A MAP approach to evidence accumulation clustering

The Evidence Accumulation Clustering (EAC) paradigm is a clustering ensemble method which derives a consensus partition from a collection of base clusterings obtained using different algorithms. It collects from the partitions in the ensemble a set of pairwise observations about the co-occurrence of objects in a same cluster and it uses these co-occurrence statistics to derive a similarity matrix, referred to as co-association matrix. The Probabilistic Evidence Accumulation for Clustering Ensembles (PEACE) algorithm is a principled approach for the extraction of a consensus clustering from the observations encoded in the co-association matrix based on a probabilistic model for the co-association matrix parameterized by the unknown assignments of objects to clusters. In this paper we extend the PEACE algorithm by deriving a consensus solution according to a MAP approach with Dirichlet priors defined for the unknown probabilistic cluster assignments. In particular, we study the positive regularization effect of Dirichlet priors on the final consensus solution with both synthetic and real benchmark data.

Utilização do algoritmo Self-Organizing Map na caracterização de organizações públicas portuguesas.

Dissertação apresentada como requisito parcial para a obtenção do grau de mestre em Estatística e Gestão de Informação.

Phytoplankton analysis of portuguese reservoirs: a cluster analysis with R

In this work, cluster analysis is applied to a real dataset of biological features of several Portuguese reservoirs. All the statistical analysis is done using R statistical software. Several metrics and methods were explored, as well as the combination of Euclidean metric and the hierarchical Ward method. Although it did not present the best combination in terms of internal and stability validation, it was still a good solution and presented good results in terms of interpretation of the problem at hand.

Caracterização da situação orçamental no poder local em indicadores orçamentais e self-organizing map.

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação.

Investigating habitat association of breeding birds using public domain satellite imagery and land cover data.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

Pentamidine (PEN) is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK) into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

Fluxus: do texto à acção. A cartografia de uma a(r)titude

Trabalho de Projecto em Ciências da Comunicação, variante Cultura Contemporânea e Novas Tecnologias

Atividade tradutológica: a (r)evolução dos últimos 20 anos

Trabalho de natureza profissional para a atribuição do Título de Especialista do Instituto Politécnico do Porto, na área de Línguas e Cuturas - Línguas e Literaturas Estrangeiras, defendido a 11-11-2015.

Stochasticity favoring the effects of the R&D strategies of the firms

We present stochastic dynamics on the production costs of Cournot competitions, based on perfect Nash equilibria of nonlinear R&D investment strategies to reduce the production costs of the firms at every period of the game. We analyse the effects that the R&D investment strategies can have in the profits of the firms along the time. We observe that, in certain cases, the uncertainty can improve the effects of the R&D strategies in the profits of the firms due to the non-linearity of the profit functions and also of the R&D parameters.

Cournot duopoly with competition in the R&D expenditures

We present a new R&D investment in a Cournot Duopoly model and we analyze the different possible types of Nash R&D investments. We observe that the new production costs region can be decomposed in three economical regions, depending on the Nash R&D investment, showing the relevance of the use of patents in new technologies.

N170 Asymmetry as an Index of Inferior Occipital Dysfunction in Patients With Symptomatic Occipital Lobe Epilepsy

Objective: Localizing epileptic foci in posterior brain epilepsy remains a difficult exercise in surgery for epilepsy evaluation. Neither clinical manifestations, neurological, EEG nor neuropsychological evaluations provide strong information about the area of onset, and fast spread of paroxysms often produces mixed features of occipital, temporal and parietal symptoms. We investigated the usefulness of the N170 event-related potential to map epileptic activity in these patients. Methods: A group of seven patients with symptomatic posterior cortex epilepsy were submitted to a high-resolution EEG (78 electrodes), with recordings of interictal spikes and face-evoked N170. Generators of spikes and N170 were localized by source analysis. Range of normal N170 asymmetry was determined in 30 healthy volunteers. Results: In 3 out of 7 patients the N170 inter-hemispheric asymmetry was outside control values. Those were the patients whose spike sources were nearest (within 3 cm) to the fusiform gyrus, while foci further away did not affect the N170 ratio. Conclusions: N170 event-related potential provides useful information about focal cortical dysfunction produced by epileptic foci located in the close neighborhood of the fusiform gyrus, but are unaffected by foci further away. Significance: The N170 evoked by faces can improve the epileptic foci localization in posterior brain epilepsy.

Toxicity of saponin isolated from Gymnema sylvestre R. Br. (Asclepiadaceae) against Culex tritaeniorhynchus Giles (Diptera: Culicidae) Japanese encephalitis vector mosquito in India

To determine the larvicidal activity of various extracts of Gymnema sylvestre against the Japanese Encephalitis vector, Culex tritaeniorynchus in Tamilnadu, India. To identify the active principle present in the promising fraction obtained in Chlorofom:Methanol extract of Fraction 2. The G. sylvestre leaf extracts were tested, employing WHO procedure against fourth instar larvae of C. tritaeniorhynchus and the larval mortalities were recorded at various concentrations (6.25, 12.5, 25.0, 50 and 100 µg/mL); the 24h LC50 values of the G. Sylvestre leaf extracts were determined following Probit analysis. It was noteworthy that treatment level 100 µg/mL exhibited highest mortality rates for the three different crude extracts and was significantly different from the mean mortalities recorded for the other concentrations. The LC50 values of 34.756 µg/mL (24.475-51.41), 31.351 µg/mL (20.634-47.043) and 28.577 µg/mL (25.159-32.308) were calculated for acetone, chloroform and methanol extract with the chi-square values of 10.301, 31.351 and 4.093 respectively. The present investigation proved that G. Sylvestre could be possibly utilized as an important component in the Vector Control Program.

Spatial and temporal analysis of recent drought using vegetation temperature condition index: case of Somali regional state of Ethiopia

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Rickettsia typhi IN RODENTS AND R. felis IN FLEAS IN YUCATÁN AS A POSSIBLE CAUSAL AGENT OF UNDEFINED FEBRILE CASES

Rickettsia typhi is the causal agent of murine typhus; a worldwide zoonotic and vector-borne infectious disease, commonly associated with the presence of domestic and wild rodents. Human cases of murine typhus in the state of Yucatán are frequent. However, there is no evidence of the presence of Rickettsia typhi in mammals or vectors in Yucatán. The presence of Rickettsia in rodents and their ectoparasites was evaluated in a small municipality of Yucatán using the conventional polymerase chain reaction technique and sequencing. The study only identified the presence of Rickettsia typhi in blood samples obtained from Rattus rattus and it reported, for the first time, the presence of R. felis in the flea Polygenis odiosus collected from Ototylomys phyllotis rodent. Additionally, Rickettsia felis was detected in the ectoparasite Ctenocephalides felis fleas parasitizing the wild rodent Peromyscus yucatanicus. This study’s results contributed to a better knowledge of Rickettsia epidemiology in Yucatán.