Role of surfactants in filtration and fouling of colloidal silica

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities

Bioinspired polyethersulfone-based hollow fiber membranes as the scaffolds in renal assist device for protein-bound toxins removal from blood

Dissertation for obtaining the Master degree in Membrane Engineering

Spectroscopic characterization of natural dyes by their non-invasive identification on pre-Columbian codices: the Maya yellow

Mesoamerican cultures had a strong tradition of written and pictorial manuscripts, called the codices. In studies already performed it was found the use of Maya Blue, made from a mixture of indigo and a clay called palygorskite, forming an incredibly stable material where the dye is trapped inside the nanotubes of the clay, after heating. However, a bigger challenge lies in the study of the yellows used, for these civilizations might have used this clay-dye mixture to produce their yellow colorants. As a first step, it was possible to provide identification, by non-invasive methods, of two colorants (a flavonoid and a carotenoid). While the flavonoid absorbed between 368-379 nm, the carotenoid would absorb around 455 nm. A temperature study also conducted allowed to set 140ºC as the desirable temperature to heat the samples without degrading them. FT-IR, conventional Raman and SERS allowed us to understand the existence of a reaction between the dyes and the clays (palygorskite and kaolinite), however it is difficult to understand it in a molecular point of view. As a second step, five species of Mexican dyes were selected on the basis of historical sources. The Maya yellow samples were produced adapting the recipe proposed by Reyes-Valerio, supporting the yellow dyes extracted from the dried plants on the clays, with addition of water, and then heated at 140ºC. It was found that the addition of water in palygorskite would increase the pH, hence deprotonating the molecules having a clear negative effect in the color. A second recipe was developed, without the addition of water; however, it was found that the use of water based binders would still alter the color of the samples with palygorskite. In this case, kaolinite without heating yield better results as a Maya yellow hybrid. It was found that the Maya chemistry might not have been the same for all the colors. The Mesoamericans might have found that different dyes could work better to their desires if matched with different clays. It was noticeable that for a clear distinction between flavonoids and carotenoids the reflectance and emission studies suffice, but when clay is added, Raman techniques will perform better. For this reason, conventional Raman and SERS were employed in order to create a database for the Mesoamerican dyestuffs for a future identification.

Aquaponics and its potential aquaculture wastewater treatment and human urine treatment

The main objective of this thesis is to study the developing fields of aquaponics and its potential for aquaculture wastewater treatment and human urine treatment. Aquaponics is a food production system which combines fish farming (aquaculture) with soilless crop farming (hydroponics). In this thesis the concept of aquaponics and the underlying processes are explained. Research on aquaculture wastewater and human urine wastewater is reviewed and its potential application with aquaponic systems is studied. An overview of the different types of aquaponic systems and current research on the field is also presented. A case study was conducted in a farm in Askeröd, Sweden, which involved building two aquaponic systems (System 1 and System 2) and a human urine-based aquaponic system (System 3), with different degrees of component complexity and sizes. The design, building and monitoring of System 1, System 2 and System 3 was documented and described in detail. Four day experiments were conducted which tested the evolution in concentration of Total Ammonia Nitrogen (NH4+/NH3), Nitrite (NO2-), Nitrate (NO3-), Phosphate (PO43-), and Dissolved Oxygen (O2) after an initial nutrient input. The goal was to assess the concentrations of these parameters after four days and compare them with relevant literature examples in the aquaculture industry and in source-separated urine research. Neither of the two aquaponic systems (System 1 and System 2) displayed all of the parameter concentrations in the last day of testing below reference values found in literature. The best performing of the aquaponic systems was the more complex system (System 2) combining the hydroponic Nutrient Film Technique with a Deep Water Culture component, with a Total Ammonia Nitrogen concentration of 0,20 mg/L, a Nitrite concentration of 0,05 mg/L, a Nitrate concentration of 1,00-5,00 mg/L, a Phosphate concentration of <0,02 mg/L and a Dissolved Oxygen concentration of 8,00 mg/L. The human urine-based aquaponic system (System 3) underperformed in achieving the reference concentration values in literature for most parameters. The removal percentage between the higher recorded values after the input addition and the final day of testing was calculated for two literature examples of separated urine treatment and System 3. The system had a removal percentage of 75% for Total Ammonia Nitrogen, 98% for Nitrite, 25% for Nitrate and 50% for Phosphate. These percentages still underperformed literature examples in most of the tested parameters. The results gathered allowed to conclude that while aquaculture wastewater treatment and human urine treatment is possible with aquaponics systems, overall these did not perform as well as some examples found in recirculating aquaculture systems and source-separated urine treatment literature. However, better measuring techniques, longer testing periods and more research is recommended in this field in order to draw an improved representative conclusion.

