In this paper, we present a semantic, metadata based knowledge discovery methodology for identifying teams of researchers from diverse backgrounds who can collaborate on interdisciplinary research projects: projects in areas that have been identified as high-impact areas at The Ohio State University. This methodology involves the semantic annotation of keywords and the postulation of semantic metrics to improve the efficiency of the path exploration algorithm as well as to rank the results. Results indicate that our methodology can discover groups of experts from diverse areas who can collaborate on translational research projects.
OBJECTIVE: Matching healthcare staff resources to patient needs in the ICU is a key factor for quality of care. We aimed to assess the impact of the staffing-to-patient ratio and workload on ICU mortality.
DESIGN: We performed a multicenter longitudinal study using routinely collected hospital data.
SETTING: Information pertaining to every patient in eight ICUs from four university hospitals from January to December 2013 was analyzed.
PATIENTS: A total of 5,718 inpatient stays were included.
MEASUREMENTS AND MAIN RESULTS: We used a shift-by-shift varying measure of the patient-to-caregiver ratio in combination with workload to establish their relationships with ICU mortality over time, excluding patients with decision to forego life-sustaining therapy. Using a multilevel Poisson regression, we quantified ICU mortality-relative risk, adjusted for patient turnover, severity, and staffing levels. The risk of death was increased by 3.5 (95% CI, 1.3-9.1) when the patient-to-nurse ratio was greater than 2.5, and it was increased by 2.0 (95% CI, 1.3-3.2) when the patient-to-physician ratio exceeded 14. The highest ratios occurred more frequently during the weekend for nurse staffing and during the night for physicians (p < 0.001). High patient turnover (adjusted relative risk, 5.6 [2.0-15.0]) and the volume of life-sustaining procedures performed by staff (adjusted relative risk, 5.9 [4.3-7.9]) were also associated with increased mortality.
CONCLUSIONS: This study proposes evidence-based thresholds for patient-to-caregiver ratios, above which patient safety may be endangered in the ICU. Real-time monitoring of staffing levels and workload is feasible for adjusting caregivers' resources to patients' needs.
BACKGROUND: Children with inflammatory bowel disease are at risk of vaccine-preventable diseases mostly due to immunosuppressive drugs.
AIM: To evaluate coverage after an awareness campaign informing patients, their parents and general practitioner about the vaccination schedule.
METHODS: Vaccination coverage was firstly evaluated and followed by an awareness campaign on the risk of infection via postal mail. The trial is a case-control study on the same patients before and after the awareness campaign. Overall, 92 children were included. A questionnaire was then completed during a routine appointment to collect data including age at diagnosis, age at data collection, treatment history, and vaccination status.
RESULTS: Vaccination rates significantly increased for vaccines against diphtheria-tetanus-poliomyelitis (92% vs. 100%), Haemophilus influenzae (88% vs. 98%), hepatitis B (52% vs. 71%), pneumococcus (36% vs. 57%), and meningococcus C (17% vs. 41%) (p<0.05). Children who were older at diagnosis were 1.26 times more likely to be up-to-date with a minimum vaccination schedule (diphtheria-tetanus-poliomyelitis, pertussis, H. influenzae, measles-mumps-rubella, tuberculosis) (p=0.002).
CONCLUSION: Informing inflammatory bowel disease patients, their parents and general practitioner about the vaccination schedule via postal mail is easy, inexpensive, reproducible, and increases vaccination coverage. This method reinforces information on the risk of infection during routine visits.
OBJECTIVES: In France, medical students regularly complain about the shortcomings of their theoretical training and the necessity of its adaptation to better fit the needs of students. The goal was to evaluate the theoretical teaching practices in postgraduate medical studies by: 1) collecting data from medical students in different medical faculties in France; 2) comparing this data with expected practices when it is possible; 3) and proposing several lines of improvement.
METHODS: A survey of theoretical practices in the 3rd cycle of medical studies was conducted by self-administered questionnaires which were free of charge, anonymous, and administered electronically from July 3 to October 31, 2013 to all medical students in France.
