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This research offers, through a bibliometric review, an overview of the latest publications on rural sanitation, aiming to assess the impact of scientific production on the subject and seek references for the formulation of management models. For this, publications from the Scopus database, the Bibliometrix tool and the VOSViewer software were used to perform evaluative and relational analyzes on the publications. This research showed the countries with the highest scientific production, the most cited, the most relevant journals, publications and works, and the most frequent keywords. In addition, the main works produced in the chosen theme were analyzed, noting that the development of management models for rural sanitation is little discussed, although relevant. Among the results, it is noteworthy that the countries with the highest scientific production on the subject are China, Brazil, the United States, the United Kingdom and India. Brazil appears in the list of countries with the most cited publications, indicating that national publications have a good impact factor. Esta investigación ofrece, a través de una revisión bibliométrica, un panorama de las últimas publicaciones sobre saneamiento rural, con el objetivo de evaluar el impacto de la producción científica sobre el tema y buscar referencias para la formulación de modelos de gestión. Para ello se utilizaron publicaciones de la base de datos Scopus, la herramienta Bibliometrix y el software VOSViewer para realizar análisis evaluativos y relacionales de las publicaciones. Esta investigación mostró los países con mayor producción científica, los más citados, las revistas, publicaciones y trabajos más relevantes, y las palabras clave más frecuentes. Además, se analizaron los principales trabajos producidos en el tema elegido, destacando que el desarrollo de modelos de gestión para el saneamiento rural es poco discutido, aunque relevante. Entre los resultados, se destaca que los países con mayor producción científica sobre el tema son China, Brasil, Estados Unidos, Reino Unido e India. Brasil aparece en la lista de países con más publicaciones citadas, lo que indica que las publicaciones nacionales tienen un buen impacto. Essa pesquisa oferece, por meio de revisão bibliométrica, um panorama das últimas publicações em saneamento rural, visando analisar a produção científica na temática e buscar referências para formulação de modelos de gestão. Para isso, utilizou-se da metodologia proposta por Treinta et al. (2014) com algumas alterações. Foi feita uma busca de publicações na base de dados Scopus com a palavra-chave “rural sanitation”. Foi utilizada a ferramenta Bibliometrix e o software VOSViewer para realizar as análises avaliativas e relacionais sobre as publicações. Essa pesquisa mostrou os países com maior produção científica, os mais citados, os periódicos, publicações e trabalhos mais relevantes e as palavras-chave mais frequentes. Ademais, as principais obras produzidas na temática escolhida foram analisadas, notando-se que o desenvolvimento de modelos de gestão para o saneamento rural foi pouco abordado, ainda que relevante. Dentre os resultados, destaca-se que os países com maior produção científica no tema foram China, Brasil, Estados Unidos, Reino Unido e Índia. O Brasil apareceu na lista dos países com publicações mais citadas, indicando que as publicações nacionais possuem bom impacto.

O aproveitamento do potencial energético presente em sistemas de abastecimento de água através de Bombas Funcionando como Turbinas (BFTs) é uma alternativa que vem apresentando viabilidade técnica e econômica devido ao custo reduzido das bombas utilizadas, porém o baixo potencial energético disponível em cada ponto e a infraestrutura necessária no local pode inviabilizar economicamente a implantação deste sistema. Para facilidade de manutenção, segurança e garantia da pressão estabelecida em normas técnicas, é necessário conter equipamentos como registros, filtro, hidrômetro e Válvula Redutora de Pressão (VRP) em sistema de by pass contido em caixa de proteção, o que pode levar na elevação do custo de implantação. Desta forma, este trabalho analisou a viabilidade econômica para a instalação da BFT e seus equipamentos anexos, considerando o potencial energético disponível, a infraestrutura presente, o custo de instalação e a geração energética futura para a seção estudada. Esta análise foi realizada através do cálculo do Valor Presente Líquido (VPL), Taxa Interna de Retorno (TIR), Custo Nivelado de Energia – ou Levelized Cost of Electricity (LCOE) – e payback, avaliando três cenários com diferentes níveis de infraestrutura no local. O cenário ideal, que considera a existência de toda infraestrutura, obteve como resultado R$ 7.251,17 de VPL, 21% de TIR, Custo Nivelado de Energia de R$ 0,55/kWh e payback de aproximadamente seis anos, com intervalo de potência de geração de 0,11 kW a 0,32 kW e geração anual de 1.772,81 kWh. O cenário que apresenta apenas a obra civil como infraestrutura existente não apresentou viabilidade econômica, resultando em um prejuízo de R$ 12.653,10, 2% de TIR e Custo Nivelado de Energia de R$ 1,58/kWh. O cenário real, que necessita a instalação de toda infraestrutura, também não apresentou viabilidade de implantação, resultando em um prejuízo de R$ 22.714,19, -1% de TIR e Custo Nivelado de Energia de R$ 2,10/kWh. The use of the potential energy embedded in water supply systems through Pumps as Turbines (PATs) is an alternative that has been showing technical and economic viability due to the reduced cost of the pumps used. However, the system implementation may become economically unviable due to low potential energy available at each point and the need to project on-site infrastructure. In order to ease of maintenance, safety and guarantee of the pressure established in technical standards it is necessary to contain equipment such as drawer, filter, water meter and Pressure Reducing Valve (PRV) registers in a by-pass system contained in a protection box, which can lead to higher deployment costs. In view of the referenced problems, this paper proposes to analyze the economic feasibility for the installation of BFT and its attached equipment, considering the available potential energy, the present infrastructure, the installation cost and the future energy generation for each section studied. This analysis will be performed by calculating the Net Present Value (NPV), Internal Rate of Return (IRR), Levelized Cost of Electricity (LCOE) and payback, measuring three scenarios with different infrastructure levels on site. The ideal scenario, that considers the existence of the entire infrastructure, obtained the result of R$ 7,251.17 (NPV), 21% of IRR, R$ 0.55/kWh levelized cost of electricity and approximately payback in six years, with power generation range of 0.11 kW up to 0.32 kW and annual generation of 1,772,81 kWh. The scenario that only presents civil works as existing infrastructure did not present deployment feasibility, resulting in a R$ 12,653.10 demage, 2% of IRR and Leveled Cost os Energy os R$ 1.58/kWh. The real scenario, which depends on the installation of the entire infrastructure, also did not present deployment feasibility, resulting in a R$ 22,714.19 damage, -1% of IRR and R$2.10/kWh Levelized Cost of Electricity (LCOE).

info:eu-repo/semantics/publishedVersion

Tese de mestrado integrado, Engenharia da Energia e do Ambiente, Universidade de Lisboa, Faculdade de Ciências, 2017 Submitted by Teresa Boa (tdboa@fc.ul.pt) on 2018-02-28T11:23:59Z No. of bitstreams: 1 ulfc124320_tm_Rafael_Carreira.pdf: 3849606 bytes, checksum: 735981dfd5207928a0987627df7db962 (MD5) Made available in DSpace on 2018-02-28T11:24:08Z (GMT). No. of bitstreams: 1 ulfc124320_tm_Rafael_Carreira.pdf: 3849606 bytes, checksum: 735981dfd5207928a0987627df7db962 (MD5) Previous issue date: 2017

PhD thesis in Biomedical Engineering, Metabolic Engineering (ME) is increasingly used to design strains for industrial biotechnology, using in silico constraint-based methods defined over genome-scale models to determine flux distributions in different conditions. However, these methods present a number of limitations related to multiple optima, futile cycles and reliance on cofactor balances. These can be overcome adding constraints to the systems, coming from experimentally measured rates. Valuable information is obtained from 13C tracer experiments, which allow to trace how labeling patterns propagate from substrates to products and how these relate to flux distributions through the application of 13C metabolic flux analysis (13C MFA). Although many software tools exist, none provides a free application that makes available the full portfolio of flux analysis methods. This work presents Constraint- Based Flux Analysis (CBFA), an open-source software application for flux analysis that implements several methods for phenotype prediction, allowing to define constraints related to measured fluxes and/or flux ratios, together with environmental conditions and gene knockouts. CBFA identifies the set of applicable methods based on the user inputs, encompassing algebraic and constraint-based methods. The integration within the OptFlux framework for ME enables to use different model formats and standards and the integration with complementary methods for phenotype simulation and visualization. To explore the information provided by 13C tracer experiments, a framework is developed that enables the integration of fluxomics data, as 13C labeling distributions, with models enriched with carbon atom transition maps. The algorithms allow to infer labeling distributions for fragments/ metabolites, building expressions for the relevant flux ratios. These can be used to generate flux ratio constraints to be added to flux analysis methods. This framework is generic not requiring any assumptions on the network or reaction reversibility. These algorithms were implemented in MetabolIc NEtwork Ratio AnaLysis (MiNeRAl), an user-friend generic tool to calculate metabolic flux ratios for any fragmentation used in GC-MS data. Both tools can thus be combined to perform tasks of 13C MFA., A Engenharia Metabólica (EM) é cada vez mais utilizada para projetar estirpes para a biotecnologia industrial, utilizando métodos baseados em restrições in silico definidos sobre modelos à escala genómica para determinar distribuições de fluxos em diferentes condições. No entanto, esses métodos apresentam várias limitações no que diz respeito a múltiplas soluções óptimas, ciclos fúteis e confiança no balanceamento de cofactores. Estas podem ser ultrapassadas através da adição de restrições aos sistemas, obtidas pela medição de fluxos experimentais. Informação relevante é obtida através de experiências de rastreamento de 13C o que permite perceber como os padrões de marcação são propagados desde os substratos para os produtos, e como estes estão relacionados com fluxos através da aplicação de análise de fluxos metabólicos baseados em 13C. Embora existam muitas ferramentas informáticas, nenhuma fornece uma aplicação livre que disponibilize um portfólio completo de métodos de análise de fluxos. Este trabalho apresenta a aplicação de código livre, CBFA, para análise de fluxos que implementa vários métodos de predição de fenótipos, permitindo a definição de restrições relacionadas com fluxos medidos e/ou rácios de fluxos, juntamente com condições ambientais e deleções de genes. Esta aplicação identifica o conjunto de métodos aplicáveis com base nos dados introduzidos pelo utilizador, contendo métodos algébricos e baseados em restrições. A integração com o OptFlux, uma ferramenta para EM, permite o uso de diferentes formatos de modelos e a integração com métodos complementares de simulação de fenótipos e visualização. Para explorar a informação obtida das experiências de carbono marcado, foi desenvolvida uma ferramenta que permite a integração de dados de fluxómica, tal como distribuição de marcação de 13C, com modelos enriquecidos com mapeamentos de transição de átomos de carbono. Os algoritmos permitem inferir a distribuição de marcação para fragmentos/ metabolitos, construindo expressões para os rácios de fluxos relevantes. Estes podem ser utilizados para gerar restrições de rácios de fluxo para serem adicionadas à métodos de análise de fluxos. Esta ferramenta é genérica e não requer qualquer assunção sobre rede ou reversibilidades das reações. Estes algoritmos foram implementados no MiNeRAl, uma aplicação informática para calcular rácios de fluxos metabólicos para qualquer fragmentação utilizada em dados de GC-MS. Ambas as ferramentas podem ser então combinadas para a execução de análise de fluxos metabólicos baseada em 13C., Fundação para a Ciência e a Tecnologia (FCT) SFRH/BD/66201/2009.

The determination of nutritional requirements of pathogenic organisms is of great significance for understanding host-pathogen interactions. Despite the knowledge obtained so far concerning amino acid requirements in H. pylori, it is still unclear which are the metabolic pathways used for biosynthesis and catabolism. Thus, information on the carbon flow in this organism is required. Glutamate is a very important metabolite in bacterial metabolism that can be used as a carbon and nitrogen source. 13C flux analysis has been largely applied to characterize phenotypes by quantifying in vivo the carbon fluxes. One of the most important applications of this approach is the identification of active pathways in less-studied organisms. Thus, in order to clarify the metabolic pathways used by H. pylori 26695, 13C labeling experiments with 13C-glutamate were conducted and labeled amino acids in biomass hydrolysates were analyzed by GC-MS. The obtained results confirmed L-glutamate as a potential sole and effective carbon source for H. pylori. Overall, all non-essential amino acids, except proline, presented a 13C labeling pattern. We hypothesized that L-proline is produced from L-arginine, while L-alanine is probably produced from pyruvate by alanine dehydrogenase. Additionally, the full usage of complete TCA cycle, under the conditions used, was also demonstrated.

Actinobacillus succinogenes, a gram-negative bacterium, is one the most promising natural producers of succinate. This chemical has been well established as a bio-based chemical platform to produce bulk chemicals (e.g. 1,4-butanediol) and other biomaterials, but the costs associated with the bioproduction of succinate are still discouraging. One of the reasons is that succinate is often produced together with other fermentative products like formate, acetate and ethanol under anaerobic conditions, which reduces the cost-effectiveness of this fermentative bioprocess1. Systems biology approaches may be required to provide valuable insights into the metabolism underlying the homofermentative production of succinate and contribute to new developments in the bio-based production of succinate2. A genome-scale model of the metabolism of A. succinogenes, accounting for 500 genes, 930 reactions, and 690 metabolites, was reconstructed and validated against published experimental data. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the metabolic network. A thorough model-driven analysis was performed to explore the metabolism under hetero- and homo-fermentative conditions. The model provided valuable insights into the metabolism of this bacterium and has the potential to predict the phenotypes of perturbed metabolic networks that promote the homo-fermentative production of succinate., This work was supported by BRIGIT (FP7 project) and PEM co-funded by the ERDF under the Operational Programme for Competitiveness Factors (COMPETE).

