ASSESSMENT OF RISK SCORES FOR THE PREDICTION AND DETECTION OF TYPE 2 DIABETES MELLITUS IN CLINICAL SETTINGS

Health and sociological indicators confirm that life expectancy is increasing, and so, the years that patients have to live with chronic diseases and co-morbidities. Type 2 Diabetes is one of the most common chronic diseases, specially linked to overweight and ages over sixty. As a metabolic disease, Type 2 Diabetes affects multiple organs by causing damage in blood vessels and nervous system at micro and macro scale. Mortality of subjects with diabetes is three times higher than the mortality for subjects with other chronic diseases. On the one hand, the management of diabetes is focused on the maintenance of the blood glucose levels under a threshold by the prescription of anti-diabetic drugs and a combination of healthy food habits and moderate physical activity. Recent studies have demonstrated the effectiveness of new strategies to delay and even prevent the onset of Type 2 Diabetes by a combination of active and healthy lifestyle on cohorts of mid to high risk subjects. On the other hand, prospective research has been driven on large groups of population to build risk scores which aim to obtain a rule for the classification of patients according to the odds for developing the disease. Currently there are more than two hundred models and risk scores for doing this, but a few have been properly evaluated in external groups and, to date, none of them has been tested on a population based study. The research study presented in this doctoral thesis strives to use externally validated risk scores for the prediction and detection of Type 2 Diabetes on a population data base in Hospital La Fe (Valencia, Spain). The study hypothesis is that the integration of existing prediction and detection risk scores on Electronic Health Records increases the early-detection of high risk cases. To evaluate this hypothesis three studies on the clinical, user and technology dimensions have been driven to evaluate the extent to which the models and the hospital is ready to exploit such models to identify high risk groups and drive efficient preventive strategies. The findings presented in this thesis suggest that Electronic Health Records are not prepared to massively feed risk models. Some of the evaluated models have shown a good classification performance, which accompanied to the well-acceptance of web-based tools and the acceptable technical performance of the information and communication technology system, suggests that after some work these models can effectively drive a new paradigm of active screening for Type 2 Diabetes.Los indicadores de salud y sociológicos confirman que la esperanza de vida está aumentando, y por lo tanto, los años que los pacientes tienen que vivir con enfermedades crónicas y comorbilidades. Diabetes tipo 2 es una de las enfermedades crónicas más comunes, especialmente relacionadas con el sobrepeso y edades superiores a los sesenta años. Como enfermedad metabólica, la diabetes tipo 2 afecta a múltiples órganos causando daño en los vasos sanguíneos y el sistema nervioso a escala micro y macro. La mortalidad de sujetos con diabetes es tres veces mayor que la mortalidad de sujetos con otras enfermedades crónicas. Por un lado, la estrategia de manejo se centra en el mantenimiento de los niveles de glucosa en sangre bajo un umbral mediante la prescripción de fármacos antidiabéticos y una combinación de hábitos alimentarios saludables y actividad física moderada. Estudios recientes han demostrado la eficacia de nuevas estrategias para retrasar e incluso prevenir la aparición de la diabetes tipo 2 mediante una combinación de estilo de vida activo y saludable en cohortes de sujetos de riesgo medio a alto. Por otro lado, la investigación prospectiva se ha dirigido a grupos de la población para construir modelos de riesgo que pretenden obtener una regla para la clasificación de las personas según las probabilidades de desarrollar la enfermedad. Actualmente hay más de doscientos modelos de riesgo para hacer esta identificación, no obstante la inmensa mayoría no han sido debidamente evaluados en grupos externos y, hasta la fecha, ninguno de ellos ha sido probado