Detecting and evaluating land cover change in the eastern half of East Timor (1972-2011)

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Forest cover monitoring in the Bara district (Nepal) with remote sensing and geographic information systems

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Neural correlations during brain activation in arithmetical tasks – an approach using electroencephalographic data

Dissertação apresentada na Faculdade de Ciências e Tecnologiea da Universidade Nova de Lisboa, para obtenção do Grau de Mestre em Engenharia Biomédica

Monitoring morphisms to support sustainable interoperability of enterprise systems

Dissertation to obtain the Master degree in Electrical Engineering and Computer Science

Insights into human carboxylesterase 2 stability and activity in vivo and in vitro

Dissertation to obtain a Master Degree in Biotechnology

Information flow analysis using data-dependent logical propositions

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Urban land use and land cover change analysis and modeling a case study area Malatya, Turkey

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

ISEGI-NOVA AR Project - Augmented Reality Aplied to the Universidade Nova de Lisboa

Project work presented as a partial requirement to obtain a Master Degree in Information Management

Infecção por Treponema pallidum: análise serológica e pesquisa de DNA

RESUMO: A sífilis é uma infecção causada por T. pallidum que pode ser transmitida por via vertical, por contacto sexual ou por sangue, e cujo diagnóstico se baseia na associação entre manifestações clinicas e testes serológicos. Neste estudo utilizaram-se os testes serológicos RPR, TPHA, FTA-Abs, um teste rápido não comercializado (Signal-Spirolipin) que pesquisa anticorpos treponémicos (CDC-T) e não treponémicos (CDC-2) em simultâneo no mesmo dispositivo e uma técnica de PCR-multiplex para a pesquisa de ADN de T. pallidum. Da comparação das técnicas serológicas constatou-se que a sensibilidade dos testes RPR e TPHA foi de 84,5% e 98% respectivamente. A especificidade foi de 77,3% para o teste RPR e de 87,5% para o teste TPHA. Na avaliação do teste rápido a comparação do teste CDC-2 com o teste RPR resultou numa taxa de concordância de 93,1% enquanto que, a do teste CDC-T com o teste TPHA foi de 94,8%. A sensibilidade e especificidade obtidas pelos testes CDC-2 e CDC-T foram de 88,7% e 65% e de 94,9% e 91,3% respectivamente. Considerando o diagnóstico de sífilis activa com base na reactividade simultânea dos testes RPR e TPHA, avaliou-se a sensibilidade do teste rápido utilizando esse mesmo critério. A sensibilidade obtida foi de 98,4% para o teste rápido e de 97,2% para a associação dos testes RPR/TPHA. A técnica de PCR-multiplex apresentou fraca sensibilidade já que em apenas 33% dos casos de sífilis foi identificado ADN de T. pallidum. O teste rápido avaliado apresentou um comportamento idêntico aos testes geralmente utilizados na rotina laboratorial tais como os utilizados neste estudo. Apresenta a vantagem de pesquisar anticorpos treponémicos e não treponémicos, ao contrário dos testes rápidos comercializados que pesquisam apenas anticorpos treponémicos. Não sendo necessário para a sua execução equipamento laboratorial especializado poderá ser de grande utilidade para o clinico a exercer em locais sem laboratório.------------- ABSTRACT: Syphilis is an infection caused by T. pallidum. Transmission may be vertical, through sexual contact or blood. The diagnosis is based in both serology and clinical manifestations. In this study, we used the serological tests RPR, TPHA, FTA-Abs and a non -commercialized rapid test (Signal-Spirolipin) to detect both treponemal (CDC-T) and non – treponemal antibodies (CDC-2) in the same device. T. pallidum DNA was identified with a multiplex PCR technique. In this study, the RPR and TPHA tests sensitivity was 84,5% and 98%, respectively, and the specificity 77,3% for the RPR test and 87,5% for TPHA test, respectively. The concordance rate was 93,1% in the comparison between the RPR and the CDC2 tests and 94,8% between the CDC-T with the TPHA tests. Sensitivity and specificity of the CDC-2 and CDC-T tests were 88,7% and 65% and 94,9% e 91,3%, respectively. Taking into account that the diagnosis of active syphilis is made when both the RPR and TPHA tests are reactive, we evaluated the sensitivity of the rapid test (CDC2 and CDCT) in the diagnosis of active syphilis, using the above described criteria. The sensitivity was 98,4 % for the rapid test and 97,2 % for the association of reactivity in both RPA and TPHA tests. The multiplex PCR technique presented a low sensitivity, with T. pallidum DNA being identified in only 33% of the syphilis cases. The rapid test evaluated in this study presented identical results to the tests generally used in the routine laboratory diagnosis, such as those used here. However, it does have the advantage of detecting both treponemal and non – treponemal antibodies what is not the case of the commercialized rapid test. Furthermore, there is no need of specialized laboratory equipment, which makes it of great utility in regions where such conditions do not exist, as in developing countries.