Hole cleaning performance monitoring during the drilling of directional wells

During drilling operation, cuttings are produced downhole and must be removed to avoid issues which can lead to Non Productive Time (NPT). Most of stuck pipe and then Bottom-Hole Assembly (BHA) lost events are hole cleaned related. There are many parameters which help determine hole cleaning conditions, but a proper selection of the key parameters will facilitate monitoring hole cleaning conditions and interventions. The aim of Hole Cleaning Monitoring is to keep track of borehole conditions including hole cleaning efficiency and wellbore stability issues during drilling operations. Adequate hole cleaning is the one of the main concerns in the underbalanced drilling operations especially for directional and horizontal wells. This dissertation addresses some hole cleaning fundamentals which will act as the basis for recommendation practice during drilling operations. Understand how parameters such as Flowrate, Rotation per Minute (RPM), Rate of Penetration (ROP) and Mud Weight are useful to improve the hole cleaning performance and how Equivalent Circulate Density (ECD), Torque & Drag (T&D) and Cuttings Volumes coming from downhole help to indicate how clean and stable the well is. For case study, hole cleaning performance or cuttings volume removal monitoring, will be based on real-time measurements of the cuttings volume removal from downhole at certain time, taking into account Flowrate, RPM, ROP and Drilling fluid or Mud properties, and then will be plotted and compared to the volume being drilled expected. ECD monitoring will dictate hole stability conditions and T&D and Cuttings Volume coming from downhole monitoring will dictate how clean the well is. T&D Modeling Software provide theoretical calculated T&D trends which will be plotted and compared to the real-time measurements. It will use the measured hookloads to perform a back-calculation of friction factors along the wellbore.

Interactive spatial decision support for sustainable agroforestry management: a case study in East Kalimantan, Indonesia

Forest managers, stakeholders and investors want to be able to evaluate economic, environmental and social benefits in order to improve the outcomes of their decisions and enhance sustainable forest management. This research developed a spatial decision support system that provides: (1) an approach to identify the most beneficial locations for agroforestry projects based on the biophysical properties and evaluate its economic, social and environmental impact; (2) a tool to inform prospective investors and stakeholders of the potential and opportunities for integrated agroforestry management; (3) a simulation environment that enables evaluation via a dashboard with the opportunity to perform interactive sensitivity analysis for key parameters of the project; (4) a 3D interactive geographic visualization of the economic, environmental and social outcomes, which facilitate understanding and eases planning. Although the tool and methodology presented are generic, a case study was performed in East Kalimantan, Indonesia. For the whole study area, it was simulated the most suitable location for three different plantation schemes: monoculture of timber, a specific recipe (cassava, banana and sugar palm) and different recipes per geographic unit. The results indicate that a mixed cropping plantation scheme, with different recipes applied to the most suitable location returns higher economic, environmental and social benefits.

