Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

Tipificação de Mycoplasma mycoides subsp. mycoides SC e detecção da sua aderência a células epiteliais pulmonares

Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Compositional and functional analysis of polycomb target chromatin

Dissertation presented to obtain the Ph.D degree in Molecular Biology

Produção de DNases extracelulares em estirpes de Streptococcus agalactiae de origem humana e bovina

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Avaliação epidemiológica dos internamentos através de um serviço de urgência de segunda linha (SII)

RESUMO: Introdução: A Comissão Nacional para a reestruturação dos Serviços de Saúde Mental em 2004, fez uma proposta de âmbito regional, ao nível da região de Saúde do Norte, levando a uma alteração da rede de referenciação hospitalar dos internamentos em psiquiatria. Métodos: Realizou-se um estudo epidemiológico longitudinal para avaliar factores preditivos de internamento através de um serviço de Urgência de Segunda Linha (SII), que de algum modo reflectisse o funcionamento dos serviços de internamento na região de Saúde do Norte, ao longo de 12 anos, nomeadamente relacionando com factores organizacionais contemplados no Plano Nacional de Saúde Mental e na reorganização da rede de referenciação hospitalar. Resultados: Durante os 12 anos do estudo, verificou-se um aumento estatisticamente significativo do número e duração de internamentos através do SII, com ponto de partida no ano 2008-2009, e de novo a partir do ano 2010-2011 (nº de internamentos), para o qual contribuiu a alteração da rede hospitalar na região de saúde do Norte, nomeadamente pelo facto do HMLemos, assumir a responsabilidade de novo, dos internamentos das áreas de Famalicão, Gondomar e Santa Maria da Feira. Em relação ao número de internamentos, e na análise exploratória, encontramos nas áreas hospitalares fora da área de influência do HMLemos, uma contribuição positiva significativa para o aumento do nº de internamentos ao longo dos anos com os Dx (290, 296, 297, 291, 309). Em relação à área do HMLemos restrita (PVC, STT, Matosinhos, Porto Ocidental), de referir a contribuição positiva significativa dos Dx 309 e 301, para o aumento do número de internamentos ao longo do tempo, sendo que a prevalência maior se mantém relacionada às Psicoses (Dx 295, 296 e 297). Não se concluiu por uma contribuição estatisticamente significativa ( positiva ou negativa), das variáveis independentes idade, sexo ou natureza do internamento em relação à variável dependente ( duração de internamentos/ano). Em relação á variável dependente (nº de internamentos/ano), relativamente aos doentes fora de área de influência do HMLemos, concluiu-se uma contribuição positiva estatisticamente significativa da variável independente idade. Conclusões: Através da análise exploratória foi possível perceber o esforço realizado pelos hospitais no sentido de melhorar a equidade e acessibilidade dos doentes à Saúde Mental, a par da reorganização da rede hospitalar. De destacar a necessidade de encontrar alternativas às situações de internamento, com menos critérios de gravidade diagnóstica, nomeadamente reforçar a importância da criação de consultas de crises nos respectivos Hospitais de Dia dos DPSM.----------------ABSTRACT:Introduction : The National Commission for the restructuring of mental health services in 2004 , has proposed at a regional level ( North Health Region), a change in the network of hospital referrals of admissions in psychiatry. Methods: We conducted a longitudinal epidemiological study to assess predictors of hospitalization through a Second Line Emergency Service ( SII) , that somehow reflect the operation of inpatient services in North Health Region, over 12 years, particularly relating to organizational factors included in the National Mental Health Plan and reorganization of the hospital referral network. Results: During the period of the study, there was a statistically significant increase in the number and duration of hospitalizations through the SII, with starting point in the year 2008-2009 and again from 2010-2011 (number of admissions) , for which counted the change of the hospital network referral in Northern health region , in particular because Hospital Magalhães Lemos (HMLemos) , took the new responsibility of admissions from areas of Famalicão, Gondomar and Santa Maria da Feira . Regarding the number of hospitalizations, in the exploratory analysis , we found in hospital areas outside the area of influence of HMLemos , a significant positive contribution to the increase in number of admissions over the years with Diagnosis of 290, 296, 297, 291 , 309 in the ICD-9. With respect to the restricted area of HMLemos (PVC, STT , Porto Ocidental and Matosinhos) , we found a significant positive contribution of Diagnosis 309 and 301, to increase the number of hospitalizations over time, with higher prevalence rates remaining the psychoses ( Dx 295, 296 and 297 ) . Did not conclude for any statistically significant contribution (positive or negative) of the independent variables age, sex and nature of admission to the dependent variable (duration of hospitalization / year). In relation to the dependent variable (number of admissions / year) relative to patients outside the area of influence of HMLemos, it was found a statistically significant positive contribution of the independent variable age . Conclusions: Through the exploratory analysis, it was possible to see the efforts made by hospitals to improve the accessibility of patients to Mental Health, throughout the hospital network reorganization. Its important to highlight the need to find alternatives to inpatient admissions in those with less gravity diagnostic criteria, reinforcing the importance of creating specific crisis consultations in Day Hospital regime.