Contract-program evaluation: Impact of the DRG classification system on hospitals' outputs

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Expressiveness improvements of OutSystems DSL query primitives

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

O erro na fase pré-analítica : amostras não conformes versus procedimentos

RESUMO: As Análises Clínicas são um precioso elemento entre os meios complementares de diagnóstico e terapêutica permitindo uma enorme panóplia de informações sobre o estado de saúde de determinado utente. O objetivo do laboratório é fornecer informação analítica sobre as amostras biológicas, sendo esta caracterizada pela sua fiabilidade, relevância e facultada em tempo útil. Assim, tratando-se de saúde, e mediante o propósito do laboratório, é notória a sua importância, bem como, a dos fatores associados para o cumprimento do mesmo. O bom desenrolar do ciclo laboratorial, compreendido pelas fases pré-analítica, analítica e pós-analítica é crucial para que o objetivo do laboratório seja cumprido com rigor e rapidez. O presente trabalho “O Erro na Fase Pré-Analítica: Amostras Não Conformes versus Procedimentos”, enquadrado no mestrado de Qualidade e Organização no Laboratório de Análises Clínicas, pretendeu enfatizar a importância da fase pré- analítica, sendo ela apontada como a primordial em erros que acabam por atrasar a saída de resultados ou por permitir que os mesmos não sejam fidedignos como se deseja, podendo acarretar falsos diagnósticos e decisões clínicas erradas. Esta fase, iniciada no pedido médico e finalizada com a chegada das amostras biológicas ao laboratório está entregue a uma diversidade de procedimentos que acarretam, por si só, uma grande diversidade de intervenientes, para além de uma variabilidade de factores que influenciam a amostra e seus resultados. Estes fatores, que podem alterar de algum modo a “veracidade” dos resultados analíticos, devem ser identificados e tidos em consideração para que estejamos convitos que os resultados auxiliam diagnósticos precisos e uma avaliação correta do estado do utente. As colheitas que por quaisquer divergências não originam amostras que cumpram o objectivo da sua recolha, não estando por isso em conformidade com o pretendido, constituem uma importante fonte de erro para esta fase pré-analítica. Neste estudo foram consultados os dados relativos a amostras de sangue e urina não conformes detetadas no laboratório, em estudo, durante o 1º trimestre de 2012, para permitir conhecer o tipo de falhas que acontecem e a sua frequência. Aos Técnicos de Análises Clínicas, colaboradores do laboratório, foi-lhes pedido que respondessem a um questionário sobre os seus procedimentos quotidianos e constituíssem, assim, a população desta 2ª parte do projeto. Preenchido e devolvido de forma anónima, este questionário pretendeu conhecer os procedimentos na tarefa de executar colheitas e, hipoteticamente, confrontá-los com as amostras não conformes verificadas. No 1ºsemestre de 2012 e num total de 25319 utentes registaram-se 146 colheitas que necessitaram de repetição por se verificarem não conformes. A “amostra não colhida” foi a não conformidade mais frequente (50%) versus a “má identificação” que registou somente 1 acontecimento. Houve ainda não conformidades que não se registaram como “preparação inadequada” e “amostra mal acondicionada”. Os técnicos revelaram-se profissionais competentes, conhecedores das tarefas a desempenhar e preocupados em executá-las com qualidade. Eliminar o erro não estará, seguramente, ao nosso alcance porém admitir a sua presença, detetá-lo e avaliar a sua frequência fará com que possamos diminuir a sua existência e melhorar a qualidade na fase pré-analítica, atribuindo-lhe a relevância que desempenha no processo laboratorial.-----------ABSTRACT:Clinical analyses are a precious element among diagnostic and therapeutic tests as they allow an enormous variety of information on the state of health of a user. The aim of the laboratory is to supply reliable, relevant and timely analytical information on biological samples. In health-related matters, in accordance with the objective of the laboratory, their importance is vital, as is the assurance that all the tools are in place for the fulfillment of its purpose. A good laboratory cycle, which includes the pre-analytical, analytical and post-analytical phases, is crucial in fulfilling the laboratory’s mission rapidly and efficiently. The present work - "Error in the pre-analytical phase: non-compliant samples versus procedures”, as part of the Master’s in Quality and Organization in the Clinical Analyses Laboratory, wishes to emphasize the importance of the pre-analytical phase, as the phase containing most errors which eventually lead to delays in the issue of results, or the one which enables those results not to be as reliable as desired, which can lead to false diagnosis and wrong clinical decisions. This phase, which starts with the medical request and ends with the arrival of the biological samples to the laboratory, entails a variety of procedures, which require the intervention of different players, not to mention a great number of factors, which influence the sample and the results. These factors, capable of somehow altering the “truth” of the analytical results, must be identified and taken into consideration so that we may ensure that the results help to make precise diagnoses and a correct evaluation of the user’s condition. Those collections which, due to any type of differences, do not originate samples capable of fulfilling their purpose, and are therefore not compliant with the objective, constitute an important source of error in this pre-analytical phase. In the present study, we consulted data from non-compliant blood and urine samples, detected at the laboratory during the 1st quarter of 2012, to find out the type of faults that happen and their frequency. The clinical analysis technicians working at the laboratory were asked to fill out a questionnaire regarding their daily procedures, forming in this way the population for this second part of the project. Completed and returned anonymously, this questionnaire intended to investigate the procedures for collections and, hypothetically, confront them with the verified non-compliant samples. In the first semester of 2012, and out of a total of 25319 users, 146 collections had to be repeated due to non-compliance. The “uncollected sample” was the most frequent non-compliance (>50%) versus “incorrect identification” which had only one occurrence. There were also unregistered non-compliance issues such as “inadequate preparation” and “inappropriately packaged sample”. The technicians proved to be competent professionals, with knowledge of the tasks they have to perform and eager to carry them out efficiently. We will certainly not be able to eliminate error, but recognizing its presence, detecting it and evaluating its frequency will help to decrease its occurrence and improve quality in the pre-analytical phase, giving it the relevance it has within the laboratory process.

A distributed platform for the volunteer execution of workflows on a local area network

Thesis submitted in fulfilment of the requirements for the Degree of Master of Science in Computer Science

Design and development of a microfluidic platform for use with colorimetric gold nanoprobe assays

Due to the importance and wide applications of the DNA analysis, there is a need to make genetic analysis more available and more affordable. As such, the aim of this PhD thesis is to optimize a colorimetric DNA biosensor based on gold nanoprobes developed in CEMOP by reducing its price and the needed volume of solution without compromising the device sensitivity and reliability, towards the point of care use. Firstly, the price of the biosensor was decreased by replacing the silicon photodetector by a low cost, solution processed TiO2 photodetector. To further reduce the photodetector price, a novel fabrication method was developed: a cost-effective inkjet printing technology that enabled to increase TiO2 surface area. Secondly, the DNA biosensor was optimized by means of microfluidics that offer advantages of miniaturization, much lower sample/reagents consumption, enhanced system performance and functionality by integrating different components. In the developed microfluidic platform, the optical path length was extended by detecting along the channel and the light was transmitted by optical fibres enabling to guide the light very close to the analysed solution. Microfluidic chip of high aspect ratio (~13), smooth and nearly vertical sidewalls was fabricated in PDMS using a SU-8 mould for patterning. The platform coupled to the gold nanoprobe assay enabled detection of Mycobacterium tuberculosis using 3 8l on DNA solution, i.e. 20 times less than in the previous state-of-the-art. Subsequently, the bio-microfluidic platform was optimized in terms of cost, electrical signal processing and sensitivity to colour variation, yielding 160% improvement of colorimetric AuNPs analysis. Planar microlenses were incorporated to converge light into the sample and then to the output fibre core increasing 6 times the signal-to-losses ratio. The optimized platform enabled detection of single nucleotide polymorphism related with obesity risk (FTO) using target DNA concentration below the limit of detection of the conventionally used microplate reader (i.e. 15 ng/μl) with 10 times lower solution volume (3 μl). The combination of the unique optical properties of gold nanoprobes with microfluidic platform resulted in sensitive and accurate sensor for single nucleotide polymorphism detection operating using small volumes of solutions and without the need for substrate functionalization or sophisticated instrumentation. Simultaneously, to enable on chip reagents mixing, a PDMS micromixer was developed and optimized for the highest efficiency, low pressure drop and short mixing length. The optimized device shows 80% of mixing efficiency at Re = 0.1 in 2.5 mm long mixer with the pressure drop of 6 Pa, satisfying requirements for the application in the microfluidic platform for DNA analysis.