RESULTS: National, inter-regional, regional and field internship educational content was absent in respectively 50.5%, 42.8%, 26.0% and 30.2% of cases. Medical students follow complementary training due to insufficient DES and/or DESC 2 training in 43.7% of cases or as part of a professional project in 54.9% of cases. The knowledge sought by medical students concerns the following crosscutting topics: career development (58.9%), practice management (50.7%), medical English (50.4%) and their specialty organization (49.9%). Fifty-four point one percent would like to be evaluated on their theoretical training on an annual basis.
CONCLUSION: The results of this first national survey give insights into the theoretical teaching conditions in postgraduate medical education in France and the aspirations of medical students.
While risk of acute kidney injury (AKI) is a well documented adverse effect of some drugs, few studies have assessed the relationship between drug-drug interactions (DDIs) and AKI. Our objective was to develop an algorithm capable of detecting potential signals on this relationship by retrospectively mining data from electronic health records.
MATERIAL AND METHODS:
Data were extracted from the clinical data warehouse (CDW) of the Hôpital Européen Georges Pompidou (HEGP). AKI was defined as the first level of the RIFLE criteria, that is, an increase ≥50 % of creatinine basis. Algorithm accuracy was tested on 20 single drugs, 10 nephrotoxic and 10 non-nephrotoxic. We then tested 45 pairs of non-nephrotoxic drugs, among the most prescribed at our hospital and representing distinct pharmacological classes for DDIs.
Sensitivity and specificity were 50 % [95 % confidence interval (CI) 23.66-76.34] and 90 % (95 % CI 59.58-98.21), respectively, for single drugs. Our algorithm confirmed a previously identified signal concerning clarithromycin and calcium-channel blockers (unadjusted odds ratio (ORu) 2.92; 95 % CI 1.11-7.69, p = 0.04). Among the 45 drug pairs investigated, we identified a signal concerning 55 patients in association with bromazepam and hydroxyzine (ORu 1.66; 95 % CI 1.23-2.23). This signal was not confirmed after a chart review. Even so, AKI and co-prescription were confirmed for 96 % (95 % CI 88-99) and 88 % (95 % CI 76-94) of these patients, respectively.
Data mining techniques on CDW can foster the detection of adverse drug reactions when drugs are used alone or in combination.
Background: The objective of this study was to measure the prevalence of inflammatory bowel disease (IBD) among patients with autism spectrum disorders (ASD), which has not been well described previously.
Methods: The rates of IBD among patients with and without ASD were measured in 4 study populations with distinct modes of ascertainment: a health care benefits company, 2 pediatric tertiary care centers, and a national ASD repository. The rates of IBD (established through International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9-CM] codes) were compared with respective controls and combined using a Stouffer meta-analysis. Clinical charts were also reviewed for IBD among patients with ICD-9-CM codes for both IBD and ASD at one of the pediatric tertiary care centers. This expert-verified rate was compared with the rate in the repository study population (where IBD diagnoses were established by expert review) and in nationally reported rates for pediatric IBD.
Results: In all of case-control study populations, the rates of IBD-related ICD-9-CM codes for patients with ASD were significantly higher than that of their respective controls (Stouffer meta-analysis, P < 0.001). Expert-verified rates of IBD among patients with ASD were 7 of 2728 patients in one study population and 16 of 7201 in a second study population. The age-adjusted prevalence of IBD among patients with ASD was higher than their respective controls and nationally reported rates of pediatric IBD.
Conclusions: Across each population with different kinds of ascertainment, there was a consistent and statistically significant increased prevalance of IBD in patients with ASD than their respective controls and nationally reported rates for pediatric IBD.
The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features.