en un estudio poblacional. El estudio de investigación presentado en esta tesis doctoral pretende utilizar modelos riesgo validados externamente para la predicción y detección de la Diabetes Tipo 2 en una base de datos poblacional del Hospital La Fe de Valencia (España). La hipótesis del estudio es que la integración de los modelos de riesgo de predicción y detección existentes la práctica clínica aumenta la detección temprana de casos de alto riesgo. Para evaluar esta hipótesis, se han realizado tres estudios sobre las dimensiones clínicas, del usuario y de la tecnología para evaluar hasta qué punto los modelos y el hospital están dispuestos a explotar dichos modelos para identificar grupos de alto riesgo y conducir estrategias preventivas eficaces. Los hallazgos presentados en esta tesis sugieren que los registros de salud electrónicos no están preparados para alimentar masivamente modelos de riesgo. Algunos de los modelos evaluados han demostrado un buen desempeño de clasificación, lo que acompañó a la buena aceptación de herramientas basadas en la web y el desempeño técnico aceptable del sistema de tecnología de información y comunicación, sugiere que después de algún trabajo estos modelos pueden conducir un nuevo paradigma de la detección activa de la Diabetes Tipo 2.Els indicadors sociològics i de salut confirmen un augment en l'esperança de vida, i per tant, dels anys que les persones han de viure amb malalties cròniques i comorbiditats. la diabetis de tipus 2 és una de les malalties cròniques més comunes, especialment relacionades amb l'excés de pes i edats superiors als seixanta anys. Com a malaltia metabòlica, la diabetis de tipus 2 afecta múltiples òrgans causant dany als vasos sanguinis i el sistema nerviós a escala micro i macro. La mortalitat de subjectes amb diabetis és tres vegades superior a la mortalitat de subjectes amb altres malalties cròniques. D'una banda, l'estratègia de maneig se centra en el manteniment dels nivells de glucosa en sang sota un llindar mitjançant la prescripció de fàrmacs antidiabètics i una combinació d'hàbits alimentaris saludables i activitat física moderada. Estudis recents han demostrat l'eficàcia de noves estratègies per a retardar i fins i tot prevenir l'aparició de la diabetis de tipus 2 mitjançant una combinació d'estil de vida actiu i saludable en cohorts de subjectes de risc mitjà a alt. D'altra banda, la investigació prospectiva s'ha dirigit a grups específics de la població per construir models de risc que pretenen obtenir una regla per a la classificació de les persones segons les probabilitats de desenvolupar la malaltia. Actualment hi ha més de dos-cents models de risc per fer aquesta identificació, però la immensa majoria no han estat degudament avaluats en grups externs i, fins ara, cap d'ells ha estat provat en un estudi poblacional. L'estudi d'investigació presentat en aquesta tesi doctoral utilitza models de risc validats externament per a la predicció i detecció de diabetis de tipus 2 en una base de dades poblacional de l'Hospital La Fe de València (Espanya). La hipòtesi de l'estudi és que la integració dels models de risc de predicció i detecció existents la pràctica clínica augmenta la detecció de casos d'alt risc. Per avaluar aquesta hipòtesi, s'han realitzat tres estudis sobre les dimensions clíniques, de l'usuari i de la tecnologia per avaluar fins a quin punt els models i l'hospital estan disposats a explotar aquests models per identificar grups d'alt risc i conduir estratègies preventives. Les troballes presentades sugereixen que els registres de salut electrònics no estan preparats per alimentar massivament models de risc. Alguns dels models avaluats han demostrat una bona classificació, el que va acompanyar a la bona acceptació d'eines basades en el web i el rendiment tècnic acceptable del sistema de tecnologia d'informació i comunicacions implementat. La conclusió es que encara es necesari treball per que aquests models poden conduir un nou paradigma de la detecció activa de la diabetis de tipus 2.Martínez Millana, A. (2017). ASSESSMENT OF RISK SCORES FOR THE PREDICTION AND DETECTION OF TYPE 2 DIABETES MELLITUS IN CLINICAL SETTINGS [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86209TESI

