MARVIN: a medical research application framework based on open source software

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Individual patient data meta-analysis of diagnostic and prognostic studies in obstetrics, gynaecology and reproductive medicine

BACKGROUND: In clinical practice a diagnosis is based on a combination of clinical history, physical examination and additional diagnostic tests. At present, studies on diagnostic research often report the accuracy of tests without taking into account the information already known from history and examination. Due to this lack of information, together with variations in design and quality of studies, conventional meta-analyses based on these studies will not show the accuracy of the tests in real practice. By using individual patient data (IPD) to perform meta-analyses, the accuracy of tests can be assessed in relation to other patient characteristics and allows the development or evaluation of diagnostic algorithms for individual patients. In this study we will examine these potential benefits in four clinical diagnostic problems in the field of gynaecology, obstetrics and reproductive medicine. METHODS/DESIGN: Based on earlier systematic reviews for each of the four clinical problems, studies are considered for inclusion. The first authors of the included studies will be invited to participate and share their original data. After assessment of validity and completeness the acquired datasets are merged. Based on these data, a series of analyses will be performed, including a systematic comparison of the results of the IPD meta-analysis with those of a conventional meta-analysis, development of multivariable models for clinical history alone and for the combination of history, physical examination and relevant diagnostic tests and development of clinical prediction rules for the individual patients. These will be made accessible for clinicians. DISCUSSION: The use of IPD meta-analysis will allow evaluating accuracy of diagnostic tests in relation to other relevant information. Ultimately, this could increase the efficiency of the diagnostic work-up, e.g. by reducing the need for invasive tests and/or improving the accuracy of the diagnostic workup. This study will assess whether these benefits of IPD meta-analysis over conventional meta-analysis can be exploited and will provide a framework for future IPD meta-analyses in diagnostic and prognostic research.

Community Research as a Factor Building Inclusive Community in Lithuania

Social and political change in Europe, increasing labour mobility, development of the new European social policy and increasingly global nature of the social problems had a profound effect on the socio-cultural and socio-educational work in community and on its objectives. In order to keep these new communitarian standards of social policy, the first steps have to be made in fostering local community with the perspective it will reach the western European communitarian level. That is the reason why university in these changes started to turn more and more to the society and first of all has put a great emphasis on the community research. This initiative was induced by non-existence of civic tradition during the communist period, the gap in the development of civil society and its culture, the weakness and the poorness of the third sector. This paper is based on the analysis of the community and civil society research conducted during recent years by the researchers of Kaunas University of Technology, Faculty of Social Sciences. The paper involves a review of the research methodology, interpretation of the received data and summary of the results. It discusses both theoretical and empirical possibilities of building and developing inclusive community.

What is Practice Research in Social Work - Definitions, Barriers and Possibilities

Practice is subject to increasing pressure to demonstrate its ability to achieve outcomes required by public policy makers. As part of this process social work practice has to engage with issues around advancing knowledge-based learning processes in a close collaboration with education and research based perspectives. This has given rise to approaches seeking to combine research methodology, field research and practical experience. Practice research is connected to both “the science of the concrete” – a field of research oriented towards subjects more than objects and “mode 2 knowledge production” – an application-oriented research where frameworks and findings are discussed by a number of partners. Practice research is defined into two approaches: practice research – collaboration between practice and research – and practitioner research – processes controlled and accomplished by practitioners. The basic stakeholders in practice research are social workers, service users, administrators, management, organisations, politicians and researchers. Accordingly, practice research is necessarily collaborative, involving a meeting point for different views, interests and needs, where complexity and dilemmas are inherent. Instead of attempting to balance or reconcile these differences, it is important to respect the differences if collaboration is to be established. The strength of both practice and research in practice research is to address these difficult challenges. The danger for both fields is to avoid and reject them.

Intelligent Virtual Patients for Training Clinical Skills

The article presents the design process of intelligent virtual human patients that are used for the enhancement of clinical skills. The description covers the development from conceptualization and character creation to technical components and the application in clinical research and training. The aim is to create believable social interactions with virtual agents that help the clinician to develop skills in symptom and ability assessment, diagnosis, interview techniques and interpersonal communication. The virtual patient fulfills the requirements of a standardized patient producing consistent, reliable and valid interactions in portraying symptoms and behaviour related to a specific clinical condition.

