Osmolality of Elemental and Semi-Elemental Formulas Supplemented with Nonprotein Energy Supplements

Elemental and semi-elemental formulas are used to feed infants with short bowel syndrome, who may not be able to tolerate feeds of more than 310 mOsm kg(-1). The present study aimed to measure the osmolality of elemental and semi-elemental formulas at different concentrations, with and without the addition of nonprotein energy supplements.

Study of membrane emulsification process as a pre-step for the microencapsulation of lipid compounds by spray drying

Dissertation presented to Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa for obtaining the master degree in Membrane Engineering

Investigation of the regulation mechanisms for bioplastics production from industrial residues

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Lime mortars with rice husk ash for ancient masonry

HMC08 - 1st Historical Mortars Conference: Characterization, Diagnosis, Conservation, Repair and Compatibility, LNEC, Lisbon, 24-26 September 2008

Evaluation of Leishmania antigens preparation and storage for use in enzyme immunoassays

The influence of time and temperature on the storage of an alkaline antigen of L.major-like and L.(V.) braziliensis promastigotes added or not of a proteases inhibitor (PMSF) was evaluted by means of an IgG-ELISA. Antibodies in assays using L. major-like antigen stored at -20oC for 6 monsths had a statistically lower geometric mean titer (GMT) and different 95% confidence interval limits (CL) than antigens stored otherwise, as assessed by the "t" statistic. The PMSF L. major-like antigen after storage for 6 months at a temperature of 4oC had the same GMT and 95% CL displayed at time zero as well as when storage for 4 and 6 months at -20oC. Significant diferences were not found when L.(V.) braziliensis antigens were stored at times and temperatures mentioned; the PMSF antigen stored for 2 months at -70oC resulted in a lower serum GMT and 95% CL than any other, as assessed by the "t" statistic. Antigen performance did not show any statistical difference associated to the addition of PMSF within the same species; the largest difference between antigens was that between PMSF-L. (V.) braziliensis and L. major-like without PMSF.

Testing the Freeze/Thaw Cycles in Lime Mortar

2nd Historic Mortars Conference - HMC 2010 and RILEM TC 203-RHM Final Workshop, Prague, September 2010

Lime mortars with heat treated clays and ceramic waste: A review

The formulation and use of lime mortars with ceramic particles has, in the past, been a very common technique. Knowledge of such used techniques and materials is fundamental for the successful rehabilitation and conservation of the built heritage. The durability that these mortars have shown encourages the study of the involved mechanisms, so that they may be adapted to the current reality. The considerable amount of waste from old ceramics factories which is sent for disposal might present an opportunity for the production of reliable improved lime mortars. In this paper a number of studies that characterize old building mortars containing ceramic fragments are reviewed. The most important research undertaken on laboratory prepared mortars with several heat treated clays types is presented, specifically with incorporated ceramic waste. Some studies on the pozzolanicity of heat treated clays are examined and the heating temperatures that seem most likely to achieve pozzolanicity are presented. It was verified that some heating temperatures currently used by ceramic industries might correspond to the temperatures that will achieve pozzolanicity.

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.

Modelling of a wastewater treatment plant using GPS-X

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

Earthen plasters: the potential of the clayey soils of barrocal region in Algarve

Due to their high adsorption capacity of water vapor, earthen plasters can act as a moisture buffer, contributing to balance the relative humidity of the indoor environment of buildings. As a consequence of this capacity earthen plasters may also contribute to the perception of thermal comfort, since a high relative humidity increases the thermal conductivity of air and restricts skin evaporation, increasing the discomfort associated with the perception of heat or cold. Simultaneously, earthen plasters may also contribute to the indoor air quality. In one hand, by mitigating health problems of the respiratory system associated with indoor environment with high relative humidity, in which increases the risk of development of microorganisms usually responsible for infections, allergies or asthma. In the other hand, by mitigating the probability of inflammation of the respiratory system airways associated to exceedingly dry indoor environments. Therefore it also becomes expectable that earthen plasters may contribute for reducing the needs for air conditioning and mechanical ventilation in buildings and, thereby, also allowing the reduction of the associated energy consumption. The «Barrocal» region, located in the sedimentary basin of Algarve, South Portugal, presents geomorphological characteristics that promote the occurrence of soils with a clay mineralogy dominated by illite, which is a clay mineral characterized by a high adsorption capacity of water vapor and low expansibility. This fact turns expectable that these soils have a high potential for interior plastering. In order to evaluate this potential four mortars were formulated with an increasing content of clayey soil extracted from a selected clay quarry from «Barrocal» region. The results from the preliminary characterization campaign confirmed the reduced linear shrinkage of these mortars, as well as their high adsorption-desorption capacity, that is positively correlated with the content of clayey soil present in mortar formulation. However, the mechanical tests showed that the mechanical resistance of these mortars should be improved, for instance through the addition of natural fibers for reinforcement, which will be investigated in future research. This research contributed to increase certainty regarding the potential of clayey soils of the «Barrocal» sub-region of Algarve to produce mortars suitable for eco-efficient interior plastering.