Resilience of logistic service providers facing a port strike: a case study

The purpose of this thesis is to study the impact of a port strike on companies that perform as logistic service providers in a supply chain (SC), here denominated 3PL (third-party logistic providers). These companies are highly dependent on ports to perform their activity, since they provide international services. Consequently, a disruption in a port can seriously impair their business. A stevedores’ strike is one of the possible disruptions that can affect ports. This study aims to analyze the negative effects caused by this disruption, and what strategies 3PLs may implement in order to keep their performance levels stable and have a quick recovery time. Within this objective, the first step will be to establish a theoretical context about the maritime port’s sector and 3PLs in a SC context, to then expand the concept of a resilient SC, and finally to develop a theoretical framework in order to better contextualize the case study. Subsequently, the impact of a port strike will be quantified by using a case study comprising three companies, covering the areas of land and sea distribution and port operations. Information from primary sources was assembled in two phases: first via e-mail and, in a second phase, through a personal interview. The information from secondary sources was obtained through television news, internet and conferences, enabling its cross-analysis. Finally, by analyzing the collected data, it will be possible to draw conclusions about the measures carried out by each company to minimize the negative effects of the strike, thus contributing to a more resilient SC. As a conclusion, a stevedores’ strike will create a snow-ball of negative effects in the SC, degrading all relevant KPIs (key performance indicators) of the 3PLs under study. No mitigation and contingency strategies available proved really effective to reduce the negative effects of a port strike disruption.

Immunohistochemistry detection of putative miR-200c and miR-203 targets in breast cancer patients

Part of this thesis will be published in the following: Gomes, B.C., Santos, B. 2015. Methods for studying microRNAs expression and their targets in formalin-fixed, paraffin-embedded (FFPE) breast cancer tissues. In Methods in Molecular Biology: Cancer Drug Resistance (Rueff, J. & Rodrigues, A.S. eds), Springer Protocols.

Frequency of Blastocystis hominis and other intestinal parasites in stool samples examined at the Parasitology Laboratory of the School of Pharmaceutical Sciences at the São Paulo State University, Araraquara

Blastocystis homins is a protozoan that causes an intestinal infection known as human blastocystosis. This infection is diagnosed by means of parasitological examination of stools and by permanent staining techniques. The present study was developed to evaluate the frequency of Blastocystis hominis infection among inhabitants of the Araraquara region, State of São Paulo, and to compare different methods for investigating this protozoan in feces samples. Evaluations on 503 stool samples were performed by means of direct fresh examination and using the techniques of Faust et al., Lutz and Rugai et al. In addition, the iron hematoxylin, trichrome and modified Kinyoun staining techniques were used. Out of the 503 samples examined, 174 (34.6%) were found to be positive for the presence of intestinal parasites. The most frequent protozoa and helminths were Entamoeba coli (14.6%) and Strongyloides stercoralis (6.7%), respectively. Blastocystis hominis was present in 23 (4.6%) fecal samples, with a predominately pasty consistency and without characterizing a condition of diarrhea. Despite the low frequency of Blastocystis hominis found in the Araraquara region, compared with other regions of Brazil, it is important to perform laboratory diagnostic tests for this protozoan. Its finding in fecal material is indicative of food and drinking water contamination. Since the transmission route for this parasite is accepted to be oral-fecal, this implies that the population needs guidance regarding hygiene and basic sanitation measures as a means for controlling health problems caused by enteroparasites.

Follow the red road of triheme cytochromes in Geobacter sulfurreducens

The bacterium Geobacter sulfurreducens (Gs) is capable of oxidizing a large variety of compounds relaying electrons out of the cytoplasm and across the membrane in a process designated as extracellular electron transfer. The Gs genome was fully sequenced and a family composed by five periplasmic triheme cytochromes c7 (designated PpcA-E) was identified. These cytochromes play an important role in the reduction of extracellular acceptors. They contain approximately 70 amino acids, three heme groups with bis-histidinyl axial coordination, and share between 57 and 77% sequence identity. The triheme cytochrome PpcA is highly abundant in Gs and is most likely the reservoir of electrons destined for outer surface. In addition to its role in electron transfer pathways this protein can perform e-/H+ energy transduction, a process that is disrupted when the strictly conserved aromatic residue phenylalanine 15 is replaced by a leucine (PpcAF15L). This Thesis focuses on the expression, purification and characterization of these proteins using Nuclear Magnetic Resonance and ultraviolet-visible spectroscopy. The orientations of the heme axial histidine ring planes and the orientation of the heme magnetic axis were determined for each Gs triheme cytochrome. The comparison of the orientations obtained in solution with the crystal structures available showed significant differences. The results obtained provide the paramagnetic constraints to include in the future refinement of the solution structure in the oxidized state. In this work was also determined the solution structure and the pH-dependent conformational changes of the PpcAF15L allowing infer the structural origin for e-/H+ energy transduction mechanism as shown by PpcA. Finally, the backbone and side chain NH signals of PpcA were used to map interactions between this protein and the putative redox partner 9,10-anthraquinone-2,6-disulfonate (AQDS). In this work a molecular interaction was identified for the first time between PpcA and AQDS, constituting the first step toward the rationalization of the Gs respiratory chain.

