Evaluation and optimization of a session-based middleware for data management

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Report of a traineeship : audit of antidepressant prescribing in Primary and Mental Care: how to address appropriateness and keep a curb on costs. A tool suitable for all contexts?

RESUMO: Este é o relatório de um estágio realizado na Autoridade de Saúde Local de Bolonha com o objectivo de desenvolver capacidades e competências na área de projectos orientados para a avaliação com base epidemiológica. As prescrições de anti-depressivos aumentaram consideravelmente em todo o mundo durante as últimas décadas. O uso cada vez maior dos agentes mais dispendiosos desempenha um papel na subida do custo dos tratamentos. A Autoridade de Saúde Local de Bolonha implementou um processo de auditoria com o objectivo de melhorar a adequação das prescrições de pacientes externos, centrando-se em dois anti-depressivos de marca ainda protegidos por patente, Escitalopram e Duloxetine. Os Departamentos de Cuidados de Saúde Primários e de Cuidados de Saúde Mental, assim como o Departamento Farmacêutico e a Unidade de Gestão Clínica, estiveram envolvidos na fase de planeamento da auditoria. O grupo da auditoria, maioritariamente composto por médicos de clínica geral e psiquiatras, reuniu e analisou provas da eficácia e segurança dos anti-depressivos. Os dados sobre as prescrições das Unidades de Cuidados de Saúde Primários e dos Centros de Saúde Mental Comunitários da Autoridade de Saúde Local (866.294 habitantes) foram comparados, em particular as taxas de consumo de Escitalopram e Duloxetine. O grupo da auditoria definiu os standards a serem abordados, os indicadores a serem avaliados e as medidas a empreender para atingir os objectivos definidos. As directrizes do NICE sobre a depressão foram escolhidas como referência. O objectivo da auditoria foi definido como evitar o Escitalopram e Duloxetine como medicamentos de primeira escolha num tratamento anti-depressivo. De modo a verificar a eficácia das medidas empreendidas foi seleccionado um indicador, consistindo numa redução de 25% das prescrições de ambos os anti-depressivos na prática clínica de pacientes externos e numa redução de 20% da variabilidade nas Unidades de Cuidados de Saúde Primários. O relatório retrospectivo pré-auditoria (Janeiro a Abril de 2012) revelou que os tratamentos com anti-depressivos para pacientes externos eram prescritos pelos médicos de clínica geral em mais de90% dos casos. As medidas da auditoria foram implementadas entre Novembro de 2012 e Maio de 2013. Algumas medidas relevantes foram integradas com a revisão da auditoria, tais como reuniões educacionais de pequena escala com os médicos de clínica geral e psiquiatras, visitas de apoio do assessor de prescrições da Autoridade de Saúde Local aos médicos de clínica geral e Centros de Saúde Mental Comunitários, panfletos para profissionais com informação retirada das directrizes clínicas do NICE, implementação de um serviço de consulta na Web para médicos de clínica geral sobre provas relativas a anti-depressivos. O relatório de feedback é aguardado em Novembro de 2013 depois de se verificar nos standards atingidos a eficácia das medidas implementadas. Foi realizada uma análise SWOT para comprovar as forças e fraquezas, as oportunidades e ameaças do processo. Como identificação de fraquezas poderá ser útil identificar estratégias relevantes para melhoria interna, para que o conhecimento das ameaças possa amortizar factores que possam ter impactos adversos que fujam ao controlo do Departamento de Saúde Mental. Uma melhor compreensão das forças e das oportunidades facilita a consecução dos objectivos estabelecidos no projecto. O primeiro, mas não o último, resultado deste processo consistiu numa maior integração entre os Cuidados de Saúde Primários e de Saúde Mental, permitindo assim que a Autoridade de Saúde Local coloque as alterações em prática.------------ABSTRACT: This is the report of a traineeship held in the Local Health Authority of Bologna with the aim to develop skills and competencies in the field of epidemiogically based evaluation oriented projects. Antidepressants prescriptions have considerably increased all over the world in the last decades. The increasing use of the most expensive agents plays a part in the rising cost of treatments. The Local Health Authority of Bologna has implemented an audit process aimed at improving the appropriateness of outpatient prescriptions focusing on the two branded antidepressants still protected by patent, Escitalopram and Duloxetine. The Primary Care and the Mental Health Care Departments, as well as the Pharmaceutical Department and the Clinical Governance Unit, were involved in the planning phase of the audit. The audit group, mainly composed of general practitioners and psychiatrists, collected and analyzed scientific evidence on effectiveness and safety of antidepressants. Data on prescriptions of Primary Care Units and Community Mental Health Centers of the Local Health Authority (866.294 inhabitants) were compared, in particular consumption rates of Escitalopram and Duloxetine. The audit group defined the standards to be addressed, the indicators to be evaluated and the actions aimed at reaching the defined goals. NICE guidelines on depression were chosen as reference. The aim of the audit was settled as avoiding Escitalopram and Duloxetine as first choice drugs starting an AD treatment. In order to check the efficacy of the actions undertaken an indicator was selected, consisting in a reduction of 25% of prescriptions of both ADs in outpatient practice and in a 20% reduction of To develop skills and competencies across Primary Care Units. The pre-audit retrospective report (January-April 2012) showed that outpatient antidepressant treatments were prescribed by GPs in over 90% of cases. Audit actions were implemented between November 2012 and May 2013. Some relevant actions have been integrated with the audit review, such as small-scale educational meetings with GPs and psychiatrists, outreach visits of the LHA prescribing adviser to GPs and CMHCs,leaflets for professionals with information extracted from NICE clinical guidelines, implementation of a web consultation service for GPs about evidence on antidepressants. The feedback report is expected in November 2013 after checking through the standards attained the effectiveness of actions implemented. A SWOT Analysis was carried out to evidence the strengths and weaknesses, opportunities and threats of the process. As identification of weaknesses may be useful to identify relevant strategies for internal improvement, so the knowledge of threats can amortize factors that may have adverse impacts beyond the control of the Mental Health Department. Better understanding of the strengths and the opportunities facilitates the achievement of the goals set in the project. The first and not least upshot of this process has consisted in further integration between Primary and Mental Health Care, thus enabling the LHA to put the change into practice.

