A demonstration case on the derivation of process-level logical architectures for ambient assisted living ecosystems

When representing the requirements for an intended software solution during the development process, a logical architecture is a model that provides an organized vision of how functionalities behave regardless of the technologies to be implemented. If the logical architecture represents an ambient assisted living (AAL) ecosystem, such representation is a complex task due to the existence of interrelated multidomains, which, most of the time, results in incomplete and incoherent user requirements. In this chap- ter, we present the results obtained when applying process-level modeling techniques to the derivation of the logical architecture for a real industrial AAL project. We adopt a V-Model–based approach that expresses the AAL requirements in a process-level perspec- tive, instead of the traditional product-level view. Additionally, we ensure compliance of the derived logical architecture with the National Institute of Standards and Technology (NIST) reference architecture as nonfunctional requirements to support the implementa- tion of the AAL architecture in cloud contexts.

Nonparametric estimation of time-dependent ROC curves conditional on a continuous covariate

The receiver-operating characteristic (ROC) curve is the most widely used measure for evaluating the performance of a diagnostic biomarker when predicting a binary disease outcome. The ROC curve displays the true positive rate (or sensitivity) and the false positive rate (or 1-specificity) for different cut-off values used to classify an individual as healthy or diseased. In time-to-event studies, however, the disease status (e.g. death or alive) of an individual is not a fixed characteristic, and it varies along the study. In such cases, when evaluating the performance of the biomarker, several issues should be taken into account: first, the time-dependent nature of the disease status; and second, the presence of incomplete data (e.g. censored data typically present in survival studies). Accordingly, to assess the discrimination power of continuous biomarkers for time-dependent disease outcomes, time-dependent extensions of true positive rate, false positive rate, and ROC curve have been recently proposed. In this work, we present new nonparametric estimators of the cumulative/dynamic time-dependent ROC curve that allow accounting for the possible modifying effect of current or past covariate measures on the discriminatory power of the biomarker. The proposed estimators can accommodate right-censored data, as well as covariate-dependent censoring. The behavior of the estimators proposed in this study will be explored through simulations and illustrated using data from a cohort of patients who suffered from acute coronary syndrome.

Autoimmune diseases and pregnancy: analysis of a series of cases

BACKGROUND: An autoimmune disease is characterized by tissue damage, caused by self-reactivity of different effector mechanisms of the immune system, namely antibodies and T cells. All autoimmune diseases, to some extent, have implications for fertility and obstetrics. Currently, due to available treatments and specialised care for pregnant women with autoimmune disease, the prognosis for both mother and child has improved significantly. However these pregnancies are always high risk. The purpose of this study is to analyse the fertility/pregnancy process of women with systemic and organ-specific autoimmune diseases and assess pathological and treatment implications. METHODS: The authors performed an analysis of the clinical records and relevant obstetric history of five patients representing five distinct autoimmune pathological scenarios, selected from Autoimmune Disease Consultation at the Hospital of Braga, and reviewed the literature. RESULTS: The five clinical cases are the following: Case 1-28 years old with systemic lupus erythematosus, and clinical remission of the disease, under medication with hydroxychloroquine, prednisolone and acetylsalicylic acid, with incomplete miscarriage at 7 weeks of gestation without signs of thrombosis. Case 2-44 years old with history of two late miscarriages, a single preterm delivery (33 weeks) and multiple thrombotic events over the years, was diagnosed with antiphospholipid syndrome after acute myocardial infarction. Case 3-31 years old with polymyositis, treated with azathioprine for 3 years with complete remission of the disease, took the informed decision to get pregnant after medical consultation and full weaning from azathioprine, and gave birth to a healthy term new-born. Case 4-38 years old pregnant woman developed Behcet's syndrome during the final 15 weeks of gestation and with disease exacerbation after delivery. Case 5-36 years old with autoimmune thyroiditis diagnosed during her first pregnancy, with difficult control over the thyroid function over the years and first trimester miscarriage, suffered a second miscarriage despite clinical stability and antibody regression. CONCLUSIONS: As described in literature, the authors found a strong association between autoimmune disease and obstetric complications, especially with systemic lupus erythematosus, antiphospholipid syndrome and autoimmune thyroiditis.

Cheese whey: a cost-effective alternative for hyaluronic acid production by Streptococcus zooepidemicus

This study focuses on the optimization of cheese whey formulated media for the production of hyaluronic acid HA by Streptococcus zooepidemicus. Culture media containing whey (W; 2.1 g/L) or whey hydrolysate (WH; 2.4 g/L) gave the highest HA productions. Both W and WH produced high yields on protein consumed, suggesting cheese whey is a good nitrogen source for S. zooepidemicus production of HA. Polysaccharide concentrations of 4.0 g/L and 3.2 g/L were produced in W and WH in a further scale-up to 5 L bioreactors, confirming the suitability of the low-cost nitrogen source. Cheese whey culture media provided high molecular weight (> 3000 kDa) HA products. This study revealed replacing the commercial peptone by the low-cost alternative could reduce HA production costs by up to a 70%compared to synthetic media.