A dashboard-based system for supporting diabetes care

[EN] Objective To describe the development, as part of the European Union MOSAIC (Models and Simulation Techniques for Discovering Diabetes Influence Factors) project, of a dashboard-based system for the management of type 2 diabetes and assess its impact on clinical practice. Methods The MOSAIC dashboard system is based on predictive modeling, longitudinal data analytics, and the reuse and integration of data from hospitals and public health repositories. Data are merged into an i2b2 data warehouse, which feeds a set of advanced temporal analytic models, including temporal abstractions, care-flow mining, drug exposure pattern detection, and risk-prediction models for type 2 diabetes complications. The dashboard has 2 components, designed for (1) clinical decision support during follow-up consultations and (2) outcome assessment on populations of interest. To assess the impact of the clinical decision support component, a pre-post study was conducted considering visit duration, number of screening examinations, and lifestyle interventions. A pilot sample of 700 Italian patients was investigated. Judgments on the outcome assessment component were obtained via focus groups with clinicians and health care managers. Results The use of the decision support component in clinical activities produced a reduction in visit duration (P¿¿¿.01) and an increase in the number of screening exams for complications (P¿<¿.01). We also observed a relevant, although nonstatistically significant, increase in the proportion of patients receiving lifestyle interventions (from 69% to 77%). Regarding the outcome assessment component, focus groups highlighted the system¿s capability of identifying and understanding the characteristics of patient subgroups treated at the center. Conclusion Our study demonstrates that decision support tools based on the integration of multiple-source data and visual and predictive analytics do improve the management of a chronic disease such as type 2 diabetes by enacting a successful implementation of the learning health care system cycle.This work was supported by the European Union in the Seventh Framework Programme, grant number 600914.Dagliati, A.; Sacchi, L.; Tibollo, V.; Cogni, G.; Teliti, M.; Martinez-Millana, A.; Traver Salcedo, V.... (2018). A dashboard-based system for supporting diabetes care. Journal of the American Medical Informatics Association. 25(5):538-547. https://doi.org/10.1093/jamia/ocx159S538547255Sim, I., Gorman, P., Greenes, R. A., Haynes, R. B., Kaplan, B., Lehmann, H., & Tang, P. C. (2001). Clinical Decision Support Systems for the Practice of Evidence-based Medicine. Journal of the American Medical Informatics Association, 8(6), 527-534. doi:10.1136/jamia.2001.0080527Palmer, A. 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Integration of Distributed Services and Hybrid Models Based on Process Choreography to Predict and Detect Type 2 Diabetes

[EN] Life expectancy is increasing and, so, the years that patients have to live with chronic diseases and co-morbidities. Type 2 diabetes is one of the most prevalent chronic diseases, specifically linked to being overweight and ages over sixty. Recent studies have demonstrated the effectiveness of new strategies to delay and even prevent the onset of type 2 diabetes by a combination of active and healthy lifestyle on cohorts of mid to high risk subjects. Prospective research has been driven on large groups of the population to build risk scores that aim to obtain a rule for the classification of patients according to the odds for developing the disease. Currently, there are more than two hundred models and risk scores for doing this, but a few have been properly evaluated in external groups and integrated into a clinical application for decision support. In this paper, we present a novel system architecture based on service choreography and hybrid modeling, which enables a distributed integration of clinical databases, statistical and mathematical engines and web interfaces to be deployed in a clinical setting. The system was assessed during an eight-week continuous period with eight endocrinologists of a hospital who evaluated up to 8080 patients with seven different type 2 diabetes risk models implemented in two mathematical engines. Throughput was assessed as a matter of technical key performance indicators, confirming the reliability and efficiency of the proposed architecture to integrate hybrid artificial intelligence tools into daily clinical routine to identify high risk subjects.The authors wish to acknowledge the consortium of the MOSAIC project (funded by the European Commission, Grant No. FP7-ICT 600914) for their commitment during concept development, which led to the development of the research reported in this manuscriptMartinez-Millana, A.; Bayo-Monton, JL.; Argente-Pla, M.; Fernández Llatas, C.; Merino-Torres, JF.; Traver Salcedo, V. (2018). Integration of Distributed Services and Hybrid Models Based on Process Choreography to Predict and Detect Type 2 Diabetes. Sensors. 18 (1)(79):1-26. https://doi.org/10.3390/s18010079S12618 (1)79Thomas, C. C., & Philipson, L. H. (2015). Update on Diabetes Classification. Medical Clinics of North America, 99(1), 1-16. doi:10.1016/j.mcna.2014.08.015Kahn, S. 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The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine learning, and causal analyses are most successful with large-scale data beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level data from many centers. MATERIALS AND METHODS: The Clinical and Translational Science Award Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level clinical data. We developed solutions to extract, aggregate, and harmonize data across organizations and data models, and created a secure data enclave to enable efficient, transparent, and reproducible collaborative analytics. RESULTS: Organized in inclusive workstreams, we created legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible COVID-19 cases; a data quality assurance and harmonization pipeline to create a single harmonized dataset; population of the secure data enclave with data, machine learning, and statistical analytics tools; dissemination mechanisms; and a synthetic data pilot to democratize data access. CONCLUSIONS: The N3C has demonstrated that a multisite collaborative learning health network can overcome barriers to rapidly build a scalable infrastructure incorporating multiorganizational clinical data for COVID-19 analytics. We expect this effort to save lives by enabling rapid collaboration among clinicians, researchers, and data scientists to identify treatments and specialized care and thereby reduce the immediate and long-term impacts of COVID-19

