TransformEHRs: a flexible methodology for building transparent ETL processes for EHR reuse

Background: During the COVID-19 pandemic, several methodologies were designed for obtaining electronic health record (EHR)-derived datasets for research. These processes are often based on black boxes, on which clinical researchers are unaware of how the data were recorded, extracted, and transformed. In order to solve this, it is essential that extract, transform, and load (ETL) processes are based on transparent, homogeneous, and formal methodologies, making them understandable, reproducible, and auditable. Objectives: This study aims to design and implement a methodology, according with FAIR Principles, for building ETL processes (focused on data extraction, selection, and transformation) for EHR reuse in a transparent and flexible manner, applicable to any clinical condition and health care organization. Methods: The proposed methodology comprises four stages: (1) analysis of secondary use models and identification of data operations, based on internationally used clinical repositories, case report forms, and aggregated datasets; (2) modeling and formalization of data operations, through the paradigm of the Detailed Clinical Models; (3) agnostic development of data operations, selecting SQL and R as programming languages; and (4) automation of the ETL instantiation, building a formal configuration file with XML. Results: First, four international projects were analyzed to identify 17 operations, necessary to obtain datasets according to the specifications of these projects from the EHR. With this, each of the data operations was formalized, using the ISO 13606 reference model, specifying the valid data types as arguments, inputs and outputs, and their cardinality. Then, an agnostic catalog of data was developed through data-oriented programming languages previously selected. Finally, an automated ETL instantiation process was built from an ETL configuration file formally defined. Conclusions: This study has provided a transparent and flexible solution to the difficulty of making the processes for obtaining EHR-derived data for secondary use understandable, auditable, and reproducible. Moreover, the abstraction carried out in this study means that any previous EHR reuse methodology can incorporate these results into them.Ministerio de Economía y Competitividad Instituto de Salud Carlos III PI18/00981, PI18/01047, PI18CIII/00019.S

In-hospital outcomes of mechanical complications in acute myocardial infarction: Analysis from a nationwide Spanish database

Background: Mechanical complications represent an important cause of mortality in myocardial infarction (MI) patients. This is a nationwide study performed to evaluate possible changes in epidemiology or prognosis of these complications with current available strategies.Methods: Information was obtained from the minimum basis data set of the Spanish National Health System, including all hospitalizations for acute myocardial infarction (AMI) from 2010 to 2015. Risk-standardized in-hospital mortality ratio was calculated using multilevel risk adjustment models.Results: A total of 241,760 AMI episodes were analyzed, MI mechanical complications were observed in 842 patients: cardiac tamponade in 587, ventricular septal rupture in 126, and mitral regurgitation due to papillary muscle or chordae tendineae rupture in 155 (there was more than one complication in 21 patients). In-hospital mortality was 59.5%. On multivariate adjustment, variables with significant impact on in-hospital mortality were: age (OR 1.06; 95% CI 1.04-1.07; p < 0.001), ST-segment elevation AMI (OR 2.91; 95% CI 1.88-4.5; p < 0.001), cardiogenic shock (OR 2.35; 95% CI 1.66-3.32; p < 0.001), cardio-respiratory failure (OR 3.48; 95% CI 2.37-5.09; p < 0.001), and chronic obstructive pulmonary disease (OR 1.85; 95% CI 1.07-3.20; p < 0.001). No significant trends in risk-adjusted in-hospital mortality were detected (IRR 0.997; p = 0.109). Cardiac intensive care unit availability and more experience with mechanical complications management were associated with lower adjusted mortality rates (56.7 ± 5.8 vs. 60.1 ± 4.5; and 57 ± 6.1 vs. 59.9 ± 5.6, respectively; p < 0.001).Conclusions: Mechanical complications occur in 3.5 per thousand AMI, with no significant trends to better survival over the past few years. Advanced age, cardiogenic shock and cardio-respiratory failure are the most important risk factors for in-hospital mortality. Higher experience and specialized cardiac intensive care units are associated with better outcomes

Impact of Heart Failure on In-Hospital Outcomes after Surgical Femoral Neck Fracture Treatment