BACKGROUND: Medline/PubMed is the most frequently used medical bibliographic research database. The aim of this study was to propose a new generic method to limit any Medline/PubMed query based on the relative impact factor and the A & B categories of the SIGAPS score. MATERIAL AND METHODS: The entire PubMed corpus was used for the feasibility study, then ten frequent diseases in terms of PubMed indexing and the citations of four Nobel prize winners. The relative impact factor (RIF) was calculated by medical specialty defined in Journal Citation Reports. The two queries, which included all the journals in category A (or A OR B), were added to any Medline/PubMed query as a central point of the feasibility study. RESULTS: Limitation using the SIGAPS category A was larger than the when using the Core Clinical Journals (CCJ): 15.65% of PubMed corpus vs 8.64% for CCJ. The response time of this limit applied to the entire PubMed corpus was less than two seconds. For five diseases out of ten, limiting the citations with the RIF was more effective than with the CCJ. For the four Nobel prize winners, limiting the citations with the RIF was more effective than the CCJ. CONCLUSION: The feasibility study to apply a new filter based on the relative impact factor on any Medline/PubMed query was positive.
OBJECTIVE: We had for objective to study HIV management (hospital, ambulatory, and mixed) and assess compliance with health insurance database.
METHOD: We conducted a retrospective study using the French Social Security (CPAM) database. The inclusion criteria were: age>18years of age, at least 2 prescriptions of antiretroviral therapy.
RESULTS: Five hundred and seventy-five patients were included: extra-hospital (12), hospital (162), mixed (401). The prescriptions were exclusively hospital issued for 76.2% of the patients. Among the mixed group patients, 91% of treatments were delivered at least once in the community, and 45.6% of biological tests were performed in private laboratories at least once. The sex ratio (2.1 vs. 1.3), the number of patients having switched antiretroviral therapy (36.7% vs. 27.8%), and the frequency of biological tests (3.1 vs. 2.6) were significantly higher in the mixed group compared to the hospital group. The mean compliance was 90% in the hospital group and 91.8% in the mixed group. The compliance was<80% for 104 patients (21.8%). Patients with≥80% compliance were older (46.1years of age vs. 42.7years of age), with more frequent biological tests (3 per year vs. 2.5 per year), and more frequent switches in treatment (35.4% vs. 26.0%).
CONCLUSION: Prescriptions of ARV were almost exclusively hospital issued. Their dispensation and biological tests were split between hospital and extra-hospital settings. Most patients demonstrated an optimal compliance. The CPAM database allows describing HIV management and assessing compliance.
PURPOSE: To test an automated method to decrease the number of false-positive (FP) signals of disproportionate reportings (SDRs) generated by co-prescription.
METHODS: Automated backward stepwise removal of reports concerning the drug associated with the highest ranked SDR for an event was tested for gastric and oesophageal haemorrhages (GOH), central nervous system haemorrhages and cerebrovascular accidents (CNSH), ischaemic coronary artery disorders and muscle pains (MP) using the reporting odds ratio in the French spontaneous reporting research database. After ranking SDRs detected in the complete dataset on the lower limit of the reporting odds ratio 95% confidence interval, reports concerning the drug with the highest ranked SDR were removed. In the dataset thus generated, SDRs were again identified, ranked and reports related to the drug involved in the newly highest ranked SDR removed. The process was repeated until no signal was detected. Initially detected SDRs eliminated using this technique were assessed regarding the summary of products characteristics and the literature to determine their FP nature.
RESULTS: Seventeen SDRs were successively eliminated for GOH, 37 for CNSH, 15 for ischaemic coronary artery disorders, and 36 for MP. Four were FP for GOH, 29 for CNSH, 7 for ACI and none were FP for MP. The positive predictive value of the backward stepwise removal procedure in identifying FP SDRs ranged from 0% (MP) to 78.4% (CNSH).
CONCLUSIONS: Although further adjustment is needed to improve the method presented herein, our results suggest that numerous FP signals because of co-prescription bias could be eliminated using an automated method.
The Patient-Centered Outcomes Research Institute (PCORI) recently launched PCORnet to establish a single inter-operable multicenter data research network that will support observational research and randomized clinical trials. This paper provides an overview of the patient-powered research networks (PPRNs), networks of patient organizations focused on a particular health condition that are interested in sharing health information and engaging in research. PPRNs will build on their foundation of trust within the patient communities and draw on their expertise, working with participants to identify true patient-centered outcomes and direct a patient-centered research agenda. The PPRNs will overcome common challenges including enrolling a diverse and representative patient population; engaging patients in governance; designing the data infrastructure; sharing data securely while protecting privacy; prioritizing research questions; scaling small networks into a larger network; and identifying pathways to sustainability. PCORnet will be the first distributed research network to bring PCOR to national scale.
BACKGROUND: Data mining in spontaneous reporting databases has shown that drug-induced liver injury is infrequently reported in children.
OBJECTIVES: Our objectives were to (i) identify drugs potentially associated with acute liver injury (ALI) in children and adolescents using electronic healthcare record (EHR) data; and (ii) to evaluate the significance and novelty of these associations.
METHODS: We identified potential cases of ALI during exposure to any prescribed/dispensed drug for individuals <18 years old from the EU-ADR network, which includes seven databases from three countries, covering the years 1996-2010. Several new methods for signal detection were applied to identify all statistically significant associations between drugs and ALI. A drug was considered statistically significantly associated with ALI, using all other time as a reference category, if the 95% CI lower band of the relative risk was >1 and in the presence of at least three exposed cases of ALI. Potentially new signals were distinguished from already known associations concerning ALI (whether in adults and/or in the paediatric population) through manual review of published literature and drug product labels.
RESULTS: The study population comprised 4,838,146 individuals aged <18 years, who contributed an overall 25,575,132 person-years of follow-up. Within this population, we identified 1,015 potential cases of ALI. Overall, 20 positive drug-ALI associations were detected. The associations between ALI and domperidone, flunisolide and human insulin were considered as potentially new signals. Citalopram and cetirizine have been previously described as hepatotoxic in adults but not in children, while all remaining associations were already known in both adults and children.
CONCLUSIONS: Data mining of multiple EHR databases for signal detection confirmed known associations between ALI and several drugs, and identified some potentially new signals in children that require further investigation through formal epidemiologic studies. This study shows that EHRs may complement traditional spontaneous reporting systems for signal detection and strengthening.
Currently, a non-invasive method to estimate the degree of interstitial fibrosis (IF) in chronic kidney disease is not available in routine. The aim of our study was to evaluate the diagnostic performance of the measurement of urinary low molecular weight (LMW) protein concentrations as a method to determine the extent of IF. The urines specimen from 162 consecutive patients who underwent renal biopsy were used in the analysis. Numerical quantification software based on the colorimetric analysis of fibrous areas was used to assess the percentage IF. Total proteinuria, albuminuria, and the urinary levels of retinol binding protein (RBP), alpha1-microglobulin (α1MG), beta 2-microglobulin (β2MG), transferrin, and IgG immunoglobulins were measured. There was a significant correlation between the degree of IF and the RBP/creatinine (creat) ratio (R2: 0.11, p<0.0001). IF was associated to a lesser extent with urinary β2MG and α1MG; however, there was no association with total proteinuria or high molecular weight (HMW) proteinuria. The correlation between IF and RBP/creat remained significant after adjustment to the estimated glomerular filtration rate, age, body mass index, α1MG, and β2MG. The specificity of the test for diagnosing a fibrosis score of >25% of the parenchyma was 95% when using a threshold of 20 mg/g creat. In conclusion, RBP appears to be a quantitative and non-invasive marker for the independent prediction of the extent of kidney IF. Because methods for the measurement of urinary RBP are available in most clinical chemistry departments, RBP measurement is appealing for implementation in the routine care of patients with chronic kidney disease.
OBJECTIVES: The aim of this research was to automate the search of publications concerning adverse drug reactions (ADR) by defining the queries used to search MEDLINE and by determining the required threshold for the number of extracted publications to confirm the drug/event association in the literature.
