualitative research, purposively selected to capture a range of year of publication, methods and methodologies, and health topics. We removed items that were duplicated, impractical to assess, and rephrased items for clarity. RESULTS: The Enhancing transparency in reporting the synthesis of qualitative research (ENTREQ) statement consists of 21 items grouped into five main domains: introduction, methods and methodology, literature search and selection, appraisal, and synthesis of findings. CONCLUSIONS: The ENTREQ statement can help researchers to report the stages most commonly associated with the synthesis of qualitative health research: searching and selecting qualitative research, quality appraisal, and methods for synthesising qualitative findings. The synthesis of qualitative research is an expanding and evolving methodological area and we would value feedback from all stakeholders for the continued development and extension of the ENTREQ statement.
BACKGROUND: Structural equation modeling (SEM) is a set of statistical techniques used to measure and analyze the relationships of observed and latent variables. Similar but more powerful than regression analyses, it examines linear causal relationships among variables, while simultaneously accounting for measurement error. The purpose of the present paper is to explicate SEM to medical and health sciences researchers and exemplify their application. FINDINGS: To facilitate its use we provide a series of steps for applying SEM to research problems. We then present three examples of how SEM has been utilized in medical and health sciences research. CONCLUSION: When many considerations are given to research planning, SEM can provide a new perspective on analyzing data and potential for advancing research in medical and health sciences.
BACKGROUND: The Medical Research Councils' framework for complex interventions has been criticized for not including theory-driven approaches to evaluation. Although the framework does include broad guidance on the use of theory, it contains little practical guidance for implementers and there have been calls to develop a more comprehensive approach. A prospective, theory-driven process of intervention design and evaluation is required to develop complex healthcare interventions which are more likely to be effective, sustainable and scalable. METHODS: We propose a theory-driven approach to the design and evaluation of complex interventions by adapting and integrating a programmatic design and evaluation tool, Theory of Change (ToC), into the MRC framework for complex interventions. We provide a guide to what ToC is, how to construct one, and how to integrate its use into research projects seeking to design, implement and evaluate complex interventions using the MRC framework. We test this approach by using ToC within two randomized controlled trials and one non-randomized evaluation of complex interventions. RESULTS: Our application of ToC in three research projects has shown that ToC can strengthen key stages of the MRC framework. It can aid the development of interventions by providing a framework for enhanced stakeholder engagement and by explicitly designing an intervention that is embedded in the local context. For the feasibility and piloting stage, ToC enables the systematic identification of knowledge gaps to generate research questions that strengthen intervention design. ToC may improve the evaluation of interventions by providing a comprehensive set of indicators to evaluate all stages of the causal pathway through which an intervention achieves impact, combining evaluations of intervention effectiveness with detailed process evaluations into one theoretical framework. CONCLUSIONS: Incorporating a ToC approach into the MRC framework holds promise for improving the design and evaluation of complex interventions, thereby increasing the likelihood that the intervention will be ultimately effective, sustainable and scalable. We urge researchers developing and evaluating complex interventions to consider using this approach, to evaluate its usefulness and to build an evidence base to further refine the methodology. TRIAL REGISTRATION: Clinical trials.gov: NCT02160249.
PURPOSE: Consensus group methods, such as the Delphi method and nominal group technique (NGT), are used to synthesize expert opinions when evidence is lacking. Despite their extensive use, these methods are inconsistently applied. Their use in medical education research has not been well studied. The authors set out to describe the use of consensus methods in medical education research and to assess the reporting quality of these methods and results. METHOD: Using scoping review methods, the authors searched the Medline, Embase, PsycInfo, PubMed, Scopus, and ERIC databases for 2009-2016. Full-text articles that focused on medical education and the keywords Delphi, RAND, NGT, or other consensus group methods were included. A standardized extraction form was used to collect article demographic data and features reflecting methodological rigor. RESULTS: Of the articles reviewed, 257 met the inclusion criteria. The Modified Delphi (105/257; 40.8%), Delphi (91/257; 35.4%), and NGT (23/257; 8.9%) methods were most often used. The most common study purpose was curriculum development or reform (68/257; 26.5%), assessment tool development (55/257; 21.4%), and defining competencies (43/257; 16.7%). The reporting quality varied, with 70.0% (180/257) of articles reporting a literature review, 27.2% (70/257) reporting what background information was provided to participants, 66.1% (170/257) describing the number of participants, 40.1% (103/257) reporting if private decisions were collected, 37.7% (97/257) reporting if formal feedback of group ratings was shared, and 43.2% (111/257) defining consensus a priori. CONCLUSIONS: Consensus methods are poorly standardized and inconsistently used in medical education research. Improved criteria for reporting are needed.