The measurement of fluxes and the understanding of their control are at the core of Metabolic Engineering (ME). In this context, this work presents two integrated open- source software tools that allow to perform tasks of metabolic flux analysis (MFA). Both are platform independent, written in Java, and interact with the OptFlux framework [1], which also facilitates their communication (Figure 1). OptFlux is a modular open-source software that incorporates tools for strain optimization, i.e., the identification of ME targets. It also provides tools to use stoichiometric metabolic models for phenotype simulation of both wild-type and mutant organisms, using methods such as the well known Flux Balance Analysis (FBA). Graphical user interfaces are made available for every operation and to check the results that are obtained. Moreover, a network visualization system is offered, where simulation results can be added to overlap the network graph. The developed tools exploit OptFluxâ??s capabilities in terms of model interaction, simulation methods and visualization features. The first proposed software, named MetabolIc NEtwork Ratio AnaLysis (MiNeRAl) (Figure 1, bottom), aims at analyzing labeling experiments to infer flux constraints that for stoichiometric models. From a set of measurements of a 13C-labelling experiment, mass isotopomer distribution vectors (MDV) are calculated. If aminoacids are measured, the measured fragments, coupled with a carbon transition map provided by the user, are used to determine their precursors, and the corresponding MDVs are calculated. Based on the set of MDVs, the software uses the carbon transitions to determine the flux ratios that produce a given metabolite through the different pathways. These ratios are probabilistic equations that translate how the 13C-labeling pattern is distributed throughout the metabolic network [2]. Since the calculation of the flux ratios is independent of the flux distribution, this software can be used independently of other flux calculation processes, and the ratios can be further exploited to reduce the degrees of freedom of systems obtained in other MFA approaches [3,4]. The main differentiating characteristics of this tool are, besides being usr-friendly, the fact that it is generic for any type of metabolite fragmentation originating from GC-MS techniques and metabolic network topology. Furthermore, the software is also able to investigate what flux ratio constraints are possible to be inferred for a certain experiment beforehand. On the other hand, the second software application here described, jMFA (Figure 1, top), is focused on using different types of experimental flux data to constrain metabolic models and improve their predictions with a variety of tools. It allows users to define constraints associated with measured fluxes and/ or flux ratios, together with environmental conditions (e.g. media) and reaction/ gene knockouts. The application identifies the set of applicable methods based on the constraints defined from user inputs, allowing to select the desired approach, encompassing algebraic and constraint- based simulation methods (such as Flux Balance Analysis and its variants). Anytime a set of constraints is selected, the software calculates the degrees of freedom of the configured system, and updates the admissible methods depending on whether the system is underdetermined, determined or overdetermined, as shown in Figure 1. A method to perform robustness analysis is also implemented. The integration of jMFA within the OptFlux framework allows the use of different model formats and the integration with complementary methods for phenotype simulation and visualization of the results. Moreover, the flux ratio constraints can be obtained from previous calculations in MiNeRAl, or manually defined by the user. The first option provides a straightforward way to integrate both applications in a ME workflow.

16th IUFoST World Congress of Food Science and Technology: Addressing Global Food Security and Wellness through Food Science and Technology, Propolis is a resinous biomass produced by honeybees from exudates of local flora. It has been used since ancient times in folk medicine and in recent years has been added to foods and beverages to improve health and prevent diseases. The chemical composition of propolis is highly variable and depends on the climate, season, specie of bee, and mainly the local flora visited by bees to collect resin. In order to identify groups of chemical similarity among samples (n=20 autumn, n=16 winter, n=19 spring, n=17 summer) of propolis produced in Santa Catarina (SC) state (southern Brazil - 2010), lyophilized ethanolic extracts (200 mg/ml, EtOH 70%, v/v) were solubilized in MeOD3 (700l) and analyzed by NMR spectroscopy. One-dimensional 1HNMR spectra were acquired at a magnetic field strength of 500,13/125,03 MHz using a Varian Inova 500 MHz equipment and standard conditions of data acquisition. The 1H-NMR peak list data set was processed under MetaboAnalyst 2.0. suite, computing the resonances at 0.80- 12ppm spectral window. Principal Components Analysis (PCA) score scatter plots (PC1 88.2% x PC2 2.2%) clearly demonstrated samples discriminated mainly according to the season of production. These results suggest that not only geographical origin is important for the classification of propolis, but the seasonal effects as well. Since seasons directly influence the flora available from where bees collect resin, the propolis chemical profile can be significantly modified over the seasons even from a same geographical origin., info:eu-repo/semantics/publishedVersion