Reactive hybrid knowledge bases

Hybrid knowledge bases are knowledge bases that combine ontologies with non-monotonic rules, allowing to join the best of both open world ontologies and close world rules. Ontologies shape a good mechanism to share knowledge on theWeb that can be understood by both humans and machines, on the other hand rules can be used, e.g., to encode legal laws or to do a mapping between sources of information. Taking into account the dynamics present today on the Web, it is important for these hybrid knowledge bases to capture all these dynamics and thus adapt themselves. To achieve that, it is necessary to create mechanisms capable of monitoring the information flow present on theWeb. Up to today, there are no such mechanisms that allow for monitoring events and performing modifications of hybrid knowledge bases autonomously. The goal of this thesis is then to create a system that combine these hybrid knowledge bases with reactive rules, aiming to monitor events and perform actions over a knowledge base. To achieve this goal, a reactive system for the SemanticWeb is be developed in a logic-programming based approach accompanied with a language for heterogeneous rule base evolution having as its basis RIF Production Rule Dialect, which is a standard for exchanging rules over theWeb.

Planning and verification of multipath routing protocols

Conventionally the problem of the best path in a network refers to the shortest path problem. However, for the vast majority of networks present nowadays this solution has some limitations which directly affect their proper functioning, as well as an inefficient use of their potentialities. Problems at the level of large networks where graphs of high complexity are commonly present as well as the appearing of new services and their respective requirements, are intrinsically related to the inability of this solution. In order to overcome the needs present in these networks, a new approach to the problem of the best path must be explored. One solution that has aroused more interest in the scientific community considers the use of multiple paths between two network nodes, where they can all now be considered as the best path between those nodes. Therefore, the routing will be discontinued only by minimizing one metric, where only one path between nodes is chosen, and shall be made by the selection of one of many paths, thereby allowing the use of a greater diversity of the present paths (obviously, if the network consents). The establishment of multi-path routing in a given network has several advantages for its operation. Its use may well improve the distribution of network traffic, improve recovery time to failure, or it can still offer a greater control of the network by its administrator. These factors still have greater relevance when networks have large dimensions, as well as when their constitution is of high complexity, such as the Internet, where multiple networks managed by different entities are interconnected. A large part of the growing need to use multipath protocols is associated to the routing made based on policies. Therefore, paths with different characteristics can be considered with equal level of preference, and thus be part of the solution for the best way problem. To perform multi-path routing using protocols based only on the destination address has some limitations but it is possible. Concepts of graph theory of algebraic structures can be used to describe how the routes are calculated and classified, enabling to model the routing problem. This thesis studies and analyzes multi-path routing protocols from the known literature and derives a new algebraic condition which allows the correct operation of these protocols without any network restriction. It also develops a range of software tools that allows the planning and the respective verification/validation of new protocols models according to the study made.