Combining WLAN fingerprint-based localization with sensor data for indoor navigation using mobile devices

This project proposes an approach for supporting Indoor Navigation Systems using Pedestrian Dead Reckoning-based methods and by analyzing motion sensor data available in most modern smartphones. Processes suggested in this investigation are able to calculate the distance traveled by a user while he or she is walking. WLAN fingerprint- based navigation systems benefit from the processes followed in this research and results achieved to reduce its workload and improve its positioning estimations.

Complex networks and data mining: toward a new perspective for the understanding of complex systems

Complex systems, i.e. systems composed of a large set of elements interacting in a non-linear way, are constantly found all around us. In the last decades, different approaches have been proposed toward their understanding, one of the most interesting being the Complex Network perspective. This legacy of the 18th century mathematical concepts proposed by Leonhard Euler is still current, and more and more relevant in real-world problems. In recent years, it has been demonstrated that network-based representations can yield relevant knowledge about complex systems. In spite of that, several problems have been detected, mainly related to the degree of subjectivity involved in the creation and evaluation of such network structures. In this Thesis, we propose addressing these problems by means of different data mining techniques, thus obtaining a novel hybrid approximation intermingling complex networks and data mining. Results indicate that such techniques can be effectively used to i) enable the creation of novel network representations, ii) reduce the dimensionality of analyzed systems by pre-selecting the most important elements, iii) describe complex networks, and iv) assist in the analysis of different network topologies. The soundness of such approach is validated through different validation cases drawn from actual biomedical problems, e.g. the diagnosis of cancer from tissue analysis, or the study of the dynamics of the brain under different neurological disorders.

