Natural antioxidants extraction and their incorporation into model pharmaceutical systems

Dissertation to obtain a Master Degree in Biotechnology

XDense: A Dense Grid Sensor Network for Distributed Feature Extraction

XXXIII Simpósio Brasileiro de Redes de Computadores e Sistemas Distribuídos (SBRC 2015). 15 to 19, May, 2015, III Workshop de Comunicação em Sistemas Embarcados Críticos. Vitória, Brasil.

Generalized Extraction of Real-Time Parameters for Homogeneous Synchronous Dataflow Graphs

23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2015). 4 to 6, Mar, 2015. Turku, Finland.

XDense: A Dense Grid Sensor Network for Distributed Feature Extraction

XXXIII Simpósio Brasileiro de Redes de Computadores e Sistemas Distribuídos (SBRC 2015), III Workshop de Comunicação em Sistemas Embarcados Críticos. Vitória, Brasil.

QuEChERS: a sample preparation for extraction of carbaryl from rat feces

Carbamate compounds are an important group of cholinesterase inhibitors. There is a need for creating awareness regarding the risks of the inadequate carbamate use in the residential areas due to potential adverse human effects. Carbaryl is a commonly used pesticide worldwide. A simple, fast, and high throughput method was developed employing liquid chromatography with fluorescence detector to determine carbaryl residues in rat feces. The extraction was performed by using a rapid, easy, cheap, effective, reliable, and safe (QuEChERS) method, using acetonitrile as the extracting solvent. The parameters for the performance of the extraction method were optimized, such as ratio of mass of sample per volume of extraction solvent, QuEChERS content, and cleanup columns. Linear response was obtained for all calibration curves (solven and matrix-matched) over the established concentration range (5 500 mg/L) with a correlation coefficients higher than 0.999. The achieved recovery was 97.9% with relative standard deviation values of 1.1% (n D 4) at 167 mg/kg fortified concentration level and the limits of detection and quantification were 27.7 and 92.3 mg/kg respectively.

New approach for vitamin E extraction in rainbow trout flesh: Application in fish fed commercial and red seaweed-supplemented diets

A vitamin E extraction method for rainbow trout flesh was optimized, validated, and applied in fish fed commercial and Gracilaria vermiculophylla-supplemented diets. Five extraction methods were compared. Vitamers were analyzed by HPLC/DAD/fluorescence. A solid-liquid extraction with n-hexane, which showed the best performance, was optimized and validated. Among the eight vitamers, only α- and γ-tocopherol were detected in muscle samples. The final method showed good linearity (>0.999), intra- (<3.1%) and inter-day precision (<2.6%), and recoveries (>96%). Detection and quantification limits were 39.9 and 121.0 ng/g of muscle, for α-tocopherol, and 111.4 ng/g and 337.6 ng/g, for γ-tocopherol, respectively. Compared to the control group, the dietary inclusion of 5% G. vermiculophylla resulted in a slight reduction of lipids in muscle and, consequently, of α- and γ-tocopherol. Nevertheless, vitamin E profile in lipids was maintained. In general, the results may be explained by the lower vitamin E level in seaweed-containing diet. Practical Applications: Based on the validation results and the low solvent consumption, the developed method can be used to analyze vitamin E in rainbow trout. The results of this work are also a valuable information source for fish feed industries and aquaculture producers, which can focus on improving seaweed inclusion in feeds as a source of vitamin E in fish muscle and, therefore, take full advantage of all bioactive components with an important role in fish health and flesh quality.

Protocol for DNA extraction of Cryptosporidium spp. oocysts in fecal samples

Molecular characterization of Cryptosporidium spp.oocysts in clinical samples is useful for public health since it allows the study of sources of contamination as well as the transmission in different geographical regions. Although widely used in developed countries, in Brazil it is restricted to academic studies, mostly using commercial kits for the extraction of genomic DNA, or in collaboration with external reference centers, rendering the method expensive and limited. The study proposes the application of the modifications recently introduced in the method improving feasibility with lower cost. This method was efficient for clinical samples preserved at -20 °C for up to six years and the low number of oocysts may be overcomed by repetitions of extraction.

Feature Extraction in Densely Sensed Environments: Extensions to Multiple Broadcast Domains

The vision of the Internet of Things (IoT) includes large and dense deployment of interconnected smart sensing and monitoring devices. This vast deployment necessitates collection and processing of large volume of measurement data. However, collecting all the measured data from individual devices on such a scale may be impractical and time consuming. Moreover, processing these measurements requires complex algorithms to extract useful information. Thus, it becomes imperative to devise distributed information processing mechanisms that identify application-specific features in a timely manner and with a low overhead. In this article, we present a feature extraction mechanism for dense networks that takes advantage of dominance-based medium access control (MAC) protocols to (i) efficiently obtain global extrema of the sensed quantities, (ii) extract local extrema, and (iii) detect the boundaries of events, by using simple transforms that nodes employ on their local data. We extend our results for a large dense network with multiple broadcast domains (MBD). We discuss and compare two approaches for addressing the challenges with MBD and we show through extensive evaluations that our proposed distributed MBD approach is fast and efficient at retrieving the most valuable measurements, independent of the number sensor nodes in the network.

Evaluation of three different DNA extraction methods from blood samples collected in dried filter paper in Plasmodium subpatent infections from the Amazon region in Brazil

Asymptomatic Plasmodium infection is a new challenge for public health in the American region. The polymerase chain reaction (PCR) is the best method for diagnosing subpatent parasitemias. In endemic areas, blood collection is hampered by geographical distances and deficient transport and storage conditions of the samples. Because DNA extraction from blood collected on filter paper is an efficient method for molecular studies in high parasitemic individuals, we investigated whether the technique could be an alternative for Plasmodium diagnosis among asymptomatic and pauciparasitemic subjects. In this report we compared three different methods (Chelex®-saponin, methanol and TRIS-EDTA) of DNA extraction from blood collected on filter paper from asymptomatic Plasmodium-infected individuals. Polymerase chain reaction assays for detection of Plasmodium species showed the best results when the Chelex®-saponin method was used. Even though the sensitivity of detection was approximately 66% and 31% for P. falciparum and P. vivax, respectively, this method did not show the effectiveness in DNA extraction required for molecular diagnosis of Plasmodium. The development of better methods for extracting DNA from blood collected on filter paper is important for the diagnosis of subpatent malarial infections in remote areas and would contribute to establishing the epidemiology of this form of infection.

EVALUATION OF FOUR DIFFERENT DNA EXTRACTION METHODS IN COAGULASE-NEGATIVE STAPHYLOCOCCI CLINICAL ISOLATES

Currently there are several methods to extract bacterial DNA based on different principles. However, the amount and the quality of the DNA obtained by each one of those methods is highly variable and microorganism dependent, as illustrated by coagulase-negative staphylococci (CoNS) which have a thick cell wall that is difficult to lyse. This study was designed to compare the quality and the amount of CoNS DNA, extracted by four different techniques: two in-house protocols and two commercial kits. DNA amount and quality determination was performed through spectrophotometry. The extracted DNA was also analyzed using agarose gel electrophoresis and by PCR. 267 isolates of CoNS were used in this study. The column method and thermal lyses showed better results with regard to DNA quality (mean ratio of A260/280 = 1.95) and average concentration of DNA (), respectively. All four methods tested provided appropriate DNA for PCR amplification, but with different yields. DNA quality is important since it allows the application of a large number of molecular biology techniques, and also it's storage for a longer period of time. In this sense the extraction method based on an extraction column presented the best results for CoNS.

Algorithms for information extraction and signal annotation on long-term biosignals using clustering techniques

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

User Profiling and Knowledge Extraction For Tourism

O sector do turismo é uma área francamente em crescimento em Portugal e que tem desenvolvido a sua divulgação e estratégia de marketing. Contudo, apenas se prende com indicadores de desempenho e de oferta instalada (número de quartos, hotéis, voos, estadias), deixando os indicadores estatísticos em segundo plano. De acordo com o “ Travel & tourism Competitiveness Report 2013”, do World Economic Forum, classifica Portugal em 72º lugar no que respeita à qualidade e cobertura da informação estatística, disponível para o sector do Turismo. Refira-se que Espanha ocupa o 3º lugar. Uma estratégia de mercado, sem base analítica, que sustente um quadro de orientações específico e objetivo, com relevante conhecimento dos mercados alvo, dificilmente é compreensível ou até mesmo materializável. A implementação de uma estrutura de Business Intelligence que permita a realização de um levantamento e tratamento de dados que possibilite relacionar e sustentar os resultados obtidos no sector do turismo revela-se fundamental e crucial, para que sejam criadas estratégias de mercado. Essas estratégias são realizadas a partir da informação dos turistas que nos visitam, e dos potenciais turistas, para que possam ser cativados no futuro. A análise das características e dos padrões comportamentais dos turistas permite definir perfis distintos e assim detetar as tendências de mercado, de forma a promover a oferta dos produtos e serviços mais adequados. O conhecimento obtido permite, por um lado criar e disponibilizar os produtos mais atrativos para oferecer aos turistas e por outro informá-los, de uma forma direcionada, da existência desses produtos. Assim, a associação de uma recomendação personalizada que, com base no conhecimento de perfis do turista proceda ao aconselhamento dos melhores produtos, revela-se como uma ferramenta essencial na captação e expansão de mercado.

Valorization of pumpkin residue by supercritical extraction of added-value compounds

Dissertação para a obtenção do Grau de Mestre em Engenharia Química e Bioquímica

Aqueous biphasic system based on cholinium ionic liquids: extraction of biologically active phenolic acids

Phenolic acids are aromatic secondary plant metabolites, widely spread throughout the plant kingdom. Due to their biological and pharmacological properties, they have been playing an important role in phytotherapy and consequently techniques for their separation and purification are in need. This thesis aims at exploring new sustainable separation processes based on ionic liquids (ILs) in the extraction of biologically active phenolic acids. For that purpose, three phenolic acids with similar chemical structures were selected: cinnamic acid, p-coumaric acid and caffeic acid. In the last years, it has been shown that ionic liquids-based aqueous biphasic systems (ABSs) are valid alternatives for the extraction, recovery and purification of biomolecules when compared to conventional ABS or extractions carried out with organic solvents. In particular, cholinium-based ILs represent a clear step towards a greener chemistry, while providing means for the implementation of efficient techniques for the separation and purification of biomolecules. In this work, ABSs were implemented using cholinium carboxylate ILs using either high charge density inorganic salt (K3PO4) or polyethylene glycol (PEG) to promote the phase separation of aqueous solutions containing three different phenolic acids. These systems allow for the evaluation of effect of chemical structure of the anion on the extraction efficiency. Only one imidazolium-based IL was used in order to establish the effect of the cation chemical structure. The selective extraction of one single acid was also researched. Overall, it was observed that phenolic acids display very complex behaviours in aqueous solutions, from dimerization to polymerization and also hetero-association are quite frequent phenomena, depending on the pH conditions. These phenomena greatly hinder the correct quantification of these acids in solution.

Automatic extraction of concepts from texts and applications

The extraction of relevant terms from texts is an extensively researched task in Text- Mining. Relevant terms have been applied in areas such as Information Retrieval or document clustering and classification. However, relevance has a rather fuzzy nature since the classification of some terms as relevant or not relevant is not consensual. For instance, while words such as "president" and "republic" are generally considered relevant by human evaluators, and words like "the" and "or" are not, terms such as "read" and "finish" gather no consensus about their semantic and informativeness. Concepts, on the other hand, have a less fuzzy nature. Therefore, instead of deciding on the relevance of a term during the extraction phase, as most extractors do, I propose to first extract, from texts, what I have called generic concepts (all concepts) and postpone the decision about relevance for downstream applications, accordingly to their needs. For instance, a keyword extractor may assume that the most relevant keywords are the most frequent concepts on the documents. Moreover, most statistical extractors are incapable of extracting single-word and multi-word expressions using the same methodology. These factors led to the development of the ConceptExtractor, a statistical and language-independent methodology which is explained in Part I of this thesis. In Part II, I will show that the automatic extraction of concepts has great applicability. For instance, for the extraction of keywords from documents, using the Tf-Idf metric only on concepts yields better results than using Tf-Idf without concepts, specially for multi-words. In addition, since concepts can be semantically related to other concepts, this allows us to build implicit document descriptors. These applications led to published work. Finally, I will present some work that, although not published yet, is briefly discussed in this document.