Semantic enrichment of knowledge sources supported by domain ontologies

This thesis introduces a novel conceptual framework to support the creation of knowledge representations based on enriched Semantic Vectors, using the classical vector space model approach extended with ontological support. One of the primary research challenges addressed here relates to the process of formalization and representation of document contents, where most existing approaches are limited and only take into account the explicit, word-based information in the document. This research explores how traditional knowledge representations can be enriched through incorporation of implicit information derived from the complex relationships (semantic associations) modelled by domain ontologies with the addition of information presented in documents. The relevant achievements pursued by this thesis are the following: (i) conceptualization of a model that enables the semantic enrichment of knowledge sources supported by domain experts; (ii) development of a method for extending the traditional vector space, using domain ontologies; (iii) development of a method to support ontology learning, based on the discovery of new ontological relations expressed in non-structured information sources; (iv) development of a process to evaluate the semantic enrichment; (v) implementation of a proof-of-concept, named SENSE (Semantic Enrichment kNowledge SourcEs), which enables to validate the ideas established under the scope of this thesis; (vi) publication of several scientific articles and the support to 4 master dissertations carried out by the department of Electrical and Computer Engineering from FCT/UNL. It is worth mentioning that the work developed under the semantic referential covered by this thesis has reused relevant achievements within the scope of research European projects, in order to address approaches which are considered scientifically sound and coherent and avoid “reinventing the wheel”.

Development of principle culture medium formulations for Saccharomyces cerevisiae

Saccharomyces cerevisiae as well as other microorganisms are frequently used in industry with the purpose of obtain different kind of products that can be applied in several areas (research investigation, pharmaceutical compounds, etc.). In order to obtain high yields for the desired product, it is necessary to make an adequate medium supplementation during the growth of the microorganisms. The higher yields are typically reached by using complex media, however the exact formulation of these media is not known. Moreover, it is difficult to control the exact composition of complex media, leading to batch-to-batch variations. So, to overcome this problem, some industries choose to use defined media, with a defined and known chemical composition. However these kind of media, many times, do not reach the same high yields that are obtained by using complex media. In order to obtain similar yield with defined media the addition of many different compounds has to be tested experimentally. Therefore, the industries use a set of empirical methods with which it is tried to formulate defined media that can reach the same high yields as complex media. In this thesis, a defined medium for Saccharomyces cerevisiae was developed using a rational design approach. In this approach a given metabolic network of Saccharomyces cerevisiae is divided into a several unique and not further decomposable sub networks of metabolic reactions that work coherently in steady state, so called elementary flux modes. The EFMtool algorithm was used in order to calculate the EFM’s for two Saccharomyces cerevisiae metabolic networks (amino acids supplemented metabolic network; amino acids non-supplemented metabolic network). For the supplemented metabolic network 1352172 EFM’s were calculated and then divided into: 1306854 EFM’s producing biomass, and 18582 EFM’s exclusively producing CO2 (cellular respiration). For the non-supplemented network 635 EFM’s were calculated and then divided into: 215 EFM’s producing biomass; 420 EFM’s producing exclusively CO2. The EFM’s of each group were normalized by the respective glucose consumption value. After that, the EFMs’ of the supplemented network were grouped again into: 30 clusters for the 1306854 EFMs producing biomass and, 20 clusters for the 18582 EFM’s producing CO2. For the non-supplemented metabolic network the respective EFM’s of each metabolic function were grouped into 10 clusters. After the clustering step, the concentrations of the other medium compounds were calculated by considering a reasonable glucose amount and by accounting for the proportionality between the compounds concentrations and the glucose ratios. The approach adopted/developed in this thesis may allow a faster and more economical way for media development.