A DSL for querying building data streams of energy, eeather and occupation data

The superfluous consumption of energy is faced by the modern society as a Socio-Economical and Environmental problem of the present days. This situation is worsening given that it is becoming clear that the tendency is to increase energy price every year. It is also noticeable that people, not necessarily proficient in technology, are not able to know where savings can be achieved, due to the absence of accessible awareness mechanisms. One of the home user concerns is to balance the need of reducing energy consumption, while producing the same activity with all the comfort and work efficiency. The common techniques to reduce the consumption are to use a less wasteful equipment, altering the equipment program to a more economical one or disconnecting appliances that are not necessary at the moment. However, there is no direct feedback from this performed actions, which leads to the situation where the user is not aware of the influence that these techniques have in the electrical bill. With the intension to give some control over the home consumption, Energy Management Systems (EMS) were developed. These systems allow the access to the consumption information and help understanding the energy waste. However, some studies have proven that these systems have a clear mismatch between the information that is presented and the one the user finds useful for his daily life, leading to demotivation of use. In order to create a solution more oriented towards the user’s demands, a specially tailored language (DSL) was implemented. This solution allows the user to acquire the information he considers useful, through the construction of questions about his energy consumption. The development of this language, following the Model Driven Development (MDD) approach, took into consideration the ideas of facility managers and home users in the phases of design and validation. These opinions were gathered through meetings with experts and a survey, which was conducted to the purpose of collecting statistics about what home users want to know.

Integrated data model and DSL modifications

Companies are increasingly more and more dependent on distributed web-based software systems to support their businesses. This increases the need to maintain and extend software systems with up-to-date new features. Thus, the development process to introduce new features usually needs to be swift and agile, and the supporting software evolution process needs to be safe, fast, and efficient. However, this is usually a difficult and challenging task for a developer due to the lack of support offered by programming environments, frameworks, and database management systems. Changes needed at the code level, database model, and the actual data contained in the database must be planned and developed together and executed in a synchronized way. Even under a careful development discipline, the impact of changing an application data model is hard to predict. The lifetime of an application comprises changes and updates designed and tested using data, which is usually far from the real, production, data. So, coding DDL and DML SQL scripts to update database schema and data, is the usual (and hard) approach taken by developers. Such manual approach is error prone and disconnected from the real data in production, because developers may not know the exact impact of their changes. This work aims to improve the maintenance process in the context of Agile Platform by Outsystems. Our goal is to design and implement new data-model evolution features that ensure a safe support for change and a sound migration process. Our solution includes impact analysis mechanisms targeting the data model and the data itself. This provides, to developers, a safe, simple, and guided evolution process.

Autochthonous visceral leishmaniasis in Brasília, Federal District, Brazil

INTRODUCTION: Visceral leishmaniasis is a public health threat in Brazil considering the high lethality rates and increasing geographical dispersion to large urban conglomerates over the past 25 years. This study aimed to confirm suspected autochthonous cases of visceral leishmaniasis reported from 2005 to 2009 among individuals living in Brasilia, Federal District. METHODS: A retrospective review of the surveillance data obtained on a regular basis and clinical records of the reported cases were performed in 2009. RESULTS: Data from entomological and canine surveys revealed the presence of both Lutzomyia longipalpis and positive serology for Leishmania in dogs within 19 of the 21 neighborhoods where human cases occurred since 2005. The review of surveillance data and medical records, together with the entomological and canine survey data, permitted confirmation of 21 autochthonous human cases in the Federal District. The disease predominantly affected children (12/21) and those from the Sobradinho region (16/21); the typical presentation of fever, hepatosplenomegaly and pancytopenia was observed in 67% of cases. Three deaths occurred during the study period. Leishmania (Leishmania) chagasi was successfully isolated from one human case and twelve canine cases. CONCLUSIONS: Visceral leishmaniasis should be considered endemic in Brasilia based on the documented epidemiological behavior herein described and the confirmed autochthony of human cases.