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment

OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine learning, and causal analyses are most successful with large-scale data beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level data from many centers. MATERIALS AND METHODS: The Clinical and Translational Science Award Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level clinical data. We developed solutions to extract, aggregate, and harmonize data across organizations and data models, and created a secure data enclave to enable efficient, transparent, and reproducible collaborative analytics. RESULTS: Organized in inclusive workstreams, we created legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible COVID-19 cases; a data quality assurance and harmonization pipeline to create a single harmonized dataset; population of the secure data enclave with data, machine learning, and statistical analytics tools; dissemination mechanisms; and a synthetic data pilot to democratize data access. CONCLUSIONS: The N3C has demonstrated that a multisite collaborative learning health network can overcome barriers to rapidly build a scalable infrastructure incorporating multiorganizational clinical data for COVID-19 analytics. We expect this effort to save lives by enabling rapid collaboration among clinicians, researchers, and data scientists to identify treatments and specialized care and thereby reduce the immediate and long-term impacts of COVID-19

Secondary use of Structured Electronic Health Records Data: From Observational Studies to Deep Learning-based Predictive Modeling

With the wide adoption of electronic health records (EHRs), researchers, as well as large healthcare organizations, governmental institutions, insurance, and pharmaceutical companies have been interested in leveraging this rich clinical data source to extract clinical evidence and develop predictive algorithms. Large vendors have been able to compile structured EHR data from sites all over the United States, de-identify these data, and make them available to data science researchers in a more usable format. For this dissertation, we leveraged one of the earliest and largest secondary EHR data sources and conducted three studies of increasing scope. In the first study, which was of limited scope, we conducted a retrospective observational study to compare the effect of three drugs on a specific population of approximately 3,000 patients. Using a novel statistical method, we found evidence that the selection of phenylephrine as the primary vasopressor to induce hypertension for the management of nontraumatic subarachnoid hemorrhage is associated with better outcomes as compared to selecting norepinephrine or dopamine. In the second study, we widened our scope, using a cohort of more than 100,000 patients to train generalizable models for the risk prediction of specific clinical events, such as heart failure in diabetes patients or pancreatic cancer. In this study, we found that recurrent neural network-based predictive models trained on expressive terminologies, which preserve a high level of granularity, are associated with better prediction performance as compared with other baseline methods, such as logistic regression. Finally, we widened our scope again, to train Med-BERT, a foundation model, on more than 20 million patients’ diagnosis data. Med-BERT was found to improve the prediction performance of downstream tasks that have a small sample size, which otherwise would limit the ability of the model to learn good representation. In conclusion, we found that we can extract useful information and train helpful deep learning-based predictive models. Given the limitations of secondary EHR data and taking into consideration that the data were originally collected for administrative and not research purposes, however, the findings need clinical validation. Therefore, clinical trials are warranted to further validate any new evidence extracted from such data sources before updating clinical practice guidelines. The implementability of the developed predictive models, which are in an early development phase, also warrants further evaluation

Facilitating and Enhancing Biomedical Knowledge Translation: An in Silico Approach to Patient-centered Pharmacogenomic Outcomes Research

Current research paradigms such as traditional randomized control trials mostly rely on relatively narrow efficacy data which results in high internal validity and low external validity. Given this fact and the need to address many complex real-world healthcare questions in short periods of time, alternative research designs and approaches should be considered in translational research. In silico modeling studies, along with longitudinal observational studies, are considered as appropriate feasible means to address the slow pace of translational research. Taking into consideration this fact, there is a need for an approach that tests newly discovered genetic tests, via an in silico enhanced translational research model (iS-TR) to conduct patient-centered outcomes research and comparative effectiveness research studies (PCOR CER). In this dissertation, it was hypothesized that retrospective EMR analysis and subsequent mathematical modeling and simulation prediction could facilitate and accelerate the process of generating and translating pharmacogenomic knowledge on comparative effectiveness of anticoagulation treatment plan(s) tailored to well defined target populations which eventually results in a decrease in overall adverse risk and improve individual and population outcomes. To test this hypothesis, a simulation modeling framework (iS-TR) was proposed which takes advantage of the value of longitudinal electronic medical records (EMRs) to provide an effective approach to translate pharmacogenomic anticoagulation knowledge and conduct PCOR CER studies. The accuracy of the model was demonstrated by reproducing the outcomes of two major randomized clinical trials for individualizing warfarin dosing. A substantial, hospital healthcare use case that demonstrates the value of iS-TR when addressing real world anticoagulation PCOR CER challenges was also presented

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe