Serviços de imagem médica suportados na cloud

Mestrado em Engenharia de Computadores e TelemáticaHoje em dia, as instituições de cuidados de saúde, utilizam a telemedicina para suportar ambientes colaborativos. Na área da imagem médica digital, a quantidade de dados tem crescido substancialmente nos últimos anos, requerendo mais infraestruturas para fornecer um serviço com a qualidade desejada. Os computadores e dispositivos com acesso à Internet estão acessíveis em qualquer altura e em qualquer lugar, criando oportunidades para partilhar e utilizar recursos online. Uma enorme quantidade de processamento computacional e armazenamento são utilizados como uma comodidade no quotidiano. Esta dissertação apresenta uma plataforma para suportar serviços de telemedicina sobre a cloud, permitindo que aplicações armazenem e comuniquem facilmente, utilizando qualquer fornecedor de cloud. Deste modo, os programadores não necessitam de se preocupar onde os recursos vão ser instalados a as suas aplicações não ficam limitadas a um único fornecedor. Foram desenvolvidas duas aplicações para tele-imagiologia com esta plataforma: repositório de imagens médicas e uma infraestrutura de comunicações entre centros hospitalares. Finalmente, a arquitetura desenvolvida é genérica e flexível permitindo facilmente a sua expansão para outras áreas aplicacionais e outros serviços de cloud.Healthcare institutions resort largely, nowadays, to telemedicine in order to support collaborative environments. In the medical imaging area, the huge amount of medical volume data has increased over the past few years, requiring high-performance infrastructures to provide services with required quality. Computing devices and Internet access are now available anywhere and at anytime, creating new opportunities to share and use online resources. A tremendous amount of ubiquitous computational power and an unprecedented number of Internet resources and services are used every day as a normal commodity. This thesis presents a telemedicine service platform over the Cloud that allows applications to store information and to communicate easier, using any Internet cloud provider. With this platform, developers do not concern where the resources will be deployed and the applications will not be restricted to a specific cloud vendor. Two tele-imagiologic applications were developed along with this platform: a medical imaging repository and an interinstitutional communications infrastructure. Lastly, the architecture developed is generic and flexible to expand to other application areas and cloud services

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

A Recommender System Based on Cohorts’ Similarity

[Abstract] Aiming to better understand the genetic and environmental associations of Alzheimer's disease, many clinical trials and scientific studies have been conducted. However, these studies are often based on a small number of participants. To address this limitation, there is an increasing demand of multi-cohorts studies, which can provide higher statistical power and clinical evidence. However, this data integration implies dealing with the diversity of cohorts structures and the wide variability of concepts. Moreover, discovering similar cohorts to extend a running study is typically a demanding task. In this paper, we present a recommendation system to allow finding similar cohorts based on profile interests. The method uses collaborative filtering mixed with context-based retrieval techniques to find relevant cohorts on scientific literature about Alzheimer's diseases. The method was validated in a set of 62 cohorts.National Science Foundation (Portugal); POCI-01-0145-FEDER-01638

IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images

Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since “seeing is believing”, it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital work-flows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer

Avaliação do potencial ecológico para a realização de culturas energéticas na zona de influência do Perímetro de Rega do Alqueva

Mestrado em Engenharia Agronómica - Agro-pecuária - Instituto Superior de AgronomiaClimate change, and the rise of global temperature, is associated with an increase in the emission of Green Houses Gases (GHG) of human origin. The transport sector is one of the highest contributors to these emissions. The use of bio fuels (made from energy crops), comes forward as a contributing solution, since it leads to globally lower emissions, when compared with the use of fossil fuels. The Alqueva (Alentejo, Portugal) irrigation perimeters (built and projected) have a high potential to grow energy crops, as a basis of analysis, due to heat and water availability. The soil and weather requirements of eight cultures were analysed: Salix spp, Populus spp, Miscanthus x giganteus, Cynara cardunculus L., Arundo donax L., Panicum virgatum L., Hibiscus cannabinus L., e Jatropha curcas L.. To estimate ecological fitness, in present and in a future scenario, a system named SISAP, developed in ISA, was used. This program crosses the soil and weather requirements of crops with environmental data. Results show that all the crops analyzed grow in the Alqueva areas, with reduced to average productivity. Miscanthus x giganteus seems to be the most interesting from an ecological standpoint

Genetic risk markers for strong biofilm-formation in clinical methicillin-resitant Staphylococcus aureus and its the association with the clonal profile

Methicillinresistant Staphylococcus aureus (MRSA) is one of the major human pathogens worldwide and its epidemiology has been the focus of numerous single and multicenter surveillance studies over the past years. In this study, a phenotypic and genotypic approach were used to determine the factors that influence adherence and biofilm production of the most common MRSA SCCmec types, and its relationship with antimicrobial resistance, virulence genes and the genetic background of S. aureus isolates. The strains used in this study were randomly selected from a collection of clinical MRSA strains recovered from patients hospitalized in the Teaching Hospital of the Federal University of Uberlandia, isolated from infections at various anatomical sites and evaluated for SCCmec type. Fifteen strains carrying different chromosomal cassettes were selected, five SCCmec II, five SCCmec III and five SCCmec IV, recovered predominantly from blood (67%), surgical site infections (27%) and pneumonia (6.0%). The SCCmec type and the presence of the virulence genes (icaA, icaD, fnbB, agr, IS256, bap) were assessed by PCR. The genetic relationship between the isolates and a possible association with the ability to form biofilm were investigated by pulsed field gel electrophoresis (PFGE). The initial adhesion and biofilm formation were examined by quantitative assays. To evaluate the correlation between the hydrophobicity and the ability of MRSA cell to adhere to an unmodified polystyrene surface, the surface tension and hydrophobicity of the strains were measured. SCCmec III and IV strains were less hydrophilic and adhered better than SCCmec II strains. The analysis of biofilm production showed that SCCmec III strains were characterized as strong biofilm producers with the average biomass of biofilm from 0.53 ± 0.12 compared with 0.04 ± 0.04 those nonproducers/ weak producers (SCCmec II e IV). The analysis of this study showed five major pulsotypes according to the PFGE with a large genomic diversity observed by the number of subtypes in each pulsotype. The presence of the genes agr I, fnb B and IS 256 in clinical MRSA SCCmec III strains, were considered as genetic risk markers for strong biofilmformation in clinical by an icaindependent biofilm pathway. To our knowledge, this study is the first to demonstrate the biofilm formation by Brazilian clinical MRSA strains recovered from nosocomial infections including molecular characterization of strains

Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC):The Hot Start experience

A fast track “Hot Start” process was implemented to launch the European Bank for Induced Pluripotent Stem Cells (EBiSC) to provide early release of a range of established control and disease linked human induced pluripotent stem cell (hiPSC) lines. Established practice amongst consortium members was surveyed to arrive at harmonised and publically accessible Standard Operations Procedures (SOPs) for tissue procurement, bio-sample tracking, iPSC expansion, cryopreservation, qualification and distribution to the research community. These were implemented to create a quality managed foundational collection of lines and associated data made available for distribution. Here we report on the successful outcome of this experience and work flow for banking and facilitating access to an otherwise disparate European resource, with lessons to benefit the international research community. eTOC: The report focuses on the EBiSC experience of rapidly establishing an operational capacity to procure, bank and distribute a foundational collection of established hiPSC lines. It validates the feasibility and defines the challenges of harnessing and integrating the capability and productivity of centres across Europe using commonly available resources currently in the field

O impacto do trabalho policial nos policias do Corpo de Intervenção

Não há sociedade moderna que se mantenha sã, sem a ordem social necessária para que os seus cidadãos consigam prosseguir com as suas aspirações de vida. Para pôr cobro a situações de desordem concertada e grave, a Polícia de Segurança Pública (PSP) tem os polícias do Corpo de Intervenção (CI), especializados para atuar em situações de grande tensão, conflito e onde as ameaças à integridade física ou à vida estão bem patentes. Importa perceber que estas situações, às quais acorrem, acarretam níveis de stress elevados, podendo levar a que estes polícias se sintam reféns de um problema psicológico. Pelo bem-estar dos homens e para que a instituição não perca os ativos humanos que têm um know how considerável, é necessário perceber os origens dos impactos destes profissionais, bem como as consequências na sua saúde. Assim, realizaram-se 20 entrevistas, a polícias que estão no serviço operacional do CI, as quais, depois de transcritas, constituíram o corpus que foi sujeito a análise de conteúdo. Os resultados mostram que o maior enfoque dos impactos tem origem no contexto do trabalho mas também no conteúdo do trabalho. Percebemos, ainda, que as estratégias de defesa passam muito pela abstração das situações ou pelo recurso a estratégias grupais, evidenciando o espírito de camaradagem desta Subunidade Operacional. Por outro lado, percebemos que os operacionais do CI sentem haver um estigma quanto à saúde mental, o que resulta em alguma relutância em procurar ajuda dentro da organização. É discutida a criação de mecanismos para minimizar este estigma, e tornar a ajuda especializada mais próxima dos polícias.No modern society can be healthy without the necessary social order for its citizens to be able to pursue their life aspirations. To put an end to situations of concerted and serious disorder that are installed, the Public Security Police (PSP) has the men of the Riot Police Unit, specialized to act in situations of great tension, conflict and where threats to physical integrity or life are clearly evident. However, it is important to realize that these situations, to which they are accustomed, bring high levels of stress, which can lead these police officers to feel hostages of a psychological problem. For the well being of the men and so that the institution does not lose human assets that have an enviable know how, it is necessary to understand the origins of the impacts of these professionals. Thus, 20 interviews were conducted, of Officers/Main Officers who are in the operational service of the IC. After the interviews had been conducted, they were transcribed, constituting the corpus that was subject to content analysis by means of a mixed procedure. From the content analysis we noticed that the biggest focus of the impacts is on questions about the work and content context. We also noticed that the defense strategies go through the abstraction of situations or group strategies, showing the spirit of camaraderie in this Operational Subunit. On the other hand, we noticed that the IC operatives feel there is a stigma about mental health, showing some reluctance to seek help within the institution. It is important to create mechanisms to dispel this stigma, and make specialized help closer to the Officers

DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners

The evolution of biomedical imaging technology is allowing the digitization of hundreds of glass slides at once. There are multiple microscope scanners available in the market including low-cost solutions that can serve small centers. Moreover, new technology is being researched to acquire images and new modalities are appearing in the market such as electron microscopy. This reality offers new diagnostics tools to clinical practice but emphasizes also the lack of multivendor system’s interoperability. Without the adoption of standard data formats and communications methods, it will be impossible to build this industry through the installation of vendor-neutral archives and the establishment of telepathology services in the cloud. The DICOM protocol is a feasible solution to the aforementioned problem because it already provides an interface for visible light and whole slide microscope imaging modalities. While some scanners currently have DICOM interfaces, the vast majority of manufacturers continue to use proprietary solutions. This article proposes an automated DICOMization pipeline that can efficiently transform distinct proprietary microscope images from CLSM, FIB-SEM, and WSI scanners into standard DICOM with their biological information maintained within their metadata. The system feasibility and performance were evaluated with fifteen distinct proprietary modalities, including stacked WSI samples. The results demonstrated that the proposed methodology is accurate and can be used in production. The normalized objects were stored through the standard communications in the Dicoogle open-source archive

IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images.

Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since "seeing is believing", it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital workflows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer