Replication vs erasure coding in data centric storage for wireless sensor networks

In-network storage of data in wireless sensor networks contributes to reduce the communications inside the network and to favor data aggregation. In this paper, we consider the use of n out of m codes and data dispersal in combination to in-network storage. In particular, we provide an abstract model of in-network storage to show how n out of m codes can be used, and we discuss how this can be achieved in five cases of study. We also define a model aimed at evaluating the probability of correct data encoding and decoding, we exploit this model and simulations to show how, in the cases of study, the parameters of the n out of m codes and the network should be configured in order to achieve correct data coding and decoding with high probability.

Metabolism of primary astrocytes studied by NMR: metabolic trafficking and neuroprotection

Dissertation presented to obtain a Ph. D. degree in Biochemistry by Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica.

Metabolic flux analysis of neural cell metabolism in primary cultures

Dissertation presented to obtain the Ph.D degree in Biochemistry, Neuroscience

Performance Model for MRC Receivers with Adaptive Modulation and Coding in Rayleigh Fading Correlated Channels with Imperfect CSIT

RTUWO Advances in Wireless and Optical Communications 2015 (RTUWO 2015). 5-6 Nov Riga, Latvia.

Role of the DHH1 Gene in the Regulation of Monocarboxylic Acids Transporters Expression in Saccharomyces cerevisiae

Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170∶301–306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.

Does Metabolic Syndrome Predict Significant Angiographic Coronary Artery Disease?

INTRODUCTION: Metabolic syndrome (MS) is an independent predictor of acute cardiovascular events. However, few studies have addressed the relationship between MS and stable angiographic coronary artery disease (CAD), which has a different pathophysiological mechanism. We aimed to study the independent predictors for significant CAD, and to analyze the impact of MS (by the AHA/NHLBI definition) on CAD. METHODS: We prospectively included 300 patients, mean age 64±9 years, 59% male, admitted for elective coronary angiography (suspected ischemic heart disease), excluding patients with known cardiac disease. All patients underwent assessment of demographic, anthropometric, and laboratory data and risk factors, and subsequently underwent coronary angiography. RESULTS: In the study population, 23.0% were diabetic, 40.5% had MS (and no diabetes) and 36.7% had neither diagnosis. Significant CAD was present in 51.3% of patients. CAD patients were older and more frequently male and diabetic, with increased triglycerides and glucose and lower HDL cholesterol. Abdominal obesity was also less prevalent. MS was not associated with the presence of CAD (OR 0.94, 95% CI 0.59-1.48, p=0.778). Of the MS components, the most important predictors of CAD were increased glucose and triglycerides. Abdominal obesity was associated with a lower risk of CAD. In a multivariate logistic regression model for CAD, independent predictors of CAD were age, male gender, glucose and triglycerides. Body mass index had a protective effect. CONCLUSIONS: Although MS is associated with cardiovascular events, the same was not found for stable angiographically proven CAD. Age, gender, diabetes and triglycerides are the most influential factors for CAD, with abdominal obesity as a protective factor.

Prevalence of Metabolic Syndrome and Diabetes on a High-Risk Population with Suspected Coronary Artery Disease

Objectivos: A prevalência de Sindroma Metabólica (SM) e diabetes é variável consoante a definição utilizada, assim como com a região geográfica e o grupo étnico estudado. Não existem estudos em indivíduos portugueses com suspeita de doença arterial coronária. Analisámos a prevalência de SM e diabetes nesta população específica de doentes, comparando também definições. Métodos: Incluíram-se no estudo 300 indivíduos, com uma idade media de 64 ± 9 anos, 59% do género masculino, admitidos para angiografia coronária electiva, tendo sido excluídos os doentes com doença cardíaca previamente conhecida. Avaliou-se a prevalência de SM e de diabetes. Resultados: A prevalência ajustada de SM foi de 39,3% (critério NCEP-ATP III), 53,8% (critério IDF) e 48,4% (critério AHA/NHLBI). A prevalência ajustada de diabetes foi de 14,8% pela definição prévia da ADA e de 36.4% com a definição mais recente. A concordância global entre as definições de SM foi de 45,3%, sendo mais elevada entre as definições da AHA/NHLBI e da NCEP-ATP III (Kappa 0,821). A prevalência de SM está altamente dependente da idade em ambos os géneros, sendo mais prevalente no género feminino. A prevalência de diabetes é também dependente da idade, sendo semelhante em ambos os géneros. O componente de SM mais frequente é a hipertensão arterial, seguido pela obesidade abdominal, elevação da glicose, colesterol-HDL baixo e finalmente elevação dos triglicéridos. É também importante referir que 60% dos doentes estavam sob terapêutica hipolipemiante (56,6% com estatinas, 1,7% com fibratos e 1,7% com ambos). A diferença mais significativa entre géneros no que diz respeito aos componentes de SM é a elevada prevalência de obesidade abdominal no género feminino. Conclusões: Nesta população de alto risco, a prevalência de SM é elevada, sendo contudo a prevalência de diabetes semelhante à registada em estudos epidemiológicos na população geral.

Full-scale biological phosphorus removal: quantification of storage polymers, microbial performance and metabolic modelling

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Yeast as a model system to study genetic and post-translational regulation of metabolic pathways in mammals

Dissertation presented to obtain the Ph.D degree in Biology

Ascaris suum: partial fractionation of metabolic antigens from "in vitro" cultured larvae

Ascaris suum metabolic antigens were obtained frorn second and early third stage larvae cultured in vitro in supplemented Eagle's minimum essential medium. Metabolic antigens harvested after 12 and 16 days from in vitro cultures were eluted through Bio-Gel Al.5. Three main elution peaks were identified, dialysed, lyophilized and injected into mice with 4% sodium alginate. Peak 11 from elution of two preparations of metabolic antigens protected mice against a chállenge infection of 10,000 A. suum embryonated eggs.

Understanding the microbial ecology and ecophysiology of enhanced biological phosphorus removal processes through metabolic modelling and experimental studies

Dissertation to obtain the degree of Master in Chemical and Biochemical Engineering

Frequency of metabolic syndrome and the food intake patterns in adults living in a rural area of Brazil

INTRODUCTION: Metabolic syndrome (MetS), a risk factor for atherosclerosis and coronary heart disease, is related to an inadequate food intake pattern. Its incidence is increasing among Brazilian adults, including those living in rural areas. Our aim was not only to describe the frequency of MetS in adults with or without MetS but also to compare their food intake pattern as assessed by the healthy eating index (HEI) and serum albumin and C reactive protein (CRP) levels. METHODS: Men and women (n = 246) living in a small village in Brazil were included. MetS was characterized according to the adult treatment panel (ATP III) criteria. Groups were compared by chi-square, student t or Mann-Whitney tests. RESULTS: MetS was diagnosed in 15.4% of the cases. The MetS group showed higher CRP (1.8±1.2 vs. 1.0±0.9 mg/dl) and lower albumin (4.3±0.3 vs. 4.4±0.3 g/dl) serum levels compared to the control group. Additionally, the MetS group showed lower scores (median[range]) in the HEI compared to the control group (53.5[31.2-78.1] vs 58[29.7-89.5], respectively). The MetS group also had decreased scores for total fat and daily variety of food intake. CONCLUSIONS: The results suggest that adults with MetS displayed chronic mild inflammation and a poorer food intake pattern than the control group.

Analysis of metabolic flux distributions in relation to the extracellular environment in Avian cells

Continuous cell lines that proliferate in chemically defined and simple media have been highly regarded as suitable alternatives for vaccine production. One such cell line is the AG1.CR.pIX avian cell line developed by PROBIOGEN. This cell line can be cultivated in a fully scalable suspension culture and adapted to grow in chemically defined, calf serum free, medium [1]–[5]. The medium composition and cultivation strategy are important factors for reaching high virus titers. In this project, a series of computational methods was used to simulate the cell’s response to different environments. The study is based on the metabolic model of the central metabolism proposed in [1]. In a first step, Metabolic Flux Analysis (MFA) was used along with measured uptake and secretion fluxes to estimate intracellular flux values. The network and data were found to be consistent. In a second step, Flux Balance Analysis (FBA) was performed to access the cell’s biological objective. The objective that resulted in the best predicted results fit to the experimental data was the minimization of oxidative phosphorylation. Employing this objective, in the next step Flux Variability Analysis (FVA) was used to characterize the flux solution space. Furthermore, various scenarios, where a reaction deletion (elimination of the compound from the media) was simulated, were performed and the flux solution space for each scenario was calculated. Growth restrictions caused by essential and non-essential amino acids were accurately predicted. Fluxes related to the essential amino acids uptake and catabolism, the lipid synthesis and ATP production via TCA were found to be essential to exponential growth. Finally, the data gathered during the previous steps were analyzed using principal component analysis (PCA), in order to assess potential changes in the physiological state of the cell. Three metabolic states were found, which correspond to zero, partial and maximum biomass growth rate. Elimination of non-essential amino acids or pyruvate from the media showed no impact on the cell’s assumed normal metabolic state.

Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes

The obligate intracellular bacterium Chlamydia trachomatis is a human pathogen of major public health significance. Strains can be classified into 15 main serovars (A to L3) that preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3), but the molecular basis behind their distinct tropism, ecological success and pathogenicity is not welldefined. Most chlamydial research demands culture in eukaryotic cell lines, but it is not known if stains become laboratory adapted. By essentially using genomics and transcriptomics, we aimed to investigate the evolutionary patterns underlying the adaptation of C. trachomatis to the different human tissues, given emphasis to the identification of molecular patterns of genes encoding hypothetical proteins, and to understand the adaptive process behind the C. trachomatis in vivo to in vitro transition. Our results highlight a positive selection-driven evolution of C. trachomatis towards nichespecific adaptation, essentially targeting host-interacting proteins, namely effectors and inclusion membrane proteins, where some of them also displayed niche-specific expression patterns. We also identified potential "ocular-specific" pseudogenes, and pointed out the major gene targets of adaptive mutations associated with LGV infections. We further observed that the in vivo-derived genetic makeup of C. trachomatis is not significantly compromised by its long-term laboratory propagation. In opposition, its introduction in vitro has the potential to affect the phenotype, likely yielding virulence attenuation. In fact, we observed a "genital-specific" rampant inactivation of the virulence gene CT135, which may impact the interpretation of data derived from studies requiring culture. Globally, the findings presented in this Ph.D. thesis contribute for the understanding of C.trachomatis adaptive evolution and provides new insights into the biological role of C. trachomatishypothetical proteins. They also launch research questions for future functional studies aiming toclarify the determinants of tissue tropism, virulence or pathogenic dissimilarities among C. trachomatisstrains.

Genome-scale metabolic network reconstruction of Polaromonas sp. strain JS666: analysis of cDCE degradation rates and design of experiments for bioremediation improvement

Release of chloroethene compounds into the environment often results in groundwater contamination, which puts people at risk of exposure by drinking contaminated water. cDCE (cis-1,2-dichloroethene) accumulation on subsurface environments is a common environmental problem due to stagnation and partial degradation of other precursor chloroethene species. Polaromonas sp. strain JS666 apparently requires no exotic growth factors to be used as a bioaugmentation agent for aerobic cDCE degradation. Although being the only suitable microorganism found capable of such, further studies are needed for improving the intrinsic bioremediation rates and fully comprehend the metabolic processes involved. In order to do so, a metabolic model, iJS666, was reconstructed from genome annotation and available bibliographic data. FVA (Flux Variability Analysis) and FBA (Flux Balance Analysis) techniques were used to satisfactory validate the predictive capabilities of the iJS666 model. The iJS666 model was able to predict biomass growth for different previously tested conditions, allowed to design key experiments which should be done for further model improvement and, also, produced viable predictions for the use of biostimulant metabolites in the cDCE biodegradation.