Using machine learning methods to improve chronic disease case definitions in primary care electronic medical records

Background: Chronic disease surveillance at the primary care level is becoming more feasible with the increased use of electronic medical records (EMRs). However, the quality of surveillance information is directly dependent on the quality of the case definitions that identify the conditions of interest. Purpose: To determine whether machine learning algorithms can produce chronic disease case definitions comparable to committee created case definitions in a primary care EMR setting. Methods: A chart review was conducted for the presence of hypertension, diabetes, osteoarthritis, and depression in a cohort of 1920 patients from the Canadian Primary Care Sentinel Surveillance Network database. The results of this chart review were used as training data. The C5.0, Classification and Regression Tree, Chi-Squared Automated Interaction Detection decision trees, Forward Stepwise logistic regression, Least Absolute Shrinkage and Selection Operator penalized logistic regression were compared using 10-fold cross validation. Sensitivity, specificity, positive predictive value and negative predictive value were estimated and compared for the four chronic conditions of interest. Results: Validity measures were similar across algorithms. For hypertension, sensitivity ranged between 93.1-96.7%, while specificity ranged from 88.8-93.2%. For diabetes, sensitivities ranged from 93.5-96.3% with specificities between 97.1-99.0%. For osteoarthritis, sensitivities ranged from 82.0-84.4% with specificities between 92.7-94.0%. For depression, sensitivities went from 81.4-88.3%, and specificities ranged from 93.4-94.9%. Compared with the committee-created case definitions, these metrics were equivalent or better using the machine learning method. Conclusions: Machine learning algorithms produced accurate case definitions comparable to committee-created case definitions. It is possible to use machine learning techniques to develop high quality case definitions from EMR data

Gastro-oesophageal reflux disease in children with neurological impairment: a retrospective cohort study

Objectives To determine the incidence and prevalence of gastro-oesophageal reflux disease (GERD) diagnosis and treatment in children with neurological impairment (NI) along with relationship to key variables.Design This is a population-based retrospective cohort study.Setting This study takes place in Alberta, Canada.Patients Children with NI were identified by hospital-based International Classification of Diseases (ICD) codes from 2006 to 2018.Main outcome measures Incidence and prevalence of a GERD diagnosis identified by: (1) hospital-based ICD-10 codes; (2) specialist claims; (3) dispensation of acid-suppressing medication (ASM). Age, gender, complex chronic conditions (CCC) and technology assistance were covariates.Results Among 10 309 children with NI, 2772 (26.9%) met the GERD definition. The unadjusted incidence rate was 52.1 per 1000 person-years (50.2–54.1). Increasing numbers of CCCs were associated with a higher risk of GERD. The HR for GERD associated with a gastrostomy tube was 4.56 (95% CI 4.15 to 5.00). Overall, 2486 (24.1%) of the children were treated with ASMs of which 1535 (61.7%) met no other GERD criteria. The incidence rate was 16.9 dispensations per year (95% CI 16.73 to 17.07). The prevalence of gastrojejunostomy tubes was 1.1% (n=121), surgical jejunostomy tubes was 0.7% (n=79) and fundoplication was 3.4% (n=351).Conclusions The incidence of GERD in children with NI greatly exceeds that of the general paediatric population. Similarly, incidence rate of medication dispensations was closer to the rates seen in adults particularly in children with multiple CCCs and gastrostomy tubes. Further research is needed to determine the appropriate use of ASMs balancing the potential for adverse effects in this population

Control of glycemia and blood pressure in British adults with diabetes mellitus and subsequent therapy choices: a comparison across health states

Abstract Background To examine the intensity of glycemic and blood pressure control in British adults with diabetes mellitus and whether control levels or treatment deintensification rates differ across health states. Methods Retrospective cohort study using primary care electronic medical records (the United Kingdom Health Improvement Network Database) for adults with diabetes diagnosed at least 6 months before the index HbA1C and systolic blood pressure (SBP) measurements (to give their primary care physicians time to achieve treatment goals). We used prescribing records for 6 months pre/post the index measurements to determine who had therapy subsequently deintensified (based on “glycemic therapy score” and “antihypertensive therapy score” derived from number and dosage of medications). Results Of 292,170 individuals with diabetes, HbA1C  7.5% and 46.6, 51.4, and 48.5% had SBP > 140 mmHg). The proportions of patients with HbA1C or SBP out of recommended treatment ranges changed little 6 months later despite frequent (median 14 per year) primary care visits. Conclusions Glycemic and hypertensive control exhibited statistically significant but small magnitude differences across frailty states. Medication deintensification was uncommon, even in frail patients below SBP and HbA1C targets. SBP levels were more likely to be outside recommended treatment ranges than glycemic levels. Trial registration As this study is a retrospective secondary analysis of electronic medical record data and not a health care intervention trial it was not registere

Correction: Age-specific global epidemiology of hydrocephalus: Systematic review, metanalysis and global birth surveillance.