Botnet cluster identification

Botnets are a group of computers infected with a specific sub-set of a malware family and controlled by one individual, called botmaster. This kind of networks are used not only, but also for virtual extorsion, spam campaigns and identity theft. They implement different types of evasion techniques that make it harder for one to group and detect botnet traffic. This thesis introduces one methodology, called CONDENSER, that outputs clusters through a self-organizing map and that identify domain names generated by an unknown pseudo-random seed that is known by the botnet herder(s). Aditionally DNS Crawler is proposed, this system saves historic DNS data for fast-flux and double fastflux detection, and is used to identify live C&Cs IPs used by real botnets. A program, called CHEWER, was developed to automate the calculation of the SVM parameters and features that better perform against the available domain names associated with DGAs. CONDENSER and DNS Crawler were developed with scalability in mind so the detection of fast-flux and double fast-flux networks become faster. We used a SVM for the DGA classififer, selecting a total of 11 attributes and achieving a Precision of 77,9% and a F-Measure of 83,2%. The feature selection method identified the 3 most significant attributes of the total set of attributes. For clustering, a Self-Organizing Map was used on a total of 81 attributes. The conclusions of this thesis were accepted in Botconf through a submited article. Botconf is known conferênce for research, mitigation and discovery of botnets tailled for the industry, where is presented current work and research. This conference is known for having security and anti-virus companies, law enforcement agencies and researchers.

Fisioterapia e ganhos em Saúde numa Unidade de Cuidados Continuados

RESUMO: Atualmente, toda a envolvência do envelhecimento, desencadeada por um aumento crescente do número de pessoas idosas, incapazes de satisfazer as exigências do autocuidado e de viver autonomamente na comunidade, torna relevante o papel da fisioterapia no suporte ao idoso. O objetivo geral deste trabalho é caracterizar a evolução do nível de independência nas atividades da vida diária (AVD’s), dos indivíduos que realizam fisioterapia numa unidade de cuidados continuados integrados (UCCI). Trata-se de uma abordagem quantitativa, observacional, longitudinal e descritiva. A população do estudo incide nos indivíduos admitidos na UCCI do Hospital do Mar (HM). Da presente população é retirada uma amostra por conveniência, num período de quatro meses, de acordo com critérios de inclusão e exclusão. Os instrumentos utilizados para a recolha de informação foram: um inquérito por questionário para o levantamento das características sócio-demográficas, de saúde e hábitos de vida; o Método de Avaliação Biopsicossocial (MAB - Classificação) para a avaliação do nível de independência nas AVD’s; e o Timed Up and Go (TUG) para a avaliação da mobilidade funcional. Os principais resultados mostraram, segundo o MAB - Classificação, diferenças significativas, entre os dois momentos de avaliação (antes da fisioterapia e no momento da alta da fisioterapia), resultando num maior nível de independência funcional nas AVD’s no momento da alta da fisioterapia. Em relação ao TUG, a média da duração do teste diminuiu no momento da alta da fisioterapia, em relação ao momento antes da fisioterapia, traduzindo-se num aumento da mobilidade funcional. Concluindo, conseguiu-se evidenciar que os indivíduos submetidos a tratamentos de fisioterapia numa UCCI, obtêm um nível de independência funcional mais elevada no momento da alta da fisioterapia, do que antes de serem objetos desta intervenção; o mesmo sucedendo, em relação à mobilidade funcional.---------------ABSTRACT: Currently, the issue aging, triggered by an increasing number of elderly people, unable to meet the demands of self-care and live independently in the community, makes relevant the role of physiotherapy in support to the elderly. The aim of this work is to characterize the evolution of the level of independence in activities of daily living (ADLs), of individuals who perform physiotherapy in long term care hospital. This is a quantitative, observational, longitudinal and descriptive approach.The population of the study focuses on individuals admitted in long-term care in Hospital do Mar. Of this population is withdrawn a convenience sample within a period of four months, according to the inclusion and exclusion criteria. The instruments used for collecting data were a questionnaire to survey the socio-demographic, health and lifestyle characteristics; Método de Avaliação Biopsicossocial (MAB - Classificação) to assess the level of independence in activities of daily living (ADLs); and the Timed Up and Go (TUG) to assess functional mobility. The main results showed, according to the MAB - Classificação, significant differences between the two time points (before physiotherapy and at discharge from physiotherapy), resulting in a higher level of functional independence in ADLs at discharge from physiotherapy. Regarding the TUG, the average duration of the test decreased at discharge from physiotherapy, relative to the time before physiotherapy, translating into an increase of functional mobility. In conclusion, we were able to show that individuals undergoing physiotherapy treatments in long-term care hospital, obtaining a higher level of functional independence at discharge from physiotherapy than before objects of this intervention; the same applies with respect to functional mobility.