BACKGROUND: ROC (receiver operating characteristic) curve analysis is well established for assessing how well a marker is capable of discriminating between individuals who experience disease onset and individuals who do not. The classical (standard) approach of ROC curve analysis considers event (disease) status and marker value for an individual as fixed over time, however in practice, both the disease status and marker value change over time. Individuals who are disease-free earlier may develop the disease later due to longer study follow-up, and also their marker value may change from baseline during follow-up. Thus, an ROC curve as a function of time is more appropriate. However, many researchers still use the standard ROC curve approach to determine the marker capability ignoring the time dependency of the disease status or the marker. METHODS: We comprehensively review currently proposed methodologies of time-dependent ROC curves which use single or longitudinal marker measurements, aiming to provide clarity in each methodology, identify software tools to carry out such analysis in practice and illustrate several applications of the methodology. We have also extended some methods to incorporate a longitudinal marker and illustrated the methodologies using a sequential dataset from the Mayo Clinic trial in primary biliary cirrhosis (PBC) of the liver. RESULTS: From our methodological review, we have identified 18 estimation methods of time-dependent ROC curve analyses for censored event times and three other methods can only deal with non-censored event times. Despite the considerable numbers of estimation methods, applications of the methodology in clinical studies are still lacking. CONCLUSIONS: The value of time-dependent ROC curve methods has been re-established. We have illustrated the methods in practice using currently available software and made some recommendations for future research.
Reporting bias represents a major problem in the assessment of health care interventions. Several prominent cases have been described in the literature, for example, in the reporting of trials of antidepressants, Class I anti-arrhythmic drugs, and selective COX-2 inhibitors. The aim of this narrative review is to gain an overview of reporting bias in the medical literature, focussing on publication bias and selective outcome reporting. We explore whether these types of bias have been shown in areas beyond the well-known cases noted above, in order to gain an impression of how widespread the problem is. For this purpose, we screened relevant articles on reporting bias that had previously been obtained by the German Institute for Quality and Efficiency in Health Care in the context of its health technology assessment reports and other research work, together with the reference lists of these articles.We identified reporting bias in 40 indications comprising around 50 different pharmacological, surgical (e.g. vacuum-assisted closure therapy), diagnostic (e.g. ultrasound), and preventive (e.g. cancer vaccines) interventions. Regarding pharmacological interventions, cases of reporting bias were, for example, identified in the treatment of the following conditions: depression, bipolar disorder, schizophrenia, anxiety disorder, attention-deficit hyperactivity disorder, Alzheimer's disease, pain, migraine, cardiovascular disease, gastric ulcers, irritable bowel syndrome, urinary incontinence, atopic dermatitis, diabetes mellitus type 2, hypercholesterolaemia, thyroid disorders, menopausal symptoms, various types of cancer (e.g. ovarian cancer and melanoma), various types of infections (e.g. HIV, influenza and Hepatitis B), and acute trauma. Many cases involved the withholding of study data by manufacturers and regulatory agencies or the active attempt by manufacturers to suppress publication. The ascertained effects of reporting bias included the overestimation of efficacy and the underestimation of safety risks of interventions.In conclusion, reporting bias is a widespread phenomenon in the medical literature. Mandatory prospective registration of trials and public access to study data via results databases need to be introduced on a worldwide scale. This will allow for an independent review of research data, help fulfil ethical obligations towards patients, and ensure a basis for fully-informed decision making in the health care system.