Structural and electron paramagnetic resonance (EPR) studies of mononuclear molybdenum enzymes from sulfate-reducing bacteria

Acc. Chem. Res., 2006, 39 (10), pp 788–796 DOI: 10.1021/ar050104k

Indicadores de prognóstico em utentes com disfunção do ombro submetidos a uma intervenção terapêutica direcionada para a estabilidade dinâmica da escápulo-torácica

RESUMO: Introdução/ Objetivo: Segundo a revisão sistemática de Chester e colaboradores (2013b)apenas dois fatores de prognóstico demonstraram uma associação consistente com o resultado que foram a duração dos sintomas e a funcionalidade na avaliação inicial. O objetivo do estudo é identificar indicadores de bom e mau prognóstico em utentes com disfunção do complexo articular do ombro (DCAO), tendo por base, aspetos da avaliação inicial do utente e critérios de alta de abolição da dor, aumento da funcionalidade e da estabilidade dinâmica considerando uma intervenção terapêutica direcionada para o aumento da estabilidade dinâmica da escápulo-torácica. Metodologia: Efetuou-se um estudo de coorte clínico retrospetivo. Para tal, aplicou-se um protocolo de intervenção terapêutica e analisou-se os resultados. A amostra foi constituída por 82 indivíduos com DCAO [53 com síndrome do conflito subacromial (SCSA) e 29 com instabilidade da glenoumeral (IGU)], residentes nos distritos de Lisboa, Setúbal e Santarém com o intuito de iniciar tratamento de fisioterapia. A análise dos dados foi efetuada tendo em consideração dois procedimentos: análise univariada (através do método de Kaplan-Meier para cada CVP) e análise multifatorial (pela análise de regressão de Cox e regressão logística nos grupos de utentes com SCSA, IGU e DCAO). Resultados: O tempo mediano de continuação no tratamento em fisioterapia foi de 7 semanas para os utentes com SCSA e 6 semanas para utentes com IGU. Segundo o teste de Logrank, na análise univariada, existem sete e oito covariáveis preditoras (CVP) com associação estatisticamente significativa (p<0,05) para o subgrupo SCSA e IGU, respectivamente. De acordo com estes resultados, a primeira parte da DASH e a SPADI são as únicas CVP com associação comuns às duas disfunções. Pela análise multifatorial e, em congruência com o teste de Wald, nenhuma das CVP contribui estatisticamente para o modelo preditivo de continuidade do tratamento de fisioterapia em qualquer um dos três modelos estudados: subgrupo SCSA, subgrupo IGU e utentes com DCAO. Conclusão: Por uma análise univariada verificou-se que existem CVP associadas à alta dos tratamentos em fisioterapia e estas não são as mesmas em ambas as DCAO. Contudo, a magnitude do efeito de cada CVP nos modelos multifatoriais definidos para os grupos de utentes com SCSA, IGU e DCAO não demonstraram valor estatisticamente significativo pelo que não foi possível determinar modelos de prognóstico em utentes com DCAO.-------------ABSTRACT: Background/ Purpose: According with the systematic review from Chester and collaborators (2013b) just two prognostic factors demonstrated a consistent association with the outcome: the duration of symptoms and functionality in the initial assessment. The purpose of the study is to identify indicators of good and poor prognosis in patients with shoulder’s dysfunctions, based on aspects of the initial assessment and discharge criteria of absence of pain, increased functionality and dynamic stability considering a therapeutic intervention used to increase the dynamic stability of scapulo-thoracic. Methodology: It was conducted a retrospective study of clinical cohort. For this purpose it was applied a protocol with therapeutic intervention and the results were analyzed. The sample consisted of 82 individuals with shoulder’s dysfunction (53 with subacromial impingement (SIMP) and 29 with shoulder instability (SINS) residing in the districts of Lisbon, Setúbal and Santarém in order to start physiotherapy. Data analysis was performed taking into account two procedures: univariate analysis [using the Kaplan-Meier method for each co-variant predictor variable (CVP)] and multifactorial analysis [analysis by Cox regression and logistic regression on groups of patients with SIMP, SINS and shoulder’s dysfunction (SD)]. Results: The median time of follow-up treatment at physical therapy was 7 weeks for patients with SIMP and 6 weeks for patients with SINS. According to the Logrank test in the univariate analysis, there are seven and eight CVP with a statistically significant association (p<0.05) for the patients with SIMP and SINS, respectively. According to these results, the first part of the DASH and SPADI are the only CVP common to both disorders association. By multifatorial analyses, and in agreement with the Wald test, none of the CVP contributes statistically to the predictive model of continuity of physiotherapy treatment in any of the three studied models: patients with SIMP, patients with SINS and patients with SD. Conclusion: In an univariate analysis, it was verified that there are CVP associated with discharge from treatments of physical therapy and these are not the same in both SD. However, the magnitude of effect of each CVP in multifactorial models for defined patients groups with SIMP, SINS and SD showed no statistically significant. Therefore, it was not possible to determine prognostic models for patients with SD.