Determinants of mother-baby relationship evaluated during pregnancy

ABSTRACT Background Mental health promotion is supported by a strong body of knowledge and is a matter of public health with the potential of a large impact on society. Mental health promotion programs should be implemented as soon as possible in life, preferably starting during pregnancy. Programs should focus on malleable determinants, introducing strategies to reduce risk factors or their impact on mother and child, and also on strengthening protective factors to increase resilience. The ambition of early detecting risk situations requires the development and use of tools to assess risk, and the creation of a responsive network of services based in primary health care, especially maternal consultation during pregnancy and the first months of the born child. The number of risk factors and the way they interact and are buffered by protective factors are relevant for the final impact. Maternal-fetal attachment (MFA) is not yet a totally understood and well operationalized concept. Methodological problems limit the comparison of data as many studies used small size samples, had an exploratory character or used different selection criteria and different measures. There is still a lack of studies in high risk populations evaluating the consequences of a weak MFA. Instead, the available studies are not very conclusive, but suggest that social support, anxiety and depression, self-esteem and self-control and sense of coherence are correlated with MFA. MFA is also correlated with health practices during pregnancy, that influence pregnancy and baby outcomes. MFA seems a relevant concept for the future mother baby interaction, but more studies are needed to clarify the concept and its operationalization. Attachment is a strong scientific concept with multiple implications for future child development, personality and relationship with others. Secure attachment is considered an essential basis of good mental health, and promoting mother-baby interaction offers an excellent opportunity to intervention programmes targeted at enhancing mental health and well-being. Understanding the process of attachment and intervening to improve attachment requires a comprehension of more proximal factors, but also a broader approach that assesses the impact of more distal social conditions on attachment and how this social impact is mediated by family functioning and mother-baby interaction. Finally, it is essential to understand how this knowledge could be translated in effective mental health promoting interventions and measures that could reach large populations of pregnant mothers and families. Strengthening emotional availability (EA) seems to be a relevant approach to improve the mother-baby relationship. In this review we have offered evidence suggesting a range of determinants of mother-infant relationship, including age, marital relationship, social disadvantages, migration, parental psychiatric disorders and the situations of abuse or neglect. Based on this theoretical background we constructed a theoretical model that included proximal and distal factors, risk and protective factors, including variables related to the mother, the father, their social support and mother baby interaction from early pregnancy until six months after birth. We selected the Antenatal Psychosocial Health Assessment (ALPHA) for use as an instrument to detect psychosocial risk during pregnancy. Method Ninety two pregnant women were recruited from the Maternal Health Consultation in Primary Health Care (PHC) at Amadora. They had three moments of assessment: at T1 (until 12 weeks of pregnancy) they filed out a questionnaire that included socio-demographic data, ALPHA, Edinburgh post-natal Depression Scale (EDPS), General Health Questionnaire (GHQ) and Sense of Coherence (SOC); at T2 (after the 20th weeks of pregnancy) they answered EDPS, SOC and MFA Scale (MFAS), and finally at T3 (6 months after birth), they repeated EDPS and SOC, and their interaction with their babies was videotaped and later evaluated using EA Scales. A statistical analysis has been done using descriptive statistics, correlation analysis, univariate logistic regression and multiple linear regression. Results The study has increased our knowledge on this particular population living in a multicultural, suburb community. It allow us to identify specific groups with a higher level of psychosocial risk, such as single or divorced women, young couples, mothers with a low level of education and those who are depressed or have a low SOC. The hypothesis that psychosocial risk is directly correlated with MFAS and that MFA is directly correlated with EA was not confirmed, neither the correlation between prenatal psychosocial risk and mother-baby EA. The study identified depression as a relevant risk factor in pregnancy and its higher prevalence in single or divorced women, immigrants and in those who have a higher global psychosocial risk. Depressed women have a poor MFA, and a lower structuring capacity and a higher hostility to their babies. In average, depression seems to reduce among pregnant women in the second part of their pregnancy. The children of immigrant mothers show a lower level of responsiveness to their mothers what could be transmitted through depression, as immigrant mothers have a higher risk of depression in the beginning of pregnancy and six months after birth. Young mothers have a low MFA and are more intrusive. Women who have a higher level of education are more sensitive and their babies showed to be more responsive. Women who are or have been submitted to abuse were found to have a higher level of MFA but their babies are less responsive to them. The study highlights the relevance of SOC as a potential protective factor while it is strongly and negatively related with a wide range of risk factors and mental health outcomes especially depression before, during and after pregnancy. Conclusions ALPHA proved to be a valid, feasible and reliable instrument to Primary Health Care (PHC) that can be used as a total sum score. We could not prove the association between psychosocial risk factors and MFA, neither between MFA and EA, or between psychosocial risk and EA. Depression and SOC seems to have a clear and opposite relevance on this process. Pregnancy can be considered as a maturational process and an opportunity to change, where adaptation processes occur, buffering risk, decreasing depression and increasing SOC. Further research is necessary to better understand interactions between variables and also to clarify a better operationalization of MFA. We recommend the use of ALPHA, SOC and EDPS in early pregnancy as a way of identifying more vulnerable women that will require additional interventions and support in order to decrease risk. At political level we recommend the reinforcement of Immigrant integration and the increment of education in women. We recommend more focus in health care and public health in mental health condition and psychosocial risk of specific groups at high risk. In PHC special attention should be paid to pregnant women who are single or divorced, very young, low educated and to immigrant mothers. This study provides the basis for an intervention programme for this population, that aims to reduce broad spectrum risk factors and to promote Mental Health in women who become pregnant. Health and mental health policies should facilitate the implementation of the suggested measures.