Epidemiological profile of acute bacterial meningitis in the state of Rio Grande do Norte, Brazil

INTRODUCTION: Acute bacterial meningitis (ABM) remains a public health problem in Brazil. To evaluate the epidemiology of ABM cases at Giselda Trigueiro Hospital, Rio Grande do Norte, a descriptive retrospective survey was conducted covering 2005 to 2008. METHODS: Clinical and laboratory data were collected from the epidemiology department of the hospital and analyzed. RESULTS: Out of 168 ABM cases, 24.4%, 10.7%, and 2.4% were, respectively, caused by Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenza b, and 5.4% by other bacteria. The mean age was 22.48 ± 18.7 years old. CONCLUSIONS: Streptococcus pneumoniae was the main causative pathogen in the young urban population.

Comparação entre sistemas de saúde oral de 8 países da união europeia e intervenções por estes desenvolvidas no seguimento das linhas de atuação definidas pela Organização Mundial de Saúde para o ano 2020

RESUMO - Hoje, facilmente se poderá constatar que as doenças orais possuem uma expressiva influência perante a saúde geral, não apenas pela presença da condição por si só, mas também a nível pessoal, social e económico. O seu reflexo traduz-se em parte, no absentismo escolar e laboral, diminuição considerável de produtividade e eficiência, falta de atenção e objetividade. Pelo que é então considerado, um grave problema de saúde pública, afetando de forma mais expressiva, grupos socioeconomicamente desfavorecidos. O acompanhamento e análise do desenvolvimento de iniciativas internacionais, no que ao seguimento das recomendações da Organização Mundial de Saúde diz respeito, poderá ser um ótimo beneficio e impulso para a identificação e aplicação de novos planos de ação. O presente projeto, pretendeu contribuir para a identificação de duas propostas de intervenção em saúde oral ajustadas ao alcance das recomendações da OMS que simultaneamente possam sejam proveitosas para a resolução dos problemas de saúde oral nacionais. Foi realizado um estudo observacional, descritivo e retrospetivo onde foram recolhidos dados acerca de 8 Sistemas de Saúde Oral europeus, previamente selecionados segundo critérios específicos, e iniciativas de saúde oral por eles desenvolvidas. Por fim, foram eleitas duas iniciativas de interesse, possíveis de aplicação futura. Os resultados do estudo apontam para a existência de diferentes iniciativas, enquadradas com as recomendações da OMS. De entre as mesmas, destaca-se uma implementada em 2009, na Suécia, que estando essencialmente assente num acessível subsidio anual fixo pago por cada indivíduo adulto, procura fundamentalmente preservar os esforços de prevenção aplicados nas últimas décadas.

Sistema de deteção de eventos adversos baseado num data warehouse

RESUMO - A Segurança do Doente tem assumido uma relevância crescente nas organizações de saúde, resultado da divulgação de diversos estudos que revelaram a magnitude deste problema e simultaneamente, de uma maior pressão por parte da opinião pública e da comunicação social. Este estudo pretende desenvolver e avaliar a performance de um sistema eletrónico de deteção de eventos adversos, baseado num Data Warehouse, por comparação com os resultados obtidos pela metodologia tradicional de revisão dos registos clínicos. O objetivo principal do trabalho consistiu em identificar um conjunto de triggers / indicadores de alerta que permitam detetar potenciais eventos adversos mais comuns. O sistema desenvolvido apresentou um Valor Preditivo Positivo de 18.2%, uma sensibilidade de 65.1% e uma especificidade de 68.6%, sendo constituído por nove indicadores baseados em informação clínica e 445 códigos do ICD-9-CM, relativos a diagnósticos e procedimentos. Apesar de terem algumas limitações, os sistemas eletrónicos de deteção de eventos adversos apresentam inúmeras potencialidades, nomeadamente a utilização em tempo real e em complemento a metodologias já existentes. Considerando a importância da problemática em análise e a necessidade de aprofundar os resultados obtidos neste trabalho de projeto, seria relevante a sua extensão a um universo mais alargado de instituições hospitalares, estando a sua replicabilidade facilitada, uma vez que o Data Warehouse tem por base um conjunto de aplicações disseminadas a nível nacional. O desenvolvimento e a consolidação dos sistemas eletrónicos de deteção de eventos adversos constitui inegavelmente uma área de futuro, com reflexos ao nível da melhoria da informação existente nas organizações e que contribuirá decisivamente para a melhoria dos cuidados de saúde prestados aos doentes.