Clinical trial design for orthodontists

High-quality research should form the basis of all clinical practice. Randomized controlled trials currently provide the gold standard for investigating the effectiveness of treatment interventions and these are increasingly being used in orthodontics. Here we discuss the reasons why this form of investigation provides the most useful evidence for assessing treatment outcome. The methods available to achieve true randomization, a fundamental component in the design of these trials, are also discussed. In addition, we focus on how to minimize bias in clinical research, not only during the design and management of a trial, but also when disseminating results. We focus on the importance of using control groups correctly and describe methods that are available to adequately power a trial. Finally, we emphasise the importance of accurate and transparent reporting, which facilitates correct communication and assessment of the evidence.

Distinct microRNA Expression Profile in Prostate Cancer Patients with Early Clinical Failure and the Impact of let-7 as Prognostic Marker in High-Risk Prostate Cancer

Background The identification of additional prognostic markers to improve risk stratification and to avoid overtreatment is one of the most urgent clinical needs in prostate cancer (PCa). MicroRNAs, being important regulators of gene expression, are promising biomarkers in various cancer entities, though the impact as prognostic predictors in PCa is poorly understood. The aim of this study was to identify specific miRNAs as potential prognostic markers in high-risk PCa and to validate their clinical impact. Methodology and Principal Findings We performed miRNA-microarray analysis in a high-risk PCa study group selected by their clinical outcome (clinical progression free survival (CPFS) vs. clinical failure (CF)). We identified seven candidate miRNAs (let-7a/b/c, miR-515-3p/5p, -181b, -146b, and -361) that showed differential expression between both groups. Further qRT-PCR analysis revealed down-regulation of members of the let-7 family in the majority of a large, well-characterized high-risk PCa cohort (n = 98). Expression of let-7a/b/and -c was correlated to clinical outcome parameters of this group. While let-7a showed no association or correlation with clinical relevant data, let-7b and let-7c were associated with CF in PCa patients and functioned partially as independent prognostic marker. Validation of the data using an independent high-risk study cohort revealed that let-7b, but not let-7c, has impact as an independent prognostic marker for BCR and CF. Furthermore, we identified HMGA1, a non-histone protein, as a new target of let-7b and found correlation of let-7b down-regulation with HMGA1 over-expression in primary PCa samples. Conclusion Our findings define a distinct miRNA expression profile in PCa cases with early CF and identified let-7b as prognostic biomarker in high-risk PCa. This study highlights the importance of let-7b as tumor suppressor miRNA in high-risk PCa and presents a basis to improve individual therapy for high-risk PCa patients.

Can prospective usability evaluation predict data errors?

Increasing amounts of clinical research data are collected by manual data entry into electronic source systems and directly from research subjects. For this manual entered source data, common methods of data cleaning such as post-entry identification and resolution of discrepancies and double data entry are not feasible. However data accuracy rates achieved without these mechanisms may be higher than desired for a particular research use. We evaluated a heuristic usability method for utility as a tool to independently and prospectively identify data collection form questions associated with data errors. The method evaluated had a promising sensitivity of 64% and a specificity of 67%. The method was used as described in the literature for usability with no further adaptations or specialization for predicting data errors. We conclude that usability evaluation methodology should be further investigated for use in data quality assurance.

Patient safety in dialysis access: education and research.

Today, a growing activity to improve patient safety in all domains of medicine is reality. This chapter deals with patient safety research in general, but is also about strategies to implement this evidence in the daily clinical work treating patients on dialysis. Good clinical research practice has been well established for some years. In the domain of dialysis access, further basic, clinical, epidemiological and health service research will be important to further improve patient safety as a whole.

Hyperthermia-related clinical trials on cancer treatment within the ClinicalTrials.gov registry

PURPOSE Hyperthermia has been shown to improve the effectiveness of chemotherapy and radiotherapy in the treatment of cancer. This paper summarises all recent clinical trials registered in the ClinicalTrials.gov registry. MATERIALS AND METHODS The records of 175,538 clinical trials registered at ClinicalTrials.gov were downloaded on 29 September 2014 and a database was established. We searched this database for hyperthermia or equivalent words. RESULTS A total of 109 trials were identified in which hyperthermia was part of the treatment regimen. Of these, 49 trials (45%) had hyperthermic intraperitoneal chemotherapy after cytoreductive surgery (HIPEC) as the primary intervention, and 14 other trials (13%) were also testing some form of intraperitoneal hyperthermic chemoperfusion. Seven trials (6%) were testing perfusion attempts to other locations (thoracic/pleural n = 4, limb n = 2, hepatic n = 1). Sixteen trials (15%) were testing regional hyperthermia, 13 trials (12%) whole body hyperthermia, seven trials (6%) superficial hyperthermia and two trials (2%) interstitial hyperthermia. One remaining trial tested laser hyperthermia. CONCLUSIONS In contrast to the general opinion, this analysis shows continuous interest and ongoing clinical research in the field of hyperthermia. Interestingly, the majority of trials focused on some form of intraperitoneal hyperthermic chemoperfusion. Despite the high number of active clinical studies, HIPEC is a topic with limited attention at the annual meetings of the European Society for Hyperthermic Oncology and the Society of Thermal Medicine. The registration of on-going clinical trials is of paramount importance for the achievement of a comprehensive overview of available clinical research activities involving hyperthermia.