Background: Femoral neck fracture (FNF) is a common condition with a rising incidence, partly due to aging of the population. It is recommended that FNF should be treated at the earliest opportunity, during daytime hours, including weekends. However, early surgery shortens the available time for preoperative medical examination. Cardiac evaluation is critical for good surgical outcomes as most of these patients are older and frail with other comorbid conditions, such as heart failure. The aim of this study was to determine the impact of heart failure on in-hospital outcomes after surgical femoral neck fracture treatment. Methods: We performed a retrospective study using the Spanish National Hospital Discharge Database, 2007–2015. We included patients older than 64 years treated for reduction and internal fixation of FNF. Demographic characteristics of patients, as well as administrative variables, related to patient’s diseases and procedures performed during the episode were evaluated. Results: A total of 234,159 episodes with FNF reduction and internal fixation were identified from Spanish National Health System hospitals during the study period; 986 (0.42%) episodes were excluded, resulting in a final study population of 233,173 episodes. Mean age was 83.7 (±7) years and 179,949 (77.2%) were women (p < 0.001). In the sample, 13,417 (5.8%) episodes had a main or secondary diagnosis of heart failure (HF) (p < 0.001). HF patients had a mean age of 86.1 (±6.3) years, significantly older than the rest (p < 0.001). All the major complications studied showed a higher incidence in patients with HF (p < 0.001). Unadjusted in-hospital mortality was 4.1%, which was significantly higher in patients with HF (18.2%) compared to those without HF (3.3%) (p < 0.001). The average length of stay (LOS) was 11.9 (±9.1) and was also significantly higher in the group with HF (16.5 ± 13.1 vs. 11.6 ± 8.7; p < 0.001). Conclusions: Patients with HF undergoing FNF surgery have longer length of stay and higher rates of both major complications and mortality than those without HF. Although their average length of stay has decreased in the last few years, their mortality rate has remained unchanged

Heart Failure Is a Poor Prognosis Risk Factor in Patients Undergoing Cholecystectomy: Results from a Spanish Data-Based Analysis

Background: The incidence of cholecystectomy is increasing as the result of the aging worldwide. Our aim was to determine the influence of heart failure on in-hospital outcomes in patients undergoing cholecystectomy in the Spanish National Health System (SNHS). Methods: We conducted a retrospective study using the Spanish National Hospital Discharge Database. Patients older than 17 years undergoing cholecystectomy in the period 2007–2015 were included. Demographic and administrative variables related to patients’ diseases as well as procedures were collected. Results: 478,111 episodes of cholecystectomy were identified according to the data from SNHS hospitals in the period evaluated. From all the episodes, 3357 (0.7%) were excluded, as the result the sample was represented by 474,754 episodes. Mean age was 58.3 (+16.5) years, and 287,734 (60.5%) were women (p < 0.001). A primary or secondary diagnosis of HF was identified in 4244 (0.89%) (p < 0.001) and mean age was 76.5 (+9.6) years. A higher incidence of all main complications studied was observed in the HF group (p < 0.001), except stroke (p = 0.753). Unadjusted in-hospital mortality was 1.1%, 12.9% in the group with HF versus 1% in the non HF group (p < 0.001). Average length of hospital stay was 5.4 (+8.9) days, and was higher in patients with HF (16.2 + 17.7 vs. 5.3 + 8.8; p < 0.001). Risk-adjusted in-hospital mortality models’ discrimination was high in both cases, with AUROC values = 0.963 (0.960–0.965) in the APRG-DRG model and AUROC = 0.965 (0.962–0.968) in the CMS adapted model. Median odds ratio (MOR) was high (1.538 and 1.533, respectively), stating an important variability of risk-adjusted outcomes among hospitals. Conclusions: The presence of HF during admission increases in hospital mortality and lengthens the hospital stay in patients undergoing cholecystectomy. However, mortality and hospital stay have significantly decreased during the study period in both groups (HF and non HF patients)

Impact of late presentation of HIV infection on short-, mid- and long-term mortality and causes of death in a multicenter national cohort: 2004–2013

SummaryObjectivesTo analyze the impact of late presentation (LP) on overall mortality and causes of death and describe LP trends and risk factors (2004–2013).MethodsCox models and logistic regression were used to analyze data from a nation-wide cohort in Spain. LP is defined as being diagnosed when CD4 < 350 cells/ml or AIDS.ResultsOf 7165 new HIV diagnoses, 46.9% (CI95%:45.7–48.0) were LP, 240 patients died.First-year mortality was the highest (aHRLP.vs.nLP = 10.3[CI95%:5.5–19.3]); between 1 and 4 years post-diagnosis, aHRLP.vs.nLP = 1.9(1.2–3.0); and >4 years, aHRLP.vs.nLP = 1.5(0.7–3.1).First-year's main cause of death was HIV/AIDS (73%); and malignancies among those surviving >4 years (32%). HIV/AIDS-related deaths were more likely in LP (59.2% vs. 25.0%; p < 0.001). LP declined from 55.9% (2004–05) to 39.4% (2012–13), and reduced in 46.1% in men who have sex with men (MSM) and 37.6% in heterosexual men, but increased in 22.6% in heterosexual women.Factors associated with LP: sex (ORMEN.vs.WOMEN = 1.4[1.2–1.7]); age (OR31–40.vs.<30 = 1.6[1.4–1.8], OR41–50.vs.<30 = 2.2[1.8–2.6], OR>50.vs.<30 = 3.6[2.9–4.4]); behavior (ORInjectedDrugUse.vs.MSM = 2.8[2.0–3.8]; ORHeterosexual.vs.MSM = 2.2[1.7–3.0]); education (ORPrimaryEducation.vs.University = 1.5[1.1–2.0], ORLowerSecondary.vs.University = 1.3[1.1–1.5]); and geographical origin (ORSub-Saharan.vs.Spain = 1.6[1.3–2.0], ORLatin-American.vs.Spain = 1.4[1.2–1.8]).ConclusionsLP is associated with higher mortality, especially short-term- and HIV/AIDS-related mortality. Mid-term-, but not long-term mortality, remained also higher in LP than nLP. LP decreased in MSM and heterosexual men, not in heterosexual women. The groups most affected by LP are low educated, non-Spanish and heterosexual women

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

Evaluación de tres sistemas de ajuste de riesgo como predictores del consumo de medicamentos y productos sanitarios en unidades polivalentes de hospitalización

ABSTRACT Background: The use of medicines and medical supplies is a significant component of health expenditure, linked to healthcare quality and efficient resource allocation. This study aimed to evaluate three risk adjustment systems predictive power of the consumption of medicines and medical supplies at polyvalent hospitalization units (PHU). Methods: This is an observational, retrospective study of the resources utilization in PHU between 2010 and 2013. We fitted linear regression models and evaluated their goodness of fit for three different predictors: Charlson Comorbidity Index (CCI), All Patients DRG (AP-DRG) and All Patients Refined DRG (APR-DRG) relative weights, and each one of them corrected by the length of stay. We analyzed hospitalization episodes included in the Minimum Basic Data Set (MBDS) from Fuenlabrada University Hospital. Data about the use of medicines and medical supplies were obtained from pharmacy and supply chain management information systems. Results: Significant correlation was found between the annual consumption and the predictors considered (r=0.879 for CCI; r=0.622 for AP-DRG and r=0.514 for APR-DRG; p<0.01). The CCI corrected by length of stay was the variable that best fit presented (Ṝ2=0.863; p<0.001). Conclusions: The best predictive ability of CCI indicates that resource utilization depends more of the concurrent presence of additional pathology than the case mix calculated for iso-resource groups.RESUMEN Fundamentos: El uso de medicamentos y productos sanitarios constituye un componente significativo del gasto sanitario, vinculado con la calidad de la atención y la asignación eficiente de los recursos. Este estudio tuvo por objetivo evaluar en tres sistemas de ajuste de riesgos la capacidad predictiva del consumo de medicamentos y productos sanitarios de los sujetos ingresados en unidades polivalentes de hospitalización. Métodos: Estudio de los consumos de las unidades polivalentes de hospitalización del Hospital de Fuenlabrada entre 2010 y 2013, utilizando información de las aplicaciones de farmacia y suministros y el Conjunto Mínimo de Datos Básicos. Se ajustaron modelos de regresión lineal para el índice de Comorbilidad de Charlson (ICH) y el peso medio de los Grupos Relacionados por el Diagnóstico All Patients (AP-GRD) y All Patiens Refined (APR_GRD), cada uno de ellos corregidos por el número de estancias. Resultados: Se comprobó la existencia de correlación estadísticamente significativa entre los consumos anuales y los predictores considerados (los coeficientes de Pearson fueron r=0,879 para ICH; r=0,622 para AP-GRD, y r=0,514 para APR-GRD; p<0,01). ICH corregido por el número de estancias fue la variable que mejor ajuste presentó para la trasformación logarítmica de los consumos (Ṝ2=0,863; p< 0,001). Conclusiones: La mayor capacidad predictiva del índice de comorbilidad de Charlson indica que el consumo de recursos depende más de la presencia concurrente de patología que de la complejidad de la casuística estimada para grupos isoconsumo, aun cuando se considere la gravedad o se corrija la complejidad resultante por la duración del episodio

SmartPITeS: Red colaborativa para la investigación e innovación en Salud Digital

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Obtención de un conjunto de datos derivados de la HCE para investigación en VIH: prueba de concepto

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