Real-world evidence in Alzheimer’s disease: the ROADMAP Data Cube

INTRODUCTION:The ROADMAP project aimed to provide an integrated overview of European real-world data on Alzheimer's disease (AD) across the disease spectrum. METHODS:Metadata were identified from data sources in catalogs of European AD projects. Priority outcomes for different stakeholders were identified through systematic literature review, patient and public consultations, and stakeholder surveys. RESULTS:Information about 66 data sources and 13 outcome domains were integrated into a Data Cube. Gap analysis identified cognitive ability, functional ability/independence, behavioral/neuropsychiatric symptoms, treatment, comorbidities, and mortality as the outcomes collected most. Data were most lacking in caregiver-related outcomes. In general, electronic health records covered a broader, less detailed data spectrum than research cohorts. DISCUSSION:This integrated real-world AD data overview provides an intuitive visual model that facilitates initial assessment and identification of gaps in relevant outcomes data to inform future prospective data collection and matching of data sources and outcomes against research protocols

TASKA: A modular task management system to support health research studies

Background: Many healthcare databases have been routinely collected over the past decades, to support clinical practice and administrative services. However, their secondary use for research is often hindered by restricted governance rules. Furthermore, health research studies typically involve many participants with complementary roles and responsibilities which require proper process management. Results: From a wide set of requirements collected from European clinical studies, we developed TASKA, a task/workflow management system that helps to cope with the socio-technical issues arising when dealing with multidisciplinary and multi-setting clinical studies. The system is based on a two-layered architecture: 1) the backend engine, which follows a micro-kernel pattern, for extensibility, and RESTful web services, for decoupling from the web clients; 2) and the client, entirely developed in ReactJS, allowing the construction and management of studies through a graphical interface. TASKA is a GNU GPL open source project, accessible at https://github.com/bioinformatics-ua/taska. A demo version is also available at https://bioinformatics.ua.pt/taska. Conclusions: The system is currently used to support feasibility studies across several institutions and countries, in the context of the European Medical Information Framework (EMIF) project. The tool was shown to simplify the set-up of health studies, the management of participants and their roles, as well as the overall governance process

A study to understand the acceptance of DICOM Structured Reports on Breast Imaging

Purpose: To create a Digital Imaging and Communication in Medicine Structured Reports (DICOM-SR) Repository and compare the acceptance of Free Text (FT) versus Structured Reports (SR) in communication of Breast Imaging findings. Materials and Methods: It was conceptualized the MamoCatalogue to the structuring of the Reports and the SR were converted into DICOM-SR and integrated with Dicoogle. After that, seven representative Breast Imaging Reports were selected and evaluated by a group of 25 Physicians. Each Physician evaluated the seven Reports, in FT and SR with a 3 months timelag, about their, Structure, Clarity and assertiveness, Diagnostic/Recommendations, Easiness of reading, Full reading, Partially reading with Breast Imaging Reporting and Data System (BI-RADS) focus and Ambiguity. Results: A DICOM-SR Repository was created and the assessment of the acceptance of the FT vs. SR revealed that there is a global trend favoring FT. Nevertheless, a group wise analysis revealed that for Gynaecologists and General Practitioners (GP) the differences between FT and SR weren't significant, unlike what happens with Radiologists. Conclusion: The DICOM-SR Repository allows the query/retrieve data for Reports and the communication with Gynaecologists and GP by SR was satisfactory. Although, Radiologists acceptance must be reinforced upon global communication and management strategy

Arquiteturas federadas para integração de dados biomédicos

Doutoramento Ciências da ComputaçãoThe last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.A adoção sucessiva das tecnologias de comunicação e de informação na área da saúde tem permitido um aumento na diversidade e na qualidade dos serviços prestados, mas, ao mesmo tempo, tem gerado uma enorme quantidade de dados, cujo valor científico está ainda por explorar. A partilha e o acesso integrado a esta informação poderá permitir a identificação de novas descobertas que possam conduzir a melhores diagnósticos e a melhores tratamentos clínicos. Esta tese propõe novos modelos de integração e de exploração de dados com vista à extração de conhecimento biomédico a partir de múltiplas fontes de dados. A primeira contribuição é uma arquitetura baseada em nuvem para partilha de serviços de imagem médica. Esta solução oferece um mecanismo de registo simplificado para fornecedores e serviços, permitindo o acesso remoto e facilitando a integração de diferentes fontes de dados. A segunda proposta é uma arquitetura baseada em sensores para integração de registos electrónicos de pacientes. Esta estratégia segue um modelo de integração federado e tem como objetivo fornecer uma solução escalável que permita a pesquisa em múltiplos sistemas de informação. Finalmente, o terceiro contributo é um sistema aberto para disponibilizar dados de pacientes num contexto europeu. Todas as soluções foram implementadas e validadas em cenários reais