From Theory to Practice: Improving the Impact of Health Services Research.

BACKGROUND: While significant strides have been made in health research, the incorporation of research evidence into healthcare decision-making has been marginal. The purpose of this paper is to provide an overview of how the utility of health services research can be improved through the use of theory. Integrating theory into health services research can improve research methodology and encourage stronger collaboration with decision-makers. DISCUSSION: Recognizing the importance of theory calls for new expectations in the practice of health services research. These include: the formation of interdisciplinary research teams; broadening the training for those who will practice health services research; and supportive organizational conditions that promote collaboration between researchers and decision makers. Further, funding bodies can provide a significant role in guiding and supporting the use of theory in the practice of health services research. SUMMARY: Institutions and researchers should incorporate the use of theory if health services research is to fulfill its potential for improving the delivery of health care.

Evaluating alternative therapies. Support/imagery and immune function in breast cancer: A pilot study

Cancer patients increasingly request alternative therapies such as imagery techniques and support groups. Although research suggests evidence of enhanced psychosocial functioning with supportive group therapy and enhanced immune function with imagery techniques, studies are anecdotal or limited to case studies or descriptive reports. The efficacy of these alternative therapies should be validated by randomized, controlled trials and the mechanisms of action mediating immune function and outcome examined.^ In a 12-month pilot study, we evaluate the feasibility of conducting a controlled study with clinical trial methodology to test the effects of imagery/relaxation and support on quality of life, emotional well-being, and immune function for women after breast cancer. Using a randomized pre-post test design with three intervention waves, we assigned women (n = 47) to either standard care (n = 15), standard care plus 6-weekly support sessions (n = 16) or imagery/relaxation sessions (n = 16).^ The primary aim of this pilot study is to determine the feasibility of conducting a clinical trial of alternative therapies in a clinical care setting. Secondary aims are to determine parameter estimates for the effects of the two treatment groups on quality of life, coping, social support, and immune function and describe methodology issues related to trials of alternative therapies.^ The research provides direction for future studies of alternative therapies by describing the recruitment, clinical trial experience, and related methodology issues. The study extends previous work by differentiating the effects of support group from mental imagery among outpatient groups who are homogeneous regarding cancer type and treatment stage. The study provides data for future longitudinal studies of disease progression by differentiating the effectiveness of interventions designed to enhance quality of life, coping, social support, and immune function and subsequently, alter the clinical course of disease. ^

TECHNOLOGY ASSESSMENT: SMALL-VOLUME INFUSION PUMPS

"Technology assessment is a comprehensive form of policy research that examines the short- and long-term social consequences of the application or use of technology" (US Congress 1967).^ This study explored a research methodology appropriate for technology assessment (TA) within the health industry. The case studied was utilization of external Small-Volume Infusion Pumps (SVIP) at a cancer treatment and research center. Primary and secondary data were collected in three project phases. In Phase I, hospital prescription records (N = 14,979) represented SVIP adoption and utilization for the years 1982-1984. The Candidate Adoption-Use (CA-U) diffusion paradigm developed for this study was germane. Compared to classic and unorthodox curves, CA-U more accurately simulated empiric experience. The hospital SVIP 1983-1984 trends denoted assurance in prescribing chemotherapy and concomitant balloon SVIP efficacy and efficiency. Abandonment of battery pumps was predicted while exponential demand for balloon SVIP was forecast for 1985-1987. In Phase II, patients using SVIP (N = 117) were prospectively surveyed from July to October 1984; the data represented a single episode of therapy. The questionnaire and indices, specifically designed to measure the impact of SVIP, evinced face validity. Compeer group data were from pre-SVIP case reviews rather than from an inpatient sample. Statistically significant results indicated that outpatients using SVIP interacted socially more than inpatients using the alternative technology. Additionally, the hospital's education program effectively taught clients to discriminate between self care and professional SVIP services. In these contexts, there was sufficient evidence that the alternative technology restricted patients activity whereas SVIP permitted patients to function more independently and in a social lifestyle, thus adding quality to life. In Phase III, diffusion forecast and patient survey findings were combined with direct observation of clinic services to profile some economic dimensions of SVIP. These three project phases provide a foundation for executing: (1) cost effectiveness analysis of external versus internal infusors, (2) institutional resource allocation, and (3) technology deployment to epidemiology-significant communities. The models and methods tested in this research of clinical technology assessment are innovative and do assess biotechnology. ^