Recently, artificial intelligence and machine learning in general have demonstrated remarkable performances in many tasks, from image processing to natural language processing, especially with the advent of deep learning (DL). Along with research progress, they have encroached upon many different fields and disciplines. Some of them require high level of accountability and thus transparency, for example, the medical sector. Explanations for machine decisions and predictions are thus needed to justify their reliability. This requires greater interpretability, which often means we need to understand the mechanism underlying the algorithms. Unfortunately, the blackbox nature of the DL is still unresolved, and many machine decisions are still poorly understood. We provide a review on interpretabilities suggested by different research works and categorize them. The different categories show different dimensions in interpretability research, from approaches that provide "obviously" interpretable information to the studies of complex patterns. By applying the same categorization to interpretability in medical research, it is hoped that: 1) clinicians and practitioners can subsequently approach these methods with caution; 2) insight into interpretability will be born with more considerations for medical practices; and 3) initiatives to push forward data-based, mathematically grounded, and technically grounded medical education are encouraged.
Background and Objectives Snowball sampling is applied when samples with the target characteristics are not easily accessible. This research describes snowball sampling as a purposeful method of data collection in qualitative research. Methods This paper is a descriptive review of previous research papers. Data were gathered using English keywords, including “review,” “declaration,” “snowball,” and “chain referral,” as well as Persian keywords that are equivalents of the following: “purposeful sampling,” “snowball,” “qualitative research,” and “descriptive review.” The databases included Google Scholar, Scopus, Irandoc, ProQuest, Science Direct, SID, MagIran, Medline, and Cochrane. The search was limited to Persian and English articles written between 2005 and 2013. Results The preliminary search yielded 433 articles from PubMed, 88 articles from Scopus, 1 article from SID, and 18 articles from MagIran. Among 125 articles, methodological and non-research articles were omitted. Finally, 11 relevant articles, which met the criteria, were selected for review. Conclusions Different methods of snowball sampling can be applied to facilitate scientific research, provide community-based data, and hold health educational programs. Snowball sampling can be effectively used to analyze vulnerable groups or individuals under special care. In fact, it allows researchers to access susceptible populations. Thus, it is suggested to consider snowball sampling strategies while working with the attendees of educational programs or samples of research studies.
BACKGROUND: The knowledge and use of qualitative description as a qualitative research approach in health services research is limited.The aim of this article is to discuss the potential benefits of a qualitative descriptive approach, to identify its strengths and weaknesses and to provide examples of use. DISCUSSION: Qualitative description is a useful qualitative method in much medical research if you keep the limitations of the approach in mind. It is especially relevant in mixed method research, in questionnaire development and in research projects aiming to gain firsthand knowledge of patients', relatives' or professionals' experiences with a particular topic. Another great advantage of the method is that it is suitable if time or resources are limited. SUMMARY: As a consequence of the growth in qualitative research in the health sciences, researchers sometimes feel obliged to designate their work as phenomenology, grounded theory, ethnography or a narrative study when in fact it is not. Qualitative description might be a useful alternative approach to consider.
The UK Medical Research Council’s widely used guidance for developing and evaluating complex interventions has been replaced by a new framework, commissioned jointly by the Medical Research Council and the National Institute for Health Research, which takes account of recent developments in theory and methods and the need to maximise the efficiency, use, and impact of research.
BACKGROUND: The aim of this study is to review the literature on known barriers and solutions that face educators when developing and implementing online learning programs for medical students and postgraduate trainees. METHODS: An integrative review was conducted over a three-month period by an inter-institutional research team. The search included ScienceDirect, Scopus, BioMedical, PubMed, Medline (EBSCO & Ovid), ERIC, LISA, EBSCO, Google Scholar, ProQuest A&I, ProQuest UK & Ireland, UL Institutional Repository (IR), UCDIR and the All Aboard Report. Search terms included online learning, medical educators, development, barriers, solutions and digital literacy. The search was carried out by two reviewers. Titles and abstracts were screened independently and reviewed with inclusion/exclusion criteria. A consensus was drawn on which articles were included. Data appraisal was performed using the Critical Appraisal Skills Programme (CASP) Qualitative Research Checklist and NHMRC Appraisal Evidence Matrix. Data extraction was completed using the Cochrane Data Extraction Form and a modified extraction tool. RESULTS: Of the 3101 abstracts identified from the search, ten full-text papers met the inclusion criteria. Data extraction was completed on seven papers of high methodological quality and on three lower quality papers. Findings suggest that the key barriers which affect the development and implementation of online learning in medical education include time constraints, poor technical skills, inadequate infrastructure, absence of institutional strategies and support and negative attitudes of all involved. Solutions to these include improved educator skills, incentives and reward for the time involved with development and delivery of online content, improved institutional strategies and support and positive attitude amongst all those involved in the development and delivery of online content. CONCLUSION: This review has identified barriers and solutions amongst medical educators to the implementation of online learning in medical education. Results can be used to inform institutional and educator practice in the development of further online learning.