Microenxertia em castanheiro

Dissertação de mestrado em Biologia Molecular, Biotecnologia e Bioempreendedorismo em Plantas

Systems biology approaches for the design of novel Saccharomyces cerevisiae winemaking strains for enhanced flavour compounds synthesis

Tese de Doutoramento em Biologia Ambiental e Molecular

Redes interorganizacionais nas políticas públicas: atores, conexões e configurações organizacionais

Tese de Doutoramento em Sociologia

Developing novel strains for butanol production

[Excerpt] The growing global demand for new energy sources combined with environmental concerns had motivated the search for alternative fuels, produced from renewable raw materials. During the last decade, ethanol was considered the next generation of biofuels. But more recently, n-butanol gained attention due to its superior fuel properties when compared with ethanol. Although n-butanol is naturally produced by solventogenic bacteria through ABE fermentation, the low productivities obtained with this bioprocess discouraged its use. Thus, most of n-butanol produced nowadays is chemical synthesized via petrochemical routes and its price is extremely sensitive to crude oil’s price. One possible approach to overcome this issue is to express non-native pathways in microbial factories. (...)

Citric acid production by Y. lipolytica W29 from crude glycerol: strain improvement by mutagenesis

[Excerpt] Citric acid, an important and versatile organic acid extensively used in several industries, is originally produced by Aspergillus niger in submerged fermentation from molasses [1]. However, Yarrowia lipolytica have been studied and demonstrate a great potential as citric acid producer from several carbon sources [1–5] including crude glycerol, a low cost byproduct from the biodiesel industry [6]. The simultaneous production of the isomer isocitric acid is the major problem in using this yeast in the citric acid production. (...)

Bioethanol production by Saccharomyces cerevisiae, Pichia stipitis and Zymomonas mobilis from delignified coconut fibre mature and lignin extraction according to biorefinery concept

In search to increase the offer of liquid, clean, renewable and sustainable energy in the world energy matrix, the use of lignocellulosic materials (LCMs) for bioethanol production arises as a valuable alternative. The objective of this work was to analyze and compare the performance of Saccharomyces cerevisiae, Pichia stipitis and Zymomonas mobilis in the production of bioethanol from coconut fibre mature (CFM) using different strategies: simultaneous saccharification and fermentation (SSF) and semi-simultaneous saccharification and fermentation (SSSF). The CFM was pretreated by hydrothermal pretreatment catalyzed with sodium hydroxide (HPCSH). The pretreated CFM was characterized by X-ray diffractometry and SEM, and the lignin recovered in the liquid phase by FTIR and TGA. After the HPCSH pretreatment (2.5% (v/v) sodium hydroxide at 180 °C for 30 min), the cellulose content was 56.44%, while the hemicellulose and lignin were reduced 69.04% and 89.13%, respectively. Following pretreatment, the obtained cellulosic fraction was submitted to SSF and SSSF. Pichia stipitis allowed for the highest ethanol yield 90.18% in SSSF, 91.17% and 91.03% were obtained with Saccharomyces cerevisiae and Zymomonas mobilis, respectively. It may be concluded that the selection of the most efficient microorganism for the obtention of high bioethanol production yields from cellulose pretreated by HPCSH depends on the operational strategy used and this pretreatment is an interesting alternative for add value of coconut fibre mature compounds (lignin, phenolics) being in accordance with the biorefinery concept.

Conversion of Cn-unsaturated into Cn-2-saturated LCFA can occur uncoupled from methanogenesis in anaerobic bioreactors

Fat, oils, and grease present in complex wastewater can be readily converted to methane, but the energy potential of these compounds is not always recyclable, due to incomplete degradation of long chain fatty acids (LCFA) released during lipids hydrolysis. Oleate (C18:1) is generally the dominant LCFA in lipid-containing wastewater, and its conversion in anaerobic bioreactors results in palmitate (C16:0) accumulation. The reason why oleate is continuously converted to palmitate without further degradation via β-oxidation is still unknown. In this work, the influence of methanogenic activity in the initial conversion steps of unsaturated LCFA was studied in 10 bioreactors continuously operated with saturated or unsaturated C16- and C18-LCFA, in the presence or absence of the methanogenic inhibitor bromoethanesulfonate (BrES). Saturated Cn-2-LCFA accumulated both in the presence and absence of BrES during the degradation of unsaturated Cn-LCFA, and represented more than 50\% of total LCFA. In the presence of BrES further conversion of saturated intermediates did not proceed, not even when prolonged batch incubation was applied. As the initial steps of unsaturated LCFA degradation proceed uncoupled from methanogenesis, accumulation of saturated LCFA can be expected. Analysis of the active microbial communities suggests a role for facultative anaerobic bacteria in the initial steps of unsaturated LCFA biodegradation. Understanding this role is now imperative to optimize methane production from LCFA.

