Towards a New Science of a Clinical Data Intelligence

In this paper we define Clinical Data Intelligence as the analysis of data generated in the clinical routine with the goal of improving patient care. We define a science of a Clinical Data Intelligence as a data analysis that permits the derivation of scientific, i.e., generalizable and reliable results. We argue that a science of a Clinical Data Intelligence is sensible in the context of a Big Data analysis, i.e., with data from many patients and with complete patient information. We discuss that Clinical Data Intelligence requires the joint efforts of knowledge engineering, information extraction (from textual and other unstructured data), and statistics and statistical machine learning. We describe some of our main results as conjectures and relate them to a recently funded research project involving two major German university hospitals.Comment: NIPS 2013 Workshop: Machine Learning for Clinical Data Analysis and Healthcare, 201

Status and potential of bacterial genomics for public health practice : a scoping review

Background: Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. Methods: In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Results: Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. Conclusions: For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance

The conduct and reporting of mediation analysis in recently published randomized controlled trials : results from a methodological systematic review

Objectives: To describe the methodological characteristics of mediation analyses (MAs) reported in recent randomized controlled trials (RCTs) and to propose recommendations on the planning, conduct, and reporting of MAs in practice. Study Design and Setting: We conducted a systematic review by searching MEDLINE (January 1, 2017, to December 1, 2018) for all reports of RCTs or secondary analyses of previously published RCTs that reported a MA. Two reviewers independently screened the title, abstracts, and full texts of the identified reports and extracted the data from the 98 eligible studies. Results: MAs were nearly always (96%) based on a traditional mediation approach. Most studies did not report a sample size calculation for the MA (96%) or assess potential treatment-by-mediator interactions (96%). In 53% of studies, mediators and outcomes were simultaneously measured. In 57% of studies, mediator-mediator and mediator-outcome confounders were adjusted for in the analysis, although adjustment was often limited to few potential confounders. About 30% of studies discussed the assumptions underlying the MA. Conclusion: The conduct and reporting of MAs remained quite heterogeneous in practice. Future MAs could benefit from a consensus-based planning, conduct, and reporting guideline for MA

Dissemination of evidence-based standards of care.

Standards of care pertain to crafting and implementing patient-centered treatment interventions. Standards of care must take into consideration the patient's gender, ethnicity, medical and dental history, insurance coverage (or socioeconomic level, if a private patient), and the timeliness of the targeted scientific evidence. This resolves into a process by which clinical decision-making about the optimal patient-centered treatment relies on the best available research evidence, and all other necessary inputs and factors to provide the best possible treatment. Standards of care must be evidence-based, and not merely based on the evidence - the dichotomy being critical in contemporary health services research and practice. Evidence-based standards of care must rest on the best available evidence that emerges from a concerted hypothesis-driven process of research synthesis and meta-analysis. Health information technology needs to become an every-day reality in health services research and practice to ensure evidence-based standards of care. Current trends indicate that user-friendly methodologies, for the dissemination of evidence-based standards of care, must be developed, tested and distributed. They should include approaches for the quantification and analysis of the textual content of systematic reviews and of their summaries in the form of critical reviews and lay-language summaries

Helminth infections, atopy, asthma and allergic diseases: protocol for a systematic review of observational studies worldwide.