BACKGROUND: The Danish National Patient Registry (DNPR) is one of the world's oldest nationwide hospital registries and is used extensively for research. Many studies have validated algorithms for identifying health events in the DNPR, but the reports are fragmented and no overview exists. OBJECTIVES: To review the content, data quality, and research potential of the DNPR. METHODS: We examined the setting, history, aims, content, and classification systems of the DNPR. We searched PubMed and the Danish Medical Journal to create a bibliography of validation studies. We included also studies that were referenced in retrieved papers or known to us beforehand. Methodological considerations related to DNPR data were reviewed. RESULTS: During 1977-2012, the DNPR registered 8,085,603 persons, accounting for 7,268,857 inpatient, 5,953,405 outpatient, and 5,097,300 emergency department contacts. The DNPR provides nationwide longitudinal registration of detailed administrative and clinical data. It has recorded information on all patients discharged from Danish nonpsychiatric hospitals since 1977 and on psychiatric inpatients and emergency department and outpatient specialty clinic contacts since 1995. For each patient contact, one primary and optional secondary diagnoses are recorded according to the International Classification of Diseases. The DNPR provides a data source to identify diseases, examinations, certain in-hospital medical treatments, and surgical procedures. Long-term temporal trends in hospitalization and treatment rates can be studied. The positive predictive values of diseases and treatments vary widely (<15%-100%). The DNPR data are linkable at the patient level with data from other Danish administrative registries, clinical registries, randomized controlled trials, population surveys, and epidemiologic field studies - enabling researchers to reconstruct individual life and health trajectories for an entire population. CONCLUSION: The DNPR is a valuable tool for epidemiological research. However, both its strengths and limitations must be considered when interpreting research results, and continuous validation of its clinical data is essential.
BACKGROUND: Choosing a suitable sample size in qualitative research is an area of conceptual debate and practical uncertainty. That sample size principles, guidelines and tools have been developed to enable researchers to set, and justify the acceptability of, their sample size is an indication that the issue constitutes an important marker of the quality of qualitative research. Nevertheless, research shows that sample size sufficiency reporting is often poor, if not absent, across a range of disciplinary fields. METHODS: A systematic analysis of single-interview-per-participant designs within three health-related journals from the disciplines of psychology, sociology and medicine, over a 15-year period, was conducted to examine whether and how sample sizes were justified and how sample size was characterised and discussed by authors. Data pertinent to sample size were extracted and analysed using qualitative and quantitative analytic techniques. RESULTS: Our findings demonstrate that provision of sample size justifications in qualitative health research is limited; is not contingent on the number of interviews; and relates to the journal of publication. Defence of sample size was most frequently supported across all three journals with reference to the principle of saturation and to pragmatic considerations. Qualitative sample sizes were predominantly - and often without justification - characterised as insufficient (i.e., 'small') and discussed in the context of study limitations. Sample size insufficiency was seen to threaten the validity and generalizability of studies' results, with the latter being frequently conceived in nomothetic terms. CONCLUSIONS: We recommend, firstly, that qualitative health researchers be more transparent about evaluations of their sample size sufficiency, situating these within broader and more encompassing assessments of data adequacy. Secondly, we invite researchers critically to consider how saturation parameters found in prior methodological studies and sample size community norms might best inform, and apply to, their own project and encourage that data adequacy is best appraised with reference to features that are intrinsic to the study at hand. Finally, those reviewing papers have a vital role in supporting and encouraging transparent study-specific reporting.