Antimicrobial use and incidence of multidrug-resistant Pseudomonas aeruginosa in a teaching hospital: an ecological approach

INTRODUCTION: Multidrug-resistant Pseudomonas aeruginosa is a major threat in healthcare settings. The use of antimicrobials can influence the incidence of resistant strains by direct and indirect mechanisms. The latter can be addressed by ecological studies. METHODS: Our group attempted to analyze the relation between the use of antipseudomonal drugs and the incidence of MDR-PA among 18 units from a 400-bed teaching hospital. The study had a retrospective, ecological design, comprising data from 2004 and 2005. Data on the use of four antimicrobials (amikacin, ciprofloxacin, ceftazidime and imipenem) were tested for correlation with the incidence of MDR-PA (defined as isolates resistant to the four antimicrobials of interest) in clinical cultures. Univariate and multivariate linear regression analyses were performed. RESULTS: Significant correlations were determined between use and resistance for all antimicrobials in the univariate analysis: amikacin (standardized correlation coefficient = 0.73, p = 0.001); ciprofloxacin (0.71, p = 0.001); ceftazidime (0.61, p = 0.007) and imipenem (0.87, p < 0.001). In multivariate analysis, only imipenem (0.67, p = 0.01) was independently related to the incidence of multidrug-resistant strains. CONCLUSIONS: These findings share similarities with those reported in individual-based observational studies, with possible implications for infection control.

SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

Comparison of Bothropoides jararaca bites with and without envenoming treated at the Vital Brazil Hospital of the Butantan Institute, State of São Paulo, Brazil

INTRODUCTION: This study analyses the cases of all bites (including dry bites) caused by Bothropoides jararaca attended at the Vital Brazil Hospital of the Butantan Institute, State of São Paulo, Brazil. METHODS: A retrospective study was conducted of patients bitten by Bothropoides jararaca (n=792) from January 1990 to December 2004. The characteristics of the snake specimen, data related to the accident and clinical manifestations on admission were obtained from patient medical records. RESULTS: The majority of the cases in this study were caused by female and juvenile snakes. No stomach contents were found in 93.4% of the snake specimens after dissection. No statistical difference was observed between the occurrence of dry bites and the maturity or sex of the snake. The median SVL of snakes in mild and moderate cases was 40.5cm and in severe cases, SVL increased to 99cm. Necrosis was more common in the digits of the feet and hands (4.8%) compared to the other body regions (1.8%). A significant difference was verified between severity and a time interval greater than six hours from the bite to hospital admission. A significant association was verified between gingival bleeding and abnormal blood coagulability. In accidents caused by adult snakes, necrosis was more frequent (7.2%) compared to accidents caused by juvenile snakes (1%). CONCLUSIONS: In this work, the association between certain epidemiological data and the evolution of biological parameters in the clinical course of Bothrops sensu latu accidents were highlighted, contributing to the improvement of snake bite assistance.

Identifying the urban communities of New York City using bikeshare data from NYC citibike

This study identifies a measure of the cultural importance of an area within a city. It does so by making use of origindestination trip data and the bike stations of the bike share system in New York City as a proxy to study the city. Rarely is movement in the city studied at such a small scale. The change in strength of the similarity of movement between each station is studied. It is the first study to provide this measure of importance for every point in the system. This measure is then related to the characteristics which make for vibrant city communities, namely highly mixed land use types. It reveals that the spatial pattern of important areas remains constant over differing time periods. Communities are then characterised by the land uses surrounding these stations with high measures of importance. Finally it identifies the areas of global cultural importance alongside the areas of local importance to the city.