Cyclooxygenase-2 immunoexpression in breast cancer : progesterone receptor influence

In breast cancer cyclooxygenase-2 expression is related with high local estrogen receptor levels and consequent poor outcomes, but the clinical relevance of cyclooxygenase-2 is still unclear. We analyzed, by immunostaining, cyclooxygenase-2 and progesterone receptor expression in 31 cases of women with invasive ductal carcinoma, from Child and Women department of Cova da Beira Medical Center. Cyclooxygenase-2 and progesterone receptor expression was observed in 64.5% and 54.8% of the tumors, respectively. We verified that tumors with progesterone receptor expression had lower size and the majority of women with these tumors had no axillary node metastasis, when compared to tumors with positive progesterone receptor. Similar results were found when a correlation between progesterone receptor, cyclooxygenase-2 and clinicopathological factors was performed. These results suggest that progesterone receptor has a protective role in breast cancer by inflammatory pathway modulation. COX-2+/PR+ seems to be a marker of better behavior in ductal invasive breast cancer. We speculate if cyclooxygenase-2 determination may have be a clinical usefulness in clinical practice. It’s expected that further studies may clarify this issue

Wavelet-Based Cancer Drug Recommender System

A natureza molecular do cancro serve de base para estudos sistemáticos de genomas cancerígenos, fornecendo valiosos insights e permitindo o desenvolvimento de tratamentos clínicos. Acima de tudo, estes estudos estão a impulsionar o uso clínico de informação genómica na escolha de tratamentos, de outro modo não expectáveis, em pacientes com diversos tipos de cancro, possibilitando a medicina de precisão. Com isso em mente, neste projeto combinamos técnicas de processamento de imagem, para aprimoramento de dados, e sistemas de recomendação para propor um ranking personalizado de drogas anticancerígenas. O sistema é implementado em Python e testado usando uma base de dados que contém registos de sensibilidade a drogas, com mais de 310.000 IC50 que, por sua vez, descrevem a resposta de mais de 300 drogas anticancerígenas em 987 linhas celulares cancerígenas. Após várias tarefas de pré-processamento, são realizadas duas experiências. A primeira experiência usa as imagens originais de microarrays de DNA e a segunda usa as mesmas imagens, mas submetidas a uma transformada wavelet. As experiências confirmam que as imagens de microarrays de DNA submetidas a transformadas wavelet melhoram o desempenho do sistema de recomendação, otimizando a pesquisa de linhas celulares cancerígenas com perfil semelhante ao da nova linha celular. Além disso, concluímos que as imagens de microarrays de DNA com transformadas de wavelet apropriadas, não apenas fornecem informações mais ricas para a pesquisa de utilizadores similares, mas também comprimem essas imagens com eficiência, otimizando os recursos computacionais. Tanto quanto é do nosso conhecimento, este projeto é inovador no que diz respeito ao uso de imagens de microarrays de DNA submetidas a transformadas wavelet, para perfilar linhas celulares num sistema de recomendação personalizado de drogas anticancerígenas

Contribution to environmental risk management of pesticides in agricultural areas of north vulnerable area of the Tejo

Mestrado em Engenharia do Ambiente - Instituto Superior de AgronomiaThis study was made to provide a better knowledge of the hazard of groundwater resources to pesticides, in agricultural ecosystems, mainly in maize and potato irrigated areas inserted in North Vulnerable zone of Tejo. The studies were developed in areas of high vulnerability to groundwater contamination. Surface and groundwater resources are intimately connected, with changes in one affecting the other. Due to the importance of the integration of ground and surface water, sampling was performed in Almonda river and “Dique dos Vinte” marsh. The registered pesticides for the main crops in the region were selected and considered to environmental modeling (model of Mackay, Bacci & Gaggi, GUS and EPRIP indices). Of the 26 pesticides and metabolites tested, three were detected in the both natural resources: atrazine, alachlor, metolachlor, reaching a maximum concentration of 0.28, 1.73 and 0.21μg/L respectively. Ecotoxicological tests were performed with the Vibrio fischeri, Pseudokirchneriella subcapitata, Daphnia magna and Chironomus riparius aquatic organisms. Toxicity effects were observed in the both natural resources. P. subcapitata was the most sensitive organism followed D. magna. This study highlights the need for a more conscientious management of the factors which determine the contamination of water resources with pesticides

Linking exposure of mediterranean freshwater ecosystems to pesticides mixtures with their environmental side-effects

Doutoramento em Engenharia do Ambiente - Instituto Superior de AgronomiaIn freshwater ecosystems associated with agricultural areas, organisms are exposed to a multitude of toxicologically and structurally distinct pesticides in concentrations that may fluctuate over time. However, the environmental risks of chemicals are traditionally evaluated and regulated on the basis of single substance. Understanding and improving the link between effects and exposure assessment is an important step in the current challenges of risk assessment in order to increase its ecological relevance. To this end, integrated approaches of different hierarchical levels of complexity and ecological realism have been developed and applied, including: exposure modelling, laboratory testing with individual organisms, species sensitivity distribution, ecosystem models and assessment of aquatic community interactions to evaluate the effects of realistic pesticide combinations on water bodies associated with rice, tomato and maize typical agroecosystems of Mediterranean conditions. Contributing to the overall knowledge of the adequacy of the prospective risk assessment and demonstrating that pesticide risk may be underestimated during the actual registration procedure. The data generated in the present study contributed to the derivation of optimized programs of measures under the scope of European legislation; the identification of sites with the highest expected impacts of pesticide mixtures; the evaluation of the major pesticide compounds that contributed mostly to the identified aquatic risks. Furthermore contribute to a deeper knowledge and unravel the effects of co-occurring chemicals, environmental and biological stressors in aquatic ecosystems considering the effects of biotic and abiotic interactions at community and ecosystem levels. The results contribute to reducing the risks of pesticides in freshwaterN/