Looking Inside The Black Box

Intensive family preservation services (IFPS), designed to stabilize at-risk families and avert out-of-home care, have been the focus of many randomized, experimental studies. The emphasis on "gold-standard" evaluation of IFPS has resulted in fewer "black box" studies that describe actual IFPS service patterns and the fidelity with which they adhere to IFPS program theory. Intervention research is important to the advancement of programs designed to protect the safety of children, improve family functioning, as well as prevent out-of-home placement. Employing a retrospective “clinical data-mining” (CDM) methodology, this exploratory study of Families First, an IFPS program, makes use of available information extracted from client records to describe interventions and service patterns provided over a two year period. This study uncovers actual IFPS service patterns, demonstrates IFPS program fidelity, as well as reveals the usefulness of CDM as a social work research methodology. These findings are particularly valuable for program planning and treatment, policy development and evidence-based practice research.

Data Accuracy in Medical Record Abstraction

Clinical Research Data Quality Literature Review and Pooled Analysis We present a literature review and secondary analysis of data accuracy in clinical research and related secondary data uses. A total of 93 papers meeting our inclusion criteria were categorized according to the data processing methods. Quantitative data accuracy information was abstracted from the articles and pooled. Our analysis demonstrates that the accuracy associated with data processing methods varies widely, with error rates ranging from 2 errors per 10,000 files to 5019 errors per 10,000 fields. Medical record abstraction was associated with the highest error rates (70–5019 errors per 10,000 fields). Data entered and processed at healthcare facilities had comparable error rates to data processed at central data processing centers. Error rates for data processed with single entry in the presence of on-screen checks were comparable to double entered data. While data processing and cleaning methods may explain a significant amount of the variability in data accuracy, additional factors not resolvable here likely exist. Defining Data Quality for Clinical Research: A Concept Analysis Despite notable previous attempts by experts to define data quality, the concept remains ambiguous and subject to the vagaries of natural language. This current lack of clarity continues to hamper research related to data quality issues. We present a formal concept analysis of data quality, which builds on and synthesizes previously published work. We further posit that discipline-level specificity may be required to achieve the desired definitional clarity. To this end, we combine work from the clinical research domain with findings from the general data quality literature to produce a discipline-specific definition and operationalization for data quality in clinical research. While the results are helpful to clinical research, the methodology of concept analysis may be useful in other fields to clarify data quality attributes and to achieve operational definitions. Medical Record Abstractor’s Perceptions of Factors Impacting the Accuracy of Abstracted Data Medical record abstraction (MRA) is known to be a significant source of data errors in secondary data uses. Factors impacting the accuracy of abstracted data are not reported consistently in the literature. Two Delphi processes were conducted with experienced medical record abstractors to assess abstractor’s perceptions about the factors. The Delphi process identified 9 factors that were not found in the literature, and differed with the literature by 5 factors in the top 25%. The Delphi results refuted seven factors reported in the literature as impacting the quality of abstracted data. The results provide insight into and indicate content validity of a significant number of the factors reported in the literature. Further, the results indicate general consistency between the perceptions of clinical research medical record abstractors and registry and quality improvement abstractors. Distributed Cognition Artifacts on Clinical Research Data Collection Forms Medical record abstraction, a primary mode of data collection in secondary data use, is associated with high error rates. Distributed cognition in medical record abstraction has not been studied as a possible explanation for abstraction errors. We employed the theory of distributed representation and representational analysis to systematically evaluate cognitive demands in medical record abstraction and the extent of external cognitive support employed in a sample of clinical research data collection forms. We show that the cognitive load required for abstraction in 61% of the sampled data elements was high, exceedingly so in 9%. Further, the data collection forms did not support external cognition for the most complex data elements. High working memory demands are a possible explanation for the association of data errors with data elements requiring abstractor interpretation, comparison, mapping or calculation. The representational analysis used here can be used to identify data elements with high cognitive demands.