As imagens do envelhecimento e as práticas idadistas em Cuidados de Saúde Primários: implicações na actividade física dos idosos

RESUMO: O envelhecimento demográfico tem vindo a aumentar em todo o mundo. Porém, constata-se que os últimos anos de vida são, frequentemente, acompanhados de situações de incapacidade que poderiam ter sido prevenidas. Apesar da importância da actividade física na saúde, verifica-se que uma grande proporção de idosos são sedentários, aumentando o risco de incapacidade. Os profissionais de saúde podem ser influenciados por imagens negativas relativas ao envelhecimento. Tal pode conduzir a práticas de discriminação, com repercussão na forma como os idosos se vêem a si próprios e, consequentemente, no seu comportamento na prática de actividade física. Este estudo tem como objectivo analisar o modo como as imagens do envelhecimento e dos idosos, bem como as práticas idadistas percebidas pelos idosos no contacto com profissionais de saúde influenciam a sua prática de actividade física. Realizou-se um estudo qualitativo, com recurso à entrevista semi-estruturada e de associação livre das palavras, sendo entrevistados 18 utentes que recorreram a um Centro de Saúde. Pelos resultados, constatou-se que uma parte considerável dos participantes (n=8) mencionou que a forma como são vistos pelos profissionais de saúde e como estes lidam consigo influencia a sua prática de actividade física. A imagem mais referida como favorecendo esta prática foi o facto de se considerarem pessoas com vontade de viver. Como principal prática favorecedora identificou-se o aconselhamento/educação para a saúde. A imagem mais mencionada como dificultando a actividade física foi a de os idosos serem deprimidos/tristes/aborrecidos e rabugentos/teimosos. As práticas mais identificadas como dificultando a actividade física foram: o desinteresse face aos problemas de saúde; o não encaminhamento para intervenções adequadas às necessidades; a indicação de que o problema de saúde é devido à idade, não o sendo; a postura autoritária em que só o profissional decide a opção terapêutica; e a verbalização de que o utente já tem muita idade para realizar uma actividade. Conclui-se que as imagens negativas do envelhecimento e dos idosos bem como a existência de práticas idadistas por parte dos profissionais de saúde, condicionam de forma negativa a prática de actividade física nos idosos.---------------ABSTRACT: The aging population has been increasing around the world. However, it appears that the last years of life are often accompanied by situations of disability, which could have been prevented. Despite the importance of physical activity on health, it appears that a large proportion of elderly people are sedentary, increasing the risk of disability. Health professionals may be influenced by negative images related to aging and that may lead to discriminatory practices with repercussion in how older people see themselves and thus their behavior as related to physical activity. This study aims to examine how the images concerning aging and older people, as well as ageist practices perceived by older people in contact with health professionals, do influence their physical activity. A qualitative study was conducted using a semi-structured interview and techniques of free word association. Eighteen primary care elderly users were interviewed. A considerable proportion of the sample (n=8) mentioned that the way health professionals see them and deal with them influences their level of physical activity. The image that most favoured this practice was that people are willing to live. Counseling/health education was identified as the main favouring practice. The image which was most often mentioned as hindering physical activity was that of elderly as being depressed, sad or bored, and grumpy or stubborn.The practices most often identified as hindering physical activity were: lack of interest regarding health problems; non-referral to appropriate intervention needs; indicating that the health problem is due to age, not being the case; authoritarian professional attitudes regarding who decides the treatment options; verbalization that the user is already to old to perform an activity. This study concludes that the negative images of aging and older people as well the existence of ageist practices by health professionals negatively affect the practice of physical activity in the elderly.