[This corrects the article DOI: 10.1371/journal.pone.0204926.]

Age-specific global epidemiology of hydrocephalus: Systematic review, metanalysis and global birth surveillance.

BACKGROUND:Hydrocephalus is a debilitating disorder, affecting all age groups. Evaluation of its global epidemiology is required for healthcare planning and resource allocation. OBJECTIVES:To define age-specific global prevalence and incidence of hydrocephalus. METHODS:Population-based studies reporting prevalence of hydrocephalus were identified (MEDLINE, EMBASE, Cochrane, and Google Scholar (1985-2017)). Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. Two authors reviewed abstracts, full text articles and abstracted data. Metanalysis and meta-regressions were used to assess associations between key variables. Heterogeneity and publication bias were assessed. Main outcome of interest was hydrocephalus prevalence among pediatric (≤ 18 years), adults (19-64 years), and elderly (≥ 65) patients. Annual hydrocephalus incidence stratified by country income level and folate fortification requirements were obtained (2003-2014) from the International Clearinghouse for Birth Defects Surveillance and Research (ICBDSR). RESULTS:Of 2,460 abstracts, 52 met review eligibility criteria (aggregate population 171,558,651). Mean hydrocephalus prevalence was 85/100,000 [95% CI 62, 116]. The prevalence was 88/100,000 [95% CI 72, 107] in pediatrics; 11/100,000 [95% CI 5, 25] in adults; and 175/100,000 [95% CI 67, 458] in the elderly. The ICBDSR-based incidence of hydrocephalus diagnosed at birth remained stable over 11 years: 81/100,000 [95% CI 69, 96]. A significantly lower incidence was identified in high-income countries. CONCLUSION:This systematic review established age-specific global hydrocephalus prevalence. While high-income countries had a lower hydrocephalus incidence according to the ICBDSR registry, folate fortification status was not associated with incidence. Our findings may inform future healthcare resource allocation and study

Assessment of endoscopic healing by using advanced technologies reflects histologic healing in ulcerative colitis.

BACKGROUND Several studies reported that Ulcerative colitis (UC) patients with endoscopic mucosal healing may still have histologic inflammation. We investigated the relationship between mucosal healing defined by modified PICaSSO (Paddington International Virtual ChromoendoScopy ScOre), Mayo Endoscopic Score (MES) and probe-based confocal laser endomicroscopy (pCLE) with histological indices in UC. METHODS A prospective study enrolling 82 UC patients (M 66%) was conducted. High definition (HD) colonoscopy was performed to evaluate the activity of the disease with MES assessed with High Definition (HD-MES) and modified PICaSSO and targeted biopsies were taken; pCLE was then performed. Receiver Operating Characteristic (ROC) curves were plotted to determine the best thresholds for modified PICaSSO and pCLE scores that predicted histological healing according to the Robarts Histopathology Index (RHI) and ECAP 'Extension, Chronicity, Activity, Plus' histology score. RESULTS A modified PICaSSO of ≤4 predicted histological healing at RHI ≤3, with sensitivity, specificity, accuracy and area under the ROC curve (AUROC) of 89.8%, 95.7%, 91.5% and 95.9% respectively. The sensitivity, specificity, accuracy and AUROC of HD-MES to predict histological healing by RHI were 81.4%, 95.7, 85.4% and 92.1%, respectively. A pCLE ≤10 predicted histological healing with sensitivity 94.9%, specificity 91.3%, accuracy of 93.9% and AUROC of 96.5%. An ECAP of ≤10 was predicted by modified PICaSSO ≤4 with accuracy of 91.5% and AUROC of 95.9%. CONCLUSION Histological healing by RHI and ECAP is accurately predicted by HD-MES and modified virtual electronic Chromoendoscopy PICaSSO,endoscopic score ; and the use of pCLE did not improve the accuracy any further