Identification of mating type genes in the bipolar basidiomycetous yeast rhodosporidium toruloides: first insight into the MAT Locus structure of the sporidiobolales

Eukaryotic Cell, Vol.7, Nº6

Development of a satellite based PM10 concentration product for urban areas

Dissertação para obtenção do Grau de Doutor em Engenharia do Ambiente

Analysis and visualization of energy use for university campus

The reduction of greenhouse gas emissions is one of the big global challenges for the next decades due to its severe impact on the atmosphere that leads to a change in the climate and other environmental factors. One of the main sources of greenhouse gas is energy consumption, therefore a number of initiatives and calls for awareness and sustainability in energy use are issued among different types of institutional and organizations. The European Council adopted in 2007 energy and climate change objectives for 20% improvement until 2020. All European countries are required to use energy with more efficiency. Several steps could be conducted for energy reduction: understanding the buildings behavior through time, revealing the factors that influence the consumption, applying the right measurement for reduction and sustainability, visualizing the hidden connection between our daily habits impacts on the natural world and promoting to more sustainable life. Researchers have suggested that feedback visualization can effectively encourage conservation with energy reduction rate of 18%. Furthermore, researchers have contributed to the identification process of a set of factors which are very likely to influence consumption. Such as occupancy level, occupants behavior, environmental conditions, building thermal envelope, climate zones, etc. Nowadays, the amount of energy consumption at the university campuses are huge and it needs great effort to meet the reduction requested by European Council as well as the cost reduction. Thus, the present study was performed on the university buildings as a use case to: a. Investigate the most dynamic influence factors on energy consumption in campus; b. Implement prediction model for electricity consumption using different techniques, such as the traditional regression way and the alternative machine learning techniques; and c. Assist energy management by providing a real time energy feedback and visualization in campus for more awareness and better decision making. This methodology is implemented to the use case of University Jaume I (UJI), located in Castellon, Spain.

Analysis and design of sinusoidal quadrature RC-oscillators

Modern telecommunication equipment requires components that operate in many different frequency bands and support multiple communication standards, to cope with the growing demand for higher data rate. Also, a growing number of standards are adopting the use of spectrum efficient digital modulations, such as quadrature amplitude modulation (QAM) and orthogonal frequency division multiplexing (OFDM). These modulation schemes require accurate quadrature oscillators, which makes the quadrature oscillator a key block in modern radio frequency (RF) transceivers. The wide tuning range characteristics of inductorless quadrature oscillators make them natural candidates, despite their higher phase noise, in comparison with LC-oscillators. This thesis presents a detailed study of inductorless sinusoidal quadrature oscillators. Three quadrature oscillators are investigated: the active coupling RC-oscillator, the novel capacitive coupling RCoscillator, and the two-integrator oscillator. The thesis includes a detailed analysis of the Van der Pol oscillator (VDPO). This is used as a base model oscillator for the analysis of the coupled oscillators. Hence, the three oscillators are approximated by the VDPO. From the nonlinear Van der Pol equations, the oscillators’ key parameters are obtained. It is analysed first the case without component mismatches and then the case with mismatches. The research is focused on determining the impact of the components’ mismatches on the oscillator key parameters: frequency, amplitude-, and quadrature-errors. Furthermore, the minimization of the errors by adjusting the circuit parameters is addressed. A novel quadrature RC-oscillator using capacitive coupling is proposed. The advantages of using the capacitive coupling are that it is noiseless, requires a small area, and has low power dissipation. The equations of the oscillation amplitude, frequency, quadrature-error, and amplitude mismatch are derived. The theoretical results are confirmed by simulation and by measurement of two prototypes fabricated in 130 nm standard complementary metal-oxide-semiconductor (CMOS) technology. The measurements reveal that the power increase due to the coupling is marginal, leading to a figure-of-merit of -154.8 dBc/Hz. These results are consistent with the noiseless feature of this coupling and are comparable to those of the best state-of-the-art RC-oscillators, in the GHz range, but with the lowest power consumption (about 9 mW). The results for the three oscillators show that the amplitude- and the quadrature-errors are proportional to the component mismatches and inversely proportional to the coupling strength. Thus, increasing the coupling strength decreases both the amplitude- and quadrature-errors. With proper coupling strength, a quadrature error below 1° and amplitude imbalance below 1% are obtained. Furthermore, the simulations show that increasing the coupling strength reduces the phase noise. Hence, there is no trade-off between phase noise and quadrature error. In the twointegrator oscillator study, it was found that the quadrature error can be eliminated by adjusting the transconductances to compensate the capacitance mismatch. However, to obtain outputs in perfect quadrature one must allow some amplitude error.