METHODS: We defined an approach based on the medical subject headings (MeSH) 'descriptor records' and 'supplementary concept records' thesaurus, using the subheadings 'chemically induced' and 'adverse effects' with the 'pharmacological action' knowledge. An expert-built validation set of true positive and true negative drug/adverse event associations (n=61) was used to validate our method.
RESULTS: Using a threshold of three of more extracted publications, the automated search method presented a sensitivity of 90% and a specificity of 100%. For nine different drug/event pairs selected, the recall of the automated search ranged from 24% to 64% and the precision from 93% to 48%.
CONCLUSIONS: This work presents a method to find previously established relationships between drugs and adverse events in the literature. Using MEDLINE, following a MeSH approach to filter the signals, is a valid option. Our contribution is available as a web service that will be integrated in the final European EU-ADR project (Exploring and Understanding Adverse Drug Reactions by integrative mining of clinical records and biomedical knowledge) automated system.
PURPOSE: Pharmacovigilance methods have advanced greatly during the last decades, making post-market drug assessment an essential drug evaluation component. These methods mainly rely on the use of spontaneous reporting systems and health information databases to collect expertise from huge amounts of real-world reports. The EU-ADR Web Platform was built to further facilitate accessing, monitoring and exploring these data, enabling an in-depth analysis of adverse drug reactions risks.
METHODS: The EU-ADR Web Platform exploits the wealth of data collected within a large-scale European initiative, the EU-ADR project. Millions of electronic health records, provided by national health agencies, are mined for specific drug events, which are correlated with literature, protein and pathway data, resulting in a rich drug-event dataset. Next, advanced distributed computing methods are tailored to coordinate the execution of data-mining and statistical analysis tasks. This permits obtaining a ranked drug-event list, removing spurious entries and highlighting relationships with high risk potential.
RESULTS: The EU-ADR Web Platform is an open workspace for the integrated analysis of pharmacovigilance datasets. Using this software, researchers can access a variety of tools provided by distinct partners in a single centralized environment. Besides performing standalone drug-event assessments, they can also control the pipeline for an improved batch analysis of custom datasets. Drug-event pairs can be substantiated and statistically analysed within the platform's innovative working environment.
CONCLUSIONS: A pioneering workspace that helps in explaining the biological path of adverse drug reactions was developed within the EU-ADR project consortium. This tool, targeted at the pharmacovigilance community, is available online at https://bioinformatics.ua.pt/euadr/.
OBJECTIVE: Data from electronic healthcare records (EHR) can be used to monitor drug safety, but in order to compare and pool data from different EHR databases, the extraction of potential adverse events must be harmonized. In this paper, we describe the procedure used for harmonizing the extraction from eight European EHR databases of five events of interest deemed to be important in pharmacovigilance: acute myocardial infarction (AMI); acute renal failure (ARF); anaphylactic shock (AS); bullous eruption (BE); and rhabdomyolysis (RHABD).
DESIGN: The participating databases comprise general practitioners' medical records and claims for hospitalization and other healthcare services. Clinical information is collected using four different disease terminologies and free text in two different languages. The Unified Medical Language System was used to identify concepts and corresponding codes in each terminology. A common database model was used to share and pool data and verify the semantic basis of the event extraction queries. Feedback from the database holders was obtained at various stages to refine the extraction queries.
MEASUREMENTS: Standardized and age specific incidence rates (IRs) were calculated to facilitate benchmarking and harmonization of event data extraction across the databases. This was an iterative process.
RESULTS: The study population comprised overall 19 647 445 individuals with a follow-up of 59 929 690 person-years (PYs). Age adjusted IRs for the five events of interest across the databases were as follows: (1) AMI: 60-148/100 000 PYs; (2) ARF: 3-49/100 000 PYs; (3) AS: 2-12/100 000 PYs; (4) BE: 2-17/100 000 PYs; and (5) RHABD: 0.1-8/100 000 PYs.