The determination of fluxes is an important parameter to define the extent to which enzymes participate in metabolic networks and to simulate organism behaviour to various types of genetic and environmental perturbations. Metabolic flux analysis is the ultimate measurement of metabolic pathway activity during steady-state conditions, operating as a valuable tool in the detection of physiological alterations and to describe cell phenotypes. Since intracellular metabolic fluxes cannot be directly measured, available methodologies often estimate fluxes by applying mass balances around intracellular metabolites and from experimentally determined nutrient uptake and product secretion rates. 13C-isotopic tracing is a technique that can also be used to measure fluxes. When cells are grown on a 13C-labeled carbon substrate, the 13C-labelling pattern in their proteinogenic amino acids can be determined through nuclear magnetic resonance or mass spectrometry (e.g.; GC-MS). In this work we adapted a sensitive and high-throughput GC-MS method for measurement of metabolic flux distribution based on methylchlorofomate (MCF) derivatization to convert the amino acids into volatile compounds. Using the 13C-labelling distribution of these compounds we determine the metabolic flux ratios in the central carbon metabolism. Great part of this work was the development of a flexible software to calculate flux ratios and estimate flux distribution in different metabolic models. Although our case studies are based on GC-MS coupled to MCF derivatization, this software is generic for different mass spectrometric methods.

Bringing biologists and text miners closer together is a major aim towards the general usage of literature mining tools. Our contribution to this aim is an end-user tool for the extraction of problem-specific biologically relevant relations. Development efforts are being focused on easy-to-use text mining workflows including commonly available entity recognisers and syntactic processors, and the construction of a userfriendly environment that enables problemspecific tailoring by biologists., Fundação para a Ciência e a Tecnologia (FCT), Systems Biology as a Driver for Industrial Biotechnology (SYSINBIO)

[Excerpt] Biomedical Text Mining. i.e., the field that deals with the automatic: retrieval and processing of biomedical literature, is perhaps one of today's most promising research fields. The automated processing of free text is not exactly a new computational issue. Text Mining has a long experience in the retrieval and processing of general text. The development of search engines and indexed directories, the compilation of dictionaries and the automatic translation of documents have impelled the development of powerful text processing techniques. Nevertheless, biomedical texts present additional challenges: the terminology does not always follows standard nomenclatures; new terms are constantly emerging; and term homonymy and synonymy (including term variants and abbreviations) make it very difficult to accurately identify entities. [...], info:eu-repo/semantics/publishedVersion

La importància històrica i patrimonial que presenta el nucli antic de la vila de Besalú no ha estat mai posada en dubte, ans el contrari. Ara bé, la seva importància com a jaciment arqueològic en potència encara no havia estat del tot demostrada. Si més no, només ens hem de capbussar en la història de les investigacions que s' hi ha realitzat per tal d'observar com 1' arqueologia ha estat —i és— una de les assignatures pendents per conèixer molt més profundament l'evolució històrica de la vila que va ser capital d'un extens comtat.

Dissertação de mestrado em Bioinformática, Understanding the metabolic processes that occur in a cell has been fundamental to rationally design organisms for the production of a desired metabolite. The improvement in biosynthesis of certain metabolites can be supported by tracing the atoms transition in different chemical conversions, and this way tackle which metabolic pathways are more efficient or most promising for manipulation. In this work, a methodology to construct metabolic maps in which the carbon atom transitions are described was implemented. The carbon atom transition map for the central metabolism of Escherichia coli and Actinobacillus succinogenes were constructed. MetaCyc and KEGG databases were explored to obtain the metabolic information necessary to construct these maps and provided support for validation at some level., Compreender os processos metabólicos que ocorrem numa célula tem sido essencial para o desenho de estirpes capazes de sintetizar produtos de elevado interesse. A síntese de um determinado metabolito pode ser avaliada pela transição de átomos ao longo das diversas conversões químicas numa ou mais vias metabólicas, de modo a identificar quais as mais eficientes ou mais promissoras para manipulação. Neste trabalho foi implementada uma metodologia para a construção de mapas de transição dos átomos de carbono, que pode ser usado conjuntamente com modelos metabólicos. Neste caso, foram construídos os mapas de transição de átomos de carbono para o metabolismo central da Escherichia coli e da Actinobacillus succinogenes. As bases de dados MetaCyc e KEGG foram exploradas para obter as informações metabólicas necessárias à construção destes mapas.