Production of medium-chain fatty acids and higher alcohols by a synthetic co-culture grown on carbon monoxide or syngas

Synthesis gas, a mixture of CO, H2, and CO2, is a promising renewable feedstock for bio-based production of organic chemicals. Production of medium-chain fatty acids can be performed via chain elongation, utilizing acetate and ethanol as main substrates. Acetate and ethanol are main products of syngas fermentation by acetogens. Therefore, syngas can be indirectly used as a substrate for the chain elongation process.

Valorization of eucalyptus wood by glycerol-organosolv pretreatment within the biorefinery concept: an integrated and intensified approach

The efficient utilization of lignocellulosic biomass and the reduction of production cost are mandatory to attain a cost-effective lignocellulose-to-ethanol process. The selection of suitable pretreatment that allows an effective fractionation of biomass and the use of pretreated material at high-solid loadings on saccharification and fermentation (SSF) processes are considered promising strategies for that purpose. Eucalyptus globulus wood was fractionated by organosolv process at 200 C for 69 min using 56% of glycerol-water. A 99% of cellulose remained in pretreated biomass and 65% of lignin was solubilized. Precipitated lignin was characterized for chemical composition and thermal behavior, showing similar features to commercial lignin. In order to produce lignocellulosic ethanol at high-gravity, a full factory design was carried to assess the liquid to solid ratio (3e9 g/g) and enzyme to solid ratio (8e16 FPU/g) on SSF of delignified Eucalyptus. High ethanol concentration (94 g/L) corresponding to 77% of conversion at 16FPU/g and LSR ¼ 3 g/g using an industrial and thermotolerant Saccharomyces cerevisiae strain was successfully produced from pretreated biomass. Process integration of a suitable pretreatment, which allows for whole biomass valorization, with intensified saccharification-fermentation stages was shown to be feasible strategy for the co-production of high ethanol titers, oligosaccharides and lignin paving the way for cost-effective Eucalyptus biorefinery.

The role of marine anaerobic bacteria and archaea in bioenergy production

The development of products from marine bioresources is gaining importance in the biotechnology sector. The global market for Marine Biotechnology products and processes was, in 2010, estimated at 2.8 billion with a cumulative annual growth rate of 510% (Børresen et al., Marine biotechnology: a new vision and strategy for Europe. Marine Board Position Paper 15. Beernem: Marine Board-ESF, 2010). Marine Biotechnology has the potential to make significant contributions towards the sustainable supply of food and energy, the solution of climate change and environmental degradation issues, and the human health. Besides the creation of jobs and wealth, it will contribute to the development of a greener economy. Thus, huge expectations anticipate the global development of marine biotechnology. The marine environment represents more than 70% of the Earths surface and includes the largest ranges of temperature, light and pressure encountered by life. These diverse marine environments still remain largely unexplored, in comparison with terrestrial habitats. Notwithstanding, efforts are being done by the scientific community to widespread the knowledge on oceans microbial life. For example, the J. Craig Venter Institute, in collaboration with the University of California, San Diego (UCSD), and Scripps Institution of Oceanography have built a state-of-the-art computational resource along with software tools to catalogue and interpret microbial life in the worlds oceans. The potential application of the marine biotechnology in the bioenergy sector is wide and, certainly, will evolve far beyond the current interest in marine algae. This chapter revises the current knowledge on marine anaerobic bacteria and archaea with a role in bio-hydrogen production, syngas fermentation and bio-electrochemical processes, three examples of bioenergy production routes.

The brewing yeast

The concept of brewing science is very recent when compared with the history of beer. It began with the microscopic observations of Louis Pasteur and evolved through the last century with improvements in engineering, microbiology, and instrumental analysis. However, the most profound insight into brewing processes only emerged in the past decades through the advances in molecular biology and genetic engineering. These techniques allowed scientists to not only affirm their experiences and past findings, but also to clarify a vast number of links between cellular structures and their role within the metabolic pathways in yeast. This chapter is therefore dedicated to the behavior of the brewing yeast during fermentation. The discussion puts together the recent findings in the core carbon and nitrogen metabolism of the model yeast Saccharomyces cerevisiae and their fermentation performance.