Transcriptional regulation of the mannosyltransferase-encoding gene pigm in inherited glycosylphosphatidylinositol (GPI) deficiency

RESUMO:O glicosilfosfatidilinositol (GPI) é um complexo glicolipídico utlizado por dezenas de proteínas, o qual medeia a sua ancoragem à superfície da célula. Proteínas de superfície celular ancoradas a GPI apresentam várias funções essenciais para a manutenção celular. A deficiência na síntese de GPI é o que caracteriza principalmente a deficiência hereditária em GPI, um grupo de doenças autossómicas raras que resultam de mutações nos genes PIGA, PIGL, PIGM, PIGV, PIGN, PIGO e PIGT, os quais sao indispensáveis para a biossíntese do GPI. Uma mutação pontual no motivo rico em GC -270 no promotor de PIGM impede a ligação do factor de transcrição (FT) Sp1 à sua sequência de reconhecimento, impondo a compactação da cromatina, associada à hipoacetilação de histonas, e consequentemente, impedindo a transcrição de PIGM. Desta forma, a adição da primeira manose ao GPI é comprometida, a síntese de GPI diminui assim como as proteínas ligadas a GPI à superficie das células. Pacientes com Deficiência Hereditária em GPI-associada a PIGM apresentam trombose e epilesia, e ausência de hemólise intravascular e anemia, sendo que estas duas últimas características definem a Hemoglobinúria Paroxística Nocturna (HPN), uma doença rara causada por mutações no gene PIGA. Embora a mutação que causa IGD seja constitutiva e esteja presente em todos os tecidos, o grau de deficiência em GPI varia entre células do mesmo tecido e entre células de tecidos diferentes. Por exemplo nos granulócitos e linfócitos B a deficiência em GPI é muito acentuada mas nos linfócitos T, fibroblastos, plaquetas e eritrócitos é aproximadamente normal, daí a ausência de hemólise intravascular. Os eventos transcricionais que estão na base da expressão diferencial da âncora GPI nas células hematopoiéticas são desconhecidos e constituem o objectivo geral desta tese. Em primeiro lugar, os resultados demonstraram que os níveis de PIGM mRNA variam entre células primárias hematopoiéticas normais. Adicionalmente, a configuração dos nucleossomas no promotor de PIGM é mais compacta em células B do que em células eritróides e tal está correlacionado com os níveis de expressão de PIGM, isto é, inferior nas células B. A presença de vários motivos de ligação para o FT específico da linhagem megacariocítica-eritróide GATA-1 no promotor de PIGM sugeriu que GATA-1 desempenha um papel regulador na sua transcrição. Os resultados mostraram que muito possivelmente GATA-1 desempenha um papel repressor em vez de activador da expressão de PIGM. Resultados preliminares sugerem que KLF1, um factor de transcrição restritamente eritróide, regula a transcrição de PIGM independentemente do motivo -270GC. Em segundo lugar, a investigação do papel dos FTs Sp demonstrou que Sp1 medeia directamente a transcrição de PIGM em ambas as células B e eritróide. Curiosamente, ao contrário do que acontece nas células B, em que a transcrição de PIGM requer a ligação do FT geral Sp1 ao motivo -270GC, nas células eritróides Sp1 regula a transcrição de PIGM ao ligar-se a montante e não ao motivo -270GC. Para além disso, demonstrou-se que Sp2 não é um regulador directo da transcrição de PIGM quer nas células B quer nas células eritróides. Estes resultados explicam a ausência de hemólise intravascular nos doentes com IGD associada a PIGM, uma das principais características que define a HPN. Por último, resultados preliminares mostraram que a repressão da transcrição de PIGM devida à mutação patogénica -270C>G está associada com a diminuição da frequência de interacções genómicas em cis entre PIGM e os seus genes “vizinhos”, sugerindo adicionalmente que a regulação de PIGM e desses genes é partilhada. No seu conjunto, os resultados apresentados nesta tese contribuem para o conhecimento do controlo transcricional de um gene housekeeping, específico-detecido, por meio de FTs genéricos e específicos de linhagem.-------------ABSTRACTC: Glycosylphosphatidylinositol (GPI) is a complex glycolipid used by dozens of proteins for cell surface anchoring. GPI-anchored proteins have various functions that are essential for the cellular maintenance. Defective GPI biosynthesis is the hallmark of inherited GPI deficiency (IGD), a group of rare autosomal diseases caused by mutations in PIGA, PIGL, PIGM, PIGV, PIGN, PIGO and PIGT, all genes indispensable for GPI biosynthesis. A point mutation in the -270GC-rich box in the core promoter of PIGM disrupts binding of the transcription factor (TF) Sp1 to it, imposing nucleosome compaction associated with histone hypoacetylation, thus abrogating transcription of PIGM. As a consequence of PIGM transcriptional repression, addition of the first mannose residue onto the GPI core and thus GPI production are impaired; and expression of GPI-anchored proteins on the surface of cells is severely impaired. Patients with PIGM-associated IGD suffer from life-threatening thrombosis and epilepsy but not intravascular haemolysis and anaemia, two defining features of paroxysmal nocturnal haemoglobinuria (PNH), a rare disease caused by somatic mutations in PIGA. Although the disease-causing mutation in IGD is constitutional and present in all tissues, the degree of GPI deficiency is variable and differs between cells of the same and of different tissues. Accordingly, GPI deficiency is severe in granulocytes and B cells but mild in T cells, fibroblasts, platelets and erythrocytes, hence the lack of intravascular haemolysis.The transcriptional events underlying differential expression of GPI in the haematopoietic cells of PIG-M-associated IGD are not known and constitute the general aim of this thesis. Firstly, I found that PIGM mRNA levels are variable amongst normal primary haematopoietic cells. In addition, the nucleosome configuration in the promoter of PIGM is more compacted in B cells than in erythroid cells and this correlated with the levels of PIGM mRNA expression, i.e., lower in B cells. The presence of several binding sites for GATA-1, a mega-erythroid lineage-specific transcription factor (TF), at the PIGM promoter suggested that GATA-1 has a role on PIGM transcription. My results showed that GATA-1 in erythroid cells is most likely a repressor rather than an activator of PIGM expression. Preliminary data suggested that KLF1, an erythroid-specific TF, regulates PIGM transcription but independently of the -270GC motif. Secondly, investigation of the role of the Sp TFs showed that Sp1 directly mediates PIGM transcriptional regulation in both B and erythroid cells. However, unlike in B cells in which active PIGM transcription requires binding of the generic TF Sp1 to the -270GC-rich box, in erythroid cells, Sp1 regulates PIGM transcription by binding upstream of but not to the -270GC-rich motif. Additionally, I showed that Sp2 is not a direct regulator of PIGM transcription in B and erythroid cells. These findings explain lack of intravascular haemolysis in PIGM-associated IGD, a defining feature of PNH. Lastly, preliminary work shows that transcriptional repression of PIG-M by the pathogenic -270C>G mutation is associated with reduced frequency of in cis genomic interactions between PIGM and its neighbouring genes, suggesting a shared regulatory link between these genes and PIGM. Altogether, the results presented in this thesis provide novel insights into tissuespecific transcriptional control of a housekeeping gene by lineage-specific and generic TFs.