Relatórios estruturados em imagiologia mamária

Mestrado em Tecnologias da Imagem MédicaO Cancro da Mama constitui o tipo de cancro que afeta o maior número de mulheres europeias e a sua deteção precoce, diagnóstico e tratamento eficazes são fundamentais. Os Structured Reports (SR) surgiram como alternativa aos Relatórios Free Text (FT) e a norma Digital Imaging and Communication in Medicine (DICOM) estendeu a sua aplicação aos SR, com o suplemento DICOM Structured Reports (DICOM SR). A presente dissertação, teve como objetivos principais a conceção de um Repositório DICOM SR e a avaliação da aceitação dos Radiologistas e não Radiologistas para Relatórios FT versus SR na comunicação de resultados em Imagiologia Mamária. A investigação compreendeu duas fases, sendo que na primeira conceptualizou-se o MamoCatalogue para a estruturação dos Relatórios de acordo com a terminologia DICOM que, à posteriori, foram convertidos em DICOM SR e integrados com o Dicoogle - Picture Archiving and Communication System (PACS) open source. Na segunda fase do estudo, foram selecionados 7 Relatórios de Mamografia e/ou Ecografia Mamária, que posteriormente foram avaliados por um grupo de 25 Médicos, Radiologistas e não Radiologistas (Ginecologia/Obstetrícia e Medicina Geral e Familiar - MGF). Cada médico apreciou os 7 Relatórios, em FT e SR, com uma distância temporal de pelo menos 3 meses e avaliou os seguintes aspetos: Estrutura do Relatório, Clareza e assertividade da linguagem, Diagnóstico e recomendações, Facilidade de leitura, Leitura do Relatório na totalidade, Leitura parcial do Relatório com avanço para a classificação BI-RADS e Existência de aspetos ambíguos. As primeiras quatro variáveis foram cotadas na escala de 5 pontos de Likert, de Nada satisfeito (1) a Totalemte satisfeito (5) e, as restantes respondidas afirmativa ou negativamente. Para o tratamento estatístico foram utilizados os softwares The Statistical Package for Social Sciences® (IBM SPSS statistics v24) e Microsoft Excel 2016® e, empregues os testes t de amostras emparelhadas, Wilcoxon, McNemar e t de amostras independentes. A integração dos documentos DICOM SR com o Dicoogle permitiu a conceção do Repositório DICOM SR, onde é possível armazenar imagens e Relatórios e, pesquisar e recuperar dados relativos aos Relatórios. A avaliação da aceitação dos Relatórios FT vs. SR revelou que, sem distinção entre as especialidades médicas, existe uma tendência global favorecendo os FT. Considerando os Médicos de Ginecologia/Obstetrícia e de MGF, estes não demonstraram diferenças significativas FT vs. SR (valor p > 0,05). Os Radiologistas apresentaram-se em média (Dp) 3,86 (0,91) satisfeitos com a Estrutura do Relatório FT e 2,84 (0,59) com a do SR, a Clareza e assertividade da linguagem utilizada apresentou uma média (Dp) de 3,92 (0,90) para os FT e de 2,94 (0,50) para os SR e, o Diagnóstico e Recomendações satisfez, em média (Dp), 4,16 (0,71) nos FT e 3,22 (0,47) nos SR. Concluiu-se que a constituição de um Repositório DICOM SR possibilita o armazenamento de Imagens e Relatórios de forma conjunta e permite a pesquisa, recuperação e consulta de dados referentes aos Relatórios, tarefas impraticáveis com os sistemas de Relato FT. Foi possível, também concluir, que os Médicos de Ginecologia/Obstetrícia e MGF aceitam, de forma semelhante, a comunicação de resultados em Imagiologia Mamária por Relatórios FT e SR. O mesmo não acontece com os Radiologistas que consideram os Relatórios FT mais claros e assertivos na comunicação de resultados e no Diagnóstico e recomendações. Assim, melhorias aos SR devem ser implementadas e estratégias que estimulem a sua aceitação pelos Radiologistas devem ser delineadas, impulsionando a comunicação global na comunidade médica e otimizando o cuidado aos pacientes.Breast Cancer is the most common type of cancer affecting european women, therefore the early detection, diagnosis and treatment efficiency are crucial. The Structured Reports (SR) emerge as an alternative of Free Text (FT) and the standard Digital Imaging and Communication in Medicine (DICOM) extend his application to SR with DICOM Structured Reports (DICOM SR). These dissertation main goals are the creation of a DICOM SR repository and the comparison of acceptance of FT versus SR by Radiologists and nonRadiologists, regarding the communication of Breast Imaging findings. The study embraces two phases. The first one, concerns the creation of MamoCatalogue that allowed structuring the Mamography and Breast Ultrassound Reports, according DICOM terminology, after converted into DICOM SR and integrated with Dicoogle - Picture Archiving and Communication System (PACS) open source. In the second phase seven representative Mamography and/or Ultrassound Breast Imaging Reports were selected and evaluated by a group of 25 physicians, Radiologists and nonRadiologists (Gynecologists and General Practitioners - GP). Each physician evaluated the seven Reports in FT and SR formats with a 3 months time-lag. A Questionnaire was designed addressing the following issues: Structure, Clarity and assertiveness, Diagnostic/Recommendations, Easiness of reading, Full Reading, Partially Reading with BIRADS focus and Ambiguity. Physicians rated the first four variables, on a 5-point Likert scale, from 1 (very dissatisfied) to 5 (totally satisfied) and the others with yes or no. The Statistical Package for Social Sciences® (SPSS vv24) and the Microsoft Excel 2016® were used for the statistical analysis, using paired t test, Wilcoxon, McNemar and t test for independent samples. A DICOM SR repository was created and integrated with Dicoogle, where search, query and retrieve operations are possible. The DICOM SR repository, also allows that Breast Images and related Reports are stored and displayed together. The statistical analysis showed a global trend favoring FT. Although, for Gynecologists and GP the differences between FT and SR weren’t significant (p value > 0.05), unlike what happens with Radiologists. The mean and standard deviation acceptance metrics for the Radiologists were as follows: 3.86 (0.91) in FT Structure and 2.84 (0.59) in SR, 3.92 (0.90) in FT Clarity and assertiveness and 2.94 (0.50) in SR and 4.16 (0.71) in FT Diagnosis/Recommendation and 3.22 (0,39) in SR. So, it is concluded that DICOM SR repository allows the storage of images and Reports, and let’s search, retrieval and query operations related to Reports data, impracticable task with FT systems. It follows, also, that Gynecologists and GP similarly accept the communication of results in Breast Imaging by FT and SR. Nevertheless, Radiologists considered FT Reports clearer and more assertive than SR in communication of Breast Imaging findings and Diagnostic/Recommendations. There are still improvements to perform in SR and its acceptance, by Radiologists, must be reinforced upon a global communication on clinical community and improvement of patient health care

Novel perspectives from existing data on early Alzheimer’s disease pathology and dementia care use

Alzheimer’s disease (AD) has a long disease duration and a progressive course. To stop or slow down cognitive decline as early as possible, intervention studies are increasingly focusing on the earliest stage of the disease. To evaluate the effectiveness of these interventions, one ideally would want to track patients from the earliest preclinical stage, where amyloid pathology exists but cognition is still intact, to the prodromal stage, where cognitive functioning is impaired, to later and increasingly severe stages of dementia. An alternative strategy is to re-use and combine data that were previously collected. Combining different data sources can improve generalizability of findings, efficiency of future clinical trials, and identification of persons best suited for treatment at different disease stages. The aim of this thesis was to examine relevant outcomes and endpoints related to amyloid pathology in pre-dementia stages, and to examine the disease trajectory and care duration after a dementia diagnosis. In this thesis, we used different data sources and data types ranging from biomarker data to registry data to examine relevant outcomes and endpoints in AD. The relevant outcomes and endpoints in this thesis are important for the monitoring of treatment effects and for personalized predictions of whether and how a patient might advance on the AD disease spectrum. Part I focuses on preclinical and prodromal stages of AD, and Part II focuses on the disease trajectory and duration of different types of care after a dementia diagnosis