Positional Amino acid frquency patterns for automatic protein annotation

Tese de mestrado, Bioinformática e Biologia computacional (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2015Today most proteins contained in protein data bases have been annotated through electronic inference. Due to the amount of data being generated by high throughput methods, electronic inference remains the only viable path to understand proteins’ biochemical functions(s), cellular location(s), participation in cellular processes, as well as, its structure and interactions. The feature learning model here proposed aims to introduce a new perspective on protein function annotation problem at a positional amino acid level. Initially, the probabilistic scores for each amino acid at each protein position is acquired, via a traditional PSI-BLAST search; this generates a PSSM with said information. Each protein’s positional amino acid frequency pattern (PAFP) is sieved through a threshold to decrease the number of PAFPs irrelevant to the protein’s function. Afterwards, these are clustered to their Euclidean closer relatives, via k-means algorithm; identifying, in this manner, s sort of fingerprint of amino acid score patterns. These are then associated to Gene Ontology terms retrieved for the training proteins, using arules package from R, i. e., establish association rules between the resulting K-means clusters of PAFPs and the Go terms. The 300 threshold for the sum of PAFPs generated 280 GO terms, with a support of 0.0005, about 30 proteins, and a confidence of 40%. These terms were used to describe 516591 proteins out of 549008 in Swiss-Prot the release of July 2015. Most GO terms were, not leaf level, but higher. The model infers far more proteins to each Go term than the ones annotated to it, however it also fails to allocate proteins annotated with the GO term, resulting in high recall levels, but not equivalently high precision. However, note that these results do not mean the inference is incorrect but in fact that there is no evidence to support it one way or the other. Also, in the training set there are 7271 GO terms with a support of at least 30 proteins, it would be expectable for the model to return a similar number of identified GO terms. Despite, falling short of what was expected, the results strongly suggest that the existence of certain PAFPs within proteins may be important for their function. It is also interesting that the strongest signal was found on terms for which the positive ratio is very low, which are typically very difficult classification problems. Results strongly suggest that it may be possible to find annotation clues by looking on amino acids substitution patterns alone. The results however were not perfect and more work will certainly be required to further validate the initial findings

Olive mill wastewater: a suitable medium for lipase production by yeasts

Fundação para a Ciência e a Tecnologia (FCT

Comparison of batch and fed-batch lipase production from olive mill wastewater by Yarrowia lipolytica and Candida cilindracea

Olive mill wastewater (OMW) is a liquid waste that results in large amounts from the olive oil manufacturing industry. The quality and quantity of OMW constituents are dependent of many factors, such as olives type and maturity, climatic conditions and region of origin, cultivation methods, and technology used for oil extraction1. From the 3-phases centrifugation process around 1.6 cubic meters of OMW per ton of olives processed are generated. These liquid wastes present an environmental problem and many solutions have been proposed for it, such as its use as culture medium for different lipolytic yeast strains (Gonçalves et al, 2009; Lopes et al, 2009). The aim of this work is the comparison of batch and fed-batch mode of operation for the lipase production and the OMW degradation by two strains, Yarrowia lipolytica W29 and Candida cylindracea CBS 7869. OMW collected from 3-phase continuous olive mills were used (COD of 30 to 261 g/L). OMW used without dilution was supplemented with ammonium chloride and yeast extract proportionally to the COD values. Batch and fed-batch cultures were conducted in a fermenter of 2 L of capacity at pH 7.2, 500 rpm, with constant or variable aeration rate for batch or fed-batch operation, respectively. Batch operation was more adequate to lipase production than fed-batch for both strains but the difference was more significant for Candida cylindracea that revealed to be the most efficient strain for lipase production. However, the final media of the fed-batch cultures presented lower values of COD and sugars indicating a higher level of organic matter degradation

Integrated urban freight logistics combining passenger and freight flows - Mathematical model proposal

The aim of this research is to propose an urban logistics distribution service which benefits from the already installed passenger transport network. This service is based upon the concept of integration of the existing passenger transport network with the urban freight process. The aim is to reduce the number of fossil combustion powered commercial vehicles traveling within city boundaries, solely for goods transportation, thus contributing to reduce negative effects of urban logistics activities, namely pollution, noise, traffic congestion and accidents. Also, integrating goods and passenger flows will promote higher efficiency rates for the passenger transport network and enhance living conditions within major urban centers. A mathematical model for the operational planning of the proposed urban logistics distribution service is proposed. This model consists of assigning origins loads (or requests) to inbound hubs (bus operator centers), transferring the inbound hubs loads to a bus service, and transferring the bus loads to bus stops, to be collected by micro-logistics operators operating environmentally friendly vehicle fleets. The objective is to minimize the total service time while assuring services synchronization along the network and balancing the loads with the system capacities.(undefined