CONCLUSIONS: The iterative harmonization process enabled a more homogeneous identification of events across differently structured databases using different coding based algorithms. This workflow can facilitate transparent and reproducible event extractions and understanding of differences between databases.
AIMS: Characteristics of sudden cardiac arrest (SCA) during sports offers a novel (and unexplored) setting to assess factors associated with disparities in outcomes across regions.
METHODS AND RESULTS: From a prospective 5-year community-based French registry concerning SCA during sports in 10-75 year-olds, we evaluated whether outcomes differed significantly between geographic regions. We then determined the extent to which variations in community-related early interventions were associated with regional variations in survival. Among 820 SCA cases studied, overall survival at hospital discharge was 15.7% (95% confidence interval, 13.2-18.2%), with considerable regional disparities (from 3.4 to 42.6%, P < 0.001). Major differences were noted regarding bystander initiation of cardiopulmonary resuscitation (15.3-80.9%, P < 0.001) and presence of initial shockable rhythm (28.6-79.1%, P < 0.001), with higher values of these being associated with better survival rates. The proportion of survivors with favourable neurological outcome at discharge was fairly uniform among survival groups (CPC-1/2, varying from 77.4 to 90.0%, P = 0.83). No difference was observed regarding subjects' characteristics and circumstances of SCA occurrence, including delays in resuscitation (collapse-to-call period). With a comparable in-hospital mortality (P = 0.44), survival at hospital discharge was highly correlated with that at hospital admission (regional variations from 7.4 to 75.0%, P < 0.001).
CONCLUSION: Major regional disparities exist in survival rates (up to 10-fold) after SCA during sports. SCA cases from regions with the highest levels of bystander resuscitation had the best survival rates to hospital admission and discharge.
BACKGROUND: The growing interest in using electronic healthcare record (EHR) databases for drug safety surveillance has spurred development of new methodologies for signal detection. Although several drugs have been withdrawn postmarketing by regulatory authorities after scientific evaluation of harms and benefits, there is no definitive list of confirmed signals (i.e. list of all known adverse reactions and which drugs can cause them). As there is no true gold standard, prospective evaluation of signal detection methods remains a challenge.
OBJECTIVE: Within the context of methods development and evaluation in the EU-ADR Project (Exploring and Understanding Adverse Drug Reactions by integrative mining of clinical records and biomedical knowledge), we propose a surrogate reference standard of drug-adverse event associations based on existing scientific literature and expert opinion.
METHODS: The reference standard was constructed for ten top-ranked events judged as important in pharmacovigilance. A stepwise approach was employed to identify which, among a list of drug-event associations, are well recognized (known positive associations) or highly unlikely ('negative controls') based on MEDLINE-indexed publications, drug product labels, spontaneous reports made to the WHO's pharmacovigilance database, and expert opinion. Only drugs with adequate exposure in the EU-ADR database network (comprising ≈60 million person-years of healthcare data) to allow detection of an association were considered. Manual verification of positive associations and negative controls was independently performed by two experts proficient in clinical medicine, pharmacoepidemiology and pharmacovigilance. A third expert adjudicated equivocal cases and arbitrated any disagreement between evaluators.
RESULTS: Overall, 94 drug-event associations comprised the reference standard, which included 44 positive associations and 50 negative controls for the ten events of interest: bullous eruptions; acute renal failure; anaphylactic shock; acute myocardial infarction; rhabdomyolysis; aplastic anaemia/pancytopenia; neutropenia/agranulocytosis; cardiac valve fibrosis; acute liver injury; and upper gastrointestinal bleeding. For cardiac valve fibrosis, there was no drug with adequate exposure in the database network that satisfied the criteria for a positive association.
CONCLUSION: A strategy for the construction of a reference standard to evaluate signal detection methods that use EHR has been proposed. The resulting reference standard is by no means definitive, however, and should be seen as dynamic. As knowledge on drug safety evolves over time and new issues in drug safety arise, this reference standard can be re-evaluated.