INTRODUCTION: Childhood infections, particularly those caused by helminths are considered to be important environmental exposures influencing the development of allergic diseases. However, epidemiological studies focusing on the relationship between helminth infections and risk of allergic diseases, performed worldwide, show inconsistent findings. Previous systematic reviews of observational studies published 10 or more years ago showed conflicting findings for effects of helminths on allergic diseases. Over the past 10 years there has been growing literature addressing this research area and these need to be considered in order to appreciate the most contemporary evidence. The objective of the current systematic review will be to provide an up-to-date synthesis of findings of observational studies investigating the influence of helminth infections on atopy, and allergic diseases. METHODS AND ANALYSIS: This systematic review protocol was registered at PROSPERO. We will search Cochrane Library, MEDLINE, EMBASE, CINAHL, AMED, ISI Web of Science, WHO Global Health Library, Scielo, IndMed, PakMediNet, KoreaMed, Ichushi for published studies from 1970 to January 2020. Bibliographies of all eligible studies will be reviewed to identify additional studies. Unpublished and ongoing research will also be searched in key databases. There will be no language or geographical restrictions regarding publications. Critical Appraisal Skills Programme quality assessment tool will be used to appraise methodological quality of included studies. A descriptive summary with data tables will be constructed, and if adequate, meta-analysis using random-effects will be performed. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist will be followed for reporting of the systematic review. ETHICS AND DISSEMINATION: Since this systematic review will be only based on published and retrievable literature, no ethics approval will be sought. The multidisciplinary team performing this systematic review will participate in relevant dissemination activities. Findings will be presented at scientific meetings and publish the systematic review in international, peer-reviewed, open-access journals. PROSPERO REGISTRATION NUMBER: CRD42020167249

Maternal smoking and the risk of still birth: systematic review and meta-analysis

BACKGROUND: Smoking in pregnancy is known to be associated with a range of adverse pregnancy outcomes, yet there is a high prevalence of smoking among pregnant women in many countries, and it remains a major public health concern. We have conducted a systematic review and meta-analysis to provide contemporary estimates of the association between maternal smoking in pregnancy and the risk of stillbirth. METHODS: We searched four databases namely MEDLINE, EMBASE, Psych Info and Web of Science for all relevant original studies published until 31(st) December 2012. We included observational studies that measured the association between maternal smoking during pregnancy and the risk of stillbirth. RESULTS: 1766 studies were screened for title analysis, of which 34 papers (21 cohorts, 8 case controls and 5 cross sectional studies) met the inclusion criteria. In meta-analysis smoking during pregnancy was significantly associated with a 47% increase in the odds of stillbirth (OR 1.47, 95% CI 1.37, 1.57, p  <  0.0001). In subgroup analysis, smoking 1-9 cig/day and ≥10 cig/day was associated with an 9% and 52% increase in the odds of stillbirth respectively. Subsequently, studies defining stillbirth at ≥ 20 weeks demonstrated a 43% increase in odds for smoking mothers compared to mothers who do not smoke, (OR 1.43, 95% CI 1.32, 1.54, p  <  0.0001), whereas studies with stillbirth defined at ≥ 24 weeks and ≥ 28 weeks showed 58% and 33% increase in the odds of stillbirth respectively. CONCLUSION: Our review confirms a dose-response effect of maternal smoking in pregnancy on risk of stillbirth. To minimise the risk of stillbirth, reducing current smoking prevalence in pregnancy should continue to be a key public health high priority

The quality of reports of medical and public health research from Palestinian institutions:A systematic review

Research reports are the most common way to communicate research findings for target readerships. Complete, accurate and transparent reporting of research studies facilitates dissemination, interpretation, translation and replication of research findings. Inadequate reporting has major consequences for clinicians, researchers, policy makers and ultimately patients. It impairs critical assessment of the validity, relevance and trustworthiness of research and so impedes its use in practice. It also limits the usability of study findings by other researchers conducting systematic reviews and meta-analyses and building on or replicating studies. In addition, inadequate reporting is one of the key contributors to avoidable waste in biomedical research. Researchers thus have an ethical obligation to research participants, funding organisations and society as a whole to report their findings in ways that are of use in practice and policy makin

Systematic review and meta-analysis of the sero-epidemiological association between Epstein-Barr virus and rheumatoid arthritis

Acknowledgements The authors would like to thank Cynthia Fraser for helping run the literature search, Dr Neil Basu for providing advice on search terms for rheumatoid arthritis and to Xueli Jia, Katie Bannister and Kubra Boza for their help with foreign language papers. The authors would also like to thank the University of Aberdeen librarians at the Foresterhill medical library for their help in locating articles used for this systematic review and meta-analysis.Peer reviewedPublisher PD