Nosocomial infection and characterization of extended-spectrum β-lactamases-producing Enterobacteriaceae in Northeast Brazil

INTRODUCTION: Extended spectrum β-lactamases (ESBLs) are enzymes that degrade β-lactam antibiotics and have been reported to be an important cause of nosocomial infection in worldwide. METHODS: During 2009, 659 enterobacteria strains were isolated from different clinical specimens and tested for ESBL production. The disk approximation test, combined disk method and addition of clavulanic acid were used for phenotypic detection of the ESBL-producing strains and PCR for detection of the blaTEM and blaCTX-M genes. RESULTS: Among the isolates, 125 were ESBL producers. The blaCTX-M and blaTEM genes were detected in 90.4% and 75% of the strains, respectively. Most strains were isolated from urine. Klebsiella pneumoniae was the most prevalent organism. Microorganisms presented high resistance to the antibiotics. CONCLUSIONS: These results support the need for extending ESBL detection methods to different pathogens of the Enterobacteriaceae family because these methods are only currently standardized by the CLSI for Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca and Proteus mirabilis. Carbapenems were the antibiotic class of choice for the treatment of infections caused by ESBL-producing Enterobacteriaceae.

Production of cytokine and chemokines by human mononuclear cells and whole blood cells after infection with Trypanosoma cruzi

INTRODUCTION: The innate immune response is the first mechanism of protection against Trypanosoma cruzi, and the interaction of inflammatory cells with parasite molecules may activate this response and modulate the adaptive immune system. This study aimed to analyze the levels of cytokines and chemokines synthesized by the whole blood cells (WBC) and peripheral blood mononuclear cells (PBMC) of individuals seronegative for Chagas disease after interaction with live T. cruzi trypomastigotes. METHODS: IL-12, IL-10, TNF-α, TGF-β, CCL-5, CCL-2, CCL-3, and CXCL-9 were measured by ELISA. Nitrite was determined by the Griess method. RESULTS: IL-10 was produced at high levels by WBC compared with PBMC, even after incubation with live trypomastigotes. Production of TNF-α by both PBMC and WBC was significantly higher after stimulation with trypomastigotes. Only PBMC produced significantly higher levels of IL-12 after parasite stimulation. Stimulation of cultures with trypomastigotes induced an increase of CXCL-9 levels produced by WBC. Nitrite levels produced by PBMC increased after the addition of parasites to the culture. CONCLUSIONS: Surface molecules of T. cruzi may induce the production of cytokines and chemokines by cells of the innate immune system through the activation of specific receptors not evaluated in this experiment. The ability to induce IL-12 and TNF-α contributes to shift the adaptive response towards a Th1 profile.